The mPower study, Parkinson disease mobile data collected using ResearchKit von Bot, Brian M., Suver, Christine, Neto, Elias Chaibub, Kellen, Michael, Klein, Arno, Bare, Christopher, Doerr, Megan, Pratap, Abhishek, Wilbanks, John, Dorsey, E. Ray, Friend, Stephen H., Trister, Andrew D.

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Hydrologic variation influences stream fish assemblage dynamics through flow regime and drought von Magoulick, Daniel D., Dekar, Matthew P., Hodges, Shawn W., Scott, Mandy K., Rabalais, Michael R., Bare, Christopher M.

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Open chromatin profiling of human postmortem brain infers functional roles for non-coding schizophrenia loci von Fullard, John F, Giambartolomei, Claudia, Hauberg, Mads E, Xu, Ke, Voloudakis, Georgios, Shao, Zhiping, Bare, Christopher, Dudley, Joel T, Mattheisen, Manuel, Robakis, Nikolaos K, Haroutunian, Vahram, Roussos, Panos

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A Predictive Model for Transcriptional Control of Physiology in a Free Living Cell von Bonneau, Richard, Facciotti, Marc T., Reiss, David J., Schmid, Amy K., Pan, Min, Kaur, Amardeep, Thorsson, Vesteinn, Shannon, Paul, Johnson, Michael H., Bare, J. Christopher, Longabaugh, William, Vuthoori, Madhavi, Whitehead, Kenia, Madar, Aviv, Suzuki, Lena, Mori, Tetsuya, Chang, Dong-Eun, DiRuggiero, Jocelyne, Johnson, Carl H., Hood, Leroy, Baliga, Nitin S.

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Simulation studies as designed experiments: the comparison of penalized regression models in the "large p, small n" setting von Chaibub Neto, Elias, Bare, J Christopher, Margolin, Adam A

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Germline contamination and leakage in whole genome somatic single nucleotide variant detection von Sendorek, Dorota H, Caloian, Cristian, Ellrott, Kyle, Bare, J Christopher, Yamaguchi, Takafumi N, Ewing, Adam D, Houlahan, Kathleen E, Norman, Thea C, Margolin, Adam A, Stuart, Joshua M, Boutros, Paul C

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Niche adaptation by expansion and reprogramming of general transcription factors von Turkarslan, Serdar, Reiss, David J, Gibbins, Goodwin, Su, Wan Lin, Pan, Min, Bare, J Christopher, Plaisier, Christopher L, Baliga, Nitin S

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Prevalence of transcription promoters within archaeal operons and coding sequences von Koide, Tie, Reiss, David J, Bare, J Christopher, Pang, Wyming Lee, Facciotti, Marc T, Schmid, Amy K, Pan, Min, Marzolf, Bruz, Van, Phu T, Lo, Fang‐Yin, Pratap, Abhishek, Deutsch, Eric W, Peterson, Amelia, Martin, Dan, Baliga, Nitin S

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Changes in the Fluorescence of Biological Particles Exposed to Environmental Conditions in the National Capitol Region von Santarpia, Joshua L., Collins, Don R., Ratnesar-Shumate, Shanna A., Glen, Crystal C., Sanchez, Andres L., Antonietti, Carlos G., Taylor, Jilliane, Taylor, Nathan F., Bare, Christopher A., Kinahan, Sean M., Rivera, Danielle N., Corson, Elizabeth, Hill, Steven C., Williamson, Chatt C., Coleman, Mark, Pan, Yong-Le

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Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection von Ewing, Adam D, Houlahan, Kathleen E, Hu, Yin, Ellrott, Kyle, Caloian, Cristian, Yamaguchi, Takafumi N, Bare, J Christopher, P'ng, Christine, Waggott, Daryl, Sabelnykova, Veronica Y, Kellen, Michael R, Norman, Thea C, Haussler, David, Friend, Stephen H, Stolovitzky, Gustavo, Margolin, Adam A, Stuart, Joshua M, Boutros, Paul C

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Integration and visualization of systems biology data in context of the genome von Bare, J Christopher, Koide, Tie, Reiss, David J, Tenenbaum, Dan, Baliga, Nitin S

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Osteoblast-like cell attachment to and calcification of novel phosphonate-containing polymeric substrates von Gemeinhart, Richard A., Bare, Christopher M., Haasch, Richard T., Gemeinhart, Ernest J.

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The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications von Bare, J Christopher, Shannon, Paul T, Schmid, Amy K, Baliga, Nitin S

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Human Immunodeficiency Virus Type 1 Nef-Mediated Downregulation of CD4 Correlates with Nef Enhancement of Viral Pathogenesis von Stoddart, Cheryl A, Geleziunas, Romas, Ferrell, Sharon, Linquist-Stepps, Valerie, Moreno, Mary E, Bare, Christopher, Xu, Weiduan, Yonemoto, Wes, Bresnahan, Patricia A, McCune, Joseph M, Greene, Warner C

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miRvestigator: web application to identify miRNAs responsible for co-regulated gene expression patterns discovered through transcriptome profiling von Plaisier, Christopher L., Bare, J. Christopher, Baliga, Nitin S.

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Global optimization of somatic variant identification in cancer genomes with a global community challenge von Boutros, Paul C, Ewing, Adam D, Ellrott, Kyle, Norman, Thea C, Dang, Kristen K, Hu, Yin, Kellen, Michael R, Suver, Christine, Bare, J Christopher, Stein, Lincoln D, Spellman, Paul T, Stolovitzky, Gustavo, Friend, Stephen H, Margolin, Adam A, Stuart, Joshua M

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Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen von Menden, Michael P., Wang, Dennis, Mason, Mike J., Szalai, Bence, Bulusu, Krishna C., Guan, Yuanfang, Yu, Thomas, Kang, Jaewoo, Jeon, Minji, Wolfinger, Russ, Nguyen, Tin, Zaslavskiy, Mikhail, Jang, In Sock, Ghazoui, Zara, Ahsen, Mehmet Eren, Vogel, Robert, Neto, Elias Chaibub, Norman, Thea, Tang, Eric K. Y., Garnett, Mathew J., Veroli, Giovanni Y. Di, Fawell, Stephen, Stolovitzky, Gustavo, Guinney, Justin, Dry, Jonathan R., Saez-Rodriguez, Julio

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Parallel evolution of transcriptome architecture during genome reorganization von Yoon, Sung Ho, Reiss, David J, Bare, J Christopher, Tenenbaum, Dan, Pan, Min, Slagel, Joseph, Moritz, Robert L, Lim, Sujung, Hackett, Murray, Menon, Angeli Lal, Adams, Michael W W, Barnebey, Adam, Yannone, Steven M, Leigh, John A, Baliga, Nitin S

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Network portal: a database for storage, analysis and visualization of biological networks von Turkarslan, Serdar, Wurtmann, Elisabeth J, Wu, Wei-Ju, Jiang, Ning, Bare, J Christopher, Foley, Karen, Reiss, David J, Novichkov, Pavel, Baliga, Nitin S

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DREAMTools: a Python package for scoring collaborative challenges [version 2; peer review: 1 approved, 2 approved with reservations] von Cokelaer, Thomas, Bansal, Mukesh, Bare, Christopher, Bilal, Erhan, Bot, Brian M, Chaibub Neto, Elias, Eduati, Federica, de la Fuente, Alberto, Gönen, Mehmet, Hill, Steven M, Hoff, Bruce, Karr, Jonathan R, Küffner, Robert, Menden, Michael P, Meyer, Pablo, Norel, Raquel, Pratap, Abhishek, Prill, Robert J, Weirauch, Matthew T, Costello, James C, Stolovitzky, Gustavo, Saez-Rodriguez, Julio

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