D. Fargo

发表

An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers

Steven A. Roberts, Sara A. Grimm, G. Getz, 2013, Nature Genetics.

Global Analysis of Short RNAs Reveals Widespread Promoter-Proximal Stalling and Arrest of Pol II in Drosophila

D. Fargo, S. Nechaev, G. dos Santos, 2010, Science.

Revealing a human p53 universe

Brian D. Bennett, Christopher A. Lavender, Sara A. Grimm, 2018, Nucleic acids research.

Comprehensive molecular characterization of urothelial bladder carcinoma

Steven J. M. Jones, Evan O. Paull, Joshua M. Stuart, 2014, Nature.

An APOBEC3A hypermutation signature is distinguishable from the signature of background mutagenesis by APOBEC3B in human cancers

Gad Getz, Kin Chan, Dmitry A. Gordenin, 2015, Nature Genetics.

Bidirectional Transcription Arises from Two Distinct Hubs of Transcription Factor Binding and Active Chromatin.

David C Fargo, D. Fargo, S. Nechaev, 2015, Molecular cell.

Pausing of RNA Polymerase II Disrupts DNA-Specified Nucleosome Organization to Enable Precise Gene Regulation

Bin Xie, Leping Li, Leping Li, 2010, Cell.

Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus)

Q. Zeng, B. Birren, B. Roe, 2010, Proceedings of the National Academy of Sciences.

Genome-wide mutagenesis resulting from topoisomerase 1-processing of unrepaired ribonucleotides in DNA.

T. Kunkel, D. Fargo, Adam B. Burkholder, 2019, DNA repair.

An Analysis of Debitage at Kosapsom Park Site (DCRU 4)

D. Fargo, 2012 .

Heterogeneous polymerase fidelity and mismatch repair bias genome variation and composition

T. Kunkel, P. Mieczkowski, D. Gordenin, 2014, Genome research.

Expanded methyl-sensitive cut counting reveals hypomethylation as an epigenetic state that highlights functional sequences of the genome

Tianyuan Wang, S. Peddada, Yuan Gao, 2011, Proceedings of the National Academy of Sciences.

Post‐transcriptional regulation of transcript abundance by a conserved member of the tristetraprolin family in Candida albicans

G. M. Wilson, P. Blackshear, Leping Li, 2015, Molecular microbiology.

An APOBEC3A hypermutation signature is distinguishable from the signature of background mutagenesis by APOBEC3B in human cancers

G. Getz, P. Mieczkowski, Jaegil Kim, 2015, Nature Genetics.

A Novel Analytical Strategy to Identify Fusion Transcripts between Repetitive Elements and Protein Coding-Exons Using RNA-Seq

Tianyuan Wang, E. Nestler, D. Fargo, 2016, PloS one.

INO80 Dependent Promoter Access Facilitates Activation of Pluripotency Genes in Embryonic Stem Cell Self-Renewal, Reprogramming, and Blastocyst Development

Raja Jothi, D. Fargo, Bingying Zhou, 2014 .

Early Bronze Age Animal Use at Lajia, a Qijia Culture Site in Qinghai Province, China

D. Fargo, Maolin Ye, Y. Lam, 2015 .

Rapid activity-induced transcription of Arc and other IEGs relies on poised RNA polymerase II

Erin M. Wissink, S. Dudek, D. Fargo, 2011, Nature Neuroscience.

Haploinsufficiency of SIRT1 Enhances Glutamine Metabolism and Promotes Cancer Development

W. Wu, Xiaoling Li, Xiangchun Li, 2017, Current Biology.

The Impact of Environmental and Endogenous Damage on Somatic Mutation Load in Human Skin Fibroblasts

Isidro Cortes-Ciriano, Steven A Roberts, Eunjung Lee, 2016, PLoS genetics.

TRIM28 regulates RNA polymerase II promoter proximal pausing and pause release

S. Levine, Christopher C. Ebmeier, D. Taatjes, 2014, Nature Structural &Molecular Biology.

Genetic modifiers of lung disease in cystic fibrosis.

Michael R Knowles, Fei Zou, Fred A Wright, 2005, The New England journal of medicine.

Intestinal Epithelial Sirtuin 1 Regulates Intestinal Inflammation During Aging in Mice by Altering the Intestinal Microbiota.

Ajay S. Gulati, L. Guarente, Xiaoling Li, 2017, Gastroenterology.

Tracking replication enzymology in vivo by genome-wide mapping of ribonucleotide incorporation

T. Kunkel, P. Mieczkowski, D. Fargo, 2014, Nature Structural &Molecular Biology.

Using ChIP-chip and ChIP-seq to study the regulation of gene expression: genome-wide localization studies reveal widespread regulation of transcription elongation.

David C Fargo, D. Fargo, K. Adelman, 2009, Methods.

Pausing of RNA polymerase II regulates mammalian developmental potential through control of signaling networks.

D. Fargo, K. Adelman, G. Hu, 2015, Molecular cell.

Defining the status of RNA polymerase at promoters.

Leighton J. Core, J. Lis, D. Fargo, 2012, Cell reports.

Chloroplast Ribosomal Protein S7 of Chlamydomonas Binds to Chloroplast mRNA Leader Sequences and May Be Involved in Translation Initiation

D. Fargo, N. W. Gillham, J. Boynton, 2001, Plant Cell.

Muver, a computational framework for accurately calling accumulated mutations

Christopher A. Lavender, Sara A. Grimm, T. Kunkel, 2018, BMC Genomics.

Downstream Antisense Transcription Predicts Genomic Features That Define the Specific Chromatin Environment at Mammalian Promoters

Brian D. Bennett, Christopher A. Lavender, D. Fargo, 2016, PLoS genetics.

The THO complex regulates pluripotency gene mRNA export and controls embryonic stem cell self-renewal and somatic cell reprogramming.

K. Hochedlinger, D. Fargo, Bingying Zhou, 2013, Cell stem cell.

DNA methylation in mice is influenced by genetics as well as sex and life experience

Brian D. Bennett, Sara A. Grimm, J. Mullikin, 2019, Nature Communications.

Regulating the regulators: the pervasive effects of Pol II pausing on stimulus-responsive gene networks.

D. Fargo, G. dos Santos, K. Adelman, 2012, Genes & development.

stimulus-responsive gene networks Regulating the regulators : the pervasive effects of Pol II pausing on Material Supplemental

G. D. Santos, D. Fargo, K. Adelman, 2012 .

INO80 facilitates pluripotency gene activation in embryonic stem cell self-renewal, reprogramming, and blastocyst development.

Raja Jothi, D. Fargo, Bingying Zhou, 2014, Cell stem cell.

Widespread transcriptional pausing and elongation control at enhancers

Christopher A. Lavender, D. Fargo, K. Adelman, 2018, Genes & development.

UV-exposure, endogenous DNA damage, and DNA replication errors shape the spectra of genome changes in human skin

D. Gordenin, L. Klimczak, D. Fargo, 2021, PLoS genetics.

ORSO (Online Resource for Social Omics): A data-driven social network connecting scientists to genomics datasets

Andrew J Shapiro, Andrew J. Shapiro, Christopher A. Lavender, 2020, PLoS Comput. Biol..

RNA polymerase II promoter-proximal pausing in mammalian long non-coding genes.

Yaoyu E. Wang, S. Levine, D. Fargo, 2016, Genomics.

Stable pausing by RNA polymerase II provides an opportunity to target and integrate regulatory signals.

D. Fargo, S. Nechaev, K. Adelman, 2013, Molecular cell.

Novel DNA motif binding activity observed in vivo with an estrogen receptor α mutant mouse.

Sara A. Grimm, Leping Li, K. Korach, 2014, Molecular endocrinology.

PAVIS: a tool for Peak Annotation and Visualization

Rasiah Loganantharaj, Leping Li, Weichun Huang, 2013, Bioinform..

Research resource: whole-genome estrogen receptor α binding in mouse uterine tissue revealed by ChIP-seq.

Sara A. Grimm, P. Bushel, Leping Li, 2012, Molecular endocrinology.

INO80 governs superenhancer-mediated oncogenic transcription and tumor growth in melanoma

Brian D. Bennett, D. Fargo, Yan Zhang, 2016, Genes & development.

A Serial shRNA Screen for Roadblocks to Reprogramming Identifies the Protein Modifier SUMO2

Brian D. Bennett, S. Elledge, J. Brumbaugh, 2016, Stem cell reports.

INO80 is required for oncogenic transcription and tumor growth in non-small cell lung cancer

Brian D. Bennett, G. Hu, D. Fargo, 2017, Oncogene.

The skin is no barrier to mixtures: Air pollutant mixtures and reported psoriasis or eczema in the Personalized Environment and Genes Study (PEGS)

K. Messier, A. Motsinger-Reif, D. Fargo, 2022, Journal of Exposure Science & Environmental Epidemiology.

Shine-Dalgarno-like sequences are not required for translation of chloroplast mRNAs in Chlamydomonas reinhardtii chloroplasts or in Escherichia coli

D. Fargo, N. W. Gillham, M. Zhang, 1998, Molecular and General Genetics MGG.

Ancestry-dependent gene expression correlates with reprogramming to pluripotency and multiple dynamic biological processes

Brian D. Bennett, E. Perez-stable, Jung S. Byun, 2020, Science Advances.

Methionine metabolism is essential for SIRT1‐regulated mouse embryonic stem cell maintenance and embryonic development

Xiaoling Li, Qing Xu, J. Locasale, 2017, The EMBO journal.

SIRT1-mediated deacetylation of CRABPII regulates cellular retinoic acid signaling and modulates embryonic stem cell differentiation.

Xiaoling Li, Qing Xu, Yingming Zhao, 2014, Molecular cell.

Questionnaire-Based Polyexposure Assessment Outperforms Polygenic Scores for Classification of Type 2 Diabetes in a Multiancestry Cohort

A. Motsinger-Reif, D. Fargo, J. Buse, 2022, Diabetes care.

CNOT3-Dependent mRNA Deadenylation Safeguards the Pluripotent State

Brian D. Bennett, Raja Jothi, D. Fargo, 2016, Stem cell reports.

Repair of multiple simultaneous double-strand breaks causes bursts of genome-wide clustered hypermutation

Cynthia J. Sakofsky, P. Mieczkowski, D. Gordenin, 2019, PLoS biology.

Race/ethnicity-stratified fine-mapping of the MHC locus reveals genetic variants associated with late-onset asthma

L. Perera, A. Motsinger-Reif, D. Fargo, 2023, Frontiers in Genetics.

Questionnaire-based exposome-wide association studies (ExWAS) reveal expected and novel risk factors associated with cardiovascular outcomes in the Personalized Environment and Genes Study.

A. Motsinger-Reif, D. Fargo, F. Akhtari, 2022, Environmental research.

The phosphorylation status of T522 modulates tissue‐specific functions of SIRT1 in energy metabolism in mice

Xiaoling Li, Qing Xu, Xiumei Guo, 2017, EMBO reports.

Mutations Altering the Predicted Secondary Structure of a Chloroplast 5′ Untranslated Region Affect Its Physical and Biochemical Properties as Well as Its Ability To Promote Translation of Reporter mRNAs Both in the Chlamydomonas reinhardtii Chloroplast and in Escherichia coli

D. Fargo, N. W. Gillham, J. Boynton, 1999, Molecular and Cellular Biology.

DNA methylation in mice is influenced by genetics as well as sex and life experience

Brian D. Bennett, Sara A. Grimm, J. Mullikin, 2019, Nature Communications.

Association of distance to swine concentrated animal feeding operations with immune-mediated diseases: An exploratory gene-environment study.

A. Motsinger-Reif, D. Fargo, M. Fessler, 2022, Environment international.

Posttranscriptional Regulation of Cell-Cell Interaction Protein-Encoding Transcripts by Zfs1p in Schizosaccharomyces pombe

P. Blackshear, Leping Li, Fatih Ozsolak, 2012, Molecular and Cellular Biology.

ORIO (Online Resource for Integrative Omics): a web-based platform for rapid integration of next generation sequencing data

Brian D. Bennett, Andrew J. Shapiro, Christopher A. Lavender, 2017, Nucleic acids research.

Online Resource for Integrative Omics ) : a web-based platform for rapid integration of next generation sequencing data

Brian D. Bennett, Andrew J. Shapiro, Christopher A. Lavender, 2017 .

Correction: Repair of multiple simultaneous double-strand breaks causes bursts of genome-wide clustered hypermutation

Cynthia J. Sakofsky, P. Mieczkowski, D. Gordenin, 2020, PLoS Biology.