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Sharing data from the Human Tumor Atlas Network through standards, infrastructure and community engagement. Nat Methods. 2025 Apr; 22(4):664-671.
de Bruijn I, Nikolov M, Lau C, Clayton A, Gibbs DL, Mitraka E, Pozhidayeva D, Lash A, Sumer SO, Altreuter J, Anton K, DeFelice M, Li X, Lisman A, Longabaugh WJR, Muhlich J, Santagata S, Nandakumar S, Sorger PK, Suver C, Doan X, Guinney J, Schultz N, Taylor AJ, Thorsson V, Cerami E, Eddy JA. PMID: 40164800.
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PubMed Mentions: Fields:
Translation:
Humans
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Robust Cluster Prediction Across Data Types Validates Association of Sex and Therapy Response in GBM. Cancers (Basel). 2025 Jan 28; 17(3).
Gibbs DL, Cioffi G, Aguilar B, Waite KA, Pan E, Mandel J, Umemura Y, Luo J, Rubin JB, Pot D, Barnholtz-Sloan J. PMID: 39941811; PMCID: PMC11815886.
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PubMed Mentions:
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Pediatric Burns - Who Requires Follow-up? A Study of Urban Pediatric Emergency Department Patients. West J Emerg Med. 2024 Jul; 25(4):634-644.
Heyming T, Dunkelman A, Gibbs D, Knudsen-Robbins C, Schomberg J, Takallou A, Lara B, Valdez B, Joe V. PMID: 39028250; PMCID: PMC11254158.
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PubMed Mentions: Fields:
Translation:
Humans
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Sharing Data from the Human Tumor Atlas Network through Standards, Infrastructure, and Community Engagement. bioRxiv. 2024 Jun 30.
de Bruijn I, Nikolov M, Lau C, Clayton A, Gibbs DL, Mitraka E, Pozhidayeva D, Lash A, Sumer SO, Altreuter J, Anton K, DeFelice M, Li X, Lisman A, R Longabaugh WJ, Muhlich J, Santagata S, Nandakumar S, Sorger PK, Suver C, Schultz N, Taylor AJ, Thorsson V, Cerami E, Eddy JA. PMID: 38979389; PMCID: PMC11230241.
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PubMed Mentions:
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Amphiregulin Switches Progenitor Cell Fate for Lineage Commitment During Gastric Mucosal Regeneration. Gastroenterology. 2024 Aug; 167(3):469-484.
Lee SH, Won Y, Gibbs D, Caldwell B, Goldstein A, Choi E, Goldenring JR. PMID: 38492892; PMCID: PMC11260537.
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PubMed Mentions:
2 Fields:
Translation:
AnimalsCells
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National Cancer Institute Imaging Data Commons: Toward Transparency, Reproducibility, and Scalability in Imaging Artificial Intelligence. Radiographics. 2023 12; 43(12):e230180.
Fedorov A, Longabaugh WJR, Pot D, Clunie DA, Pieper SD, Gibbs DL, Bridge C, Herrmann MD, Homeyer A, Lewis R, Aerts HJWL, Krishnaswamy D, Thiriveedhi VK, Ciausu C, Schacherer DP, Bontempi D, Pihl T, Wagner U, Farahani K, Kim E, Kikinis R. PMID: 37999984; PMCID: PMC10716669.
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PubMed Mentions:
7 Fields:
Translation:
Humans
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Single-cell gene set scoring with nearest neighbor graph smoothed data (gssnng). Bioinform Adv. 2023; 3(1):vbad150.
Gibbs DL, Strasser MK, Huang S. PMID: 37886712; PMCID: PMC10599965.
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PubMed Mentions:
1
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Polyclonal lymphoid expansion drives paraneoplastic autoimmunity in neuroblastoma. Cell Rep. 2023 08 29; 42(8):112879.
Rosenberg MI, Greenstein E, Buchkovich M, Peres A, Santoni-Rugiu E, Yang L, Mikl M, Vaksman Z, Gibbs DL, Reshef D, Salovin A, Irwin MS, Naranjo A, Ulitsky I, de Alarcon PA, Matthay KK, Weigman V, Yaari G, Panzer JA, Friedman N, Maris JM. PMID: 37537844; PMCID: PMC10551040.
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PubMed Mentions:
3 Fields:
Translation:
Humans
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Concerted epithelial and stromal changes during progression of Barrett's Esophagus to invasive adenocarcinoma exposed by multi-scale, multi-omics analysis. bioRxiv. 2023 Jun 11.
Strasser MK, Gibbs DL, Gascard P, Bons J, Hickey JW, Schürch CM, Tan Y, Black S, Chu P, Ozkan A, Basisty N, Sangwan V, Rose J, Shah S, Camilleri-Broet S, Fiset PO, Bertos N, Berube J, Djambazian H, Li R, Oikonomopoulos S, Fels-Elliott DR, Vernovsky S, Shimshoni E, Collyar D, Russell A, Ragoussis I, Stachler M, Goldenring JR, McDonald S, Ingber DE, Schilling B, Nolan GP, Tlsty TD, Huang S, Ferri LE. PMID: 37333362; PMCID: PMC10274886.
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PubMed Mentions:
1
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No more bull: pediatric head injuries as a result of mechanical bull rides. Childs Nerv Syst. 2023 01; 39(1):1-4.
Xu JC, Vargas AJ, Waunch A, Gibbs DL, Cappon JP, Loudon WG, Magge SN. PMID: 35680683.
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PubMed Mentions: Fields:
Translation:
HumansAnimals
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A functional module states framework reveals transcriptional states for drug and target prediction. Cell Rep. 2022 01 18; 38(3):110269.
Qin G, Knijnenburg TA, Gibbs DL, Moser R, Monnat RJ, Kemp CJ, Shmulevich I. PMID: 35045296.
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PubMed Mentions:
1 Fields:
Translation:
HumansCells
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Patient-Specific Cell Communication Networks Associate With Disease Progression in Cancer. Front Genet. 2021; 12:667382.
Gibbs DL, Aguilar B, Thorsson V, Ratushny AV, Shmulevich I. PMID: 34512714; PMCID: PMC8429851.
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PubMed Mentions:
2
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Analysis of Unintentional Falls in Pediatric Population and Predictors of Morbidity. J Surg Res. 2021 11; 267:48-55.
Farzaneh C, Schomberg J, Sullivan B, Yu PT, Loudon W, Duong WQ, Gibbs D, Guner YS. PMID: 34130238.
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PubMed Mentions: Fields:
Translation:
Humans
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PRoBE the cloud toolkit: finding the best biomarkers of drug response within a breast cancer clinical trial. JAMIA Open. 2021 Apr; 4(2):ooab038.
O'Grady N, Gibbs DL, Abdilleh K, Asare A, Asare S, Venters S, Brown-Swigart L, Hirst GL, Wolf D, Yau C, van 't Veer LJ, Esserman L, Basu A. PMID: 34095775; PMCID: PMC8172495.
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PubMed Mentions:
1
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Are routine chest X-rays following chest tube removal necessary in asymptomatic pediatric patients? Pediatr Surg Int. 2021 May; 37(5):631-637.
Kanamori LM, Guner Y, Gibbs D, Schomberg J. PMID: 33385243.
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PubMed Mentions:
3 Fields:
Translation:
Humans
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Prolonged hospital length of stay in pediatric trauma: a model for targeted interventions. Pediatr Res. 2021 08; 90(2):464-471.
Gibbs D, Ehwerhemuepha L, Moreno T, Guner Y, Yu P, Schomberg J, Wallace E, Feaster W. PMID: 33184499.
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PubMed Mentions:
7 Fields:
Translation:
Humans
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CRI iAtlas: an interactive portal for immuno-oncology research. F1000Res. 2020; 9:1028.
Eddy JA, Thorsson V, Lamb AE, Gibbs DL, Heimann C, Yu JX, Chung V, Chae Y, Dang K, Vincent BG, Shmulevich I, Guinney J. PMID: 33214875; PMCID: PMC7658727.
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PubMed Mentions:
34 Fields:
Translation:
HumansCells
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A multicenter mixed-effects model for inference and prediction of 72-h return visits to the emergency department for adult patients with trauma-related diagnoses. J Orthop Surg Res. 2020 Aug 14; 15(1):331.
Yaghmaei E, Ehwerhemuepha L, Feaster W, Gibbs D, Rakovski C. PMID: 32795327; PMCID: PMC7427714.
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PubMed Mentions:
5 Fields:
Translation:
Humans
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A generalizable data-driven multicellular model of pancreatic ductal adenocarcinoma. Gigascience. 2020 07 01; 9(7).
Aguilar B, Gibbs DL, Reiss DJ, McConnell M, Danziger SA, Dervan A, Trotter M, Bassett D, Hershberg R, Ratushny AV, Shmulevich I. PMID: 32696951; PMCID: PMC7374045.
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PubMed Mentions:
15 Fields:
Translation:
Humans
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Intrinsic Genetic and Transcriptomic Patterns Reflect Tumor Immune Subtypes Facilitating Exploring Possible Combinatory Therapy. Front Mol Biosci. 2020; 7:53.
Xu Y, Li D, Liu Z, Gibbs DL, Xie L, Qin G. PMID: 32391377; PMCID: PMC7191006.
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PubMed Mentions:
1
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ADAPTS: Automated deconvolution augmentation of profiles for tissue specific cells. PLoS One. 2019; 14(11):e0224693.
Danziger SA, Gibbs DL, Shmulevich I, McConnell M, Trotter MWB, Schmitz F, Reiss DJ, Ratushny AV. PMID: 31743345; PMCID: PMC6863530.
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PubMed Mentions:
16 Fields:
Translation:
Humans
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A Pan-Cancer Approach to Predict Responsiveness to Immune Checkpoint Inhibitors by Machine Learning. Cancers (Basel). 2019 Oct 15; 11(10).
Polano M, Chierici M, Dal Bo M, Gentilini D, Di Cintio F, Baboci L, Gibbs DL, Furlanello C, Toffoli G. PMID: 31618839; PMCID: PMC6827166.
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PubMed Mentions:
27
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The Immune Landscape of Cancer. Immunity. 2019 Aug 20; 51(2):411-412.
Thorsson V, Gibbs DL, Brown SD, Wolf D, Bortone DS, Ou Yang TH, Porta-Pardo E, Gao GF, Plaisier CL, Eddy JA, Ziv E, Culhane AC, Paull EO, Sivakumar IKA, Gentles AJ, Malhotra R, Farshidfar F, Colaprico A, Parker JS, Mose LE, Vo NS, Liu J, Liu Y, Rader J, Dhankani V, Reynolds SM, Bowlby R, Califano A, Cherniack AD, Anastassiou D, Bedognetti D, Mokrab Y, Newman AM, Rao A, Chen K, Krasnitz A, Hu H, Malta TM, Noushmehr H, Pedamallu CS, Bullman S, Ojesina AI, Lamb A, Zhou W, Shen H, Choueiri TK, Weinstein JN, Guinney J, Saltz J, Holt RA, Rabkin CS, Cancer Genome Atlas Research Network, Lazar AJ, Serody JS, Demicco EG, Disis ML, Vincent BG, Shmulevich I. PMID: 31433971.
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PubMed Mentions:
252 Fields:
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Genomic and molecular characterization of preterm birth. Proc Natl Acad Sci U S A. 2019 03 19; 116(12):5819-5827.
Knijnenburg TA, Vockley JG, Chambwe N, Gibbs DL, Humphries C, Huddleston KC, Klein E, Kothiyal P, Tasseff R, Dhankani V, Bodian DL, Wong WSW, Glusman G, Mauldin DE, Miller M, Slagel J, Elasady S, Roach JC, Kramer R, Leinonen K, Linthorst J, Baveja R, Baker R, Solomon BD, Eley G, Iyer RK, Maxwell GL, Bernard B, Shmulevich I, Hood L, Niederhuber JE. PMID: 30833390; PMCID: PMC6431191.
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PubMed Mentions:
36 Fields:
Translation:
HumansCells
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Flexibility of Boolean Network Reservoir Computers in Approximating Arbitrary Recursive and Non-Recursive Binary Filters. Entropy (Basel). 2018 Dec 11; 20(12).
Echlin M, Aguilar B, Notarangelo M, Gibbs DL, Shmulevich I. PMID: 33266678; PMCID: PMC7512538.
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PubMed Mentions:
5
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Integrative Molecular Characterization of Malignant Pleural Mesothelioma. Cancer Discov. 2018 12; 8(12):1548-1565.
Hmeljak J, Sanchez-Vega F, Hoadley KA, Shih J, Stewart C, Heiman D, Tarpey P, Danilova L, Drill E, Gibb EA, Bowlby R, Kanchi R, Osmanbeyoglu HU, Sekido Y, Takeshita J, Newton Y, Graim K, Gupta M, Gay CM, Diao L, Gibbs DL, Thorsson V, Iype L, Kantheti H, Severson DT, Ravegnini G, Desmeules P, Jungbluth AA, Travis WD, Dacic S, Chirieac LR, Galateau-Sallé F, Fujimoto J, Husain AN, Silveira HC, Rusch VW, Rintoul RC, Pass H, Kindler H, Zauderer MG, Kwiatkowski DJ, Bueno R, Tsao AS, Creaney J, Lichtenberg T, Leraas K, Bowen J, TCGA Research Network, Felau I, Zenklusen JC, Akbani R, Cherniack AD, Byers LA, Noble MS, Fletcher JA, Robertson AG, Shen R, Aburatani H, Robinson BW, Campbell P, Ladanyi M. PMID: 30322867; PMCID: PMC6310008.
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PubMed Mentions:
266 Fields:
Translation:
Humans
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Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics. Cell. 2018 04 05; 173(2):305-320.e10.
Ding L, Bailey MH, Porta-Pardo E, Thorsson V, Colaprico A, Bertrand D, Gibbs DL, Weerasinghe A, Huang KL, Tokheim C, Cortés-Ciriano I, Jayasinghe R, Chen F, Yu L, Sun S, Olsen C, Kim J, Taylor AM, Cherniack AD, Akbani R, Suphavilai C, Nagarajan N, Stuart JM, Mills GB, Wyczalkowski MA, Vincent BG, Hutter CM, Zenklusen JC, Hoadley KA, Wendl MC, Shmulevich L, Lazar AJ, Wheeler DA, Getz G, Cancer Genome Atlas Research Network. PMID: 29625049; PMCID: PMC5916814.
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PubMed Mentions:
181 Fields:
Translation:
HumansCells
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The Immune Landscape of Cancer. Immunity. 2018 04 17; 48(4):812-830.e14.
Thorsson V, Gibbs DL, Brown SD, Wolf D, Bortone DS, Ou Yang TH, Porta-Pardo E, Gao GF, Plaisier CL, Eddy JA, Ziv E, Culhane AC, Paull EO, Sivakumar IKA, Gentles AJ, Malhotra R, Farshidfar F, Colaprico A, Parker JS, Mose LE, Vo NS, Liu J, Liu Y, Rader J, Dhankani V, Reynolds SM, Bowlby R, Califano A, Cherniack AD, Anastassiou D, Bedognetti D, Mokrab Y, Newman AM, Rao A, Chen K, Krasnitz A, Hu H, Malta TM, Noushmehr H, Pedamallu CS, Bullman S, Ojesina AI, Lamb A, Zhou W, Shen H, Choueiri TK, Weinstein JN, Guinney J, Saltz J, Holt RA, Rabkin CS, Cancer Genome Atlas Research Network, Lazar AJ, Serody JS, Demicco EG, Disis ML, Vincent BG, Shmulevich I. PMID: 29628290; PMCID: PMC5982584.
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PubMed Mentions:
2860 Fields:
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The ISB Cancer Genomics Cloud: A Flexible Cloud-Based Platform for Cancer Genomics Research. Cancer Res. 2017 11 01; 77(21):e7-e10.
Reynolds SM, Miller M, Lee P, Leinonen K, Paquette SM, Rodebaugh Z, Hahn A, Gibbs DL, Slagel J, Longabaugh WJ, Dhankani V, Reyes M, Pihl T, Backus M, Bookman M, Deflaux N, Bingham J, Pot D, Shmulevich I. PMID: 29092928; PMCID: PMC5780183.
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PubMed Mentions:
31 Fields:
Translation:
Humans
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Solving the influence maximization problem reveals regulatory organization of the yeast cell cycle. PLoS Comput Biol. 2017 Jun; 13(6):e1005591.
Gibbs DL, Shmulevich I. PMID: 28628618; PMCID: PMC5495484.
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PubMed Mentions:
2 Fields:
Translation:
AnimalsCells
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Combining dependent P-values with an empirical adaptation of Brown's method. Bioinformatics. 2016 09 01; 32(17):i430-i436.
Poole W, Gibbs DL, Shmulevich I, Bernard B, Knijnenburg TA. PMID: 27587659; PMCID: PMC5013915.
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PubMed Mentions:
58 Fields:
Translation:
Humans
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Using Incomplete Trios to Boost Confidence in Family Based Association Studies. Front Genet. 2016; 7:34.
Dhankani V, Gibbs DL, Knijnenburg T, Kramer R, Vockley J, Niederhuber J, Shmulevich I, Bernard B. PMID: 27047537; PMCID: PMC4796035.
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PubMed Mentions:
1
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Multi-omic network signatures of disease. Front Genet. 2014 Jan 07; 4:309.
Gibbs DL, Gralinski L, Baric RS, McWeeney SK. PMID: 24432028; PMCID: PMC3882664.
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PubMed Mentions:
10
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Protein co-expression network analysis (ProCoNA). J Clin Bioinforma. 2013 Jun 01; 3(1):11.
Gibbs DL, Baratt A, Baric RS, Kawaoka Y, Smith RD, Orwoll ES, Katze MG, McWeeney SK. PMID: 23724967; PMCID: PMC3695838.
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PubMed Mentions:
14
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Management of rectal stenosis with endoscopic balloon dilatation. J Pediatr Surg. 2013 Apr; 48(4):e13-6.
Hidas G, Gibbs D, Alireza A, Khoury AE. PMID: 23583158.
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PubMed Mentions:
3 Fields:
Translation:
Humans
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Multilaboratory study of the Biomic automated well-reading instrument versus MicroScan WalkAway for reading MicroScan antimicrobial susceptibility and identification panels. J Clin Microbiol. 2013 May; 51(5):1548-54.
Fader RC, Weaver E, Fossett R, Toyras M, Vanderlaan J, Gibbs D, Wang A, Thierjung N. PMID: 23486713; PMCID: PMC3647896.
View in:
PubMed Mentions:
3 Fields:
Translation:
Cells
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Copy number variation analysis in 98 individuals with PHACE syndrome. J Invest Dermatol. 2013 Mar; 133(3):677-684.
Siegel DH, Shieh JTC, Kwon EK, Baselga E, Blei F, Cordisco M, Dobyns WB, Duffy KJ, Garzon MC, Gibbs DL, Grimmer JF, Hayflick SJ, Krol AL, Kwok PY, Lorier R, Matter A, McWeeney S, Metry D, Mitchell S, Pope E, Santoro JL, Stevenson DA, Bayrak-Toydemir P, Wilmot B, Worthey EA, Frieden IJ, Drolet BA, Broeckel U. PMID: 23096700; PMCID: PMC3971866.
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PubMed Mentions:
11 Fields:
Translation:
HumansCells
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Geographic variation in the frequency of isolation and fluconazole and voriconazole susceptibilities of Candida glabrata: an assessment from the ARTEMIS DISK Global Antifungal Surveillance Program. Diagn Microbiol Infect Dis. 2010 Jun; 67(2):162-71.
Pfaller MA, Diekema DJ, Gibbs DL, Newell VA, Barton R, Bijie H, Bille J, Chang SC, da Luz Martins M, Duse A, Dzierzanowska D, Ellis D, Finquelievich J, Gould I, Gur D, Hoosen A, Lee K, Mallatova N, Mallie M, Peng NG, Petrikos G, Santiago A, Trupl J, VanDen Abeele AM, Wadula J, Zaidi M, Global Antifungal Surveillance Group. PMID: 20338711.
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PubMed Mentions:
20 Fields:
Translation:
HumansAnimals
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Evaluation of the Biomic V3 microbiology system for identification of selected species on BBL CHROMagar orientation agar and CHROMagar MRSA medium. J Clin Microbiol. 2008 Oct; 46(10):3488-90.
Baron EJ, D'Souza H, Wang AQ, Gibbs DL. PMID: 18701661; PMCID: PMC2566125.
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PubMed Mentions:
2 Fields:
Translation:
HumansCells
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Comparison of the susceptibilities of Candida spp. to fluconazole and voriconazole in a 4-year global evaluation using disk diffusion. J Clin Microbiol. 2003 Dec; 41(12):5623-32.
Hazen KC, Baron EJ, Colombo AL, Girmenia C, Sanchez-Sousa A, del Palacio A, de Bedout C, Gibbs DL, Global Antifungal Surveillance Group. PMID: 14662952; PMCID: PMC309015.
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PubMed Mentions:
31 Fields:
Translation:
HumansAnimalsCells
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Selective delivery of CB300638, a cyclopenta[g]quinazoline-based thymidylate synthase inhibitor into human tumor cell lines overexpressing the alpha-isoform of the folate receptor. Cancer Res. 2003 Jul 01; 63(13):3612-8.
Theti DS, Bavetsias V, Skelton LA, Titley J, Gibbs D, Jansen G, Jackman AL. PMID: 12839949.
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PubMed Mentions:
5 Fields:
Translation:
HumansCells