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The search results on this publication page are automated on a monthly schedule based on acknowledgement of NIH Common Fund award numbers and intramural awards. Therefore, this list is not an exhaustive or error-free account of the program’s publications.
Epigenomics (768)
| Publication Title | Authors | Journal | Publication Date | Page No | PubMedID |
|---|---|---|---|---|---|
| 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, Kyunghee | The Journal of experimental medicine. | 2017 May 01; | 28461595 | |
| 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, Ting | Nature 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 Gregory | eLife. | 2017 03 27; | 28346137 | |
| Epigenomic annotation of noncoding mutations identifies mutated pathways in primary liver cancer. | Lowdon, Rebecca F; Wang, Ting | PloS one. | 2017; | 28333948 | |
| Monobodies and other synthetic binding proteins for expanding protein science. | Sha, Fern; Salzman, Gabriel; Gupta, Ankit; Koide, Shohei | Protein science : a publication of the Protein Society. | 2017 May; | 28249355 | |
| 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 G | Nucleic 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, Bosiljka | eLife. | 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, Kathrin | Cell. | 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 D | Tissue engineering. Part A. | 2017 Jan 17; | 28095751 | |
| 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, Ting | Neoplasia (New York, N.Y.). | 2017 Feb; | 28088687 | |
| 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 S | Cell. | 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, Aviv | Cell. | 2016 Dec 15; | 27984732 | |
| 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 A | Science (New York, N.Y.). | 2017 Jan 06; | 27980086 | |
| LOVTRAP: A Versatile Method to Control Protein Function with Light. | Wang, Hui; Hahn, Klaus M | Current protocols in cell biology. | ; | 27906450 | |
| 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, Bing | Cell reports. | 2016 Nov 15; | 27851967 | |
| Genetic engineering: Chemical control for CRISPR editing. | Hilton, Isaac B; Gersbach, Charles A | Nature 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, Norbert | Nature 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 S | Nature 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, Da | Nature. | 2016 Oct 19; | 27760116 | |
| 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 K | Science (New York, N.Y.). | ; | 27738015 | |
| 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, Manolis | Nature biotechnology. | 2016 Nov; | 27701403 | |
| 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 S | eLife. | 2016 Sep 23; | 27661255 | |
| Engineering and Application of LOV2-Based Photoswitches. | Zimmerman, S P; Kuhlman, B; Yumerefendi, H | Methods in enzymology. | 2016; | 27586333 | |
| 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 J | Genes & 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 T | Genes & development. | 2016 Aug 01; | 27542829 | |
| 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, Brian | Biochemistry. | 2016 Sep 20; | 27529180 | |
| 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 A | Cell stem cell. | 2016 Sep 1; | 27524438 | |
| 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, Hiroko | Scientific reports. | 2016 Aug 12; | 27516062 | |
| 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 M | Nature methods. | 2016 Sep; | 27427858 | |
| Go in! Go out! Inducible control of nuclear localization. | Di Ventura, Barbara; Kuhlman, Brian | Current 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 A | Nature 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 J | BMC bioinformatics. | 2016; | 27358049 | |
| 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 P | G3 (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, Eleazar | Bioinformatics (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, Marta | Breast cancer research and treatment. | 2016 Jul; | 27283835 | |
| Chromatin Domains: The Unit of Chromosome Organization. | Dixon, Jesse R; Gorkin, David U; Ren, Bing | Molecular cell. | 2016 Jun 2; | 27259200 | |
| 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 A | Cell. | 2016 Jun 2; | 27238023 | |
| CRISPR/Cas9 for Human Genome Engineering and Disease Research. | Xiong, Xin; Chen, Meng; Lim, Wendell A; Zhao, Dehua; Qi, Lei S | Annual 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 K | Science (New York, N.Y.). | 2016 May 20; | 27199432 | |
| All Things in Moderation: Prevention of Intestinal Adenomas by DNA Hypomethylation. | Lee, Kwang-Ho; Laird, Peter W | Cancer prevention research (Philadelphia, Pa.). | 2016 Jul; | 27190044 | |
| 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 E | Journal of cell science. | 2016 Jun 15; | 27173494 | |
| 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 M | Nucleic 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, Ricardo | eLife. | 2016 Apr 28; | 27130520 | |
| Vitamin D and androgen receptor-targeted therapy for triple-negative breast cancer. | Thakkar, A; Wang, B; Picon-Ruiz, M; Buchwald, P; Ince, Tan A | Breast cancer research and treatment. | 2016 May; | 27120467 | |
| 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, Brian | Nature chemical biology. | 2016 Jun; | 27089030 | |
| Evolution of Epigenetic Regulation in Vertebrate Genomes. | Lowdon, Rebecca F; Jang, Hyo Sik; Wang, Ting | Trends Genet | 2016 May | P:269-83 | 27080453 |
| 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 A | Alzheimer'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, Bo | Nature 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 S | eLife. | 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, Jingyun | Medicine. | 2016 Mar; | 26986136 | |
| 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 R | Cell stem cell. | 2016 Apr 7; | 26971820 | |
| Molecular circuitry of stem cell fate in skeletal muscle regeneration, ageing and disease. | Almada, Albert E; Wagers, Amy J | Nature 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, Miguel | Cell 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, Ting | G3 (Bethesda) | 2016 | P:973-86 | 26888867 |
| 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 J | Oncogene. | 2016 Feb 15; | 26876208 | |
| ATR-101 disrupts mitochondrial functions in adrenocortical carcinoma cells and in vivo. | Cheng, Yunhui; Kerppola, Raili Emilia; Kerppola, Tom Klaus | Endocrine-related cancer. | 2016 Apr; | 26843528 | |
| Editing the epigenome: technologies for programmable transcription and epigenetic modulation. | Thakore, Pratiksha I; Black, Joshua B; Hilton, Isaac B; Gersbach, Charles A | Nature methods. | 2016 Feb; | 26820547 | |
| 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 N | The American journal of clinical nutrition. | 2016 Feb; | 26791180 | |
| 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, Katalin | Cell reports. | 2016 Feb 2; | 861-71 | 26776520 |
| 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, Bo | Nucleic 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, Yue | Scientific 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 J | Developmental cell. | 2015 Dec 21; | 26702833 | |
| Genome editing: the end of the beginning. | Doudna, Jennifer A; Gersbach, Charles A | Genome biology. | 2015; | 292 | 26700220 |
| PET Neurochemical Imaging Modes. | Placzek, Michael S; Zhao, Wenjun; Wey, Hsiao-Ying; Morin, Thomas M; Hooker, Jacob M | Seminars in nuclear medicine. | 2016 Jan; | 20-7 | 26687854 |
| 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, Steve | Aging. | 2015 Dec; | 26684672 | |
| Beyond editing: repurposing CRISPR-Cas9 for precision genome regulation and interrogation. | Dominguez, Antonia A; Lim, Wendell A; Qi, Lei S | Nature reviews. Molecular cell biology. | 2016 Jan; | 26670017 | |
| 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, Jonathan | Nature neuroscience. | 2016 Jan; | 48-54 | 26619357 |
| 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; Ca | Genome biology. | 2015; | 263 | 26607552 |
| 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 A | Stem cell reports. | 2015 Nov 10; | 763-75 | 26603904 |
| 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, Ryan | Journal of abnormal psychology. | 2015 Nov; | 860-77 | 26595473 |
| 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, Jingyun | Medicine. | 2015 Nov; | e2028 | 26579811 |
| 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 D | Neurobiology of aging. | 2015 Dec; | 3121-9 | 26553823 |
| Complete haplotype phasing of the MHC and KIR loci with targeted HaploSeq. | Selvaraj, Siddarth; Schmitt, Anthony D; Dixon, Jesse R; Ren, Bing | BMC genomics. | 2015; | 900 | 26541200 |
| 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, Joanna | eLife. | 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 C | Proceedings of the National Academy of Sciences of the United States of America. | 2015 Nov 10; | 14018-23 | 26508642 |
| 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 A | Nature methods. | 2015 Dec; | 1143-9 | 26501517 |
| 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, Steven | Nature communications. | 2015; | 8733 | 26490019 |
| 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 K | Molecular psychiatry. | 2016 Jan; | 26481319 | |
| 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, Brian | ACS synthetic biology. | 2016 Jan 15; | 53-64 | 26474029 |
| Piezoelectric Versus Conventional Rotary Techniques for Impacted Third Molar Extraction: A Meta-analysis of Randomized Controlled Trials. | Jiang, Qian; Qiu, Yating; Yang, Chi; Yang, Jingyun; Chen, Minjie; Zhang, Zhiyuan | Medicine. | 2015 Oct; | e1685 | 26469902 |
| Ribosome profiling reveals the what, when, where and how of protein synthesis. | Brar, Gloria A; Weissman, Jonathan S | Nature 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 J | Oncotarget. | 2015 Oct 20; | 32878-89 | 26460735 |
| 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 S | PLoS genetics. | 2015 Oct; | e1005573 | 26451733 |
| 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, Lynda | Cancer discovery. | 2015 Dec; | 26450788 | |
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| The 3D Genome in Transcriptional Regulation and Pluripotency. | Gorkin, David U; Leung, Danny; Ren, Bing | Cell stem cell | 2014 Jun 5 | 762-775 | 24905166 |
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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 E | PloS one | 2014 | e93846 | 24796678 |
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| A phase Ib study of the effects of black raspberries on rectal polyps in patients with familial adenomatous polyposis. | Wang, Li-Shu; Burke, Carol A; Hasson, Henrietta; Kuo, Chieh-Ti; Molmenti, Christine L Sardo; Seguin, Claire; Liu, Pengyuan; Huang, Tim H-M; Frankel, Wendy L; Stoner, Gary D | Cancer prevention research (Philadelphia, Pa.) | 2014 Jul | 666-74 | 24764585 |
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| Aggregate culture of human embryonic stem cell-derived hepatocytes in suspension are an improved in vitro model for drug metabolism and toxicity testing. | Sengupta, Srikumar; Johnson, Brian Patrick; Swanson, Scott Allen; Stewart, Ron; Bradfield, Christopher Alan; Thomson, James Alexander | Toxicological sciences : an official journal of the Society of Toxicology | 2014 Jul | 236-45 | 24752503 |
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| KAP1 represses differentiation-inducible genes in embryonic stem cells through cooperative binding with PRC1 and derepresses pluripotency-associated genes. | Cheng, Bo; Ren, Xiaojun; Kerppola, Tom K | Molecular and cellular biology | 2014 Mar 31 | NULL | 24687849 |
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| Epigenetics: a new way to look at kidney diseases. | Beckerman, Pazit; Ko, Yi-An; Susztak, Katalin | Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association | 2014 Mar 27 | NULL | 24675284 |
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| An epigenetic mechanism of resistance to targeted therapy in T cell acute lymphoblastic leukemia. | Knoechel, Birgit; Roderick, Justine E; Williamson, Kaylyn E; Zhu, Jiang; Lohr, Jens G; Cotton, Matthew J; Gillespie, Shawn M; Fernandez, Daniel; Ku, Manching; Wang, Hongfang; Piccioni, Federica; Silver, Serena J; Jain, Mohit; Pearson, Daniel; Kluk, Michae | Nature genetics | 2014 Apr | 364-70 | 24584072 |
| Noncoding RNAs and LRRFIP1 Regulate TNF Expression. | Shi, Lihua; Song, Li; Fitzgerald, Michael; Maurer, Kelly; Bagashev, Asen; Sullivan, Kathleen E | Journal of immunology (Baltimore, Md. : 1950) | 2014 Apr 1 | 3057-67 | 24567534 |
| Association of Genetic Variants in GN*3 with Functional Dyspepsia: A Meta-Analysis. | Dai, Fei; Liu, Yaping; Shi, Haitao; Ge, Shuqiong; Song, Jun; Dong, Lei; Yang, Jingyun | Digestive diseases and sciences | 2014 Feb 21 | NULL | 24557575 |
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| Kinase-mediated changes in nucleosome conformation trigger chromatin decondensation via poly(ADP-ribosyl)ation. | Thomas, Colin J; Kotova, Elena; Andrake, Mark; Adolf-Bryfogle, Jared; Glaser, Robert; Regnard, Catherine; Tulin, Alexei V | Molecular cell | 2014 Mar 6 | 831-42 | 24508391 |
| Minor grove binding ligands disrupt PARP-1 activation pathways. | Kirsanov, Kirill I; Kotova, Elena; Makhov, Petr; Golovine, Konstantin; Lesovaya, Ekaterina A; Kolenko, Vladimir M; Yakubovskaya, Marianna G; Tulin, Alexei V | Oncotarget | 2014 Jan 30 | 428-37 | 24504413 |
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| Notch ties a knot on fistula maturation. | Dember, Laura M; Susztak, Katalin | Journal of the American Society of Nephrology : JASN. | 2014 Apr; | 648-50 | 24480826 |
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| Taxonomy of breast cancer based on normal cell phenotype predicts outcome. | Santagata, Sandro; Thakkar, Ankita; Ergonul, Ayse; Wang, Bin; Woo, Terri; Hu, Rong; Harrell, J Chuck; McNamara, George; Schwede, Matthew; Culhane, Aedin C; Kindelberger, David; Rodig, Scott; Richardson, Andrea; Schnitt, Stuart J; Tamimi, Rulla M; Ince, Ta | The Journal of clinical investigation | 2014 Feb 3 | 859-70 | 24463450 |
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| What we talk about when we talk about fat. | Rosen, Evan D; Spiegelman, Bruce M | Cell | 2014 Jan 16 | 20-44 | 24439368 |
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| Seasonal changes in gene expression represent cell-type composition in whole blood. | De Jong, Simone; Neeleman, Marjolein; Luykx, Jurjen J; ten Berg, Maarten J; Strengman, Eric; Den Breeijen, Hanneke H; Stijvers, Leon C; Buizer-Voskamp, Jacobine E; Bakker, Steven C; Kahn, Rene S; Horvath, Steve; Van Solinge, Wouter W; Ophoff, Roel A | Human molecular genetics | 2014 May 15 | 2721-8 | 24399446 |
| Comparison and quantitative verification of mapping algorithms for whole-genome bisulfite sequencing. | Kunde-Ramamoorthy, Govindarajan; Coarfa, Cristian; Laritsky, Eleonora; Kessler, Noah J; Harris, R Alan; Xu, Mingchu; Chen, Rui; Shen, Lanlan; Milosavljevic, Aleksandar; Waterland, Robert A | Nucleic acids research | 2014 Apr | e43 | 24391148 |
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| Hypomethylation of the IL17RC Promoter in Peripheral Blood Leukocytes Is Not A Hallmark of Age-Related Macular Degeneration. | Oliver, Verity F; Franchina, Maria; Jaffe, Andrew E; Branham, Kari E; Othman, Mohammad; Heckenlively, John R; Swaroop, Anand; Campochiaro, Betsy; Vote, Brendan J; Craig, Jamie E; Saffery, Richard; Mackey, David A; Qian, Jiang; Zack, Donald J; Hewitt, Alex | Cell reports | 2013 Dec 26 | 1527-35 | 24373284 |
| Doxorubicin, DNA torsion, and chromatin dynamics. | Yang, Fan; Teves, Sheila S; Kemp, Christopher J; Henikoff, Steven | Biochimica et biophysica acta | 2014 Jan | 84-9 | 24361676 |
| Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. | Chen, Baohui; Gilbert, Luke A; Cimini, Beth A; Schnitzbauer, Joerg; Zhang, Wei; Li, Gene-Wei; Park, Jason; Blackburn, Elizabeth H; Weissman, Jonathan S; Qi, Lei S; Huang, Bo | Cell | 2013 Dec 19 | 1479-91 | 24360272 |
| Characterizing the strand-specific distribution of non-CpG methylation in human pluripotent cells. | Guo, Weilong; Chung, Wen-Yu; Qian, Minping; Pellegrini, Matteo; Zhang, Michael Q | Nucleic acids research | 2014 Mar | 3009-16 | 24343027 |
| High-resolution mapping of transcription factor binding sites on native chromatin. | Kasinathan, Sivakanthan; Orsi, Guillermo A; Zentner, Gabriel E; Ahmad, Kami; Henikoff, Steven | Nature methods | 2013 Dec 15 | NULL | 24336359 |
| Genome-wide localization of small molecules. | Anders, Lars; Guenther, Matthew G; Qi, Jun; Fan, Zi Peng; Marineau, Jason J; Rahl, Peter B; Loven, Jakob; Sigova, Alla A; Smith, William B; Lee, Tong Ihn; Bradner, James E; Young, Richard A | Nature biotechnology | 2014 Jan | 92-6 | 24336317 |
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| Gene expression signature of normal cell-of-origin predicts ovarian tumor outcomes. | Merritt, Melissa A; Bentink, Stefan; Schwede, Matthew; Iwanicki, Marcin P; Quackenbush, John; Woo, Terri; Agoston, Elin S; Reinhardt, Ferenc; Crum, Christopher P; Berkowitz, Ross S; Mok, Samuel C; Witt, Abigail E; Jones, Michelle A; Wang, Bin; Ince, Tan A | PloS one | 2013 | e80314 | 24303006 |
| An improved synthesis of 1'-[18F]fluoroethyl-*-D-lactose ([18F]-FEL) for positron emission tomography imaging of pancreatic cancer. | Turkman, Nashaat; Gelovani, Juri G; Alauddin, Mian M | Journal of labelled compounds & radiopharmaceuticals | 2013 Jun 15 | 351-5 | 24285438 |
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| Black raspberries protectively regulate methylation of Wnt pathway genes in precancerous colon tissue. | Wang, Li-Shu; Kuo, Chieh-Ti; Huang, Tim H-M; Yearsley, Martha; Oshima, Kiyoko; Stoner, Gary D; Yu, Jianhua; Lechner, John F; Huang, Yi-Wen | Cancer prevention research (Philadelphia, Pa.) | 2013 Dec | 1317-27 | 24129635 |
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| Cytosine methylation changes in enhancer regions of core pro-fibrotic genes characterize kidney fibrosis development. | Ko, Yi-An; Mohtat, Davoud; Suzuki, Masako; Park, Ae Seo Deok; Izquierdo, Maria Concepcion; Han, Sang Youb; Kang, Hyun Mi; Si, Han; Hostetter, Thomas; Pullman, James M; Fazzari, Melissa; Verma, Amit; Zheng, Deyou; Greally, John M; Susztak, Katalin | Genome biology | 2013 | R108 | 24098934 |
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| Identification of novel imprinted differentially methylated regions by global analysis of human-parthenogenetic-induced pluripotent stem cells. | Stelzer, Yonatan; Ronen, Daniel; Bock, Christoph; Boyle, Patrick; Meissner, Alexander; Benvenisty, Nissim | Stem cell reports. | 2013; | 79-89 | 24052944 |
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| Epigenomics: The Science of No-Longer-Junk DNA. Why Study it in Chronic Kidney Disease? | Ko, Yi-An; Susztak, Katalin | Seminars in nephrology | 2013 Jul | 354-62 | 24011577 |
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| Long non-coding RNA HNF1A-AS1 regulates proliferation and migration in oesophageal adenocarcinoma cells. | Yang, Xue; Song, Jee Hoon; Cheng, Yulan; Wu, Wenjing; Bhagat, Tushar; Yu, Yiting; Abraham, John M; Ibrahim, Sariat; Ravich, William; Roland, Bani Chander; Khashab, Mouen; Singh, Vikesh K; Shin, Eun Ji; Yang, Xiao; Verma, Amit K; Meltzer, Stephen J; Mori, | Gut | 2014 Jun | 881-90 | 24000294 |
| Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues. | Hon, Gary C; Rajagopal, Nisha; Shen, Yin; McCleary, David F; Yue, Feng; Dang, My D; Ren, Bing | Nature genetics | 2013 Oct | 1198-206 | 23995138 |
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| Quantitative Proteomics Identifies Activation of Hallmark Pathways of Cancer in Patient Melanoma. | Byrum, Stephanie D; Larson, Signe K; Avaritt, Nathan L; Moreland, Linley E; Mackintosh, Samuel G; Cheung, Wang L; Tackett, Alan J | Journal of proteomics & bioinformatics | 2013 Mar 1 | 43-50 | 23976835 |
| A selective HDAC 1/2 inhibitor modulates chromatin and gene expression in brain and alters mouse behavior in two mood-related tests. | Schroeder, Frederick A; Lewis, Michael C; Fass, Daniel M; Wagner, Florence F; Zhang, Yan-Ling; Hennig, Krista M; Gale, Jennifer; Zhao, Wen-Ning; Reis, Surya; Barker, Douglas D; Berry-Scott, Erin; Kim, Sung Won; Clore, Elizabeth L; Hooker, Jacob M; Holson, | PloS one | 2013 | e71323 | 23967191 |
| Recombinant antibodies to histone post-translational modifications. | Hattori, Takamitsu; Taft, Joseph M; Swist, Kalina M; Luo, Hao; Witt, Heather; Slattery, Matthew; Koide, Akiko; Ruthenburg, Alexander J; Krajewski, Krzysztof; Strahl, Brian D; White, Kevin P; Farnham, Peggy J; Zhao, Yingming; Koide, Shohei | Nature methods | 2013 Oct | 992-5 | 23955773 |
| Developmental fate and cellular maturity encoded in human regulatory DNA landscapes. | Stergachis, Andrew B; Neph, Shane; Reynolds, Alex; Humbert, Richard; Miller, Brady; Paige, Sharon L; Vernot, Benjamin; Cheng, Jeffrey B; Thurman, Robert E; Sandstrom, Richard; Haugen, Eric; Heimfeld, Shelly; Murry, Charles E; Akey, Joshua M; Stamatoyannop | Cell | 2013 Aug 15 | 888-903 | 23953118 |
| Amplification of distant estrogen response elements deregulates target genes associated with tamoxifen resistance in breast cancer. | Hsu, Pei-Yin; Hsu, Hang-Kai; Lan, Xun; Juan, Liran; Yan, Pearlly S; Labanowska, Jadwiga; Heerema, Nyla; Hsiao, Tzu-Hung; Chiu, Yu-Chiao; Chen, Yidong; Liu, Yunlong; Li, Lang; Li, Rong; Thompson, Ian M; Nephew, Kenneth P; Sharp, Zelton D; Kirma, Nameer B; | Cancer cell | 2013 Aug 12 | 197-212 | 23948299 |
| A genome-wide siRNA screen identifies proteasome addiction as a vulnerability of basal-like triple-negative breast cancer cells. | Petrocca, Fabio; Altschuler, Gabriel; Tan, Shen Mynn; Mendillo, Marc L; Yan, Haoheng; Jerry, D Joseph; Kung, Andrew L; Hide, Winston; Ince, Tan A; Lieberman, Judy | Cancer cell | 2013 Aug 12 | 182-96 | 23948298 |
| H1 histones: current perspectives and challenges. | Harshman, Sean W; Young, Nicolas L; Parthun, Mark R; Freitas, Michael A | Nucleic acids research | 2013 Nov | 9593-609 | 23945933 |
| Double minute chromosomes in glioblastoma multiforme are revealed by precise reconstruction of oncogenic amplicons. | Sanborn, J Zachary; Salama, Sofie R; Grifford, Mia; Brennan, Cameron W; Mikkelsen, Tom; Jhanwar, Suresh; Katzman, Sol; Chin, Lynda; Haussler, David | Cancer research | 2013 Oct 1 | 6036-45 | 23940299 |
| Charting a dynamic DNA methylation landscape of the human genome. | Ziller, Michael J; Gu, Hongcang; Muller, Fabian; Donaghey, Julie; Tsai, Linus T-Y; Kohlbacher, Oliver; De Jager, Philip L; Rosen, Evan D; Bennett, David A; Bernstein, Bradley E; Gnirke, Andreas; Meissner, Alexander | Nature | 2013 Aug 22 | 477-81 | 23925113 |
| Bimolecular fluorescence complementation (BiFC) analysis of protein interactions in live cells. | Kerppola, Tom K | Cold Spring Harbor protocols | 2013 Aug | 727-31 | 23906917 |
| Whole-body pharmacokinetics of HDAC inhibitor drugs, butyric acid, valproic acid and 4-phenylbutyric acid measured with carbon-11 labeled analogs by PET. | Kim, Sung Won; Hooker, Jacob M; Otto, Nicola; Win, Khaing; Muench, Lisa; Shea, Colleen; Carter, Pauline; King, Payton; Reid, Alicia E; Volkow, Nora D; Fowler, Joanna S | Nuclear medicine and biology | 2013 Jul 29 | NULL | 23906667 |
| The effects of carbon dioxide and temperature on microRNA expression in Arabidopsis development. | May, Patrick; Liao, Will; Wu, Yijin; Shuai, Bin; McCombie, W Richard; Zhang, Michael Q; Liu, Qiong A | Nature communications | 2013 | 2145 | 23900278 |
| Methylomics of gene expression in human monocytes. | Liu, Yongmei; Ding, Jingzhong; Reynolds, Lindsay M; Lohman, Kurt; Register, Thomas C; De La Fuente, Alberto; Howard, Timothy D; Hawkins, Greg A; Cui, Wei; Morris, Jessica; Smith, Shelly G; Barr, R Graham; Kaufman, Joel D; Burke, Gregory L; Post, Wendy; Sh | Human molecular genetics | 2013 Dec 15 | 5065-74 | 23900078 |
| Endoglin promoter hypermethylation identifies a field defect in human primary esophageal cancer. | Jin, Zhe; Zhao, Zhenfu; Cheng, Yulan; Dong, Ming; Zhang, Xiaojing; Wang, Liang; Fan, Xinmin; Feng, Xianling; Mori, Yuriko; Meltzer, Stephen J | Cancer | 2013 Jul 24 | NULL | 23893879 |
| DNA unmethylome profiling by covalent capture of CpG sites. | Kriukiene, Edita; Labrie, Viviane; Khare, Tarang; Urbanaviciute, Giedre; Lapinaite, Audrone; Koncevicius, Karolis; Li, Daofeng; Wang, Ting; Pai, Shraddha; Ptak, Carolyn; Gordevicius, Juozas; Wang, Sun-Chong; Petronis, Arturas; Klimasauskas, Saulius | Nature communications | 2013 | 2190 | 23877302 |
| An epigenetic trap stabilizes singular olfactory receptor expression. | Lyons, David B; Allen, William E; Goh, Tracie; Tsai, Lulu; Barnea, Gilad; Lomvardas, Stavros | Cell | 2013 Jul 18 | 325-36 | 23870122 |
| Developmental biology. Enhancing pluripotency and lineage specification. | Xie, Wei; Ren, Bing | Science (New York, N.Y.) | 2013 Jul 19 | 245-7 | 23869010 |
| Browsing (Epi)genomes: a guide to data resources and epigenome browsers for stem cell researchers. | Karnik, Rahul; Meissner, Alexander | Cell stem cell | 2013 Jul 3 | 14-21 | 23827707 |
| Poised Chromatin at the ZEB1 Promoter Enables Breast Cancer Cell Plasticity and Enhances Tumorigenicity. | Chaffer, Christine L; Marjanovic, Nemanja D; Lee, Tony; Bell, George; Kleer, Celina G; Reinhardt, Ferenc; D'Alessio, Ana C; Young, Richard A; Weinberg, Robert A | Cell | 2013 Jul 3 | 61-74 | 23827675 |
| Pervasive transcription of the human genome produces thousands of previously unidentified long intergenic noncoding RNAs. | Hangauer, Matthew J; Vaughn, Ian W; McManus, Michael T | PLoS genetics | 2013 Jun | e1003569 | 23818866 |
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| FDG-PET imaging reveals local brain glucose utilization is altered by class I histone deacetylase inhibitors. | Schroeder, Frederick A; Chonde, Daniel B; Riley, Misha M; Moseley, Christian K; Granda, Michael L; Wilson, Colin M; Wagner, Florence F; Zhang, Yan-Ling; Gale, Jennifer; Holson, Edward B; Haggarty, Stephen J; Hooker, Jacob M | Neuroscience letters | 2013 Jun 25 | NULL | 23810801 |
| Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods. | Stevens, Michael; Cheng, Jeffrey B; Li, Daofeng; Xie, Mingchao; Hong, Chibo; Maire, Cecile L; Ligon, Keith L; Hirst, Martin; Marra, Marco A; Costello, Joseph F; Wang, Ting | Genome research | 2013 Sep | 1541-53 | 23804401 |
| Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm. | Zhang, Bo; Zhou, Yan; Lin, Nan; Lowdon, Rebecca F; Hong, Chibo; Nagarajan, Raman P; Cheng, Jeffrey B; Li, Daofeng; Stevens, Michael; Lee, Hyung Joo; Xing, Xiaoyun; Zhou, Jia; Sundaram, Vasavi; Elliott, Ginell; Gu, Junchen; Shi, Taoping; Gascard, Philippe; | Genome research | 2013 Sep | 1522-40 | 23804400 |
| Class I HDAC imaging using [ ( 3) H]CI-994 autoradiography. | Wang, Yajie; Zhang, Yan-Ling; Hennig, Krista; Gale, Jennifer P; Hong, Yijia; Cha, Anna; Riley, Misha; Wagner, Florence; Haggarty, Stephen J; Holson, Edward; Hooker, Jacob | Epigenetics : official journal of the DNA Methylation Society | 2013 Jun 11 | NULL | 23803584 |
| 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, Riitta | Immunity | 2013 Jun 27 | 1271-84 | 23791644 |
| 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 : CJASN | 2013 Sep | 1603-5 | 23788618 |
| 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 R | Molecular and cellular biology | 2013 Aug | 3286-98 | 23775118 |
| ARF inhibits the growth and malignant progression of non-small-cell lung carcinoma. | Busch, S E; Moser, R D; Gurley, K E; Kelly-Spratt, K S; Liggitt, H D; Kemp, C J | Oncogene | 2013 Jun 10 | NULL | 23752194 |
| DNA methylation data analysis and its application to cancer research. | Ma, Xiaotu; Wang, Yi-Wei; Zhang, Michael Q; Gazdar, Adi F | Epigenomics | 2013 Jun | 301-16 | 23750645 |
| Density-dependent cooperative non-specific binding in solid-phase SELEX affinity selection. | Ozer, Abdullah; White, Brian S; Lis, John T; Shalloway, David | Nucleic acids research | 2013 Aug | 7167-75 | 23737446 |
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| DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape. | Xie, Mingchao; Hong, Chibo; Zhang, Bo; Lowdon, Rebecca F; Xing, Xiaoyun; Li, Daofeng; Zhou, Xin; Lee, Hyung Joo; Maire, Cecile L; Ligon, Keith L; Gascard, Philippe; Sigaroudinia, Mahvash; Tlsty, Thea D; Kadlecek, Theresa; Weiss, Arthur; O'Geen, Henriette; | Nature genetics | 2013 Jul | 836-41 | 23708189 |
| 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 neuroscience | 2013 May 23 | 848-850 | 23708142 |
| An aberrant transcription factor network essential for Wnt signaling and stem cell maintenance in glioblastoma. | Rheinbay, Esther; Suva, Mario L; Gillespie, Shawn M; Wakimoto, Hiroaki; Patel, Anoop P; Shahid, Mohammad; Oksuz, Ozgur; Rabkin, Samuel D; Martuza, Robert L; Rivera, Miguel N; Louis, David N; Kasif, Simon; Chi, Andrew S; Bernstein, Bradley E | Cell reports | 2013 May 30 | 1567-79 | 23707066 |
| Stochastic gene expression in mammals: lessons from olfaction. | Magklara, Angeliki; Lomvardas, Stavros | Trends in cell biology | 2013 May 17 | 23689023 | |
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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; N | Cell | 2013 May 23 | 1134-48 | 23664764 |
| Transcriptional and epigenetic dynamics during specification of human embryonic stem cells. | Gifford, Casey A; Ziller, Michael J; Gu, Hongcang; Trapnell, Cole; Donaghey, Julie; Tsankov, Alexander; Shalek, Alex K; Kelley, David R; Shishkin, Alexander A; Issner, Robbyn; Zhang, Xiaolan; Coyne, Michael; Fostel, Jennifer L; Holmes, Laurie; Meldrim, Ji | Cell | 2013 May 23 | 1149-63 | 23664763 |
| A data-driven approach to preprocessing Illumina 450K methylation array data. | Pidsley, Ruth; Y Wong, Chloe C; Volta, Manuela; Lunnon, Katie; Mill, Jonathan; Schalkwyk, Leonard C | BMC genomics | 2013 | 293 | 23631413 |
| CMS: a web-based system for visualization and analysis of genome-wide methylation data of human cancers. | Gu, Fei; Doderer, Mark S; Huang, Yi-Wen; Roa, Juan C; Goodfellow, Paul J; Kizer, E Lynette; Huang, Tim H M; Chen, Yidong | PloS one | 2013 | e60980 | 23630576 |
| Exploring long-range genome interactions using the WashU Epigenome Browser. | Zhou, Xin; Lowdon, Rebecca F; Li, Daofeng; Lawson, Heather A; Madden, Pamela A F; Costello, Joseph F; Wang, Ting | Nature methods | 2013 May | 375-6 | 23629413 |
| 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 J | Asian Pacific journal of cancer prevention : APJCP | 2013 | 679-83 | 23621218 |
| Single-molecule analysis of combinatorial epigenomic states in normal and tumor cells. | Murphy, Patrick J; Cipriany, Benjamin R; Wallin, Christopher B; Ju, Chan Yang; Szeto, Kylan; Hagarman, James A; Benitez, Jaime J; Craighead, Harold G; Soloway, Paul D | Proceedings of the National Academy of Sciences of the United States of America | 2013 May 7 | 7772-7 | 23610441 |
| Sex difference in daily rhythms of clock gene expression in the aged human cerebral cortex. | Lim, Andrew S P; Myers, Amanda J; Yu, Lei; Buchman, Aron S; Duffy, Jeanne F; De Jager, Philip L; Bennett, David A | Journal of biological rhythms | 2013 Apr | 117-29 | 23606611 |
| Doxorubicin Enhances Nucleosome Turnover around Promoters. | Yang, Fan; Kemp, Christopher J; Henikoff, Steven | Current biology : CB | 2013 May 6 | 782-7 | 23602475 |
| 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 A | Molecular & cellular proteomics : MCP | 2013 Aug | 2048-59 | 23592332 |
| 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 D | Nucleic acids research | 2013 Jun | e116 | 23589626 |
| Consistent decrease in global DNA methylation and hydroxymethylation in the hippocampus of Alzheimer's disease patients. | Chouliaras, Leonidas; Mastroeni, Diego; Delvaux, Elaine; Grover, Andrew; Kenis, Gunter; Hof, Patrick R; Steinbusch, Harry W M; Coleman, Paul D; Rutten, Bart P F; van den Hove, Daniel L A | Neurobiology of aging | 2013 Sep | 2091-9 | 23582657 |
| Selective inhibition of tumor oncogenes by disruption of super-enhancers. | Loven, Jakob; Hoke, Heather A; Lin, Charles Y; Lau, Ashley; Orlando, David A; Vakoc, Christopher R; Bradner, James E; Lee, Tong Ihn; Young, Richard A | Cell | 2013 Apr 11 | 320-34 | 23582323 |
| Master transcription factors and mediator establish super-enhancers at key cell identity genes. | Whyte, Warren A; Orlando, David A; Hnisz, Denes; Abraham, Brian J; Lin, Charles Y; Kagey, Michael H; Rahl, Peter B; Lee, Tong Ihn; Young, Richard A | Cell | 2013 Apr 11 | 307-19 | 23582322 |
| An Inflection Point in Gene Discovery Efforts for Neurodegenerative Diseases: From Syndromic Diagnoses Toward Endophenotypes and the Epigenome. | De Jager, Philip L; Bennett, David A | JAMA neurology | 2013 Apr 9 | 1-8 | 23571780 |
| 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; Murre | JAMA : the journal of the American Medical Association | 2013 Apr 10 | 1483-92 | 23571587 |
| 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 B | Carcinogenesis | 2013 Aug | 1717-27 | 23568951 |
| Interplay between the cancer genome and epigenome. | Shen, Hui; Laird, Peter W | Cell | 2013 Mar 28 | 38-55 | 23540689 |
| Epigenetic reprogramming in cancer. | Suva, Mario L; Riggi, Nicolo; Bernstein, Bradley E | Science (New York, N.Y.) | 2013 Mar 29 | 1567-70 | 23539597 |
| RFECS: a random-forest based algorithm for enhancer identification from chromatin state. | Rajagopal, Nisha; Xie, Wei; Li, Yan; Wagner, Uli; Wang, Wei; Stamatoyannopoulos, John; Ernst, Jason; Kellis, Manolis; Ren, Bing | PLoS computational biology | 2013 Mar | e1002968 | 23526891 |
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| Rare somatic cells from human breast tissue exhibit extensive lineage plasticity. | Roy, Somdutta; Gascard, Philippe; Dumont, Nancy; Zhao, Jianxin; Pan, Deng; Petrie, Sarah; Margeta, Marta; Tlsty, Thea D | Proceedings of the National Academy of Sciences of the United States of America | 2013 Mar 19 | 4598-603 | 23487770 |
| Alternative Approaches in Gene Discovery and Characterization in Alzheimer's Disease. | Ertekin-Taner, Nilufer; De Jager, Phillip L; Yu, Lei; Bennett, David A | Current genetic medicine reports | 2013 Mar | 39-51 | 23482655 |
| Comparative annotation of functional regions in the human genome using epigenomic data. | Won, Kyoung-Jae; Zhang, Xian; Wang, Tao; Ding, Bo; Raha, Debasish; Snyder, Michael; Ren, Bing; Wang, Wei | Nucleic acids research | 2013 Apr | 4423-32 | 23482391 |
| Confounding by repetitive elements and CpG islands does not explain the association between hypomethylation and genomic instability. | Harris, R Alan; Shaw, Chad; Li, Jian; Cheung, Sau Wai; Coarfa, Cristian; Jeong, Mira; Goodell, Margaret A; White, Lisa D; Patel, Ankita; Kang, Sung-Hae; Chinault, A Craig; Gambin, Tomasz; Gambin, Anna; Lupski, James R; Milosavljevic, Aleksandar | PLoS genetics | 2013 Feb | e1003333 | 23468659 |
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| Lysine succinylation and lysine malonylation in histones. | Xie, Zhongyu; Dai, Junbiao; Dai, Lunzhi; Tan, Minjia; Cheng, Zhongyi; Wu, Yeming; Boeke, Jef D; Zhao, Yingming | Molecular & cellular proteomics : MCP | 2012 May | 100-7 | 22389435 |
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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 L | Journal of neuroimmunology. | 2012 Jul 15; | 9-Feb | 22297167 |
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| Commentary: The seven plagues of epigenetic epidemiology. | Heijmans, Bastiaan T; Mill, Jonathan | International journal of epidemiology | 2012 Feb | 74-8 | 22269254 |
| Minireview: Epigenetics of obesity and diabetes in humans. | Slomko, Howard; Heo, Hye J; Einstein, Francine H | Endocrinology | 2012 Mar | 1025-30 | 22253427 |
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| Thermal stability of fibroblast growth factor protein is a determinant factor in regulating self-renewal, differentiation, and reprogramming in human pluripotent stem cells. | Chen, Guokai; Gulbranson, Daniel R; Yu, Pengzhi; Hou, Zhonggang; Thomson, James A | Stem cells (Dayton, Ohio) | 2012 Apr | 623-30 | 22213113 |
| Current status and future prospects for epigenetic psychopharmacology. | Boks, Marco P; de Jong, Noelle M; Kas, Martien J H; Vinkers, Christiaan H; Fernandes, Cathy; Kahn, Rene S; Mill, Jonathan; Ophoff, Roel A | Epigenetics : official journal of the DNA Methylation Society | 2012 Jan 1 | 20-8 | 22207355 |
| 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 J | Endocrine-related cancer | 2012 Feb | L5-9 | 22194443 |
| K16-biotinylated histone H4 is overrepresented in repeat regions and participates in the repression of transcriptionally competent genes in human Jurkat lymphoid cells. | Rios-Avila, Luisa; Pestinger, Valerie; Zempleni, Janos | The Journal of nutritional biochemistry | 2012 Dec | 1559-64 | 22192339 |
| RNA aptamers that functionally interact with green fluorescent protein and its derivatives. | Shui, Bo; Ozer, Abdullah; Zipfel, Warren; Sahu, Nevedita; Singh, Avtar; Lis, John T; Shi, Hua; Kotlikoff, Michael I | Nucleic acids research | 2012 Mar | e39 | 22189104 |
| Assessment of free energy predictors for ligand binding to a methyllysine histone code reader. | Gao C, Herold JM, Kireev D. | J Comput Chem | 2012 Mar 5 | 659-65 | 22183769 |
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| Genomic distribution and inter-sample variation of non-CpG methylation across human cell types. | Ziller, Michael J; Muller, Fabian; Liao, Jing; Zhang, Yingying; Gu, Hongcang; Bock, Christoph; Boyle, Patrick; Epstein, Charles B; Bernstein, Bradley E; Lengauer, Thomas; Gnirke, Andreas; Meissner, Alexander | PLoS genetics | 2011 Dec | e1002389 | 22174693 |
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| Aberrant methylation of the PTPRO gene in peripheral blood as a potential biomarker in esophageal squamous cell carcinoma patients. | You, Yan-Jie; Chen, Yu-Ping; Zheng, Xiao-Xuan; Meltzer, Stephen J; Zhang, Hao | Cancer letters | 2012 Feb 28 | 138-44 | 22099875 |
| NSD2 links dimethylation of histone H3 at lysine 36 to oncogenic programming. | Kuo, Alex J; Cheung, Peggie; Chen, Kaifu; Zee, Barry M; Kioi, Mitomu; Lauring, Josh; Xi, Yuanxin; Park, Ben Ho; Shi, Xiaobing; Garcia, Benjamin A; Li, Wei; Gozani, Or | Molecular cell | 2011 Nov 18 | 609-20 | 22099308 |
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| Heat shock reduces stalled RNA polymerase II and nucleosome turnover genome-wide. | Teves, Sheila S; Henikoff, Steven | Genes & development | 2011 Nov 15 | 2387-97 | 22085965 |
| 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-Hsiu | PloS one | 2011 | e26799 | 22073196 |
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| 5-Hydroxymethylcytosine is strongly depleted in human cancers but its levels do not correlate with IDH1 mutations. | Jin, Seung-Gi; Jiang, Yong; Qiu, Runxiang; Rauch, Tibor A; Wang, Yinsheng; Schackert, Gabriele; Krex, Dietmar; Lu, Qiang; Pfeifer, Gerd P | Cancer research | 2011 Dec 15 | 7360-5 | 22052461 |
| High levels of nuclear heat-shock factor 1 (HSF1) are associated with poor prognosis in breast cancer. | Santagata, Sandro; Hu, Rong; Lin, Nancy U; Mendillo, Marc L; Collins, Laura C; Hankinson, Susan E; Schnitt, Stuart J; Whitesell, Luke; Tamimi, Rulla M; Lindquist, Susan; Ince, Tan A | Proceedings of the National Academy of Sciences of the United States of America | 2011 Nov 8 | 18378-83 | 22042860 |
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| Transfer-printing of single DNA molecule arrays on graphene for high-resolution electron imaging and analysis. | Cerf, Aline; Alava, Thomas; Barton, Robert A; Craighead, Harold G | Nano letters | 2011 Oct 12 | 4232-8 | 21919532 |
| 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 W | Journal of gastroenterology and hepatology | 2012 Apr | 773-80 | 21916995 |
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| The first identification of lysine malonylation substrates and its regulatory enzyme. | Peng C, Lu Z, Xie Z, Cheng Z, Chen Y, Tan M, Luo H, Zhang Y, He W, Yang K, Zwaans BM, Tishkoff D, Ho L, Lombard D, He TC, Dai J, Verdin E, Ye Y, Zhao Y. | Mol Cell Proteomics | 2011 Dec | M111.012658 | 21908771 |
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| 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 J | Journal of cutaneous pathology | 2011 Nov | 933-6 | 21883366 |
| 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 V | Cell research | 2011 Oct | 1393-409 | 21876557 |
| Neuronal activity modifies the DNA methylation landscape in the adult brain. | Guo, Junjie U; Ma, Dengke K; Mo, Huan; Ball, Madeleine P; Jang, Mi-Hyeon; Bonaguidi, Michael A; Balazer, Jacob A; Eaves, Hugh L; Xie, Bin; Ford, Eric; Zhang, Kun; Ming, Guo-li; Gao, Yuan; Song, Hongjun | Nature neuroscience. | 2011 Oct; | 1345-51 | 21874013 |
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| PARP1 genomics: chromatin immunoprecipitation approach using anti-PARP1 antibody (ChIP and ChIP-seq). | Lodhi, Niraj; Tulin, Alexei V | Methods in molecular biology (Clifton, N.J.) | 2011 | 191-208 | 21870262 |
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| Long noncoding RNA, polycomb, and the ghosts haunting INK4b-ARF-INK4a expression. | Aguilo F, Zhou MM, Walsh MJ. | Cancer Res | 2011 Aug 15 | 5365-9 | 21828241 |
| Perinephric and epididymal fat affect hepatic metabolism in rats. | Ben-Shlomo, Shani; Einstein, Francine H; Zvibel, Isabel; Atias, Dikla; Shlomai, Amir; Halpern, Zamir; Barzilai, Nir; Fishman, Sigal | Obesity (Silver Spring, Md.) | 2012 Jan | 151-6 | 21818154 |
| Genome-wide analysis of interferon regulatory factor I binding in primary human monocytes. | Shi, Lihua; Perin, Juan C; Leipzig, Jeremy; Zhang, Zhe; Sullivan, Kathleen E | Gene | 2011 Nov 1 | 21-8 | 21803131 |
| 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, Janos | Biochemical and biophysical research communications | 2011 Aug 19 | 115-20 | 21802411 |
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| Regulation of embryonic stem cell self-renewal and pluripotency by leukaemia inhibitory factor. | Hirai, Hiroyuki; Karian, Peter; Kikyo, Nobuaki | The Biochemical journal | 2011 Aug 15 | 11-23 | 21793804 |
| Germline mutations in MSR1, ASCC1, and CTHRC1 in patients with Barrett esophagus and esophageal adenocarcinoma. | Orloff, Mohammed; Peterson, Charissa; He, Xin; Ganapathi, Shireen; Heald, Brandie; Yang, Yi-ran; Bebek, Gurkan; Romigh, Todd; Song, Jee Hoon; Wu, Wenjing; David, Stefan; Cheng, Yulan; Meltzer, Stephen J; Eng, Charis | JAMA : the journal of the American Medical Association | 2011 Jul 27 | 410-9 | 21791690 |
| 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, Huidong | Nucleic acids research | 2011 Oct | e127 | 21785137 |
| Cytosine methylation in miR-153 gene promoters increases the expression of holocarboxylase synthetase, thereby increasing the abundance of histone H4 biotinylation marks in HEK-293 human kidney cells. | Bao, Baolong; Rodriguez-Melendez, Rocio; Zempleni, Janos | The Journal of nutritional biochemistry | 2012 Jun | 635-9 | 21764280 |
| Transcriptome analysis of human diabetic kidney disease. | Woroniecka, Karolina I; Park, Ae Seo Deok; Mohtat, Davoud; Thomas, David B; Pullman, James M; Susztak, Katalin | Diabetes | 2011 Sep | 2354-69 | 21752957 |
| 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, Elliott | Proceedings of the National Academy of Sciences of the United States of America | 2011 Sep 6 | 14902-7 | 21746931 |
| 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, Ir | Nature chemical biology | 2011 Aug | 566-74 | 21743462 |
| 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 C | Proceedings of the National Academy of Sciences of the United States of America | 2011 Sep 6 | 14908-13 | 21737748 |
| 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, Nobuaki | Stem cells (Dayton, Ohio) | 2011 Sep | 1349-61 | 21732495 |
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