Author details

Full Name

James B Brown

Affiliation

ORCID

Career Start Year

2007

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
35789323	Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements.	Nat Genet	2022
36346220	Two neuronal peptides encoded from a single transcript regulate mitochondrial complex III in <i>Drosophila</i>.	Elife	2022
34819611	An integrated host-microbiome response to atrazine exposure mediates toxicity in Drosophila.	Commun Biol	2021
33782488	Influence of soil heterogeneity on soybean plant development and crop yield evaluated using time-series of UAV and ground-based geophysical imagery.	Scientific Reports	2021
34341363	An infrared spectral biomarker accurately predicts neurodegenerative disease class in the absence of overt symptoms.	Scientific Reports	2021
33758256	Selective time-dependent changes in activity and cell-specific gene expression in human postmortem brain.	Sci Rep	2021
33339542	Roundup causes embryonic development failure and alters metabolic pathways and gut microbiota functionality in non-target species.	Microbiome	2020
31906859	A comprehensive epigenomic analysis of phenotypically distinguishable, genetically identical female and male Daphnia pulex.	BMC Genomics	2020
32170312	*-DCC: A platform to collect, annotate, and explore a large variety of sequencing experiments.	Gigascience	2020
31669395	Vision of a near future: Bridging the human health-environment divide. Toward an integrated strategy to understand mechanisms across species for chemical safety assessment.	Toxicol In Vitro	2020
32338428	Multigenerational Exposures of Daphnia Magna to Pristine and Aged Silver Nanoparticles: Epigenetic Changes and Phenotypical Ageing Related Effects.	Small	2020
32754192	A Long Non-coding RNA, <i>LOC157273</i>, Is an Effector Transcript at the Chromosome 8p23.1-<i>PPP1R3B</i> Metabolic Traits and Type 2 Diabetes Risk Locus.	Front Genet	2020
32793173	Iron Supplementation Eliminates Antagonistic Interactions Between Root-Associated Bacteria.	Front Microbiol	2020
31515332	Complete Genome Sequence of <i>Agrobacterium</i> sp. Strain 33MFTa1.1, Isolated from <i>Thlaspi arvense</i> Roots.	Microbiol Resour Announc	2019
30598455	Exploiting regulatory heterogeneity to systematically identify enhancers with high accuracy.	Proc Natl Acad Sci U S A	2019
29494619	Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease.	PLoS Comput Biol	2018
28746735	Early transcriptional response pathways in Daphnia magna are coordinated in networks of crustacean-specific genes.	Mol Ecol	2018
30060190	Pattern of DNA Methylation in Daphnia: Evolutionary Perspective.	Genome Biol Evol	2018
29959282	An important class of intron retention events in human erythroblasts is regulated by cryptic exons proposed to function as splicing decoys.	RNA	2018
29351989	Iterative random forests to discover predictive and stable high-order interactions.	Proceedings of the National Academy of Sciences of the United States of America	2018
28140384	Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors.	Sci Data	2017
29016359	Age-related gene expression in luminal epithelial cells is driven by a microenvironment made from myoepithelial cells.	Aging	2017
27892936	Influence of early life exposure, host genetics and diet on the mouse gut microbiome and metabolome.	Nat Microbiol	2016
27164179	Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors.	Sci Data	2016
26772746	Diverse Hormone Response Networks in 41 Independent Drosophila Cell Lines.	G3 (Bethesda)	2016
27577169	Centromere and kinetochore gene misexpression predicts cancer patient survival and response to radiotherapy and chemotherapy.	Nat Commun	2016
26294687	Extensive cross-regulation of post-transcriptional regulatory networks in Drosophila.	Genome Res	2015
25631608	Low-frequency and rare exome chip variants associate with fasting glucose and type 2 diabetes susceptibility.	Nat Commun	2015
26133010	Lessons from modENCODE.	Annu Rev Genomics Hum Genet	2015
26548763	Identification of genetic factors that modify motor performance and body weight using Collaborative Cross mice.	Sci Rep	2015
25164755	Comparative analysis of the transcriptome across distant species.	Nature	2014
25275320	Promoter analysis reveals globally differential regulation of human long non-coding RNA and protein-coding genes.	PLoS One	2014
24633242	Genome-guided transcript assembly by integrative analysis of RNA sequence data.	Nat Biotechnol	2014
24985915	Comparative validation of the D. melanogaster modENCODE transcriptome annotation.	Genome Res	2014
24670639	Diversity and dynamics of the Drosophila transcriptome.	Nature	2014
23236164	DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila.	Proc Natl Acad Sci U S A	2012
22685694	Global patterns of tissue-specific alternative polyadenylation in Drosophila.	Cell Rep	2012
22955991	ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.	Genome Res	2012
22955988	The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression.	Genome Res	2012
22955977	Long noncoding RNAs are rarely translated in two human cell lines.	Genome Res	2012
22950945	Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors.	Genome Biol	2012
22950368	Modeling gene expression using chromatin features in various cellular contexts.	Genome Biol	2012
22135461	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
22279750	[Splice sites are overrepresented in Pasilla binding motif clusters in D. melanogaster genes].	Biofizika	2011
21179090	The developmental transcriptome of Drosophila melanogaster.	Nature	2011
21177961	Genome-wide analysis of promoter architecture in Drosophila melanogaster.	Genome Res	2011
20684787	Nonparametric identification of regulatory interactions from spatial and temporal gene expression data.	BMC Bioinformatics	2010
19805447	An overview of recent developments in genomics and associated statistical methods.	Philos Trans A Math Phys Eng Sci	2009
19627575	Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions.	Genome Biol	2009
17571346	Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.	Nature	2007