James B. Brown

发表

Non Parametric Methods for Genomic Inference

Peter J. Bickel, Nancy R. Zhang, James B. Brown, 2007 .

Exploiting regulatory heterogeneity to systematically identify enhancers with high accuracy

William W. Fisher, Mark D. Biggin, James B. Brown, 2018, bioRxiv.

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

William Stafford Noble, Nancy R. Zhang, Stephen C. J. Parker, 2007, Nature.

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

David G. Knowles, James B. Brown, Hagen U. Tilgner, 2012, Genome research.

An overview of recent developments in genomics and associated statistical methods

James B. Brown, P. Bickel, Haiyan Huang, 2009, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome.

Colin N. Dewey, Richard A. Moore, James B. Brown, 2007, Genome research.

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

Marc D. Perry, James B. Brown, Timothy E. Reddy, 2012, Genome research.

An Integrated Encyclopedia of DNA Elements in the Human Genome

Raymond K. Auerbach, William Stafford Noble, Stephen C. J. Parker, 2012, Nature.

Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions

James B. Brown, D. W. Knowles, P. Bickel, 2009, Genome Biology.

Measuring reproducibility of high-throughput experiments

Peter J. Bickel, Haiyan Huang, James B. Brown, 2011, 1110.4705.

DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila

James B. Brown, P. Bickel, J. Stamatoyannopoulos, 2012, Proceedings of the National Academy of Sciences.

Subsampling methods for genomic inference

Nancy R. Zhang, James B. Brown, P. Bickel, 2010, 1101.0947.

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors

Kevin Y. Yip, James B. Brown, P. Bickel, 2012, Genome Biology.

Long noncoding RNAs are rarely translated in two human cell lines

James B. Brown, Morgan C. Giddings, P. Bickel, 2012, Genome research.

Modeling gene expression using chromatin features in various cellular contexts

James B. Brown, Melissa C. Greven, E. Birney, 2012, Genome Biology.

A Long Non-coding RNA, LOC157273, Is an Effector Transcript at the Chromosome 8p23.1-PPP1R3B Metabolic Traits and Type 2 Diabetes Risk Locus

James B. Brown, L. Lipovich, J. Rotter, 2020, Frontiers in Genetics.

Low-frequency and rare exome chip variants associate with fasting glucose and type 2 diabetes susceptibility

Inês Barroso, Jiyoung Heo, Beverley Balkau, 2015, Nature communications.

Lessons from modENCODE.

James B. Brown, Susan E Celniker, James B Brown, 2015, Annual review of genomics and human genetics.

Comparative Analysis of the Transcriptome across Distant Species

Peter J. Bickel, Raymond K. Auerbach, Peter J. Park, 2014, Nature.

Global patterns of tissue-specific alternative polyadenylation in Drosophila.

James B. Brown, S. Celniker, E. Lai, 2012, Cell reports.

The Developmental Transcriptome of Drosophila melanogaster

Peter J. Bickel, Li Yang, Thomas R. Gingeras, 2010, Nature.

Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation

James B. Brown, P. Bickel, Haiyan Huang, 2011, Proceedings of the National Academy of Sciences.

Diversity and dynamics of the Drosophila transcriptome

James B. Brown, Benjamin W. Booth, Marcus H. Stoiber, 2014, Nature.

Satellite-derived foresummer drought sensitivity of plant productivity in Rocky Mountain headwater catchments: spatial heterogeneity and geological-geomorphological control

James B. Brown, K. Williams, B. Enquist, 2020, Environmental Research Letters.

Comparative validation of the D. melanogaster modENCODE transcriptome annotation

James B. Brown, P. Bickel, Manolis Kellis, 2014, Genome research.

Iterative random forests to discover predictive and stable high-order interactions

James B. Brown, Sumanta Basu, Karl Kumbier, 2017, Proceedings of the National Academy of Sciences.

An Overview of Recent Developments in Genomics and the Statistical Methods that Bear on Them

James B. Brown, P. Bickel, Haiyan Huang, 2009 .

Qunhua Li and associated statistical methods An overview of recent developments in genomics

James B. Brown, P. Bickel, Haiyan Huang, 2009 .

Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors

Luisa Orsini, Ram Podicheti, John K. Colbourne, 2016, Scientific Data.

Genome-wide analysis of promoter architecture in Drosophila melanogaster.

Piero Carninci, Timo Lassmann, Justen Andrews, 2011, Genome research.

Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease

Carsten O. Daub, Vladimir B. Bajic, Tom C. Freeman, 2016, bioRxiv.

iterative Random Forests to discover predictive and stable high-order interactions

Bin Yu, Sumanta Basu, Karl Kumbier, 2017 .

Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors

Luisa Orsini, Ram Podicheti, John K. Colbourne, 2017, Scientific Data.

MEASURING REPRODUCIBILITY OF HIGH-THROUGHPUT

Peter J. Bickel, James B. Brown, Haiyan Huang, 2010 .

Identification and analysis of functional elements in 1 % of the human genome by the ENCODE pilot project The ENCODE Project Consortium *

Colin N. Dewey, James B. Brown, Anason S. Halees, 2007 .

MODA: MOdule Differential Analysis for weighted gene co-expression network

Zhisong Pan, Guyu Hu, Luisa Orsini, 2016 .

Centromere and kinetochore gene misexpression predicts cancer patient survival and response to radiotherapy and chemotherapy

Wei Zhu, Ke Liu, Gary H. Karpen, 2016, Nature Communications.

Promoter Analysis Reveals Globally Differential Regulation of Human Long Non-Coding RNA and Protein-Coding Genes

Vladimir B. Bajic, Leonard Lipovich, Tanvir Alam, 2014, PloS one.

Review of and Recommendations for Monitoring Contaminants and their Effects in the San Francisco Bay−Delta

James B. Brown, A. Whitehead, T. Young, 2019, San Francisco Estuary and Watershed Science.

A comprehensive epigenomic analysis of phenotypically distinguishable, genetically identical female and male Daphnia pulex

James B. Brown, J. Colbourne, M. Pfrender, 2020, BMC Genomics.

Iterative Random Forests to detect predictive and stable high-order interactions

James B. Brown, Sumanta Basu, Karl Kumbier, 2017 .

Roundup causes embryonic development failure and alters metabolic pathways and gut microbiota functionality in non-target species

James B. Brown, Jiarui Zhou, A. Suppa, 2020, Microbiome.

A Long Non-coding RNA, LOC157273, Is an Effector Transcript at the Chromosome 8p23.1-PPP1R3B Metabolic Traits and Type 2 Diabetes Risk Locus

James B. Brown, Erica L. Kleinbrink, L. Lipovich, 2020, bioRxiv.

Lawrence Berkeley National Laboratory Recent Work Title Extensive cross-regulation of post-transcriptional regulatory networks in Drosophila Permalink

James B. Brown, Marcus H. Stoiber, P. Bickel, 2015 .

Multigenerational Exposures of Daphnia Magna to Pristine and Aged Silver Nanoparticles: Epigenetic Changes and Phenotypical Ageing Related Effects.

James B. Brown, Laura-Jayne A. Ellis, I. Lynch, 2020, Small.

Toward an integrated strategy to understand mechanisms across 2 species for chemical safety assessment

James B. Brown, Timothy E. H. Allen, R. Judson, 2019 .

Integration of RNA-seq and Ribosome Profiling to Characterize Transcriptional and Translational Estrogen Responses of Genes in Human Breast Cancer

James B. Brown, S. Choo, L. Lipovich, 2020 .

Iron Supplementation Eliminates Antagonistic Interactions Between Root-Associated Bacteria

James B. Brown, A. Deutschbauer, M. Bissell, 2020, Frontiers in Microbiology.

Diversity and dynamics of the Drosophila transcriptome Please share how this access benefits you. Your story matters

James B. Brown, Eads, Benjamin W. Booth, 2014 .

Molecular and functional characterization of the Drosophila melanogaster conserved smORFome

James B. Brown, N. Perrimon, Richard Weiszmann, 2022, bioRxiv.

Multigenerational Exposure to Nano‐TiO 2 Induces Ageing as a Stress Response Mitigated by Environmental Interactions

James B. Brown, Laura-Jayne A. Ellis, I. Lynch, 2021, Advanced NanoBiomed Research.

Roundup causes embryonic development failure, activates tumorigenesis pathways and alters gut microbiota functionality in non-target species

James B. Brown, Jiarui Zhou, A. Suppa, 2020 .

Early transcriptional response pathways in Daphnia magna are coordinated in networks of crustacean‐specific genes

James B. Brown, Marcus H. Stoiber, D. Rusch, 2018, Molecular ecology.

University of Birmingham Pattern of DNA methylation in Daphnia

James B. Brown, O. S. Solari, J. Colbourne, 2018 .

Sparse Canonical Correlation Analysis via Concave Minimization pdf

Peter J. Bickel, James B. Brown, James B. Brown, 2019, ArXiv.

Genome-guided transcript assembly from integrative analysis of RNA sequence data

James B. Brown, Benjamin W. Booth, Marcus H. Stoiber, 2014, Nature Biotechnology.

Complete Genome Sequence of Agrobacterium sp. Strain 33MFTa1.1, Isolated from Thlaspi arvense Roots

James B. Brown, S. Tringe, S. Celniker, 2019, Microbiology Resource Announcements.

An infrared spectral biomarker accurately predicts neurodegenerative disease class in the absence of overt symptoms

James B. Brown, Renaud Schuck, E. Barnard, 2021, Scientific Reports.

Refining interaction search through signed iterative Random Forests

Bin Yu, Sumanta Basu, Karl Kumbier, 2018, bioRxiv.

Rhizobacteria Mediate the Phytotoxicity of a Range of Biorefinery‐Relevant Compounds

James B. Brown, M. Bissell, K. Wan, 2019, Environmental toxicology and chemistry.

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Martin S. Taylor, Jay W. Shin, Thomas J. Ha, 2021, Nature Communications.

Selective time-dependent changes in activity and cell-specific gene expression in human postmortem brain

K. D. Narayan, James B. Brown, S. Celniker, 2021, Scientific Reports.

An important class of intron retention events in human erythroblasts is regulated by cryptic exons proposed to function as splicing decoys

James B. Brown, Gene W. Yeo, Benjamin W. Booth, 2018, bioRxiv.

Vision of a near future: Bridging the human health-environment divide. Toward an integrated strategy to understand mechanisms across species for chemical safety assessment.

Imran Shah, Andrew White, Francesco Falciani, 2020, Toxicology in vitro : an international journal published in association with BIBRA.

Extensive cross-regulation of post-transcriptional regulatory networks in Drosophila

James B. Brown, Michael O Duff, Brenton R Graveley, 2015, Genome research.

Exploiting regulatory heterogeneity to systematically identify enhancers with high accuracy

Sumanta Basu, James B. Brown, Richard Weiszmann, 2018, Proceedings of the National Academy of Sciences.

Pattern of DNA Methylation in Daphnia: Evolutionary Perspective

James B. Brown, J. Colbourne, M. Pfrender, 2018, Genome biology and evolution.

modENCODE consortia ChIP-seq guidelines and practices of the ENCODE and Material Supplemental

James B. Brown, Timothy E. Reddy, P. Bickel, 2012 .

Influence of early life exposure, host genetics and diet on the mouse gut microbiome and metabolome

Young-Mo Kim, Elhanan Borenstein, Thomas O Metz, 2016, Nature Microbiology.

A comprehensive epigenomic analysis of phenotypically distinguishable, genetically identical female and male Daphnia pulex

James B. Brown, J. Colbourne, M. Pfrender, 2020, BMC Genomics.

James B. Brown, Rosalyn W. Sayaman, Marcus H. Stoiber, 2017, Aging.

BasecRAWller: Streaming Nanopore Basecalling Directly from Raw Signal

James B. Brown, Marcus H. Stoiber, James B. Brown, 2017, bioRxiv.

*-DCC: A platform to collect, annotate, and explore a large variety of sequencing experiments

James B Brown, James B. Brown, Matthias Hörtenhuber, 2020, GigaScience.

An integrated host-microbiome response to atrazine exposure mediates toxicity in Drosophila

James B. Brown, Ralf J. M. Weber, Benjamin W. Booth, 2021, Communications Biology.

Identification of genetic factors that modify motor performance and body weight using Collaborative Cross mice

James B. Brown, S. Celniker, A. Snijders, 2015, Scientific Reports.

Frontiers in RNA biology: Advances from a small fly Drosophila melanogaster

James B. Brown, S. Celniker, S. E. Celniker, 2016 .

Influence of soil heterogeneity on soybean plant development and crop yield evaluated using time-series of UAV and ground-based geophysical imagery

James B. Brown, Richard G. Ham, S. Hubbard, 2021, Scientific Reports.

Estrogen distinctly regulates transcription and translation of lncRNAs and pseudogenes in breast cancer cells.

James B. Brown, S. Choo, L. Lipovich, 2022, Genomics.

University of Birmingham Multigenerational exposures of Daphnia magna to pristine and aged silver nanoparticles

James B. Brown, Laura-Jayne A. Ellis, I. Lynch, 2020 .

Nonparametric identification of regulatory interactions from spatial and temporal gene expression data

James Brown, Claire J. Tomlin, Charless C. Fowlkes, 2010, BMC Bioinformatics.

Signed iterative random forests to identify enhancer-associated transcription factor binding

James B. Brown, E. Frise, Sumanta Basu, 2018, 1810.07287.

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors

Kevin Y. Yip, James B. Brown, E. Birney, 2012, Genome Biology.

Sequential Imputation of Missing Spatio-Temporal Precipitation Data Using Random Forests

Scott L. Painter, Dipankar Dwivedi, James B. Brown, 2020, Frontiers in Water.

Iterative Random Forests to detect predictive and stable high-order interactions

James B. Brown, Sumanta Basu, Bin-Xia Yu, 2017 .

DE-FPCA: Testing Gene Differential Expression and Exon Usage Through Functional Principal Component Analysis

Peter J. Bickel, Hao Xiong, James B. Brown, 2014 .

The wicked problem of biodiversity and ecosystem services in a changing world

William A. Stubbings, Stefan Krause, Niamh Eastwood, 2020 .

Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation

James B. Brown, P. Bickel, Haiyan Huang, 2011, Proceedings of the National Academy of Sciences.

BLOCCS: Block Sparse Canonical Correlation Analysis With Application To Interpretable Omics Integration

James B. Brown, O. S. Solari, Rojin Safavi, 2019, ArXiv.

Modeling gene expression using chromatin features in various cellular contexts

James B. Brown, Melissa C. Greven, E. Birney, 2012, Genome Biology.