James B. Brown - Publications

Affiliations: 
2008 University of California, Berkeley, Berkeley, CA 

39 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Choo SW, Zhong Y, Sendler E, Goustin AS, Cai J, Ju D, Brown JB, Kosir MA, Giordo R, Lipovich L. Estrogen distinctly regulates transcription and translation of lncRNAs and pseudogenes in breast cancer cells. Genomics. 110421. PMID 35779786 DOI: 10.1016/j.ygeno.2022.110421  0.331
2021 Dachet F, Brown JB, Valyi-Nagy T, Narayan KD, Serafini A, Boley N, Gingeras TR, Celniker SE, Mohapatra G, Loeb JA. Selective time-dependent changes in activity and cell-specific gene expression in human postmortem brain. Scientific Reports. 11: 6078. PMID 33758256 DOI: 10.1038/s41598-021-85801-6  0.726
2020 Manning AK, Goustin AS, Kleinbrink EL, Thepsuwan P, Cai J, Ju D, Leong A, Udler MS, Brown JB, Goodarzi MO, Rotter JI, Sladek R, Meigs JB, Lipovich L. A Long Non-coding RNA, , Is an Effector Transcript at the Chromosome 8p23.1- Metabolic Traits and Type 2 Diabetes Risk Locus. Frontiers in Genetics. 11: 615. PMID 32754192 DOI: 10.3389/Fgene.2020.00615  0.382
2020 Hörtenhuber M, Mukarram AK, Stoiber MH, Brown JB, Daub CO. *-DCC: A platform to collect, annotate, and explore a large variety of sequencing experiments. Gigascience. 9. PMID 32170312 DOI: 10.1093/Gigascience/Giaa024  0.324
2018 Arbel H, Basu S, Fisher WW, Hammonds AS, Wan KH, Park S, Weiszmann R, Booth BW, Keranen SV, Henriquez C, Shams Solari O, Bickel PJ, Biggin MD, Celniker SE, Brown JB. Exploiting regulatory heterogeneity to systematically identify enhancers with high accuracy. Proceedings of the National Academy of Sciences of the United States of America. PMID 30598455 DOI: 10.1073/Pnas.1808833115  0.599
2018 Kvist J, Athanàsio CG, Solari OS, Brown JB, Colbourne JK, Pfrender ME, Mirbahai L. Pattern of DNA methylation in Daphnia: Evolutionary perspective. Genome Biology and Evolution. PMID 30060190 DOI: 10.1093/Gbe/Evy155  0.372
2018 Parra M, Booth BW, Weiszmann R, Yee BA, Yeo GW, Brown JB, Celniker SE, Conboy JG. An important class of intron retention events in human erythroblasts is regulated by cryptic exons proposed to function as splicing decoys. Rna (New York, N.Y.). PMID 29959282 DOI: 10.1261/Rna.066951.118  0.472
2018 Basu S, Kumbier K, Brown JB, Yu B. Iterative random forests to discover predictive and stable high-order interactions. Proceedings of the National Academy of Sciences of the United States of America. PMID 29351989 DOI: 10.1073/Pnas.1711236115  0.393
2017 Orsini L, Brown JB, Shams Solari O, Li D, He S, Podicheti R, Stoiber MH, Spanier KI, Gilbert D, Jansen M, Rusch D, Pfrender ME, Colbourne JK, Frilander MJ, Kvist J, et al. Early transcriptional response pathways in Daphnia magna are coordinated in networks of crustacean specific genes. Molecular Ecology. PMID 28746735 DOI: 10.1111/Mec.14261  0.354
2017 Orsini L, Gilbert D, Podicheti R, Jansen M, Brown JB, Solari OS, Spanier KI, Colbourne JK, Rusch DB, Decaestecker E, Asselman J, De Schamphelaere KA, Ebert D, Haag CR, Kvist J, et al. Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors. Scientific Data. 4: 170006. PMID 28140384 DOI: 10.1038/Sdata.2017.6  0.356
2017 Zhang W, Mao J, Zhu W, Jain AK, Liu K, Brown JB, Karpen GH. Abstract 3456: Centromere gene misregulation is a major source of chromosomal instability in human cancers and predicts patient response to specific therapies Cancer Research. 77: 3456-3456. DOI: 10.1158/1538-7445.Am2017-3456  0.306
2016 Zhang W, Mao JH, Zhu W, Jain AK, Liu K, Brown JB, Karpen GH. Centromere and kinetochore gene misexpression predicts cancer patient survival and response to radiotherapy and chemotherapy. Nature Communications. 7: 12619. PMID 27577169 DOI: 10.1038/Ncomms12619  0.304
2016 Orsini L, Gilbert D, Podicheti R, Jansen M, Brown JB, Solari OS, Spanier KI, Colbourne JK, Rush D, Decaestecker E, Asselman J, De Schamphelaere KA, Ebert D, Haag CR, Kvist J, et al. Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors. Scientific Data. 3: 160030. PMID 27164179 DOI: 10.1038/Sdata.2016.30  0.443
2015 Stoiber MH, Olson S, May GE, Duff MO, Manent J, Obar R, Guruharsha K, Artavanis-Tsakonas S, Brown JB, Graveley BR, Celniker SE. Extensive cross-regulation of post-transcriptional regulatory networks in Drosophila. Genome Research. PMID 26294687 DOI: 10.1101/Gr.182675.114  0.42
2015 Brown JB, Celniker SE. Lessons from modENCODE. Annual Review of Genomics and Human Genetics. PMID 26133010 DOI: 10.1146/Annurev-Genom-090413-025448  0.475
2014 Alam T, Medvedeva YA, Jia H, Brown JB, Lipovich L, Bajic VB. Promoter analysis reveals globally differential regulation of human long non-coding RNA and protein-coding genes. Plos One. 9: e109443. PMID 25275320 DOI: 10.1371/Journal.Pone.0109443  0.499
2014 Gerstein MB, Rozowsky J, Yan KK, Wang D, Cheng C, Brown JB, Davis CA, Hillier L, Sisu C, Li JJ, Pei B, Harmanci AO, Duff MO, Djebali S, Alexander RP, et al. Comparative analysis of the transcriptome across distant species. Nature. 512: 445-8. PMID 25164755 DOI: 10.1038/Nature13424  0.783
2014 Chen ZX, Sturgill D, Qu J, Jiang H, Park S, Boley N, Suzuki AM, Fletcher AR, Plachetzki DC, FitzGerald PC, Artieri CG, Atallah J, Barmina O, Brown JB, Blankenburg KP, et al. Comparative validation of the D. melanogaster modENCODE transcriptome annotation. Genome Research. 24: 1209-23. PMID 24985915 DOI: 10.1101/Gr.159384.113  0.785
2014 Brown JB, Boley N, Eisman R, May GE, Stoiber MH, Duff MO, Booth BW, Wen J, Park S, Suzuki AM, Wan KH, Yu C, Zhang D, Carlson JW, Cherbas L, et al. Diversity and dynamics of the Drosophila transcriptome. Nature. 512: 393-9. PMID 24670639 DOI: 10.1038/Nature12962  0.792
2014 Boley N, Stoiber MH, Booth BW, Wan KH, Hoskins RA, Bickel PJ, Celniker SE, Brown JB. Genome-guided transcript assembly by integrative analysis of RNA sequence data. Nature Biotechnology. 32: 341-6. PMID 24633242 DOI: 10.1038/Nbt.2850  0.803
2012 Fisher WW, Li JJ, Hammonds AS, Brown JB, Pfeiffer BD, Weiszmann R, MacArthur S, Thomas S, Stamatoyannopoulos JA, Eisen MB, Bickel PJ, Biggin MD, Celniker SE. DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila. Proceedings of the National Academy of Sciences of the United States of America. 109: 21330-5. PMID 23236164 DOI: 10.1073/Pnas.1209589110  0.71
2012 Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Research. 22: 1813-31. PMID 22955991 DOI: 10.1101/Gr.136184.111  0.598
2012 Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG, Lagarde J, Veeravalli L, Ruan X, Ruan Y, Lassmann T, ... ... Brown JB, et al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Research. 22: 1775-89. PMID 22955988 DOI: 10.1101/Gr.132159.111  0.496
2012 Bánfai B, Jia H, Khatun J, Wood E, Risk B, Gundling WE, Kundaje A, Gunawardena HP, Yu Y, Xie L, Krajewski K, Strahl BD, Chen X, Bickel P, Giddings MC, ... Brown JB, et al. Long noncoding RNAs are rarely translated in two human cell lines. Genome Research. 22: 1646-57. PMID 22955977 DOI: 10.1101/Gr.134767.111  0.61
2012 Yip KY, Cheng C, Bhardwaj N, Brown JB, Leng J, Kundaje A, Rozowsky J, Birney E, Bickel P, Snyder M, Gerstein M. Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors. Genome Biology. 13: R48. PMID 22950945 DOI: 10.1186/Gb-2012-13-9-R48  0.63
2012 Dong X, Greven MC, Kundaje A, Djebali S, Brown JB, Cheng C, Gingeras TR, Gerstein M, Guigó R, Birney E, Weng Z. Modeling gene expression using chromatin features in various cellular contexts. Genome Biology. 13: R53. PMID 22950368 DOI: 10.1186/Gb-2012-13-9-R53  0.439
2012 Smibert P, Miura P, Westholm JO, Shenker S, May G, Duff MO, Zhang D, Eads BD, Carlson J, Brown JB, Eisman RC, Andrews J, Kaufman T, Cherbas P, Celniker SE, et al. Global patterns of tissue-specific alternative polyadenylation in Drosophila. Cell Reports. 1: 277-89. PMID 22685694 DOI: 10.1016/J.Celrep.2012.01.001  0.436
2011 Polishchuk MS, Brown JB, Favorov AV, Bickel PJ, Tumanian VG. [Splice sites are overrepresented in Pasilla binding motif clusters in D. melanogaster genes]. Biofizika. 56: 1065-70. PMID 22279750  0.525
2011 Li JJ, Jiang CR, Brown JB, Huang H, Bickel PJ. Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation. Proceedings of the National Academy of Sciences of the United States of America. 108: 19867-72. PMID 22135461 DOI: 10.1073/Pnas.1113972108  0.679
2011 Graveley BR, Brooks AN, Carlson JW, Duff MO, Landolin JM, Yang L, Artieri CG, van Baren MJ, Boley N, Booth BW, Brown JB, Cherbas L, Davis CA, Dobin A, Li R, et al. The developmental transcriptome of Drosophila melanogaster. Nature. 471: 473-9. PMID 21179090 DOI: 10.1038/Nature09715  0.802
2011 Hoskins RA, Landolin JM, Brown JB, Sandler JE, Takahashi H, Lassmann T, Yu C, Booth BW, Zhang D, Wan KH, Yang L, Boley N, Andrews J, Kaufman TC, Graveley BR, et al. Genome-wide analysis of promoter architecture in Drosophila melanogaster. Genome Research. 21: 182-92. PMID 21177961 DOI: 10.1101/Gr.112466.110  0.792
2011 Li Q, Brown JB, Huang H, Bickel PJ. Measuring reproducibility of high-throughput experiments Annals of Applied Statistics. 5: 1752-1779. DOI: 10.1214/11-Aoas466  0.547
2011 Polishchuk MS, Brown JB, Favorov AV, Bickel PJ, Tumanyan VG. Splice sites are overrepresented in Pasilla binding motif clusters in D. melanogaster genes Biophysics. 56: 1043-1046. DOI: 10.1134/S0006350911060145  0.503
2010 Aswani A, Keränen SVE, Brown J, Fowlkes CC, Knowles DW, Biggin MD, Bickel P, Tomlin CJ. Nonparametric identification of regulatory interactions from spatial and temporal gene expression data Bmc Bioinformatics. 11. PMID 20684787 DOI: 10.1186/1471-2105-11-413  0.604
2010 Bickel PJ, Boley N, Brown JB, Huang H, Zhang NR. Subsampling methods for genomic inference Annals of Applied Statistics. 4: 1660-1697. DOI: 10.1214/10-Aoas363  0.759
2009 Bickel PJ, Brown JB, Huang H, Li Q. An overview of recent developments in genomics and associated statistical methods Philosophical Transactions of the Royal Society a: Mathematical, Physical and Engineering Sciences. 367: 4313-4337. PMID 19805447 DOI: 10.1098/Rsta.2009.0164  0.607
2009 MacArthur S, Li XY, Li J, Brown JB, Chu HC, Zeng L, Grondona BP, Hechmer A, Simirenko L, Keränen SV, Knowles DW, Stapleton M, Bickel P, Biggin MD, Eisen MB. Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions. Genome Biology. 10: R80. PMID 19627575 DOI: 10.1186/Gb-2009-10-7-R80  0.694
2007 Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, ... ... Brown JB, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447: 799-816. PMID 17571346 DOI: 10.1038/Nature05874  0.662
2007 Margulies EH, Cooper GM, Asimenos G, Thomas DJ, Dewey CN, Siepel A, Birney E, Keefe D, Schwartz AS, Hou M, Taylor J, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, ... ... Brown JB, et al. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Research. 17: 760-74. PMID 17567995 DOI: 10.1101/Gr.6034307  0.623
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