The Encyclopedia of DNA elements (ENCODE): data portal update von Davis, Carrie A, Hitz, Benjamin C, Sloan, Cricket A, Chan, Esther T, Davidson, Jean M, Gabdank, Idan, Hilton, Jason A, Jain, Kriti, Baymuradov, Ulugbek K, Narayanan, Aditi K, Onate, Kathrina C, Graham, Keenan, Miyasato, Stuart R, Dreszer, Timothy R, Strattan, J Seth, Jolanki, Otto, Tanaka, Forrest Y, Cherry, J Michael

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Saccharomyces Genome Database: the genomics resource of budding yeast von Cherry, J. Michael, Hong, Eurie L., Amundsen, Craig, Balakrishnan, Rama, Binkley, Gail, Chan, Esther T., Christie, Karen R., Costanzo, Maria C., Dwight, Selina S., Engel, Stacia R., Fisk, Dianna G., Hirschman, Jodi E., Hitz, Benjamin C., Karra, Kalpana, Krieger, Cynthia J., Miyasato, Stuart R., Nash, Rob S., Park, Julie, Skrzypek, Marek S., Simison, Matt, Weng, Shuai, Wong, Edith D.

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New developments on the Encyclopedia of DNA Elements (ENCODE) data portal von Luo, Yunhai, Hitz, Benjamin C, Gabdank, Idan, Hilton, Jason A, Kagda, Meenakshi S, Lam, Bonita, Myers, Zachary, Sud, Paul, Jou, Jennifer, Lin, Khine, Baymuradov, Ulugbek K, Graham, Keenan, Litton, Casey, Miyasato, Stuart R, Strattan, J Seth, Jolanki, Otto, Lee, Jin-Wook, Tanaka, Forrest Y, Adenekan, Philip, O’Neill, Emma, Cherry, J Michael

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H3K4me3 Breadth Is Linked to Cell Identity and Transcriptional Consistency von Benayoun, Bérénice A., Pollina, Elizabeth A., Ucar, Duygu, Mahmoudi, Salah, Karra, Kalpana, Wong, Edith D., Devarajan, Keerthana, Daugherty, Aaron C., Kundaje, Anshul B., Mancini, Elena, Hitz, Benjamin C., Gupta, Rakhi, Rando, Thomas A., Baker, Julie C., Snyder, Michael P., Cherry, J. Michael, Brunet, Anne

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Annotation of functional variation in personal genomes using RegulomeDB von Boyle, Alan P, Hong, Eurie L, Hariharan, Manoj, Cheng, Yong, Schaub, Marc A, Kasowski, Maya, Karczewski, Konrad J, Park, Julie, Hitz, Benjamin C, Weng, Shuai, Cherry, J Michael, Snyder, Michael

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Effects of hot isostatic pressing on the elastic modulus and tensile properties of 316L parts made by powder bed laser fusion von Lavery, N.P., Cherry, J., Mehmood, S., Davies, H., Girling, B., Sackett, E., Brown, S.G.R., Sienz, J.

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AGAPE (Automated Genome Analysis PipelinE) for pan-genome analysis of Saccharomyces cerevisiae von Song, Giltae, Dickins, Benjamin J A, Demeter, Janos, Engel, Stacia, Gallagher, Jennifer, Choe, Kisurb, Dunn, Barbara, Snyder, Michael, Cherry, J Michael

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YeastMine--an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit von Balakrishnan, Rama, Park, Julie, Karra, Kalpana, Hitz, Benjamin C, Binkley, Gail, Hong, Eurie L, Sullivan, Julie, Micklem, Gos, Cherry, J Michael

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Investigation into the effect of process parameters on microstructural and physical properties of 316L stainless steel parts by selective laser melting von Cherry, J. A., Davies, H. M., Mehmood, S., Lavery, N. P., Brown, S. G. R., Sienz, J.

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A gene ontology inferred from molecular networks von Dutkowski, Janusz, Kramer, Michael, Surma, Michal A, Balakrishnan, Rama, Cherry, J Michael, Krogan, Nevan J, Ideker, Trey

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Evaluating the Clinical Validity of Gene-Disease Associations: An Evidence-Based Framework Developed by the Clinical Genome Resource von Strande, Natasha T., Riggs, Erin Rooney, Buchanan, Adam H., Ceyhan-Birsoy, Ozge, DiStefano, Marina, Dwight, Selina S., Goldstein, Jenny, Ghosh, Rajarshi, Seifert, Bryce A., Sneddon, Tam P., Wright, Matt W., Milko, Laura V., Cherry, J. Michael, Giovanni, Monica A., Murray, Michael F., O’Daniel, Julianne M., Ramos, Erin M., Santani, Avni B., Scott, Alan F., Plon, Sharon E., Rehm, Heidi L., Martin, Christa L., Berg, Jonathan S.

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Brain Responses to Food Logos in Obese and Healthy Weight Children von Bruce, Amanda S., PhD, Lepping, Rebecca J., MA, Bruce, Jared M., PhD, Cherry, J. Bradley C., JD, Martin, Laura E., PhD, Davis, Ann M., PhD, MPH, ABPP, Brooks, William M., PhD, Savage, Cary R., PhD

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Integrative Meta-Assembly Pipeline (IMAP): Chromosome-level genome assembler combining multiple de novo assemblies von Song, Giltae, Lee, Jongin, Kim, Juyeon, Kang, Seokwoo, Lee, Hoyong, Kwon, Daehong, Lee, Daehwan, Lang, Gregory I, Cherry, J Michael, Kim, Jaebum

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Saccharomyces genome database update: server architecture, pan-genome nomenclature, and external resources von Wong, Edith D, Miyasato, Stuart R, Aleksander, Suzi, Karra, Kalpana, Nash, Robert S, Skrzypek, Marek S, Weng, Shuai, Engel, Stacia R, Cherry, J Michael

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Annotating and prioritizing human non-coding variants with RegulomeDB v.2 von Dong, Shengcheng, Zhao, Nanxiang, Spragins, Emma, Kagda, Meenakshi S., Li, Mingjie, Assis, Pedro, Jolanki, Otto, Luo, Yunhai, Cherry, J. Michael, Boyle, Alan P., Hitz, Benjamin C.

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Data Sanitization to Reduce Private Information Leakage from Functional Genomics von Gürsoy, Gamze, Emani, Prashant, Brannon, Charlotte M., Jolanki, Otto A., Harmanci, Arif, Strattan, J. Seth, Cherry, J. Michael, Miranker, Andrew D., Gerstein, Mark

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A guide to best practices for Gene Ontology (GO) manual annotation von Balakrishnan, Rama, Harris, Midori A, Huntley, Rachael, Van Auken, Kimberly, Cherry, J Michael

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ENCODE data at the ENCODE portal von Sloan, Cricket A, Chan, Esther T, Davidson, Jean M, Malladi, Venkat S, Strattan, J Seth, Hitz, Benjamin C, Gabdank, Idan, Narayanan, Aditi K, Ho, Marcus, Lee, Brian T, Rowe, Laurence D, Dreszer, Timothy R, Roe, Greg, Podduturi, Nikhil R, Tanaka, Forrest, Hong, Eurie L, Cherry, J Michael

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GO::TermFinder—open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes von Boyle, Elizabeth I., Weng, Shuai, Gollub, Jeremy, Jin, Heng, Botstein, David, Cherry, J. Michael, Sherlock, Gavin

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Bird rookery nutrient over-enrichment as a potential accelerant of mangrove cay decline in Belize von Simpson, L. T., Canty, S. W. J., Cissell, J. R., Steinberg, M. K., Cherry, J. A., Feller, I. C.

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