Brown Group @ LBNL
Publications
Brown Lab Member
Co-senior or Co-first Author
 
  • Stoiber MH, May G, Duff M, Obar R, Artavanis-Tsakonas S, Brown JB, Graveley BR, Celniker SE. “Extensive cross-regulation in Drosophila post-transcriptional regulatory networks”. Genome Research. 2015. Provisionally Accepted.
  • Brown JB, Celniker SE. “Lessons from modENCODE”. Annual Reviews of Genomics and Human Genetics. 2015.
  • Wessel J, et al. “Low-frequency and rare exome chip variants associate with fasting glucose and type 2 diabetes susceptibility”. Nat Commun. 2015.
  • 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, Eads BD, Miller D, Mockaitis K, Roberts J, Davis CA, Frise E, Hammonds AS, Olson S, Shenker S, Sturgill D, Samsonova AA, Weiszmann R, Robinson G, Hernandez J, Andrews J, Bickel PJ, Carninci P, Cherbas P, Gingeras TR, Hoskins RA, Kaufman TC, Lai EC, Oliver B, Perrimon N, Graveley BR, Celniker SE. “Diversity and Dynamics of the Drosophila Transcriptome”. Nature. 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”. Nat Biotechnol. 2014.
  • Gerstein MB, Rozowsky J, Yan KK, Wang D, Cheng C, Brown JB, Davis CA, Hillier L, et al. “Comparative analysis of the transcriptome across distant species”. Nature. 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. 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, Clough E, et al. “Comparative validation of the D. melanogaster modENCODE transcriptome annotation”. Genome Res. 2014.
  • Bánfai B, Jia H, Khatun J, Wood E, Risk B, Gundling WE Jr, Kundaje A, Gunawardena HP, Yu Y, Xie L, Krajewski K, Strahl BD, Chen X, Bickel P, Giddings MC, Brown JB, Lipovich L. "Long noncoding RNAs are rarely translated in two human cell lines". Genome Res. 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”. Proc Natl Acad Sci USA. 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 Biol. 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 Biol. 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, Graveley BR, Lai EC. "Global patterns of tissue-specific alternative polyadenylation in Drosophila". Cell Rep. 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, Gerstein M, Gertz J, Hartemink AJ, Hoffman MM, Iyer VR, Jung YL, Karmakar S, et al. "ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia", Genome Res. 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, Carninci P, Brown JB, Lipovich L, Gonzalez JM, Thomas M, Davis CA, Shiekhattar R, et al. "The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression." Genome Res. 2012.
  • ENCODE Project Consortium. "An integrated encyclopedia of DNA elements in the human genome." Nature. 2012.
  • Atherton J, Boley N, Brown JB, Ogawa N, Davidson SM, Eisen MB, Biggin MD, Bickel P. "A model for sequential evolution of ligands by exponential enrichment (SELEX) data." Ann. Appl. Stat. 2012.
  • Graveley BR, et al. "The developmental transcriptome of Drosophila melanogaster". Nature. 2011.
  • The ENCODE Project Consortium. "A User's Guide to the Encyclopedia of DNA Elements (ENCODE)". PLoS Biol. 2011.
  • Li Q, Brown JB, Huang H, Bickel PJ. "Measuring Reproducibility of High-Throughput Experiments." Ann. Appl. Stat. 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." Proc Natl Acad Sci U S A. 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, Bickel PJ, Carninci P, Carlson JW, Celniker SE. "Genome-wide analysis of promoter architecture in Drosophila melanogaster". Genome Research, 2010.
  • Bickel PJ, Boley N, Brown JB, Huang H, and Zhang NR. "Subsampling methods for genomic inference." Ann. Appl. Stat. 2010.
  • Aswani A, Keränen S, Brown J, Fowlkes C, Knowles DW, Biggin MD, Bickel P and Tomlin CJ. "Nonparametric identification of regulatory interactions from spatial and temporal gene expression data." BMC Bioinformatics. 2010.
  • 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. 2009.
  • The ENCODE Project Consortium. "Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project." Nature. 2007.
  • Margulies EH, et al. "Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome". Genome Research. 2007.