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Epigenomics (438)
Publication TitleAuthorsJournalPublication DatePage NoPubMedID
Nuclear architecture as an epigenetic regulator of neural development and function.Alexander, J M; Lomvardas, SNeuroscience2014 Apr 439-5024486963
Noncoding RNAs and LRRFIP1 Regulate TNF Expression.Shi, Lihua; Song, Li; Fitzgerald, Michael; Maurer, Kelly; Bagashev, Asen; Sullivan, Kathleen EJournal of immunology (Baltimore, Md. : 1950)2014 Apr 13057-6724567534
SILAC Peptide Ratio Calculator: A Tool for SILAC Quantitation of Peptides and Post-Translational Modifications.Guan, Xiaoyan; Rastogi, Neha; Parthun, Mark R; Freitas, Michael AJournal of proteome research2014 Feb 7506-1624328097
Taxonomy of breast cancer based on normal cell phenotype predicts outcome.Santagata, Sandro; Thakkar, Ankita; Ergonul, Ayse; Wang, Bin; Woo, Terri; Hu, Rong; Harrell, J Chuck; McNamara, George; Schwede, Matthew; Culhane, Aedin C; Kindelberger, David; Rodig, Scott; Richardson, Andrea; Schnitt, Stuart J; Tamimi, Rulla M; Ince, TaThe Journal of clinical investigation2014 Feb 3859-7024463450
What we talk about when we talk about fat.Rosen, Evan D; Spiegelman, Bruce MCell2014 Jan 1620-4424439368
Understanding the epigenetic syntax for the genetic alphabet in the kidney.Susztak, KatalinJournal of the American Society of Nephrology : JASN2014 Jan7-Oct24179169
Exomic analysis of myxoid liposarcomas, synovial sarcomas, and osteosarcomas.Joseph, Christine G; Hwang, Heejung; Jiao, Yuchen; Wood, Laura D; Kinde, Isaac; Wu, Jian; Mandahl, Nils; Luo, Jinyong; Hruban, Ralph H; Diaz Jr, Luis A; He, Tong-Chuan; Vogelstein, Bert; Kinzler, Kenneth W; Mertens, Fredrik; Papadopoulos, NickolasGenes, chromosomes & cancer2014 Jan15-2424190505
Genome-wide localization of small molecules.Anders, Lars; Guenther, Matthew G; Qi, Jun; Fan, Zi Peng; Marineau, Jason J; Rahl, Peter B; Loven, Jakob; Sigova, Alla A; Smith, William B; Lee, Tong Ihn; Bradner, James E; Young, Richard ANature biotechnology2014 Jan92-624336317
Doxorubicin, DNA torsion, and chromatin dynamics.Yang, Fan; Teves, Sheila S; Kemp, Christopher J; Henikoff, StevenBiochimica et biophysica acta2014 Jan84-924361676
MYC and transcription elongation.Rahl, Peter B; Young, Richard ACold Spring Harbor perspectives in medicine2014 Jana02099024384817
Hypomethylation of the IL17RC Promoter in Peripheral Blood Leukocytes Is Not A Hallmark of Age-Related Macular Degeneration.Oliver, Verity F; Franchina, Maria; Jaffe, Andrew E; Branham, Kari E; Othman, Mohammad; Heckenlively, John R; Swaroop, Anand; Campochiaro, Betsy; Vote, Brendan J; Craig, Jamie E; Saffery, Richard; Mackey, David A; Qian, Jiang; Zack, Donald J; Hewitt, AlexCell reports2013 Dec 261527-3524373284
Dynamic Imaging of Genomic Loci in Living Human Cells by an Optimized CRISPR/Cas System.Chen, Baohui; Gilbert, Luke A; Cimini, Beth A; Schnitzbauer, Joerg; Zhang, Wei; Li, Gene-Wei; Park, Jason; Blackburn, Elizabeth H; Weissman, Jonathan S; Qi, Lei S; Huang, BoCell2013 Dec 191479-9124360272
STAR: an integrated solution to management and visualization of sequencing data.Wang, Tao; Liu, Jie; Shen, Li; Tonti-Filippini, Julian; Zhu, Yun; Jia, Haiyang; Lister, Ryan; Whitaker, John W; Ecker, Joseph R; Millar, A Harvey; Ren, Bing; Wang, WeiBioinformatics (Oxford, England)2013 Dec 153204-1024078702
Radionuclide labeling and evaluation of candidate radioligands for PET imaging of histone deacetylase in the brain.Seo, Young Jun; Muench, Lisa; Reid, Alicia; Chen, Jinzhu; Kang, Yeona; Hooker, Jacob M; Volkow, Nora D; Fowler, Joanna S; Kim, Sung WonBioorganic & medicinal chemistry letters2013 Dec 156700-524210501
High-resolution mapping of transcription factor binding sites on native chromatin.Kasinathan, Sivakanthan; Orsi, Guillermo A; Zentner, Gabriel E; Ahmad, Kami; Henikoff, StevenNature methods2013 Dec 15NULL24336359
Locus-specific editing of histone modifications at endogenous enhancers.Mendenhall, Eric M; Williamson, Kaylyn E; Reyon, Deepak; Zou, James Y; Ram, Oren; Joung, J Keith; Bernstein, Bradley ENature biotechnology2013 Dec1133-624013198
Black raspberries protectively regulate methylation of Wnt pathway genes in precancerous colon tissue.Wang, Li-Shu; Kuo, Chieh-Ti; Huang, Tim H-M; Yearsley, Martha; Oshima, Kiyoko; Stoner, Gary D; Yu, Jianhua; Lechner, John F; Huang, Yi-WenCancer prevention research (Philadelphia, Pa.)2013 Dec1317-2724129635
Mot1 redistributes TBP from TATA-containing to TATA-less promoters.Zentner, Gabriel E; Henikoff, StevenMolecular and cellular biology2013 Dec4996-500424144978
Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing.Selvaraj, Siddarth; R Dixon, Jesse; Bansal, Vikas; Ren, BingNature biotechnology2013 Dec1111-824185094
Mechanisms of cohesin-mediated gene regulation and lessons learned from cohesinopathies.Ball Jr, Alexander R; Chen, Yen-Yun; Yokomori, KyokoBiochimica et biophysica acta2013 Nov 22NULL24269489
A high-resolution map of the three-dimensional chromatin interactome in human cells.Jin, Fulai; Li, Yan; Dixon, Jesse R; Selvaraj, Siddarth; Ye, Zhen; Lee, Ah Young; Yen, Chia-An; Schmitt, Anthony D; Espinoza, Celso A; Ren, BingNature2013 Nov 14290-424141950
Super-enhancers in the control of cell identity and disease.Hnisz, Denes; Abraham, Brian J; Lee, Tong Ihn; Lau, Ashley; Saint-Andre, Violaine; Sigova, Alla A; Hoke, Heather A; Young, Richard ACell2013 Nov 7934-4724119843
A sequence variant in the phospholipase C epsilon C2 domain is associated with esophageal carcinoma and esophagitis.Wang, Li-Dong; Bi, Xiuli; Song, Xin; Pohl, Nicole M; Cheng, Yulan; Zhou, Yixing; Shears, Stephen; Ansong, Emmanuel; Xing, Mengtao; Wang, Shaomeng; Xu, Xiao-Chun; Huang, Peng; Xu, Liyan; Wang, Liang; Fan, Zongmin; Zhao, Xueke; Dong, Huali; Meltzer, StephenMolecular carcinogenesis2013 NovE80-623390063
H1 histones: current perspectives and challenges.Harshman, Sean W; Young, Nicolas L; Parthun, Mark R; Freitas, Michael ANucleic acids research2013 Nov9593-60923945933
CDKN2A/p16 inactivation mechanisms and their relationship to smoke exposure and molecular features in non-small-cell lung cancer.Tam, Kit W; Zhang, Wei; Soh, Junichi; Stastny, Victor; Chen, Min; Sun, Han; Thu, Kelsie; Rios, Jonathan J; Yang, Chenchen; Marconett, Crystal N; Selamat, Suhaida A; Laird-Offringa, Ite A; Taguchi, Ayumu; Hanash, Samir; Shames, David; Ma, Xiaotu; Zhang, MiJournal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer2013 Nov1378-8824077454
Aberrant methylation of the Ras-related associated with diabetes gene in human primary esophageal cancer.Jin, Zhe; Feng, Xianling; Jian, Qianhe; Cheng, Yulan; Gao, Yan; Zhang, Xiaojing; Wang, Liang; Zhang, Yuan; Huang, Weiling; Fan, Xinmin; Chen, Si; Yu, Huimin; Zhao, Zhenfu; Dong, Ming; Liu, Jie; Mori, Yuriko; Meltzer, Stephen JAnticancer research2013 Nov5199-20324222170
The human protein PRR14 tethers heterochromatin to the nuclear lamina during interphase and mitotic exit.Poleshko, Andrey; Mansfield, Katelyn M; Burlingame, Caroline C; Andrake, Mark D; Shah, Neil R; Katz, Richard ACell reports2013 Oct 31292-30124209742
Double minute chromosomes in glioblastoma multiforme are revealed by precise reconstruction of oncogenic amplicons.Sanborn, J Zachary; Salama, Sofie R; Grifford, Mia; Brennan, Cameron W; Mikkelsen, Tom; Jhanwar, Suresh; Katzman, Sol; Chin, Lynda; Haussler, DavidCancer research2013 Oct 16036-4523940299
Recombinant antibodies to histone post-translational modifications.Hattori, Takamitsu; Taft, Joseph M; Swist, Kalina M; Luo, Hao; Witt, Heather; Slattery, Matthew; Koide, Akiko; Ruthenburg, Alexander J; Krajewski, Krzysztof; Strahl, Brian D; White, Kevin P; Farnham, Peggy J; Zhao, Yingming; Koide, ShoheiNature methods2013 Oct992-523955773
Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues.Hon, Gary C; Rajagopal, Nisha; Shen, Yin; McCleary, David F; Yue, Feng; Dang, My D; Ren, BingNature genetics2013 Oct1198-20623995138
Micro- and nanoscale devices for the investigation of epigenetics and chromatin dynamics.Aguilar, Carlos A; Craighead, Harold GNature nanotechnology2013 Oct709-1824091454
Mapping human epigenomes.Rivera, Chloe M; Ren, BingCell2013 Sep 2639-5524074860
A universal DNA-based protein detection system.Tran, Thua N N; Cui, Jinhui; Hartman, Mark R; Peng, Songming; Funabashi, Hisakage; Duan, Faping; Yang, Dayong; March, John C; Lis, John T; Cui, Haixin; Luo, DanJournal of the American Chemical Society2013 Sep 2514008-1123978265
Visualizing epigenetics: Current advances and advantages in HDAC PET imaging techniques.Wang, C; Schroeder, F A; Hooker, J MNeuroscience2013 Sep 17NULL24051365
Epigenetic studies in Alzheimer's disease: Current findings, caveats, and considerations for future studies.Lunnon, Katie; Mill, JonathanAmerican journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics2013 Sep 13NULL24038819
Consistent decrease in global DNA methylation and hydroxymethylation in the hippocampus of Alzheimer's disease patients.Chouliaras, Leonidas; Mastroeni, Diego; Delvaux, Elaine; Grover, Andrew; Kenis, Gunter; Hof, Patrick R; Steinbusch, Harry W M; Coleman, Paul D; Rutten, Bart P F; van den Hove, Daniel L ANeurobiology of aging2013 Sep2091-923582657
Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm.Zhang, Bo; Zhou, Yan; Lin, Nan; Lowdon, Rebecca F; Hong, Chibo; Nagarajan, Raman P; Cheng, Jeffrey B; Li, Daofeng; Stevens, Michael; Lee, Hyung Joo; Xing, Xiaoyun; Zhou, Jia; Sundaram, Vasavi; Elliott, Ginell; Gu, Junchen; Shi, Taoping; Gascard, Philippe;Genome research2013 Sep1522-4023804400
Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods.Stevens, Michael; Cheng, Jeffrey B; Li, Daofeng; Xie, Mingchao; Hong, Chibo; Maire, Cecile L; Ligon, Keith L; Hirst, Martin; Marra, Marco A; Costello, Joseph F; Wang, TingGenome research2013 Sep1541-5323804401
Charting a dynamic DNA methylation landscape of the human genome.Ziller, Michael J; Gu, Hongcang; Muller, Fabian; Donaghey, Julie; Tsai, Linus T-Y; Kohlbacher, Oliver; De Jager, Philip L; Rosen, Evan D; Bennett, David A; Bernstein, Bradley E; Gnirke, Andreas; Meissner, AlexanderNature2013 Aug 22477-8123925113
Developmental fate and cellular maturity encoded in human regulatory DNA landscapes.Stergachis, Andrew B; Neph, Shane; Reynolds, Alex; Humbert, Richard; Miller, Brady; Paige, Sharon L; Vernot, Benjamin; Cheng, Jeffrey B; Thurman, Robert E; Sandstrom, Richard; Haugen, Eric; Heimfeld, Shelly; Murry, Charles E; Akey, Joshua M; StamatoyannopCell2013 Aug 15888-90323953118
A genome-wide siRNA screen identifies proteasome addiction as a vulnerability of basal-like triple-negative breast cancer cells.Petrocca, Fabio; Altschuler, Gabriel; Tan, Shen Mynn; Mendillo, Marc L; Yan, Haoheng; Jerry, D Joseph; Kung, Andrew L; Hide, Winston; Ince, Tan A; Lieberman, JudyCancer cell2013 Aug 12182-9623948298
Amplification of distant estrogen response elements deregulates target genes associated with tamoxifen resistance in breast cancer.Hsu, Pei-Yin; Hsu, Hang-Kai; Lan, Xun; Juan, Liran; Yan, Pearlly S; Labanowska, Jadwiga; Heerema, Nyla; Hsiao, Tzu-Hung; Chiu, Yu-Chiao; Chen, Yidong; Liu, Yunlong; Li, Lang; Li, Rong; Thompson, Ian M; Nephew, Kenneth P; Sharp, Zelton D; Kirma, Nameer B; Cancer cell2013 Aug 12197-21223948299
Holocarboxylase synthetase interacts physically with euchromatic histone-lysine N-methyltransferase, linking histone biotinylation with methylation events.Li, Yong; Hassan, Yousef I; Moriyama, Hideaki; Zempleni, JanosThe Journal of nutritional biochemistry2013 Aug1446-5223337344
Epigenetic deregulation of the anaplastic lymphoma kinase gene modulates mesenchymal characteristics of oral squamous cell carcinomas.Huang, Tze-Ta; Gonzales, Cara B; Gu, Fei; Hsu, Ya-Ting; Jadhav, Rohit R; Wang, Chiou-Miin; Redding, Spencer W; Tseng, Chih-En; Lee, Ching-Chih; Thompson, Ian M; Chen, Hau-Ren; Huang, Tim Hui-Ming; Kirma, Nameer BCarcinogenesis2013 Aug1717-2723568951
Discovery of histone modification crosstalk networks by stable isotope labeling of amino acids in cell culture mass spectrometry (SILAC MS).Guan, Xiaoyan; Rastogi, Neha; Parthun, Mark R; Freitas, Michael AMolecular & cellular proteomics : MCP2013 Aug2048-5923592332
Density-dependent cooperative non-specific binding in solid-phase SELEX affinity selection.Ozer, Abdullah; White, Brian S; Lis, John T; Shalloway, DavidNucleic acids research2013 Aug7167-7523737446
Sites of acetylation on newly synthesized histone H4 are required for chromatin assembly and DNA damage response signaling.Ge, Zhongqi; Nair, Devi; Guan, Xiaoyan; Rastogi, Neha; Freitas, Michael A; Parthun, Mark RMolecular and cellular biology2013 Aug3286-9823775118
From promises to practical strategies in epigenetic epidemiology.Mill, Jonathan; Heijmans, Bastiaan TNature reviews. Genetics2013 Aug585-9423817309
Comparative anatomy of chromosomal domains with imprinted and non-imprinted allele-specific DNA methylation.Paliwal, Anupam; Temkin, Alexis M; Kerkel, Kristi; Yale, Alexander; Yotova, Iveta; Drost, Natalia; Lax, Simon; Nhan-Chang, Chia-Ling; Powell, Charles; Borczuk, Alain; Aviv, Abraham; Wapner, Ronald; Chen, Xiaowei; Nagy, Peter L; Schork, Nicholas; Do, CathePLoS genetics2013 Auge100362224009515
Whole-body pharmacokinetics of HDAC inhibitor drugs, butyric acid, valproic acid and 4-phenylbutyric acid measured with carbon-11 labeled analogs by PET.Kim, Sung Won; Hooker, Jacob M; Otto, Nicola; Win, Khaing; Muench, Lisa; Shea, Colleen; Carter, Pauline; King, Payton; Reid, Alicia E; Volkow, Nora D; Fowler, Joanna SNuclear medicine and biology2013 Jul 29NULL23906667
Identification and assessment of markers of biotin status in healthy adults.Eng, Wei Kay; Giraud, David; Schlegel, Vicki L; Wang, Dong; Lee, Bo Hyun; Zempleni, JanosThe British journal of nutrition2013 Jul 28321-923302490
Endoglin promoter hypermethylation identifies a field defect in human primary esophageal cancer.Jin, Zhe; Zhao, Zhenfu; Cheng, Yulan; Dong, Ming; Zhang, Xiaojing; Wang, Liang; Fan, Xinmin; Feng, Xianling; Mori, Yuriko; Meltzer, Stephen JCancer2013 Jul 24NULL23893879
Developmental biology. Enhancing pluripotency and lineage specification.Xie, Wei; Ren, BingScience (New York, N.Y.)2013 Jul 19245-723869010
An epigenetic trap stabilizes singular olfactory receptor expression.Lyons, David B; Allen, William E; Goh, Tracie; Tsai, Lulu; Barnea, Gilad; Lomvardas, StavrosCell2013 Jul 18325-3623870122
Poised Chromatin at the ZEB1 Promoter Enables Breast Cancer Cell Plasticity and Enhances Tumorigenicity.Chaffer, Christine L; Marjanovic, Nemanja D; Lee, Tony; Bell, George; Kleer, Celina G; Reinhardt, Ferenc; D'Alessio, Ana C; Young, Richard A; Weinberg, Robert ACell2013 Jul 361-7423827675
Browsing (Epi)genomes: a guide to data resources and epigenome browsers for stem cell researchers.Karnik, Rahul; Meissner, AlexanderCell stem cell2013 Jul 314-2123827707
DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape.Xie, Mingchao; Hong, Chibo; Zhang, Bo; Lowdon, Rebecca F; Xing, Xiaoyun; Li, Daofeng; Zhou, Xin; Lee, Hyung Joo; Maire, Cecile L; Ligon, Keith L; Gascard, Philippe; Sigaroudinia, Mahvash; Tlsty, Thea D; Kadlecek, Theresa; Weiss, Arthur; O'Geen, Henriette;Nature genetics2013 Jul836-4123708189
Epigenomics: The Science of No-Longer-Junk DNA. Why Study it in Chronic Kidney Disease?Ko, Yi-An; Susztak, KatalinSeminars in nephrology2013 Jul354-6224011577
Global chromatin state analysis reveals lineage-specific enhancers during the initiation of human T helper 1 and T helper 2 cell polarization.Hawkins, R David; Larjo, Antti; Tripathi, Subhash K; Wagner, Ulrich; Luu, Ying; Lonnberg, Tapio; Raghav, Sunil K; Lee, Leonard K; Lund, Riikka; Ren, Bing; Lahdesmaki, Harri; Lahesmaa, RiittaImmunity2013 Jun 271271-8423791644
FDG-PET imaging reveals local brain glucose utilization is altered by class I histone deacetylase inhibitors.Schroeder, Frederick A; Chonde, Daniel B; Riley, Misha M; Moseley, Christian K; Granda, Michael L; Wilson, Colin M; Wagner, Florence F; Zhang, Yan-Ling; Gale, Jennifer; Holson, Edward B; Haggarty, Stephen J; Hooker, Jacob MNeuroscience letters2013 Jun 25NULL23810801
An improved synthesis of 1'-[18F]fluoroethyl-*-D-lactose ([18F]-FEL) for positron emission tomography imaging of pancreatic cancer.Turkman, Nashaat; Gelovani, Juri G; Alauddin, Mian MJournal of labelled compounds & radiopharmaceuticals2013 Jun 15351-524285438
Class I HDAC imaging using [ ( 3) H]CI-994 autoradiography.Wang, Yajie; Zhang, Yan-Ling; Hennig, Krista; Gale, Jennifer P; Hong, Yijia; Cha, Anna; Riley, Misha; Wagner, Florence; Haggarty, Stephen J; Holson, Edward; Hooker, JacobEpigenetics : official journal of the DNA Methylation Society2013 Jun 11NULL23803584
ARF inhibits the growth and malignant progression of non-small-cell lung carcinoma.Busch, S E; Moser, R D; Gurley, K E; Kelly-Spratt, K S; Liggitt, H D; Kemp, C JOncogene2013 Jun 10NULL23752194
Density-dependent cooperative non-specific binding in solid-phase SELEX affinity selection.Ozer, Abdullah; White, Brian S; Lis, John T; Shalloway, DavidNucleic acids research2013 Jun 3NULL23737446
Defined, serum-free conditions for in vitro culture of primary human T-ALL blasts.Yost, A J; Shevchuk, O O; Gooch, R; Gusscott, S; You, M J; Ince, T A; Aster, J C; Weng, A PLeukemia2013 Jun1437-4023246990
Synaptic genes are extensively downregulated across multiple brain regions in normal human aging and Alzheimer's disease.Berchtold, Nicole C; Coleman, Paul D; Cribbs, David H; Rogers, Joseph; Gillen, Daniel L; Cotman, Carl WNeurobiology of aging2013 Jun1653-6123273601
Differential processing of amyloid precursor protein in brain and in peripheral blood leukocytes.Delvaux, Elaine; Bentley, Karen; Stubbs, Victoria; Sabbagh, Marwan; Coleman, Paul DNeurobiology of aging2013 Jun1680-623298733
Genome organization and long-range regulation of gene expression by enhancers.Smallwood, Andrea; Ren, BingCurrent opinion in cell biology2013 Jun387-9423465541
Laser capture microdissection-reduced representation bisulfite sequencing (LCM-RRBS) maps changes in DNA methylation associated with gonadectomy-induced adrenocortical neoplasia in the mouse.Schillebeeckx, Maximiliaan; Schrade, Anja; Lobs, Ann-Kathrin; Pihlajoki, Marjut; Wilson, David B; Mitra, Robi DNucleic acids research2013 June11623589626
DNA methylation data analysis and its application to cancer research.Ma, Xiaotu; Wang, Yi-Wei; Zhang, Michael Q; Gazdar, Adi FEpigenomics2013 Jun301-1623750645
Pervasive transcription of the human genome produces thousands of previously unidentified long intergenic noncoding RNAs.Hangauer, Matthew J; Vaughn, Ian W; McManus, Michael TPLoS genetics2013 June100356923818866
An aberrant transcription factor network essential for Wnt signaling and stem cell maintenance in glioblastoma.Rheinbay, Esther; Suva, Mario L; Gillespie, Shawn M; Wakimoto, Hiroaki; Patel, Anoop P; Shahid, Mohammad; Oksuz, Ozgur; Rabkin, Samuel D; Martuza, Robert L; Rivera, Miguel N; Louis, David N; Kasif, Simon; Chi, Andrew S; Bernstein, Bradley ECell reports2013 May 301567-7923707066
Transcriptional and epigenetic dynamics during specification of human embryonic stem cells.Gifford, Casey A; Ziller, Michael J; Gu, Hongcang; Trapnell, Cole; Donaghey, Julie; Tsankov, Alexander; Shalek, Alex K; Kelley, David R; Shishkin, Alexander A; Issner, Robbyn; Zhang, Xiaolan; Coyne, Michael; Fostel, Jennifer L; Holmes, Laurie; Meldrim, JiCell2013 May 231149-6323664763
Epigenomic analysis of multilineage differentiation of human embryonic stem cells.Xie, Wei; Schultz, Matthew D; Lister, Ryan; Hou, Zhonggang; Rajagopal, Nisha; Ray, Pradipta; Whitaker, John W; Tian, Shulan; Hawkins, R David; Leung, Danny; Yang, Hongbo; Wang, Tao; Lee, Ah Young; Swanson, Scott A; Zhang, Jiuchun; Zhu, Yun; Kim, Audrey; NCell2013 May 231134-4823664764
CD33 Alzheimer's disease locus: altered monocyte function and amyloid biology.Bradshaw, Elizabeth M; Chibnik, Lori B; Keenan, Brendan T; Ottoboni, Linda; Raj, Towfique; Tang, Anna; Rosenkrantz, Laura L; Imboywa, Selina; Lee, Michelle; Von Korff, Alina; The Alzheimer Disease Neuroimaging Initiative; Morris, Martha C; Evans, Denis A;Nature neuroscience2013 May 23848-85023708142
Stochastic gene expression in mammals: lessons from olfaction.Magklara, Angeliki; Lomvardas, StavrosTrends in cell biology2013 May 1723689023
Role of Macrophage Receptor with Collagenous Structure in Innate Immune Tolerance.Jing, Jian; Yang, Ivana V; Hui, Lucy; Patel, Jay A; Evans, Christopher M; Prikeris, Rytis; Kobzik, Lester; O'Connor, Brian P; Schwartz, David AJournal of immunology (Baltimore, Md. : 1950)2013 May 1023667110
Single-molecule analysis of combinatorial epigenomic states in normal and tumor cells.Murphy, Patrick J; Cipriany, Benjamin R; Wallin, Christopher B; Ju, Chan Yang; Szeto, Kylan; Hagarman, James A; Benitez, Jaime J; Craighead, Harold G; Soloway, Paul DProceedings of the National Academy of Sciences of the United States of America2013 May 77772-723610441
Doxorubicin Enhances Nucleosome Turnover around Promoters.Yang, Fan; Kemp, Christopher J; Henikoff, StevenCurrent biology : CB2013 May 6782-723602475
Hypomethylation of noncoding DNA regions and overexpression of the long noncoding RNA, AFAP1-AS1, in Barrett's esophagus and esophageal adenocarcinoma.Wu, Wenjing; Bhagat, Tushar D; Yang, Xue; Song, Jee Hoon; Cheng, Yulan; Agarwal, Rachana; Abraham, John M; Ibrahim, Sariat; Bartenstein, Matthias; Hussain, Zulfiqar; Suzuki, Masako; Yu, Yiting; Chen, Wei; Eng, Charis; Greally, John; Verma, Amit; Meltzer, Gastroenterology2013 May956-966.e423333711
Exploring long-range genome interactions using the WashU Epigenome Browser.Zhou, Xin; Lowdon, Rebecca F; Li, Daofeng; Lawson, Heather A; Madden, Pamela A F; Costello, Joseph F; Wang, TingNature methods2013 May375-623629413
Master transcription factors and mediator establish super-enhancers at key cell identity genes.Whyte, Warren A; Orlando, David A; Hnisz, Denes; Abraham, Brian J; Lin, Charles Y; Kagey, Michael H; Rahl, Peter B; Lee, Tong Ihn; Young, Richard ACell2013 Apr 11307-1923582322
Selective inhibition of tumor oncogenes by disruption of super-enhancers.Loven, Jakob; Hoke, Heather A; Lin, Charles Y; Lau, Ashley; Orlando, David A; Vakoc, Christopher R; Bradner, James E; Lee, Tong Ihn; Young, Richard ACell2013 Apr 11320-3423582323
Variants in the ATP-binding cassette transporter (ABCA7), apolipoprotein E ýý4,and the risk of late-onset Alzheimer disease in African Americans.Reitz, Christiane; Jun, Gyungah; Naj, Adam; Rajbhandary, Ruchita; Vardarajan, Badri Narayan; Wang, Li-San; Valladares, Otto; Lin, Chiao-Feng; Larson, Eric B; Graff-Radford, Neill R; Evans, Denis; De Jager, Philip L; Crane, Paul K; Buxbaum, Joseph D; MurreJAMA : the journal of the American Medical Association2013 Apr 101483-9223571587
An Inflection Point in Gene Discovery Efforts for Neurodegenerative Diseases: From Syndromic Diagnoses Toward Endophenotypes and the Epigenome.De Jager, Philip L; Bennett, David AJAMA neurology2013 Apr 91-823571780
Genome organizing function of SATB1 in tumor progression.Kohwi-Shigematsu, Terumi; Poterlowicz, Krzysztof; Ordinario, Ellen; Han, Hye-Jung; Botchkarev, Vladimir A; Kohwi, YoshinoriSeminars in cancer biology2013 Apr72-922771615
Comparative annotation of functional regions in the human genome using epigenomic data.Won, Kyoung-Jae; Zhang, Xian; Wang, Tao; Ding, Bo; Raha, Debasish; Snyder, Michael; Ren, Bing; Wang, WeiNucleic acids research2013 Apr4423-3223482391
Sex difference in daily rhythms of clock gene expression in the aged human cerebral cortex.Lim, Andrew S P; Myers, Amanda J; Yu, Lei; Buchman, Aron S; Duffy, Jeanne F; De Jager, Philip L; Bennett, David AJournal of biological rhythms2013 Apr117-2923606611
Identification of small molecule inhibitors of Jumonji AT-rich interactive domain 1B (JARID1B) histone demethylase by a sensitive high throughput screen.Sayegh, Joyce; Cao, Jian; Zou, Mike Ran; Morales, Alfonso; Blair, Lauren P; Norcia, Michael; Hoyer, Denton; Tackett, Alan J; Merkel, Jane S; Yan, QinThe Journal of biological chemistry2013 Mar 299408-1723408432
Epigenetic reprogramming in cancer.Suva, Mario L; Riggi, Nicolo; Bernstein, Bradley EScience (New York, N.Y.)2013 Mar 291567-7023539597
Interplay between the cancer genome and epigenome.Shen, Hui; Laird, Peter WCell2013 Mar 2838-5523540689
Multiplexed microcolumn-based process for efficient selection of RNA aptamers.Latulippe, David R; Szeto, Kylan; Ozer, Abdullah; Duarte, Fabiana M; Kelly, Christopher V; Pagano, John M; White, Brian S; Shalloway, David; Lis, John T; Craighead, Harold GAnalytical chemistry2013 Mar 193417-2423398198
Rare somatic cells from human breast tissue exhibit extensive lineage plasticity.Roy, Somdutta; Gascard, Philippe; Dumont, Nancy; Zhao, Jianxin; Pan, Deng; Petrie, Sarah; Margeta, Marta; Tlsty, Thea DProceedings of the National Academy of Sciences of the United States of America2013 Mar 194598-60323487770
Myogenin recruits the histone chaperone facilitates chromatin transcription (FACT) to promote nucleosome disassembly at muscle-specific genes.Lolis, Alexandra A; Londhe, Priya; Beggs, Benjamin C; Byrum, Stephanie D; Tackett, Alan J; Davie, Judith KThe Journal of biological chemistry2013 Mar 157676-8723364797
Transcriptional regulation and its misregulation in disease.Lee, Tong Ihn; Young, Richard ACell2013 Mar 141237-5123498934
The UCSC genome browser and associated tools.Kuhn, Robert M; Haussler, David; Kent, W JamesBriefings in bioinformatics2013 Mar144-6122908213
Enrichment of meiotic recombination hotspot sequences by avidin capture technology.Camara Teixeira, Daniel; Malkaram, Sridhar A; Zempleni, JanosGene2013 Mar 1101-623270922
DNA methylation: roles in mammalian development.Smith, Zachary D; Meissner, AlexanderNature reviews. Genetics2013 Mar204-2023400093
Regulation of nucleosome dynamics by histone modifications.Zentner, Gabriel E; Henikoff, StevenNature structural & molecular biology2013 Mar259-6623463310
Alternative Approaches in Gene Discovery and Characterization in Alzheimer's Disease.Ertekin-Taner, Nilufer; De Jager, Phillip L; Yu, Lei; Bennett, David ACurrent genetic medicine reports2013 Mar39-5123482655
RFECS: a random-forest based algorithm for enhancer identification from chromatin state.Rajagopal, Nisha; Xie, Wei; Li, Yan; Wagner, Uli; Wang, Wei; Stamatoyannopoulos, John; Ernst, Jason; Kellis, Manolis; Ren, BingPLoS computational biology2013 Mare100296823526891
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Crebinostat: a novel cognitive enhancer that inhibits histone deacetylase activity and modulates chromatin-mediated neuroplasticity.Fass, Daniel M; Reis, Surya A; Ghosh, Balaram; Hennig, Krista M; Joseph, Nadine F; Zhao, Wen-Ning; Nieland, Thomas J F; Guan, Ji-Song; Kuhnle, Chelsea E Groves; Tang, Weiping; Barker, Douglas D; Mazitschek, Ralph; Schreiber, Stuart L; Tsai, Li-Huei; HaggaNeuropharmacology2013 Jan81-9622771460
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Genome-wide map of quantified epigenetic changes during in vitro chondrogenic differentiation of primary human mesenchymal stem cells.Herlofsen, Sarah R; Bryne, Jan Christian; Hoiby, Torill; Wang, Li; Issner, Robbyn; Zhang, Xiaolan; Coyne, Michael J; Boyle, Patrick; Gu, Hongcang; Meza-Zepeda, Leonardo A; Collas, Philippe; Mikkelsen, Tarjei S; Brinchmann, Jan EBMC genomics201310523414147
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A selective HDAC 1/2 inhibitor modulates chromatin and gene expression in brain and alters mouse behavior in two mood-related tests.Schroeder, Frederick A; Lewis, Michael C; Fass, Daniel M; Wagner, Florence F; Zhang, Yan-Ling; Hennig, Krista M; Gale, Jennifer; Zhao, Wen-Ning; Reis, Surya; Barker, Douglas D; Berry-Scott, Erin; Kim, Sung Won; Clore, Elizabeth L; Hooker, Jacob M; Holson,PloS one2013e7132323967191
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Cytosine methylation changes in enhancer regions of core pro-fibrotic genes characterize kidney fibrosis development.Ko, Yi-An; Mohtat, Davoud; Suzuki, Masako; Park, Ae Seo Deok; Izquierdo, Maria Concepcion; Han, Sang Youb; Kang, Hyun Mi; Si, Han; Hostetter, Thomas; Pullman, James M; Fazzari, Melissa; Verma, Amit; Zheng, Deyou; Greally, John M; Susztak, KatalinGenome biology2013R10824098934
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A maternal high-fat diet modulates fetal SIRT1 histone and protein deacetylase activity in nonhuman primates.Suter, Melissa A; Chen, Aishe; Burdine, Marie S; Choudhury, Mahua; Harris, R Alan; Lane, Robert H; Friedman, Jacob E; Grove, Kevin L; Tackett, Alan J; Aagaard, Kjersti MFASEB journal : official publication of the Federation of American Societies for Experimental Biology2012 Dec5106-1422982377
Epigenetic mechanisms and the development of asthma.Yang, Ivana V; Schwartz, David AThe Journal of allergy and clinical immunology2012 Dec1243-5523026498
sarA-mediated repression of protease production plays a key role in the pathogenesis of Staphylococcus aureus USA300 isolates.Zielinska, Agnieszka K; Beenken, Karen E; Mrak, Lara N; Spencer, Horace J; Post, Ginell R; Skinner, Robert A; Tackett, Alan J; Horswill, Alexander R; Smeltzer, Mark SMolecular microbiology2012 Dec1183-9623075270
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Surveying the epigenomic landscape, one base at a time.Zentner, Gabriel E; Henikoff, StevenGenome biology2012 Oct 2225023088423
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5-hmC in the brain is abundant in synaptic genes and shows differences at the exon-intron boundary.Khare, Tarang; Pai, Shraddha; Koncevicius, Karolis; Pal, Mrinal; Kriukiene, Edita; Liutkeviciute, Zita; Irimia, Manuel; Jia, Peixin; Ptak, Carolyn; Xia, Menghang; Tice, Raymond; Tochigi, Mamoru; Morera, Solange; Nazarians, Anaies; Belsham, Denise; Wong, Albert H C; Blencowe, Benjamin J; Wang, Sun Chong; Kapranov, Philipp; Kustra, Rafal; Labrie, Viviane; Klimasauskas, Saulius; Petronis, ArturasNature structural & molecular biology2012 Oct1037-4322961382
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A multi-tissue analysis identifies HLA complex group 9 gene methylation differences in bipolar disorder.Kaminsky, Z; Tochigi, M; Jia, P; Pal, M; Mill, J; Kwan, A; Ioshikhes, I; Vincent, J B; Kennedy, J L; Strauss, J; Pai, S; Wang, S-C; Petronis, AMolecular psychiatry2012 Jul728-4021647149
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Repair problems in podocytes: Wnt, Notch, and glomerulosclerosis.Kato, Hideki; Susztak, KatalinSeminars in nephrology2012 Jul350-622958489
The clonal and mutational evolution spectrum of primary triple-negative breast cancers.Shah, Sohrab P; Roth, Andrew; Goya, Rodrigo; Oloumi, Arusha; Ha, Gavin; Zhao, Yongjun; Turashvili, Gulisa; Ding, Jiarui; Tse, Kane; Haffari, Gholamreza; Bashashati, Ali; Prentice, Leah M; Khattra, Jaswinder; Burleigh, Angela; Yap, Damian; Bernard, VirginiNature2012 Jun 21395-922495314
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Cytosine methylation in miR-153 gene promoters increases the expression of holocarboxylase synthetase, thereby increasing the abundance of histone H4 biotinylation marks in HEK-293 human kidney cells.Bao, Baolong; Rodriguez-Melendez, Rocio; Zempleni, JanosThe Journal of nutritional biochemistry2012 Jun635-921764280
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Aberrant methylation of the PTPRO gene in peripheral blood as a potential biomarker in esophageal squamous cell carcinoma patients.You, Yan-Jie; Chen, Yu-Ping; Zheng, Xiao-Xuan; Meltzer, Stephen J; Zhang, HaoCancer letters2012 Feb 28138-4422099875
Histone H3R2 symmetric dimethylation and histone H3K4 trimethylation are tightly correlated in eukaryotic genomes.Yuan, Chih-Chi; Matthews, Adam G W; Jin, Yi; Chen, Chang Feng; Chapman, Brad A; Ohsumi, Toshiro K; Glass, Karen C; Kutateladze, Tatiana G; Borowsky, Mark L; Struhl, Kevin; Oettinger, Marjorie ACell reports2012 Feb 2383-9022720264
Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation in the mouse genome.Xie, Wei; Barr, Cathy L; Kim, Audrey; Yue, Feng; Lee, Ah Young; Eubanks, James; Dempster, Emma L; Ren, BingCell2012 Feb 17816-3122341451
RRBSMAP: a fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing.Xi, Yuanxin; Bock, Christoph; Muller, Fabian; Sun, Deqiang; Meissner, Alexander; Li, WeiBioinformatics (Oxford, England)2012 Feb 1430-222155871
Epigenomic program of Barrett's-associated neoplastic progression reveals possible involvement of insulin signaling pathways.Agarwal, Rachana; Jin, Zhe; Yang, Jian; Mori, Yuriko; Song, Jee Hoon; Kumar, Sahil; Sato, Masato; Cheng, Yulan; Olaru, Alexandru V; Abraham, John M; Verma, Amit; Meltzer, Stephen JEndocrine-related cancer2012 FebL5-922194443
Commentary: The seven plagues of epigenetic epidemiology.Heijmans, Bastiaan T; Mill, JonathanInternational journal of epidemiology2012 Feb74-822269254
Epigenetic and genetic variation at the IGF2/H19 imprinting control region on 11p15.5 is associated with cerebellum weight.Pidsley, Ruth; Dempster, Emma; Troakes, Claire; Al-Sarraj, Safa; Mill, JonathanEpigenetics : official journal of the DNA Methylation Society2012 Feb155-6322395465
DNA methylation shows genome-wide association of NFIX, RAPGEF2 and MSRB3 with gestational age at birth.Lee, Hwajin; Jaffe, Andrew E; Feinberg, Jason I; Tryggvadottir, Rakel; Brown, Shannon; Montano, Carolina; Aryee, Martin J; Irizarry, Rafael A; Herbstman, Julie; Witter, Frank R; Goldman, Lynn R; Feinberg, Andrew P; Fallin, M DanieleInternational journal of epidemiology2012 Feb188-9922422452
Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies.Jaffe, Andrew E; Murakami, Peter; Lee, Hwajin; Leek, Jeffrey T; Fallin, M Daniele; Feinberg, Andrew P; Irizarry, Rafael AInternational journal of epidemiology2012 Feb200-922422453
Perinephric and epididymal fat affect hepatic metabolism in rats.Ben-Shlomo, Shani; Einstein, Francine H; Zvibel, Isabel; Atias, Dikla; Shlomai, Amir; Halpern, Zamir; Barzilai, Nir; Fishman, SigalObesity (Silver Spring, Md.)2012 Jan151-621818154
The UCSC Genome Browser database: extensions and updates 2011.Dreszer, Timothy R; Karolchik, Donna; Zweig, Ann S; Hinrichs, Angie S; Raney, Brian J; Kuhn, Robert M; Meyer, Laurence R; Wong, Mathew; Sloan, Cricket A; Rosenbloom, Kate R; Roe, Greg; Rhead, Brooke; Pohl, Andy; Malladi, Venkat S; Li, Chin H; Learned, KatNucleic acids research2012 JanD918-2322086951
Analysis of stable and transient protein-protein interactions.Byrum, Stephanie; Smart, Sherri K; Larson, Signe; Tackett, Alan JMethods in molecular biology (Clifton, N.J.)2012143-5222183593
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An integrative variant analysis suite for whole exome next-generation sequencing data.Challis, Danny; Yu, Jin; Evani, Uday S; Jackson, Andrew R; Paithankar, Sameer; Coarfa, Cristian; Milosavljevic, Aleksandar; Gibbs, Richard A; Yu, FuliBMC bioinformatics2012822239737
Visualizing cell architecture and molecular location using soft x-ray tomography and correlated cryo-light microscopy.McDermott, Gerry; Le Gros, Mark A; Larabell, Carolyn AAnnual review of physical chemistry2012225-3922242730
Application of MassSQUIRM for quantitative measurements of lysine demethylase activity.Blair, Lauren P; Avaritt, Nathan L; Tackett, Alan JJournal of visualized experiments : JoVE201222433969
The transcription factor encyclopedia.Yusuf, Dimas; Butland, Stefanie L; Swanson, Magdalena I; Bolotin, Eugene; Ticoll, Amy; Cheung, Warren A; Zhang, Xiao Yu Cindy; Dickman, Christopher T D; Fulton, Debra L; Lim, Jonathan S; Schnabl, Jake M; Ramos, Oscar H P; Vasseur-Cognet, Mireille; de LeeuGenome biology2012R2422458515
Efficient iPS cell production with the MyoD transactivation domain in serum-free culture.Hirai, Hiroyuki; Katoku-Kikyo, Nobuko; Karian, Peter; Firpo, Meri; Kikyo, NobuakiPloS one2012e3414922479546
Impact of the location of CpG methylation within the GSTP1 gene on its specificity as a DNA marker for hepatocellular carcinoma.Jain, Surbhi; Chen, Sitong; Chang, Kung-Chao; Lin, Yih-Jyh; Hu, Chi-Tan; Boldbaatar, Batbold; Hamilton, James P; Lin, Selena Y; Chang, Ting-Tsung; Chen, Shun-Hua; Song, Wei; Meltzer, Stephen J; Block, Timothy M; Su, Ying-HsiuPloS one2012e3578922536438
Genomic hypomethylation in the human germline associates with selective structural mutability in the human genome.Li, Jian; Harris, R Alan; Cheung, Sau Wai; Coarfa, Cristian; Jeong, Mira; Goodell, Margaret A; White, Lisa D; Patel, Ankita; Kang, Sung-Hae; Shaw, Chad; Chinault, A Craig; Gambin, Tomasz; Gambin, Anna; Lupski, James R; Milosavljevic, AleksandarPLoS genetics2012e100269222615578
Use of laser capture microdissection for analysis of retinal mRNA/miRNA expression and DNA methylation.Hackler Jr, Laszlo; Masuda, Tomohiro; Oliver, Verity F; Merbs, Shannath L; Zack, Donald JMethods in molecular biology (Clifton, N.J.)2012289-30422688715
IS-seq: a novel high throughput survey of in vivo IS6110 transposition in multiple Mycobacterium tuberculosis genomes.Reyes, Alejandro; Sandoval, Andrea; Cubillos-Ruiz, Andres; Varley, Katherine E; Hernandez-Neuta, Ivan; Samper, Sofia; Martin, Carlos; Garcia, Maria Jesus; Ritacco, Viviana; Lopez, Lucelly; Robledo, Jaime; Zambrano, Maria Mercedes; Mitra, Robi D; Del PortiBMC genomics201224922703188
Functional annotation of the human brain methylome identifies tissue-specific epigenetic variation across brain and blood.Davies, Matthew N; Volta, Manuela; Pidsley, Ruth; Lunnon, Katie; Dixit, Abhishek; Lovestone, Simon; Coarfa, Cristian; Harris, R Alan; Milosavljevic, Aleksandar; Troakes, Claire; Al-Sarraj, Safa; Dobson, Richard; Schalkwyk, Leonard C; Mill, JonathanGenome biology2012R4322703893
Establishment of LIF-dependent human iPS cells closely related to basic FGF-dependent authentic iPS cells.Hirai, Hiroyuki; Firpo, Meri; Kikyo, NobuakiPloS one2012e3902222720020
Detection of rare genomic variants from pooled sequencing using SPLINTER.Vallania, Francesco; Ramos, Enrique; Cresci, Sharon; Mitra, Robi D; Druley, Todd EJournal of visualized experiments : JoVE201222760212
A random change point model for cognitive decline in Alzheimer's disease and mild cognitive impairment.Yu, Lei; Boyle, Patricia; Wilson, Robert S; Segawa, Eisuke; Leurgans, Sue; De Jager, Philip L; Bennett, David ANeuroepidemiology201273-8322814083
BCLAF1 is a radiation-induced H2AX-interacting partner involved in ýýH2AX-mediated regulation of apoptosis and DNA repair.Lee, Y Y; Yu, Y B; Gunawardena, H P; Xie, L; Chen, XCell death & disease2012e35922833098
High-fat or ethinyl-oestradiol intake during pregnancy increases mammary cancer risk in several generations of offspring.de Assis, Sonia; Warri, Anni; Cruz, M Idalia; Laja, Olusola; Tian, Ye; Zhang, Bai; Wang, Yue; Huang, Tim Hui-Ming; Hilakivi-Clarke, LeenaNature communications2012105322968699
Online tools for bioinformatics analyses in nutrition sciences.Malkaram, Sridhar A; Hassan, Yousef I; Zempleni, JanosAdvances in nutrition (Bethesda, Md.)2012654-6522983844
Atlas2 Cloud: a framework for personal genome analysis in the cloud.Evani, Uday S; Challis, Danny; Yu, Jin; Jackson, Andrew R; Paithankar, Sameer; Bainbridge, Matthew N; Jakkamsetti, Adinarayana; Pham, Peter; Coarfa, Cristian; Milosavljevic, Aleksandar; Yu, FuliBMC genomics2012S1923134663
A modulator based regulatory network for ERýý signaling pathway.Wu, Heng-Yi; Zheng, Pengyue; Jiang, Guanglong; Liu, Yunlong; Nephew, Kenneth P; Huang, Tim H M; Li, LangBMC genomics2012S623134758
Genetic analysis of DNA methylation and gene expression levels in whole blood of healthy human subjects.van Eijk, Kristel R; de Jong, Simone; Boks, Marco P M; Langeveld, Terry; Colas, Fabrice; Veldink, Jan H; de Kovel, Carolien G F; Janson, Esther; Strengman, Eric; Langfelder, Peter; Kahn, Rene S; van den Berg, Leonard H; Horvath, Steve; Ophoff, Roel ABMC genomics201263623157493
Hierarchical modularity in ERýý transcriptional network is associated with distinct functions and implicates clinical outcomes.Tang, Binhua; Hsu, Hang-Kai; Hsu, Pei-Yin; Bonneville, Russell; Chen, Su-Shing; Huang, Tim H-M; Jin, Victor XScientific reports201287523166858
A novel Bayesian change-point algorithm for genome-wide analysis of diverse ChIPseq data types.Xing, Haipeng; Liao, Willey; Mo, Yifan; Zhang, Michael QJournal of visualized experiments : JoVE2012e427323271069
Disease-associated epigenetic changes in monozygotic twins discordant for schizophrenia and bipolar disorder.Dempster, Emma L; Pidsley, Ruth; Schalkwyk, Leonard C; Owens, Sheena; Georgiades, Anna; Kane, Fergus; Kalidindi, Sridevi; Picchioni, Marco; Kravariti, Eugenia; Toulopoulou, Timothea; Murray, Robin M; Mill, JonathanHuman molecular genetics2011 Dec 154786-9621908516
5-Hydroxymethylcytosine is strongly depleted in human cancers but its levels do not correlate with IDH1 mutations.Jin, Seung-Gi; Jiang, Yong; Qiu, Runxiang; Rauch, Tibor A; Wang, Yinsheng; Schackert, Gabriele; Krex, Dietmar; Lu, Qiang; Pfeifer, Gerd PCancer research2011 Dec 157360-522052461
The first identification of lysine malonylation substrates and its regulatory enzyme.Peng C, Lu Z, Xie Z, Cheng Z, Chen Y, Tan M, Luo H, Zhang Y, He W, Yang K, Zwaans BM, Tishkoff D, Ho L, Lombard D, He TC, Dai J, Verdin E, Ye Y, Zhao Y.Mol Cell Proteomics2011 DecM111.01265821908771
Biotinylation is a natural, albeit rare, modification of human histones.Kuroishi, Toshinobu; Rios-Avila, Luisa; Pestinger, Valerie; Wijeratne, Subhashinee S K; Zempleni, JanosMolecular genetics and metabolism2011 Dec537-4521930408
Sensitive single-molecule protein quantification and protein complex detection in a microarray format.Tessler, Lee A; Mitra, Robi DProteomics2011 Dec4731-522038904
The Human Epigenome Browser at Washington University.Zhou, Xin; Maricque, Brett; Xie, Mingchao; Li, Daofeng; Sundaram, Vasavi; Martin, Eric A; Koebbe, Brian C; Nielsen, Cydney; Hirst, Martin; Farnham, Peggy; Kuhn, Robert M; Zhu, Jingchun; Smirnov, Ivan; Kent, W James; Haussler, David; Madden, Pamela A F; CoNature methods2011 Dec989-9022127213
Genomic distribution and inter-sample variation of non-CpG methylation across human cell types.Ziller, Michael J; Muller, Fabian; Liao, Jing; Zhang, Yingying; Gu, Hongcang; Bock, Christoph; Boyle, Patrick; Epstein, Charles B; Bernstein, Bradley E; Lengauer, Thomas; Gnirke, Andreas; Meissner, AlexanderPLoS genetics2011 Dece100238922174693
NSD2 links dimethylation of histone H3 at lysine 36 to oncogenic programming.Kuo, Alex J; Cheung, Peggie; Chen, Kaifu; Zee, Barry M; Kioi, Mitomu; Lauring, Josh; Xi, Yuanxin; Park, Ben Ho; Shi, Xiaobing; Garcia, Benjamin A; Li, Wei; Gozani, OrMolecular cell2011 Nov 18609-2022099308
Heat shock reduces stalled RNA polymerase II and nucleosome turnover genome-wide.Teves, Sheila S; Henikoff, StevenGenes & development2011 Nov 152387-9722085965
High levels of nuclear heat-shock factor 1 (HSF1) are associated with poor prognosis in breast cancer.Santagata, Sandro; Hu, Rong; Lin, Nancy U; Mendillo, Marc L; Collins, Laura C; Hankinson, Susan E; Schnitt, Stuart J; Whitesell, Luke; Tamimi, Rulla M; Lindquist, Susan; Ince, Tan AProceedings of the National Academy of Sciences of the United States of America2011 Nov 818378-8322042860
Development of an internet based system for modeling biotin metabolism using Bayesian networks.Zhou, Jinglei; Wang, Dong; Schlegel, Vicki; Zempleni, JanosComputer methods and programs in biomedicine2011 Nov254-921356565
Genome-wide analysis of interferon regulatory factor I binding in primary human monocytes.Shi, Lihua; Perin, Juan C; Leipzig, Jeremy; Zhang, Zhe; Sullivan, Kathleen EGene2011 Nov 121-821803131
A quantitative proteomic analysis of FFPE melanoma.Byrum, Stephanie; Avaritt, Nathan L; Mackintosh, Samuel G; Munkberg, Josie M; Badgwell, Brian D; Cheung, Wang L; Tackett, Alan JJournal of cutaneous pathology2011 Nov933-621883366
Single DNA molecule patterning for high-throughput epigenetic mapping.Cerf, Aline; Cipriany, Benjamin R; Benitez, Jaime J; Craighead, Harold GAnalytical chemistry2011 Nov 18073-721981444
Pioneer transcription factors: establishing competence for gene expression.Zaret, Kenneth S; Carroll, Jason SGenes & development2011 Nov 12227-4122056668
Nanogel surface coatings for improved single-molecule imaging substrates.Tessler, Lee A; Donahoe, Casey D; Garcia, Daniel J; Jun, Young-Shin; Elbert, Donald L; Mitra, Robi DJournal of the Royal Society, Interface / the Royal Society2011 Oct 71400-821325313
Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing.Lee, Eun-Joon; Pei, Lirong; Srivastava, Gyan; Joshi, Trupti; Kushwaha, Garima; Choi, Jeong-Hyeon; Robertson, Keith D; Wang, Xinguo; Colbourne, John K; Zhang, Lu; Schroth, Gary P; Xu, Dong; Zhang, Kun; Shi, HuidongNucleic acids research2011 Octe12721785137
Cohesin: a critical chromatin organizer in mammalian gene regulation.Chien, Richard; Zeng, Weihua; Ball, Alexander R; Yokomori, KyokoBiochemistry and cell biology = Biochimie et biologie cellulaire2011 Oct445-5821851156
Dynamic chromatin states in human ES cells reveal potential regulatory sequences and genes involved in pluripotency.Hawkins, R David; Hon, Gary C; Yang, Chuhu; Antosiewicz-Bourget, Jessica E; Lee, Leonard K; Ngo, Que-Minh; Klugman, Sarit; Ching, Keith A; Edsall, Lee E; Ye, Zhen; Kuan, Samantha; Yu, Pengzhi; Liu, Hui; Zhang, Xinmin; Green, Roland D; Lobanenkov, Victor VCell research2011 Oct1393-40921876557
Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification.Tan, Minjia; Luo, Hao; Lee, Sangkyu; Jin, Fulai; Yang, Jeong Soo; Montellier, Emilie; Buchou, Thierry; Cheng, Zhongyi; Rousseaux, Sophie; Rajagopal, Nisha; Lu, Zhike; Ye, Zhen; Zhu, Qin; Wysocka, Joanna; Ye, Yang; Khochbin, Saadi; Ren, Bing; Zhao, YingminCell2011 Sep 161016-2821925322
Genome-wide analysis reveals conserved and divergent features of Notch1/RBPJ binding in human and murine T-lymphoblastic leukemia cells.Wang, Hongfang; Zou, James; Zhao, Bo; Johannsen, Eric; Ashworth, Todd; Wong, Hoifung; Pear, Warren S; Schug, Jonathan; Blacklow, Stephen C; Arnett, Kelly L; Bernstein, Bradley E; Kieff, Elliott; Aster, Jon CProceedings of the National Academy of Sciences of the United States of America2011 Sep 614908-1321737748
Epstein-Barr virus exploits intrinsic B-lymphocyte transcription programs to achieve immortal cell growth.Zhao, Bo; Zou, James; Wang, Hongfang; Johannsen, Eric; Peng, Chih-wen; Quackenbush, John; Mar, Jessica C; Morton, Cynthia Casson; Freedman, Matthew L; Blacklow, Stephen C; Aster, Jon C; Bernstein, Bradley E; Kieff, ElliottProceedings of the National Academy of Sciences of the United States of America2011 Sep 614902-721746931
Monocyte polarization: the relationship of genome-wide changes in H4 acetylation with polarization.Zhang, Z; Song, L; Maurer, K; Bagashev, A; Sullivan, K EGenes and immunity2011 Sep445-5621451557
Radical acceleration of nuclear reprogramming by chromatin remodeling with the transactivation domain of MyoD.Hirai, Hiroyuki; Tani, Tetsuya; Katoku-Kikyo, Nobuko; Kellner, Steven; Karian, Peter; Firpo, Meri; Kikyo, NobuakiStem cells (Dayton, Ohio)2011 Sep1349-6121732495
Transcriptome analysis of human diabetic kidney disease.Woroniecka, Karolina I; Park, Ae Seo Deok; Mohtat, Davoud; Thomas, David B; Pullman, James M; Susztak, KatalinDiabetes2011 Sep2354-6921752957
Human holocarboxylase synthetase with a start site at methionine-58 is the predominant nuclear variant of this protein and has catalytic activity.Bao, Baolong; Wijeratne, Subhashinee S K; Rodriguez-Melendez, Rocio; Zempleni, JanosBiochemical and biophysical research communications2011 Aug 19115-2021802411
Regulation of embryonic stem cell self-renewal and pluripotency by leukaemia inhibitory factor.Hirai, Hiroyuki; Karian, Peter; Kikyo, NobuakiThe Biochemical journal2011 Aug 1511-2321793804
Long noncoding RNA, polycomb, and the ghosts haunting INK4b-ARF-INK4a expression.Aguilo F, Zhou MM, Walsh MJ.Cancer Res2011 Aug 155365-921828241
Structural basis of SETD6-mediated regulation of the NF-kB network via methyl-lysine signaling.Chang, Yanqi; Levy, Dan; Horton, John R; Peng, Junmin; Zhang, Xing; Gozani, Or; Cheng, XiaodongNucleic acids research2011 Aug6380-921515635
Increased methylation variation in epigenetic domains across cancer types.Hansen, Kasper Daniel; Timp, Winston; Bravo, Hector Corrada; Sabunciyan, Sarven; Langmead, Benjamin; McDonald, Oliver G; Wen, Bo; Wu, Hao; Liu, Yun; Diep, Dinh; Briem, Eirikur; Zhang, Kun; Irizarry, Rafael A; Feinberg, Andrew PNature genetics2011 Aug768-7521706001
A chemical probe selectively inhibits G9a and GLP methyltransferase activity in cells.Vedadi, Masoud; Barsyte-Lovejoy, Dalia; Liu, Feng; Rival-Gervier, Sylvie; Allali-Hassani, Abdellah; Labrie, Viviane; Wigle, Tim J; Dimaggio, Peter A; Wasney, Gregory A; Siarheyeva, Alena; Dong, Aiping; Tempel, Wolfram; Wang, Sun-Chong; Chen, Xin; Chau, IrNature chemical biology2011 Aug566-7421743462
Selection of proteins with desired properties from natural proteome libraries using mRNA display.Cotten, Steven W; Zou, Jianwei; Valencia, C Alexander; Liu, RiheNature protocols2011 Aug1163-8221799486
Germline mutations in MSR1, ASCC1, and CTHRC1 in patients with Barrett esophagus and esophageal adenocarcinoma.Orloff, Mohammed; Peterson, Charissa; He, Xin; Ganapathi, Shireen; Heald, Brandie; Yang, Yi-ran; Bebek, Gurkan; Romigh, Todd; Song, Jee Hoon; Wu, Wenjing; David, Stefan; Cheng, Yulan; Meltzer, Stephen J; Eng, CharisJAMA : the journal of the American Medical Association2011 Jul 27410-921791690
The DNA methylome.Pelizzola, Mattia; Ecker, Joseph RFEBS letters2011 Jul 71994-200021056564
Genomic mapping of 5-hydroxymethylcytosine in the human brain.Jin, Seung-Gi; Wu, Xiwei; Li, Arthur X; Pfeifer, Gerd PNucleic acids research2011 Jul5015-2421378125
Epigenetic mechanisms in Alzheimer's disease.Mastroeni, Diego; Grover, Andrew; Delvaux, Elaine; Whiteside, Charisse; Coleman, Paul D; Rogers, JosephNeurobiology of aging2011 Jul1161-8021482442
Toward an integrated genetic and epigenetic approach to Alzheimer's disease.Mill, JonathanNeurobiology of aging2011 Jul1188-9121497948
The epigenetics of Alzheimer's disease--additional considerations.Rogers, Joseph; Mastroeni, Diego; Grover, Andrew; Delvaux, Elaine; Whiteside, Charisse; Coleman, Paul DNeurobiology of aging2011 Jul1196-721497949
Probing the role of HDACs and mechanisms of chromatin-mediated neuroplasticity.Haggarty, Stephen J; Tsai, Li-HueiNeurobiology of learning and memory2011 Jul41-5221545841
The role of holocarboxylase synthetase in genome stability is mediated partly by epigenomic synergies between methylation and biotinylation events.Zempleni, Janos; Li, Yong; Xue, Jing; Cordonier, Elizabeth LEpigenetics : official journal of the DNA Methylation Society2011 Jul892-421555910
Opposing roles of FoxP1 and Nfat3 in transcriptional control of cardiomyocyte hypertrophy.Bai, Shoumei; Kerppola, Tom KMolecular and cellular biology2011 Jul3068-8021606195
Targeted gene correction of laminopathy-associated LMNA mutations in patient-specific iPSCs.Liu, Guang-Hui; Suzuki, Keiichiro; Qu, Jing; Sancho-Martinez, Ignacio; Yi, Fei; Li, Mo; Kumar, Sachin; Nivet, Emmanuel; Kim, Jessica; Soligalla, Rupa Devi; Dubova, Ilir; Goebl, April; Plongthongkum, Nongluk; Fung, Ho-Lim; Zhang, Kun; Loring, Jeanne F; LauCell stem cell2011 Jun 3688-9421596650
Identification of holocarboxylase synthetase chromatin binding sites in human mammary cell lines using the DNA adenine methyltransferase identification technology.Singh, Dipika; Pannier, Angela K; Zempleni, JanosAnalytical biochemistry2011 Jun 155-921303649
Estrogen-mediated epigenetic repression of the imprinted gene cyclin-dependent kinase inhibitor 1C in breast cancer cells.Rodriguez, Benjamin A T; Weng, Yu-I; Liu, Ta-Ming; Zuo, Tao; Hsu, Pei-Yin; Lin, Ching-Hung; Cheng, Ann-Lii; Cui, Hengmi; Yan, Pearlly S; Huang, Tim H-MCarcinogenesis2011 Jun812-2121304052
The ATRX-ADD domain binds to H3 tail peptides and reads the combined methylation state of K4 and K9.Dhayalan A, Tamas R, Bock I, Tattermusch A, Dimitrova E, Kudithipudi S, Ragozin S, Jeltsch A.Hum Mol Genet2011 Jun 12195-20321421568
Emerging patterns of epigenomic variation.Milosavljevic, AleksandarTrends in genetics : TIG2011 Jun242-5021507501
Advantages of mRNA display selections over other selection techniques for investigation of protein-protein interactions.Wang, Hui; Liu, RiheExpert review of proteomics2011 Jun335-4621679115
Cohesin mediates chromatin interactions that regulate mammalian ýý-globin expression.Chien, Richard; Zeng, Weihua; Kawauchi, Shimako; Bender, M A; Santos, Rosaysela; Gregson, Heather C; Schmiesing, John A; Newkirk, Daniel A; Kong, Xiangduo; Ball Jr, Alexander R; Calof, Anne L; Lander, Arthur D; Groudine, Mark T; Yokomori, KyokoThe Journal of biological chemistry2011 May 2017870-821454523
Genome-wide regulation of 5hmC, 5mC, and gene expression by Tet1 hydroxylase in mouse embryonic stem cells.Xu, Yufei; Wu, Feizhen; Tan, Li; Kong, Lingchun; Xiong, Lijun; Deng, Jie; Barbera, Andrew J; Zheng, Lijuan; Zhang, Haikuo; Huang, Stephen; Min, Jinrong; Nicholson, Thomas; Chen, Taiping; Xu, Guoliang; Shi, Yang; Zhang, Kun; Shi, Yujiang GenoMolecular cell2011 May 20451-6421514197
Epigenetic control of gene expression in the lung.Yang, Ivana V; Schwartz, David AAmerican journal of respiratory and critical care medicine2011 May 151295-30121596832
An epigenetic signature for monoallelic olfactory receptor expression.Magklara, Angeliki; Yen, Angela; Colquitt, Bradley M; Clowney, E Josephine; Allen, William; Markenscoff-Papadimitriou, Eirene; Evans, Zoe A; Kheradpour, Pouya; Mountoufaris, George; Carey, Catriona; Barnea, Gilad; Kellis, Manolis; Lomvardas, StavrosCell2011 May 13555-7021529909
Holocarboxylase synthetase is a chromatin protein and interacts directly with histone H3 to mediate biotinylation of K9 and K18.Bao, Baolong; Pestinger, Valerie; Hassan, Yousef I; Borgstahl, Gloria E O; Kolar, Carol; Zempleni, JanosThe Journal of nutritional biochemistry2011 May470-520688500
Fetal environment, epigenetics, and pediatric renal disease.Woroniecki, Robert; Gaikwad, Anil Bhanudas; Susztak, KatalinPediatric nephrology (Berlin, Germany)2011 May705-1121174217
Nucleosome fragility reveals novel functional states of chromatin and poises genes for activation.Xi, Yuanxin; Yao, Jianhui; Chen, Rui; Li, Wei; He, XiangweiGenome research2011 May718-2421363969
REST interacts with Cbx proteins and regulates polycomb repressive complex 1 occupancy at RE1 elements.Ren, Xiaojun; Kerppola, Tom KMolecular and cellular biology2011 May2100-1021402785
Calling Cards enable multiplexed identification of the genomic targets of DNA-binding proteins.Wang, Haoyi; Mayhew, David; Chen, Xuhua; Johnston, Mark; Mitra, Robi DavidGenome research2011 May748-5521471402
Chemically defined conditions for human iPSC derivation and culture.Chen, Guokai; Gulbranson, Daniel R; Hou, Zhonggang; Bolin, Jennifer M; Ruotti, Victor; Probasco, Mitchell D; Smuga-Otto, Kimberly; Howden, Sara E; Diol, Nicole R; Propson, Nicholas E; Wagner, Ryan; Lee, Garrett O; Antosiewicz-Bourget, Jessica; Teng, JoyceNature methods2011 May424-921478862
Recapitulation of premature ageing with iPSCs from Hutchinson-Gilford progeria syndrome.Liu, Guang-Hui; Barkho, Basam Z; Ruiz, Sergio; Diep, Dinh; Qu, Jing; Yang, Sheng-Lian; Panopoulos, Athanasia D; Suzuki, Keiichiro; Kurian, Leo; Walsh, Christopher; Thompson, James; Boue, Stephanie; Fung, Ho Lim; Sancho-Martinez, Ignacio; Zhang, Kun; YatesNature2011 Apr 14221-521346760
Small-molecule ligands of methyl-lysine binding proteins.Herold JM, Wigle TJ, Norris JL, Lam R, Korboukh VK, Gao C, Ingerman LA, Kireev DB, Senisterra G, Vedadi M, Tripathy A, Brown PJ, Arrowsmith CH, Jin J, Janzen WP, Frye SV.J Med Chem2011 Apr 142504-1121417280
Biophysical probes reveal a compromise" nature of the methyl-lysine binding pocket in L3MBTL1."Gao C, Herold JM, Kireev D, Wigle T, Norris JL, Frye S.J Am Chem Soc2011 Apr 135357-6221428286
Drosophila histone H2A variant (H2Av) controls poly(ADP-ribose) polymerase 1 (PARP1) activation in chromatin.Kotova, Elena; Lodhi, Niraj; Jarnik, Michael; Pinnola, Aaron D; Ji, Yingbiao; Tulin, Alexei VProceedings of the National Academy of Sciences of the United States of America2011 Apr 126205-1021444826
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Novel histone biotinylation marks are enriched in repeat regions and participate in repression of transcriptionally competent genes.Pestinger, Valerie; Wijeratne, Subhashinee S K; Rodriguez-Melendez, Rocio; Zempleni, JanosThe Journal of nutritional biochemistry2011 Apr328-3320691578
Visualization by BiFC of different C/EBPýý dimers and their interaction with HP1ýý reveals a differential subnuclear distribution of complexes in living cells.Susperreguy, Sebastian; Prendes, Luciana P; Desbats, Maria A; Charo, Nancy L; Brown, Karen; MacDougald, Ormond A; Kerppola, Tom; Schwartz, Jessica; Piwien-Pilipuk, GracielaExperimental cell research2011 Apr 1706-2321122806
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The histone methyltransferase SETDB1 is recurrently amplified in melanoma and accelerates its onset.Ceol CJ, Houvras Y, Jane-Valbuena J, Bilodeau S, Orlando DA, Battisti V, Fritsch L, Lin WM, Hollmann TJ, Ferré F, Bourque C, Burke CJ, Turner L, Uong A, Johnson LA, Beroukhim R, Mermel CH, Loda M, Ait-Si-Ali S, Garraway LA, Young RA, Zon LI.Nature2011 Mar 24513-721430779
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An assessment of histone-modification antibody quality.Egelhofer, Thea A; Minoda, Aki; Klugman, Sarit; Lee, Kyungjoon; Kolasinska-Zwierz, Paulina; Alekseyenko, Artyom A; Cheung, Ming-Sin; Day, Daniel S; Gadel, Sarah; Gorchakov, Andrey A; Gu, Tingting; Kharchenko, Peter V; Kuan, Samantha; Latorre, Isabel; LindNature structural & molecular biology2011 Jan91-321131980
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The role of histone H4 biotinylation in the structure of nucleosomes.Filenko, Nina A; Kolar, Carol; West, John T; Smith, S Abbie; Hassan, Yousef I; Borgstahl, Gloria E O; Zempleni, Janos; Lyubchenko, Yuri LPloS one2011e1629921298003
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Characterization of the contradictory chromatin signatures at the 3' exons of zinc finger genes.Blahnik, Kimberly R; Dou, Lei; Echipare, Lorigail; Iyengar, Sushma; O'Geen, Henriette; Sanchez, Erica; Zhao, Yongjun; Marra, Marco A; Hirst, Martin; Costello, Joseph F; Korf, Ian; Farnham, Peggy JPloS one2011e1712121347206
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Characterization of single-nucleotide variation in Indian-origin rhesus macaques (Macaca mulatta).Fawcett, Gloria L; Raveendran, Muthuswamy; Deiros, David Rio; Chen, David; Yu, Fuli; Harris, Ronald Alan; Ren, Yanru; Muzny, Donna M; Reid, Jeffrey G; Wheeler, David A; Worley, Kimberly C; Shelton, Steven E; Kalin, Ned H; Milosavljevic, Aleksandar; Gibbs,BMC genomics201131121668978
PARP1 genomics: chromatin immunoprecipitation approach using anti-PARP1 antibody (ChIP and ChIP-seq).Lodhi, Niraj; Tulin, Alexei VMethods in molecular biology (Clifton, N.J.)2011191-20821870262
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Methylation of the CpG sites only on the sense strand of the APC gene is specific for hepatocellular carcinoma.Jain, Surbhi; Chang, Ting-Tsung; Hamilton, James P; Lin, Selena Y; Lin, Yih-Jyh; Evans, Alison A; Selaru, Florin M; Lin, Pin-Wen; Chen, Shun-Hua; Block, Timothy M; Hu, Chi-Tan; Song, Wei; Meltzer, Stephen J; Su, Ying-HsiuPloS one2011e2679922073196
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Keeping it in the family: diverse histone recognition by conserved structural folds.Yap KL, Zhou MM.Crit Rev Biochem Mol Biol2010 Dec488-50520923397
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The first global screening of protein substrates bearing protein-bound 3,4-Dihydroxyphenylalanine in Escherichia coli and human mitochondria.Lee, Sangkyu; Chen, Yue; Luo, Hao; Wu, Andrew A; Wilde, Michael; Schumacker, Paul T; Zhao, YingmingJournal of proteome research2010 Nov 55705-1420818827
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Epigenetic influences of low-dose bisphenol A in primary human breast epithelial cells.Weng, Yu-I; Hsu, Pei-Yin; Liyanarachchi, Sandya; Liu, Joseph; Deatherage, Daniel E; Huang, Yi-Wen; Zuo, Tao; Rodriguez, Benjamin; Lin, Ching-Hung; Cheng, Ann-Lii; Huang, Tim H-MToxicology and applied pharmacology2010 Oct 15111-2120678512
SILAC-based quantitative proteomic approach to identify potential biomarkers from the esophageal squamous cell carcinoma secretome.Kashyap, Manoj Kumar; Harsha, H C; Renuse, Santosh; Pawar, Harsh; Sahasrabuddhe, Nandini A; Kim, Min-Sik; Marimuthu, Arivusudar; Keerthikumar, Shivakumar; Muthusamy, Babylakshmi; Kandasamy, Kumaran; Subbannayya, Yashwanth; Prasad, Thottethodi Subrahmanya Cancer biology & therapy2010 Oct 15796-81020686364
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Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.Harris, R Alan; Wang, Ting; Coarfa, Cristian; Nagarajan, Raman P; Hong, Chibo; Downey, Sara L; Johnson, Brett E; Fouse, Shaun D; Delaney, Allen; Zhao, Yongjun; Olshen, Adam; Ballinger, Tracy; Zhou, Xin; Forsberg, Kevin J; Gu, Junchen; Echipare, Lorigail; Nature biotechnology2010 Oct1097-10520852635
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The Dnmt3a PWWP domain reads histone 3 lysine 36 trimethylation and guides DNA methylation.Dhayalan A, Rajavelu A, Rathert P, Tamas R, Jurkowska RZ, Ragozin S, Jeltsch A.J Biol Chem2010 Aug 2026114-2020547484
Protein lysine methyltransferase G9a inhibitors: design, synthesis, and structure activity relationships of 2,4-diamino-7-aminoalkoxy-quinazolines.Liu F, Chen X, Allali-Hassani A, Quinn AM, Wigle TJ, Wasney GA, Dong A, Senisterra G, Chau I, Siarheyeva A, Norris JL, Kireev DB, Jadhav A, Herold JM, Janzen WP, Arrowsmith CH, Frye SV, Brown PJ, Simeonov A, Vedadi M, Jin J.J Med Chem2010 Aug 125844-5720614940
Rapid visualization and large-scale profiling of bacterial lipoproteins with chemical reporters.Rangan, Kavita J; Yang, Yu-Ying; Charron, Guillaume; Hang, Howard CJournal of the American Chemical Society2010 Aug 1110628-920230003
Actin-myosin contractility is responsible for the reduced viability of dissociated human embryonic stem cells.Chen, Guokai; Hou, Zhonggang; Gulbranson, Daniel R; Thomson, James ACell stem cell2010 Aug 6240-820682449
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Palmitoylome profiling reveals S-palmitoylation-dependent antiviral activity of IFITM3.Yount, Jacob S; Moltedo, Bruno; Yang, Yu-Ying; Charron, Guillaume; Moran, Thomas M; Lopez, Carolina B; Hang, Howard CNature chemical biology2010 Aug610-420601941
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Adding a lysine mimic in the design of potent inhibitors of histone lysine methyltransferases.Chang, Yanqi; Ganesh, Thota; Horton, John R; Spannhoff, Astrid; Liu, Jin; Sun, Aiming; Zhang, Xing; Bedford, Mark T; Shinkai, Yoichi; Snyder, James P; Cheng, XiaodongJournal of molecular biology2010 Jul 21-720434463
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Biotin requirements are lower in human Jurkat lymphoid cells but homeostatic mechanisms are similar to those of HepG2 liver cells.Mall, Gaganpreet Kaur; Chew, Yap Ching; Zempleni, JanosThe Journal of nutrition2010 Jun1086-9220357078
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Distinct epigenomic landscapes of pluripotent and lineage-committed human cells.Hawkins, R David; Hon, Gary C; Lee, Leonard K; Ngo, Queminh; Lister, Ryan; Pelizzola, Mattia; Edsall, Lee E; Kuan, Samantha; Luu, Ying; Klugman, Sarit; Antosiewicz-Bourget, Jessica; Ye, Zhen; Espinoza, Celso; Agarwahl, Saurabh; Shen, Li; Ruotti, Victor; WCell stem cell2010 May 7479-9120452322
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K12-biotinylated histone H4 is enriched in telomeric repeats from human lung IMR-90 fibroblasts.Wijeratne, Subhashinee S K; Camporeale, Gabriela; Zempleni, JanosThe Journal of nutritional biochemistry2010 Apr310-619369050
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Structure of the MADS-box/MEF2 domain of MEF2A bound to DNA and its implication for myocardin recruitment.Wu Y, Dey R, Han A, Jayathilaka N, Philips M, Ye J, Chen L.J Mol Biol2010 Mar 26520-3320132824
Bioorthogonal chemical reporters for monitoring protein acetylation.Yang, Yu-Ying; Ascano, Janice M; Hang, Howard CJournal of the American Chemical Society2010 Mar 243640-120192265
Rational conversion of affinity reagents into label-free sensors for Peptide motifs by designed allostery.Huang, Jin; Koide, ShoheiACS chemical biology2010 Mar 19273-720143785
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Proteomic dissection of cell type-specific H2AX-interacting protein complex associated with hepatocellular carcinoma.Yang, Xiaoli; Zou, Peng; Yao, Jun; Yun, Dong; Bao, Huimin; Du, Ruyun; Long, Jing; Chen, XianJournal of proteome research2010 Mar 51402-1520000738
Global H4 acetylation analysis by ChIP-chip in systemic lupus erythematosus monocytes.Zhang, Z; Song, L; Maurer, K; Petri, M A; Sullivan, K EGenes and immunity2010 Mar124-3319710693
The polypeptide Syn67 interacts physically with human holocarboxylase synthetase, but is not a target for biotinylation.Hassan, Yousef I; Moriyama, Hideaki; Zempleni, JanosArchives of biochemistry and biophysics2010 Mar 135-4120026029
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Jarid2/Jumonji coordinates control of PRC2 enzymatic activity and target gene occupancy in pluripotent cells.Peng, Jamy C; Valouev, Anton; Swigut, Tomek; Zhang, Junmei; Zhao, Yingming; Sidow, Arend; Wysocka, JoannaCell2009 Dec 241290-30220064375
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Biotin tagging coupled with amino acid-coded mass tagging for efficient and precise screening of interaction proteome in mammalian cells.He, Yu-Fei; Bao, Hui-Min; Xiao, Xiao-Feng; Zuo, Shuai; Du, Ru-Yun; Tang, Si-Wei; Yang, Peng-Yuan; Chen, XianProteomics2009 Dec5414-2419834888
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Chromosomal abnormalities and novel disease-related regions in progression from Barrett's esophagus to esophageal adenocarcinoma.Akagi, Tadayuki; Ito, Tetsuo; Kato, Motohiro; Jin, Zhe; Cheng, Yulan; Kan, Takatsugu; Yamamoto, Go; Olaru, Alexandru; Kawamata, Norihiko; Boult, Jessica; Soukiasian, Harmik J; Miller, Carl W; Ogawa, Seishi; Meltzer, Stephen J; Koeffler, H PhillipInternational journal of cancer. Journal international du cancer2009 Nov 152349-5919670330
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Structural basis for exquisite specificity of affinity clamps, synthetic binding proteins generated through directed domain-interface evolution.Huang, Jin; Makabe, Koki; Biancalana, Matthew; Koide, Akiko; Koide, ShoheiJournal of molecular biology2009 Oct 91221-3119646997
Epithelial-mesenchymal transition and podocyte loss in diabetic kidney disease.Reidy, Kimberly; Susztak, KatalinAmerican journal of kidney diseases : the official journal of the National Kidney Foundation2009 Oct590-319781451
Parylene peel-off arrays to probe the role of cell-cell interactions in tumour angiogenesis.Tan CP, Seo BR, Brooks DJ, Chandler EM, Craighead HG, Fischbach C.Integr Biol (Camb)2009 Oct587-9420023775
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A noncanonical bromodomain in the AAA ATPase protein Yta7 directs chromosomal positioning and barrier chromatin activity.Gradolatto, Angeline; Smart, Sherri K; Byrum, Stephanie; Blair, Lauren P; Rogers, Richard S; Kolar, Elizabeth A; Lavender, Heather; Larson, Signe K; Aitchison, John D; Taverna, Sean D; Tackett, Alan JMolecular and cellular biology2009 Sep4604-1119581291
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The ankyrin repeat domain of Huntingtin interacting protein 14 contains a surface aromatic cage, a potential site for methyl-lysine binding.Gao, Tiyu; Collins, Robert E; Horton, John R; Zhang, Xing; Zhang, Rongguang; Dhayalan, Arunkumar; Tamas, Raluca; Jeltsch, Albert; Cheng, XiaodongProteins2009 Aug 15772-719434754
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Identification and verification of lysine propionylation and butyrylation in yeast core histones using PTMap software.Zhang, Kai; Chen, Yue; Zhang, Zhihong; Zhao, YingmingJournal of proteome research2009 Feb900-619113941
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Epigenomic profiling reveals DNA-methylation changes associated with major psychosis.Mill, Jonathan; Tang, Thomas; Kaminsky, Zachary; Khare, Tarang; Yazdanpanah, Simin; Bouchard, Luigi; Jia, Peixin; Assadzadeh, Abbas; Flanagan, James; Schumacher, Axel; Wang, Sun-Chong; Petronis, ArturasAmerican journal of human genetics2008 Mar696-71118319075
Lysine propionylation and butyrylation are novel post-translational modifications in histones.Chen, Yue; Sprung, Robert; Tang, Yi; Ball, Haydn; Sangras, Bhavani; Kim, Sung Chan; Falck, John R; Peng, Junmin; Gu, Wei; Zhao, YingmingMolecular & cellular proteomics : MCP2007 May812-917267393
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