Iterative random forests to discover predictive and stable high-order interactions von Basu, Sumanta, Kumbier, Karl, Brown, James B., Yu, Bin

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Centromere and kinetochore gene misexpression predicts cancer patient survival and response to radiotherapy and chemotherapy von Zhang, Weiguo, Mao, Jian-Hua, Zhu, Wei, Jain, Anshu K., Liu, Ke, Brown, James B., Karpen, Gary H.

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Long noncoding RNAs are rarely translated in two human cell lines von Bánfai, Balázs, Jia, Hui, Khatun, Jainab, Wood, Emily, Risk, Brian, Gundling, Jr, William E, Kundaje, Anshul, Gunawardena, Harsha P, Yu, Yanbao, Xie, Ling, Krajewski, Krzysztof, Strahl, Brian D, Chen, Xian, Bickel, Peter, Giddings, Morgan C, Brown, James B, Lipovich, Leonard

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Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models von Garvin, Michael R., Prates, Erica T., Pavicic, Mirko, Jones, Piet, Amos, B. Kirtley, Geiger, Armin, Shah, Manesh B., Streich, Jared, Gazolla, Joao Gabriel Felipe Machado, Kainer, David, Cliff, Ashley, Romero, Jonathon, Keith, Nathan, Brown, James B., Jacobson, Daniel

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Lessons from modENCODE von Brown, James B, Celniker, Susan E

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Selective time-dependent changes in activity and cell-specific gene expression in human postmortem brain von Dachet, Fabien, Brown, James B., Valyi-Nagy, Tibor, Narayan, Kunwar D., Serafini, Anna, Boley, Nathan, Gingeras, Thomas R., Celniker, Susan E., Mohapatra, Gayatry, Loeb, Jeffrey A.

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Promoter analysis reveals globally differential regulation of human long non-coding RNA and protein-coding genes von Alam, Tanvir, Medvedeva, Yulia A, Jia, Hui, Brown, James B, Lipovich, Leonard, Bajic, Vladimir B

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Global Patterns of Tissue-Specific Alternative Polyadenylation in Drosophila von Smibert, Peter, Miura, Pedro, Westholm, Jakub O., Shenker, Sol, May, Gemma, Duff, Michael O., Zhang, Dayu, Eads, Brian D., Carlson, Joe, Brown, James B., Eisman, Robert C., Andrews, Justen, Kaufman, Thomas, Cherbas, Peter, Celniker, Susan E., Graveley, Brenton R., Lai, Eric C.

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Molecular and functional characterization of the Drosophila melanogaster conserved smORFome von Bosch, Justin A., Keith, Nathan, Escobedo, Felipe, Fisher, William W., LaGraff, James Thai, Rabasco, Jorden, Wan, Kenneth H., Weiszmann, Richard, Wu, Yulun, Hu, Yanhui, Kondo, Shu, Brown, James B., Perrimon, Norbert, Celniker, Susan E.

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Molecular and functional characterization of the Drosophila melanogaster conserved smORFome von Bosch, Justin A., Keith, Nathan, Escobedo, Felipe, Fisher, William W., LaGraff, James Thai, Rabasco, Jorden, Wan, Kenneth H., Weiszmann, Richard, Wu, Yulun, Hu, Yanhui, Kondo, Shu, Brown, James B., Perrimon, Norbert, Celniker, Susan E.

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A comprehensive epigenomic analysis of phenotypically distinguishable, genetically identical female and male Daphnia pulex von Kvist, Jouni, Athanasio, Camila Goncalves, Pfrender, Michael E., Brown, James B., Colbourne, John K., Mirbahai, Leda

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A novel random forest approach to revealing interactions and controls on chlorophyll concentration and bacterial communities during coastal phytoplankton blooms von Cheng, Yiwei, Bhoot, Ved N., Kumbier, Karl, Sison-Mangus, Marilou P., Brown, James B., Kudela, Raphael, Newcomer, Michelle E.

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Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions von MacArthur, Stewart, Li, Xiao-Yong, Li, Jingyi, Brown, James B, Chu, Hou Cheng, Zeng, Lucy, Grondona, Brandi P, Hechmer, Aaron, Simirenko, Lisa, Keränen, Soile V E, Knowles, David W, Stapleton, Mark, Bickel, Peter, Biggin, Mark D, Eisen, Michael B

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DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila von Fisher, William W., Li, Jingyi Jessica, Hammonds, Ann S., Brown, James B., Pfeiffer, Barret D., Weiszmann, Richard, MacArthur, Stewart, Thomas, Sean, Stamatoyannopoulos, John A., Eisen, Michael B., Bickel, Peter J., Biggin, Mark D., Celniker, Susan E.

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Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation von Li, Jingyi Jessica, Jiang, Ci-Ren, Brown, James B, Huang, Haiyan, Bickel, Peter J

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Genome-wide analysis of promoter architecture in Drosophila melanogaster von Hoskins, Roger A, Landolin, Jane M, Brown, James B, Sandler, Jeremy E, Takahashi, Hazuki, Lassmann, Timo, Yu, Charles, Booth, Benjamin W, Zhang, Dayu, Wan, Kenneth H, Yang, Li, Boley, Nathan, Andrews, Justen, Kaufman, Thomas C, Graveley, Brenton R, Bickel, Peter J, Carninci, Piero, Carlson, Joseph W, Celniker, Susan E

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Vision of a near future: Bridging the human health–environment divide. Toward an integrated strategy to understand mechanisms across species for chemical safety assessment von Rivetti, Claudia, Allen, Timothy E.H., Brown, James B., Butler, Emma, Carmichael, Paul L., Colbourne, John K., Dent, Matthew, Falciani, Francesco, Gunnarsson, Lina, Gutsell, Steve, Harrill, Joshua A., Hodges, Geoff, Jennings, Paul, Judson, Richard, Kienzler, Aude, Margiotta-Casaluci, Luigi, Muller, Iris, Owen, Stewart F., Rendal, Cecilie, Russell, Paul J., Scott, Sharon, Sewell, Fiona, Shah, Imran, Sorrel, Ian, Viant, Mark R., Westmoreland, Carl, White, Andrew, Campos, Bruno

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An infrared spectral biomarker accurately predicts neurodegenerative disease class in the absence of overt symptoms von Lovergne, Lila, Ghosh, Dhruba, Schuck, Renaud, Polyzos, Aris A., Chen, Andrew D., Martin, Michael C., Barnard, Edward S., Brown, James B., McMurray, Cynthia T.

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Roundup causes embryonic development failure and alters metabolic pathways and gut microbiota functionality in non-target species von Suppa, Antonio, Kvist, Jouni, Li, Xiaojing, Dhandapani, Vignesh, Almulla, Hanan, Tian, Antoine Y., Kissane, Stephen, Zhou, Jiarui, Perotti, Alessio, Mangelson, Hayley, Langford, Kyle, Rossi, Valeria, Brown, James B., Orsini, Luisa

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Machine-Learning Functional Zonation Approach for Characterizing Terrestrial–Aquatic Interfaces: Application to Lake Erie von Enguehard, Léa, Falco, Nicola, Schmutz, Myriam, Newcomer, Michelle E., Ladau, Joshua, Brown, James B., Bourgeau-Chavez, Laura, Wainwright, Haruko M.

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