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Correction: Repair of multiple simultaneous double-strand breaks causes bursts of genome-wide clustered hypermutation.
Published in:
2020
By:
- Sakofsky, Cynthia J.;
- Saini, Natalie;
- Klimczak, Leszek J.;
- Chan, Kin;
- Malc, Ewa P.;
- Mieczkowski, Piotr A.;
- Burkholder, Adam B.;
- Fargo, David;
- Gordenin, Dmitry A.
Publication type:
Correction Notice
Repair of multiple simultaneous double-strand breaks causes bursts of genome-wide clustered hypermutation.
Published in:
PLoS Biology, 2019, v. 17, n. 9, p. 1, doi. 10.1371/journal.pbio.3000464
By:
- Sakofsky, Cynthia J.;
- Saini, Natalie;
- Klimczak, Leszek J.;
- Chan, Kin;
- Malc, Ewa P.;
- Mieczkowski, Piotr A.;
- Burkholder, Adam B.;
- Fargo, David;
- Gordenin, Dmitry A.
Publication type:
Article
Revealing a human p53 universe.
Published in:
Nucleic Acids Research, 2018, v. 46, n. 16, p. 8153, doi. 10.1093/nar/gky720
By:
- Nguyen, Thuy-Ai T;
- Grimm, Sara A;
- Bushel, Pierre R;
- Li, Jianying;
- Li, Yuanyuan;
- Bennett, Brian D;
- Lavender, Christopher A;
- Ward, James M;
- Fargo, David C;
- Anderson, Carl W
Publication type:
Article
ORIO (Online Resource for Integrative Omics): a web-based platform for rapid integration of next generation sequencing data.
Published in:
Nucleic Acids Research, 2017, v. 45, n. 10, p. 5678, doi. 10.1093/nar/gkx270
By:
- Lavender, Christopher A.;
- Shapiro, Andrew J.;
- Burkholder, Adam B.;
- Bennett, Brian D.;
- Adelman, Karen;
- Fargo, David C.
Publication type:
Article
An APOBEC3A hypermutation signature is distinguishable from the signature of background mutagenesis by APOBEC3B in human cancers.
Published in:
Nature Genetics, 2015, v. 47, n. 9, p. 1067, doi. 10.1038/ng.3378
By:
- Sterling, Joan F;
- Malc, Ewa P;
- Fargo, David C;
- Mieczkowski, Piotr A;
- Kwiatkowski, David J;
- Saini, Natalie;
- Kim, Jaegil;
- Roberts, Steven A;
- Getz, Gad;
- Chan, Kin;
- Gordenin, Dmitry A;
- Klimczak, Leszek J
Publication type:
Article
An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers.
Published in:
Nature Genetics, 2013, v. 45, n. 9, p. 970, doi. 10.1038/ng.2702
By:
- Roberts, Steven A;
- Lawrence, Michael S;
- Klimczak, Leszek J;
- Grimm, Sara A;
- Fargo, David;
- Stojanov, Petar;
- Kiezun, Adam;
- Kryukov, Gregory V;
- Carter, Scott L;
- Saksena, Gordon;
- Harris, Shawn;
- Shah, Ruchir R;
- Resnick, Michael A;
- Getz, Gad;
- Gordenin, Dmitry A
Publication type:
Article
Tracking replication enzymology in vivo by genome-wide mapping of ribonucleotide incorporation.
Published in:
Nature Structural & Molecular Biology, 2015, v. 22, n. 3, p. 185, doi. 10.1038/nsmb.2957
By:
- Clausen, Anders R;
- Lujan, Scott A;
- Burkholder, Adam B;
- Orebaugh, Clinton D;
- Williams, Jessica S;
- Clausen, Maryam F;
- Malc, Ewa P;
- Mieczkowski, Piotr A;
- Fargo, David C;
- Smith, Duncan J;
- Kunkel, Thomas A
Publication type:
Article
TRIM28 regulates RNA polymerase II promoter-proximal pausing and pause release.
Published in:
Nature Structural & Molecular Biology, 2014, v. 21, n. 10, p. 876, doi. 10.1038/nsmb.2878
By:
- Bunch, Heeyoun;
- Zheng, Xiaofeng;
- Burkholder, Adam;
- Dillon, Simon T;
- Motola, Shmulik;
- Birrane, Gabriel;
- Ebmeier, Christopher C;
- Levine, Stuart;
- Fargo, David;
- Hu, Guang;
- Taatjes, Dylan J;
- Calderwood, Stuart K
Publication type:
Article
UV-exposure, endogenous DNA damage, and DNA replication errors shape the spectra of genome changes in human skin.
Published in:
PLoS Genetics, 2021, v. 17, n. 1, p. 1, doi. 10.1371/journal.pgen.1009302
By:
- Saini, Natalie;
- Giacobone, Camille K.;
- Klimczak, Leszek J.;
- Papas, Brian N.;
- Burkholder, Adam B.;
- Li, Jian-Liang;
- Fargo, David C.;
- Bai, Re;
- Gerrish, Kevin;
- Innes, Cynthia L.;
- Schurman, Shepherd H.;
- Gordenin, Dmitry A.
Publication type:
Article
The phosphorylation status of T522 modulates tissue-specific functions of SIRT1 in energy metabolism in mice.
Published in:
EMBO Reports, 2017, v. 18, n. 5, p. 841, doi. 10.15252/embr.201643803
By:
- Lu, Jing;
- Xu, Qing;
- Ji, Ming;
- Guo, Xiumei;
- Xu, Xiaojiang;
- Fargo, David C;
- Li, Xiaoling
Publication type:
Article
Post-transcriptional regulation of transcript abundance by a conserved member of the tristetraprolin family in C andida albicans.
Published in:
Molecular Microbiology, 2015, v. 95, n. 6, p. 1036, doi. 10.1111/mmi.12913
By:
- Wells, Melissa L.;
- Washington, Onica L.;
- Hicks, Stephanie N.;
- Nobile, Clarissa J.;
- Hartooni, Nairi;
- Wilson, Gerald M.;
- Zucconi, Beth E.;
- Huang, Weichun;
- Li, Leping;
- Fargo, David C.;
- Blackshear, Perry J.
Publication type:
Article
Methionine metabolism is essential for SIRT1-regulated mouse embryonic stem cell maintenance and embryonic development.
Published in:
EMBO Journal, 2017, v. 36, n. 21, p. 3175, doi. 10.15252/embj.201796708
By:
- Tang, Shuang;
- Fang, Yi;
- Huang, Gang;
- Xu, Xiaojiang;
- Padilla‐Banks, Elizabeth;
- Fan, Wei;
- Xu, Qing;
- Sanderson, Sydney M;
- Foley, Julie F;
- Dowdy, Scotty;
- McBurney, Michael W;
- Fargo, David C;
- Williams, Carmen J;
- Locasale, Jason W;
- Guan, Ziqiang;
- Li, Xiaoling
Publication type:
Article
Muver, a computational framework for accurately calling accumulated mutations.
Published in:
BMC Genomics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12864-018-4753-3
By:
- Burkholder, Adam B.;
- Lujan, Scott A.;
- Lavender, Christopher A.;
- Grimm, Sara A.;
- Kunkel, Thomas A.;
- Fargo, David C.
Publication type:
Article
A Novel Analytical Strategy to Identify Fusion Transcripts between Repetitive Elements and Protein Coding-Exons Using RNA-Seq.
Published in:
PLoS ONE, 2016, v. 11, n. 7, p. 1, doi. 10.1371/journal.pone.0159028
By:
- Wang, Tianyuan;
- Santos, Janine H.;
- Feng, Jian;
- Fargo, David C.;
- Shen, Li;
- Riadi, Gonzalo;
- Keeley, Elizabeth;
- Rosh, Zachary S.;
- Nestler, Eric J.;
- Woychik, Richard P.
Publication type:
Article
Rapid activity-induced transcription of Arc and other IEGs relies on poised RNA polymerase II.
Published in:
Nature Neuroscience, 2011, v. 14, n. 7, p. 848, doi. 10.1038/nn.2839
By:
- Saha, Ramendra N.;
- Wissink, Erin M.;
- Bailey, Emma R.;
- Zhao, Meilan;
- Fargo, David C.;
- Hwang, Ji-Yeon;
- Daigle, Kelly R.;
- Fenn, J Daniel;
- Adelman, Karen;
- Dudek, Serena M.
Publication type:
Article
Race/ethnicity-stratified fine-mapping of the MHC locus reveals genetic variants associated with late-onset asthma.
Published in:
Frontiers in Genetics, 2023, p. 1, doi. 10.3389/fgene.2023.1173676
By:
- Lee, Eunice Y.;
- Wonson Choi;
- Burkholder, Adam B.;
- Perera, Lalith;
- Mack, Jasmine A.;
- Miller, Frederick W.;
- Fessler, Michael B.;
- Cook, Donald N.;
- Karmaus, Peer W. F.;
- Hideki Nakano;
- Garantziotis, Stavros;
- Madenspacher, Jennifer H.;
- House, John S.;
- Akhtari, Farida S.;
- Schmitt, Charles S.;
- Fargo, David C.;
- Hall, Janet E.;
- Motsinger-Reif, Alison A.
Publication type:
Article
Questionnaire-Based Polyexposure Assessment Outperforms Polygenic Scores for Classification of Type 2 Diabetes in a Multiancestry Cohort.
Published in:
Diabetes Care, 2023, v. 46, n. 5, p. 929, doi. 10.2337/dc22-0295
By:
- Akhtari, Farida S.;
- Lloyd, Dillon;
- Burkholder, Adam;
- Tong, Xiaoran;
- House, John S.;
- Lee, Eunice Y.;
- Buse, John;
- Schurman, Shepherd H.;
- Fargo, David C.;
- Schmitt, Charles P.;
- Hall, Janet;
- Motsinger-Reif, Alison A.
Publication type:
Article
ORSO (Online Resource for Social Omics): A data-driven social network connecting scientists to genomics datasets.
Published in:
PLoS Computational Biology, 2020, v. 16, n. 1, p. 1, doi. 10.1371/journal.pcbi.1007571
By:
- Lavender, Christopher A.;
- Shapiro, Andrew J.;
- Day, Frank S.;
- Fargo, David C.
Publication type:
Article
PAVIS: a tool for Peak Annotation and Visualization.
Published in:
Bioinformatics, 2013, v. 29, n. 23, p. 3097, doi. 10.1093/bioinformatics/btt520
By:
- Huang, Weichun;
- Loganantharaj, Rasiah;
- Schroeder, Bryce;
- Fargo, David;
- Li, Leping
Publication type:
Article
The Impact of Environmental and Endogenous Damage on Somatic Mutation Load in Human Skin Fibroblasts.
Published in:
PLoS Genetics, 2016, v. 12, n. 10, p. 1, doi. 10.1371/journal.pgen.1006385
By:
- Saini, Natalie;
- Roberts, Steven A.;
- Klimczak, Leszek J.;
- Chan, Kin;
- Grimm, Sara A.;
- Dai, Shuangshuang;
- Fargo, David C.;
- Boyer, Jayne C.;
- Kaufmann, William K.;
- Taylor, Jack A.;
- Lee, Eunjung;
- Cortes-Ciriano, Isidro;
- Park, Peter J.;
- Schurman, Shepherd H.;
- Malc, Ewa P.;
- Mieczkowski, Piotr A.;
- Gordenin, Dmitry A.
Publication type:
Article
Downstream Antisense Transcription Predicts Genomic Features That Define the Specific Chromatin Environment at Mammalian Promoters.
Published in:
PLoS Genetics, 2016, v. 12, n. 8, p. 1, doi. 10.1371/journal.pgen.1006224
By:
- Lavender, Christopher A.;
- Cannady, Kimberly R.;
- Hoffman, Jackson A.;
- Trotter, Kevin W.;
- Gilchrist, Daniel A.;
- Bennett, Brian D.;
- Burkholder, Adam B.;
- Burd, Craig J.;
- Fargo, David C.;
- Archer, Trevor K.
Publication type:
Article

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