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James B. Brown
James B. Brown
Lawrence Berkeley National Laboratory; UC Berkeley; Arva Intelligence, Inc.
Verified email at lbl.gov - Homepage
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Cited by
Year
An integrated encyclopedia of DNA elements in the human genome
ENCODE Project Consortium
Nature 489 (7414), 57, 2012
137742012
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
Management Group Liefer Laura A. 51 Wetterstrand Kris A. 51 Good Peter J. 51 ...
nature 447 (7146), 799-816, 2007
59892007
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
52522012
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
21872012
The developmental transcriptome of Drosophila melanogaster
BR Graveley, AN Brooks, JW Carlson, MO Duff, JM Landolin, L Yang, ...
Nature 471 (7339), 473-479, 2011
16672011
Measuring reproducibility of high-throughput experiments
Q Li, JB Brown, H Huang, PJ Bickel
10912011
Diversity and dynamics of the Drosophila transcriptome
JB Brown, N Boley, R Eisman, GE May, MH Stoiber, MO Duff, BW Booth, ...
Nature 512 (7515), 393-399, 2014
7162014
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
4532012
Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic …
S MacArthur, XY Li, J Li, JB Brown, HC Chu, L Zeng, BP Grondona, ...
Genome biology 10, 1-26, 2009
3962009
Comparative analysis of the transcriptome across distant species
MB Gerstein, J Rozowsky, KK Yan, D Wang, C Cheng, JB Brown, ...
Nature 512 (7515), 445-448, 2014
3242014
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, 1-17, 2012
3212012
Iterative random forests to discover predictive and stable high-order interactions
S Basu, K Kumbier, JB Brown, B Yu
Proceedings of the National Academy of Sciences 115 (8), 1943-1948, 2018
3152018
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, 1-22, 2012
2962012
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
2752011
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
2602012
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
2482007
De novo Identification of DNA Modifications Enabled by Genome-Guided Nanopore Signal Processing
M Stoiber, J Quick, R Egan, J Eun Lee, S Celniker, RK Neely, N Loman, ...
BioRxiv, 094672, 2016
2402016
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 (1), 5897, 2015
2242015
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
1822011
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 (1), 12619, 2016
1742016
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Articles 1–20