Publications

Rozenblatt-Rosen O, Regev A, Oberdoerffer P, Nawy T, Hupalowska A, Rood JE, Ashenberg O, Cerami E, Coffey RJ, Demir E, Ding L, Esplin ED, Ford JM, Goecks J, Ghosh S, Gray JW, Guinney J, Hanlon SE, Hughes SK, Hwang ES, Iacobuzio-Donahue CA, Jané-Valbuena J, Johnson BE, Lau KS, Lively T, Mazzilli SA, Pe'er D, Santagata S, Shalek AK, Schapiro D, Snyder MP, Sorger PK, Spira AE, Srivastava S, Tan K, West RB, Williams EH; Human Tumor Atlas Network. The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution. Cell. April 2020; 181(2):236-249
Wagner AH, Walsh B, Mayfield G, Tamborero D, Sonkin D, Krysiak K, Deu-Pons J, Duren RP, Gao J, McMurry J, Patterson S, Del Vecchio Fitz C, Pitel BA, Sezerman OU, Ellrott K, Warner JL, Rieke DT, Aittokallio T, Cerami E, Ritter DI, Schriml LM, Freimuth RR, Haendel M, Raca G, Madhavan S, Baudis M, Beckmann JS, Dienstmann R, Chakravarty D, Li XS, Mockus S, Elemento O, Schultz N, Lopez-Bigas N, Lawler M, Goecks J, Griffith M, Griffith OL, Margolin AA; Variant Interpretation for Cancer Consortium.. A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer. Nature Genetics. April 2020; 52(4):448-457
Goecks J, Jalili V, Heiser LM, Gray JW.. How Machine Learning Will Transform Biomedicine. Cell. April 2020; 181(1):92-101
Jalili V, Afgan E, Taylor J, Goecks J.. Cloud Bursting Galaxy: Federated Identity and Access Management. Bioinformatics. January 2020; 36(1):1-9
Liu Y, Sargent L, Leung W, Elgin SCR, Goecks J.. G-OnRamp: A Galaxy-based platform for collaborative annotation of eukaryotic genomes. Bioinformatics. November 2019; 35(21):4422-4423
Afgan E, Jalili V, Goonasekera N, Taylor J, and Goecks J. Federated Galaxy: Biomedical Computing at the Frontier. 2018 IEEE International Conference on Cloud Computing. June 2018; 1:871-874
Afgan E, Baker D, Batut B, van den Beek M, Bouvier D, Čech M, Chilton J, Clements D, Coraor N, Grüning B, Guerler A, Hillman-Jackson J, Hiltemann S, Jalili V, Rasche H, Soranzo N, Taylor J, Goecks J, Taylor J, Nekrutenko A, and Blankenberg D. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Research. May 2018;
Nekrutenko A, Team G, Goecks J, Taylor J, Blankenberg D. Biology Needs Evolutionary Software Tools: Let’s Build Them Right. Molecular Biology and Evolution. April 2018; msy084
Jalili V, Matteucci M, Goecks J, Deldjoo Y, Ceri S. Next Generation Indexing for Genomic Intervals. IEEE Transactions on Knowledge and Data Engineering. December 2017;
Alterovitz G, … Goecks J, …., Mazumder, R. Enabling precision medicine via standard communication of HTS provenance, analysis, and results. PLoS Biology. December 2017;
Grüning B, Chilton J, Köster J, Dale R, Soranzo N, van den Beek M, Goecks J, Backofen R, Nekrutenko A, Taylor J. Practical Computational Reproducibility in the Life Sciences. Cell Systems. December 2017; 6(6):631-635
Jalili V, Matteucci M, Masseroli M, and Ceri S. Explorative visual analytics on interval-based genomic data and their metadata. BMC Bioinformatics. December 2017; 18(1):536
Simonyan V, Goecks J, and Mazumder R. Bio-compute objects-a step towards evaluation and validation of bio-medical scientific computations. PDA Journal of Pharmaceutical Science and Technology. December 2016;
Afgan E, Baker D, van den Beek M, Blankenberg D, Bouvier D, Čech M, Chilton J, Clements D, Coraor N, Eberhard C, Grüning B, Guerler A, Hillman-Jackson J, Von Kuster G, Rasche E, Soranzo N, Turaga N, Taylor J, Nekrutenko A, and Goecks J. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Research. May 2016; 44(W1)
Yan C, Pattabiraman N, Goecks J, Lam P, Nayak A, Pan Y, Torcivia-Rodriguez J, Voskanian A, Wan Q, Mazumder R. Impact of germline and somatic missense variations on drug binding sites. The Pharmacogenomics Journal. January 2016;
Budd A, Corpas M, Brazas MD, Fuller JC, Goecks J, Mulder NJ, Michaut M, Ouellette BF, Pawlik A, and Blomberg N. A Quick Guide for Building a Successful Bioinformatics Community. PLOS Computational Biology. February 2015; 11(2)
Goecks J, El-Rayes BF, Maithel SK, Khoury HJ, Taylor J, and Rossi MR. Open pipelines for integrated tumor genome profiles reveal differences between pancreatic cancer tumors and cell lines. Cancer Medicine. January 2015; 4(3):392-403
Goecks J, Eberhard C, Too T, The Galaxy Team, Nekrutenko A, and Taylor J. Web-based Visual Analysis for High-throughput Genomics. BMC Genomics. June 2013; 14(1):397
Goecks J, Mortimer NT, Mobley JA, Bowersock GJ, Taylor J, and Schlenke TA. Integrative Approach Reveals Composition of Endoparasitoid Wasp Venoms. PLoS ONE. May 2013; 8(5):e64125
Mortimer NT, Goecks J, Kacsoh BZ, Mobley JA, Bowersock GJ, Taylor J, and Schlenke TA. Parasitoid Wasp Venom SERCA Regulates Drosophila Calcium Levels and Inhibits Cellular Immunity. Proceedings of the National Academy of Science USA. May 2013; 110(23):9427–9432
Goecks J, Coraor N, The Galaxy Team, Nekrutenko A, and Taylor J. NGS analyses by visualization with Trackster. Nature Biotechnology. November 2012; 30:1036-1039
Goecks J, Li K, Clements D, The Galaxy Team, and Taylor J. The Galaxy Track Browser: Transforming the Genome Browser from Visualization Tool to Analysis Tool. 2011 IEEE Symposium on Biological Data Visualization. October 2011;
Afgan E, Goecks J, Baker D, Coraor N, The Galaxy Team, Nekrutenko A, and Taylor J. Galaxy - a Gateway to Tools in e-Science. Guide to e-Science: Next Generation Scientific Research and Discovery. May 2011;
Goecks J, Nekrutenko A, Taylor J, and The Galaxy Team. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biology. August 2010; 11(8)