Michael Paul Snyder

Title(s)Visiting Professor, Medicine
SchoolSchool of Medicine
Address1001 Health Sciences Road
Irvine CA 92697-3950
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Emerging Technologies and Future Directions in Interorgan Crosstalk Cardiometabolic Research. Circ Res. 2025 May 23; 136(11):1494-1506. Bae H, Nguyen CM, Ruiz-Orera J, Mills NL, Snyder MP, Jang C, Shah SH, Hübner N, Seldin M. PMID: 40403107; PMCID: PMC12101523.
      View in: PubMed   Mentions:    Fields:    
    2. Dissecting the genetic complexity of myalgic encephalomyelitis/chronic fatigue syndrome via deep learning-powered genome analysis. medRxiv. 2025 May 11. Zhang S, Jahanbani F, Chander V, Kjellberg M, Liu M, Glass KA, Iu DS, Ahmed F, Li H, Maynard RD, Chou T, Cooper-Knock J, Zhang MJ, Thota D, Zeineh M, Grenier JK, Grimson A, Hanson MR, Snyder MP. PMID: 40321247; PMCID: PMC12047926.
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    3. Predicting Placenta Accreta Spectrum Disorder Through Machine Learning Using Metabolomic and Lipidomic Profiling and Clinical Characteristics. Obstet Gynecol. 2025 Jun 01; 145(6):721-731. Miller S, Lyell D, Maric I, Lancaster S, Sylvester K, Contrepois K, Kruger S, Burgess J, Stevenson D, Aghaeepour N, Snyder M, Zhang E, Badillo K, Silver R, Einerson BD, Bianco K. PMID: 40373320.
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    4. Altered maturation and activation state of circulating monocytes is associated with their enhanced recruitment in pulmonary arterial hypertension. Respir Res. 2025 Apr 15; 26(1):148. Harper RL, Zhou X, Marciano DP, Cao A, Wang L, Chen G, Adil MS, Zhou W, Maguire P, Deivanayagam S, Yu Q, Viswanathan V, Yang D, Martin M, Isobe S, Otsuki S, Burgess J, Inglis A, Kelley D, Del Rosario PA, Hsi A, Haddad F, Zamanian RT, Boehm M, Snyder MP, Rabinovitch M. PMID: 40234964; PMCID: PMC11998417.
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    5. Microbiome-Immune Interaction in Pulmonary Arterial Hypertension: What Have We Missed? Research (Wash D C). 2025; 8:0669. Zhou X, Tian W, Gu S, Rabinovitch M, Nicolls MR, Snyder MP. PMID: 40207016; PMCID: PMC11979341.
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    6. Human Body Single-Cell Atlas of 3D Genome Organization and DNA Methylation. bioRxiv. 2025 Mar 24. Zhou J, Wu Y, Liu H, Tian W, Castanon RG, Bartlett A, Zhang Z, Yao G, Shi D, Clock B, Marcotte S, Nery JR, Liem M, Claffey N, Boggeman L, Barragan C, Drigo RAE, Weimer AK, Shi M, Cooper-Knock J, Zhang S, Snyder MP, Preissl S, Ren B, O'Connor C, Chen S, Luo C, Dixon JR, Ecker JR. PMID: 40196612; PMCID: PMC11974725.
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    7. Glial Contribution to the Pathogenesis of Post-Operative Delirium Revealed by Multi-omic Analysis of Brain Tissue from Neurosurgery Patients. bioRxiv. 2025 Mar 14. Ishii T, Wang T, Shibata K, Nishitani S, Yamanashi T, Wahba NE, Seki T, Thompson KJ, Yamanishi K, Nishiguchi T, Shimura A, Aoyama B, Gorantla N, Phuong NJ, Nguyen HD, Santiago TA, Nishizawa Y, Nagao T, Howard MA, Kawasaki H, Hino K, Ikeda A, Snyder MP, Shinozaki G. PMID: 40161597; PMCID: PMC11952519.
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    8. Publisher Correction: The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles. Genome Biol. 2025 Feb 13; 26(1):31. Schreiber JM, Boix CA, Wook Lee J, Li H, Guan Y, Chang CC, Chang JC, Hawkins-Hooker A, Schölkopf B, Schweikert G, Carulla MR, Canakoglu A, Guzzo F, Nanni L, Masseroli M, Carman MJ, Pinoli P, Hong C, Yip KY, Spence JP, Batra SS, Song YS, Mahony S, Zhang Z, Tan W, Shen Y, Sun Y, Shi M, Adrian J, Sandstrom RS, Farrell NP, Halow JM, Lee K, Jiang L, Yang X, Epstein CB, Strattan JS, Bernstein BE, Snyder MP, Kellis M, Noble WS, Kundaje AB, ENCODE Imputation Challenge Participants. PMID: 39948633; PMCID: PMC11827186.
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    9. Author Correction: Global loss of promoter-enhancer connectivity and rebalancing of gene expression during early colorectal cancer carcinogenesis. Nat Cancer. 2025 Feb; 6(2):404. Zhu Y, Lee H, White S, Weimer AK, Monte E, Horning A, Nevins SA, Esplin ED, Paul K, Krieger G, Shipony Z, Chiu R, Laquindanum R, Karathanos TV, Chua MWY, Mills M, Ladabaum U, Longacre T, Shen J, Jaimovich A, Lipson D, Kundaje A, Greenleaf WJ, Curtis C, Ford JM, Snyder MP. PMID: 39865177; PMCID: PMC11864971.
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    10. Evaluation of a biomarker for amyotrophic lateral sclerosis derived from a hypomethylated DNA signature of human motor neurons. BMC Med Genomics. 2025 Jan 14; 18(1):10. Harvey C, Nowak A, Zhang S, Moll T, Weimer AK, Barcons AM, Souza CDS, Ferraiuolo L, Kenna K, Zaitlen N, Caggiano C, Shaw PJ, Snyder MP, Mill J, Hannon E, Cooper-Knock J. PMID: 39810183; PMCID: PMC11734586.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    11. VISTA-induced tumor suppression by a four amino acid intracellular motif. bioRxiv. 2025 Jan 05. Zhao Y, Andoh T, Charles F, Reddy P, Paul K, Goar H, Durdana I, Golder C, Hardy A, Juntilla MM, Yang SR, Lin CY, Sagiv-Barfi I, Geller BS, Moore S, Thakkar D, Boyd-Kirkup JD, Peng Y, Ford JM, Telli ML, Zhang S, Kurian AW, West RB, Yue T, Lipchik AM, Snyder MP, Gruber JJ. PMID: 39803490; PMCID: PMC11722267.
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    12. An Expanded Registry of Candidate cis-Regulatory Elements for Studying Transcriptional Regulation. bioRxiv. 2024 Dec 26. Moore JE, Pratt HE, Fan K, Phalke N, Fisher J, Elhajjajy SI, Andrews G, Gao M, Shedd N, Fu Y, Lacadie MC, Meza J, Ganna M, Choudhury E, Swofford R, Farrell NP, Pampari A, Ramalingam V, Reese F, Borsari B, Yu M, Wattenberg E, Ruiz-Romero M, Razavi-Mohseni M, Xu J, Galeev T, Beer MA, Guigó R, Gerstein M, Engreitz J, Ljungman M, Reddy TE, Snyder MP, Epstein CB, Gaskell E, Bernstein BE, Dickel DE, Visel A, Pennacchio LA, Mortazavi A, Kundaje A, Weng Z. PMID: 39763870; PMCID: PMC11703161.
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    13. Dynamic human gut microbiome and immune shifts during an immersive psychosocial intervention program. Brain Behav Immun. 2025 Mar; 125:428-443. Zhou X, Ganz AB, Rayner A, Cheng TY, Oba H, Rolnik B, Lancaster S, Lu X, Li Y, Johnson JS, Hoyd R, Spakowicz DJ, Slavich GM, Snyder MP. PMID: 39701328; PMCID: PMC11903166.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    14. Improving design and normalization of multiplex proteomics study. bioRxiv. 2024 Dec 10. Fang H, Shih MC, Jiang L, da Veiga Leprevost F, Jian R, Chan J, Nesvizhskii AI, Snyder MP, Tang H. PMID: 39713300; PMCID: PMC11661083.
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    15. California Stress, Trauma, and Resilience Study (CalSTARS) protocol: A multiomics-based cross-sectional investigation and randomized controlled trial to elucidate the biology of ACEs and test a precision intervention for reducing stress and enhancing resilience. Stress. 2024 Jan; 27(1):2401788. Kim LY, Schüssler-Fiorenza Rose SM, Mengelkoch S, Moriarity DP, Gassen J, Alley JC, Roos LG, Jiang T, Alavi A, Thota DD, Zhang X, Perelman D, Kodish T, Krupnick JL, May M, Bowman K, Hua J, Liao YJ, Lieberman AF, Butte AJ, Lester P, Thyne SM, Hilton JF, Snyder MP, Slavich GM. PMID: 39620249.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCTClinical Trials
    16. Evaluation of a biomarker for amyotrophic lateral sclerosis derived from a hypomethylated DNA signature of human motor neurons. Res Sq. 2024 Nov 26. Harvey C, Nowak A, Zhang S, Moll T, Weimer AK, Barcons AM, Dos Santos Souza C, Ferraiuolo L, Kenna K, Zaitlen N, Caggiano C, Shaw PJ, Snyder MP, Mill J, Hannon E, Cooper-Knock J. PMID: 39649175; PMCID: PMC11623773.
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    17. Longitudinal urine metabolic profiling and gestational age prediction in human pregnancy. Brief Bioinform. 2024 Nov 22; 26(1). Shen X, Chen S, Liang L, Avina M, Zackriah H, Jelliffe-Pawlowski L, Rand L, Snyder MP. PMID: 39955767; PMCID: PMC11830194.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    18. Single-cell spatial mapping reveals alteration of cell type composition and tissue microenvironment during early colorectal cancer formation. bioRxiv. 2024 Nov 21. Guha TK, Esplin ED, Horning AM, Chiu R, Paul K, Weimer AK, Becker WR, Laquindanum R, Mills MA, Glen Esplin D, Shen J, Monte E, White S, Karathanos TV, Cotter D, Bi J, Ladabaum U, Longacre TA, Curtis C, Greenleaf WJ, Ford JM, Snyder MP. PMID: 39605357; PMCID: PMC11601668.
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    19. Interlaboratory comparison of standardised metabolomics and lipidomics analyses in human and rodent blood using the MxP® Quant 500 kit. bioRxiv. 2024 Nov 14. Zararsiz GE, Lintelmann J, Cecil A, Kirwan J, Poschet G, Gegner HM, Schuchardt S, Guan XL, Saigusa D, Wishart D, Zheng J, Mandal R, Adams K, Thompson JW, Snyder MP, Contrepois K, Chen S, Ashrafi N, Akyol S, Yilmaz A, Graham SF, O'Connell TM, Kalecký K, Bottiglieri T, Limonciel A, Pham HT, Koal T, Adamski J, Kastenmüller G. PMID: 39605511; PMCID: PMC11601468.
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    20. Short-chain fatty acid metabolites propionate and butyrate are unique epigenetic regulatory elements linking diet, metabolism and gene expression. bioRxiv. 2024 Nov 14. Nshanian M, Gruber JJ, Geller BS, Chleilat F, Lancaster S, White SM, Alexandrova L, Camarillo JM, Kelleher NL, Zhao Y, Snyder MP. PMID: 38293216; PMCID: PMC10827076.
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    21. Global loss of promoter-enhancer connectivity and rebalancing of gene expression during early colorectal cancer carcinogenesis. Nat Cancer. 2024 11; 5(11):1697-1712. Zhu Y, Lee H, White S, Weimer AK, Monte E, Horning A, Nevins SA, Esplin ED, Paul K, Krieger G, Shipony Z, Chiu R, Laquindanum R, Karathanos TV, Chua MWY, Mills M, Ladabaum U, Longacre T, Shen J, Jaimovich A, Lipson D, Kundaje A, Greenleaf WJ, Curtis C, Ford JM, Snyder MP. PMID: 39478119; PMCID: PMC11584406.
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    22. Multiomic analysis of familial adenomatous polyposis reveals molecular pathways associated with early tumorigenesis. Nat Cancer. 2024 11; 5(11):1737-1753. Esplin ED, Hanson C, Wu S, Horning AM, Barapour N, Nevins SA, Jiang L, Contrepois K, Lee H, Guha TK, Hu Z, Laquindanum R, Mills MA, Chaib H, Chiu R, Jian R, Chan J, Ellenberger M, Becker WR, Bahmani B, Khan A, Michael B, Weimer AK, Esplin DG, Shen J, Lancaster S, Monte E, Karathanos TV, Ladabaum U, Longacre TA, Kundaje A, Curtis C, Greenleaf WJ, Ford JM, Snyder MP. PMID: 39478120; PMCID: PMC11584401.
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    23. Detection and analysis of complex structural variation in human genomes across populations and in brains of donors with psychiatric disorders. Cell. 2024 Nov 14; 187(23):6687-6706.e25. Zhou B, Arthur JG, Guo H, Kim T, Huang Y, Pattni R, Wang T, Kundu S, Luo JXJ, Lee H, Nachun DC, Purmann C, Monte EM, Weimer AK, Qu PP, Shi M, Jiang L, Yang X, Fullard JF, Bendl J, Girdhar K, Kim M, Chen X, PsychENCODE Consortium, Greenleaf WJ, Duncan L, Ji HP, Zhu X, Song G, Montgomery SB, Palejev D, Zu Dohna H, Roussos P, Kundaje A, Hallmayer JF, Snyder MP, Wong WH, Urban AE. PMID: 39353437; PMCID: PMC11608572.
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    24. Achieving Inclusive Healthcare through Integrating Education and Research with AI and Personalized Curricula. medRxiv. 2024 Aug 01. Bahmani A, Cha K, Alavi A, Dixit A, Ross A, Park R, Goncalves F, Ma S, Saxman P, Nair R, Akhavan-Sarraf R, Zhou X, Wang M, Contrepois K, Than JLP, Monte E, Rodriguez DJF, Lai J, Babu M, Tondar A, Rose SMS, Akbari I, Zhang X, Yegnashankaran K, Yracheta J, Dale K, Miller AD, Edmiston S, McGhee EM, Nebeker C, Wu JC, Kundaje A, Snyder M. PMID: 39211867; PMCID: PMC11361244.
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    25. predicTTE: An accessible and optimal tool for time-to-event prediction in neurological diseases. bioRxiv. 2024 Jul 23. Weinreich M, McDonough H, Yacovzada N, Magen I, Cohen Y, Harvey C, Gornall S, Boddy S, Alix J, Mohseni N, Kurz JM, Kenna KP, Zhang S, Iacoangeli A, Al-Khleifat A, Snyder MP, Hobson E, Al-Chalabi A, Hornstein E, Elhaik E, Shaw PJ, McDermott C, Cooper-Knock J. PMID: 39091819; PMCID: PMC11291041.
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    26. PRC2-AgeIndex as a universal biomarker of aging and rejuvenation. Nat Commun. 2024 Jul 16; 15(1):5956. Moqri M, Cipriano A, Simpson DJ, Rasouli S, Murty T, de Jong TA, Nachun D, de Sena Brandine G, Ying K, Tarkhov A, Aberg KA, van den Oord E, Zhou W, Smith A, Mackall C, Gladyshev VN, Horvath S, Snyder MP, Sebastiano V. PMID: 39009581; PMCID: PMC11250797.
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    27. Dynamic Human Gut Microbiome and Immune Shifts During an Immersive Psychosocial Therapeutic Program. bioRxiv. 2024 Jun 27. Zhou X, Ganz AB, Rayner A, Cheng TY, Oba H, Rolnik B, Lancaster S, Lu X, Li Y, Johnson JS, Hoyd R, Spakowicz DJ, Slavich GM, Snyder MP. PMID: 38979211; PMCID: PMC11230355.
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    28. The ENCODE mouse postnatal developmental time course identifies regulatory programs of cell types and cell states. bioRxiv. 2024 Jun 14. Rebboah E, Rezaie N, Williams BA, Weimer AK, Shi M, Yang X, Liang HY, Dionne LA, Reese F, Trout D, Jou J, Youngworth I, Reinholdt L, Morabito S, Snyder MP, Wold BJ, Mortazavi A. PMID: 38915583; PMCID: PMC11195270.
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    29. Integrated platform for multiscale molecular imaging and phenotyping of the human brain. Science. 2024 06 14; 384(6701):eadh9979. Park J, Wang J, Guan W, Gjesteby LA, Pollack D, Kamentsky L, Evans NB, Stirman J, Gu X, Zhao C, Marx S, Kim ME, Choi SW, Snyder M, Chavez D, Su-Arcaro C, Tian Y, Park CS, Zhang Q, Yun DH, Moukheiber M, Feng G, Yang XW, Keene CD, Hof PR, Ghosh SS, Frosch MP, Brattain LJ, Chung K. PMID: 38870291; PMCID: PMC11830150.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    30. Post-GWAS multiomic functional investigation of the TNIP1 locus in Alzheimer's disease highlights a potential role for GPX3. Alzheimers Dement. 2024 07; 20(7):5044-5053. Panyard DJ, Reus LM, Ali M, Liu J, Deming YK, Lu Q, Kollmorgen G, Carboni M, Wild N, Visser PJ, Bertram L, Zetterberg H, Blennow K, Gobom J, Western D, Sung YJ, Carlsson CM, Johnson SC, Asthana S, Cruchaga C, Tijms BM, Engelman CD, Snyder MP. PMID: 38809917; PMCID: PMC11247664.
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    31. Personalized transcriptome signatures in a cardiomyopathy stem cell biobank. bioRxiv. 2024 May 14. Monte E, Furihata T, Wang G, Perea-Gil I, Wei E, Chaib H, Nair R, Guevara JV, Mares R, Cheng X, Zhuge Y, Black K, Serrano R, Dagan-Rosenfeld O, Maguire P, Mercola M, Karakikes I, Wu JC, Snyder MP. PMID: 38798547; PMCID: PMC11118309.
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    32. Deconvolution of polygenic risk score in single cells unravels cellular and molecular heterogeneity of complex human diseases. bioRxiv. 2024 May 14. Zhang S, Shu H, Zhou J, Rubin-Sigler J, Yang X, Liu Y, Cooper-Knock J, Monte E, Zhu C, Tu S, Li H, Tong M, Ecker JR, Ichida JK, Shen Y, Zeng J, Tsao PS, Snyder MP. PMID: 38798507; PMCID: PMC11118500.
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    33. Oxidative Stress is a shared characteristic of ME/CFS and Long COVID. bioRxiv. 2024 May 05. Shankar V, Wilhelmy J, Curtis EJ, Michael B, Cervantes L, Mallajosyula VA, Davis RW, Snyder M, Younis S, Robinson WH, Shankar S, Mischel PS, Bonilla H, Davis MM. PMID: 38746454; PMCID: PMC11092775.
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    34. Molecular adaptations in response to exercise training are associated with tissue-specific transcriptomic and epigenomic signatures. Cell Genom. 2024 Jun 12; 4(6):100421. Nair VD, Pincas H, Smith GR, Zaslavsky E, Ge Y, Amper MAS, Vasoya M, Chikina M, Sun Y, Raja AN, Mao W, Gay NR, Esser KA, Smith KS, Zhao B, Wiel L, Singh A, Lindholm ME, Amar D, Montgomery S, Snyder MP, Walsh MJ, Sealfon SC, MoTrPAC Study Group. PMID: 38697122; PMCID: PMC11228891.
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    35. Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease. Cell Host Microbe. 2024 Apr 10; 32(4):506-526.e9. Zhou X, Shen X, Johnson JS, Spakowicz DJ, Agnello M, Zhou W, Avina M, Honkala A, Chleilat F, Chen SJ, Cha K, Leopold S, Zhu C, Chen L, Lyu L, Hornburg D, Wu S, Zhang X, Jiang C, Jiang L, Jiang L, Jian R, Brooks AW, Wang M, Contrepois K, Gao P, Rose SMS, Tran TDB, Nguyen H, Celli A, Hong BY, Bautista EJ, Dorsett Y, Kavathas PB, Zhou Y, Sodergren E, Weinstock GM, Snyder MP. PMID: 38479397; PMCID: PMC11022754.
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    36. Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease. bioRxiv. 2024 Feb 01. Zhou X, Shen X, Johnson JS, Spakowicz DJ, Agnello M, Zhou W, Avina M, Honkala A, Chleilat F, Chen SJ, Cha K, Leopold S, Zhu C, Chen L, Lyu L, Hornburg D, Wu S, Zhang X, Jiang C, Jiang L, Jiang L, Jian R, Brooks AW, Wang M, Contrepois K, Gao P, Schüssler-Fiorenza Rose SM, Binh Tran TD, Nguyen H, Celli A, Hong BY, Bautista EJ, Dorsett Y, Kavathas P, Zhou Y, Sodergren E, Weinstock GM, Snyder MP. PMID: 38352363; PMCID: PMC10862915.
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    37. NGLY1 mutations cause protein aggregation in human neurons. Cell Rep. 2023 12 26; 42(12):113466. Manole A, Wong T, Rhee A, Novak S, Chin SM, Tsimring K, Paucar A, Williams A, Newmeyer TF, Schafer ST, Rosh I, Kaushik S, Hoffman R, Chen S, Wang G, Snyder M, Cuervo AM, Andrade L, Manor U, Lee K, Jones JR, Stern S, Marchetto MC, Gage FH. PMID: 38039131; PMCID: PMC10826878.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    38. Reduced FOXF1 links unrepaired DNA damage to pulmonary arterial hypertension. Nat Commun. 2023 11 21; 14(1):7578. Isobe S, Nair RV, Kang HY, Wang L, Moonen JR, Shinohara T, Cao A, Taylor S, Otsuki S, Marciano DP, Harper RL, Adil MS, Zhang C, Lago-Docampo M, Körbelin J, Engreitz JM, Snyder MP, Rabinovitch M. PMID: 37989727; PMCID: PMC10663616.
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    39. Wearable Devices: Implications for Precision Medicine and the Future of Health Care. Annu Rev Med. 2024 Jan 29; 75:401-415. Babu M, Lautman Z, Lin X, Sobota MHB, Snyder MP. PMID: 37983384.
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    40. Multi-omic identification of key transcriptional regulatory programs during endurance exercise training. bioRxiv. 2023 Oct 23. Smith GR, Zhao B, Lindholm ME, Raja A, Viggars M, Pincas H, Gay NR, Sun Y, Ge Y, Nair VD, Sanford JA, Amper MAS, Vasoya M, Smith KS, Montgomery S, Zaslavsky E, Bodine SC, Esser KA, Walsh MJ, Snyder MP, MoTrPAC Study Group. PMID: 36711841; PMCID: PMC9882056.
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    41. Biomarkers of aging for the identification and evaluation of longevity interventions. Cell. 2023 08 31; 186(18):3758-3775. Moqri M, Herzog C, Poganik JR, Biomarkers of Aging Consortium, Justice J, Belsky DW, Higgins-Chen A, Moskalev A, Fuellen G, Cohen AA, Bautmans I, Widschwendter M, Ding J, Fleming A, Mannick J, Han JJ, Zhavoronkov A, Barzilai N, Kaeberlein M, Cummings S, Kennedy BK, Ferrucci L, Horvath S, Verdin E, Maier AB, Snyder MP, Sebastiano V, Gladyshev VN. PMID: 37657418; PMCID: PMC11088934.
      View in: PubMed   Mentions: 148     Fields:    Translation:Humans
    42. Organization of the human intestine at single-cell resolution. Nature. 2023 Jul; 619(7970):572-584. Hickey JW, Becker WR, Nevins SA, Horning A, Perez AE, Zhu C, Zhu B, Wei B, Chiu R, Chen DC, Cotter DL, Esplin ED, Weimer AK, Caraccio C, Venkataraaman V, Schürch CM, Black S, Brbic M, Cao K, Chen S, Zhang W, Monte E, Zhang NR, Ma Z, Leskovec J, Zhang Z, Lin S, Longacre T, Plevritis SK, Lin Y, Nolan GP, Greenleaf WJ, Snyder M. PMID: 37468586; PMCID: PMC10356619.
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    43. Multiomic signals associated with maternal epidemiological factors contributing to preterm birth in low- and middle-income countries. Sci Adv. 2023 05 24; 9(21):eade7692. Espinosa CA, Khan W, Khanam R, Das S, Khalid J, Pervin J, Kasaro MP, Contrepois K, Chang AL, Phongpreecha T, Michael B, Ellenberger M, Mehmood U, Hotwani A, Nizar A, Kabir F, Wong RJ, Becker M, Berson E, Culos A, De Francesco D, Mataraso S, Ravindra N, Thuraiappah M, Xenochristou M, Stelzer IA, Maric I, Dutta A, Raqib R, Ahmed S, Rahman S, Hasan ASMT, Ali SM, Juma MH, Rahman M, Aktar S, Deb S, Price JT, Wise PH, Winn VD, Druzin ML, Gibbs RS, Darmstadt GL, Murray JC, Stringer JSA, Gaudilliere B, Snyder MP, Angst MS, Rahman A, Baqui AH, Jehan F, Nisar MI, Vwalika B, Sazawal S, Shaw GM, Stevenson DK, Aghaeepour N. PMID: 37224249; PMCID: PMC10208584.
      View in: PubMed   Mentions: 11     Fields:    Translation:Humans
    44. The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity. bioRxiv. 2023 May 16. Reese F, Williams B, Balderrama-Gutierrez G, Wyman D, Çelik MH, Rebboah E, Rezaie N, Trout D, Razavi-Mohseni M, Jiang Y, Borsari B, Morabito S, Liang HY, McGill CJ, Rahmanian S, Sakr J, Jiang S, Zeng W, Carvalho K, Weimer AK, Dionne LA, McShane A, Bedi K, Elhajjajy SI, Upchurch S, Jou J, Youngworth I, Gabdank I, Sud P, Jolanki O, Strattan JS, Kagda MS, Snyder MP, Hitz BC, Moore JE, Weng Z, Bennett D, Reinholdt L, Ljungman M, Beer MA, Gerstein MB, Pachter L, Guigó R, Wold BJ, Mortazavi A. PMID: 37292896; PMCID: PMC10245583.
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    45. The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles. Genome Biol. 2023 04 18; 24(1):79. Schreiber JM, Boix CA, Wook Lee J, Li H, Guan Y, Chang CC, Chang JC, Hawkins-Hooker A, Schölkopf B, Schweikert G, Carulla MR, Canakoglu A, Guzzo F, Nanni L, Masseroli M, Carman MJ, Pinoli P, Hong C, Yip KY, Spence JP, Batra SS, Song YS, Mahony S, Zhang Z, Tan W, Shen Y, Sun Y, Shi M, Adrian J, Sandstrom RS, Farrell NP, Halow JM, Lee K, Jiang L, Yang X, Epstein CB, Strattan JS, Bernstein BE, Snyder MP, Kellis M, Noble WS, Kundaje AB, ENCODE Imputation Challenge Participants. PMID: 37072822; PMCID: PMC10111747.
      View in: PubMed   Mentions:
    46. Withdrawal of 'Precision Neoantigen Discovery Using Large-scale Immunopeptidomes and Composite Modeling of MHC Peptide Presentation'. Mol Cell Proteomics. 2023 04; 22(4):100511. Pyke RM, Mellacheruvu D, Dea S, Abbott CW, Zhang SV, Phillips NA, Harris J, Bartha G, Desai S, McClory R, West J, Snyder MP, Chen R, Boyle SM. PMID: 37019059; PMCID: PMC10114503.
      View in: PubMed   Mentions:
    47. Proinflammatory polarization of monocytes by particulate air pollutants is mediated by induction of trained immunity in pediatric asthma. Allergy. 2023 07; 78(7):1922-1933. Movassagh H, Prunicki M, Kaushik A, Zhou X, Dunham D, Smith EM, He Z, Aleman Muench GR, Shi M, Weimer AK, Cao S, Andorf S, Feizi A, Snyder MP, Soroosh P, Mellins ED, Nadeau KC. PMID: 36929161.
      View in: PubMed   Mentions:
    48. Precision Neoantigen Discovery Using Large-Scale Immunopeptidomes and Composite Modeling of MHC Peptide Presentation. Mol Cell Proteomics. 2023 04; 22(4):100506. Pyke RM, Mellacheruvu D, Dea S, Abbott C, Zhang SV, Phillips NA, Harris J, Bartha G, Desai S, McClory R, West J, Snyder MP, Chen R, Boyle SM. PMID: 36796642; PMCID: PMC10114598.
      View in: PubMed   Mentions:
    49. Integration of spatial and single-cell data across modalities with weak linkage. bioRxiv. 2023 Jan 16. Chen S, Zhu B, Huang S, Hickey JW, Lin KZ, Snyder M, Greenleaf WJ, Nolan GP, Zhang NR, Ma Z. PMID: 36711792; PMCID: PMC9882150.
      View in: PubMed   Mentions:
    50. Recurrent repeat expansions in human cancer genomes. Nature. 2023 01; 613(7942):96-102. Erwin GS, Gürsoy G, Al-Abri R, Suriyaprakash A, Dolzhenko E, Zhu K, Hoerner CR, White SM, Ramirez L, Vadlakonda A, Vadlakonda A, von Kraut K, Park J, Brannon CM, Sumano DA, Kirtikar RA, Erwin AA, Metzner TJ, Yuen RKC, Fan AC, Leppert JT, Eberle MA, Gerstein M, Snyder MP. PMID: 36517591.
      View in: PubMed   Mentions: 32     Fields:    Translation:HumansCells
    51. Distinct factors associated with short-term and long-term weight loss induced by low-fat or low-carbohydrate diet intervention. Cell Rep Med. 2022 12 20; 3(12):100870. Li X, Perelman D, Leong AK, Fragiadakis G, Gardner CD, Snyder MP. PMID: 36516846; PMCID: PMC9798029.
      View in: PubMed   Mentions: 10     Fields:    Translation:Humans
    52. Early prediction and longitudinal modeling of preeclampsia from multiomics. Patterns (N Y). 2022 Dec 09; 3(12):100655. Maric I, Contrepois K, Moufarrej MN, Stelzer IA, Feyaerts D, Han X, Tang A, Stanley N, Wong RJ, Traber GM, Ellenberger M, Chang AL, Fallahzadeh R, Nassar H, Becker M, Xenochristou M, Espinosa C, De Francesco D, Ghaemi MS, Costello EK, Culos A, Ling XB, Sylvester KG, Darmstadt GL, Winn VD, Shaw GM, Relman DA, Quake SR, Angst MS, Snyder MP, Stevenson DK, Gaudilliere B, Aghaeepour N. PMID: 36569558; PMCID: PMC9768681.
      View in: PubMed   Mentions: 17  
    53. Endogenous Retroviral Elements Generate Pathologic Neutrophils in Pulmonary Arterial Hypertension. Am J Respir Crit Care Med. 2022 10 15; 206(8):1019-1034. Taylor S, Isobe S, Cao A, Contrepois K, Benayoun BA, Jiang L, Wang L, Melemenidis S, Ozen MO, Otsuki S, Shinohara T, Sweatt AJ, Kaplan J, Moonen JR, Marciano DP, Gu M, Miyagawa K, Hayes B, Sierra RG, Kupitz CJ, Del Rosario PA, Hsi A, Thompson AAR, Ariza ME, Demirci U, Zamanian RT, Haddad F, Nicolls MR, Snyder MP, Rabinovitch M. PMID: 35696338; PMCID: PMC9801997.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansAnimalsCells
    54. Performance effectiveness of vital parameter combinations for early warning of sepsis-an exhaustive study using machine learning. JAMIA Open. 2022 Dec; 5(4):ooac080. Rangan ES, Pathinarupothi RK, Anand KJS, Snyder MP. PMID: 36267121; PMCID: PMC9566305.
      View in: PubMed   Mentions:
    55. Chimpanzee and pig-tailed macaque iPSCs: Improved culture and generation of primate cross-species embryos. Cell Rep. 2022 08 30; 40(9):111264. Roodgar M, Suchy FP, Nguyen LH, Bajpai VK, Sinha R, Vilches-Moure JG, Van Bortle K, Bhadury J, Metwally A, Jiang L, Jian R, Chiang R, Oikonomopoulos A, Wu JC, Weissman IL, Mankowski JL, Holmes S, Loh KM, Nakauchi H, VandeVoort CA, Snyder MP. PMID: 36044843; PMCID: PMC10075238.
      View in: PubMed   Mentions: 4     Fields:    Translation:AnimalsCells
    56. KLF4 recruits SWI/SNF to increase chromatin accessibility and reprogram the endothelial enhancer landscape under laminar shear stress. Nat Commun. 2022 08 23; 13(1):4941. Moonen JR, Chappell J, Shi M, Shinohara T, Li D, Mumbach MR, Zhang F, Nair RV, Nasser J, Mai DH, Taylor S, Wang L, Metzger RJ, Chang HY, Engreitz JM, Snyder MP, Rabinovitch M. PMID: 35999210; PMCID: PMC9399231.
      View in: PubMed   Mentions:
    57. TidyMass an object-oriented reproducible analysis framework for LC-MS data. Nat Commun. 2022 07 28; 13(1):4365. Shen X, Yan H, Wang C, Gao P, Johnson CH, Snyder MP. PMID: 35902589; PMCID: PMC9334349.
      View in: PubMed   Mentions:
    58. KMT2D-NOTCH Mediates Coronary Abnormalities in Hypoplastic Left Heart Syndrome. Circ Res. 2022 07 22; 131(3):280-282. Yu Z, Zhou X, Liu Z, Pastrana-Gomez V, Liu Y, Guo M, Tian L, Nelson TJ, Wang N, Mital S, Chitayat D, Wu JC, Rabinovitch M, Wu SM, Snyder MP, Miao Y, Gu M. PMID: 35762338; PMCID: PMC9308708.
      View in: PubMed   Mentions:
    59. Multiomic analysis reveals cell-type-specific molecular determinants of COVID-19 severity. Cell Syst. 2022 08 17; 13(8):598-614.e6. Zhang S, Cooper-Knock J, Weimer AK, Shi M, Kozhaya L, Unutmaz D, Harvey C, Julian TH, Furini S, Frullanti E, Fava F, Renieri A, Gao P, Shen X, Timpanaro IS, Kenna KP, Baillie JK, Davis MM, Tsao PS, Snyder MP. PMID: 35690068; PMCID: PMC9163145.
      View in: PubMed   Mentions:
    60. A cancer-associated RNA polymerase III identity drives robust transcription and expression of snaR-A noncoding RNA. Nat Commun. 2022 05 30; 13(1):3007. Van Bortle K, Marciano DP, Liu Q, Chou T, Lipchik AM, Gollapudi S, Geller BS, Monte E, Kamakaka RT, Snyder MP. PMID: 35637192; PMCID: PMC9151912.
      View in: PubMed   Mentions:
    61. Author Correction: Perspectives on ENCODE. Nature. 2022 May; 605(7909):E4. ENCODE Project Consortium, Snyder MP, Gingeras TR, Moore JE, Weng Z, Gerstein MB, Ren B, Hardison RC, Stamatoyannopoulos JA, Graveley BR, Feingold EA, Pazin MJ, Pagan M, Gilchrist DA, Hitz BC, Cherry JM, Bernstein BE, Mendenhall EM, Zerbino DR, Frankish A, Flicek P, Myers RM. PMID: 35474002; PMCID: PMC9095462.
      View in: PubMed   Mentions:
    62. A machine learning algorithm with subclonal sensitivity reveals widespread pan-cancer human leukocyte antigen loss of heterozygosity. Nat Commun. 2022 04 12; 13(1):1925. Pyke RM, Mellacheruvu D, Dea S, Abbott CW, McDaniel L, Bhave DP, Zhang SV, Levy E, Bartha G, West J, Snyder MP, Chen RO, Boyle SM. PMID: 35414054; PMCID: PMC9005524.
      View in: PubMed   Mentions:
    63. Low expression of EXOSC2 protects against clinical COVID-19 and impedes SARS-CoV-2 replication. bioRxiv. 2022 Mar 07. Moll T, Odon V, Harvey C, Collins MO, Peden A, Franklin J, Graves E, Marshall JNG, Souza CDS, Zhang S, Azzouz M, Gordon D, Krogan N, Ferraiuolo L, Snyder MP, Shaw PJ, Rehwinkel J, Cooper-Knock J. PMID: 35291294; PMCID: PMC8923113.
      View in: PubMed   Mentions:
    64. Genome-wide identification of the genetic basis of amyotrophic lateral sclerosis. Neuron. 2022 03 16; 110(6):992-1008.e11. Zhang S, Cooper-Knock J, Weimer AK, Shi M, Moll T, Marshall JNG, Harvey C, Nezhad HG, Franklin J, Souza CDS, Ning K, Wang C, Li J, Dilliott AA, Farhan S, Elhaik E, Pasniceanu I, Livesey MR, Eitan C, Hornstein E, Kenna KP, Project MinE ALS Sequencing Consortium, Veldink JH, Ferraiuolo L, Shaw PJ, Snyder MP. PMID: 35045337; PMCID: PMC9017397.
      View in: PubMed   Mentions:
    65. Design and Methods of the Validating Injury to the Renal Transplant Using Urinary Signatures (VIRTUUS) Study in Children. Transplant Direct. 2021 Dec; 7(12):e791. Kumar J, Contrepois K, Snyder M, Grimm PC, Moudgil A, Smith JM, Bobrowski AE, Verghese PS, Hooper D, Ingulli E, Lestz R, Weng P, Reason JL, Blydt-Hansen TD, Suthanthiran M, Keating B, Amaral S. PMID: 34805493; PMCID: PMC8601357.
      View in: PubMed   Mentions: 3  
    66. Heterogeneity of Diabetes: β-Cells, Phenotypes, and Precision Medicine: Proceedings of an International Symposium of the Canadian Institutes of Health Research's Institute of Nutrition, Metabolism and Diabetes and the U.S. National Institutes of Health's National Institute of Diabetes and Digestive and Kidney Diseases. Diabetes. 2021 11 13. Cefalu WT, Andersen DK, Arreaza-Rubín G, Pin CL, Sato S, Verchere CB, Woo M, Rosenblum ND, Symposium planning committee, moderators, and speakers:, Rosenblum N, Cefalu W, Andersen DK, Arreaza-Rubín G, Dhara C, James SP, Makarchuk MJ, Pin CL, Sato S, Verchere B, Woo M, Powers A, Estall J, Hoesli C, Millman J, Linnemann A, Johnson J, Pin CL, Hawkins M, Woo M, Gloyn A, Cefalu W, Rosenblum N, Huising MO, Benninger RKP, Almaça J, Hull-Meichle RL, MacDonald P, Lynn F, Melero-Martin J, Yoshihara E, Stabler C, Sander M, Evans-Molina C, Engin F, Thompson P, Shalev A, Redondo MJ, Nadeau K, Bellin M, Udler MS, Dennis J, Dash S, Zhou W, Snyder M, Booth G, Butte A, Florez J. PMID: 34957490.
      View in: PubMed   Mentions: 3     Fields:    
    67. The dynamic, combinatorial cis-regulatory lexicon of epidermal differentiation. Nat Genet. 2021 11; 53(11):1564-1576. Kim DS, Risca VI, Reynolds DL, Chappell J, Rubin AJ, Jung N, Donohue LKH, Lopez-Pajares V, Kathiria A, Shi M, Zhao Z, Deep H, Sharmin M, Rao D, Lin S, Chang HY, Snyder MP, Greenleaf WJ, Kundaje A, Khavari PA. PMID: 34650237; PMCID: PMC8763320.
      View in: PubMed   Mentions:
    68. A scalable, secure, and interoperable platform for deep data-driven health management. Nat Commun. 2021 10 01; 12(1):5757. Bahmani A, Alavi A, Buergel T, Upadhyayula S, Wang Q, Ananthakrishnan SK, Alavi A, Celis D, Gillespie D, Young G, Xing Z, Nguyen MHH, Haque A, Mathur A, Payne J, Mazaheri G, Li JK, Kotipalli P, Liao L, Bhasin R, Cha K, Rolnik B, Celli A, Dagan-Rosenfeld O, Higgs E, Zhou W, Berry CL, Van Winkle KG, Contrepois K, Ray U, Bettinger K, Datta S, Li X, Snyder MP. PMID: 34599181; PMCID: PMC8486823.
      View in: PubMed   Mentions:
    69. Chromatin accessibility associates with protein-RNA correlation in human cancer. Nat Commun. 2021 09 30; 12(1):5732. Sanghi A, Gruber JJ, Metwally A, Jiang L, Reynolds W, Sunwoo J, Orloff L, Chang HY, Kasowski M, Snyder MP. PMID: 34593797; PMCID: PMC8484618.
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    70. Structured elements drive extensive circular RNA translation. Mol Cell. 2021 10 21; 81(20):4300-4318.e13. Chen CK, Cheng R, Demeter J, Chen J, Weingarten-Gabbay S, Jiang L, Snyder MP, Weissman JS, Segal E, Jackson PK, Chang HY. PMID: 34437836; PMCID: PMC8567535.
      View in: PubMed   Mentions: 126     Fields:    Translation:HumansCells
    71. Five-year pediatric use of a digital wearable fitness device: lessons from a pilot case study. JAMIA Open. 2021 Jul; 4(3):ooab054. Butte KD, Bahmani A, Butte AJ, Li X, Snyder MP. PMID: 34350390; PMCID: PMC8327370.
      View in: PubMed   Mentions: 2  
    72. Prediction of Immunotherapy Response in Melanoma through Combined Modeling of Neoantigen Burden and Immune-Related Resistance Mechanisms. Clin Cancer Res. 2021 08 01; 27(15):4265-4276. Abbott CW, Boyle SM, Pyke RM, McDaniel LD, Levy E, Navarro FCP, Mellacheruvu D, Zhang SV, Tan M, Santiago R, Rusan ZM, Milani P, Bartha G, Harris J, McClory R, Snyder MP, Jang S, Chen R. PMID: 34341053; PMCID: PMC9401549.
      View in: PubMed   Mentions:
    73. The Exposome in the Era of the Quantified Self. Annu Rev Biomed Data Sci. 2021 07 20; 4:255-277. Zhang X, Gao P, Snyder MP. PMID: 34465170.
      View in: PubMed   Mentions:
    74. Common and rare variant analyses combined with single-cell multiomics reveal cell-type-specific molecular mechanisms of COVID-19 severity. medRxiv. 2021 Jun 21. Zhang S, Cooper-Knock J, Weimer AK, Harvey C, Julian TH, Wang C, Li J, Furini S, Frullanti E, Fava F, Renieri A, Pan C, Song J, Billing-Ross P, Gao P, Shen X, Timpanaro IS, Kenna KP, VA Million Veteran Program, GEN-COVID Network, Davis MM, Tsao PS, Snyder MP. PMID: 34189540; PMCID: PMC8240695.
      View in: PubMed   Mentions:
    75. Withdrawn: Precision Neoantigen Discovery Using Large-scale Immunopeptidomes and Composite Modeling of MHC Peptide Presentation. Mol Cell Proteomics. 2021; 20:100111. Pyke RM, Mellacheruvu D, Dea S, Abbott CW, Zhang SV, Phillips NA, Harris J, Bartha G, Desai S, McClory R, West J, Snyder MP, Chen R, Boyle SM. PMID: 34126241; PMCID: PMC8318994.
      View in: PubMed   Mentions:
    76. Early detection of SARS-CoV-2 and other infections in solid organ transplant recipients and household members using wearable devices. Transpl Int. 2021 06; 34(6):1019-1031. Keating BJ, Mukhtar EH, Elftmann ED, Eweje FR, Gao H, Ibrahim LI, Kathawate RG, Lee AC, Li EH, Moore KA, Nair N, Chaluvadi V, Reason J, Zanoni F, Honkala AT, Al-Ali AK, Abdullah Alrubaish F, Ahmad Al-Mozaini M, Al-Muhanna FA, Al-Romaih K, Goldfarb SB, Kellogg R, Kiryluk K, Kizilbash SJ, Kohut TJ, Kumar J, O'Connor MJ, Rand EB, Redfield RR, Rolnik B, Rossano J, Sanchez PG, Alavi A, Bahmani A, Bogu GK, Brooks AW, Metwally AA, Mishra T, Marks SD, Montgomery RA, Fishman JA, Amaral S, Jacobson PA, Wang M, Snyder MP. PMID: 33735480; PMCID: PMC8250335.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCellsPHPublic Health
    77. Integrated trajectories of the maternal metabolome, proteome, and immunome predict labor onset. Sci Transl Med. 2021 05 05; 13(592). Stelzer IA, Ghaemi MS, Han X, Ando K, Hédou JJ, Feyaerts D, Peterson LS, Rumer KK, Tsai ES, Ganio EA, Gaudillière DK, Tsai AS, Choisy B, Gaigne LP, Verdonk F, Jacobsen D, Gavasso S, Traber GM, Ellenberger M, Stanley N, Becker M, Culos A, Fallahzadeh R, Wong RJ, Darmstadt GL, Druzin ML, Winn VD, Gibbs RS, Ling XB, Sylvester K, Carvalho B, Snyder MP, Shaw GM, Stevenson DK, Contrepois K, Angst MS, Aghaeepour N, Gaudillière B. PMID: 33952678; PMCID: PMC8136601.
      View in: PubMed   Mentions: 67     Fields:    Translation:Humans
    78. ALDH1A3 Coordinates Metabolism With Gene Regulation in Pulmonary Arterial Hypertension. Circulation. 2021 05 25; 143(21):2074-2090. Li D, Shao NY, Moonen JR, Zhao Z, Shi M, Otsuki S, Wang L, Nguyen T, Yan E, Marciano DP, Contrepois K, Li CG, Wu JC, Snyder MP, Rabinovitch M. PMID: 33764154; PMCID: PMC8289565.
      View in: PubMed   Mentions:
    79. Understanding how biologic and social determinants affect disparities in preterm birth and outcomes of preterm infants in the NICU. Semin Perinatol. 2021 06; 45(4):151408. Stevenson DK, Aghaeepour N, Maric I, Angst MS, Darmstadt GL, Druzin ML, Gaudilliere B, Ling XB, Moufarrej MN, Peterson LS, Quake SR, Relman DA, Snyder MP, Sylvester KG, Shaw GM, Wong RJ. PMID: 33875265; PMCID: PMC9159791.
      View in: PubMed   Mentions:
    80. CTLA-4 expression by B-1a B cells is essential for immune tolerance. Nat Commun. 2021 01 22; 12(1):525. Yang Y, Li X, Ma Z, Wang C, Yang Q, Byrne-Steele M, Hong R, Min Q, Zhou G, Cheng Y, Qin G, Youngyunpipatkul JV, Wing JB, Sakaguchi S, Toonstra C, Wang LX, Vilches-Moure JG, Wang D, Snyder MP, Wang JY, Han J, Herzenberg LA. PMID: 33483505; PMCID: PMC7822855.
      View in: PubMed   Mentions:
    81. PPARγ-p53-Mediated Vasculoregenerative Program to Reverse Pulmonary Hypertension. Circ Res. 2021 02 05; 128(3):401-418. Hennigs JK, Cao A, Li CG, Shi M, Mienert J, Miyagawa K, Körbelin J, Marciano DP, Chen PI, Roughley M, Elliott MV, Harper RL, Bill MA, Chappell J, Moonen JR, Diebold I, Wang L, Snyder MP, Rabinovitch M. PMID: 33322916; PMCID: PMC7908816.
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    82. Cell-free DNA (cfDNA) and Exosome Profiling from a Year-Long Human Spaceflight Reveals Circulating Biomarkers. iScience. 2020 Dec 18; 23(12):101844. Bezdan D, Grigorev K, Meydan C, Pelissier Vatter FA, Cioffi M, Rao V, MacKay M, Nakahira K, Burnham P, Afshinnekoo E, Westover C, Butler D, Mozsary C, Donahoe T, Foox J, Mishra T, Lucotti S, Rana BK, Melnick AM, Zhang H, Matei I, Kelsen D, Yu K, Lyden DC, Taylor L, Bailey SM, Snyder MP, Garrett-Bakelman FE, Ossowski S, De Vlaminck I, Mason CE. PMID: 33376973; PMCID: PMC7756145.
      View in: PubMed   Mentions: 28  
    83. Human-engineered Treg-like cells suppress FOXP3-deficient T cells but preserve adaptive immune responses in vivo. Clin Transl Immunology. 2020; 9(11):e1214. Sato Y, Passerini L, Piening BD, Uyeda MJ, Goodwin M, Gregori S, Snyder MP, Bertaina A, Roncarolo MG, Bacchetta R. PMID: 33304583; PMCID: PMC7688376.
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    84. A high-stringency blueprint of the human proteome. Nat Commun. 2020 10 16; 11(1):5301. Adhikari S, Nice EC, Deutsch EW, Lane L, Omenn GS, Pennington SR, Paik YK, Overall CM, Corrales FJ, Cristea IM, Van Eyk JE, Uhlén M, Lindskog C, Chan DW, Bairoch A, Waddington JC, Justice JL, LaBaer J, Rodriguez H, He F, Kostrzewa M, Ping P, Gundry RL, Stewart P, Srivastava S, Srivastava S, Nogueira FCS, Domont GB, Vandenbrouck Y, Lam MPY, Wennersten S, Vizcaino JA, Wilkins M, Schwenk JM, Lundberg E, Bandeira N, Marko-Varga G, Weintraub ST, Pineau C, Kusebauch U, Moritz RL, Ahn SB, Palmblad M, Snyder MP, Aebersold R, Baker MS. PMID: 33067450; PMCID: PMC7568584.
      View in: PubMed   Mentions: 108     Fields:    Translation:Humans
    85. Deep longitudinal multiomics profiling reveals two biological seasonal patterns in California. Nat Commun. 2020 10 01; 11(1):4933. Sailani MR, Metwally AA, Zhou W, Rose SMS, Ahadi S, Contrepois K, Mishra T, Zhang MJ, Kidzinski L, Chu TJ, Snyder MP. PMID: 33004787; PMCID: PMC7529769.
      View in: PubMed   Mentions:
    86. Candidate variants in TUB are associated with familial tremor. PLoS Genet. 2020 09; 16(9):e1009010. Sailani MR, Jahanbani F, Abbott CW, Lee H, Zia A, Rego S, Winkelmann J, Hopfner F, Khan TN, Katsanis N, Müller SH, Berg D, Lyman KM, Mychajliw C, Deuschl G, Bernstein JA, Kuhlenbäumer G, Snyder MP. PMID: 32956375; PMCID: PMC7529431.
      View in: PubMed   Mentions:
    87. Perspectives on ENCODE. Nature. 2020 07; 583(7818):693-698. ENCODE Project Consortium, Snyder MP, Gingeras TR, Moore JE, Weng Z, Gerstein MB, Ren B, Hardison RC, Stamatoyannopoulos JA, Graveley BR, Feingold EA, Pazin MJ, Pagan M, Gilchrist DA, Hitz BC, Cherry JM, Bernstein BE, Mendenhall EM, Zerbino DR, Frankish A, Flicek P, Myers RM. PMID: 32728248; PMCID: PMC7410827.
      View in: PubMed   Mentions: 79     Fields:    Translation:HumansAnimalsCells
    88. An integrative ENCODE resource for cancer genomics. Nat Commun. 2020 07 29; 11(1):3696. Zhang J, Lee D, Dhiman V, Jiang P, Xu J, McGillivray P, Yang H, Liu J, Meyerson W, Clarke D, Gu M, Li S, Lou S, Xu J, Lochovsky L, Ung M, Ma L, Yu S, Cao Q, Harmanci A, Yan KK, Sethi A, Gürsoy G, Schoenberg MR, Rozowsky J, Warrell J, Emani P, Yang YT, Galeev T, Kong X, Liu S, Li X, Krishnan J, Feng Y, Rivera-Mulia JC, Adrian J, Broach JR, Bolt M, Moran J, Fitzgerald D, Dileep V, Liu T, Mei S, Sasaki T, Trevilla-Garcia C, Wang S, Wang Y, Zang C, Wang D, Klein RJ, Snyder M, Gilbert DM, Yip K, Cheng C, Yue F, Liu XS, White KP, Gerstein M. PMID: 32728046; PMCID: PMC7391744.
      View in: PubMed   Mentions: 78     Fields:    Translation:HumansCells
    89. Landscape of cohesin-mediated chromatin loops in the human genome. Nature. 2020 07; 583(7818):737-743. Grubert F, Srivas R, Spacek DV, Kasowski M, Ruiz-Velasco M, Sinnott-Armstrong N, Greenside P, Narasimha A, Liu Q, Geller B, Sanghi A, Kulik M, Sa S, Rabinovitch M, Kundaje A, Dalton S, Zaugg JB, Snyder M. PMID: 32728247; PMCID: PMC7410831.
      View in: PubMed   Mentions:
    90. A limited set of transcriptional programs define major cell types. Genome Res. 2020 07; 30(7):1047-1059. Breschi A, Muñoz-Aguirre M, Wucher V, Davis CA, Garrido-Martín D, Djebali S, Gillis J, Pervouchine DD, Vlasova A, Dobin A, Zaleski C, Drenkow J, Danyko C, Scavelli A, Reverter F, Snyder MP, Gingeras TR, Guigó R. PMID: 32759341; PMCID: PMC7397875.
      View in: PubMed   Mentions:
    91. Molecular Choreography of Acute Exercise. Cell. 2020 05 28; 181(5):1112-1130.e16. Contrepois K, Wu S, Moneghetti KJ, Hornburg D, Ahadi S, Tsai MS, Metwally AA, Wei E, Lee-McMullen B, Quijada JV, Chen S, Christle JW, Ellenberger M, Balliu B, Taylor S, Durrant MG, Knowles DA, Choudhry H, Ashland M, Bahmani A, Enslen B, Amsallem M, Kobayashi Y, Avina M, Perelman D, Schüssler-Fiorenza Rose SM, Zhou W, Ashley EA, Montgomery SB, Chaib H, Haddad F, Snyder MP. PMID: 32470399; PMCID: PMC7299174.
      View in: PubMed   Mentions: 170     Fields:    Translation:HumansCells
    92. Remodeling of active endothelial enhancers is associated with aberrant gene-regulatory networks in pulmonary arterial hypertension. Nat Commun. 2020 04 03; 11(1):1673. Reyes-Palomares A, Gu M, Grubert F, Berest I, Sa S, Kasowski M, Arnold C, Shuai M, Srivas R, Miao S, Li D, Snyder MP, Rabinovitch M, Zaugg JB. PMID: 32245974; PMCID: PMC7125148.
      View in: PubMed   Mentions:
    93. Cumulative Lifetime Burden of Cardiovascular Disease From Early Exposure to Air Pollution. J Am Heart Assoc. 2020 03 17; 9(6):e014944. Kim JB, Prunicki M, Haddad F, Dant C, Sampath V, Patel R, Smith E, Akdis C, Balmes J, Snyder MP, Wu JC, Nadeau KC. PMID: 32174249; PMCID: PMC7335506.
      View in: PubMed   Mentions: 37     Fields:    Translation:HumansPHPublic Health
    94. Multiomic immune clockworks of pregnancy. Semin Immunopathol. 2020 08; 42(4):397-412. Peterson LS, Stelzer IA, Tsai AS, Ghaemi MS, Han X, Ando K, Winn VD, Martinez NR, Contrepois K, Moufarrej MN, Quake S, Relman DA, Snyder MP, Shaw GM, Stevenson DK, Wong RJ, Arck P, Angst MS, Aghaeepour N, Gaudilliere B. PMID: 32020337; PMCID: PMC7508753.
      View in: PubMed   Mentions: 40     Fields:    Translation:Humans
    95. Global metabolic profiling to model biological processes of aging in twins. Aging Cell. 2020 01; 19(1):e13073. Bunning BJ, Contrepois K, Lee-McMullen B, Dhondalay GKR, Zhang W, Tupa D, Raeber O, Desai M, Nadeau KC, Snyder MP, Andorf S. PMID: 31746094; PMCID: PMC6974708.
      View in: PubMed   Mentions:
    96. Mitigation of off-target toxicity in CRISPR-Cas9 screens for essential non-coding elements. Nat Commun. 2019 Sep 06; 10(1):4063. Tycko J, Wainberg M, Marinov GK, Ursu O, Hess GT, Ego BK, Li A, Truong A, Trevino AE, Spees K, Yao D, Kaplow IM, Greenside PG, Morgens DW, Phanstiel DH, Snyder MP, Bintu L, Greenleaf WJ, Kundaje A, Bassik MC. PMID: 31492858; PMCID: PMC6731277.
      View in: PubMed   Mentions:
    97. Phenotypically Silent Bone Morphogenetic Protein Receptor 2 Mutations Predispose Rats to Inflammation-Induced Pulmonary Arterial Hypertension by Enhancing the Risk for Neointimal Transformation. Circulation. 2019 10 22; 140(17):1409-1425. Tian W, Jiang X, Sung YK, Shuffle E, Wu TH, Kao PN, Tu AB, Dorfmüller P, Cao A, Wang L, Peng G, Kim Y, Zhang P, Chappell J, Pasupneti S, Dahms P, Maguire P, Chaib H, Zamanian R, Peters-Golden M, Snyder MP, Voelkel NF, Humbert M, Rabinovitch M, Nicolls MR. PMID: 31462075; PMCID: PMC6803052.
      View in: PubMed   Mentions:
    98. Simultaneous RNA purification and size selection using on-chip isotachophoresis with an ionic spacer. Lab Chip. 2019 08 21; 19(16):2741-2749. Han CM, Catoe D, Munro SA, Khnouf R, Snyder MP, Santiago JG, Salit ML, Cenik C. PMID: 31328753; PMCID: PMC7272188.
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    99. A longitudinal big data approach for precision health. Nat Med. 2019 05; 25(5):792-804. Schüssler-Fiorenza Rose SM, Contrepois K, Moneghetti KJ, Zhou W, Mishra T, Mataraso S, Dagan-Rosenfeld O, Ganz AB, Dunn J, Hornburg D, Rego S, Perelman D, Ahadi S, Sailani MR, Zhou Y, Leopold SR, Chen J, Ashland M, Christle JW, Avina M, Limcaoco P, Ruiz C, Tan M, Butte AJ, Weinstock GM, Slavich GM, Sodergren E, McLaughlin TL, Haddad F, Snyder MP. PMID: 31068711; PMCID: PMC6713274.
      View in: PubMed   Mentions: 192     Fields:    Translation:HumansCells
    100. Author Correction: Novel mutations in PIEZO1 cause an autosomal recessive generalized lymphatic dysplasia with non-immune hydrops fetalis. Nat Commun. 2019 Apr 26; 10(1):1951. Fotiou E, Martin-Almedina S, Simpson MA, Lin S, Gordon K, Brice G, Atton G, Jeffery I, Rees DC, Mignot C, Vogt J, Homfray T, Snyder MP, Rockson SG, Jeffery S, Mortimer PS, Mansour S, Ostergaard P. PMID: 31028252; PMCID: PMC6486644.
      View in: PubMed   Mentions:
    101. The NASA Twins Study: A multidimensional analysis of a year-long human spaceflight. Science. 2019 04 12; 364(6436). Garrett-Bakelman FE, Darshi M, Green SJ, Gur RC, Lin L, Macias BR, McKenna MJ, Meydan C, Mishra T, Nasrini J, Piening BD, Rizzardi LF, Sharma K, Siamwala JH, Taylor L, Vitaterna MH, Afkarian M, Afshinnekoo E, Ahadi S, Ambati A, Arya M, Bezdan D, Callahan CM, Chen S, Choi AMK, Chlipala GE, Contrepois K, Covington M, Crucian BE, De Vivo I, Dinges DF, Ebert DJ, Feinberg JI, Gandara JA, George KA, Goutsias J, Grills GS, Hargens AR, Heer M, Hillary RP, Hoofnagle AN, Hook VYH, Jenkinson G, Jiang P, Keshavarzian A, Laurie SS, Lee-McMullen B, Lumpkins SB, MacKay M, Maienschein-Cline MG, Melnick AM, Moore TM, Nakahira K, Patel HH, Pietrzyk R, Rao V, Saito R, Salins DN, Schilling JM, Sears DD, Sheridan CK, Stenger MB, Tryggvadottir R, Urban AE, Vaisar T, Van Espen B, Zhang J, Ziegler MG, Zwart SR, Charles JB, Kundrot CE, Scott GBI, Bailey SM, Basner M, Feinberg AP, Lee SMC, Mason CE, Mignot E, Rana BK, Smith SM, Snyder MP, Turek FW. PMID: 30975860; PMCID: PMC7580864.
      View in: PubMed   Mentions: 405     Fields:    Translation:HumansCells
    102. Smooth Muscle Contact Drives Endothelial Regeneration by BMPR2-Notch1-Mediated Metabolic and Epigenetic Changes. Circ Res. 2019 01 18; 124(2):211-224. Miyagawa K, Shi M, Chen PI, Hennigs JK, Zhao Z, Wang M, Li CG, Saito T, Taylor S, Sa S, Cao A, Wang L, Snyder MP, Rabinovitch M. PMID: 30582451; PMCID: PMC6400637.
      View in: PubMed   Mentions:
    103. High Throughput Sequencing and Assessing Disease Risk. Cold Spring Harb Perspect Med. 2019 01 02; 9(1). Rego SM, Snyder MP. PMID: 29959131; PMCID: PMC6314070.
      View in: PubMed   Mentions:
    104. Personalized Metabolomics. Methods Mol Biol. 2019; 1978:447-456. Marciano DP, Snyder MP. PMID: 31119679.
      View in: PubMed   Mentions:
    105. Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy. Bioinformatics. 2019 01 01; 35(1):95-103. Ghaemi MS, DiGiulio DB, Contrepois K, Callahan B, Ngo TTM, Lee-McMullen B, Lehallier B, Robaczewska A, Mcilwain D, Rosenberg-Hasson Y, Wong RJ, Quaintance C, Culos A, Stanley N, Tanada A, Tsai A, Gaudilliere D, Ganio E, Han X, Ando K, McNeil L, Tingle M, Wise P, Maric I, Sirota M, Wyss-Coray T, Winn VD, Druzin ML, Gibbs R, Darmstadt GL, Lewis DB, Partovi Nia V, Agard B, Tibshirani R, Nolan G, Snyder MP, Relman DA, Quake SR, Shaw GM, Stevenson DK, Angst MS, Gaudilliere B, Aghaeepour N. PMID: 30561547; PMCID: PMC6298056.
      View in: PubMed   Mentions: 106     Fields:    Translation:HumansCells
    106. High-frequency actionable pathogenic exome variants in an average-risk cohort. Cold Spring Harb Mol Case Stud. 2018 12; 4(6). Rego S, Dagan-Rosenfeld O, Zhou W, Sailani MR, Limcaoco P, Colbert E, Avina M, Wheeler J, Craig C, Salins D, Röst HL, Dunn J, McLaughlin T, Steinmetz LM, Bernstein JA, Snyder MP. PMID: 30487145; PMCID: PMC6318774.
      View in: PubMed   Mentions:
    107. Identification of phagocytosis regulators using magnetic genome-wide CRISPR screens. Nat Genet. 2018 12; 50(12):1716-1727. Haney MS, Bohlen CJ, Morgens DW, Ousey JA, Barkal AA, Tsui CK, Ego BK, Levin R, Kamber RA, Collins H, Tucker A, Li A, Vorselen D, Labitigan L, Crane E, Boyle E, Jiang L, Chan J, Rincón E, Greenleaf WJ, Li B, Snyder MP, Weissman IL, Theriot JA, Collins SR, Barres BA, Bassik MC. PMID: 30397336; PMCID: PMC6719718.
      View in: PubMed   Mentions: 91     Fields:    Translation:HumansAnimalsCells
    108. Disruption of mesoderm formation during cardiac differentiation due to developmental exposure to 13-cis-retinoic acid. Sci Rep. 2018 08 28; 8(1):12960. Liu Q, Van Bortle K, Zhang Y, Zhao MT, Zhang JZ, Geller BS, Gruber JJ, Jiang C, Wu JC, Snyder MP. PMID: 30154523; PMCID: PMC6113333.
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    109. Natural Selection Has Differentiated the Progesterone Receptor among Human Populations. Am J Hum Genet. 2018 07 05; 103(1):45-57. Li J, Hong X, Mesiano S, Muglia LJ, Wang X, Snyder M, Stevenson DK, Shaw GM. PMID: 29937092; PMCID: PMC6035283.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansAnimals
    110. Personal Omics for Precision Health. Circ Res. 2018 04 27; 122(9):1169-1171. Kellogg RA, Dunn J, Snyder MP. PMID: 29700064.
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    111. NF90/ILF3 is a transcription factor that promotes proliferation over differentiation by hierarchical regulation in K562 erythroleukemia cells. PLoS One. 2018; 13(3):e0193126. Wu TH, Shi L, Adrian J, Shi M, Nair RV, Snyder MP, Kao PN. PMID: 29590119; PMCID: PMC5873942.
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    112. Circular DNA elements of chromosomal origin are common in healthy human somatic tissue. Nat Commun. 2018 03 14; 9(1):1069. Møller HD, Mohiyuddin M, Prada-Luengo I, Sailani MR, Halling JF, Plomgaard P, Maretty L, Hansen AJ, Snyder MP, Pilegaard H, Lam HYK, Regenberg B. PMID: 29540679; PMCID: PMC5852086.
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    113. SETD7 Drives Cardiac Lineage Commitment through Stage-Specific Transcriptional Activation. Cell Stem Cell. 2018 03 01; 22(3):428-444.e5. Lee J, Shao NY, Paik DT, Wu H, Guo H, Termglinchan V, Churko JM, Kim Y, Kitani T, Zhao MT, Zhang Y, Wilson KD, Karakikes I, Snyder MP, Wu JC. PMID: 29499155; PMCID: PMC5929163.
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    114. Biallelic Mutations in ATP5F1D, which Encodes a Subunit of ATP Synthase, Cause a Metabolic Disorder. Am J Hum Genet. 2018 03 01; 102(3):494-504. Oláhová M, Yoon WH, Thompson K, Jangam S, Fernandez L, Davidson JM, Kyle JE, Grove ME, Fisk DG, Kohler JN, Holmes M, Dries AM, Huang Y, Zhao C, Contrepois K, Zappala Z, Frésard L, Waggott D, Zink EM, Kim YM, Heyman HM, Stratton KG, Webb-Robertson BM, Undiagnosed Diseases Network, Snyder M, Merker JD, Montgomery SB, Fisher PG, Feichtinger RG, Mayr JA, Hall J, Barbosa IA, Simpson MA, Deshpande C, Waters KM, Koeller DM, Metz TO, Morris AA, Schelley S, Cowan T, Friederich MW, McFarland R, Van Hove JLK, Enns GM, Yamamoto S, Ashley EA, Wangler MF, Taylor RW, Bellen HJ, Bernstein JA, Wheeler MT. PMID: 29478781; PMCID: PMC6117612.
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    115. WISP3 mutation associated with pseudorheumatoid dysplasia. Cold Spring Harb Mol Case Stud. 2018 02; 4(1). Sailani MR, Chappell J, Jingga I, Narasimha A, Zia A, Lynch JL, Mazrouei S, Bernstein JA, Aryani O, Snyder MP. PMID: 29092958; PMCID: PMC5793776.
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    116. Integrative Personal Omics Profiles during Periods of Weight Gain and Loss. Cell Syst. 2018 Feb 28; 6(2):157-170.e8. Piening BD, Zhou W, Contrepois K, Röst H, Gu Urban GJ, Mishra T, Hanson BM, Bautista EJ, Leopold S, Yeh CY, Spakowicz D, Banerjee I, Chen C, Kukurba K, Perelman D, Craig C, Colbert E, Salins D, Rego S, Lee S, Zhang C, Wheeler J, Sailani MR, Liang L, Abbott C, Gerstein M, Mardinoglu A, Smith U, Rubin DL, Pitteri S, Sodergren E, McLaughlin TL, Weinstock GM, Snyder MP. PMID: 29361466; PMCID: PMC6021558.
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    117. A genome-wide association study identifies only two ancestry specific variants associated with spontaneous preterm birth. Sci Rep. 2018 01 09; 8(1):226. Rappoport N, Toung J, Hadley D, Wong RJ, Fujioka K, Reuter J, Abbott CW, Oh S, Hu D, Eng C, Huntsman S, Bodian DL, Niederhuber JE, Hong X, Zhang G, Sikora-Wohfeld W, Gignoux CR, Wang H, Oehlert J, Jelliffe-Pawlowski LL, Gould JB, Darmstadt GL, Wang X, Bustamante CD, Snyder MP, Ziv E, Patsopoulos NA, Muglia LJ, Burchard E, Shaw GM, O'Brodovich HM, Stevenson DK, Butte AJ, Sirota M. PMID: 29317701; PMCID: PMC5760643.
      View in: PubMed   Mentions: 27     Fields:    Translation:HumansCells
    118. Long-Read Sequencing of Human Cytomegalovirus Transcriptome Reveals RNA Isoforms Carrying Distinct Coding Potentials. Sci Rep. 2017 11 22; 7(1):15989. Balázs Z, Tombácz D, Szucs A, Csabai Z, Megyeri K, Petrov AN, Snyder M, Boldogkoi Z. PMID: 29167532; PMCID: PMC5700075.
      View in: PubMed   Mentions: 45     Fields:    Translation:HumansCells
    119. Identification of a novel mutation in the APTX gene associated with ataxia-oculomotor apraxia. Cold Spring Harb Mol Case Stud. 2017 Nov; 3(6). Inlora J, Sailani MR, Khodadadi H, Teymurinezhad A, Takahashi S, Bernstein JA, Garshasbi M, Snyder MP. PMID: 28652255; PMCID: PMC5701303.
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    120. Cell Type-Specific Chromatin Signatures Underline Regulatory DNA Elements in Human Induced Pluripotent Stem Cells and Somatic Cells. Circ Res. 2017 Nov 10; 121(11):1237-1250. Zhao MT, Shao NY, Hu S, Ma N, Srinivasan R, Jahanbani F, Lee J, Zhang SL, Snyder MP, Wu JC. PMID: 29030344; PMCID: PMC5773062.
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    121. Transcriptomic and epigenomic differences in human induced pluripotent stem cells generated from six reprogramming methods. Nat Biomed Eng. 2017 Oct; 1(10):826-837. Churko JM, Lee J, Ameen M, Gu M, Venkatasubramanian M, Diecke S, Sallam K, Im H, Wang G, Gold JD, Salomonis N, Snyder MP, Wu JC. PMID: 30263871; PMCID: PMC6155993.
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    122. Lineage-specific dynamic and pre-established enhancer-promoter contacts cooperate in terminal differentiation. Nat Genet. 2017 Oct; 49(10):1522-1528. Rubin AJ, Barajas BC, Furlan-Magaril M, Lopez-Pajares V, Mumbach MR, Howard I, Kim DS, Boxer LD, Cairns J, Spivakov M, Wingett SW, Shi M, Zhao Z, Greenleaf WJ, Kundaje A, Snyder M, Chang HY, Fraser P, Khavari PA. PMID: 28805829; PMCID: PMC5715812.
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    123. Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis. Nat Commun. 2017 07 05; 8(1):59. Sahraeian SME, Mohiyuddin M, Sebra R, Tilgner H, Afshar PT, Au KF, Bani Asadi N, Gerstein MB, Wong WH, Snyder MP, Schadt E, Lam HYK. PMID: 28680106; PMCID: PMC5498581.
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    124. A Case Report of Hypoglycemia and Hypogammaglobulinemia: DAVID Syndrome in a Patient With a Novel NFKB2 Mutation. J Clin Endocrinol Metab. 2017 07 01; 102(7):2127-2130. Lal RA, Bachrach LK, Hoffman AR, Inlora J, Rego S, Snyder MP, Lewis DB. PMID: 28472507; PMCID: PMC11651530.
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    125. Genome-Wide Temporal Profiling of Transcriptome and Open Chromatin of Early Cardiomyocyte Differentiation Derived From hiPSCs and hESCs. Circ Res. 2017 Aug 04; 121(4):376-391. Liu Q, Jiang C, Xu J, Zhao MT, Van Bortle K, Cheng X, Wang G, Chang HY, Wu JC, Snyder MP. PMID: 28663367; PMCID: PMC5576565.
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    126. Isolated Congenital Anosmia and CNGA2 Mutation. Sci Rep. 2017 06 01; 7(1):2667. Sailani MR, Jingga I, MirMazlomi SH, Bitarafan F, Bernstein JA, Snyder MP, Garshasbi M. PMID: 28572688; PMCID: PMC5454015.
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    127. Histone variant H2A.J accumulates in senescent cells and promotes inflammatory gene expression. Nat Commun. 2017 05 10; 8:14995. Contrepois K, Coudereau C, Benayoun BA, Schuler N, Roux PF, Bischof O, Courbeyrette R, Carvalho C, Thuret JY, Ma Z, Derbois C, Nevers MC, Volland H, Redon CE, Bonner WM, Deleuze JF, Wiel C, Bernard D, Snyder MP, Rübe CE, Olaso R, Fenaille F, Mann C. PMID: 28489069; PMCID: PMC5436145.
      View in: PubMed   Mentions: 98     Fields:    Translation:HumansAnimalsCells
    128. Genome-scale measurement of off-target activity using Cas9 toxicity in high-throughput screens. Nat Commun. 2017 May 05; 8:15178. Morgens DW, Wainberg M, Boyle EA, Ursu O, Araya CL, Tsui CK, Haney MS, Hess GT, Han K, Jeng EE, Li A, Snyder MP, Greenleaf WJ, Kundaje A, Bassik MC. PMID: 28474669; PMCID: PMC5424143.
      View in: PubMed   Mentions: 177     Fields:    Translation:HumansCells
    129. Induced Pluripotent Stem Cell Model of Pulmonary Arterial Hypertension Reveals Novel Gene Expression and Patient Specificity. Am J Respir Crit Care Med. 2017 04 01; 195(7):930-941. Sa S, Gu M, Chappell J, Shao NY, Ameen M, Elliott KA, Li D, Grubert F, Li CG, Taylor S, Cao A, Ma Y, Fong R, Nguyen L, Wu JC, Snyder MP, Rabinovitch M. PMID: 27779452; PMCID: PMC5387706.
      View in: PubMed   Mentions:
    130. De novo and rare mutations in the HSPA1L heat shock gene associated with inflammatory bowel disease. Genome Med. 2017 01 26; 9(1):8. Takahashi S, Andreoletti G, Chen R, Munehira Y, Batra A, Afzal NA, Beattie RM, Bernstein JA, Ennis S, Snyder M. PMID: 28126021; PMCID: PMC5270254.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansCells
    131. Association of AHSG with alopecia and mental retardation (APMR) syndrome. Hum Genet. 2017 03; 136(3):287-296. Reza Sailani M, Jahanbani F, Nasiri J, Behnam M, Salehi M, Sedghi M, Hoseinzadeh M, Takahashi S, Zia A, Gruber J, Lynch JL, Lam D, Winkelmann J, Amirkiai S, Pang B, Rego S, Mazroui S, Bernstein JA, Snyder MP. PMID: 28054173.
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    132. Patient-Specific iPSC-Derived Endothelial Cells Uncover Pathways that Protect against Pulmonary Hypertension in BMPR2 Mutation Carriers. Cell Stem Cell. 2017 04 06; 20(4):490-504.e5. Gu M, Shao NY, Sa S, Li D, Termglinchan V, Ameen M, Karakikes I, Sosa G, Grubert F, Lee J, Cao A, Taylor S, Ma Y, Zhao Z, Chappell J, Hamid R, Austin ED, Gold JD, Wu JC, Snyder MP, Rabinovitch M. PMID: 28017794; PMCID: PMC5500296.
      View in: PubMed   Mentions:
    133. A common class of transcripts with 5'-intron depletion, distinct early coding sequence features, and N1-methyladenosine modification. RNA. 2017 03; 23(3):270-283. Cenik C, Chua HN, Singh G, Akef A, Snyder MP, Palazzo AF, Moore MJ, Roth FP. PMID: 27994090; PMCID: PMC5311483.
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    134. Simul-seq: combined DNA and RNA sequencing for whole-genome and transcriptome profiling. Nat Methods. 2016 Nov; 13(11):953-958. Reuter JA, Spacek DV, Pai RK, Snyder MP. PMID: 27723755; PMCID: PMC5734913.
      View in: PubMed   Mentions:
    135. Transcriptome Profiling of Patient-Specific Human iPSC-Cardiomyocytes Predicts Individual Drug Safety and Efficacy Responses In Vitro. Cell Stem Cell. 2016 09 01; 19(3):311-25. Matsa E, Burridge PW, Yu KH, Ahrens JH, Termglinchan V, Wu H, Liu C, Shukla P, Sayed N, Churko JM, Shao N, Woo NA, Chao AS, Gold JD, Karakikes I, Snyder MP, Wu JC. PMID: 27545504; PMCID: PMC5087997.
      View in: PubMed   Mentions:
    136. Genome assembly from synthetic long read clouds. Bioinformatics. 2016 06 15; 32(12):i216-i224. Kuleshov V, Snyder MP, Batzoglou S. PMID: 27307620; PMCID: PMC4908351.
      View in: PubMed   Mentions:
    137. Identification of significantly mutated regions across cancer types highlights a rich landscape of functional molecular alterations. Nat Genet. 2016 Feb; 48(2):117-25. Araya CL, Cenik C, Reuter JA, Kiss G, Pande VS, Snyder MP, Greenleaf WJ. PMID: 26691984; PMCID: PMC4731297.
      View in: PubMed   Mentions:
    138. Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome. Nat Biotechnol. 2016 Jan; 34(1):64-9. Kuleshov V, Jiang C, Zhou W, Jahanbani F, Batzoglou S, Snyder M. PMID: 26655498; PMCID: PMC4884093.
      View in: PubMed   Mentions:
    139. Identification of Human Neuronal Protein Complexes Reveals Biochemical Activities and Convergent Mechanisms of Action in Autism Spectrum Disorders. Cell Syst. 2015 Nov 25; 1(5):361-374. Li J, Ma Z, Shi M, Malty RH, Aoki H, Minic Z, Phanse S, Jin K, Wall DP, Zhang Z, Urban AE, Hallmayer J, Babu M, Snyder M. PMID: 26949739; PMCID: PMC4776331.
      View in: PubMed   Mentions: 28     Fields:    
    140. H3K4me3 Breadth Is Linked to Cell Identity and Transcriptional Consistency. Cell. 2015 Nov 19; 163(5):1281-1286. Benayoun BA, Pollina EA, Ucar D, Mahmoudi S, Karra K, Wong ED, Devarajan K, Daugherty AC, Kundaje AB, Mancini E, Hitz BC, Gupta R, Rando TA, Baker JC, Snyder MP, Cherry JM, Brunet A. PMID: 28930648.
      View in: PubMed   Mentions: 23     Fields:    
    141. Disease Variant Landscape of a Large Multiethnic Population of Moyamoya Patients by Exome Sequencing. G3 (Bethesda). 2015 Nov 03; 6(1):41-9. Shoemaker LD, Clark MJ, Patwardhan A, Chandratillake G, Garcia S, Chen R, Morgan AA, Leng N, Kirk S, Chen R, Cook DJ, Snyder M, Steinberg GK. PMID: 26530418; PMCID: PMC4704723.
      View in: PubMed   Mentions:
    142. Novel mutations in PIEZO1 cause an autosomal recessive generalized lymphatic dysplasia with non-immune hydrops fetalis. Nat Commun. 2015 Sep 03; 6:8085. Fotiou E, Martin-Almedina S, Simpson MA, Lin S, Gordon K, Brice G, Atton G, Jeffery I, Rees DC, Mignot C, Vogt J, Homfray T, Snyder MP, Rockson SG, Jeffery S, Mortimer PS, Mansour S, Ostergaard P. PMID: 26333996; PMCID: PMC4568316.
      View in: PubMed   Mentions:
    143. Exome Sequencing of Neonatal Blood Spots and the Identification of Genes Implicated in Bronchopulmonary Dysplasia. Am J Respir Crit Care Med. 2015 Sep 01; 192(5):589-96. Li J, Yu KH, Oehlert J, Jeliffe-Pawlowski LL, Gould JB, Stevenson DK, Snyder M, Shaw GM, O'Brodovich HM. PMID: 26030808; PMCID: PMC4595691.
      View in: PubMed   Mentions: 43     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    144. Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans. Genome Res. 2015 Nov; 25(11):1610-21. Cenik C, Cenik ES, Byeon GW, Grubert F, Candille SI, Spacek D, Alsallakh B, Tilgner H, Araya CL, Tang H, Ricci E, Snyder MP. PMID: 26297486; PMCID: PMC4617958.
      View in: PubMed   Mentions:
    145. RNA Sequencing Analysis Detection of a Novel Pathway of Endothelial Dysfunction in Pulmonary Arterial Hypertension. Am J Respir Crit Care Med. 2015 Aug 01; 192(3):356-66. Rhodes CJ, Im H, Cao A, Hennigs JK, Wang L, Sa S, Chen PI, Nickel NP, Miyagawa K, Hopper RK, Tojais NF, Li CG, Gu M, Spiekerkoetter E, Xian Z, Chen R, Zhao M, Kaschwich M, Del Rosario PA, Bernstein D, Zamanian RT, Wu JC, Snyder MP, Rabinovitch M. PMID: 26030479; PMCID: PMC4584250.
      View in: PubMed   Mentions:
    146. Achieving high-sensitivity for clinical applications using augmented exome sequencing. Genome Med. 2015; 7:71. Patwardhan A, Harris J, Leng N, Bartha G, Church DM, Luo S, Haudenschild C, Pratt M, Zook J, Salit M, Tirch J, Morra M, Chervitz S, Li M, Clark M, Garcia S, Chandratillake G, Kirk S, Ashley E, Snyder M, Altman R, Bustamante C, Butte AJ, West J, Chen R. PMID: 26269718; PMCID: PMC4534066.
      View in: PubMed   Mentions: 30     Fields:    Translation:Humans
    147. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature. 2015 Jul 23; 523(7561):486-90. Buenrostro JD, Wu B, Litzenburger UM, Ruff D, Gonzales ML, Snyder MP, Chang HY, Greenleaf WJ. PMID: 26083756; PMCID: PMC4685948.
      View in: PubMed   Mentions:
    148. Comprehensive transcriptome analysis using synthetic long-read sequencing reveals molecular co-association of distant splicing events. Nat Biotechnol. 2015 Jul; 33(7):736-42. Tilgner H, Jahanbani F, Blauwkamp T, Moshrefi A, Jaeger E, Chen F, Harel I, Bustamante CD, Rasmussen M, Snyder MP. PMID: 25985263; PMCID: PMC4832928.
      View in: PubMed   Mentions:
    149. Prospective multicenter study of a synthetic bioabsorbable anal fistula plug to treat cryptoglandular transsphincteric anal fistulas. Dis Colon Rectum. 2015 Mar; 58(3):344-51. Stamos MJ, Snyder M, Robb BW, Ky A, Singer M, Stewart DB, Sonoda T, Abcarian H. PMID: 25664714.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCTClinical Trials
    150. Integrated systems analysis reveals a molecular network underlying autism spectrum disorders. Mol Syst Biol. 2014 Dec 30; 10:774. Li J, Shi M, Ma Z, Zhao S, Euskirchen G, Ziskin J, Urban A, Hallmayer J, Snyder M. PMID: 25549968; PMCID: PMC4300495.
      View in: PubMed   Mentions: 75     Fields:    Translation:HumansAnimalsCells
    151. Exome sequencing and genome-wide copy number variant mapping reveal novel associations with sensorineural hereditary hearing loss. BMC Genomics. 2014 Dec 20; 15:1155. Haraksingh RR, Jahanbani F, Rodriguez-Paris J, Gelernter J, Nadeau KC, Oghalai JS, Schrijver I, Snyder MP. PMID: 25528277; PMCID: PMC4367882.
      View in: PubMed   Mentions: 15     Fields:    Translation:Humans
    152. Principles of regulatory information conservation between mouse and human. Nature. 2014 Nov 20; 515(7527):371-375. Cheng Y, Ma Z, Kim BH, Wu W, Cayting P, Boyle AP, Sundaram V, Xing X, Dogan N, Li J, Euskirchen G, Lin S, Lin Y, Visel A, Kawli T, Yang X, Patacsil D, Keller CA, Giardine B, mouse ENCODE Consortium, Kundaje A, Wang T, Pennacchio LA, Weng Z, Hardison RC, Snyder MP. PMID: 25409826; PMCID: PMC4343047.
      View in: PubMed   Mentions: 175     Fields:    Translation:HumansAnimalsCells
    153. A comparative encyclopedia of DNA elements in the mouse genome. Nature. 2014 Nov 20; 515(7527):355-64. Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, Rynes E, Kirilusha A, Marinov GK, Williams BA, Trout D, Amrhein H, Fisher-Aylor K, Antoshechkin I, DeSalvo G, See LH, Fastuca M, Drenkow J, Zaleski C, Dobin A, Prieto P, Lagarde J, Bussotti G, Tanzer A, Denas O, Li K, Bender MA, Zhang M, Byron R, Groudine MT, McCleary D, Pham L, Ye Z, Kuan S, Edsall L, Wu YC, Rasmussen MD, Bansal MS, Kellis M, Keller CA, Morrissey CS, Mishra T, Jain D, Dogan N, Harris RS, Cayting P, Kawli T, Boyle AP, Euskirchen G, Kundaje A, Lin S, Lin Y, Jansen C, Malladi VS, Cline MS, Erickson DT, Kirkup VM, Learned K, Sloan CA, Rosenbloom KR, Lacerda de Sousa B, Beal K, Pignatelli M, Flicek P, Lian J, Kahveci T, Lee D, Kent WJ, Ramalho Santos M, Herrero J, Notredame C, Johnson A, Vong S, Lee K, Bates D, Neri F, Diegel M, Canfield T, Sabo PJ, Wilken MS, Reh TA, Giste E, Shafer A, Kutyavin T, Haugen E, Dunn D, Reynolds AP, Neph S, Humbert R, Hansen RS, De Bruijn M, Selleri L, Rudensky A, Josefowicz S, Samstein R, Eichler EE, Orkin SH, Levasseur D, Papayannopoulou T, Chang KH, Skoultchi A, Gosh S, Disteche C, Treuting P, Wang Y, Weiss MJ, Blobel GA, Cao X, Zhong S, Wang T, Good PJ, Lowdon RF, Adams LB, Zhou XQ, Pazin MJ, Feingold EA, Wold B, Taylor J, Mortazavi A, Weissman SM, Stamatoyannopoulos JA, Snyder MP, Guigo R, Gingeras TR, Gilbert DM, Hardison RC, Beer MA, Ren B, Mouse ENCODE Consortium. PMID: 25409824; PMCID: PMC4266106.
      View in: PubMed   Mentions: 929     Fields:    Translation:HumansAnimalsCells
    154. Comparison of the transcriptional landscapes between human and mouse tissues. Proc Natl Acad Sci U S A. 2014 Dec 02; 111(48):17224-9. Lin S, Lin Y, Nery JR, Urich MA, Breschi A, Davis CA, Dobin A, Zaleski C, Beer MA, Chapman WC, Gingeras TR, Ecker JR, Snyder MP. PMID: 25413365; PMCID: PMC4260565.
      View in: PubMed   Mentions: 218     Fields:    Translation:HumansAnimalsCells
    155. Genome-wide map of regulatory interactions in the human genome. Genome Res. 2014 Dec; 24(12):1905-17. Heidari N, Phanstiel DH, He C, Grubert F, Jahanbani F, Kasowski M, Zhang MQ, Snyder MP. PMID: 25228660; PMCID: PMC4248309.
      View in: PubMed   Mentions:
    156. Comparative analysis of regulatory information and circuits across distant species. Nature. 2014 Aug 28; 512(7515):453-6. Boyle AP, Araya CL, Brdlik C, Cayting P, Cheng C, Cheng Y, Gardner K, Hillier LW, Janette J, Jiang L, Kasper D, Kawli T, Kheradpour P, Kundaje A, Li JJ, Ma L, Niu W, Rehm EJ, Rozowsky J, Slattery M, Spokony R, Terrell R, Vafeados D, Wang D, Weisdepp P, Wu YC, Xie D, Yan KK, Feingold EA, Good PJ, Pazin MJ, Huang H, Bickel PJ, Brenner SE, Reinke V, Waterston RH, Gerstein M, White KP, Kellis M, Snyder M. PMID: 25164757; PMCID: PMC4336544.
      View in: PubMed   Mentions: 103     Fields:    Translation:HumansAnimalsCells
    157. Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease. Proc Natl Acad Sci U S A. 2014 Aug 19; 111(33):E3366. Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, Giddings MC, Gilbert DM, Gingeras TR, Green ED, Guigo R, Hubbard T, Kent J, Lieb JD, Myers RM, Pazin MJ, Ren B, Stamatoyannopoulos J, Weng Z, White KP, Hardison RC. PMID: 25275169; PMCID: PMC4143047.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    158. Genomic analysis of fibrolamellar hepatocellular carcinoma. Hum Mol Genet. 2015 Jan 01; 24(1):50-63. Xu L, Hazard FK, Zmoos AF, Jahchan N, Chaib H, Garfin PM, Rangaswami A, Snyder MP, Sage J. PMID: 25122662; PMCID: PMC4262492.
      View in: PubMed   Mentions: 48     Fields:    Translation:HumansCells
    159. H3K4me3 breadth is linked to cell identity and transcriptional consistency. Cell. 2014 Jul 31; 158(3):673-88. Benayoun BA, Pollina EA, Ucar D, Mahmoudi S, Karra K, Wong ED, Devarajan K, Daugherty AC, Kundaje AB, Mancini E, Hitz BC, Gupta R, Rando TA, Baker JC, Snyder MP, Cherry JM, Brunet A. PMID: 25083876; PMCID: PMC4137894.
      View in: PubMed   Mentions: 276     Fields:    Translation:HumansAnimalsCells
    160. Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A. 2014 Apr 29; 111(17):6131-8. Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, Giddings MC, Gilbert DM, Gingeras TR, Green ED, Guigo R, Hubbard T, Kent J, Lieb JD, Myers RM, Pazin MJ, Ren B, Stamatoyannopoulos JA, Weng Z, White KP, Hardison RC. PMID: 24753594; PMCID: PMC4035993.
      View in: PubMed   Mentions: 335     Fields:    Translation:HumansCells
    161. Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes. Nat Biotechnol. 2014 Jun; 32(6):562-8. Buenrostro JD, Araya CL, Chircus LM, Layton CJ, Chang HY, Snyder MP, Greenleaf WJ. PMID: 24727714; PMCID: PMC4414031.
      View in: PubMed   Mentions:
    162. Mutations in NGLY1 cause an inherited disorder of the endoplasmic reticulum-associated degradation pathway. Genet Med. 2014 Oct; 16(10):751-8. Enns GM, Shashi V, Bainbridge M, Gambello MJ, Zahir FR, Bast T, Crimian R, Schoch K, Platt J, Cox R, Bernstein JA, Scavina M, Walter RS, Bibb A, Jones M, Hegde M, Graham BH, Need AC, Oviedo A, Schaaf CP, Boyle S, Butte AJ, Chen R, Chen R, Clark MJ, Haraksingh R, FORGE Canada Consortium, Cowan TM, He P, Langlois S, Zoghbi HY, Snyder M, Gibbs RA, Freeze HH, Goldstein DB. PMID: 24651605; PMCID: PMC4243708.
      View in: PubMed   Mentions: 102     Fields:    Translation:HumansCells
    163. Clinical interpretation and implications of whole-genome sequencing. JAMA. 2014 Mar 12; 311(10):1035-45. Dewey FE, Grove ME, Pan C, Goldstein BA, Bernstein JA, Chaib H, Merker JD, Goldfeder RL, Enns GM, David SP, Pakdaman N, Ormond KE, Caleshu C, Kingham K, Klein TE, Whirl-Carrillo M, Sakamoto K, Wheeler MT, Butte AJ, Ford JM, Boxer L, Ioannidis JP, Yeung AC, Altman RB, Assimes TL, Snyder M, Ashley EA, Quertermous T. PMID: 24618965; PMCID: PMC4119063.
      View in: PubMed   Mentions: 223     Fields:    Translation:Humans
    164. Landscape and variation of RNA secondary structure across the human transcriptome. Nature. 2014 Jan 30; 505(7485):706-9. Wan Y, Qu K, Zhang QC, Flynn RA, Manor O, Ouyang Z, Zhang J, Spitale RC, Snyder MP, Segal E, Chang HY. PMID: 24476892; PMCID: PMC3973747.
      View in: PubMed   Mentions: 305     Fields:    Translation:HumansCells
    165. PATH-SCAN: a reporting tool for identifying clinically actionable variants. Pac Symp Biocomput. 2014; 229-40. Daneshjou R, Zappala Z, Kukurba K, Boyle SM, Ormond KE, Klein TE, Snyder M, Bustamante CD, Altman RB, Montgomery SB. PMID: 24297550; PMCID: PMC4008882.
      View in: PubMed   Mentions:
    166. Specific plasma autoantibody reactivity in myelodysplastic syndromes. Sci Rep. 2013 Nov 22; 3:3311. Mias GI, Chen R, Zhang Y, Sridhar K, Sharon D, Xiao L, Im H, Snyder MP, Greenberg PL. PMID: 24264604; PMCID: PMC3837310.
      View in: PubMed   Mentions:
    167. A single-molecule long-read survey of the human transcriptome. Nat Biotechnol. 2013 Nov; 31(11):1009-14. Sharon D, Tilgner H, Grubert F, Snyder M. PMID: 24108091; PMCID: PMC4075632.
      View in: PubMed   Mentions:
    168. Defective sphingosine 1-phosphate receptor 1 (S1P1) phosphorylation exacerbates TH17-mediated autoimmune neuroinflammation. Nat Immunol. 2013 Nov; 14(11):1166-72. Garris CS, Wu L, Acharya S, Arac A, Blaho VA, Huang Y, Moon BS, Axtell RC, Ho PP, Steinberg GK, Lewis DB, Sobel RA, Han DK, Steinman L, Snyder MP, Hla T, Han MH. PMID: 24076635; PMCID: PMC4014310.
      View in: PubMed   Mentions: 84     Fields:    Translation:HumansAnimalsCells
    169. Comprehensive whole-genome sequencing of an early-stage primary myelofibrosis patient defines low mutational burden and non-recurrent candidate genes. Haematologica. 2013 Nov; 98(11):1689-96. Merker JD, Roskin KM, Ng D, Pan C, Fisk DG, King JJ, Hoh R, Stadler M, Okumoto LM, Abidi P, Hewitt R, Jones CD, Gojenola L, Clark MJ, Zhang B, Cherry AM, George TI, Snyder M, Boyd SD, Zehnder JL, Fire AZ, Gotlib J. PMID: 23872309; PMCID: PMC3815168.
      View in: PubMed   Mentions:
    170. Impacts of variation in the human genome on gene regulation. J Mol Biol. 2013 Nov 01; 425(21):3970-7. Haraksingh RR, Snyder MP. PMID: 23871684.
      View in: PubMed   Mentions:
    171. Identification of genes critical for resistance to infection by West Nile virus using RNA-Seq analysis. Viruses. 2013 Jul 08; 5(7):1664-81. Qian F, Chung L, Zheng W, Bruno V, Alexander RP, Wang Z, Wang X, Kurscheid S, Zhao H, Fikrig E, Gerstein M, Snyder M, Montgomery RR. PMID: 23881275; PMCID: PMC3738954.
      View in: PubMed   Mentions:
    172. Overview of high throughput sequencing technologies to elucidate molecular pathways in cardiovascular diseases. Circ Res. 2013 Jun 07; 112(12):1613-23. Churko JM, Mantalas GL, Snyder MP, Wu JC. PMID: 23743227; PMCID: PMC3831009.
      View in: PubMed   Mentions:
    173. Systematic functional regulatory assessment of disease-associated variants. Proc Natl Acad Sci U S A. 2013 Jun 04; 110(23):9607-12. Karczewski KJ, Dudley JT, Kukurba KR, Chen R, Butte AJ, Montgomery SB, Snyder M. PMID: 23690573; PMCID: PMC3677437.
      View in: PubMed   Mentions: 56     Fields:    Translation:HumansCells
    174. Accurate identification and analysis of human mRNA isoforms using deep long read sequencing. G3 (Bethesda). 2013 Mar; 3(3):387-97. Tilgner H, Raha D, Habegger L, Mohiuddin M, Gerstein M, Snyder M. PMID: 23450794; PMCID: PMC3583448.
      View in: PubMed   Mentions:
    175. Tissue-specific direct targets of Caenorhabditis elegans Rb/E2F dictate distinct somatic and germline programs. Genome Biol. 2013 Jan 23; 14(1):R5. Kudron M, Niu W, Lu Z, Wang G, Gerstein M, Snyder M, Reinke V. PMID: 23347407; PMCID: PMC4053757.
      View in: PubMed   Mentions:
    176. Exome sequencing by targeted enrichment. Curr Protoc Mol Biol. 2013; Chapter 7:Unit7.12. Clark MJ, Chen R, Snyder M. PMID: 23547016.
      View in: PubMed   Mentions:
    177. Role of the vagus in the reduced pancreatic exocrine function in copper-deficient rats. Am J Physiol Gastrointest Liver Physiol. 2013 Feb 15; 304(4):G437-48. Babic T, Bhagat R, Wan S, Browning KN, Snyder M, Fortna SR, Travagli RA. PMID: 23275611; PMCID: PMC6842873.
      View in: PubMed   Mentions:
    178. Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors. Genome Biol. 2012 Sep 26; 13(9):R48. Yip KY, Cheng C, Bhardwaj N, Brown JB, Leng J, Kundaje A, Rozowsky J, Birney E, Bickel P, Snyder M, Gerstein M. PMID: 22950945; PMCID: PMC3491392.
      View in: PubMed   Mentions:
    179. Architecture of the human regulatory network derived from ENCODE data. Nature. 2012 Sep 06; 489(7414):91-100. Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R, Min R, Alves P, Abyzov A, Addleman N, Bhardwaj N, Boyle AP, Cayting P, Charos A, Chen DZ, Cheng Y, Clarke D, Eastman C, Euskirchen G, Frietze S, Fu Y, Gertz J, Grubert F, Harmanci A, Jain P, Kasowski M, Lacroute P, Leng JJ, Lian J, Monahan H, O'Geen H, Ouyang Z, Partridge EC, Patacsil D, Pauli F, Raha D, Ramirez L, Reddy TE, Reed B, Shi M, Slifer T, Wang J, Wu L, Yang X, Yip KY, Zilberman-Schapira G, Batzoglou S, Sidow A, Farnham PJ, Myers RM, Weissman SM, Snyder M. PMID: 22955619; PMCID: PMC4154057.
      View in: PubMed   Mentions: 808     Fields:    Translation:HumansCells
    180. Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Res. 2012 Sep; 22(9):1798-812. Wang J, Zhuang J, Iyer S, Lin X, Whitfield TW, Greven MC, Pierce BG, Dong X, Kundaje A, Cheng Y, Rando OJ, Birney E, Myers RM, Noble WS, Snyder M, Weng Z. PMID: 22955990; PMCID: PMC3431495.
      View in: PubMed   Mentions:
    181. Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs. Genome Res. 2012 Sep; 22(9):1616-25. Tilgner H, Knowles DG, Johnson R, Davis CA, Chakrabortty S, Djebali S, Curado J, Snyder M, Gingeras TR, Guigó R. PMID: 22955974; PMCID: PMC3431479.
      View in: PubMed   Mentions:
    182. Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Res. 2012 Sep; 22(9):1658-67. Cheng C, Alexander R, Min R, Leng J, Yip KY, Rozowsky J, Yan KK, Dong X, Djebali S, Ruan Y, Davis CA, Carninci P, Lassman T, Gingeras TR, Guigó R, Birney E, Weng Z, Snyder M, Gerstein M. PMID: 22955978; PMCID: PMC3431483.
      View in: PubMed   Mentions:
    183. Annotation of functional variation in personal genomes using RegulomeDB. Genome Res. 2012 Sep; 22(9):1790-7. Boyle AP, Hong EL, Hariharan M, Cheng Y, Schaub MA, Kasowski M, Karczewski KJ, Park J, Hitz BC, Weng S, Cherry JM, Snyder M. PMID: 22955989; PMCID: PMC3431494.
      View in: PubMed   Mentions:
    184. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 2012 Sep; 22(9):1813-31. Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, Gerstein M, Gertz J, Hartemink AJ, Hoffman MM, Iyer VR, Jung YL, Karmakar S, Kellis M, Kharchenko PV, Li Q, Liu T, Liu XS, Ma L, Milosavljevic A, Myers RM, Park PJ, Pazin MJ, Perry MD, Raha D, Reddy TE, Rozowsky J, Shoresh N, Sidow A, Slattery M, Stamatoyannopoulos JA, Tolstorukov MY, White KP, Xi S, Farnham PJ, Lieb JD, Wold BJ, Snyder M. PMID: 22955991; PMCID: PMC3431496.
      View in: PubMed   Mentions: 1086     Fields:    Translation:HumansAnimals
    185. An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol. 2012 Aug 13; 13(8):418. Mouse ENCODE Consortium, Stamatoyannopoulos JA, Snyder M, Hardison R, Ren B, Gingeras T, Gilbert DM, Groudine M, Bender M, Kaul R, Canfield T, Giste E, Johnson A, Zhang M, Balasundaram G, Byron R, Roach V, Sabo PJ, Sandstrom R, Stehling AS, Thurman RE, Weissman SM, Cayting P, Hariharan M, Lian J, Cheng Y, Landt SG, Ma Z, Wold BJ, Dekker J, Crawford GE, Keller CA, Wu W, Morrissey C, Kumar SA, Mishra T, Jain D, Byrska-Bishop M, Blankenberg D, Lajoie BR, Jain G, Sanyal A, Chen KB, Denas O, Taylor J, Blobel GA, Weiss MJ, Pimkin M, Deng W, Marinov GK, Williams BA, Fisher-Aylor KI, Desalvo G, Kiralusha A, Trout D, Amrhein H, Mortazavi A, Edsall L, McCleary D, Kuan S, Shen Y, Yue F, Ye Z, Davis CA, Zaleski C, Jha S, Xue C, Dobin A, Lin W, Fastuca M, Wang H, Guigo R, Djebali S, Lagarde J, Ryba T, Sasaki T, Malladi VS, Cline MS, Kirkup VM, Learned K, Rosenbloom KR, Kent WJ, Feingold EA, Good PJ, Pazin M, Lowdon RF, Adams LB. PMID: 22889292; PMCID: PMC3491367.
      View in: PubMed   Mentions: 296     Fields:    Translation:HumansAnimals
    186. VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment. Bioinformatics. 2012 Sep 01; 28(17):2267-9. Habegger L, Balasubramanian S, Chen DZ, Khurana E, Sboner A, Harmanci A, Rozowsky J, Clarke D, Snyder M, Gerstein M. PMID: 22743228; PMCID: PMC3426844.
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    187. Patient-specific induced pluripotent stem cells as a model for familial dilated cardiomyopathy. Sci Transl Med. 2012 Apr 18; 4(130):130ra47. Sun N, Yazawa M, Liu J, Han L, Sanchez-Freire V, Abilez OJ, Navarrete EG, Hu S, Wang L, Lee A, Pavlovic A, Lin S, Chen R, Hajjar RJ, Snyder MP, Dolmetsch RE, Butte MJ, Ashley EA, Longaker MT, Robbins RC, Wu JC. PMID: 22517884; PMCID: PMC3657516.
      View in: PubMed   Mentions: 392     Fields:    Translation:HumansCells
    188. Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell. 2012 Mar 16; 148(6):1293-307. Chen R, Mias GI, Li-Pook-Than J, Jiang L, Lam HY, Chen R, Miriami E, Karczewski KJ, Hariharan M, Dewey FE, Cheng Y, Clark MJ, Im H, Habegger L, Balasubramanian S, O'Huallachain M, Dudley JT, Hillenmeyer S, Haraksingh R, Sharon D, Euskirchen G, Lacroute P, Bettinger K, Boyle AP, Kasowski M, Grubert F, Seki S, Garcia M, Whirl-Carrillo M, Gallardo M, Blasco MA, Greenberg PL, Snyder P, Klein TE, Altman RB, Butte AJ, Ashley EA, Gerstein M, Nadeau KC, Tang H, Snyder M. PMID: 22424236; PMCID: PMC3341616.
      View in: PubMed   Mentions: 536     Fields:    Translation:HumansCells
    189. Tcf7 is an important regulator of the switch of self-renewal and differentiation in a multipotential hematopoietic cell line. PLoS Genet. 2012; 8(3):e1002565. Wu JQ, Seay M, Schulz VP, Hariharan M, Tuck D, Lian J, Du J, Shi M, Ye Z, Gerstein M, Snyder MP, Weissman S. PMID: 22412390; PMCID: PMC3297581.
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    190. Detecting and annotating genetic variations using the HugeSeq pipeline. Nat Biotechnol. 2012 Mar 07; 30(3):226-9. Lam HY, Pan C, Clark MJ, Lacroute P, Chen R, Haraksingh R, O'Huallachain M, Gerstein MB, Kidd JM, Bustamante CD, Snyder M. PMID: 22398614; PMCID: PMC4720384.
      View in: PubMed   Mentions:
    191. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell. 2012 Jan 20; 148(1-2):84-98. Li G, Ruan X, Auerbach RK, Sandhu KS, Zheng M, Wang P, Poh HM, Goh Y, Lim J, Zhang J, Sim HS, Peh SQ, Mulawadi FH, Ong CT, Orlov YL, Hong S, Zhang Z, Landt S, Raha D, Euskirchen G, Wei CL, Ge W, Wang H, Davis C, Fisher-Aylor KI, Mortazavi A, Gerstein M, Gingeras T, Wold B, Sun Y, Fullwood MJ, Cheung E, Liu E, Sung WK, Snyder M, Ruan Y. PMID: 22265404; PMCID: PMC3339270.
      View in: PubMed   Mentions: 741     Fields:    Translation:HumansCells
    192. Performance comparison of whole-genome sequencing platforms. Nat Biotechnol. 2011 Dec 18; 30(1):78-82. Lam HY, Clark MJ, Chen R, Chen R, Natsoulis G, O'Huallachain M, Dewey FE, Habegger L, Ashley EA, Gerstein MB, Butte AJ, Ji HP, Snyder M. PMID: 22178993; PMCID: PMC4076012.
      View in: PubMed   Mentions: 172     Fields:    Translation:Humans
    193. Genome-wide mapping of copy number variation in humans: comparative analysis of high resolution array platforms. PLoS One. 2011; 6(11):e27859. Haraksingh RR, Abyzov A, Gerstein M, Urban AE, Snyder M. PMID: 22140474; PMCID: PMC3227574.
      View in: PubMed   Mentions:
    194. Construction and analysis of an integrated regulatory network derived from high-throughput sequencing data. PLoS Comput Biol. 2011 Nov; 7(11):e1002190. Cheng C, Yan KK, Hwang W, Qian J, Bhardwaj N, Rozowsky J, Lu ZJ, Niu W, Alves P, Kato M, Snyder M, Gerstein M. PMID: 22125477; PMCID: PMC3219617.
      View in: PubMed   Mentions:
    195. Performance comparison of exome DNA sequencing technologies. Nat Biotechnol. 2011 Sep 25; 29(10):908-14. Clark MJ, Chen R, Lam HY, Karczewski KJ, Chen R, Euskirchen G, Butte AJ, Snyder M. PMID: 21947028; PMCID: PMC4127531.
      View in: PubMed   Mentions: 246     Fields:    Translation:HumansCells
    196. Phased whole-genome genetic risk in a family quartet using a major allele reference sequence. PLoS Genet. 2011 Sep; 7(9):e1002280. Dewey FE, Chen R, Cordero SP, Ormond KE, Caleshu C, Karczewski KJ, Whirl-Carrillo M, Wheeler MT, Dudley JT, Byrnes JK, Cornejo OE, Knowles JW, Woon M, Sangkuhl K, Gong L, Thorn CF, Hebert JM, Capriotti E, David SP, Pavlovic A, West A, Thakuria JV, Ball MP, Zaranek AW, Rehm HL, Church GM, West JS, Bustamante CD, Snyder M, Altman RB, Klein TE, Butte AJ, Ashley EA. PMID: 21935354; PMCID: PMC3174201.
      View in: PubMed   Mentions: 85     Fields:    Translation:HumansCells
    197. AlleleSeq: analysis of allele-specific expression and binding in a network framework. Mol Syst Biol. 2011 Aug 02; 7:522. Rozowsky J, Abyzov A, Wang J, Alves P, Raha D, Harmanci A, Leng J, Bjornson R, Kong Y, Kitabayashi N, Bhardwaj N, Rubin M, Snyder M, Gerstein M. PMID: 21811232; PMCID: PMC3208341.
      View in: PubMed   Mentions:
    198. Cooperative transcription factor associations discovered using regulatory variation. Proc Natl Acad Sci U S A. 2011 Aug 09; 108(32):13353-8. Karczewski KJ, Tatonetti NP, Landt SG, Yang X, Slifer T, Altman RB, Snyder M. PMID: 21828005; PMCID: PMC3156166.
      View in: PubMed   Mentions:
    199. Identification of genomic indels and structural variations using split reads. BMC Genomics. 2011 Jul 25; 12:375. Zhang ZD, Du J, Lam H, Abyzov A, Urban AE, Snyder M, Gerstein M. PMID: 21787423; PMCID: PMC3161018.
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    200. A large gene network in immature erythroid cells is controlled by the myeloid and B cell transcriptional regulator PU.1. PLoS Genet. 2011 Jun; 7(6):e1001392. Wontakal SN, Guo X, Will B, Shi M, Raha D, Mahajan MC, Weissman S, Snyder M, Steidl U, Zheng D, Skoultchi AI. PMID: 21695229; PMCID: PMC3111485.
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    201. Diverse protein kinase interactions identified by protein microarrays reveal novel connections between cellular processes. Genes Dev. 2011 Apr 01; 25(7):767-78. Fasolo J, Sboner A, Sun MG, Yu H, Chen R, Sharon D, Kim PM, Gerstein M, Snyder M. PMID: 21460040; PMCID: PMC3070938.
      View in: PubMed   Mentions:
    202. The CRIT framework for identifying cross patterns in systems biology and application to chemogenomics. Genome Biol. 2011; 12(3):R32. Gianoulis TA, Agarwal A, Snyder M, Gerstein MB. PMID: 21453526; PMCID: PMC3129682.
      View in: PubMed   Mentions:
    203. Diverse roles and interactions of the SWI/SNF chromatin remodeling complex revealed using global approaches. PLoS Genet. 2011 Mar; 7(3):e1002008. Euskirchen GM, Auerbach RK, Davidov E, Gianoulis TA, Zhong G, Rozowsky J, Bhardwaj N, Gerstein MB, Snyder M. PMID: 21408204; PMCID: PMC3048368.
      View in: PubMed   Mentions:
    204. CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res. 2011 Jun; 21(6):974-84. Abyzov A, Urban AE, Snyder M, Gerstein M. PMID: 21324876; PMCID: PMC3106330.
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    205. Mapping copy number variation by population-scale genome sequencing. Nature. 2011 Feb 03; 470(7332):59-65. Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva LM, Iqbal Z, Kang S, Kidd JM, Konkel MK, Korn J, Khurana E, Kural D, Lam HY, Leng J, Li R, Li Y, Lin CY, Luo R, Mu XJ, Nemesh J, Peckham HE, Rausch T, Scally A, Shi X, Stromberg MP, Stütz AM, Urban AE, Walker JA, Wu J, Zhang Y, Zhang ZD, Batzer MA, Ding L, Marth GT, McVean G, Sebat J, Snyder M, Wang J, Ye K, Eichler EE, Gerstein MB, Hurles ME, Lee C, McCarroll SA, Korbel JO, 1000 Genomes Project. PMID: 21293372; PMCID: PMC3077050.
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    206. Measuring the evolutionary rewiring of biological networks. PLoS Comput Biol. 2011 Jan 06; 7(1):e1001050. Shou C, Bhardwaj N, Lam HY, Yan KK, Kim PM, Snyder M, Gerstein MB. PMID: 21253555; PMCID: PMC3017101.
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    207. Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans. Genome Res. 2011 Feb; 21(2):245-54. Niu W, Lu ZJ, Zhong M, Sarov M, Murray JI, Brdlik CM, Janette J, Chen C, Alves P, Preston E, Slightham C, Jiang L, Hyman AA, Kim SK, Waterston RH, Gerstein M, Snyder M, Reinke V. PMID: 21177963; PMCID: PMC3032928.
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    208. Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data. Genome Res. 2011 Feb; 21(2):276-85. Lu ZJ, Yip KY, Wang G, Shou C, Hillier LW, Khurana E, Agarwal A, Auerbach R, Rozowsky J, Cheng C, Kato M, Miller DM, Slack F, Snyder M, Waterston RH, Reinke V, Gerstein MB. PMID: 21177971; PMCID: PMC3032931.
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    209. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science. 2010 Dec 24; 330(6012):1775-87. Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R, Rechtsteiner A, Ikegami K, Alves P, Chateigner A, Perry M, Morris M, Auerbach RK, Feng X, Leng J, Vielle A, Niu W, Rhrissorrakrai K, Agarwal A, Alexander RP, Barber G, Brdlik CM, Brennan J, Brouillet JJ, Carr A, Cheung MS, Clawson H, Contrino S, Dannenberg LO, Dernburg AF, Desai A, Dick L, Dosé AC, Du J, Egelhofer T, Ercan S, Euskirchen G, Ewing B, Feingold EA, Gassmann R, Good PJ, Green P, Gullier F, Gutwein M, Guyer MS, Habegger L, Han T, Henikoff JG, Henz SR, Hinrichs A, Holster H, Hyman T, Iniguez AL, Janette J, Jensen M, Kato M, Kent WJ, Kephart E, Khivansara V, Khurana E, Kim JK, Kolasinska-Zwierz P, Lai EC, Latorre I, Leahey A, Lewis S, Lloyd P, Lochovsky L, Lowdon RF, Lubling Y, Lyne R, MacCoss M, Mackowiak SD, Mangone M, McKay S, Mecenas D, Merrihew G, Miller DM, Muroyama A, Murray JI, Ooi SL, Pham H, Phippen T, Preston EA, Rajewsky N, Rätsch G, Rosenbaum H, Rozowsky J, Rutherford K, Ruzanov P, Sarov M, Sasidharan R, Sboner A, Scheid P, Segal E, Shin H, Shou C, Slack FJ, Slightam C, Smith R, Spencer WC, Stinson EO, Taing S, Takasaki T, Vafeados D, Voronina K, Wang G, Washington NL, Whittle CM, Wu B, Yan KK, Zeller G, Zha Z, Zhong M, Zhou X, modENCODE Consortium, Ahringer J, Strome S, Gunsalus KC, Micklem G, Liu XS, Reinke V, Kim SK, Hillier LW, Henikoff S, Piano F, Snyder M, Stein L, Lieb JD, Waterston RH. PMID: 21177976; PMCID: PMC3142569.
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    210. RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries. Bioinformatics. 2011 Jan 15; 27(2):281-3. Habegger L, Sboner A, Gianoulis TA, Rozowsky J, Agarwal A, Snyder M, Gerstein M. PMID: 21134889; PMCID: PMC3018817.
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    211. Extensive in vivo metabolite-protein interactions revealed by large-scale systematic analyses. Cell. 2010 Nov 12; 143(4):639-50. Li X, Gianoulis TA, Yip KY, Gerstein M, Snyder M. PMID: 21035178; PMCID: PMC3005334.
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    212. Annotating non-coding regions of the genome. Nat Rev Genet. 2010 Aug; 11(8):559-71. Alexander RP, Fang G, Rozowsky J, Snyder M, Gerstein MB. PMID: 20628352.
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    213. MOTIPS: automated motif analysis for predicting targets of modular protein domains. BMC Bioinformatics. 2010 May 11; 11:243. Lam HY, Kim PM, Mok J, Tonikian R, Sidhu SS, Turk BE, Snyder M, Gerstein MB. PMID: 20459839; PMCID: PMC2882932.
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    214. Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells. Nat Struct Mol Biol. 2010 May; 17(5):635-40. Moqtaderi Z, Wang J, Raha D, White RJ, Snyder M, Weng Z, Struhl K. PMID: 20418883; PMCID: PMC3350333.
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    215. Variation in transcription factor binding among humans. Science. 2010 Apr 09; 328(5975):232-5. Kasowski M, Grubert F, Heffelfinger C, Hariharan M, Asabere A, Waszak SM, Habegger L, Rozowsky J, Shi M, Urban AE, Hong MY, Karczewski KJ, Huber W, Weissman SM, Gerstein MB, Korbel JO, Snyder M. PMID: 20299548; PMCID: PMC2938768.
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    216. Personal genome sequencing: current approaches and challenges. Genes Dev. 2010 Mar 01; 24(5):423-31. Snyder M, Du J, Gerstein M. PMID: 20194435; PMCID: PMC2827837.
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    217. Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing. Proc Natl Acad Sci U S A. 2010 Mar 16; 107(11):5254-9. Wu JQ, Habegger L, Noisa P, Szekely A, Qiu C, Hutchison S, Raha D, Egholm M, Lin H, Weissman S, Cui W, Gerstein M, Snyder M. PMID: 20194744; PMCID: PMC2841935.
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    218. Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response. PLoS Genet. 2010 Feb 19; 6(2):e1000848. Zhong M, Niu W, Lu ZJ, Sarov M, Murray JI, Janette J, Raha D, Sheaffer KL, Lam HY, Preston E, Slightham C, Hillier LW, Brock T, Agarwal A, Auerbach R, Hyman AA, Gerstein M, Mango SE, Kim SK, Waterston RH, Reinke V, Snyder M. PMID: 20174564; PMCID: PMC2824807.
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    219. Deciphering protein kinase specificity through large-scale analysis of yeast phosphorylation site motifs. Sci Signal. 2010 Feb 16; 3(109):ra12. Mok J, Kim PM, Lam HY, Piccirillo S, Zhou X, Jeschke GR, Sheridan DL, Parker SA, Desai V, Jwa M, Cameroni E, Niu H, Good M, Remenyi A, Ma JL, Sheu YJ, Sassi HE, Sopko R, Chan CS, De Virgilio C, Hollingsworth NM, Lim WA, Stern DF, Stillman B, Andrews BJ, Gerstein MB, Snyder M, Turk BE. PMID: 20159853; PMCID: PMC2846625.
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    220. Close association of RNA polymerase II and many transcription factors with Pol III genes. Proc Natl Acad Sci U S A. 2010 Feb 23; 107(8):3639-44. Raha D, Wang Z, Moqtaderi Z, Wu L, Zhong G, Gerstein M, Struhl K, Snyder M. PMID: 20139302; PMCID: PMC2840497.
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    221. Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library. Nat Biotechnol. 2010 Jan; 28(1):47-55. Lam HY, Mu XJ, Stütz AM, Tanzer A, Cayting PD, Snyder M, Kim PM, Korbel JO, Gerstein MB. PMID: 20037582; PMCID: PMC2951730.
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    222. EBNA1 regulates cellular gene expression by binding cellular promoters. Proc Natl Acad Sci U S A. 2009 Dec 29; 106(52):22421-6. Canaan A, Haviv I, Urban AE, Schulz VP, Hartman S, Zhang Z, Palejev D, Deisseroth AB, Lacy J, Snyder M, Gerstein M, Weissman SM. PMID: 20080792; PMCID: PMC2799695.
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    223. Mapping accessible chromatin regions using Sono-Seq. Proc Natl Acad Sci U S A. 2009 Sep 01; 106(35):14926-31. Auerbach RK, Euskirchen G, Rozowsky J, Lamarre-Vincent N, Moqtaderi Z, Lefrançois P, Struhl K, Gerstein M, Snyder M. PMID: 19706456; PMCID: PMC2736440.
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    224. The genetic architecture of Down syndrome phenotypes revealed by high-resolution analysis of human segmental trisomies. Proc Natl Acad Sci U S A. 2009 Jul 21; 106(29):12031-6. Korbel JO, Tirosh-Wagner T, Urban AE, Chen XN, Kasowski M, Dai L, Grubert F, Erdman C, Gao MC, Lange K, Sobel EM, Barlow GM, Aylsworth AS, Carpenter NJ, Clark RD, Cohen MY, Doran E, Falik-Zaccai T, Lewin SO, Lott IT, McGillivray BC, Moeschler JB, Pettenati MJ, Pueschel SM, Rao KW, Shaffer LG, Shohat M, Van Riper AJ, Warburton D, Weissman S, Gerstein MB, Snyder M, Korenberg JR. PMID: 19597142; PMCID: PMC2709665.
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    225. Integrating sequencing technologies in personal genomics: optimal low cost reconstruction of structural variants. PLoS Comput Biol. 2009 Jul; 5(7):e1000432. Du J, Bjornson RD, Zhang ZD, Kong Y, Snyder M, Gerstein MB. PMID: 19593373; PMCID: PMC2700963.
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    226. Unlocking the secrets of the genome. Nature. 2009 Jun 18; 459(7249):927-30. Celniker SE, Dillon LA, Gerstein MB, Gunsalus KC, Henikoff S, Karpen GH, Kellis M, Lai EC, Lieb JD, MacAlpine DM, Micklem G, Piano F, Snyder M, Stein L, White KP, Waterston RH, modENCODE Consortium. PMID: 19536255; PMCID: PMC2843545.
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    227. Dynamic and complex transcription factor binding during an inducible response in yeast. Genes Dev. 2009 Jun 01; 23(11):1351-63. Ni L, Bruce C, Hart C, Leigh-Bell J, Gelperin D, Umansky L, Gerstein MB, Snyder M. PMID: 19487574; PMCID: PMC2701586.
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    228. Personal phenotypes to go with personal genomes. Mol Syst Biol. 2009; 5:273. Snyder M, Weissman S, Gerstein M. PMID: 19455137; PMCID: PMC2694681.
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    229. Distinct genomic aberrations associated with ERG rearranged prostate cancer. Genes Chromosomes Cancer. 2009 Apr; 48(4):366-80. Demichelis F, Setlur SR, Beroukhim R, Perner S, Korbel JO, Lafargue CJ, Pflueger D, Pina C, Hofer MD, Sboner A, Svensson MA, Rickman DS, Urban A, Snyder M, Meyerson M, Lee C, Gerstein MB, Kuefer R, Rubin MA. PMID: 19156837; PMCID: PMC2674964.
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    230. PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Genome Biol. 2009 Feb 23; 10(2):R23. Korbel JO, Abyzov A, Mu XJ, Carriero N, Cayting P, Zhang Z, Snyder M, Gerstein MB. PMID: 19236709; PMCID: PMC2688268.
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    231. Quantifying environmental adaptation of metabolic pathways in metagenomics. Proc Natl Acad Sci U S A. 2009 Feb 03; 106(5):1374-9. Gianoulis TA, Raes J, Patel PV, Bjornson R, Korbel JO, Letunic I, Yamada T, Paccanaro A, Jensen LJ, Snyder M, Bork P, Gerstein MB. PMID: 19164758; PMCID: PMC2629784.
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    232. Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing. BMC Genomics. 2009 Jan 21; 10:37. Lefrançois P, Euskirchen GM, Auerbach RK, Rozowsky J, Gibson T, Yellman CM, Gerstein M, Snyder M. PMID: 19159457; PMCID: PMC2656530.
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    233. A myelopoiesis-associated regulatory intergenic noncoding RNA transcript within the human HOXA cluster. Blood. 2009 Mar 12; 113(11):2526-34. Zhang X, Lian Z, Padden C, Gerstein MB, Rozowsky J, Snyder M, Gingeras TR, Kapranov P, Weissman SM, Newburger PE. PMID: 19144990; PMCID: PMC2656274.
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    234. PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol. 2009 Jan; 27(1):66-75. Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein MB. PMID: 19122651; PMCID: PMC2924752.
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    235. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2009 Jan; 10(1):57-63. Wang Z, Gerstein M, Snyder M. PMID: 19015660; PMCID: PMC2949280.
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    236. Mismatch oligonucleotides in human and yeast: guidelines for probe design on tiling microarrays. BMC Genomics. 2008 Dec 31; 9:635. Seringhaus M, Rozowsky J, Royce T, Nagalakshmi U, Jee J, Snyder M, Gerstein M. PMID: 19117516; PMCID: PMC2642824.
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    237. MAPK target networks in Arabidopsis thaliana revealed using functional protein microarrays. Genes Dev. 2009 Jan 01; 23(1):80-92. Popescu SC, Popescu GV, Bachan S, Zhang Z, Gerstein M, Snyder M, Dinesh-Kumar SP. PMID: 19095804; PMCID: PMC2632172.
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    238. MSB: a mean-shift-based approach for the analysis of structural variation in the genome. Genome Res. 2009 Jan; 19(1):106-17. Wang LY, Abyzov A, Korbel JO, Snyder M, Gerstein M. PMID: 19037015; PMCID: PMC2612956.
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    239. High-resolution copy-number variation map reflects human olfactory receptor diversity and evolution. PLoS Genet. 2008 Nov; 4(11):e1000249. Hasin Y, Olender T, Khen M, Gonzaga-Jauregui C, Kim PM, Urban AE, Snyder M, Gerstein MB, Lancet D, Korbel JO. PMID: 18989455; PMCID: PMC2570968.
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    240. Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history. Genome Res. 2008 Dec; 18(12):1865-74. Kim PM, Lam HY, Urban AE, Korbel JO, Affourtit J, Grubert F, Chen X, Weissman S, Snyder M, Gerstein MB. PMID: 18842824; PMCID: PMC2593581.
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    241. Modeling ChIP sequencing in silico with applications. PLoS Comput Biol. 2008 Aug 22; 4(8):e1000158. Zhang ZD, Rozowsky J, Snyder M, Chang J, Gerstein M. PMID: 18725927; PMCID: PMC2507756.
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    242. The current excitement about copy-number variation: how it relates to gene duplications and protein families. Curr Opin Struct Biol. 2008 Jun; 18(3):366-74. Korbel JO, Kim PM, Chen X, Urban AE, Weissman S, Snyder M, Gerstein MB. PMID: 18511261; PMCID: PMC2577873.
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    243. A genomic analysis of RNA polymerase II modification and chromatin architecture related to 3' end RNA polyadenylation. Genome Res. 2008 Aug; 18(8):1224-37. Lian Z, Karpikov A, Lian J, Mahajan MC, Hartman S, Gerstein M, Snyder M, Weissman SM. PMID: 18487515; PMCID: PMC2493437.
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    244. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science. 2008 Jun 06; 320(5881):1344-9. Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M. PMID: 18451266; PMCID: PMC2951732.
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    245. Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res. 2008 Mar; 18(3):393-403. Johnson DS, Li W, Gordon DB, Bhattacharjee A, Curry B, Ghosh J, Brizuela L, Carroll JS, Brown M, Flicek P, Koch CM, Dunham I, Bieda M, Xu X, Farnham PJ, Kapranov P, Nix DA, Gingeras TR, Zhang X, Holster H, Jiang N, Green RD, Song JS, McCuine SA, Anton E, Nguyen L, Trinklein ND, Ye Z, Ching K, Hawkins D, Ren B, Scacheri PC, Rozowsky J, Karpikov A, Euskirchen G, Weissman S, Gerstein M, Snyder M, Yang A, Moqtaderi Z, Hirsch H, Shulha HP, Fu Y, Weng Z, Struhl K, Myers RM, Lieb JD, Liu XS. PMID: 18258921; PMCID: PMC2259103.
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    246. Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome. Genome Biol. 2008 Jan 03; 9(1):R3. Wu JQ, Du J, Rozowsky J, Zhang Z, Urban AE, Euskirchen G, Weissman S, Gerstein M, Snyder M. PMID: 18173853; PMCID: PMC2395237.
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    247. Paired-end mapping reveals extensive structural variation in the human genome. Science. 2007 Oct 19; 318(5849):420-6. Korbel JO, Urban AE, Affourtit JP, Godwin B, Grubert F, Simons JF, Kim PM, Palejev D, Carriero NJ, Du L, Taillon BE, Chen Z, Tanzer A, Saunders AC, Chi J, Yang F, Carter NP, Hurles ME, Weissman SM, Harkins TT, Gerstein MB, Egholm M, Snyder M. PMID: 17901297; PMCID: PMC2674581.
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    248. Divergence of transcription factor binding sites across related yeast species. Science. 2007 Aug 10; 317(5839):815-9. Borneman AR, Gianoulis TA, Zhang ZD, Yu H, Rozowsky J, Seringhaus MR, Wang LY, Gerstein M, Snyder M. PMID: 17690298.
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    249. Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms. Funct Integr Genomics. 2007 Oct; 7(4):335-45. Borneman AR, Zhang ZD, Rozowsky J, Seringhaus MR, Gerstein M, Snyder M. PMID: 17638031.
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    250. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007 Jun 14; 447(7146):799-816. ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA, NISC Comparative Sequencing Program, Baylor College of Medicine Human Genome Sequencing Center, Washington University Genome Sequencing Center, Broad Institute, Children's Hospital Oakland Research Institute, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ. PMID: 17571346; PMCID: PMC2212820.
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    251. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods. 2007 Aug; 4(8):651-7. Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A, Thiessen N, Griffith OL, He A, Marra M, Snyder M, Jones S. PMID: 17558387.
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    252. Systematic prediction and validation of breakpoints associated with copy-number variants in the human genome. Proc Natl Acad Sci U S A. 2007 Jun 12; 104(24):10110-5. Korbel JO, Urban AE, Grubert F, Du J, Royce TE, Starr P, Zhong G, Emanuel BS, Weissman SM, Snyder M, Gerstein MB. PMID: 17551006; PMCID: PMC1891248.
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    253. Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies. Genome Res. 2007 Jun; 17(6):898-909. Euskirchen GM, Rozowsky JS, Wei CL, Lee WH, Zhang ZD, Hartman S, Emanuelsson O, Stolc V, Weissman S, Gerstein MB, Ruan Y, Snyder M. PMID: 17568005; PMCID: PMC1891348.
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    254. Structured RNAs in the ENCODE selected regions of the human genome. Genome Res. 2007 Jun; 17(6):852-64. Washietl S, Pedersen JS, Korbel JO, Stocsits C, Gruber AR, Hackermüller J, Hertel J, Lindemeyer M, Reiche K, Tanzer A, Ucla C, Wyss C, Antonarakis SE, Denoeud F, Lagarde J, Drenkow J, Kapranov P, Gingeras TR, Guigó R, Snyder M, Gerstein MB, Reymond A, Hofacker IL, Stadler PF. PMID: 17568003; PMCID: PMC1891344.
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    255. Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome Res. 2007 Jun; 17(6):839-51. Zheng D, Frankish A, Baertsch R, Kapranov P, Reymond A, Choo SW, Lu Y, Denoeud F, Antonarakis SE, Snyder M, Ruan Y, Wei CL, Gingeras TR, Guigó R, Harrow J, Gerstein MB. PMID: 17568002; PMCID: PMC1891343.
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    256. Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions. Genome Res. 2007 Jun; 17(6):787-97. Zhang ZD, Paccanaro A, Fu Y, Weissman S, Weng Z, Chang J, Snyder M, Gerstein MB. PMID: 17567997; PMCID: PMC1891338.
      View in: PubMed   Mentions:
    257. The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci. Genome Res. 2007 Jun; 17(6):732-45. Rozowsky JS, Newburger D, Sayward F, Wu J, Jordan G, Korbel JO, Nagalakshmi U, Yang J, Zheng D, Guigó R, Gingeras TR, Weissman S, Miller P, Snyder M, Gerstein MB. PMID: 17567993; PMCID: PMC1891334.
      View in: PubMed   Mentions:
    258. What is a gene, post-ENCODE? History and updated definition. Genome Res. 2007 Jun; 17(6):669-81. Gerstein MB, Bruce C, Rozowsky JS, Zheng D, Du J, Korbel JO, Emanuelsson O, Zhang ZD, Weissman S, Snyder M. PMID: 17567988.
      View in: PubMed   Mentions:
    259. Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome. Genome Res. 2007 Jun; 17(6):720-31. Trinklein ND, Karaöz U, Wu J, Halees A, Force Aldred S, Collins PJ, Zheng D, Zhang ZD, Gerstein MB, Snyder M, Myers RM, Weng Z. PMID: 17567992; PMCID: PMC1891333.
      View in: PubMed   Mentions:
    260. Getting connected: analysis and principles of biological networks. Genes Dev. 2007 May 01; 21(9):1010-24. Zhu X, Gerstein M, Snyder M. PMID: 17473168.
      View in: PubMed   Mentions:
    261. New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis. Genes Dev. 2007 Mar 01; 21(5):601-14. Smith MG, Gianoulis TA, Pukatzki S, Mekalanos JJ, Ornston LN, Gerstein M, Snyder M. PMID: 17344419; PMCID: PMC1820901.
      View in: PubMed   Mentions:
    262. Differential binding of calmodulin-related proteins to their targets revealed through high-density Arabidopsis protein microarrays. Proc Natl Acad Sci U S A. 2007 Mar 13; 104(11):4730-5. Popescu SC, Popescu GV, Bachan S, Zhang Z, Seay M, Gerstein M, Snyder M, Dinesh-Kumar SP. PMID: 17360592; PMCID: PMC1838668.
      View in: PubMed   Mentions:
    263. Tilescope: online analysis pipeline for high-density tiling microarray data. Genome Biol. 2007; 8(5):R81. Zhang ZD, Rozowsky J, Lam HY, Du J, Snyder M, Gerstein M. PMID: 17501994; PMCID: PMC1929149.
      View in: PubMed   Mentions:
    264. Positional artifacts in microarrays: experimental verification and construction of COP, an automated detection tool. Nucleic Acids Res. 2007; 35(2):e8. Yu H, Nguyen K, Royce T, Qian J, Nelson K, Snyder M, Gerstein M. PMID: 17158151; PMCID: PMC1802630.
      View in: PubMed   Mentions:
    265. Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome. Genome Res. 2007 Jun; 17(6):886-97. Emanuelsson O, Nagalakshmi U, Zheng D, Rozowsky JS, Urban AE, Du J, Lian Z, Stolc V, Weissman S, Snyder M, Gerstein MB. PMID: 17119069; PMCID: PMC1891347.
      View in: PubMed   Mentions:
    266. A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledge. Bioinformatics. 2006 Dec 15; 22(24):3016-24. Du J, Rozowsky JS, Korbel JO, Zhang ZD, Royce TE, Schultz MH, Snyder M, Gerstein M. PMID: 17038339.
      View in: PubMed   Mentions:
    267. TOS9 regulates white-opaque switching in Candida albicans. Eukaryot Cell. 2006 Oct; 5(10):1674-87. Srikantha T, Borneman AR, Daniels KJ, Pujol C, Wu W, Seringhaus MR, Gerstein M, Yi S, Snyder M, Soll DR. PMID: 16950924; PMCID: PMC1595353.
      View in: PubMed   Mentions:
    268. Predicting essential genes in fungal genomes. Genome Res. 2006 Sep; 16(9):1126-35. Seringhaus M, Paccanaro A, Borneman A, Snyder M, Gerstein M. PMID: 16899653; PMCID: PMC1557763.
      View in: PubMed   Mentions:
    269. Genomic analysis of insertion behavior and target specificity of mini-Tn7 and Tn3 transposons in Saccharomyces cerevisiae. Nucleic Acids Res. 2006 Apr 28; 34(8):e57. Seringhaus M, Kumar A, Hartigan J, Snyder M, Gerstein M. PMID: 16648358; PMCID: PMC1450332.
      View in: PubMed   Mentions:
    270. High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays. Proc Natl Acad Sci U S A. 2006 Mar 21; 103(12):4534-9. Urban AE, Korbel JO, Selzer R, Richmond T, Hacker A, Popescu GV, Cubells JF, Green R, Emanuel BS, Gerstein MB, Weissman SM, Snyder M. PMID: 16537408; PMCID: PMC1450206.
      View in: PubMed   Mentions:
    271. Target hub proteins serve as master regulators of development in yeast. Genes Dev. 2006 Feb 15; 20(4):435-48. Borneman AR, Leigh-Bell JA, Yu H, Bertone P, Gerstein M, Snyder M. PMID: 16449570; PMCID: PMC1369046.
      View in: PubMed   Mentions:
    272. ProCAT: a data analysis approach for protein microarrays. Genome Biol. 2006; 7(11):R110. Zhu X, Gerstein M, Snyder M. PMID: 17109749; PMCID: PMC1794587.
      View in: PubMed   Mentions:
    273. BoCaTFBS: a boosted cascade learner to refine the binding sites suggested by ChIP-chip experiments. Genome Biol. 2006; 7(11):R102. Wang LY, Snyder M, Gerstein M. PMID: 17078876; PMCID: PMC1794589.
      View in: PubMed   Mentions:
    274. Extrapolating traditional DNA microarray statistics to tiling and protein microarray technologies. Methods Enzymol. 2006; 411:282-311. Royce TE, Rozowsky JS, Luscombe NM, Emanuelsson O, Yu H, Zhu X, Snyder M, Gerstein MB. PMID: 16939796.
      View in: PubMed   Mentions:
    275. Design optimization methods for genomic DNA tiling arrays. Genome Res. 2006 Feb; 16(2):271-81. Bertone P, Trifonov V, Rozowsky JS, Schubert F, Emanuelsson O, Karro J, Kao MY, Snyder M, Gerstein M. PMID: 16365382; PMCID: PMC1361723.
      View in: PubMed   Mentions:
    276. Biochemical and genetic analysis of the yeast proteome with a movable ORF collection. Genes Dev. 2005 Dec 01; 19(23):2816-26. Gelperin DM, White MA, Wilkinson ML, Kon Y, Kung LA, Wise KJ, Lopez-Hoyo N, Jiang L, Piccirillo S, Yu H, Gerstein M, Dumont ME, Phizicky EM, Snyder M, Grayhack EJ. PMID: 16322557; PMCID: PMC1315389.
      View in: PubMed   Mentions:
    277. Global analysis of protein phosphorylation in yeast. Nature. 2005 Dec 01; 438(7068):679-84. Ptacek J, Devgan G, Michaud G, Zhu H, Zhu X, Fasolo J, Guo H, Jona G, Breitkreutz A, Sopko R, McCartney RR, Schmidt MC, Rachidi N, Lee SJ, Mah AS, Meng L, Stark MJ, Stern DF, De Virgilio C, Tyers M, Andrews B, Gerstein M, Schweitzer B, Predki PF, Snyder M. PMID: 16319894.
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    278. Global changes in STAT target selection and transcription regulation upon interferon treatments. Genes Dev. 2005 Dec 15; 19(24):2953-68. Hartman SE, Bertone P, Nath AK, Royce TE, Gerstein M, Weissman S, Snyder M. PMID: 16319195; PMCID: PMC1315400.
      View in: PubMed   Mentions:
    279. A pilot study of transcription unit analysis in rice using oligonucleotide tiling-path microarray. Plant Mol Biol. 2005 Sep; 59(1):137-49. Stolc V, Li L, Wang X, Li X, Su N, Tongprasit W, Han B, Xue Y, Li J, Snyder M, Gerstein M, Wang J, Deng XW. PMID: 16217608.
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    280. Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping. Trends Genet. 2005 Aug; 21(8):466-75. Royce TE, Rozowsky JS, Bertone P, Samanta M, Stolc V, Weissman S, Snyder M, Gerstein M. PMID: 15979196; PMCID: PMC1855044.
      View in: PubMed   Mentions:
    281. Applications of DNA tiling arrays to experimental genome annotation and regulatory pathway discovery. Chromosome Res. 2005; 13(3):259-74. Bertone P, Gerstein M, Snyder M. PMID: 15868420.
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    282. DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states. Proc Natl Acad Sci U S A. 2004 Dec 21; 101(51):17771-6. White EJ, Emanuelsson O, Scalzo D, Royce T, Kosak S, Oakeley EJ, Weissman S, Gerstein M, Groudine M, Snyder M, Schübeler D. PMID: 15591350; PMCID: PMC539744.
      View in: PubMed   Mentions:
    283. Global identification of human transcribed sequences with genome tiling arrays. Science. 2004 Dec 24; 306(5705):2242-6. Bertone P, Stolc V, Royce TE, Rozowsky JS, Urban AE, Zhu X, Rinn JL, Tongprasit W, Samanta M, Weissman S, Gerstein M, Snyder M. PMID: 15539566.
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    284. Regulation of gene expression by a metabolic enzyme. Science. 2004 Oct 15; 306(5695):482-4. Hall DA, Zhu H, Zhu X, Royce T, Gerstein M, Snyder M. PMID: 15486299.
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    285. Large-scale mutagenesis of the yeast genome using a Tn7-derived multipurpose transposon. Genome Res. 2004 Oct; 14(10A):1975-86. Kumar A, Seringhaus M, Biery MC, Sarnovsky RJ, Umansky L, Piccirillo S, Heidtman M, Cheung KH, Dobry CJ, Gerstein MB, Craig NL, Snyder M. PMID: 15466296; PMCID: PMC524422.
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    286. Genomic analysis of regulatory network dynamics reveals large topological changes. Nature. 2004 Sep 16; 431(7006):308-12. Luscombe NM, Babu MM, Yu H, Snyder M, Teichmann SA, Gerstein M. PMID: 15372033.
      View in: PubMed   Mentions:
    287. Major molecular differences between mammalian sexes are involved in drug metabolism and renal function. Dev Cell. 2004 Jun; 6(6):791-800. Rinn JL, Rozowsky JS, Laurenzi IJ, Petersen PH, Zou K, Zhong W, Gerstein M, Snyder M. PMID: 15177028.
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    288. CREB binds to multiple loci on human chromosome 22. Mol Cell Biol. 2004 May; 24(9):3804-14. Euskirchen G, Royce TE, Bertone P, Martone R, Rinn JL, Nelson FK, Sayward F, Luscombe NM, Miller P, Gerstein M, Weissman S, Snyder M. PMID: 15082775; PMCID: PMC387762.
      View in: PubMed   Mentions:
    289. Fast optimal genome tiling with applications to microarray design and homology search. J Comput Biol. 2004; 11(4):766-85. Berman P, Bertone P, Dasgupta B, Gerstein M, Kao MY, Snyder M. PMID: 15579244.
      View in: PubMed   Mentions:
    290. A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science. 2003 Oct 17; 302(5644):449-53. Jansen R, Yu H, Greenbaum D, Kluger Y, Krogan NJ, Chung S, Emili A, Snyder M, Greenblatt JF, Gerstein M. PMID: 14564010.
      View in: PubMed   Mentions: 381     Fields:    Translation:AnimalsCells
    291. Distribution of NF-kappaB-binding sites across human chromosome 22. Proc Natl Acad Sci U S A. 2003 Oct 14; 100(21):12247-52. Martone R, Euskirchen G, Bertone P, Hartman S, Royce TE, Luscombe NM, Rinn JL, Nelson FK, Miller P, Gerstein M, Weissman S, Snyder M. PMID: 14527995; PMCID: PMC218744.
      View in: PubMed   Mentions:
    292. ExpressYourself: A modular platform for processing and visualizing microarray data. Nucleic Acids Res. 2003 Jul 01; 31(13):3477-82. Luscombe NM, Royce TE, Bertone P, Echols N, Horak CE, Chang JT, Snyder M, Gerstein M. PMID: 12824348; PMCID: PMC169034.
      View in: PubMed   Mentions:
    293. Genomics. Defining genes in the genomics era. Science. 2003 Apr 11; 300(5617):258-60. Snyder M, Gerstein M. PMID: 12690176.
      View in: PubMed   Mentions:
    294. The transcriptional activity of human Chromosome 22. Genes Dev. 2003 Feb 15; 17(4):529-40. Rinn JL, Euskirchen G, Bertone P, Martone R, Luscombe NM, Hartman S, Harrison PM, Nelson FK, Miller P, Gerstein M, Weissman S, Snyder M. PMID: 12600945; PMCID: PMC195998.
      View in: PubMed   Mentions:
    295. Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae. Genes Dev. 2002 Dec 01; 16(23):3017-33. Horak CE, Luscombe NM, Qian J, Bertone P, Piccirrillo S, Gerstein M, Snyder M. PMID: 12464632; PMCID: PMC187492.
      View in: PubMed   Mentions:
    296. Functional profiling of the Saccharomyces cerevisiae genome. Nature. 2002 Jul 25; 418(6896):387-91. Giaever G, Chu AM, Ni L, Connelly C, Riles L, Véronneau S, Dow S, Lucau-Danila A, Anderson K, André B, Arkin AP, Astromoff A, El-Bakkoury M, Bangham R, Benito R, Brachat S, Campanaro S, Curtiss M, Davis K, Deutschbauer A, Entian KD, Flaherty P, Foury F, Garfinkel DJ, Gerstein M, Gotte D, Güldener U, Hegemann JH, Hempel S, Herman Z, Jaramillo DF, Kelly DE, Kelly SL, Kötter P, LaBonte D, Lamb DC, Lan N, Liang H, Liao H, Liu L, Luo C, Lussier M, Mao R, Menard P, Ooi SL, Revuelta JL, Roberts CJ, Rose M, Ross-Macdonald P, Scherens B, Schimmack G, Shafer B, Shoemaker DD, Sookhai-Mahadeo S, Storms RK, Strathern JN, Valle G, Voet M, Volckaert G, Wang CY, Ward TR, Wilhelmy J, Winzeler EA, Yang Y, Yen G, Youngman E, Yu K, Bussey H, Boeke JD, Snyder M, Philippsen P, Davis RW, Johnston M. PMID: 12140549.
      View in: PubMed   Mentions: 1869     Fields:    Translation:Animals
    297. Subcellular localization of the yeast proteome. Genes Dev. 2002 Mar 15; 16(6):707-19. Kumar A, Agarwal S, Heyman JA, Matson S, Heidtman M, Piccirillo S, Umansky L, Drawid A, Jansen R, Liu Y, Cheung KH, Miller P, Gerstein M, Roeder GS, Snyder M. PMID: 11914276; PMCID: PMC155358.
      View in: PubMed   Mentions:
    298. A question of size: the eukaryotic proteome and the problems in defining it. Nucleic Acids Res. 2002 Mar 01; 30(5):1083-90. Harrison PM, Kumar A, Lang N, Snyder M, Gerstein M. PMID: 11861898; PMCID: PMC101239.
      View in: PubMed   Mentions:
    299. GATA-1 binding sites mapped in the beta-globin locus by using mammalian chIp-chip analysis. Proc Natl Acad Sci U S A. 2002 Mar 05; 99(5):2924-9. Horak CE, Mahajan MC, Luscombe NM, Gerstein M, Weissman SM, Snyder M. PMID: 11867748; PMCID: PMC122449.
      View in: PubMed   Mentions:
    300. A small reservoir of disabled ORFs in the yeast genome and its implications for the dynamics of proteome evolution. J Mol Biol. 2002 Feb 22; 316(3):409-19. Harrison P, Kumar A, Lan N, Echols N, Snyder M, Gerstein M. PMID: 11866506.
      View in: PubMed   Mentions:
    301. YMD: a microarray database for large-scale gene expression analysis. Proc AMIA Symp. 2002; 140-4. Cheung KH, White K, Hager J, Gerstein M, Reinke V, Nelson K, Masiar P, Srivastava R, Li Y, Li J, Zhao H, Li J, Allison DB, Snyder M, Miller P, Williams K. PMID: 12463803; PMCID: PMC2244579.
      View in: PubMed   Mentions:
    302. An integrated approach for finding overlooked genes in yeast. Nat Biotechnol. 2002 Jan; 20(1):58-63. Kumar A, Harrison PM, Cheung KH, Lan N, Echols N, Bertone P, Miller P, Gerstein MB, Snyder M. PMID: 11753363.
      View in: PubMed   Mentions:
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