Michael Cherry

J. Michael Cherry, PhD, Professor, Department of Genetics, Stanford University School of Medicine

Research Description: Dr. Cherry’s research focuses on the integration of biological knowledge and published experimental results into software/database environments that provide access to these data with sophisticated tools. His lab currently focuses on the curation for all literature on budding yeast, unification of biological nomenclature, data coordination for human epigenomics and single-cell assays and their results, and integration of these results. His research group includes Scientific Biocurators, Software Engineers, Data Wranglers and Bioinformatic Analysts that serve the biological research and teaching communities via development and maintenance of online public resources such as the ENCODE Portal and SGD database. He is currently PI for of the NIH ENCODE project’s Data Coordination Center (DCC), Saccharomyces Genome Database, CZI Lattice database for single-cell results, RegulomeDB, as well as co-Investigator on Gene Ontology Consortium and the Alliance of Genomic Resources. His role in SDRC is to advise an experienced group of professionals in the Genomics and Analysis Core, including his Department of Genetics colleagues Hassan Chaib and Mike Snyder to provide the best resources possible to facilitate diabetes-related research.

Selected relevant publications (Stanford DRC Members in BOLD):

  1. ENCODE Project Consortium, Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, Shen Y, He Y, Mackiewicz M, Pauli-Behn F, Williams BA, Mortazavi A, Keller CA, Zhang XO, Elhajjajy SI, Huey J, Dickel DE, Snetkova V, Wei X, Wang X, Rivera-Mulia JC, Rozowsky J, Zhang J, Chhetri SB, Zhang J, Victorsen A, White KP, Visel A, Yeo GW, Burge CB, Lécuyer E, Gilbert DM, Dekker J, Rinn J, Mendenhall EM, Ecker JR, Kellis M, Klein RJ, Noble WS, Kundaje A, Guigó R, Farnham PJ, Cherry JM, Myers RM, Ren B, Graveley BR, Gerstein MB, Pennacchio LA, Snyder MP, Bernstein BE, Wold B, Hardison RC, Gingeras TR, Stamatoyannopoulos JA, Weng Z. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 2020 Jul;583(7818):699-710. doi: 10.1038/s41586-020-2493-4. PMID: 32728249; PMCID: PMC7410828. 

  2. 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. Perspectives on ENCODE. Nature. 2020 Jul;583(7818):693-698. doi: 10.1038/s41586-020-2449-8. PMID: 32728248; PMCID: PMC7410827.