James B. Brown
James B. Brown
University of Birmingham (UK), Lawrence Berkeley National Laboratory (US), UC Berkeley (US)
Verified email at lbl.gov - Homepage
TitleCited byYear
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
ENCODE Project Consortium
Nature 447 (7146), 799, 2007
48272007
The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression
T Derrien, R Johnson, G Bussotti, A Tanzer, S Djebali, H Tilgner, ...
Genome research 22 (9), 1775-1789, 2012
28872012
The developmental transcriptome of Drosophila melanogaster
BR Graveley, AN Brooks, JW Carlson, MO Duff, JM Landolin, L Yang, ...
Nature 471 (7339), 473, 2011
11412011
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
SG Landt, GK Marinov, A Kundaje, P Kheradpour, F Pauli, S Batzoglou, ...
Genome research 22 (9), 1813-1831, 2012
10882012
Measuring reproducibility of high-throughput experiments
Q Li, JB Brown, H Huang, PJ Bickel
The annals of applied statistics 5 (3), 1752-1779, 2011
4832011
Diversity and dynamics of the Drosophila transcriptome
JB Brown, N Boley, R Eisman, GE May, MH Stoiber, MO Duff, BW Booth, ...
Nature 512 (7515), 393, 2014
3502014
Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions
S MacArthur, XY Li, J Li, JB Brown, HC Chu, L Zeng, BP Grondona, ...
Genome biology 10 (7), R80, 2009
3182009
Long noncoding RNAs are rarely translated in two human cell lines
B Bánfai, H Jia, J Khatun, E Wood, B Risk, WE Gundling, A Kundaje, ...
Genome research 22 (9), 1646-1657, 2012
3042012
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
EH Margulies, GM Cooper, G Asimenos, DJ Thomas, CN Dewey, A Siepel, ...
Genome research 17 (6), 760-774, 2007
2312007
Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors
KY Yip, C Cheng, N Bhardwaj, JB Brown, J Leng, A Kundaje, J Rozowsky, ...
Genome biology 13 (9), R48, 2012
2202012
Modeling gene expression using chromatin features in various cellular contexts
X Dong, MC Greven, A Kundaje, S Djebali, JB Brown, C Cheng, ...
Genome biology 13 (9), R53, 2012
2072012
Comparative analysis of the transcriptome across distant species
MB Gerstein, J Rozowsky, KK Yan, D Wang, C Cheng, JB Brown, ...
Nature 512 (7515), 445, 2014
2032014
Genome-wide analysis of promoter architecture in Drosophila melanogaster
RA Hoskins, JM Landolin, JB Brown, JE Sandler, H Takahashi, ...
Genome research 21 (2), 182-192, 2011
1812011
Global patterns of tissue-specific alternative polyadenylation in Drosophila
P Smibert, P Miura, JO Westholm, S Shenker, G May, MO Duff, D Zhang, ...
Cell reports 1 (3), 277-289, 2012
1722012
Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation
JJ Li, CR Jiang, JB Brown, H Huang, PJ Bickel
Proceedings of the National Academy of Sciences 108 (50), 19867-19872, 2011
1372011
Low-frequency and rare exome chip variants associate with fasting glucose and type 2 diabetes susceptibility
J Wessel, AY Chu, SM Willems, S Wang, H Yaghootkar, JA Brody, ...
Nature communications 6, 5897, 2015
1282015
Comparative validation of the D. melanogaster modENCODE transcriptome annotation
ZX Chen, D Sturgill, J Qu, H Jiang, S Park, N Boley, AM Suzuki, ...
Genome research 24 (7), 1209-1223, 2014
902014
Subsampling methods for genomic inference
PJ Bickel, N Boley, JB Brown, H Huang, NR Zhang
The Annals of Applied Statistics 4 (4), 1660-1697, 2010
692010
Promoter analysis reveals globally differential regulation of human long non-coding RNA and protein-coding genes
T Alam, YA Medvedeva, H Jia, JB Brown, L Lipovich, VB Bajic
PloS one 9 (10), e109443, 2014
592014
Centromere and kinetochore gene misexpression predicts cancer patient survival and response to radiotherapy and chemotherapy
W Zhang, JH Mao, W Zhu, AK Jain, K Liu, JB Brown, GH Karpen
Nature communications 7, 12619, 2016
582016
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