Epigenomics (912)
Publication TitleAuthorsJournalPublication DatePage NoPubMedID
Pulling the genome in opposite directions to dissect gene networks.Gersbach, Charles A; Barrangou, RodolpheGenome biology.2018 Mar 26;29580291
Global delay in nascent strand DNA methylation.Charlton, Jocelyn; Downing, Timothy L; Smith, Zachary D; Gu, Hongcang; Clement, Kendell; Pop, Ramona; Akopian, Veronika; Klages, Sven; Santos, David P; Tsankov, Alexander M; Timmermann, Bernd; Ziller, Michael J; Kiskinis, Evangelos; Gnirke, Andreas; Meissner, AlexanderNature structural & molecular biology.2018 Mar 12;29531288
CRISPR-based methods for high-throughput annotation of regulatory DNA.Klann, Tyler S; Black, Joshua B; Gersbach, Charles ACurrent opinion in biotechnology.2018 Feb 28;29500989
Transcription start site profiling uncovers divergent transcription and enhancer-associated RNAs in Drosophila melanogaster.Meers, Michael P; Adelman, Karen; Duronio, Robert J; Strahl, Brian D; McKay, Daniel J; Matera, A GregoryBMC genomics.2018 02 21;29466941
Zika Virus Alters DNA Methylation of Neural Genes in an Organoid Model of the Developing Human Brain.Janssens, Sylvie; Schotsaert, Michael; Karnik, Rahul; Balasubramaniam, Vinod; Dejosez, Marion; Meissner, Alexander; García-Sastre, Adolfo; Zwaka, Thomas PmSystems.2018 Jan-Feb;29435496
A mixed modality approach towards Xi reactivation for Rett syndrome and other X-linked disorders.Carrette, Lieselot L G; Wang, Chen-Yu; Wei, Chunyao; Press, William; Ma, Weiyuan; Kelleher 3rd, Raymond J; Lee, Jeannie TProceedings of the National Academy of Sciences of the United States of America.2018 Jan 23;29282321
CRISPR Approaches to Small Molecule Target Identification.Jost, Marco; Weissman, Jonathan SACS chemical biology.2018 Feb 16;29261286
Control of microtubule dynamics using an optogenetic microtubule plus end-F-actin cross-linker.Adikes, Rebecca C; Hallett, Ryan A; Saway, Brian F; Kuhlman, Brian; Slep, Kevin CThe Journal of cell biology.2018 Feb 05;29259096
Transposable Element Mediated Innovation in Gene Regulatory Landscapes of Cells: Re-Visiting the ''Gene-Battery'' Model.Sundaram, Vasavi; Wang, TingBioEssays : news and reviews in molecular, cellular and developmental biology.2018 Jan;29206283
Landscape of the regulatory elements for lysine 2-hydroxyisobutyrylation pathway.Huang, He; Luo, Zhouqing; Qi, Shankang; Huang, Jing; Xu, Peng; Wang, Xiuxuan; Gao, Li; Li, Fangyi; Wang, Jian; Zhao, Wenhui; Gu, Wei; Chen, Zhucheng; Dai, Lunzhi; Dai, Junbiao; Zhao, YingmingCell research.2018 Jan;29192674
Functional Redundancy of Variant and Canonical Histone H3 Lysine 9 Modification in Drosophila.Penke, Taylor J R; McKay, Daniel J; Strahl, Brian D; Matera, A Gregory; Duronio, Robert JGenetics.2018 Jan;29133298
Epigenome-wide association studies identify DNA methylation associated with kidney function.Chu, Audrey Y; Tin, Adrienne; Schlosser, Pascal; Ko, Yi-An; Qiu, Chengxiang; Yao, Chen; Joehanes, Roby; Grams, Morgan E; Liang, Liming; Gluck, Caroline A; Liu, Chunyu; Coresh, Josef; Hwang, Shih-Jen; Levy, Daniel; Boerwinkle, Eric; Pankow, James S; Yang, Qiong; Fornage, Myriam; Fox, Caroline S; Susztak, Katalin; Köttgen, AnnaNature communications.2017 Nov 03;29097680
Association Between Brain Gene Expression, DNA Methylation, and Alteration of Ex Vivo Magnetic Resonance Imaging Transverse Relaxation in Late-Life Cognitive Decline.Yu, Lei; Dawe, Robert J; Boyle, Patricia A; Gaiteri, Chris; Yang, Jingyun; Buchman, Aron S; Schneider, Julie A; Arfanakis, Konstantinos; De Jager, Philip L; Bennett, David AJAMA neurology.2017 Dec 01;29084334
Inducible and multiplex gene regulation using CRISPR-Cpf1-based transcription factors.Tak, Y Esther; Kleinstiver, Benjamin P; Nuñez, James K; Hsu, Jonathan Y; Horng, Joy E; Gong, Jingyi; Weissman, Jonathan S; Joung, J KeithNature methods.2017 Dec;29083402
Association of Bone Metabolic Markers With Diabetic Retinopathy and Diabetic Macular Edema in Elderly Chinese Individuals With Type 2 Diabetes Mellitus.Zhang, Xiao; Yang, Jingyun; Zhong, Yong; Xu, Lingling; Wang, Ou; Huang, Ping; Li, Chunying; Qu, Bin; Wang, Jing; Zheng, Caixia; Niu, Meng; Yu, WeihongThe American journal of the medical sciences.2017 Oct;29078839
Combined CRISPRi/a-Based Chemical Genetic Screens Reveal that Rigosertib Is a Microtubule-Destabilizing Agent.Jost, Marco; Chen, Yuwen; Gilbert, Luke A; Horlbeck, Max A; Krenning, Lenno; Menchon, Grégory; Rai, Ankit; Cho, Min Y; Stern, Jacob J; Prota, Andrea E; Kampmann, Martin; Akhmanova, Anna; Steinmetz, Michel O; Tanenbaum, Marvin E; Weissman, Jonathan SMolecular cell.2017 Oct 05;28985505
The REMOTE-control system: a system for reversible and tunable control of endogenous gene expression in mice.Lee, Kwang-Ho; Oghamian, Shirley; Park, Jin-A; Kang, Liang; Laird, Peter WNucleic acids research.2017 Dec 01;28981717
Human Kidney Tubule-Specific Gene Expression Based Dissection of Chronic Kidney Disease Traits.Beckerman, Pazit; Qiu, Chengxiang; Park, Jihwan; Ledo, Nora; Ko, Yi-An; Park, Ae-Seo Deok; Han, Sang-Youb; Choi, Peter; Palmer, Matthew; Susztak, KatalinEBioMedicine.2017 Oct;28970079
Epigenetic restriction of extraembryonic lineages mirrors the somatic transition to cancer.Smith, Zachary D; Shi, Jiantao; Gu, Hongcang; Donaghey, Julie; Clement, Kendell; Cacchiarelli, Davide; Gnirke, Andreas; Michor, Franziska; Meissner, AlexanderNature.2017 09 28;28959968
A Single-Chain Photoswitchable CRISPR-Cas9 Architecture for Light-Inducible Gene Editing and Transcription.Zhou, Xin X; Zou, Xinzhi; Chung, Hokyung K; Gao, Yuchen; Liu, Yanxia; Qi, Lei S; Lin, Michael ZACS chemical biology.2018 Feb 16;28938067
Cooperative interactions enable singular olfactory receptor expression in mouse olfactory neurons.Monahan, Kevin; Schieren, Ira; Cheung, Jonah; Mumbey-Wafula, Alice; Monuki, Edwin S; Lomvardas, StavroseLife.2017 Sep 21;28933695
Tissue-specific DNA methylation is conserved across human, mouse, and rat, and driven by primary sequence conservation.Zhou, Jia; Sears, Renee L; Xing, Xiaoyun; Zhang, Bo; Li, Daofeng; Rockweiler, Nicole B; Jang, Hyo Sik; Choudhary, Mayank N K; Lee, Hyung Joo; Lowdon, Rebecca F; Arand, Jason; Tabers, Brianne; Gu, C Charles; Cicero, Theodore J; Wang, TingBMC genomics.2017 Sep 12;28899353
Genome Engineering for Personalized Arthritis Therapeutics.Adkar, Shaunak S; Brunger, Jonathan M; Willard, Vincent P; Wu, Chia-Lung; Gersbach, Charles A; Guilak, FarshidTrends in molecular medicine.2017 Oct;28887050
MicroRNAs Induce a Permissive Chromatin Environment that Enables Neuronal Subtype-Specific Reprogramming of Adult Human Fibroblasts.Abernathy, Daniel G; Kim, Woo Kyung; McCoy, Matthew J; Lake, Allison M; Ouwenga, Rebecca; Lee, Seong Won; Xing, Xiaoyun; Li, Daofeng; Lee, Hyung Joo; Heuckeroth, Robert O; Dougherty, Joseph D; Wang, Ting; Yoo, Andrew SCell stem cell.2017 Sep 07;28886366
Denoising genome-wide histone ChIP-seq with convolutional neural networks.Koh, Pang Wei; Pierson, Emma; Kundaje, AnshulBioinformatics (Oxford, England).2017 Jul 15;28881977
An Engineered Optogenetic Switch for Spatiotemporal Control of Gene Expression, Cell Differentiation, and Tissue Morphogenesis.Polstein, Lauren R; Juhas, Mark; Hanna, Gabi; Bursac, Nenad; Gersbach, Charles AACS synthetic biology.2017 Nov 17;28793186
Neuronal-expressed microRNA-targeted pseudogenes compete with coding genes in the human brain.Barbash, S; Simchovitz, A; Buchman, A S; Bennett, D A; Shifman, S; Soreq, HTranslational psychiatry.2017 Aug 08;28786976
Emerging Infections and Pertinent Infections Related to Travel for Patients with Primary Immunodeficiencies.Sullivan, Kathleen E; Bassiri, Hamid; Bousfiha, Ahmed A; Costa-Carvalho, Beatriz T; Freeman, Alexandra F; Hagin, David; Lau, Yu L; Lionakis, Michail S; Moreira, Ileana; Pinto, Jorge A; de Moraes-Pinto, M Isabel; Rawat, Amit; Reda, Shereen M; Reyes, Saul Oswaldo Lugo; Seppänen, Mikko; Tang, Mimi L KJournal of clinical immunology.2017 Oct;28786026
Correcting nucleotide-specific biases in high-throughput sequencing data.Wang, Jeremy R; Quach, Bryan; Furey, Terrence SBMC bioinformatics.2017 Aug 01;28764645
A High Fat Diet During Pregnancy and Lactation Induces Cardiac and Renal Abnormalities in GLUT4 +/- Male Mice.Kruse, Michael; Fiallo, Ariana; Tao, Jianling; Susztak, Katalin; Amann, Kerstin; Katz, Ellen B; Charron, Maureen JKidney & blood pressure research.2017;28750406
Whole exome sequencing identified genetic variations in Chinese hemangioblastoma patients.Ma, Dexuan; Yang, Jingyun; Wang, Ying; Huang, Xiang; Du, Guhong; Zhou, LiangfuAmerican journal of medical genetics. Part A.2017 Oct;28742274
Increasing the level of peroxisome proliferator-activated receptor ? coactivator-1? in podocytes results in collapsing glomerulopathy.Li, Szu-Yuan; Park, Jihwan; Qiu, Chengxiang; Han, Seung Hyeok; Palmer, Matthew B; Arany, Zoltan; Susztak, KatalinJCI insight.2017 Jul 20;28724797
ATR-101 inhibits cholesterol efflux and cortisol secretion by ATP-binding cassette transporters, causing cytotoxic cholesterol accumulation in adrenocortical carcinoma cells.Burns, Veronica Elizabeth; Kerppola, Tom KlausBritish journal of pharmacology.2017 Oct;28710789
The environment, epigenome, and asthma.Yang, Ivana V; Lozupone, Catherine A; Schwartz, David AThe Journal of allergy and clinical immunology.2017 Jul;28673400
Dissecting the role of non-coding RNAs in the accumulation of amyloid and tau neuropathologies in Alzheimer's disease.Patrick, Ellis; Rajagopal, Sathyapriya; Wong, Hon-Kit Andus; McCabe, Cristin; Xu, Jishu; Tang, Anna; Imboywa, Selina H; Schneider, Julie A; Pochet, Nathalie; Krichevsky, Anna M; Chibnik, Lori B; Bennett, David A; De Jager, Philip LMolecular neurodegeneration.2017 07 01;28668092
Transcriptomic profiles of aging in naïve and memory CD4+ cells from mice.Taylor, Jackson; Reynolds, Lindsay; Hou, Li; Lohman, Kurt; Cui, Wei; Kritchevsky, Stephen; McCall, Charles; Liu, YongmeiImmunity & ageing : I & A.2017;28642803
DNA methyltransferase 3b regulates articular cartilage homeostasis by altering metabolism.Shen, Jie; Wang, Cuicui; Li, Daofeng; Xu, Taotao; Myers, Jason; Ashton, John M; Wang, Ting; Zuscik, Michael J; McAlinden, Audrey; O'Keefe, Regis JJCI insight.2017 Jun 15;28614801
EpiCompare: An online tool to define and explore genomic regions with tissue or cell type-specific epigenomic features.He, Yu; Wang, TingBioinformatics (Oxford, England).2017 Jun 09;28605501
DNMT and HDAC inhibitors induce cryptic transcription start sites encoded in long terminal repeats.Brocks, David; Schmidt, Christopher R; Daskalakis, Michael; Jang, Hyo Sik; Shah, Nakul M; Li, Daofeng; Li, Jing; Zhang, Bo; Hou, Yiran; Laudato, Sara; Lipka, Daniel B; Schott, Johanna; Bierhoff, Holger; Assenov, Yassen; Helf, Monika; Ressnerova, Alzbeta; Nature genetics.2017 Jul;28604729
Uncovering the transcriptomic and epigenomic landscape of nicotinic receptor genes in non-neuronal tissues.Zhang, Bo; Madden, Pamela; Gu, Junchen; Xing, Xiaoyun; Sankar, Savita; Flynn, Jennifer; Kroll, Kristen; Wang, TingBMC genomics.2017 Jun 05;28583088
SERPINB2 is regulated by dynamic interactions with pause-release proteins and enhancer RNAs.Shii, Lihua; Song, Li; Maurer, Kelly; Zhang, Zhe; Sullivan, Kathleen EMolecular immunology.2017 Aug;28578223
Genetic-Variation-Driven Gene-Expression Changes Highlight Genes with Important Functions for Kidney Disease.Ko, Yi-An; Yi, Huiguang; Qiu, Chengxiang; Huang, Shizheng; Park, Jihwan; Ledo, Nora; Köttgen, Anna; Li, Hongzhe; Rader, Daniel J; Pack, Michael A; Brown, Christopher D; Susztak, KatalinAmerican journal of human genetics.2017 Jun 01;28575649
Neuroprotective effects respond to cerebral ischemia without susceptibility to HB-tumorigenesis in VHL heterozygous knockout mice.Wang, Ying; Yang, Jingyun; Du, Guhong; Ma, Dexuan; Zhou, LiangfuMolecular carcinogenesis.2017 Oct;28574654
Genetic architecture of epigenetic and neuronal ageing rates in human brain regions.Lu, Ake T; Hannon, Eilis; Levine, Morgan E; Crimmins, Eileen M; Lunnon, Katie; Mill, Jonathan; Geschwind, Daniel H; Horvath, SteveNature communications.2017 May 18;28516910
Genetic interaction mapping in mammalian cells using CRISPR interference.Du, Dan; Roguev, Assen; Gordon, David E; Chen, Meng; Chen, Si-Han; Shales, Michael; Shen, John Paul; Ideker, Trey; Mali, Prashant; Qi, Lei S; Krogan, Nevan JNature methods.2017 Jun;28481362
ETV2/ER71 regulates hematopoietic regeneration by promoting hematopoietic stem cell proliferation.Xu, Can-Xin; Lee, Tae-Jin; Sakurai, Nagisa; Krchma, Karen; Liu, Fang; Li, Daofeng; Wang, Ting; Choi, KyungheeThe Journal of experimental medicine.2017 May 01;28461595
Activity of distinct growth factor receptor network components in breast tumors uncovers two biologically relevant subtypes.Rahman, Mumtahena; MacNeil, Shelley M; Jenkins, David F; Shrestha, Gajendra; Wyatt, Sydney R; McQuerry, Jasmine A; Piccolo, Stephen R; Heiser, Laura M; Gray, Joe W; Johnson, W Evan; Bild, Andrea HGenome medicine.2017 04 26;28446242
Systematic Epigenomic Analysis Reveals Chromatin States Associated with Melanoma Progression.Fiziev, Petko; Akdemir, Kadir C; Miller, John P; Keung, Emily Z; Samant, Neha S; Sharma, Sneha; Natale, Christopher A; Terranova, Christopher J; Maitituoheti, Mayinuer; Amin, Samirkumar B; Martinez-Ledesma, Emmanuel; Dhamdhere, Mayura; Axelrad, Jacob B; SCell reports.2017 Apr 25;28445736
Kidney triglyceride accumulation in the fasted mouse is dependent upon serum free fatty acids.Scerbo, Diego; Son, Ni-Huiping; Sirwi, Alaa; Zeng, Lixia; Sas, Kelli M; Cifarelli, Vincenza; Schoiswohl, Gabriele; Huggins, Lesley-Ann; Gumaste, Namrata; Hu, Yunying; Pennathur, Subramaniam; Abumrad, Nada A; Kershaw, Erin E; Hussain, M Mahmood; Susztak, KJournal of lipid research.2017 Jun;28404638
CRISPR-Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome.Klann, Tyler S; Black, Joshua B; Chellappan, Malathi; Safi, Alexias; Song, Lingyun; Hilton, Isaac B; Crawford, Gregory E; Reddy, Timothy E; Gersbach, Charles ANature biotechnology.2017 Jun;28369033
Population Epigenetics.Greally, John MCurrent opinion in systems biology.2017 Feb;28367533
Precision Medicine Approaches to Diabetic Kidney Disease: Tissue as an Issue.Gluck, Caroline; Ko, Yi-An; Susztak, KatalinCurrent diabetes reports.2017 05;28364354
Small-Magnitude Effect Sizes in Epigenetic End Points are Important in Children's Environmental Health Studies: The Children's Environmental Health and Disease Prevention Research Center's Epigenetics Working Group.Breton, Carrie V; Marsit, Carmen J; Faustman, Elaine; Nadeau, Kari; Goodrich, Jaclyn M; Dolinoy, Dana C; Herbstman, Julie; Holland, Nina; LaSalle, Janine M; Schmidt, Rebecca; Yousefi, Paul; Perera, Frederica; Joubert, Bonnie R; Wiemels, Joseph; Taylor, Michele; Yang, Ivana V; Chen, Rui; Hew, Kinjal M; Freeland, Deborah M Hussey; Miller, Rachel; Murphy, Susan KEnvironmental health perspectives.2017 Apr;28362264
Functional cis-regulatory modules encoded by mouse-specific endogenous retrovirus.Sundaram, Vasavi; Choudhary, Mayank N K; Pehrsson, Erica; Xing, Xiaoyun; Fiore, Christopher; Pandey, Manishi; Maricque, Brett; Udawatta, Methma; Ngo, Duc; Chen, Yujie; Paguntalan, Asia; Ray, Tammy; Hughes, Ava; Cohen, Barak A; Wang, TingNature communications.2017 Mar 28;28348391
Histone gene replacement reveals a post-transcriptional role for H3K36 in maintaining metazoan transcriptome fidelity.Meers, Michael P; Henriques, Telmo; Lavender, Christopher A; McKay, Daniel J; Strahl, Brian D; Duronio, Robert J; Adelman, Karen; Matera, A GregoryeLife.2017 03 27;28346137
Visualization of the Genomic Loci That Are Bound by Specific Multiprotein Complexes by Bimolecular Fluorescence Complementation Analysis on Drosophila Polytene Chromosomes.Deng, Huai; Kerppola, Tom KMethods in enzymology.2017;28336073
Epigenomic annotation of noncoding mutations identifies mutated pathways in primary liver cancer.Lowdon, Rebecca F; Wang, TingPloS one.2017;28333948
Susceptibility to neurofibrillary tangles: role of the PTPRD locus and limited pleiotropy with other neuropathologies.Chibnik, L B; White, C C; Mukherjee, S; Raj, T; Yu, L; Larson, E B; Montine, T J; Keene, C D; Sonnen, J; Schneider, J A; Crane, P K; Shulman, J M; Bennett, D A; De Jager, P LMolecular psychiatry.2017 Mar 21;28322283
The Nasal Methylome: A Key to Understanding Allergic Asthma.Yang, Ivana V; Richards, Adam; Davidson, Elizabeth J; Stevens, Allen D; Kolakowski, Christena A; Martin, Richard J; Schwartz, David AAmerican journal of respiratory and critical care medicine.2017 03 15;28294656
Monobodies and other synthetic binding proteins for expanding protein science.Sha, Fern; Salzman, Gabriel; Gupta, Ankit; Koide, ShoheiProtein science : a publication of the Protein Society.2017 May;28249355
Transgenic expression of human APOL1 risk variants in podocytes induces kidney disease in mice.Beckerman, Pazit; Bi-Karchin, Jing; Park, Ae Seo Deok; Qiu, Chengxiang; Dummer, Patrick D; Soomro, Irfana; Boustany-Kari, Carine M; Pullen, Steven S; Miner, Jeffrey H; Hu, Chien-An A; Rohacs, Tibor; Inoue, Kazunori; Ishibe, Shuta; Saleem, Moin A; Palmer, Matthew B; Cuervo, Ana Maria; Kopp, Jeffrey B; Susztak, KatalinNature medicine.2017 Apr;28218918
A high-throughput small molecule screen identifies synergism between DNA methylation and Aurora kinase pathways for X reactivation.Lessing, Derek; Dial, Thomas O; Wei, Chunyao; Payer, Bernhard; Carrette, Lieselot L G; Kesner, Barry; Szanto, Attila; Jadhav, Ajit; Maloney, David J; Simeonov, Anton; Theriault, Jimmy; Hasaka, Thomas; Bedalov, Antonio; Bartolomei, Marisa S; Lee, Jeannie TProceedings of the National Academy of Sciences of the United States of America.2016 Dec 13;28182563
Transcriptional heterogeneity in the lactase gene within cell-type is linked to the epigenome.Oh, Edward; Jeremian, Richie; Oh, Gabriel; Groot, Daniel; Susic, Miki; Lee, KwangHo; Foy, Kelly; Laird, Peter W; Petronis, Arturas; Labrie, VivianeScientific reports.2017 Jan 31;28139744
Genome-Wide Association of Copy Number Polymorphisms and Kidney Function.Li, Man; Carey, Jacob; Cristiano, Stephen; Susztak, Katalin; Coresh, Josef; Boerwinkle, Eric; Kao, Wen Hong L; Beaty, Terri H; Köttgen, Anna; Scharpf, Robert BPloS one.2017;28135296
sNASP and ASF1A function through both competitive and compatible modes of histone binding.Bowman, Andrew; Koide, Akiko; Goodman, Jay S; Colling, Meaghan E; Zinne, Daria; Koide, Shohei; Ladurner, Andreas GNucleic acids research.2017 Jan 25;28123037
Layer-specific chromatin accessibility landscapes reveal regulatory networks in adult mouse visual cortex.Gray, Lucas T; Yao, Zizhen; Nguyen, Thuc Nghi; Kim, Tae Kyung; Zeng, Hongkui; Tasic, BosiljkaeLife.2017 Jan 23;28112643
Cooperative Binding of Transcription Factors Orchestrates Reprogramming.Chronis, Constantinos; Fiziev, Petko; Papp, Bernadett; Butz, Stefan; Bonora, Giancarlo; Sabri, Shan; Ernst, Jason; Plath, KathrinCell.2017 Jan 26;28111071
CRISPR-Based Epigenome Editing of Cytokine Receptors for the Promotion of Cell Survival and Tissue Deposition in Inflammatory Environments.Farhang, Niloofar; Brunger, Jonathan M; Stover, Joshua D; Thakore, Pratiksha I; Lawrence, Brandon; Guilak, Farshid; Gersbach, Charles A; Setton, Lori A; Bowles, Robert DTissue engineering. Part A.2017 Jan 17;28095751
Epigenetic Research in Neuropsychiatric Disorders: the ''Tissue Issue''.Bakulski, Kelly M; Halladay, Alycia; Hu, Valerie W; Mill, Jonathan; Fallin, M DanieleCurrent behavioral neuroscience reports.2016 Sep;28093577
Whole-Genome DNA Methylation Profiling Identifies Epigenetic Signatures of Uterine Carcinosarcoma.Li, Jing; Xing, Xiaoyun; Li, Daofeng; Zhang, Bo; Mutch, David G; Hagemann, Ian S; Wang, TingNeoplasia (New York, N.Y.).2017 Feb;28088687
Schizophrenia-associated methylomic variation: molecular signatures of disease and polygenic risk burden across multiple brain regions.Viana, Joana; Hannon, Eilis; Dempster, Emma; Pidsley, Ruth; Macdonald, Ruby; Knox, Olivia; Spiers, Helen; Troakes, Claire; Al-Saraj, Safa; Turecki, Gustavo; Schalkwyk, Leonard C; Mill, JonathanHuman molecular genetics.2017 01 01;28011714
DeFCoM: analysis and modeling of transcription factor binding sites using a motif-centric genomic footprinter.Quach, Bryan; Furey, Terrence SBioinformatics (Oxford, England).2017 Apr 01;27993786
Developing Treatments for Chronic Kidney Disease in the 21st Century.Breyer, Matthew D; Susztak, KatalinSeminars in nephrology.2016 Nov;27987541
A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response.Adamson, Britt; Norman, Thomas M; Jost, Marco; Cho, Min Y; Nuñez, James K; Chen, Yuwen; Villalta, Jacqueline E; Gilbert, Luke A; Horlbeck, Max A; Hein, Marco Y; Pak, Ryan A; Gray, Andrew N; Gross, Carol A; Dixit, Atray; Parnas, Oren; Regev, Aviv; Weissman, Jonathan SCell.2016 Dec 15;27984733
Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens.Dixit, Atray; Parnas, Oren; Li, Biyu; Chen, Jenny; Fulco, Charles P; Jerby-Arnon, Livnat; Marjanovic, Nemanja D; Dionne, Danielle; Burks, Tyler; Raychowdhury, Raktima; Adamson, Britt; Norman, Thomas M; Lander, Eric S; Weissman, Jonathan S; Friedman, Nir; Regev, AvivCell.2016 Dec 15;27984732
''Gap hunting'' to characterize clustered probe signals in Illumina methylation array data.Andrews, Shan V; Ladd-Acosta, Christine; Feinberg, Andrew P; Hansen, Kasper D; Fallin, M DanieleEpigenetics & chromatin.2016;27980682
CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells.Liu, S John; Horlbeck, Max A; Cho, Seung Woo; Birk, Harjus S; Malatesta, Martina; He, Daniel; Attenello, Frank J; Villalta, Jacqueline E; Cho, Min Y; Chen, Yuwen; Mandegar, Mohammad A; Olvera, Michael P; Gilbert, Luke A; Conklin, Bruce R; Chang, Howard Y; Weissman, Jonathan S; Lim, Daniel AScience (New York, N.Y.).2017 Jan 06;27980086
Trans-acting epigenetic effects of chromosomal aneuploidies: lessons from Down syndrome and mouse models.Do, Catherine; Xing, Zhuo; Yu, Y Eugene; Tycko, BenjaminEpigenomics.2017 Feb;27911079
Notch Pathway Is Activated via Genetic and Epigenetic Alterations and Is a Therapeutic Target in Clear Cell Renal Cancer.Bhagat, Tushar D; Zou, Yiyu; Huang, Shizheng; Park, Jihwan; Palmer, Matthew B; Hu, Caroline; Li, Weijuan; Shenoy, Niraj; Giricz, Orsolya; Choudhary, Gaurav; Yu, Yiting; Ko, Yi-An; Izquierdo, María C; Park, Ae Seo Deok; Vallumsetla, Nishanth; Laurence, Remi; Lopez, Robert; Suzuki, Masako; Pullman, James; Kaner, Justin; Gartrell, Benjamin; Hakimi, A Ari; Greally, John M; Patel, Bharvin; Benhadji, Karim; Pradhan, Kith; Verma, Amit; Susztak, KatalinThe Journal of biological chemistry.2017 01 20;27909050
LOVTRAP: A Versatile Method to Control Protein Function with Light.Wang, Hui; Hahn, Klaus MCurrent protocols in cell biology.;27906450
Long-term outdoor air pollution and DNA methylation in circulating monocytes: results from the Multi-Ethnic Study of Atherosclerosis (MESA).Chi, Gloria C; Liu, Yongmei; MacDonald, James W; Barr, R Graham; Donohue, Kathleen M; Hensley, Mark D; Hou, Lifang; McCall, Charles E; Reynolds, Lindsay M; Siscovick, David S; Kaufman, Joel DEnvironmental health : a global access science source.2016 12 01;27903268
Circadian alterations during early stages of Alzheimer's disease are associated with aberrant cycles of DNA methylation in BMAL1.Cronin, Peter; McCarthy, Michael J; Lim, Andrew S P; Salmon, David P; Galasko, Douglas; Masliah, Eliezer; De Jager, Philip L; Bennett, David A; Desplats, PaulaAlzheimer's & dementia : the journal of the Alzheimer's Association.2017 Jun;27883893
Soft X-Ray Tomography Reveals Gradual Chromatin Compaction and Reorganization during Neurogenesis In Vivo.Le Gros, Mark A; Clowney, E Josephine; Magklara, Angeliki; Yen, Angela; Markenscoff-Papadimitriou, Eirene; Colquitt, Bradley; Myllys, Markko; Kellis, Manolis; Lomvardas, Stavros; Larabell, Carolyn ACell reports.2016 Nov 15;27851973
Epigenomic Deconvolution of Breast Tumors Reveals Metabolic Coupling between Constituent Cell Types.Onuchic, Vitor; Hartmaier, Ryan J; Boone, David N; Samuels, Michael L; Patel, Ronak Y; White, Wendy M; Garovic, Vesna D; Oesterreich, Steffi; Roth, Matt E; Lee, Adrian V; Milosavljevic, AleksandarCell reports.2016 11 15;27851969
A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome.Schmitt, Anthony D; Hu, Ming; Jung, Inkyung; Xu, Zheng; Qiu, Yunjiang; Tan, Catherine L; Li, Yun; Lin, Shin; Lin, Yiing; Barr, Cathy L; Ren, BingCell reports.2016 Nov 15;27851967
A DNA methylation biomarker of alcohol consumption.Liu, C; Marioni, R E; Hedman, Å K; Pfeiffer, L; Tsai, P-C; Reynolds, L M; Just, A C; Duan, Q; Boer, C G; Tanaka, T; Elks, C E; Aslibekyan, S; Brody, J A; Kühnel, B; Herder, C; Almli, L M; Zhi, D; Wang, Y; Huan, T; Yao, C; Mendelson, M M; Joehanes, R; Liang, L; Love, S-A; Guan, W; Shah, S; McRae, A F; Kretschmer, A; Prokisch, H; Strauch, K; Peters, A; Visscher, P M; Wray, N R; Guo, X; Wiggins, K L; Smith, A K; Binder, E B; Ressler, K J; Irvin, M R; Absher, D M; Hernandez, D; Ferrucci, L; Bandinelli, S; Lohman, K; Ding, J; Trevisi, L; Gustafsson, S; Sandling, J H; Stolk, L; Uitterlinden, A G; Yet, I; Castillo-Fernandez, J E; Spector, T D; Schwartz, J D; Vokonas, P; Lind, L; Li, Y; Fornage, M; Arnett, D K; Wareham, N J; Sotoodehnia, N; Ong, K K; van Meurs, J B J; Conneely, K N; Baccarelli, A A; Deary, I J; Bell, J T; North, K E; Liu, Y; Waldenberger, M; London, S J; Ingelsson, E; Levy, DMolecular psychiatry.2016 Nov 15;27843151
Genetic engineering: Chemical control for CRISPR editing.Hilton, Isaac B; Gersbach, Charles ANature chemical biology.2017 Jan;27820804
Loss-of-function genetic tools for animal models: cross-species and cross-platform differences.Housden, Benjamin E; Muhar, Matthias; Gemberling, Matthew; Gersbach, Charles A; Stainier, Didier Y R; Seydoux, Geraldine; Mohr, Stephanie E; Zuber, Johannes; Perrimon, NorbertNature reviews. Genetics.2017 01;27795562
Complex transcriptional modulation with orthogonal and inducible dCas9 regulators.Gao, Yuchen; Xiong, Xin; Wong, Spencer; Charles, Emeric J; Lim, Wendell A; Qi, Lei SNature methods.2016 Dec;27776111
Chromosome conformation elucidates regulatory relationships in developing human brain.Won, Hyejung; de la Torre-Ubieta, Luis; Stein, Jason L; Parikshak, Neelroop N; Huang, Jerry; Opland, Carli K; Gandal, Michael J; Sutton, Gavin J; Hormozdiari, Farhad; Lu, Daning; Lee, Changhoon; Eskin, Eleazar; Voineagu, Irina; Ernst, Jason; Geschwind, DaNature.2016 Oct 19;27760116
The long noncoding RNA Tug1 connects metabolic changes with kidney disease in podocytes.Li, Szu Yuan; Susztak, KatalinThe Journal of clinical investigation.2016 Nov 01;27760046
The nasal methylome and childhood atopic asthma.Yang, Ivana V; Pedersen, Brent S; Liu, Andrew H; O'Connor, George T; Pillai, Dinesh; Kattan, Meyer; Misiak, Rana Tawil; Gruchalla, Rebecca; Szefler, Stanley J; Khurana Hershey, Gurjit K; Kercsmar, Carolyn; Richards, Adam; Stevens, Allen D; Kolakowski, Christena A; Makhija, Melanie; Sorkness, Christine A; Krouse, Rebecca Z; Visness, Cynthia; Davidson, Elizabeth J; Hennessy, Corinne E; Martin, Richard J; Togias, Alkis; Busse, William W; Schwartz, David AThe Journal of allergy and clinical immunology.2016 Oct 13;27745942
Molecular classification of Crohn's disease reveals two clinically relevant subtypes.Weiser, Matthew; Simon, Jeremy M; Kochar, Bharati; Tovar, Adelaide; Israel, Jennifer W; Robinson, Adam; Gipson, Gregory R; Schaner, Matthew S; Herfarth, Hans H; Sartor, R Balfour; McGovern, Dermot P B; Rahbar, Reza; Sadiq, Timothy S; Koruda, Mark J; Furey, Terrence S; Sheikh, Shehzad ZGut.2018 Jan;27742763
Epigenomic and transcriptional control of insulin resistance.Rosen, E DJournal of internal medicine.2016 Nov;27739225
Detection of human adaptation during the past 2000 years.Field, Yair; Boyle, Evan A; Telis, Natalie; Gao, Ziyue; Gaulton, Kyle J; Golan, David; Yengo, Loic; Rocheleau, Ghislain; Froguel, Philippe; McCarthy, Mark I; Pritchard, Jonathan KScience (New York, N.Y.).;27738015
SOX2, OCT3/4 and NANOG expression and cellular plasticity in rare human somatic cells requires CD73.Pan, Deng; Roy, Somdutta; Gascard, Philippe; Zhao, Jianxin; Chen-Tanyolac, Chira; Tlsty, Thea DCellular signalling.2016 Dec;27705752
Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions.Ernst, Jason; Melnikov, Alexandre; Zhang, Xiaolan; Wang, Li; Rogov, Peter; Mikkelsen, Tarjei S; Kellis, ManolisNature biotechnology.2016 Nov;27701403
Identification of a cancer stem cell-specific function for the histone deacetylases, HDAC1 and HDAC7, in breast and ovarian cancer.Witt, A E; Lee, C-W; Lee, T I; Azzam, D J; Wang, B; Caslini, C; Petrocca, F; Grosso, J; Jones, M; Cohick, E B; Gropper, A B; Wahlestedt, C; Richardson, A L; Shiekhattar, R; Young, R A; Ince, T AOncogene.2017 Mar 23;27694895
Association of genetic variants in the receptor for advanced glycation end products gene with diabetic retinopathy: A meta-analysis.Yu, Weihong; Yang, Jingyun; Sui, Wenda; Qu, Bin; Huang, Ping; Chen, YouxinMedicine.2016 Sep;27684793
Rescue of Early bace-1 and Global DNA Demethylation by S-Adenosylmethionine Reduces Amyloid Pathology and Improves Cognition in an Alzheimer's Model.Do Carmo, Sonia; Hanzel, Cecilia E; Jacobs, Marie L; Machnes, Ziv; Iulita, M Florencia; Yang, Jingyun; Yu, Lei; Ducatenzeiler, Adriana; Danik, Marc; Breuillaud, Lionel S; Bennett, David A; Szyf, Moshe; Cuello, A ClaudioScientific reports.2016 Sep 29;27681803
Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation.Horlbeck, Max A; Gilbert, Luke A; Villalta, Jacqueline E; Adamson, Britt; Pak, Ryan A; Chen, Yuwen; Fields, Alexander P; Park, Chong Yon; Corn, Jacob E; Kampmann, Martin; Weissman, Jonathan SeLife.2016 Sep 23;27661255
Epigenetic Signatures of Cigarette Smoking.Joehanes, Roby; Just, Allan C; Marioni, Riccardo E; Pilling, Luke C; Reynolds, Lindsay M; Mandaviya, Pooja R; Guan, Weihua; Xu, Tao; Elks, Cathy E; Aslibekyan, Stella; Moreno-Macias, Hortensia; Smith, Jennifer A; Brody, Jennifer A; Dhingra, Radhika; Yousefi, Paul; Pankow, James S; Kunze, Sonja; Shah, Sonia H; McRae, Allan F; Lohman, Kurt; Sha, Jin; Absher, Devin M; Ferrucci, Luigi; Zhao, Wei; Demerath, Ellen W; Bressler, Jan; Grove, Megan L; Huan, Tianxiao; Liu, Chunyu; Mendelson, Michael M; Yao, Chen; Kiel, Douglas P; Peters, Annette; Wang-Sattler, Rui; Visscher, Peter M; Wray, Naomi R; Starr, John M; Ding, Jingzhong; Rodriguez, Carlos J; Wareham, Nicholas J; Irvin, Marguerite R; Zhi, Degui; Barrdahl, Myrto; Vineis, Paolo; Ambatipudi, Srikant; Uitterlinden, André G; Hofman, Albert; Schwartz, Joel; Colicino, Elena; Hou, Lifang; Vokonas, Pantel S; Hernandez, Dena G; Singleton, Andrew B; Bandinelli, Stefania; Turner, Stephen T; Ware, Erin B; Smith, Alicia K; Klengel, Torsten; Binder, Elisabeth B; Psaty, Bruce M; Taylor, Kent D; Gharib, Sina A; Swenson, Brenton R; Liang, Liming; DeMeo, Dawn L; O'Connor, George T; Herceg, Zdenko; Ressler, Kerry J; Conneely, Karen N; Sotoodehnia, Nona; Kardia, Sharon L R; Melzer, David; Baccarelli, Andrea A; van Meurs, Joyce B J; Romieu, Isabelle; Arnett, Donna K; Ong, Ken K; Liu, Yongmei; Waldenberger, Melanie; Deary, Ian J; Fornage, Myriam; Levy, Daniel; London, Stephanie JCirculation. Cardiovascular genetics.2016 Oct;27651444
Secondhand Tobacco Smoke Exposure Associations With DNA Methylation of the Aryl Hydrocarbon Receptor Repressor.Reynolds, Lindsay M; Magid, Hoda S; Chi, Gloria C; Lohman, Kurt; Barr, R Graham; Kaufman, Joel D; Hoeschele, Ina; Blaha, Michael J; Navas-Acien, Ana; Liu, YongmeiNicotine & tobacco research : official journal of the Society for Research on Nicotine and Tobacco.2017 Apr 01;27613907
Engineering and Application of LOV2-Based Photoswitches.Zimmerman, S P; Kuhlman, B; Yumerefendi, HMethods in enzymology.2016;27586333
Genome-wide mapping and analysis of chromosome architecture.Schmitt, Anthony D; Hu, Ming; Ren, BingNature reviews. Molecular cell biology.2016 12;27580841
An integrated genetic-epigenetic analysis of schizophrenia: evidence for co-localization of genetic associations and differential DNA methylation.Hannon, Eilis; Dempster, Emma; Viana, Joana; Burrage, Joe; Smith, Adam R; Macdonald, Ruby; St Clair, David; Mustard, Colette; Breen, Gerome; Therman, Sebastian; Kaprio, Jaakko; Toulopoulou, Timothea; Hulshoff Pol, Hilleke E; Bohlken, Marc M; Kahn, Rene S; Nenadic, Igor; Hultman, Christina M; Murray, Robin M; Collier, David A; Bass, Nick; Gurling, Hugh; McQuillin, Andrew; Schalkwyk, Leonard; Mill, JonathanGenome biology.2016 Aug 30;27572077
Direct interrogation of the role of H3K9 in metazoan heterochromatin function.Penke, Taylor J R; McKay, Daniel J; Strahl, Brian D; Matera, A Gregory; Duronio, Robert JGenes & development.2016 Aug 15;27566777
Female mice lacking Xist RNA show partial dosage compensation and survive to term.Yang, Lin; Kirby, James E; Sunwoo, Hongjae; Lee, Jeannie TGenes & development.2016 Aug 01;27542829
BatchQC: interactive software for evaluating sample and batch effects in genomic data.Manimaran, Solaiappan; Selby, Heather Marie; Okrah, Kwame; Ruberman, Claire; Leek, Jeffrey T; Quackenbush, John; Haibe-Kains, Benjamin; Bravo, Hector Corrada; Johnson, W EvanBioinformatics (Oxford, England).2016 Dec 15;27540268
Tuning the Binding Affinities and Reversion Kinetics of a Light Inducible Dimer Allows Control of Transmembrane Protein Localization.Zimmerman, Seth P; Hallett, Ryan A; Bourke, Ashley M; Bear, James E; Kennedy, Matthew J; Kuhlman, BrianBiochemistry.2016 Sep 20;27529180
Waking up dormant tumor suppressor genes with zinc fingers, TALEs and the CRISPR/dCas9 system.Garcia-Bloj, Benjamin; Moses, Colette; Sgro, Agustin; Plani-Lam, Janice; Arooj, Mahira; Duffy, Ciara; Thiruvengadam, Shreyas; Sorolla, Anabel; Rashwan, Rabab; Mancera, Ricardo L; Leisewitz, Andrea; Swift-Scanlan, Theresa; Corvalan, Alejandro H; Blancafort, PilarOncotarget.2016 Sep 13;27528034
Charon Mediates Immune Deficiency-Driven PARP-1-Dependent Immune Responses in Drosophila.Ji, Yingbiao; Thomas, Colin; Tulin, Nikita; Lodhi, Niraj; Boamah, Ernest; Kolenko, Vladimir; Tulin, Alexei VJournal of immunology (Baltimore, Md. : 1950).2016 Sep 15;27527593
Targeted Epigenetic Remodeling of Endogenous Loci by CRISPR/Cas9-Based Transcriptional Activators Directly Converts Fibroblasts to Neuronal Cells.Black, Joshua B; Adler, Andrew F; Wang, Hong-Gang; D'Ippolito, Anthony M; Hutchinson, Hunter A; Reddy, Timothy E; Pitt, Geoffrey S; Leong, Kam W; Gersbach, Charles ACell stem cell.2016 Sep 1;27524438
Increased DNA methylation near TREM2 is consistently seen in the superior temporal gyrus in Alzheimer's disease brain.Smith, Adam R; Smith, Rebecca G; Condliffe, Daniel; Hannon, Eilis; Schalkwyk, Leonard; Mill, Jonathan; Lunnon, KatieNeurobiology of aging.2016 Nov;27522519
Inhibition of DNA Methyltransferases Blocks Mutant Huntingtin-Induced Neurotoxicity.Pan, Yanchun; Daito, Takuji; Sasaki, Yo; Chung, Yong Hee; Xing, Xiaoyun; Pondugula, Santhi; Swamidass, S Joshua; Wang, Ting; Kim, Albert H; Yano, HirokoScientific reports.2016 Aug 12;27516062
An epigenetic clock analysis of race/ethnicity, sex, and coronary heart disease.Horvath, Steve; Gurven, Michael; Levine, Morgan E; Trumble, Benjamin C; Kaplan, Hillard; Allayee, Hooman; Ritz, Beate R; Chen, Brian; Lu, Ake T; Rickabaugh, Tammy M; Jamieson, Beth D; Sun, Dianjianyi; Li, Shengxu; Chen, Wei; Quintana-Murci, Lluis; Fagny, Maud; Kobor, Michael S; Tsao, Philip S; Reiner, Alexander P; Edlefsen, Kerstin L; Absher, Devin; Assimes, Themistocles LGenome biology.2016 Aug 11;27511193
Insights into neuroepigenetics through human histone deacetylase PET imaging.Wey, Hsiao-Ying; Gilbert, Tonya M; Zürcher, Nicole R; She, Angela; Bhanot, Anisha; Taillon, Brendan D; Schroeder, Fredrick A; Wang, Changing; Haggarty, Stephen J; Hooker, Jacob MScience translational medicine.2016 08 10;27510902
Hypomethylation coordinates antagonistically with hypermethylation in cancer development: a case study of leukemia.Kushwaha, Garima; Dozmorov, Mikhail; Wren, Jonathan D; Qiu, Jing; Shi, Huidong; Xu, DongHuman genomics.2016 Jul 25;27461342
Highly Multiplexed RNA Aptamer Selection using a Microplate-based Microcolumn Device.Reinholt, Sarah J; Ozer, Abdullah; Lis, John T; Craighead, Harold GScientific reports.2016 Jul 19;27432610
LOVTRAP: an optogenetic system for photoinduced protein dissociation.Wang, Hui; Vilela, Marco; Winkler, Andreas; Tarnawski, Miroslaw; Schlichting, Ilme; Yumerefendi, Hayretin; Kuhlman, Brian; Liu, Rihe; Danuser, Gaudenz; Hahn, Klaus MNature methods.2016 Sep;27427858
Long-term clinical outcomes of laparoscopy-assisted distal gastrectomy versus open distal gastrectomy for early gastric cancer: A comprehensive systematic review and meta-analysis of randomized control trials.Lu, Wei; Gao, Jian; Yang, Jingyun; Zhang, Yijian; Lv, Wenjie; Mu, Jiasheng; Dong, Ping; Liu, YingbinMedicine.2016 Jul;27399073
Go in! Go out! Inducible control of nuclear localization.Di Ventura, Barbara; Kuhlman, BrianCurrent opinion in chemical biology.2016 Jun 30;27372352
Ligand-binding domains of nuclear receptors facilitate tight control of split CRISPR activity.Nguyen, Duy P; Miyaoka, Yuichiro; Gilbert, Luke A; Mayerl, Steven J; Lee, Brian H; Weissman, Jonathan S; Conklin, Bruce R; Wells, James ANature communications.2016 Jul 01;27363581
Reference-free deconvolution of DNA methylation data and mediation by cell composition effects.Houseman, E Andres; Kile, Molly L; Christiani, David C; Ince, Tan A; Kelsey, Karl T; Marsit, Carmen JBMC bioinformatics.2016;27358049
An evaluation of processing methods for HumanMethylation450 BeadChip data.Liu, Jie; Siegmund, Kimberly DBMC genomics.2016 06 22;27334613
Whole Genome Sequencing Identifies a Novel Factor Required for Secretory Granule Maturation in Tetrahymena thermophila.Kontur, Cassandra; Kumar, Santosh; Lan, Xun; Pritchard, Jonathan K; Turkewitz, Aaron PG3 (Bethesda, Md.).2016 Aug 09;27317773
Using genomic annotations increases statistical power to detect eGenes.Duong, Dat; Zou, Jennifer; Hormozdiari, Farhad; Sul, Jae Hoon; Ernst, Jason; Han, Buhm; Eskin, EleazarBioinformatics (Oxford, England).2016 Jun 15;27307612
Breast cancers from black women exhibit higher numbers of immunosuppressive macrophages with proliferative activity and of crown-like structures associated with lower survival compared to non-black Latinas and Caucasians.Koru-Sengul, Tulay; Santander, Ana M; Miao, Feng; Sanchez, Lidia G; Jorda, Merce; Glück, Stefan; Ince, Tan A; Nadji, Mehrad; Chen, Zhibin; Penichet, Manuel L; Cleary, Margot P; Torroella-Kouri, MartaBreast cancer research and treatment.2016 Jul;27283835
Genetic variants in Alzheimer disease - molecular and brain network approaches.Gaiteri, Chris; Mostafavi, Sara; Honey, Christopher J; De Jager, Philip L; Bennett, David ANature reviews. Neurology.2016 Jul;27282653
Chromatin Domains: The Unit of Chromosome Organization.Dixon, Jesse R; Gorkin, David U; Ren, BingMolecular cell.2016 Jun 2;27259200
Paf15 expression correlates with rectal cancer prognosis, cell proliferation and radiation response.Yan, Rong; Zhu, Kun; Dang, Chengxue; Lan, Ke; Wang, Haonan; Yuan, Dawei; Chen, Wei; Meltzer, Stephen J; Li, KangOncotarget.2016 Jun 21;27246972
Pediatric Obesity-Related Asthma: The Role of Metabolic Dysregulation.Vijayakanthi, Nandini; Greally, John M; Rastogi, DeepaPediatrics.2016 May;27244776
A Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria.Peters, Jason M; Colavin, Alexandre; Shi, Handuo; Czarny, Tomasz L; Larson, Matthew H; Wong, Spencer; Hawkins, John S; Lu, Candy H S; Koo, Byoung-Mo; Marta, Elizabeth; Shiver, Anthony L; Whitehead, Evan H; Weissman, Jonathan S; Brown, Eric D; Qi, Lei S; Huang, Kerwyn Casey; Gross, Carol ACell.2016 Jun 2;27238023
The next generation of therapeutics for chronic kidney disease.Breyer, Matthew D; Susztak, KatalinNature reviews. Drug discovery.2016 08;27230798
CRISPR/Cas9 for Human Genome Engineering and Disease Research.Xiong, Xin; Chen, Meng; Lim, Wendell A; Zhao, Dehua; Qi, Lei SAnnual review of genomics and human genetics.2016 Aug 31;27216776
Coregulation of tandem duplicate genes slows evolution of subfunctionalization in mammals.Lan, Xun; Pritchard, Jonathan KScience (New York, N.Y.).2016 May 20;27199432
All Things in Moderation: Prevention of Intestinal Adenomas by DNA Hypomethylation.Lee, Kwang-Ho; Laird, Peter WCancer prevention research (Philadelphia, Pa.).2016 Jul;27190044
Diabetic kidney disease.Thomas, Merlin C; Brownlee, Michael; Susztak, Katalin; Sharma, Kumar; Jandeleit-Dahm, Karin A M; Zoungas, Sophia; Rossing, Peter; Groop, Per-Henrik; Cooper, Mark ENature reviews. Disease primers.2015 07 30;27188921
Activation of the pluripotency factor OCT4 in smooth muscle cells is atheroprotective.Cherepanova, Olga A; Gomez, Delphine; Shankman, Laura S; Swiatlowska, Pamela; Williams, Jason; Sarmento, Olga F; Alencar, Gabriel F; Hess, Daniel L; Bevard, Melissa H; Greene, Elizabeth S; Murgai, Meera; Turner, Stephen D; Geng, Yong-Jian; Bekiranov, Stefan; Connelly, Jessica J; Tomilin, Alexey; Owens, Gary KNature medicine.2016 06;27183216
The Association Between Genetic Polymorphism rs703842 in CYP27B1 and Multiple Sclerosis: A Meta-Analysis.Jiang, Tao; Li, Lizhuo; Wang, Ying; Zhao, Chuntao; Yang, Jundong; Ma, Dexuan; Guan, Yanlei; Zhao, Dan; Bao, Yijun; Wang, Yunjie; Yang, JingyunMedicine.2016 May;27175669
Lamellipodia are crucial for haptotactic sensing and response.King, Samantha J; Asokan, Sreeja B; Haynes, Elizabeth M; Zimmerman, Seth P; Rotty, Jeremy D; Alb Jr, James G; Tagliatela, Alicia; Blake, Devon R; Lebedeva, Irina P; Marston, Daniel; Johnson, Heath E; Parsons, Maddy; Sharpless, Norman E; Kuhlman, Brian; Haugh, Jason M; Bear, James EJournal of cell science.2016 Jun 15;27173494
Lactase nonpersistence is directed by DNA-variation-dependent epigenetic aging.Labrie, Viviane; Buske, Orion J; Oh, Edward; Jeremian, Richie; Ptak, Carolyn; Gasi?nas, Giedrius; Maleckas, Almantas; Petereit, R?ta; ?virbliene, Aida; Adamonis, K?stutis; Kriukien?, Edita; Koncevi?ius, Karolis; Gordevi?ius, Juozas; Nair, Akhil; Zhang, Aiping; Ebrahimi, Sasha; Oh, Gabriel; ?ik?nys, Virginijus; Kup?inskas, Limas; Brudno, Michael; Petronis, ArturasNature structural & molecular biology.2016 06;27159559
Alterations to chromatin in intestinal macrophages link IL-10 deficiency to inappropriate inflammatory responses.Simon, Jeremy M; Davis, James P; Lee, Saangyoung E; Schaner, Matthew R; Gipson, Gregory R; Weiser, Matthew; Sartor, R Balfour; Herfarth, Hans H; Rahbar, Reza; Sadiq, Timothy S; Koruda, Mark J; McGovern, Dermot P; Lieb, Jason D; Mohlke, Karen L; Furey, Terrence S; Sheikh, Shehzad ZEuropean journal of immunology.2016 08;27159132
Novel method to ascertain chromatin accessibility at specific genomic loci from frozen brain homogenates and laser capture microdissected defined cells.Delvaux, Elaine; Mastroeni, Diego; Nolz, Jennifer; Coleman, Paul DNeuroepigenetics.2016 Jun;27158594
Mechanisms and Disease Associations of Haplotype-Dependent Allele-Specific DNA Methylation.Do, Catherine; Lang, Charles F; Lin, John; Darbary, Huferesh; Krupska, Izabela; Gaba, Aulona; Petukhova, Lynn; Vonsattel, Jean-Paul; Gallagher, Mary P; Goland, Robin S; Clynes, Raphael A; Dwork, Andrew; Kral, John G; Monk, Catherine; Christiano, Angela M; Tycko, BenjaminAmerican journal of human genetics.2016 May 05;27153397
Developmental signalling pathways in renal fibrosis: the roles of Notch, Wnt and Hedgehog.Edeling, Maria; Ragi, Grace; Huang, Shizheng; Pavenstädt, Hermann; Susztak, KatalinNature reviews. Nephrology.2016 07;27140856
Taking Stock of Regulatory Variation.Maurano, Matthew T; Stamatoyannopoulos, John ACell systems.2015 Jul 29;27135686
Methylation of histone H4 lysine 20 by PR-Set7 ensures the integrity of late replicating sequence domains in Drosophila.Li, Yulong; Armstrong, Robin L; Duronio, Robert J; MacAlpine, David MNucleic acids research.2016 Sep 06;27131378
Nucleosome breathing and remodeling constrain CRISPR-Cas9 function.Isaac, R Stefan; Jiang, Fuguo; Doudna, Jennifer A; Lim, Wendell A; Narlikar, Geeta J; Almeida, RicardoeLife.2016 Apr 28;27130520
Epigenetic assimilation in the aging human brain.Oh, Gabriel; Ebrahimi, Sasha; Wang, Sun-Chong; Cortese, Rene; Kaminsky, Zachary A; Gottesman, Irving I; Burke, James R; Plassman, Brenda L; Petronis, ArtGenome biology.2016 Apr 28;27122015
Vitamin D and androgen receptor-targeted therapy for triple-negative breast cancer.Thakkar, A; Wang, B; Picon-Ruiz, M; Buchwald, P; Ince, Tan ABreast cancer research and treatment.2016 May;27120467
Metabolic Regulation of Gene Expression by Histone Lysine ?-Hydroxybutyrylation.Xie, Zhongyu; Zhang, Di; Chung, Dongjun; Tang, Zhanyun; Huang, He; Dai, Lunzhi; Qi, Shankang; Li, Jingya; Colak, Gozde; Chen, Yue; Xia, Chunmei; Peng, Chao; Ruan, Haibin; Kirkey, Matt; Wang, Danli; Jensen, Lindy M; Kwon, Oh Kwang; Lee, Sangkyu; Pletcher, Scott D; Tan, Minjia; Lombard, David B; White, Kevin P; Zhao, Hongyu; Li, Jia; Roeder, Robert G; Yang, Xiaoyong; Zhao, YingmingMolecular cell.2016 04 21;27105115
Light-induced nuclear export reveals rapid dynamics of epigenetic modifications.Yumerefendi, Hayretin; Lerner, Andrew Michael; Zimmerman, Seth Parker; Hahn, Klaus; Bear, James E; Strahl, Brian D; Kuhlman, BrianNature chemical biology.2016 Jun;27089030
Allele-Skewed DNA Modification in the Brain: Relevance to a Schizophrenia GWAS.Gagliano, Sarah A; Ptak, Carolyn; Mak, Denise Y F; Shamsi, Mehrdad; Oh, Gabriel; Knight, Joanne; Boutros, Paul C; Petronis, ArturasAmerican journal of human genetics.2016 May 05;27087318
Evolution of Epigenetic Regulation in Vertebrate Genomes.Lowdon, Rebecca F; Jang, Hyo Sik; Wang, TingTrends Genet2016 MayP:269-8327080453
Podocytes: the Weakest Link in Diabetic Kidney Disease?Lin, Jamie S; Susztak, KatalinCurrent diabetes reports.2016 May;27053072
Mitotic bookmarking: maintaining post-mitotic reprogramming of transcription reactivation.Lodhi, Niraj; Ji, Yingbiao; Tulin, AlexeiCurrent molecular biology reports.2016 Mar;27042400
Methylation profiles in peripheral blood CD4+ lymphocytes versus brain: The relation to Alzheimer's disease pathology.Yu, Lei; Chibnik, Lori B; Yang, Jingyun; McCabe, Cristin; Xu, Jishu; Schneider, Julie A; De Jager, Philip L; Bennett, David AAlzheimer's & dementia : the journal of the Alzheimer's Association.2016 Mar 24;27016692
Versatile protein tagging in cells with split fluorescent protein.Kamiyama, Daichi; Sekine, Sayaka; Barsi-Rhyne, Benjamin; Hu, Jeffrey; Chen, Baohui; Gilbert, Luke A; Ishikawa, Hiroaki; Leonetti, Manuel D; Marshall, Wallace F; Weissman, Jonathan S; Huang, BoNature communications.2016;26988139
Nucleosomes impede Cas9 access to DNA in vivo and in vitro.Horlbeck, Max A; Witkowsky, Lea B; Guglielmi, Benjamin; Replogle, Joseph M; Gilbert, Luke A; Villalta, Jacqueline E; Torigoe, Sharon E; Tjian, Robert; Weissman, Jonathan SeLife.2016;26987018
The Association Between Genetic Variants in the Dopaminergic System and Posttraumatic Stress Disorder: A Meta-Analysis.Li, Lizhuo; Bao, Yijun; He, Songbai; Wang, Gang; Guan, Yanlei; Ma, Dexuan; Wang, Pengfei; Huang, Xiaolong; Tao, Shanwei; Zhang, Dewei; Liu, Qiwen; Wang, Yunjie; Yang, JingyunMedicine.2016 Mar;26986136
Occupational cognitive requirements and late-life cognitive aging.Pool, Lindsay R; Weuve, Jennifer; Wilson, Robert S; Bültmann, Ute; Evans, Denis A; Mendes de Leon, Carlos FNeurology.2016 04 12;26984944
CRISPR Interference Efficiently Induces Specific and Reversible Gene Silencing in Human iPSCs.Mandegar, Mohammad A; Huebsch, Nathaniel; Frolov, Ekaterina B; Shin, Edward; Truong, Annie; Olvera, Michael P; Chan, Amanda H; Miyaoka, Yuichiro; Holmes, Kristin; Spencer, C Ian; Judge, Luke M; Gordon, David E; Eskildsen, Tilde V; Villalta, Jacqueline E; Horlbeck, Max A; Gilbert, Luke A; Krogan, Nevan J; Sheikh, Søren P; Weissman, Jonathan S; Qi, Lei S; So, Po-Lin; Conklin, Bruce RCell stem cell.2016 Apr 7;26971820
Constructing 3D interaction maps from 1D epigenomes.Zhu, Yun; Chen, Zhao; Zhang, Kai; Wang, Mengchi; Medovoy, David; Whitaker, John W; Ding, Bo; Li, Nan; Zheng, Lina; Wang, WeiNature communications.2016;26960733
Molecular circuitry of stem cell fate in skeletal muscle regeneration, ageing and disease.Almada, Albert E; Wagers, Amy JNature reviews. Molecular cell biology.2016 May;26956195
YAP Induces Human Naive Pluripotency.Qin, Han; Hejna, Miroslav; Liu, Yanxia; Percharde, Michelle; Wossidlo, Mark; Blouin, Laure; Durruthy-Durruthy, Jens; Wong, Priscilla; Qi, Zhongxia; Yu, Jingwei; Qi, Lei S; Sebastiano, Vittorio; Song, Jun S; Ramalho-Santos, MiguelCell reports.2016 Mar 15;26947063
Mapping of Variable DNA Methylation Across Multiple Cell Types Defines a Dynamic Regulatory Landscape of the Human Genome.Gu, Junchen; Stevens, Michael; Xing, Xiaoyun; Li, Daofeng; Zhang, Bo; Payton, Jacqueline E; Oltz, Eugene M; Jarvis, James N; Jiang, Kaiyu; Cicero, Theodore; Costello, Joseph F; Wang, TingG3 (Bethesda)2016P:973-8626888867
Variation in 5-hydroxymethylcytosine across human cortex and cerebellum.Lunnon, Katie; Hannon, Eilis; Smith, Rebecca G; Dempster, Emma; Wong, Chloe; Burrage, Joe; Troakes, Claire; Al-Sarraj, Safa; Kepa, Agnieszka; Schalkwyk, Leonard; Mill, JonathanGenome biology.2016 Feb 16;26883014
Epigenetic regulation of mitochondrial function in neurodegenerative disease: New insights from advances in genomic technologies.Devall, Matthew; Roubroeks, Janou; Mill, Jonathan; Weedon, Michael; Lunnon, KatieNeuroscience letters.2016 Jun 20;26876477
Long non-coding antisense RNA KRT7-AS is activated in gastric cancers and supports cancer cell progression by increasing KRT7 expression.Huang, B; Song, J H; Cheng, Y; Abraham, J M; Ibrahim, S; Sun, Z; Ke, X; Meltzer, S JOncogene.2016 Feb 15;26876208
Antigen clasping by two antigen-binding sites of an exceptionally specific antibody for histone methylation.Hattori, Takamitsu; Lai, Darson; Dementieva, Irina S; Montaño, Sherwin P; Kurosawa, Kohei; Zheng, Yupeng; Akin, Louesa R; ?wist-Rosowska, Kalina M; Grzybowski, Adrian T; Koide, Akiko; Krajewski, Krzysztof; Strahl, Brian D; Kelleher, Neil L; Ruthenburg, Alexander J; Koide, ShoheiProceedings of the National Academy of Sciences of the United States of America.2016 Feb 23;26862167
ATR-101 disrupts mitochondrial functions in adrenocortical carcinoma cells and in vivo.Cheng, Yunhui; Kerppola, Raili Emilia; Kerppola, Tom KlausEndocrine-related cancer.2016 Apr;26843528
H3K4 tri-methylation breadth at transcription start sites impacts the transcriptome of systemic lupus erythematosus.Zhang, Zhe; Shi, Lihua; Dawany, Noor; Kelsen, Judith; Petri, Michelle A; Sullivan, Kathleen EClinical epigenetics.2016;26839600
Genetic associations at 53 loci highlight cell types and biological pathways relevant for kidney function.Pattaro, Cristian (see original citation for additional authors)Nature communications.2016 Jan 21;26831199
Editing the epigenome: technologies for programmable transcription and epigenetic modulation.Thakore, Pratiksha I; Black, Joshua B; Hilton, Isaac B; Gersbach, Charles ANature methods.2016 Feb;26820547
A full Bayesian partition model for identifying hypo- and hyper-methylated loci from single nucleotide resolution sequencing data.Wang, Henan; He, Chong; Kushwaha, Garima; Xu, Dong; Qiu, JingBMC bioinformatics.2016;26818685
Dissecting structure-activity-relationships of crebinostat: Brain penetrant HDAC inhibitors for neuroepigenetic regulation.Ghosh, Balaram; Zhao, Wen-Ning; Reis, Surya A; Patnaik, Debasis; Fass, Daniel M; Tsai, Li-Huei; Mazitschek, Ralph; Haggarty, Stephen JBioorganic & medicinal chemistry letters.2016 Feb 15;26804233
Interaction of methylation-related genetic variants with circulating fatty acids on plasma lipids: a meta-analysis of 7 studies and methylation analysis of 3 studies in the Cohorts for Heart and Aging Research in Genomic Epidemiology consortium.Ma, Yiyi; Follis, Jack L; Smith, Caren E; Tanaka, Toshiko; Manichaikul, Ani W; Chu, Audrey Y; Samieri, Cecilia; Zhou, Xia; Guan, Weihua; Wang, Lu; Biggs, Mary L; Chen, Yii-Der I; Hernandez, Dena G; Borecki, Ingrid; Chasman, Daniel I; Rich, Stephen S; Ferrucci, Luigi; Irvin, Marguerite Ryan; Aslibekyan, Stella; Zhi, Degui; Tiwari, Hemant K; Claas, Steven A; Sha, Jin; Kabagambe, Edmond K; Lai, Chao-Qiang; Parnell, Laurence D; Lee, Yu-Chi; Amouyel, Philippe; Lambert, Jean-Charles; Psaty, Bruce M; King, Irena B; Mozaffarian, Dariush; McKnight, Barbara; Bandinelli, Stefania; Tsai, Michael Y; Ridker, Paul M; Ding, Jingzhong; Mstat, Kurt Lohmant; Liu, Yongmei; Sotoodehnia, Nona; Barberger-Gateau, Pascale; Steffen, Lyn M; Siscovick, David S; Absher, Devin; Arnett, Donna K; Ordovás, José M; Lemaitre, Rozenn NThe American journal of clinical nutrition.2016 Feb;26791180
Tissue-specific patterns of allelically-skewed DNA methylation.Marzi, Sarah J; Meaburn, Emma L; Dempster, Emma L; Lunnon, Katie; Paya-Cano, Jose L; Smith, Rebecca G; Volta, Manuela; Troakes, Claire; Schalkwyk, Leonard C; Mill, JonathanEpigenetics.2016;26786711
Sox9-Positive Progenitor Cells Play a Key Role in Renal Tubule Epithelial Regeneration in Mice.Kang, Hyun Mi; Huang, Shizheng; Reidy, Kimberly; Han, Seung Hyeok; Chinga, Frank; Susztak, KatalinCell reports.2016 Feb 2;861-7126776520
Expanding the CRISPR imaging toolset with Staphylococcus aureus Cas9 for simultaneous imaging of multiple genomic loci.Chen, Baohui; Hu, Jeffrey; Almeida, Ricardo; Liu, Harrison; Balakrishnan, Sanjeev; Covill-Cooke, Christian; Lim, Wendell A; Huang, BoNucleic acids research.2016 Jan 5;26740581
Mathematical modelling of transcriptional heterogeneity identifies novel markers and subpopulations in complex tissues.Wang, Niya; Hoffman, Eric P; Chen, Lulu; Chen, Li; Zhang, Zhen; Liu, Chunyu; Yu, Guoqiang; Herrington, David M; Clarke, Robert; Wang, YueScientific reports.2016;26739359
Genetic and Epigenetic Variation, but Not Diet, Shape the Sperm Methylome.Shea, Jeremy M; Serra, Ryan W; Carone, Benjamin R; Shulha, Hennady P; Kucukural, Alper; Ziller, Michael J; Vallaster, Markus P; Gu, Hongcang; Tapper, Andrew R; Gardner, Paul D; Meissner, Alexander; Garber, Manuel; Rando, Oliver JDevelopmental cell.2015 Dec 21;26702833
Epithelial Plasticity versus EMT in Kidney Fibrosis.Huang, Shizheng; Susztak, KatalinTrends in molecular medicine.2016 Jan;26700490
Genome editing: the end of the beginning.Doudna, Jennifer A; Gersbach, Charles AGenome biology.2015;29226700220
PET Neurochemical Imaging Modes.Placzek, Michael S; Zhao, Wenjun; Wey, Hsiao-Ying; Morin, Thomas M; Hooker, Jacob MSeminars in nuclear medicine.2016 Jan;20-726687854
Epigenetic age of the pre-frontal cortex is associated with neuritic plaques, amyloid load, and Alzheimer's disease related cognitive functioning.Levine, Morgan E; Lu, Ake T; Bennett, David A; Horvath, SteveAging.2015 Dec;26684672
Development of a Fluorinated Class-I HDAC Radiotracer Reveals Key Chemical Determinants of Brain Penetrance.Strebl, Martin G; Wang, Changning; Schroeder, Frederick A; Placzek, Michael S; Wey, Hsiao-Ying; Van de Bittner, Genevieve C; Neelamegam, Ramesh; Hooker, Jacob MACS chemical neuroscience.2016 05 18;26675505
Beyond editing: repurposing CRISPR-Cas9 for precision genome regulation and interrogation.Dominguez, Antonia A; Lim, Wendell A; Qi, Lei SNature reviews. Molecular cell biology.2016 Jan;26670017
Down-Regulated Phosphoglycerate Kinase 1 Expression Is Associated With Poor Prognosis in Patients With Gallbladder Cancer.Lu, Wei; Gao, Jian; Yang, Jingyun; Cao, Yang; Jiang, Lin; Li, Maolan; Zhang, Yijian; Zhou, Jian; Liu, YingbinMedicine.2015 Dec;26656369
In Utero Cigarette Smoke Affects Allergic Airway Disease But Does Not Alter the Lung Methylome.Eyring, Kenneth R; Pedersen, Brent S; Yang, Ivana V; Schwartz, David APloS one.2015;26642056
Genome-wide Association Studies Identify Genetic Loci Associated With Albuminuria in Diabetes.Teumer, Alexander; Tin, Adrienne; Sorice, Rossella; Gorski, Mathias; Yeo, Nan Cher; Chu, Audrey Y; Li, Man; Li, Yong; Mijatovic, Vladan; Ko, Yi-An; Taliun, Daniel; Luciani, Alessandro; Chen, Ming-Huei; Yang, Qiong; Foster, Meredith C; Olden, Matthias; Hiraki, Linda T; Tayo, Bamidele O; Fuchsberger, Christian; Dieffenbach, Aida Karina; Shuldiner, Alan R; Smith, Albert V; Zappa, Allison M; Lupo, Antonio; Kollerits, Barbara; Ponte, Belen; Stengel, Bénédicte; Krämer, Bernhard K; Paulweber, Bernhard; Mitchell, Braxton D; Hayward, Caroline; Helmer, Catherine; Meisinger, Christa; Gieger, Christian; Shaffer, Christian M; Müller, Christian; Langenberg, Claudia; Ackermann, Daniel; Siscovick, David; DCCT/EDIC; Boerwinkle, Eric; Kronenberg, Florian; Ehret, Georg B; Homuth, Georg; Waeber, Gerard; Navis, Gerjan; Gambaro, Giovanni; Malerba, Giovanni; Eiriksdottir, Gudny; Li, Guo; Wichmann, H Erich; Grallert, Harald; Wallaschofski, Henri; Völzke, Henry; Brenner, Herrmann; Kramer, Holly; Mateo Leach, I; Rudan, Igor; Hillege, Hans L; Beckmann, Jacques S; Lambert, Jean Charles; Luan, Jian'an; Zhao, Jing Hua; Chalmers, John; Coresh, Josef; Denny, Joshua C; Butterbach, Katja; Launer, Lenore J; Ferrucci, Luigi; Kedenko, Lyudmyla; Haun, Margot; Metzger, Marie; Woodward, Mark; Hoffman, Matthew J; Nauck, Matthias; Waldenberger, Melanie; Pruijm, Menno; Bochud, Murielle; Rheinberger, Myriam; Verweij, Niek; Wareham, Nicholas J; Endlich, Nicole; Soranzo, Nicole; Polasek, Ozren; van der Harst, Pim; Pramstaller, Peter Paul; Vollenweider, Peter; Wild, Philipp S; Gansevoort, Ron T; Rettig, Rainer; Biffar, Reiner; Carroll, Robert J; Katz, Ronit; Loos, Ruth J F; Hwang, Shih-Jen; Coassin, Stefan; Bergmann, Sven; Rosas, Sylvia E; Stracke, Sylvia; Harris, Tamara B; Corre, Tanguy; Zeller, Tanja; Illig, Thomas; Aspelund, Thor; Tanaka, Toshiko; Lendeckel, Uwe; Völker, Uwe; Gudnason, Vilmundur; Chouraki, Vincent; Koenig, Wolfgang; Kutalik, Zoltan; O'Connell, Jeffrey R; Parsa, Afshin; Heid, Iris M; Paterson, Andrew D; de Boer, Ian H; Devuyst, Olivier; Lazar, Jozef; Endlich, Karlhans; Susztak, Katalin; Tremblay, Johanne; Hamet, Pavel; Jacob, Howard J; Böger, Carsten A; Fox, Caroline S; Pattaro, Cristian; Köttgen, AnnaDiabetes.2016 Mar;26631737
Methylation QTLs in the developing brain and their enrichment in schizophrenia risk loci.Hannon, Eilis; Spiers, Helen; Viana, Joana; Pidsley, Ruth; Burrage, Joe; Murphy, Therese M; Troakes, Claire; Turecki, Gustavo; O'Donovan, Michael C; Schalkwyk, Leonard C; Bray, Nicholas J; Mill, JonathanNature neuroscience.2016 Jan;48-5426619357
Trans effects of chromosome aneuploidies on DNA methylation patterns in human Down syndrome and mouse models.Mendioroz, Maite; Do, Catherine; Jiang, Xiaoling; Liu, Chunhong; Darbary, Huferesh K; Lang, Charles F; Lin, John; Thomas, Anna; Abu-Amero, Sayeda; Stanier, Philip; Temkin, Alexis; Yale, Alexander; Liu, Meng-Min; Li, Yang; Salas, Martha; Kerkel, Kristi; CaGenome biology.2015;26326607552
A Systematic Approach to Identify Candidate Transcription Factors that Control Cell Identity.D'Alessio, Ana C; Fan, Zi Peng; Wert, Katherine J; Baranov, Petr; Cohen, Malkiel A; Saini, Janmeet S; Cohick, Evan; Charniga, Carol; Dadon, Daniel; Hannett, Nancy M; Young, Michael J; Temple, Sally; Jaenisch, Rudoff; Lee, Tong Ihn; Young, Richard AStem cell reports.2015 Nov 10;763-7526603904
Monoacylglycerol lipase (MGLL) polymorphism rs604300 interacts with childhood adversity to predict cannabis dependence symptoms and amygdala habituation: Evidence from an endocannabinoid system-level analysis.Carey, Caitlin E; Agrawal, Arpana; Zhang, Bo; Conley, Emily D; Degenhardt, Louisa; Heath, Andrew C; Li, Daofeng; Lynskey, Michael T; Martin, Nicholas G; Montgomery, Grant W; Wang, Ting; Bierut, Laura J; Hariri, Ahmad R; Nelson, Elliot C; Bogdan, RyanJournal of abnormal psychology.2015 Nov;860-7726595473
The Association Between Apolipoprotein E and Functional Outcome After Traumatic Brain Injury: A Meta-Analysis.Li, Lizhuo; Bao, Yijun; He, Songbai; Wang, Gang; Guan, Yanlei; Ma, Dexuan; Wu, Rile; Wang, Pengfei; Huang, Xiaolong; Tao, Shanwei; Liu, Qiwen; Wang, Yunjie; Yang, JingyunMedicine.2015 Nov;e202826579811
CpG methylation differences between neurons and glia are highly conserved from mouse to human.Kessler, Noah J; Van Baak, Timothy E; Baker, Maria S; Laritsky, Eleonora; Coarfa, Cristian; Waterland, Robert AHuman molecular genetics.2016 Jan 15;26566671
Identification of differentially methylated loci using wavelet-based functional mixed models.Lee, Wonyul; Morris, Jeffrey SBioinformatics (Oxford, England).2016 Mar 01;26559505
Aberrant intracellular localization of H3k4me3 demonstrates an early epigenetic phenomenon in Alzheimer's disease.Mastroeni, Diego; Delvaux, Elaine; Nolz, Jennifer; Tan, Yuyan; Grover, Andrew; Oddo, Salvatore; Coleman, Paul DNeurobiology of aging.2015 Dec;3121-926553823
Complete haplotype phasing of the MHC and KIR loci with targeted HaploSeq.Selvaraj, Siddarth; Schmitt, Anthony D; Dixon, Jesse R; Ren, BingBMC genomics.2015;90026541200
ETO family protein Mtgr1 mediates Prdm14 functions in stem cell maintenance and primordial germ cell formation.Nady, Nataliya; Gupta, Ankit; Ma, Ziyang; Swigut, Tomek; Koide, Akiko; Koide, Shohei; Wysocka, JoannaeLife.2015;26523391
Perinatal deiodinase 2 expression in hepatocytes defines epigenetic susceptibility to liver steatosis and obesity.Fonseca, Tatiana L; Fernandes, Gustavo W; McAninch, Elizabeth A; Bocco, Barbara M L C; Abdalla, Sherine M; Ribeiro, Miriam O; Mohácsik, Petra; Fekete, Csaba; Li, Daofeng; Xing, Xiaoyun; Wang, Ting; Gereben, Balázs; Bianco, Antonio CProceedings of the National Academy of Sciences of the United States of America.2015 Nov 10;14018-2326508642
Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo.Maurano, Matthew T; Haugen, Eric; Sandstrom, Richard; Vierstra, Jeff; Shafer, Anthony; Kaul, Rajinder; Stamatoyannopoulos, John ANature genetics.2015 Dec;26502339
Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements.Thakore, Pratiksha I; D'Ippolito, Anthony M; Song, Lingyun; Safi, Alexias; Shivakumar, Nishkala K; Kabadi, Ami M; Reddy, Timothy E; Crawford, Gregory E; Gersbach, Charles ANature methods.2015 Dec;1143-926501517
ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo.Zentner, Gabriel E; Kasinathan, Sivakanthan; Xin, Beibei; Rohs, Remo; Henikoff, StevenNature communications.2015;873326490019
Psychiatric genetics in China: achievements and challenges.Liu, C; Saffen, D; Schulze, T G; Burmeister, M; Sham, P C; Yao, Y-G; Kuo, P-H; Chen, C; An, Y; Dai, J; Yue, W; Li, M X; Xue, H; Su, B; Chen, L; Shi, Y; Qiao, M; Liu, T; Xia, K; Chan, R C KMolecular psychiatry.2016 Jan;26481319
Methylomic analysis of monozygotic twins discordant for childhood psychotic symptoms.Fisher, Helen L; Murphy, Therese M; Arseneault, Louise; Caspi, Avshalom; Moffitt, Terrie E; Viana, Joana; Hannon, Eilis; Pidsley, Ruth; Burrage, Joe; Dempster, Emma L; Wong, Chloe C Y; Pariante, Carmine M; Mill, JonathanEpigenetics.2015;26479702
Correlating in Vitro and in Vivo Activities of Light-Inducible Dimers: A Cellular Optogenetics Guide.Hallett, Ryan A; Zimmerman, Seth P; Yumerefendi, Hayretin; Bear, James E; Kuhlman, BrianACS synthetic biology.2016 Jan 15;53-6426474029
Ribosome profiling reveals the what, when, where and how of protein synthesis.Brar, Gloria A; Weissman, Jonathan SNature reviews. Molecular cell biology.2015 Nov;26465719
Integrated miRNA profiling and bioinformatics analyses reveal potential causative miRNAs in gastric adenocarcinoma.Zhang, Xiaojing; Peng, Yin; Jin, Zhe; Huang, Weiling; Cheng, Yulan; Liu, Yudan; Feng, Xianling; Yang, Mengting; Huang, Yong; Zhao, Zhenfu; Wang, Liang; Wei, Yanjie; Fan, Xinmin; Zheng, Duo; Meltzer, Stephen JOncotarget.2015 Oct 20;32878-8926460735
Interindividual methylomic variation across blood, cortex, and cerebellum: implications for epigenetic studies of neurological and neuropsychiatric phenotypes.Hannon, Eilis; Lunnon, Katie; Schalkwyk, Leonard; Mill, JonathanEpigenetics.2015;26457534
Parent-of-Origin Effects of the APOB Gene on Adiposity in Young Adults.Hochner, Hagit; Allard, Catherine; Granot-Hershkovitz, Einat; Chen, Jinbo; Sitlani, Colleen M; Sazdovska, Sandra; Lumley, Thomas; McKnight, Barbara; Rice, Kenneth; Enquobahrie, Daniel A; Meigs, James B; Kwok, Pui; Hivert, Marie-France; Borecki, Ingrid B; Gomez, Felicia; Wang, Ting; van Duijn, Cornelia; Amin, Najaf; Rotter, Jerome I; Stamatoyannopoulos, John; Meiner, Vardiella; Manor, Orly; Dupuis, Josée; Friedlander, Yechiel; Siscovick, David SPLoS genetics.2015 Oct;e100557326451733
Dual Roles of RNF2 in Melanoma Progression.Rai, Kunal; Akdemir, Kadir C; Kwong, Lawrence N; Fiziev, Petko; Wu, Chang-Jiun; Keung, Emily Z; Sharma, Sneha; Samant, Neha S; Williams, Maura; Axelrad, Jacob B; Shah, Amiksha; Yang, Dong; Grimm, Elizabeth A; Barton, Michelle C; Milton, Denai R; Heffernan, Timothy P; Horner, James W; Ekmekcioglu, Suhendan; Lazar, Alexander J; Ernst, Jason; Chin, LyndaCancer discovery.2015 Dec;26450788
Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes.Yao, Lijing; Berman, Benjamin P; Farnham, Peggy JCritical reviews in biochemistry and molecular biology.2015;550-7326446758
Design, Assembly, and Characterization of TALE-Based Transcriptional Activators and Repressors.Thakore, Pratiksha I; Gersbach, Charles AMethods in molecular biology (Clifton, N.J.).2016;71-8826443215
The Development of TALE Nucleases for Biotechnology.Ousterout, David G; Gersbach, Charles AMethods in molecular biology (Clifton, N.J.).2016;27-4226443211
Monocyte enhancers are highly altered in systemic lupus erythematosus.Shi, Lihua; Zhang, Zhe; Song, Li; Leung, Yiu Tak; Petri, Michelle A; Sullivan, Kathleen EEpigenomics.2015;921-3526442457
Animal Models of Chemical Carcinogenesis: Driving Breakthroughs in Cancer Research for 100 Years.Kemp, Christopher JCold Spring Harbor protocols.2015 Oct;865-7426430259
Enabling functional genomics with genome engineering.Hilton, Isaac B; Gersbach, Charles AGenome research.2015 Oct;1442-5526430154
TQ inhibits hepatocellular carcinoma growth in vitro and in vivo via repression of Notch signaling.Ke, Xiquan; Zhao, Yan; Lu, Xinlan; Wang, Zhe; Liu, Yuanyuan; Ren, Mudan; Lu, Guifang; Zhang, Dan; Sun, Zhenguo; Xu, Zhipeng; Song, Jee Hoon; Cheng, Yulan; Meltzer, Stephen J; He, ShuixiangOncotarget.2015 Oct 20;32610-2126416455
methylPipe and compEpiTools: a suite of R packages for the integrative analysis of epigenomics data.Kishore, Kamal; de Pretis, Stefano; Lister, Ryan; Morelli, Marco J; Bianchi, Valerio; Amati, Bruno; Ecker, Joseph R; Pelizzola, MattiaBMC bioinformatics.2015;31326415965
Structure and specificity of the RNA-guided endonuclease Cas9 during DNA interrogation, target binding and cleavage.Josephs, Eric A; Kocak, D Dewran; Fitzgibbon, Christopher J; McMenemy, Joshua; Gersbach, Charles A; Marszalek, Piotr ENucleic acids research.2015 Oct 15;8924-4126384421
The New State of the Art: Cas9 for Gene Activation and Repression.La Russa, Marie F; Qi, Lei SMolecular and cellular biology.2015 Nov;3800-926370509
Bacterial CRISPR: accomplishments and prospects.Peters, Jason M; Silvis, Melanie R; Zhao, Dehua; Hawkins, John S; Gross, Carol A; Qi, Lei SCurrent opinion in microbiology.2015 Oct;121-626363124
Labelling and optical erasure of synaptic memory traces in the motor cortex.Hayashi-Takagi, Akiko; Yagishita, Sho; Nakamura, Mayumi; Shirai, Fukutoshi; Wu, Yi I; Loshbaugh, Amanda L; Kuhlman, Brian; Hahn, Klaus M; Kasai, HaruoNature.2015 Sep 17;26352471
BACOM2.0 facilitates absolute normalization and quantification of somatic copy number alterations in heterogeneous tumor.Fu, Yi; Yu, Guoqiang; Levine, Douglas A; Wang, Niya; Shih, Ie-Ming; Zhang, Zhen; Clarke, Robert; Wang, YueScientific reports.2015;1395526350498
Impact of a cis-associated gene expression SNP on chromosome 20q11.22 on bipolar disorder susceptibility, hippocampal structure and cognitive performance.Li, Ming; Luo, Xiong-Jian; Landén, Mikael; Bergen, Sarah E; Hultman, Christina M; Li, Xiao; Zhang, Wen; Yao, Yong-Gang; Zhang, Chen; Liu, Jiewei; Mattheisen, Manuel; Cichon, Sven; Mühleisen, Thomas W; Degenhardt, Franziska A; Nöthen, Markus M; Schulze, Thomas G; Grigoroiu-Serbanescu, Maria; Li, Hao; Fuller, Chris K; Chen, Chunhui; Dong, Qi; Chen, Chuansheng; Jamain, Stéphane; Leboyer, Marion; Bellivier, Frank; Etain, Bruno; Kahn, Jean-Pierre; Henry, Chantal; Preisig, Martin; Kutalik, Zoltán; Castelao, Enrique; Wright, Adam; Mitchell, Philip B; Fullerton, Janice M; Schofield, Peter R; Montgomery, Grant W; Medland, Sarah E; Gordon, Scott D; Martin, Nicholas G; MooDS Consortium; Swedish Bipolar Study Group; Rietschel, Marcella; Liu, Chunyu; Kleinman, Joel E; Hyde, Thomas M; Weinberger, Daniel R; Su, BingThe British journal of psychiatry : the journal of mental science.2016 Feb;26338991
DNA Methylation of the Aryl Hydrocarbon Receptor Repressor Associations With Cigarette Smoking and Subclinical Atherosclerosis.Reynolds, Lindsay M; Wan, Ma; Ding, Jingzhong; Taylor, Jackson R; Lohman, Kurt; Su, Dan; Bennett, Brian D; Porter, Devin K; Gimple, Ryan; Pittman, Gary S; Wang, Xuting; Howard, Timothy D; Siscovick, David; Psaty, Bruce M; Shea, Steven; Burke, Gregory L; JCirculation. Cardiovascular genetics.2015 Oct;707-1626307030
Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions.Grubert, Fabian; Zaugg, Judith B; Kasowski, Maya; Ursu, Oana; Spacek, Damek V; Martin, Alicia R; Greenside, Peyton; Srivas, Rohith; Phanstiel, Doug H; Pekowska, Aleksandra; Heidari, Nastaran; Euskirchen, Ghia; Huber, Wolfgang; Pritchard, Jonathan K; BustaCell.2015 Aug 27;1051-6526300125
Spatiotemporal control of estrogen-responsive transcription in ER?-positive breast cancer cells.Hsu, P-Y; Hsu, H-K; Hsiao, T-H; Ye, Z; Wang, E; Profit, A L; Jatoi, I; Chen, Y; Kirma, N B; Jin, V X; Sharp, Z D; Huang, T H-MOncogene.2016 05 05;26300005
Life course socioeconomic status and DNA methylation in genes related to stress reactivity and inflammation: The multi-ethnic study of atherosclerosis.Needham, Belinda L; Smith, Jennifer A; Zhao, Wei; Wang, Xu; Mukherjee, Bhramar; Kardia, Sharon L R; Shively, Carol A; Seeman, Teresa E; Liu, Yongmei; Diez Roux, Ava VEpigenetics.2015;958-6926295359
Notch1 and Notch2 in Podocytes Play Differential Roles During Diabetic Nephropathy Development.Sweetwyne, Mariya T; Gruenwald, Antje; Niranjan, Thiruvur; Nishinakamura, Ryuichi; Strobl, Lothar J; Susztak, KatalinDiabetes.2015 Dec;26293507
LINE-1 expression and retrotransposition in Barrett's esophagus and esophageal carcinoma.Doucet-O'Hare, Tara T; Rodi?, Nemanja; Sharma, Reema; Darbari, Isha; Abril, Gabriela; Choi, Jungbin A; Young Ahn, Ji; Cheng, Yulan; Anders, Robert A; Burns, Kathleen H; Meltzer, Stephen J; Kazazian Jr, Haig HProceedings of the National Academy of Sciences of the United States of America.2015 Sep 1;E4894-90026283398
Systematic chromatin state comparison of epigenomes associated with diverse properties including sex and tissue type.Yen, Angela; Kellis, ManolisNature communications.2015;797326282110
Comparative analyses of CTCF and BORIS occupancies uncover two distinct classes of CTCF binding genomic regions.Pugacheva, Elena M; Rivero-Hinojosa, Samuel; Espinoza, Celso A; Méndez-Catalá, Claudia Fabiola; Kang, Sungyun; Suzuki, Teruhiko; Kosaka-Suzuki, Natsuki; Robinson, Susan; Nagarajan, Vijayaraj; Ye, Zhen; Boukaba, Abdelhalim; Rasko, John E J; Strunnikov, AleGenome biology.2015;16126268681
Role of DNA Methylation in Modulating Transcription Factor Occupancy.Maurano, Matthew T; Wang, Hao; John, Sam; Shafer, Anthony; Canfield, Theresa; Lee, Kristen; Stamatoyannopoulos, John ACell reports.2015 Aug 18;1184-9526257180
Evidence of CNIH3 involvement in opioid dependence.Nelson, E C; Agrawal, A; Heath, A C; Bogdan, R; Sherva, R; Zhang, B; Al-Hasani, R; Bruchas, M R; Chou, Y-L; Demers, C H; Carey, C E; Conley, E D; Fakira, A K; Farrer, L A; Goate, A; Gordon, S; Henders, A K; Hesselbrock, V; Kapoor, M; Lynskey, M T; Madden, P A F; Moron, J A; Rice, J P; Saccone, N L; Schwab, S G; Shand, F L; Todorov, A A; Wallace, L; Wang, T; Wray, N R; Zhou, X; Degenhardt, L; Martin, N G; Hariri, A R; Kranzler, H R; Gelernter, J; Bierut, L J; Clark, D J; Montgomery, G WMolecular psychiatry.2015 Aug 4;26239289
Klotho: a tumor suppressor and modulator of the Wnt/?-catenin pathway in human hepatocellular carcinoma.Tang, Xiaowei; Wang, Yun; Fan, Zhining; Ji, Guozhong; Wang, Min; Lin, Jie; Huang, Shu; Meltzer, Stephen JLaboratory investigation; a journal of technical methods and pathology.2016 Feb;26237271
Identification of Global DNA Methylation Signatures in Glioblastoma-Derived Cancer Stem Cells.Lee, Eun-Joon; Rath, Prakash; Liu, Jimei; Ryu, Dungsung; Pei, Lirong; Noonepalle, Satish K; Shull, Austin Y; Feng, Qi; Litofsky, N Scott; Miller, Douglas C; Anthony, Douglas C; Kirk, Mark D; Laterra, John; Deng, Libin; Xin, Hong-Bo; Wang, Xinguo; Choi, Jeong-Hyeon; Shi, HuidongJournal of genetics and genomics = Yi chuan xue bao.2015 Jul 20;355-7126233891
Epigenetic Signatures as Biomarkers of Exposure.Ladd-Acosta, ChristineCurrent environmental health reports.2015 Jun;117-2526231361
Heat shock factor 1 induces cancer stem cell phenotype in breast cancer cell lines.Wang, Bin; Lee, Chung-Wei; Witt, Abigail; Thakkar, Ankita; Ince, Tan ABreast cancer research and treatment.2015 Aug;57-6626223813
Synthetic biology approaches to engineer T cells.Wu, Chia-Yung; Rupp, Levi J; Roybal, Kole T; Lim, Wendell ACurrent opinion in immunology.2015 Aug;123-3026218616
CRISPR-ERA: a comprehensive design tool for CRISPR-mediated gene editing, repression and activation.Liu, Honglei; Wei, Zheng; Dominguez, Antonia; Li, Yanda; Wang, Xiaowo; Qi, Lei SBioinformatics (Oxford, England).2015 Nov 15;3676-826209430
Alternative preprocessing of RNA-Sequencing data in The Cancer Genome Atlas leads to improved analysis results.Rahman, Mumtahena; Jackson, Laurie K; Johnson, W Evan; Li, Dean Y; Bild, Andrea H; Piccolo, Stephen RBioinformatics (Oxford, England).2015 Nov 15;3666-7226209429
Endotoxin tolerance in monocytes can be mitigated by ?2-interferon.Shi, Lihua; Song, Li; Maurer, Kelly; Sharp, James; Zhang, Zhe; Sullivan, Kathleen EJournal of leukocyte biology.2015 Oct;651-926206900
Genomic analysis reveals distinct mechanisms and functional classes of SOX10-regulated genes in melanocytes.Fufa, Temesgen D; Harris, Melissa L; Watkins-Chow, Dawn E; Levy, Denise; Gorkin, David U; Gildea, Derek E; Song, Lingyun; Safi, Alexias; Crawford, Gregory E; Sviderskaya, Elena V; Bennett, Dorothy C; Mccallion, Andrew S; Loftus, Stacie K; Pavan, William JHuman molecular genetics.2015 Oct 1;5433-5026206884
Quantitative assessment of RNA-protein interactions with high-throughput sequencing-RNA affinity profiling.Ozer, Abdullah; Tome, Jacob M; Friedman, Robin C; Gheba, Dan; Schroth, Gary P; Lis, John TNature protocols.2015 Aug;1212-3326182240
MicroRNAs Classify Different Disease Behavior Phenotypes of Crohn's Disease and May Have Prognostic Utility.Peck, Bailey C E; Weiser, Matthew; Lee, Saangyoung E; Gipson, Gregory R; Iyer, Vishal B; Sartor, Ryan B; Herfarth, Hans H; Long, Millie D; Hansen, Jonathan J; Isaacs, Kim L; Trembath, Dimitri G; Rahbar, Reza; Sadiq, Timothy S; Furey, Terrence S; SethupathInflammatory bowel diseases.2015 Sep;2178-8726164662
Alterations of a Cellular Cholesterol Metabolism Network Are a Molecular Feature of Obesity-Related Type 2 Diabetes and Cardiovascular Disease.Ding, Jingzhong; Reynolds, Lindsay M; Zeller, Tanja; Müller, Christian; Lohman, Kurt; Nicklas, Barbara J; Kritchevsky, Stephen B; Huang, Zhiqing; de la Fuente, Alberto; Soranzo, Nicola; Settlage, Robert E; Chuang, Chia-Chi; Howard, Timothy; Xu, Ning; GoodDiabetes.2015 Oct;3464-7426153245
Alzheimer's loci: epigenetic associations and interaction with genetic factors.Chibnik, Lori B; Yu, Lei; Eaton, Matthew L; Srivastava, Gyan; Schneider, Julie A; Kellis, Manolis; Bennett, David A; De Jager, Philip LAnnals of clinical and translational neurology.2015 Jun;636-4726125039
Chromosomes. A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation.Minajigi, Anand; Froberg, John E; Wei, Chunyao; Sunwoo, Hongjae; Kesner, Barry; Colognori, David; Lessing, Derek; Payer, Bernhard; Boukhali, Myriam; Haas, Wilhelm; Lee, Jeannie TScience (New York, N.Y.).2015 Jul 17;26089354
Population dynamics of cancer cells with cell state conversions.Zhou, Da; Wu, Dingming; Li, Zhe; Qian, Minping; Zhang, Michael QQuantitative biology.2013 Sep;201-20826085954
Control of Protein Activity and Cell Fate Specification via Light-Mediated Nuclear Translocation.Yumerefendi, Hayretin; Dickinson, Daniel J; Wang, Hui; Zimmerman, Seth P; Bear, James E; Goldstein, Bob; Hahn, Klaus; Kuhlman, BrianPloS one.2015;e012844326083500
Characterization of twenty-five ovarian tumour cell lines that phenocopy primary tumours.Ince, Tan A; Sousa, Aurea D; Jones, Michelle A; Harrell, J Chuck; Agoston, Elin S; Krohn, Marit; Selfors, Laura M; Liu, Wenbin; Chen, Ken; Yong, Mao; Buchwald, Peter; Wang, Bin; Hale, Katherine S; Cohick, Evan; Sergent, Petra; Witt, Abigail; Kozhekbaeva, Nature communications.2015;741926080861
High Precision DNA Modification Analysis of HCG9 in Major Psychosis.Pal, Mrinal; Ebrahimi, Sasha; Oh, Gabriel; Khare, Tarang; Zhang, Aiping; Kaminsky, Zachary A; Wang, Sun-Chong; Petronis, ArturasSchizophrenia bulletin.2016 Jan;26078387
Differential DNA methylation identified in the blood and retina of AMD patients.Oliver, Verity F; Jaffe, Andrew E; Song, Jin; Wang, Guohua; Zhang, Pingwu; Branham, Kari E; Swaroop, Anand; Eberhart, Charles G; Zack, Donald J; Qian, Jiang; Merbs, Shannath LEpigenetics.2015;698-70726067391
Irregular 24-hour activity rhythms and the metabolic syndrome in older adults.Sohail, Shahmir; Yu, Lei; Bennett, David A; Buchman, Aron S; Lim, Andrew S PChronobiology international.2015;802-1326061588
Deletion of Lkb1 in Renal Tubular Epithelial Cells Leads to CKD by Altering Metabolism.Han, Seung Hyeok; Malaga-Dieguez, Laura; Chinga, Frank; Kang, Hyun Mi; Tao, Jianling; Reidy, Kimberly; Susztak, KatalinJournal of the American Society of Nephrology : JASN.2016 Feb;26054542
Phosphorus-32, a clinically available drug, inhibits cancer growth by inducing DNA double-strand breakage.Cheng, Yulan; Kiess, Ana P; Herman, Joseph M; Pomper, Martin G; Meltzer, Stephen J; Abraham, John MPloS one.2015;e012815226030880
Human body epigenome maps reveal noncanonical DNA methylation variation.Schultz, Matthew D; He, Yupeng; Whitaker, John W; Hariharan, Manoj; Mukamel, Eran A; Leung, Danny; Rajagopal, Nisha; Nery, Joseph R; Urich, Mark A; Chen, Huaming; Lin, Shin; Lin, Yiing; Jung, Inkyung; Schmitt, Anthony D; Selvaraj, Siddarth; Ren, Bing; Sejnowski, Terrence J; Wang, Wei; Ecker, Joseph RNature.2015 Jul 9;212-626030523
GATA factors in endocrine neoplasia.Pihlajoki, Marjut; Färkkilä, Anniina; Soini, Tea; Heikinheimo, Markku; Wilson, David BMolecular and cellular endocrinology.2016 Feb 05;26027919
Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators.Polstein, Lauren R; Perez-Pinera, Pablo; Kocak, D Dewran; Vockley, Christopher M; Bledsoe, Peggy; Song, Lingyun; Safi, Alexias; Crawford, Gregory E; Reddy, Timothy E; Gersbach, Charles AGenome research.2015 Aug;1158-6926025803
Association of DNA methylation in the brain with age in older persons is confounded by common neuropathologies.Yang, Jingyun; Yu, Lei; Gaiteri, Christopher; Srivastava, Gyan P; Chibnik, Lori B; Leurgans, Sue E; Schneider, Julie A; Meissner, Alexander; De Jager, Philip L; Bennett, David AThe international journal of biochemistry & cell biology.2015 May 21;26003740
Inferring regulatory element landscapes and transcription factor networks from cancer methylomes.Yao, Lijing; Shen, Hui; Laird, Peter W; Farnham, Peggy J; Berman, Benjamin PGenome biology.2015;10525994056
Targeted Transcriptional Repression in Bacteria Using CRISPR Interference (CRISPRi).Hawkins, John S; Wong, Spencer; Peters, Jason M; Almeida, Ricardo; Qi, Lei SMethods in molecular biology (Clifton, N.J.).2015;349-6225981485
Longitudinal epigenetic and gene expression profiles analyzed by three-component analysis reveal down-regulation of genes involved in protein translation in human aging.Jung, Marc; Jin, Seung-Gi; Zhang, Xiaoying; Xiong, Wenying; Gogoshin, Grigoriy; Rodin, Andrei S; Pfeifer, Gerd PNucleic acids research.2015 Sep 3;e10025977295
Cognitive aging in older Black and White persons.Wilson, Robert S; Capuano, Ana W; Sytsma, Joel; Bennett, David A; Barnes, Lisa LPsychology and aging.2015 Jun;279-8525961876
The evolving understanding of the contribution of lipid metabolism to diabetic kidney disease.Stadler, Krisztian; Goldberg, Ira J; Susztak, KatalinCurrent diabetes reports.2015 Jul;4025957525
Chemosensory receptor specificity and regulation.Dalton, Ryan P; Lomvardas, StavrosAnnual review of neuroscience.2015 Jul 8;331-4925938729
A unique chromatin complex occupies young ?-satellite arrays of human centromeres.Henikoff, Jorja G; Thakur, Jitendra; Kasinathan, Sivakanthan; Henikoff, StevenScience advances.2015 Feb 12;25927077
Prenatal mercury concentration is associated with changes in DNA methylation at TCEANC2 in newborns.Bakulski, Kelly M; Lee, HwaJin; Feinberg, Jason I; Wells, Ellen M; Brown, Shannon; Herbstman, Julie B; Witter, Frank R; Halden, Rolf U; Caldwell, Kathleen; Mortensen, Mary Ellen; Jaffe, Andrew E; Moye Jr, John; Caulfield, Laura E; Pan, Yi; Goldman, Lynn RInternational journal of epidemiology.2015 Aug;1249-6225906783
Transcriptomic profiles of aging in purified human immune cells.Reynolds, Lindsay M; Ding, Jingzhong; Taylor, Jackson R; Lohman, Kurt; Soranzo, Nicola; de la Fuente, Alberto; Liu, Tie Fu; Johnson, Craig; Barr, R Graham; Register, Thomas C; Donohue, Kathleen M; Talor, Monica V; Cihakova, Daniela; Gu, Charles; Divers, Jasmin; Siscovick, David; Burke, Gregory; Post, Wendy; Shea, Steven; Jacobs Jr, David R; Hoeschele, Ina; McCall, Charles E; Kritchevsky, Stephen B; Herrington, David; Tracy, Russell P; Liu, YongmeiBMC genomics.2015;33325898983
MIRA-seq for DNA methylation analysis of CpG islands.Jung, Marc; Kadam, Swati; Xiong, Wenying; Rauch, Tibor A; Jin, Seung-Gi; Pfeifer, Gerd PEpigenomics.2015 Apr 17;12-Jan25881900
Paternal sperm DNA methylation associated with early signs of autism risk in an autism-enriched cohort.Feinberg, Jason I; Bakulski, Kelly M; Jaffe, Andrew E; Tryggvadottir, Rakel; Brown, Shannon C; Goldman, Lynn R; Croen, Lisa A; Hertz-Picciotto, Irva; Newschaffer, Craig J; Daniele Fallin, M; Feinberg, Andrew PInternational journal of epidemiology.2015 Aug;1199-21025878217
Regulation of chromatin accessibility and Zic binding at enhancers in the developing cerebellum.Frank, Christopher L; Liu, Fang; Wijayatunge, Ranjula; Song, Lingyun; Biegler, Matthew T; Yang, Marty G; Vockley, Christopher M; Safi, Alexias; Gersbach, Charles A; Crawford, Gregory E; West, Anne ENature neuroscience.2015 May;647-5625849986
Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers.Hilton, Isaac B; D'Ippolito, Anthony M; Vockley, Christopher M; Thakore, Pratiksha I; Crawford, Gregory E; Reddy, Timothy E; Gersbach, Charles ANature biotechnology.2015 May;510-725849900
Genes with de novo mutations are shared by four neuropsychiatric disorders discovered from NPdenovo database.Li, Jinchen; Cai, Tao; Jiang, Yi; Chen, Huiqian; He, Xin; Chen, Chao; Li, Xianfeng; Shao, Qianzhi; Ran, Xia; Li, Zhongshan; Xia, Kun; Liu, Chunyu; Sun, Zhong Sheng; Wu, JinyuMolecular psychiatry.2016 Feb;25849321
An anti-silencer- and SATB1-dependent chromatin hub regulates Rag1 and Rag2 gene expression during thymocyte development.Hao, Bingtao; Naik, Abani Kanta; Watanabe, Akiko; Tanaka, Hirokazu; Chen, Liang; Richards, Hunter W; Kondo, Motonari; Taniuchi, Ichiro; Kohwi, Yoshinori; Kohwi-Shigematsu, Terumi; Krangel, Michael SThe Journal of experimental medicine.2015 May 4;809-2425847946
Epigenetic priming of enhancers predicts developmental competence of hESC-derived endodermal lineage intermediates.Wang, Allen; Yue, Feng; Li, Yan; Xie, Ruiyu; Harper, Thomas; Patel, Nisha A; Muth, Kayla; Palmer, Jeffrey; Qiu, Yunjiang; Wang, Jinzhao; Lam, Dieter K; Raum, Jeffrey C; Stoffers, Doris A; Ren, Bing; Sander, MaikeCell stem cell.2015 Apr 2;386-9925842977
Genome Modification in Enterococcus faecalis OG1RF Assessed by Bisulfite Sequencing and Single-Molecule Real-Time Sequencing.Huo, Wenwen; Adams, Hannah M; Zhang, Michael Q; Palmer, Kelli LJournal of bacteriology.2015 Jun;1939-5125825433
Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells.Liao, Jing; Karnik, Rahul; Gu, Hongcang; Ziller, Michael J; Clement, Kendell; Tsankov, Alexander M; Akopian, Veronika; Gifford, Casey A; Donaghey, Julie; Galonska, Christina; Pop, Ramona; Reyon, Deepak; Tsai, Shengdar Q; Mallard, William; Joung, J Keith; Rinn, John L; Gnirke, Andreas; Meissner, AlexanderNature genetics.2015 May;469-7825822089
Induction of hematopoietic and endothelial cell program orchestrated by ETS transcription factor ER71/ETV2.Liu, Fang; Li, Daofeng; Yu, Yik Yeung Lawrence; Kang, Inyoung; Cha, Min-Ji; Kim, Ju Young; Park, Changwon; Watson, Dennis K; Wang, Ting; Choi, KyungheeEMBO reports.2015 May;654-6925802403
DNA methylation and childhood asthma in the inner city.Yang, Ivana V; Pedersen, Brent S; Liu, Andrew; O'Connor, George T; Teach, Stephen J; Kattan, Meyer; Misiak, Rana Tawil; Gruchalla, Rebecca; Steinbach, Suzanne F; Szefler, Stanley J; Gill, Michelle A; Calatroni, Agustin; David, Gloria; Hennessy, Corinne E;The Journal of allergy and clinical immunology.2015 Jul;69-8025769910
Kinetic Analysis and Quantification of [¹¹C]Martinostat for in Vivo HDAC Imaging of the Brain.Wey, Hsiao-Ying; Wang, Changning; Schroeder, Frederick A; Logan, Jean; Price, Julie C; Hooker, Jacob MACS chemical neuroscience.2015 May 20;708-1525768025
Physical activity, motor function, and white matter hyperintensity burden in healthy older adults.Fleischman, Debra A; Yang, Jingyun; Arfanakis, Konstantinos; Arvanitakis, Zoe; Leurgans, Sue E; Turner, Arlener D; Barnes, Lisa L; Bennett, David A; Buchman, Aron SNeurology.2015 Mar 31;1294-30025762710
An epigenome-wide association study of total serum immunoglobulin E concentration.Liang, Liming; Willis-Owen, Saffron A G; Laprise, Catherine; Wong, Kenny C C; Davies, Gwyneth A; Hudson, Thomas J; Binia, Aristea; Hopkin, Julian M; Yang, Ivana V; Grundberg, Elin; Busche, Stephan; Hudson, Marie; Ronnblom, Lars; Pastinen, Tomi M; Schwartz, David A; Lathrop, G Mark; Moffatt, Miriam F; Cookson, William O C MNature.2015 Apr 30;670-425707804
Anthracyclines induce double-strand DNA breaks at active gene promoters.Yang, Fan; Kemp, Christopher J; Henikoffa, StevenMutation research.2015 Mar;15-Sep25705119
Developmental enhancers revealed by extensive DNA methylome maps of zebrafish early embryos.Lee, Hyung Joo; Lowdon, Rebecca F; Maricque, Brett; Zhang, Bo; Stevens, Michael; Li, Daofeng; Johnson, Stephen L; Wang, TingNature communications.2015 Feb 20;631525697895
PRIMEGENSw3: a web-based tool for high-throughput primer and probe design.Kushwaha, Garima; Srivastava, Gyan Prakash; Xu, DongMethods in molecular biology (Clifton, N.J.).2015;181-9925697661
Cell-of-origin chromatin organization shapes the mutational landscape of cancer.Polak, Paz; Karli?, Rosa; Koren, Amnon; Thurman, Robert; Sandstrom, Richard; Lawrence, Michael S; Reynolds, Alex; Rynes, Eric; Vlahovi?ek, Kristian; Stamatoyannopoulos, John A; Sunyaev, Shamil RNature.2015 Feb 19;360-425693567
Integrative analysis of haplotype-resolved epigenomes across human tissues.Leung, Danny; Jung, Inkyung; Rajagopal, Nisha; Schmitt, Anthony; Selvaraj, Siddarth; Lee, Ah Young; Yen, Chia-An; Lin, Shin; Lin, Yiing; Qiu, Yunjiang; Xie, Wei; Yue, Feng; Hariharan, Manoj; Ray, Pradipta; Kuan, Samantha; Edsall, Lee; Yang, Hongbo; Chi, Neil C; Zhang, Michael Q; Ecker, Joseph R; Ren, BingNature.2015 Feb 19;350-425693566
Transcription factor binding dynamics during human ES cell differentiation.Tsankov, Alexander M; Gu, Hongcang; Akopian, Veronika; Ziller, Michael J; Donaghey, Julie; Amit, Ido; Gnirke, Andreas; Meissner, AlexanderNature.2015 Feb 19;344-925693565
Chromatin architecture reorganization during stem cell differentiation.Dixon, Jesse R; Jung, Inkyung; Selvaraj, Siddarth; Shen, Yin; Antosiewicz-Bourget, Jessica E; Lee, Ah Young; Ye, Zhen; Kim, Audrey; Rajagopal, Nisha; Xie, Wei; Diao, Yarui; Liang, Jing; Zhao, Huimin; Lobanenkov, Victor V; Ecker, Joseph R; Thomson, James A; Ren, BingNature.2015 Feb 19;331-625693564
Integrative analysis of 111 reference human epigenomes.Roadmap Epigenomics Consortium; Kundaje, Anshul; Meuleman, Wouter; Ernst, Jason; Bilenky, Misha; Yen, Angela; Heravi-Moussavi, Alireza; Kheradpour, Pouya; Zhang, Zhizhuo; Wang, Jianrong; Ziller, Michael J; Amin, Viren; Whitaker, John W; Schultz, Matthew D; Ward, Lucas D; Sarkar, Abhishek; Quon, Gerald; Sandstrom, Richard S; Eaton, Matthew L; Wu, Yi-Chieh; Pfenning, Andreas R; Wang, Xinchen; Claussnitzer, Melina; Liu, Yaping; Coarfa, Cristian; Harris, R Alan; Shoresh, Noam; Epstein, Charles B; Gjoneska, Elizabeta; Leung, Danny; Xie, Wei; Hawkins, R David; Lister, Ryan; Hong, Chibo; Gascard, Philippe; Mungall, Andrew J; Moore, Richard; Chuah, Eric; Tam, Angela; Canfield, Theresa K; Hansen, R Scott; Kaul, Rajinder; Sabo, Peter J; Bansal, Mukul S; Carles, Annaick; Dixon, Jesse R; Farh, Kai-How; Feizi, Soheil; Karlic, Rosa; Kim, Ah-Ram; Kulkarni, Ashwinikumar; Li, Daofeng; Lowdon, Rebecca; Elliott, GiNell; Mercer, Tim R; Neph, Shane J; Onuchic, Vitor; Polak, Paz; Rajagopal, Nisha; Ray, Pradipta; Sallari, Richard C; Siebenthall, Kyle T; Sinnott-Armstrong, Nicholas A; Stevens, Michael; Thurman, Robert E; Wu, Jie; Zhang, Bo; Zhou, Xin; Beaudet, Arthur E; Boyer, Laurie A; De Jager, Philip L; Farnham, Peggy J; Fisher, Susan J; Haussler, David; Jones, Steven J M; Li, Wei; Marra, Marco A; McManus, Michael T; Sunyaev, Shamil; Thomson, James A; Tlsty, Thea D; Tsai, Li-Huei; Wang, Wei; Waterland, Robert A; Zhang, Michael Q; Chadwick, Lisa H; Bernstein, Bradley E; Costello, Joseph F; Ecker, Joseph R; Hirst, Martin; Meissner, Alexander; Milosavljevic, Aleksandar; Ren, Bing; Stamatoyannopoulos, John A; Wang, Ting; Kellis, ManolisNature.2015 Feb 19;317-3025693563
Epigenomic footprints across 111 reference epigenomes reveal tissue-specific epigenetic regulation of lincRNAs.Amin, Viren; Harris, R Alan; Onuchic, Vitor; Jackson, Andrew R; Charnecki, Tim; Paithankar, Sameer; Lakshmi Subramanian, Sai; Riehle, Kevin; Coarfa, Cristian; Milosavljevic, AleksandarNature communications.2015;637025691256
Intermediate DNA methylation is a conserved signature of genome regulation.Elliott, GiNell; Hong, Chibo; Xing, Xiaoyun; Zhou, Xin; Li, Daofeng; Coarfa, Cristian; Bell, Robert J A; Maire, Cecile L; Ligon, Keith L; Sigaroudinia, Mahvash; Gascard, Philippe; Tlsty, Thea D; Harris, R Alan; Schalkwyk, Leonard C; Bilenky, Misha; Mill, Jonathan; Farnham, Peggy J; Kellis, Manolis; Marra, Marco A; Milosavljevic, Aleksandar; Hirst, Martin; Stormo, Gary D; Wang, Ting; Costello, Joseph FNature communications.2015;636325691127
Epigenetic and transcriptional determinants of the human breast.Gascard, Philippe; Bilenky, Misha; Sigaroudinia, Mahvash; Zhao, Jianxin; Li, Luolan; Carles, Annaick; Delaney, Allen; Tam, Angela; Kamoh, Baljit; Cho, Stephanie; Griffith, Malachi; Chu, Andy; Robertson, Gordon; Cheung, Dorothy; Li, Irene; Heravi-Moussavi, Alireza; Moksa, Michelle; Mingay, Matthew; Hussainkhel, Angela; Davis, Brad; Nagarajan, Raman P; Hong, Chibo; Echipare, Lorigail; O'Geen, Henriette; Hangauer, Matthew J; Cheng, Jeffrey B; Neel, Dana; Hu, Donglei; McManus, Michael T; Moore, Richard; Mungall, Andrew; Ma, Yussanne; Plettner, Patrick; Ziv, Elad; Wang, Ting; Farnham, Peggy J; Jones, Steven J M; Marra, Marco A; Tlsty, Thea D; Costello, Joseph F; Hirst, MartinNature communications.2015;635125690954
Epigenomic annotation of genetic variants using the Roadmap Epigenome Browser.Zhou, Xin; Li, Daofeng; Zhang, Bo; Lowdon, Rebecca F; Rockweiler, Nicole B; Sears, Renee L; Madden, Pamela A F; Smirnov, Ivan; Costello, Joseph F; Wang, TingNature biotechnology.2015 Apr;345-625690851
Quantitative proteomic analysis of histone modifications.Huang, He; Lin, Shu; Garcia, Benjamin A; Zhao, YingmingChemical reviews.2015 Mar 25;2376-41825688442
Stable oncogenic silencing in vivo by programmable and targeted de novo DNA methylation in breast cancer.Stolzenburg, S; Beltran, A S; Swift-Scanlan, T; Rivenbark, A G; Rashwan, R; Blancafort, POncogene.2015 Feb 16;25684141
Functional Proteomic Analysis of Repressive Histone Methyltransferase Complexes Reveals ZNF518B as a G9A Regulator.Maier, Verena K; Feeney, Caitlin M; Taylor, Jordan E; Creech, Amanda L; Qiao, Jana W; Szanto, Attila; Das, Partha P; Chevrier, Nicholas; Cifuentes-Rojas, Catherine; Orkin, Stuart H; Carr, Steven A; Jaffe, Jacob D; Mertins, Philipp; Lee, Jeannie TMolecular & cellular proteomics : MCP.2015 Jun;1435-4625680957
Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression.Libbrecht, Maxwell W; Ay, Ferhat; Hoffman, Michael M; Gilbert, David M; Bilmes, Jeffrey A; Noble, William StaffordGenome research.2015 Apr;544-5725677182
Interrogating the function of metazoan histones using engineered gene clusters.McKay, Daniel J; Klusza, Stephen; Penke, Taylor J R; Meers, Michael P; Curry, Kaitlin P; McDaniel, Stephen L; Malek, Pamela Y; Cooper, Stephen W; Tatomer, Deirdre C; Lieb, Jason D; Strahl, Brian D; Duronio, Robert J; Matera, A GregoryDevelopmental cell.2015 Feb 9;373-8625669886
Novel antioxidants protect mitochondria from the effects of oligomeric amyloid beta and contribute to the maintenance of epigenome function.Mastroeni, Diego; Khdour, Omar M; Arce, Pablo M; Hecht, Sidney M; Coleman, Paul DACS chemical neuroscience.2015 Apr 15;588-9825668062
A light-inducible CRISPR-Cas9 system for control of endogenous gene activation.Polstein, Lauren R; Gersbach, Charles ANature chemical biology.2015 Mar;198-20025664691
Small molecules enhance CRISPR genome editing in pluripotent stem cells.Yu, Chen; Liu, Yanxia; Ma, Tianhua; Liu, Kai; Xu, Shaohua; Zhang, Yu; Liu, Honglei; La Russa, Marie; Xie, Min; Ding, Sheng; Qi, Lei SCell stem cell.2015 Feb 5;142-725658371
The TMEM106B locus and TDP-43 pathology in older persons without FTLD.Yu, Lei; De Jager, Philip L; Yang, Jingyun; Trojanowski, John Q; Bennett, David A; Schneider, Julie ANeurology.2015 Mar 3;927-3425653292
Genetics and epigenetics of circadian rhythms and their potential roles in neuropsychiatric disorders.Liu, Chunyu; Chung, MichaelNeuroscience bulletin.2015 Feb;141-5925652815
Inhibitor of DNA Binding 4 (ID4) is highly expressed in human melanoma tissues and may function to restrict normal differentiation of melanoma cells.Peretz, Yuval; Wu, Hong; Patel, Shayan; Bellacosa, Alfonso; Katz, Richard APloS one.2015;e011683925642713
Aging and DNA methylation.Jung, Marc; Pfeifer, Gerd PBMC biology.2015;725637097
Interferon regulatory factor 1 and histone H4 acetylation in systemic lupus erythematosus.Leung, Yiu Tak; Shi, Lihua; Maurer, Kelly; Song, Li; Zhang, Zhe; Petri, Michelle; Sullivan, Kathleen EEpigenetics : official journal of the DNA Methylation Society.2015;191-925611806
(Epi)genomics approaches and their applications.Meissner, AlexanderMethods (San Diego, Calif.).2015 Jan 15;2-Jan25597875
Characterization and target identification of a DNA aptamer that labels pluripotent stem cells.Hou, Zhonggang; Meyer, Susanne; Propson, Nicholas E; Nie, Jeff; Jiang, Peng; Stewart, Ron; Thomson, James ACell research.2015 Mar;390-325591927
Blood methylomic signatures of presymptomatic dementia in elderly subjects with type 2 diabetes mellitus.Lunnon, Katie; Smith, Rebecca G; Cooper, Itzik; Greenbaum, Lior; Mill, Jonathan; Beeri, Michal SchnaiderNeurobiology of aging.2015 Mar;1600.e1-425585531
Genomic discovery of potent chromatin insulators for human gene therapy.Liu, Mingdong; Maurano, Matthew T; Wang, Hao; Qi, Heyuan; Song, Chao-Zhong; Navas, Patrick A; Emery, David W; Stamatoyannopoulos, John A; Stamatoyannopoulos, GeorgeNature biotechnology.2015 Feb;198-20325580597
Normal cell-type epigenetics and breast cancer classification: a case study of cell mixture-adjusted analysis of DNA methylation data from tumors.Houseman, Eugene Andrés; Ince, Tan ACancer informatics.2014;25574126
Considering the kinetics of mRNA synthesis in the analysis of the genome and epigenome reveals determinants of co-transcriptional splicing.Davis-Turak, Jeremy C; Allison, Karmel; Shokhirev, Maxim N; Ponomarenko, Petr; Tsimring, Lev S; Glass, Christopher K; Johnson, Tracy L; Hoffmann, AlexanderNucleic acids research.2015 Jan;699-70725541195
Dissecting neural differentiation regulatory networks through epigenetic footprinting.Ziller, Michael J; Edri, Reuven; Yaffe, Yakey; Donaghey, Julie; Pop, Ramona; Mallard, William; Issner, Robbyn; Gifford, Casey A; Goren, Alon; Xing, Jeffrey; Gu, Hongcang; Cacchiarelli, Davide; Tsankov, Alexander M; Epstein, Charles; Rinn, John L; Mikkelsen, Tarjei S; Kohlbacher, Oliver; Gnirke, Andreas; Bernstein, Bradley E; Elkabetz, Yechiel; Meissner, AlexanderNature.2015 Feb 19;355-925533951
Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds.Zalatan, Jesse G; Lee, Michael E; Almeida, Ricardo; Gilbert, Luke A; Whitehead, Evan H; La Russa, Marie; Tsai, Jordan C; Weissman, Jonathan S; Dueber, John E; Qi, Lei S; Lim, Wendell ACell.2015 Jan 15;339-5025533786
The mitochondrial epigenome: a role in Alzheimer's disease?Devall, Matthew; Mill, Jonathan; Lunnon, KatieEpigenomics.2014;665-7525531259
A common set of distinct features that characterize noncoding RNAs across multiple species.Hu, Long; Di, Chao; Kai, Mingxuan; Yang, Yu-Cheng T; Li, Yang; Qiu, Yunjiang; Hu, Xihao; Yip, Kevin Y; Zhang, Michael Q; Lu, Zhi JohnNucleic acids research.2015 Jan;104-1425505163
Identification of nuclear hormone receptor pathways causing insulin resistance by transcriptional and epigenomic analysis.Kang, Sona; Tsai, Linus T; Zhou, Yiming; Evertts, Adam; Xu, Su; Griffin, Michael J; Issner, Robbyn; Whitton, Holly J; Garcia, Benjamin A; Epstein, Charles B; Mikkelsen, Tarjei S; Rosen, Evan DNature cell biology.2015 Jan;44-5625503565
Toying with fate: Redirecting the differentiation of adrenocortical progenitor cells into gonadal-like tissue.Rohrig, Theresa; Pihlajoki, Marjut; Ziegler, Ricarda; Cochran, Rebecca S; Schrade, Anja; Schillebeeckx, Maximiliaan; Mitra, Robi D; Heikinheimo, Markku; Wilson, David BMolecular and cellular endocrinology.2015 Jun 15;165-7725498963
Enhanced MyoD-Induced Transdifferentiation to a Myogenic Lineage by Fusion to a Potent Transactivation Domain.Kabadi, Ami M; Thakore, Pratiksha I; Vockley, Christopher M; Ousterout, David G; Gibson, Tyler M; Guilak, Farshid; Reddy, Timothy E; Gersbach, Charles AACS synthetic biology.2015 Jun 19;689-9925494287
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SORBS1 gene, a new candidate for diabetic nephropathy: results from a multi-stage genome-wide association study in patients with type 1 diabetes.Germain, Marine; Pezzolesi, Marcus G; Sandholm, Niina; McKnight, Amy J; Susztak, Katalin; Lajer, Maria; Forsblom, Carol; Marre, Michel; Parving, Hans-Henrik; Rossing, Peter; Toppila, Iiro; Skupien, Jan; Roussel, Ronan; Ko, Yi-An; Ledo, Nora; Folkersen, Lasse; Civelek, Mete; Maxwell, Alexander P; Tregouet, David-Alexandre; Groop, Per-Henrik; Tarnow, Lise; Hadjadj, SamyDiabetologia.2015 Mar;543-825476525
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Combining MeDIP-seq and MRE-seq to investigate genome-wide CpG methylation.Li, Daofeng; Zhang, Bo; Xing, Xiaoyun; Wang, TingMethods (San Diego, Calif.).2015 Jan 15;29-4025448294
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Identification of schizophrenia-associated loci by combining DNA methylation and gene expression data from whole blood.van Eijk, Kristel R; de Jong, Simone; Strengman, Eric; Buizer-Voskamp, Jacobine E; Kahn, Rene S; Boks, Marco P; Horvath, Steve; Ophoff, Roel AEuropean journal of human genetics : EJHG.2015 Aug;1106-1025424713
Regulatory network decoded from epigenomes of surface ectoderm-derived cell types.Lowdon, Rebecca F; Zhang, Bo; Bilenky, Misha; Mauro, Thea; Li, Daofeng; Gascard, Philippe; Sigaroudinia, Mahvash; Farnham, Peggy J; Bastian, Boris C; Tlsty, Thea D; Marra, Marco A; Hirst, Martin; Costello, Joseph F; Wang, Ting; Cheng, Jeffrey BNature communications.2014;544225421844
Sequencing the cancer methylome.Shull, Austin Y; Noonepalle, Satish K; Lee, Eun-Joon; Choi, Jeong-Hyeon; Shi, HuidongMethods in molecular biology (Clifton, N.J.).2015;627-5125421684
Defective fatty acid oxidation in renal tubular epithelial cells has a key role in kidney fibrosis development.Kang, Hyun Mi; Ahn, Seon Ho; Choi, Peter; Ko, Yi-An; Han, Seung Hyeok; Chinga, Frank; Park, Ae Seo Deok; Tao, Jianling; Sharma, Kumar; Pullman, James; Bottinger, Erwin P; Goldberg, Ira J; Susztak, KatalinNature medicine.2015 Jan;25419705
Proteomics-Based Identification of Differentially Abundant Proteins from Human Keratinocytes Exposed to Arsenic Trioxide.Udensi, Udensi K; Tackett, Alan J; Byrum, Stephanie; Avaritt, Nathan L; Sengupta, Deepanwita; Moreland, Linley W; Tchounwou, Paul B; Isokpehi, Raphael DJournal of proteomics & bioinformatics.2014 Jul;166-17825419056
Interferon regulatory factor 1 marks activated genes and can induce target gene expression in systemic lupus erythematosus.Zhang, Zhe; Shi, Lihua; Song, Li; Ephrem, Elshaddai; Petri, Michelle; Sullivan, Kathleen EArthritis & rheumatology (Hoboken, N.J.).2015 Mar;785-9625418955
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Aberrantly expressed mRNAs and long non-coding RNAs in patients with invasive ductal breast carcinoma: a pilot study.Chen, Xuedong; Yang, Jingyun; Qian, Liyuan; Cao, TianzhuMolecular medicine reports.2015 Mar;2185-9025411894
Principles of regulatory information conservation between mouse and human.Cheng, Yong; Ma, Zhihai; Kim, Bong-Hyun; Wu, Weisheng; Cayting, Philip; Boyle, Alan P; Sundaram, Vasavi; Xing, Xiaoyun; Dogan, Nergiz; Li, Jingjing; Euskirchen, Ghia; Lin, Shin; Lin, Yiing; Visel, Axel; Kawli, Trupti; Yang, Xinqiong; Patacsil, Dorrelyn; KNature.2014 Nov 20;371-525409826
A comparative encyclopedia of DNA elements in the mouse genome.Yue, Feng; Cheng, Yong; Breschi, Alessandra; Vierstra, Jeff; Wu, Weisheng; Ryba, Tyrone; Sandstrom, Richard; Ma, Zhihai; Davis, Carrie; Pope, Benjamin D; Shen, Yin; Pervouchine, Dmitri D; Djebali, Sarah; Thurman, Robert E; Kaul, Rajinder; Rynes, Eric; KirNature.2014 Nov 20;355-6425409824
Specific gene repression by CRISPRi system transferred through bacterial conjugation.Ji, Weiyue; Lee, Derrick; Wong, Eric; Dadlani, Priyanka; Dinh, David; Huang, Verna; Kearns, Kendall; Teng, Sherry; Chen, Susan; Haliburton, John; Heimberg, Graham; Heineike, Benjamin; Ramasubramanian, Anusuya; Stevens, Thomas; Helmke, Kara J; Zepeda, Veronica; Qi, Lei S; Lim, Wendell AACS synthetic biology.2014 Dec 19;929-3125409531
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24-hour rhythms of DNA methylation and their relation with rhythms of RNA expression in the human dorsolateral prefrontal cortex.Lim, Andrew S P; Srivastava, Gyan P; Yu, Lei; Chibnik, Lori B; Xu, Jishu; Buchman, Aron S; Schneider, Julie A; Myers, Amanda J; Bennett, David A; De Jager, Philip LPLoS genetics.2014 Nov;e100479225375876
Association of Brain DNA methylation in SORL1, ABCA7, HLA-DRB5, SLC24A4, and BIN1 with pathological diagnosis of Alzheimer disease.Yu, Lei; Chibnik, Lori B; Srivastava, Gyan P; Pochet, Nathalie; Yang, Jingyun; Xu, Jishu; Kozubek, James; Obholzer, Nikolaus; Leurgans, Sue E; Schneider, Julie A; Meissner, Alexander; De Jager, Philip L; Bennett, David AJAMA neurology.2015 Jan;15-2425365775
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Methylomic profiling of human brain tissue supports a neurodevelopmental origin for schizophrenia.Pidsley, Ruth; Viana, Joana; Hannon, Eilis; Spiers, Helen; Troakes, Claire; Al-Saraj, Safa; Mechawar, Naguib; Turecki, Gustavo; Schalkwyk, Leonard C; Bray, Nicholas J; Mill, JonathanGenome biology.2014;48325347937
The meta-epigenomic structure of purified human stem cell populations is defined at cis-regulatory sequences.Wijetunga, N Ari; Delahaye, Fabien; Zhao, Yong M; Golden, Aaron; Mar, Jessica C; Einstein, Francine H; Greally, John MNature communications.2014;519525327398
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Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation.Gilbert, Luke A; Horlbeck, Max A; Adamson, Britt; Villalta, Jacqueline E; Chen, Yuwen; Whitehead, Evan H; Guimaraes, Carla; Panning, Barbara; Ploegh, Hidde L; Bassik, Michael C; Qi, Lei S; Kampmann, Martin; Weissman, Jonathan SCell.2014 Oct 23;647-6125307932
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Novel markers of gonadectomy-induced adrenocortical neoplasia in the mouse and ferret.Schillebeeckx, Maximiliaan; Pihlajoki, Marjut; Gretzinger, Elisabeth; Yang, Wei; Thol, Franziska; Hiller, Theresa; Lobs, Ann-Kathrin; Rohrig, Theresa; Schrade, Anja; Cochran, Rebecca; Jay, Patrick Y; Heikinheimo, Markku; Mitra, Robi D; Wilson, David BMolecular and cellular endocrinology.2015 Jan 5;122-3025289806
Comparative DNA methylome analysis of endometrial carcinoma reveals complex and distinct deregulation of cancer promoters and enhancers.Zhang, Bo; Xing, XiaoYun; Li, Jing; Lowdon, Rebecca F; Zhou, Yan; Lin, Nan; Zhang, Baoxue; Sundaram, Vasavi; Chiappinelli, Katherine B; Hagemann, Ian S; Mutch, David G; Goodfellow, Paul J; Wang, TingBMC genomics.2014;86825286960
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Normal cell phenotypes of breast epithelial cells provide the foundation of a breast cancer taxonomy.Santagata, Sandro; Ince, Tan AExpert review of anticancer therapy.2014 Dec;1385-925263303
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Functional genomic annotation of genetic risk loci highlights inflammation and epithelial biology networks in CKD.Ledo, Nora; Ko, Yi-An; Park, Ae-Seo Deok; Kang, Hyun-Mi; Han, Sang-Youb; Choi, Peter; Susztak, KatalinJournal of the American Society of Nephrology : JASN.2015 Mar;692-71425231882
Relation of DASH- and Mediterranean-like dietary patterns to cognitive decline in older persons.Tangney, Christy C; Li, Hong; Wang, Yamin; Barnes, Lisa; Schneider, Julie A; Bennett, David A; Morris, Martha CNeurology.2014 Oct 14;1410-625230996
In vivo imaging of histone deacetylases (HDACs) in the central nervous system and major peripheral organs.Wang, Changning; Schroeder, Frederick A; Wey, Hsiao-Ying; Borra, Ronald; Wagner, Florence F; Reis, Surya; Kim, Sung Won; Holson, Edward B; Haggarty, Stephen J; Hooker, Jacob MJournal of medicinal chemistry.2014 Oct 9;7999-800925203558
PET imaging demonstrates histone deacetylase target engagement and clarifies brain penetrance of known and novel small molecule inhibitors in rat.Schroeder, F A; Wang, C; Van de Bittner, G C; Neelamegam, R; Takakura, W R; Karunakaran, A; Wey, H Y; Reis, S A; Gale, J; Zhang, Y L; Holson, E B; Haggarty, S J; Hooker, J MACS chemical neuroscience.2014 Oct 15;1055-6225188794
Effect of breastfeeding on childhood BMI and obesity: the China Family Panel Studies.Jing, Huiquan; Xu, Hongwei; Wan, Junmin; Yang, Yang; Ding, Hua; Chen, Minyan; Li, Lizhuo; Lv, Ping; Hu, Jingwei; Yang, JingyunMedicine.2014 Aug;e5525170931
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Methylomic profiling implicates cortical deregulation of ANK1 in Alzheimer's disease.Lunnon, Katie; Smith, Rebecca; Hannon, Eilis; De Jager, Philip L; Srivastava, Gyan; Volta, Manuela; Troakes, Claire; Al-Sarraj, Safa; Burrage, Joe; Macdonald, Ruby; Condliffe, Daniel; Harries, Lorna W; Katsel, Pavel; Haroutunian, Vahram; Kaminsky, ZacharyNature neuroscience2014 Sep1164-117025129077
Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci.De Jager, Philip L; Srivastava, Gyan; Lunnon, Katie; Burgess, Jeremy; Schalkwyk, Leonard C; Yu, Lei; Eaton, Matthew L; Keenan, Brendan T; Ernst, Jason; McCabe, Cristin; Tang, Anna; Raj, Towfique; Replogle, Joseph; Brodeur, Wendy; Gabriel, Stacey; Chai, High S; Younkin, Curtis; Younkin, Steven G; Zou, Fanggeng; Szyf, Moshe; Epstein, Charles B; Schneider, Julie A; Bernstein, Bradley E; Meissner, Alex; Ertekin-Taner, Nilufer; Chibnik, Lori B; Kellis, Manolis; Mill, Jonathan; Bennett, David ANature neuroscience.2014 Sep;1156-6325129075
Functional kinomics identifies candidate therapeutic targets in head and neck cancer.Moser, Russell; Xu, Chang; Kao, Michael; Annis, James; Lerma, Luisa Angelica; Schaupp, Christopher M; Gurley, Kay E; Jang, In Sock; Biktasova, Asel; Yarbrough, Wendell G; Margolin, Adam A; Grandori, Carla; Kemp, Christopher J; Mendez, EduardoClinical cancer research : an official journal of the American Association for Cancer Research2014 Aug 154274-8825125259
Multiplex CRISPR/Cas9-based genome engineering from a single lentiviral vector.Kabadi, Ami M; Ousterout, David G; Hilton, Isaac B; Gersbach, Charles ANucleic acids research.2014 Oct 29;e14725122746
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Distinct and predictive histone lysine acetylation patterns at promoters, enhancers, and gene bodies.Rajagopal, Nisha; Ernst, Jason; Ray, Pradipta; Wu, Jie; Zhang, Michael; Kellis, Manolis; Ren, BingG3 (Bethesda, Md.).2014 Nov;2051-6325122670
DNA Modification Study of Major Depressive Disorder: Beyond Locus-by-Locus Comparisons.Oh, Gabriel; Wang, Sun-Chong; Pal, Mrinal; Chen, Zheng Fei; Khare, Tarang; Tochigi, Mamoru; Ng, Catherine; Yang, Yeqing A; Kwan, Andrew; Kaminsky, Zachary A; Mill, Jonathan; Gunasinghe, Cerisse; Tackett, Jennifer L; Gottesman, Irving I; Willemsen, Gonneke; de Geus, Eco J C; Vink, Jacqueline M; Slagboom, P Eline; Wray, Naomi R; Heath, Andrew C; Montgomery, Grant W; Turecki, Gustavo; Martin, Nicholas G; Boomsma, Dorret I; McGuffin, Peter; Kustra, Rafal; Petronis, ArtBiological psychiatry.2015 Feb 1;246-5525108803
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A PWWP domain-containing protein targets the NuA3 acetyltransferase complex via histone H3 lysine 36 trimethylation to coordinate transcriptional elongation at coding regions.Gilbert, Tonya M; McDaniel, Stephen L; Byrum, Stephanie D; Cades, Jessica A; Dancy, Blair C R; Wade, Herschel; Tackett, Alan J; Strahl, Brian D; Taverna, Sean DMolecular & cellular proteomics : MCP.2014 Nov;2883-9525104842
New Technologies Provide Quantum Changes in the Scale, Speed, and Success of SELEX Methods and Aptamer Characterization.Ozer, Abdullah; Pagano, John M; Lis, John TMolecular therapy. Nucleic acids.2014;e18325093707
Analysis of interactions between the epigenome and structural mutability of the genome using Genboree Workbench tools.Coarfa, Cristian; Pichot, Christina; Jackson, Andrew; Tandon, Arpit; Amin, Viren; Raghuraman, Sriram; Paithankar, Sameer; Lee, Adrian V; McGuire, Sean E; Milosavljevic, AleksandarBMC bioinformatics.2014;S225080362
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Visualization of the Drosophila dKeap1-CncC interaction on chromatin illumines cooperative, xenobiotic-specific gene activation.Deng, Huai; Kerppola, Tom KDevelopment (Cambridge, England).2014 Aug;3277-8825063457
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A chemical strategy for the cell-based detection of HDAC activity.Diyabalanage, Himashinie V K; Van de Bittner, Genevieve C; Ricq, Emily L; Hooker, Jacob MACS chemical biology2014 Jun 201257-6225056147
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Copy number polymorphisms near SLC2A9 are associated with serum uric acid concentrations.Scharpf, Robert B; Mireles, Lynn; Yang, Qiong; Kottgen, Anna; Ruczinski, Ingo; Susztak, Katalin; Halper-Stromberg, Eitan; Tin, Adrienne; Cristiano, Stephen; Chakravarti, Aravinda; Boerwinkle, Eric; Fox, Caroline S; Coresh, Josef; Linda Kao, Wen HongBMC genetics.2014;8125007794
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Activating human genes with zinc finger proteins, transcription activator-like effectors and CRISPR/Cas9 for gene therapy and regenerative medicine.Gersbach, Charles A; Perez-Pinera, PabloExpert opinion on therapeutic targets2014 Aug835-924917359
Kidney cancer is characterized by aberrant methylation of tissue-specific enhancers that are prognostic for overall survival.Hu, Caroline Y; Mohtat, Davoud; Yu, Yiting; Ko, Yi-An; Shenoy, Niraj; Bhattacharya, Sanchari; Izquierdo, Maria C; Park, Ae Seo Deok; Giricz, Orsolya; Vallumsetla, Nishanth; Gundabolu, Krishna; Ware, Kristin; Bhagat, Tushar D; Suzuki, Masako; Pullman, James; Liu, X Shirley; Greally, John M; Susztak, Katalin; Verma, AmitClinical cancer research : an official journal of the American Association for Cancer Research.2014 Aug 15;4349-6024916699
The 3D Genome in Transcriptional Regulation and Pluripotency.Gorkin, David U; Leung, Danny; Ren, BingCell stem cell2014 Jun 5762-77524905166
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The SLE transcriptome exhibits evidence of chronic endotoxin exposure and has widespread dysregulation of non-coding and coding RNAs.Shi, Lihua; Zhang, Zhe; Yu, Angela M; Wang, Wei; Wei, Zhi; Akhter, Ehtisham; Maurer, Kelly; Costa Reis, Patricia; Song, Li; Petri, Michelle; Sullivan, Kathleen EPloS one2014e9384624796678
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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
Diabetic nephropathy: a national dialogue.Breyer, Matthew D; Coffman, Thomas M; Flessner, Michael F; Fried, Linda F; Harris, Raymond C; Ketchum, Christian J; Kretzler, Matthias; Nelson, Robert G; Sedor, John R; Susztak, Katalin; Kidney Research National Dialogue (KRND)Clinical journal of the American Society of Nephrology : CJASN2013 Sep1603-523788618
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
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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
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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
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Evidence for enhanced telomerase activity in Barrett's esophagus with dysplasia and adenocarcinoma.Merchant, Nipun B; Dutta, Sudhir K; Girotra, Mohit; Arora, Manish; Meltzer, Stephen JAsian Pacific journal of cancer prevention : APJCP2013679-8323621218
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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
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
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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
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
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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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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
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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
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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
Histone acetyltransferase cofactor Trrap maintains self-renewal and restricts differentiation of embryonic stem cells.Sawan, Carla; Hernandez-Vargas, Hector; Murr, Rabih; Lopez, Fabrice; Vaissiere, Thomas; Ghantous, Akram Y; Cuenin, Cyrille; Imbert, Jean; Wang, Zhao-Qi; Ren, Bing; Herceg, ZdenkoStem cells (Dayton, Ohio).2013 May;979-9123362228
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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
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
Genome-wide chromatin state transitions associated with developmental and environmental cues.Zhu, Jiang; Adli, Mazhar; Zou, James Y; Verstappen, Griet; Coyne, Michael; Zhang, Xiaolan; Durham, Timothy; Miri, Mohammad; Deshpande, Vikram; De Jager, Philip L; Bennett, David A; Houmard, Joseph A; Muoio, Deborah M; Onder, Tamer T; Camahort, Ray; Cowan,Cell2013 Jan 31642-5423333102
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The simplest explanation: passive DNA demethylation in PGCs.Smith, Zachary D; Meissner, AlexanderThe EMBO journal2013 Feb 6318-2123299938
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
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
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Functional characterization of piggyBat from the bat Myotis lucifugus unveils an active mammalian DNA transposon.Mitra, Rupak; Li, Xianghong; Kapusta, Aurelie; Mayhew, David; Mitra, Robi D; Feschotte, Cedric; Craig, Nancy LProceedings of the National Academy of Sciences of the United States of America2013 Jan 2234-923248290
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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
'Leveling' the playing field for analyses of single-base resolution DNA methylomes.Schultz, Matthew D; Schmitz, Robert J; Ecker, Joseph RTrends in genetics : TIG2012 Dec583-523131467
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Passaging and colony expansion of human pluripotent stem cells by enzyme-free dissociation in chemically defined culture conditions.Beers, Jeanette; Gulbranson, Daniel R; George, Nicole; Siniscalchi, Lauren I; Jones, Jeffrey; Thomson, James A; Chen, GuokaiNature protocols2012 Nov2029-4023099485
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Progressive degeneration of human neural stem cells caused by pathogenic LRRK2.Liu, Guang-Hui; Qu, Jing; Suzuki, Keiichiro; Nivet, Emmanuel; Li, Mo; Montserrat, Nuria; Yi, Fei; Xu, Xiuling; Ruiz, Sergio; Zhang, Weiqi; Wagner, Ulrich; Kim, Audrey; Ren, Bing; Li, Ying; Goebl, April; Kim, Jessica; Soligalla, Rupa Devi; Dubova, Ilir; ThNature2012 Nov 22603-723075850
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
Broad ranges of affinity and specificity of anti-histone antibodies revealed by a quantitative peptide immunoprecipitation assay.Nishikori, Shingo; Hattori, Takamitsu; Fuchs, Stephen M; Yasui, Norihisa; Wojcik, John; Koide, Akiko; Strahl, Brian D; Koide, ShoheiJournal of molecular biology2012 Dec 14391-923041298
Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling.Boyle, Patrick; Clement, Kendell; Gu, Hongcang; Smith, Zachary D; Ziller, Michael; Fostel, Jennifer L; Holmes, Laurie; Meldrim, Jim; Kelley, Fontina; Gnirke, Andreas; Meissner, AlexanderGenome biology.2012;R9223034176
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Combination therapy: histone deacetylase inhibitors and platinum-based chemotherapeutics for cancer.Diyabalanage, Himashinie V K; Granda, Michael L; Hooker, Jacob MCancer letters2013 Feb 11-823032720
Epigenetic mechanisms and the development of asthma.Yang, Ivana V; Schwartz, David AThe Journal of allergy and clinical immunology2012 Dec1243-5523026498
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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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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
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
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Exploring the role of the epigenome in multiple sclerosis: a window onto cell-specific transcriptional potential.Kaliszewska, Anna; De Jager, Philip LJournal of neuroimmunology.2012 Jul 15;9-Feb22297167
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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
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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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Identification of the putative intestinal stem cell marker doublecortin and CaM kinase-like-1 in Barrett's esophagus and esophageal adenocarcinoma.Vega, Kenneth J; May, Randal; Sureban, Sripathi M; Lightfoot, Stan A; Qu, Dongfeng; Reed, Alessandra; Weygant, Nathaniel; Ramanujam, Rama; Souza, Rhonda; Madhoun, Mohammad; Whorton, Joshua; Anant, Shrikant; Meltzer, Stephen J; Houchen, Courtney WJournal of gastroenterology and hepatology2012 Apr773-8021916995
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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
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
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
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Biotin requirements for DNA damage prevention.Zempleni J, Teixeira DC, Kuroishi T, Cordonier EL, Baier S.Mutat Res2012 May 158-6021871906
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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
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
Long noncoding RNA, polycomb, and the ghosts haunting INK4b-ARF-INK4a expression.Aguilo F, Zhou MM, Walsh MJ.Cancer Res2011 Aug 155365-921828241
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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
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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
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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
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
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
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
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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
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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
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
Opposing roles of FoxP1 and Nfat3 in transcriptional control of cardiomyocyte hypertrophy.Bai, Shoumei; Kerppola, Tom KMolecular and cellular biology2011 Jul3068-8021606195
Epigenetic control of gene expression in the lung.Yang, Ivana V; Schwartz, David AAmerican journal of respiratory and critical care medicine2011 May 151295-30121596832
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
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
Probing the role of HDACs and mechanisms of chromatin-mediated neuroplasticity.Haggarty, Stephen J; Tsai, Li-HueiNeurobiology of learning and memory2011 Jul41-5221545841
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
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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
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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
Toward an integrated genetic and epigenetic approach to Alzheimer's disease.Mill, JonathanNeurobiology of aging2011 Jul1188-9121497948
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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
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
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
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
Tracing the footsteps of glomerular insulin signaling in diabetic kidney disease.Chang, Gene-Yuan; Park, Ae Seo Deok; Susztak, KatalinKidney international2011 Apr802-421451535
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
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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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
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
Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling.Gu, Hongcang; Smith, Zachary D; Bock, Christoph; Boyle, Patrick; Gnirke, Andreas; Meissner, AlexanderNature protocols2011 Apr468-8121412275
Structure and functions of powerful transactivators: VP16, MyoD and FoxA.Hirai, Hiroyuki; Tani, Tetsuya; Kikyo, NobuakiThe International journal of developmental biology20101589-9621404180
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
Genomic mapping of 5-hydroxymethylcytosine in the human brain.Jin, Seung-Gi; Wu, Xiwei; Li, Arthur X; Pfeifer, Gerd PNucleic acids research2011 Jul5015-2421378125
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
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
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
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
Diabetes in pregnancy: glycemia control guidelines and rationale.Karakash, Scarlett D; Einstein, Francine HCurrent opinion in endocrinology, diabetes, and obesity2011 Apr99-10321330917
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Reprogramming of the paternal genome upon fertilization involves genome-wide oxidation of 5-methylcytosine.Iqbal, Khursheed; Jin, Seung-Gi; Pfeifer, Gerd P; Szabo, Piroska EProceedings of the National Academy of Sciences of the United States of America2011 Mar 13642-721321204
ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads.Miller, Christopher A; Hampton, Oliver; Coarfa, Cristian; Milosavljevic, AleksandarPloS one2011e1632721305028
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
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
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
Reference Maps of human ES and iPS cell variation enable high-throughput characterization of pluripotent cell lines.Bock, Christoph; Kiskinis, Evangelos; Verstappen, Griet; Gu, Hongcang; Boulting, Gabriella; Smith, Zachary D; Ziller, Michael; Croft, Gist F; Amoroso, Mackenzie W; Oakley, Derek H; Gnirke, Andreas; Eggan, Kevin; Meissner, AlexanderCell2011 Feb 4439-5221295703
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Epigenetic silencing mediated through activated PI3K/AKT signaling in breast cancer.Zuo, Tao; Liu, Ta-Ming; Lan, Xun; Weng, Yu-I; Shen, Rulong; Gu, Fei; Huang, Yi-Wen; Liyanarachchi, Sandya; Deatherage, Daniel E; Hsu, Pei-Yin; Taslim, Cenny; Ramaswamy, Bhuvaneswari; Shapiro, Charles L; Lin, Huey-Jen L; Cheng, Alfred S L; Jin, Victor X; HCancer research2011 Mar 11752-6221216892
A 96-well plate assay for high-throughput analysis of holocarboxylase synthetase activity.Rios-Avila, Luisa; Prince, Sara A; Wijeratne, Subhashinee S K; Zempleni, JanosClinica chimica acta; international journal of clinical chemistry2011 Apr 11735-921195703
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Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin.Riddle, Nicole C; Minoda, Aki; Kharchenko, Peter V; Alekseyenko, Artyom A; Schwartz, Yuri B; Tolstorukov, Michael Y; Gorchakov, Andrey A; Jaffe, Jacob D; Kennedy, Cameron; Linder-Basso, Daniela; Peach, Sally E; Shanower, Gregory; Zheng, Haiyan; Kuroda, MiGenome research2011 Feb147-6321177972
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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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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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Proteomic analysis of fatty-acylated proteins in mammalian cells with chemical reporters reveals S-acylation of histone H3 variants.Wilson, John P; Raghavan, Anuradha S; Yang, Yu-Ying; Charron, Guillaume; Hang, Howard CMolecular & cellular proteomics : MCP2011 MarM110.00119821076176
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Identification of novel loci for Alzheimer disease and replication of CLU, PICALM, and BIN1 in Caribbean Hispanic individuals.Lee, Joseph H; Cheng, Rong; Barral, Sandra; Reitz, Christiane; Medrano, Martin; Lantigua, Rafael; Jimenez-Velazquez, Ivonne Z; Rogaeva, Ekaterina; St George-Hyslop, Peter H; Mayeux, RichardArchives of neurology.2011 Mar;320-821059989
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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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