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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.
Title | Authors | Journal | PubMedID | Publication Date |
---|---|---|---|---|
Modeling of mitochondrial genetic polymorphisms reveals induction of heteroplasmy by pleiotropic disease locus 10398A>G. | Smullen, Molly; Olson, Meagan N; Murray, Liam F; Suresh, Madhusoodhanan; Yan, Guang; Dawes, Pepper; Barton, Nathaniel J; Mason, Jivanna N; Zhang, Yucheng; Fernandez-Fontaine, Aria A; Church, George M; Mastroeni, Diego; Wang, Qi; Lim, Elaine T; Chan, Yingleong; Readhead, Benjamin | Scientific reports | 37369829 | 2023 Jun 27 |
Mendelian Randomization and Transcriptome-Wide Association Analysis Identified Genes That Were Pleiotropically Associated with Intraocular Pressure. | Yang, Zhikun; Zhang, Zhewei; Zhu, Yining; Yuan, Guangwei; Yang, Jingyun; Yu, Weihong | Genes | 37239387 | 2023 Apr 30 |
DNA methylation markers for kidney function and progression of diabetic kidney disease. | Li, Kelly Yichen; Tam, Claudia Ha Ting; Liu, Hongbo; Day, Samantha; Lim, Cadmon King Poo; So, Wing Yee; Huang, Chuiguo; Jiang, Guozhi; Shi, Mai; Lee, Heung Man; TRANSCEND Consortium; Lan, Hui-Yao; Szeto, Cheuk-Chun; Hanson, Robert L; Nelson, Robert G; Susztak, Katalin; Chan, Juliana C N; Yip, Kevin Y; Ma, Ronald C W | Nature communications | 37188670 | 2023 May 15 |
Epigenetic changes in sperm are associated with paternal and child quantitative autistic traits in an autism-enriched cohort. | Feinberg, Jason I; Schrott, Rose; Ladd-Acosta, Christine; Newschaffer, Craig J; Hertz-Picciotto, Irva; Croen, Lisa A; Daniele Fallin, M; Feinberg, Andrew P; Volk, Heather E | Molecular psychiatry | 37100868 | 2023 Apr 27 |
Treatment effects of soluble guanylate cyclase modulation on diabetic kidney disease at single-cell resolution. | Balzer, Michael S; Pavkovic, Mira; Frederick, Julia; Abedini, Amin; Freyberger, Alexius; Vienenkötter, Julia; Mathar, Ilka; Siudak, Krystyna; Eitner, Frank; Sandner, Peter; Grundmann, Manuel; Susztak, Katalin | Cell reports. Medicine | 37023747 | 2023 Apr 18 |
Unbiased Human Kidney Tissue Proteomics Identifies Matrix Metalloproteinase 7 as a Kidney Disease Biomarker. | Hirohama, Daigoro; Abedini, Amin; Moon, Salina; Surapaneni, Aditya; Dillon, Simon T; Vassalotti, Allison; Liu, Hongbo; Doke, Tomohito; Martinez, Victor; Md Dom, Zaipul; Karihaloo, Anil; Palmer, Matthew B; Coresh, Josef; Grams, Morgan E; Niewczas, Monika A; Susztak, Katalin | Journal of the American Society of Nephrology : JASN | 37022120 | 2023 Apr 05 |
The Type 2 Diabetes Knowledge Portal: An open access genetic resource dedicated to type 2 diabetes and related traits. | Costanzo, Maria C; von Grotthuss, Marcin; Massung, Jeffrey; Jang, Dongkeun; Caulkins, Lizz; Koesterer, Ryan; Gilbert, Clint; Welch, Ryan P; Kudtarkar, Parul; Hoang, Quy; Boughton, Andrew P; Singh, Preeti; Sun, Ying; Duby, Marc; Moriondo, Annie; Nguyen, Trang; Smadbeck, Patrick; Alexander, Benjamin R; Brandes, MacKenzie; Carmichael, Mary; Dornbos, Peter; Green, Todd; Huellas-Bruskiewicz, Kenneth C; Ji, Yue; Kluge, Alexandria; McMahon, Aoife C; Mercader, Josep M; Ruebenacker, Oliver; Sengupta, Sebanti; Spalding, Dylan; Taliun, Daniel; AMP-T2D Consortium; Smith, Philip; Thomas, Melissa K; Akolkar, Beena; Brosnan, M Julia; Cherkas, Andriy; Chu, Audrey Y; Fauman, Eric B; Fox, Caroline S; Kamphaus, Tania Nayak; Miller, Melissa R; Nguyen, Lynette; Parsa, Afshin; Reilly, Dermot F; Ruetten, Hartmut; Wholley, David; Zaghloul, Norann A; Abecasis, Gonçalo R; Altshuler, David; Keane, Thomas M; McCarthy, Mark I; Gaulton, Kyle J; Florez, Jose C; Boehnke, Michael; Burtt, Noël P; Flannick, Jason | Cell metabolism | 36963395 | 2023 Apr 04 |
NAD+ precursor supplementation prevents mtRNA/RIG-I-dependent inflammation during kidney injury. | Doke, Tomohito; Mukherjee, Sarmistha; Mukhi, Dhanunjay; Dhillon, Poonam; Abedini, Amin; Davis, James G; Chellappa, Karthikeyani; Chen, Beishan; Baur, Joseph A; Susztak, Katalin | Nature metabolism | 36914909 | 2023 Mar |
Multi-omic characterization of brain changes in the vascular endothelial growth factor family during aging and Alzheimer's disease. | Seto, Mabel; Dumitrescu, Logan; Mahoney, Emily R; Sclafani, Annah M; De Jager, Philip L; Menon, Vilas; Koran, Mary E I; Robinson, Renã A; Ruderfer, Douglas M; Cox, Nancy J; Seyfried, Nicholas T; Jefferson, Angela L; Schneider, Julie A; Bennett, David A; Petyuk, Vladislav A; Hohman, Timothy J | Neurobiology of aging | 36905877 | 2023 Jun |
Molecular pathways that drive diabetic kidney disease. | Mohandes, Samer; Doke, Tomohito; Hu, Hailong; Mukhi, Dhanunjay; Dhillon, Poonam; Susztak, Katalin | The Journal of clinical investigation | 36787250 | 2023 Feb 15 |
Worsened Outcome in Patients with Membranous Nephropathy Carrying Apolipoprotein L1 High-Risk Genotype. | Susztak, Katalin | Clinical journal of the American Society of Nephrology : CJASN | 36764286 | 2023 Mar 01 |
Increased levels of endogenous retroviruses trigger fibroinflammation and play a role in kidney disease development. | Dhillon, Poonam; Mulholland, Kelly Ann; Hu, Hailong; Park, Jihwan; Sheng, Xin; Abedini, Amin; Liu, Hongbo; Vassalotti, Allison; Wu, Junnan; Susztak, Katalin | Nature communications | 36732547 | 2023 Feb 02 |
Exploring genes for immunoglobulin A nephropathy: a summary data-based mendelian randomization and FUMA analysis. | Zhang, Qian; Zhang, Kang; Zhu, Yining; Yuan, Guangwei; Yang, Jingyun; Zhang, Minmin | BMC medical genomics | 36709307 | 2023 Jan 29 |
Integrated DNA Methylation/RNA Profiling in Middle Temporal Gyrus of Alzheimer's Disease. | Piras, Ignazio S; Brokaw, Danielle; Kong, Yinfei; Weisenberger, Daniel J; Krate, Jonida; Delvaux, Elaine; Mahurkar, Swapna; Blattler, Adam; Siegmund, Kimberly D; Sue, Lucia; Serrano, Geidy E; Beach, Thomas G; Laird, Peter W; Huentelman, Matthew J; Coleman, Paul D | Cellular and molecular neurobiology | 36596913 | 2023 Jul |
Neuroimmune transcriptome changes in patient brains of psychiatric and neurological disorders. | Chen, Yu; Dai, Jiacheng; Tang, Longfei; Mikhailova, Tatiana; Liang, Qiuman; Li, Miao; Zhou, Jiaqi; Kopp, Richard F; Weickert, Cynthia; Chen, Chao; Liu, Chunyu | Molecular psychiatry | 36424395 | 2022 Nov 24 |
Differential Gene Expression and DNA Methylation in the Risk of Depression in LOAD Patients. | Upadhya, Suraj; Gingerich, Daniel; Lutz, Michael William; Chiba-Falek, Ornit | Biomolecules | 36421693 | 2022 Nov 12 |
Metabolomic and lipidomic signatures in autosomal dominant and late-onset Alzheimer's disease brains. | Novotny, Brenna C; Fernandez, Maria Victoria; Wang, Ciyang; Budde, John P; Bergmann, Kristy; Eteleeb, Abdallah M; Bradley, Joseph; Webster, Carol; Ebl, Curtis; Norton, Joanne; Gentsch, Jen; Dube, Umber; Wang, Fengxian; Morris, John C; Bateman, Randall J; Perrin, Richard J; McDade, Eric; Xiong, Chengjie; Chhatwal, Jasmeer; Dominantly Inherited Alzheimer Network (DIAN) Study Group; Alzheimer's Disease Neuroimaging Initiative; and the Alzheimer's Disease Metabolomics Consortium (ADMC); Goate, Alison; Farlow, Martin; Schofield, Peter; Chui, Helena; Karch, Celeste M; Cruchaga, Carlos; Benitez, Bruno A; Harari, Oscar | Alzheimer's & dementia : the journal of the Alzheimer's Association | 36251323 | 2023 May |
Associations between accelerated parental biologic age, autism spectrum disorder, social traits, and developmental and cognitive outcomes in their children. | Song, Ashley Y; Bakulski, Kelly; Feinberg, Jason I; Newschaffer, Craig; Croen, Lisa A; Hertz-Picciotto, Irva; Schmidt, Rebecca J; Farzadegan, Homayoon; Lyall, Kristen; Fallin, M Daniele; Volk, Heather E; Ladd-Acosta, Christine | Autism research : official journal of the International Society for Autism Research | 36189953 | 2022 Dec |
Integrative Co-methylation Network Analysis Identifies Novel DNA Methylation Signatures and Their Target Genes in Alzheimer's Disease. | Kim, Jun Pyo; Kim, Bo-Hyun; Bice, Paula J; Seo, Sang Won; Bennett, David A; Saykin, Andrew J; Nho, Kwangsik | Biological psychiatry | 36150909 | 2022 Jun 24 |
Risperidone-induced changes in DNA methylation in peripheral blood from first-episode schizophrenia patients parallel changes in neuroimaging and cognitive phenotypes. | Hu, Maolin; Xia, Yan; Zong, Xiaofen; Sweeney, John A; Bishop, Jeffrey R; Liao, Yanhui; Giase, Gina; Li, Bingshan; Rubin, Leah H; Wang, Yunpeng; Li, Zongchang; He, Ying; Chen, Xiaogang; Liu, Chunyu; Chen, Chao; Tang, Jinsong | Psychiatry research | 36075150 | 2022 Nov |
Genome-wide meta-analyses reveal novel loci for verbal short-term memory and learning. | Lahti, Jari; Tuominen, Samuli; Yang, Qiong; Pergola, Giulio; Ahmad, Shahzad; Amin, Najaf; Armstrong, Nicola J; Beiser, Alexa; Bey, Katharina; Bis, Joshua C; Boerwinkle, Eric; Bressler, Jan; Campbell, Archie; Campbell, Harry; Chen, Qiang; Corley, Janie; Cox, Simon R; Davies, Gail; De Jager, Philip L; Derks, Eske M; Faul, Jessica D; Fitzpatrick, Annette L; Fohner, Alison E; Ford, Ian; Fornage, Myriam; Gerring, Zachary; Grabe, Hans J; Grodstein, Francine; Gudnason, Vilmundur; Simonsick, Eleanor; Holliday, Elizabeth G; Joshi, Peter K; Kajantie, Eero; Kaprio, Jaakko; Karell, Pauliina; Kleineidam, Luca; Knol, Maria J; Kochan, Nicole A; Kwok, John B; Leber, Markus; Lam, Max; Lee, Teresa; Li, Shuo; Loukola, Anu; Luck, Tobias; Marioni, Riccardo E; Mather, Karen A; Medland, Sarah; Mirza, Saira S; Nalls, Mike A; Nho, Kwangsik; O'Donnell, Adrienne; Oldmeadow, Christopher; Painter, Jodie; Pattie, Alison; Reppermund, Simone; Risacher, Shannon L; Rose, Richard J; Sadashivaiah, Vijay; Scholz, Markus; Satizabal, Claudia L; Schofield, Peter W; Schraut, Katharina E; Scott, Rodney J; Simino, Jeannette; Smith, Albert V; Smith, Jennifer A; Stott, David J; Surakka, Ida; Teumer, Alexander; Thalamuthu, Anbupalam; Trompet, Stella; Turner, Stephen T; van der Lee, Sven J; Villringer, Arno; Völker, Uwe; Wilson, Robert S; Wittfeld, Katharina; Vuoksimaa, Eero; Xia, Rui; Yaffe, Kristine; Yu, Lei; Zare, Habil; Zhao, Wei; Ames, David; Attia, John; Bennett, David A; Brodaty, Henry; Chasman, Daniel I; Goldman, Aaron L; Hayward, Caroline; Ikram, M Arfan; Jukema, J Wouter; Kardia, Sharon L R; Lencz, Todd; Loeffler, Markus; Mattay, Venkata S; Palotie, Aarno; Psaty, Bruce M; Ramirez, Alfredo; Ridker, Paul M; Riedel-Heller, Steffi G; Sachdev, Perminder S; Saykin, Andrew J; Scherer, Martin; Schofield, Peter R; Sidney, Stephen; Starr, John M; Trollor, Julian; Ulrich, William; Wagner, Michael; Weir, David R; Wilson, James F; Wright, Margaret J; Weinberger, Daniel R; Debette, Stephanie; Eriksson, Johan G; Mosley Jr, Thomas H; Launer, Lenore J; van Duijn, Cornelia M; Deary, Ian J; Seshadri, Sudha; Räikkönen, Katri | Molecular psychiatry | 35974141 | 2022 Nov |
RNASE6 is a novel modifier of APOE-ε4 effects on cognition. | Seto, Mabel; Weiner, Rebecca L; Dumitrescu, Logan; Mahoney, Emily R; Hansen, Shania L; Janve, Vaibhav; Khan, Omair A; Liu, Dandan; Wang, Yanling; Menon, Vilas; De Jager, Philip L; Schneider, Julie A; Bennett, David A; Gifford, Katherine A; Jefferson, Angela L; Hohman, Timothy J | Neurobiology of aging | 35896049 | 2022 10 |
Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stability. | de Mendoza, Alex; Nguyen, Trung Viet; Ford, Ethan; Poppe, Daniel; Buckberry, Sam; Pflueger, Jahnvi; Grimmer, Matthew R; Stolzenburg, Sabine; Bogdanovic, Ozren; Oshlack, Alicia; Farnham, Peggy J; Blancafort, Pilar; Lister, Ryan | Genome biology | 35883107 | 2022 07 26 |
[11C]Martinostat PET analysis reveals reduced HDAC I availability in Alzheimer's disease. | Pascoal, Tharick A; Chamoun, Mira; Lax, Elad; Wey, Hsiao-Ying; Shin, Monica; Ng, Kok Pin; Kang, Min Su; Mathotaarachchi, Sulantha; Benedet, Andrea L; Therriault, Joseph; Lussier, Firoza Z; Schroeder, Frederick A; DuBois, Jonathan M; Hightower, Baileigh G; Gilbert, Tonya M; Zürcher, Nicole R; Wang, Changning; Hopewell, Robert; Chakravarty, Mallar; Savard, Melissa; Thomas, Emilie; Mohaddes, Sara; Farzin, Sarah; Salaciak, Alyssa; Tullo, Stephanie; Cuello, A Claudio; Soucy, Jean-Paul; Massarweh, Gassan; Hwang, Heungsun; Kobayashi, Eliane; Hyman, Bradley T; Dickerson, Bradford C; Guiot, Marie-Christine; Szyf, Moshe; Gauthier, Serge; Hooker, Jacob M; Rosa-Neto, Pedro | Nature communications | 35853847 | 2022 07 19 |
Epigenetic and Transcriptomic Programming of HSC Quiescence Signaling in Large for Gestational Age Neonates. | Pelletier, Alexandre; Carrier, Arnaud; Zhao, Yongmei; Canouil, Mickaël; Derhourhi, Mehdi; Durand, Emmanuelle; Berberian-Ferrato, Lionel; Greally, John; Hughes, Francine; Froguel, Philippe; Bonnefond, Amélie; Delahaye, Fabien | International journal of molecular sciences | 35806330 | 2022 Jun 30 |
Keap1 moderates the transcription of virus induced genes through G9a-GLP and NFκB p50 recruitment. | Burns, Veronica Elizabeth; Kerppola, Tom Klaus | Immunology | 35751391 | 2022 Sep |
The association between aging-related monocyte transcriptional networks and comorbidity burden: the Multi-Ethnic Study of Atherosclerosis (MESA). | Ding, Jingzhong; Lohman, Kurt; Molina, Anthony; Delbono, Osvaldo; Bertoni, Alain; Shea, Steven; Post, Wendy; Guo, Xiuqing; Barr, R Graham; Manichaikul, Ani W; Pankow, James S; Rotter, Jerome I; Hoeschele, Ina; Kritchevsky, Stephen B; Liu, Yongmei | GeroScience | 35737188 | 2023 Feb |
Epigenomic and transcriptomic analyses define core cell types, genes and targetable mechanisms for kidney disease. | Liu, Hongbo; Doke, Tomohito; Guo, Dong; Sheng, Xin; Ma, Ziyuan; Park, Joseph; Vy, Ha My T; Nadkarni, Girish N; Abedini, Amin; Miao, Zhen; Palmer, Matthew; Voight, Benjamin F; Li, Hongzhe; Brown, Christopher D; Ritchie, Marylyn D; Shu, Yan; Susztak, Katalin | Nature genetics | 35710981 | 2022 07 |
Developmental Pathways Are Epigenetically Reprogrammed during Lung Cancer Brain Metastasis. | Karlow, Jennifer A; Devarakonda, Siddhartha; Xing, Xiaoyun; Jang, Hyo Sik; Govindan, Ramaswamy; Watson, Mark; Wang, Ting | Cancer research | 35706127 | 2022 Aug 03 |
Single-cell analysis identifies the interaction of altered renal tubules with basophils orchestrating kidney fibrosis. | Doke, Tomohito; Abedini, Amin; Aldridge, Daniel L; Yang, Ya-Wen; Park, Jihwan; Hernandez, Christina M; Balzer, Michael S; Shrestra, Rojesh; Coppock, Gaia; Rico, Juan M Inclan; Han, Seung Yub; Kim, Junhyong; Xin, Sheng; Piliponsky, Adrian M; Angelozzi, Marco; Lefebvre, Veronique; Siracusa, Mark C; Hunter, Christopher A; Susztak, Katalin | Nature immunology | 35552540 | 2022 May 12 |
The multifaceted role of kidney tubule mitochondrial dysfunction in kidney disease development. | Doke, Tomohito; Susztak, Katalin | Trends in cell biology | 35473814 | 2022 Oct |
Antisense oligonucleotides ameliorate kidney dysfunction in podocyte-specific APOL1 risk variant mice. | Yang, Ya-Wen; Poudel, Bibek; Frederick, Julia; Dhillon, Poonam; Shrestha, Rojesh; Ma, Ziyuan; Wu, Junnan; Okamoto, Koji; Kopp, Jeffrey B; Booten, Sheri L; Gattis, Danielle; Watt, Andrew T; Palmer, Matthew; Aghajan, Mariam; Susztak, Katalin | Molecular therapy : the journal of the American Society of Gene Therapy | 35450819 | 2022 Jul 06 |
Distinct developmental phenotypes result from mutation of Set8/KMT5A and histone H4 lysine 20 in Drosophila melanogaster. | Crain, Aaron T; Klusza, Stephen; Armstrong, Robin L; Santa Rosa, Priscila; Temple, Brenda R S; Strahl, Brian D; McKay, Daniel J; Matera, A Gregory; Duronio, Robert J | Genetics | 35404465 | 2022 May 31 |
New insights into the genetic etiology of Alzheimer's disease and related dementias. | Bellenguez, Céline; Küçükali, Fahri; Jansen, Iris E; Kleineidam, Luca; Moreno-Grau, Sonia; Amin, Najaf; Naj, Adam C; Campos-Martin, Rafael; Grenier-Boley, Benjamin; Andrade, Victor; Holmans, Peter A; Boland, Anne; Damotte, Vincent; van der Lee, Sven J; Costa, Marcos R; Kuulasmaa, Teemu; Yang, Qiong; de Rojas, Itziar; Bis, Joshua C; Yaqub, Amber; Prokic, Ivana; Chapuis, Julien; Ahmad, Shahzad; Giedraitis, Vilmantas; Aarsland, Dag; Garcia-Gonzalez, Pablo; Abdelnour, Carla; Alarcón-Martín, Emilio; Alcolea, Daniel; Alegret, Montserrat; Alvarez, Ignacio; Álvarez, Victoria; Armstrong, Nicola J; Tsolaki, Anthoula; Antúnez, Carmen; Appollonio, Ildebrando; Arcaro, Marina; Archetti, Silvana; Pastor, Alfonso Arias; Arosio, Beatrice; Athanasiu, Lavinia; Bailly, Henri; Banaj, Nerisa; Baquero, Miquel; Barral, Sandra; Beiser, Alexa; Pastor, Ana Belén; Below, Jennifer E; Benchek, Penelope; Benussi, Luisa; Berr, Claudine; Besse, Céline; Bessi, Valentina; Binetti, Giuliano; Bizarro, Alessandra; Blesa, Rafael; Boada, Mercè; Boerwinkle, Eric; Borroni, Barbara; Boschi, Silvia; Bossù, Paola; Bråthen, Geir; Bressler, Jan; Bresner, Catherine; Brodaty, Henry; Brookes, Keeley J; Brusco, Luis Ignacio; Buiza-Rueda, Dolores; Bûrger, Katharina; Burholt, Vanessa; Bush, William S; Calero, Miguel; Cantwell, Laura B; Chene, Geneviève; Chung, Jaeyoon; Cuccaro, Michael L; Carracedo, Ángel; Cecchetti, Roberta; Cervera-Carles, Laura; Charbonnier, Camille; Chen, Hung-Hsin; Chillotti, Caterina; Ciccone, Simona; Claassen, Jurgen A H R; Clark, Christopher; Conti, Elisa; Corma-Gómez, Anaïs; Costantini, Emanuele; Custodero, Carlo; Daian, Delphine; Dalmasso, Maria Carolina; Daniele, Antonio; Dardiotis, Efthimios; Dartigues, Jean-François; de Deyn, Peter Paul; de Paiva Lopes, Katia; de Witte, Lot D; Debette, Stéphanie; Deckert, Jürgen; Del Ser, Teodoro; Denning, Nicola; DeStefano, Anita; Dichgans, Martin; Diehl-Schmid, Janine; Diez-Fairen, Mónica; Rossi, Paolo Dionigi; Djurovic, Srdjan; Duron, Emmanuelle; Düzel, Emrah; Dufouil, Carole; Eiriksdottir, Gudny; Engelborghs, Sebastiaan; Escott-Price, Valentina; Espinosa, Ana; Ewers, Michael; Faber, Kelley M; Fabrizio, Tagliavini; Nielsen, Sune Fallgaard; Fardo, David W; Farotti, Lucia; Fenoglio, Chiara; Fernández-Fuertes, Marta; Ferrari, Raffaele; Ferreira, Catarina B; Ferri, Evelyn; Fin, Bertrand; Fischer, Peter; Fladby, Tormod; Fließbach, Klaus; Fongang, Bernard; Fornage, Myriam; Fortea, Juan; Foroud, Tatiana M; Fostinelli, Silvia; Fox, Nick C; Franco-Macías, Emlio; Bullido, María J; Frank-García, Ana; Froelich, Lutz; Fulton-Howard, Brian; Galimberti, Daniela; García-Alberca, Jose Maria; García-González, Pablo; Garcia-Madrona, Sebastian; Garcia-Ribas, Guillermo; Ghidoni, Roberta; Giegling, Ina; Giorgio, Giaccone; Goate, Alison M; Goldhardt, Oliver; Gomez-Fonseca, Duber; González-Pérez, Antonio; Graff, Caroline; Grande, Giulia; Green, Emma; Grimmer, Timo; Grünblatt, Edna; Grunin, Michelle; Gudnason, Vilmundur; Guetta-Baranes, Tamar; Haapasalo, Annakaisa; Hadjigeorgiou, Georgios; Haines, Jonathan L; Hamilton-Nelson, Kara L; Hampel, Harald; Hanon, Olivier; Hardy, John; Hartmann, Annette M; Hausner, Lucrezia; Harwood, Janet; Heilmann-Heimbach, Stefanie; Helisalmi, Seppo; Heneka, Michael T; Hernández, Isabel; Herrmann, Martin J; Hoffmann, Per; Holmes, Clive; Holstege, Henne; Vilas, Raquel Huerto; Hulsman, Marc; Humphrey, Jack; Biessels, Geert Jan; Jian, Xueqiu; Johansson, Charlotte; Jun, Gyungah R; Kastumata, Yuriko; Kauwe, John; Kehoe, Patrick G; Kilander, Lena; Ståhlbom, Anne Kinhult; Kivipelto, Miia; Koivisto, Anne; Kornhuber, Johannes (see original citation for additional authors) | Nature genetics | 35379992 | 2022 04 |
Local connectivity and synaptic dynamics in mouse and human neocortex. | Campagnola, Luke; Seeman, Stephanie C; Chartrand, Thomas; Kim, Lisa; Hoggarth, Alex; Gamlin, Clare; Ito, Shinya; Trinh, Jessica; Davoudian, Pasha; Radaelli, Cristina; Kim, Mean-Hwan; Hage, Travis; Braun, Thomas; Alfiler, Lauren; Andrade, Julia; Bohn, Phillip; Dalley, Rachel; Henry, Alex; Kebede, Sara; Alice, Mukora; Sandman, David; Williams, Grace; Larsen, Rachael; Teeter, Corinne; Daigle, Tanya L; Berry, Kyla; Dotson, Nadia; Enstrom, Rachel; Gorham, Melissa; Hupp, Madie; Dingman Lee, Samuel; Ngo, Kiet; Nicovich, Philip R; Potekhina, Lydia; Ransford, Shea; Gary, Amanda; Goldy, Jeff; McMillen, Delissa; Pham, Trangthanh; Tieu, Michael; Siverts, La'Akea; Walker, Miranda; Farrell, Colin; Schroedter, Martin; Slaughterbeck, Cliff; Cobb, Charles; Ellenbogen, Richard; Gwinn, Ryder P; Keene, C Dirk; Ko, Andrew L; Ojemann, Jeffrey G; Silbergeld, Daniel L; Carey, Daniel; Casper, Tamara; Crichton, Kirsten; Clark, Michael; Dee, Nick; Ellingwood, Lauren; Gloe, Jessica; Kroll, Matthew; Sulc, Josef; Tung, Herman; Wadhwani, Katherine; Brouner, Krissy; Egdorf, Tom; Maxwell, Michelle; McGraw, Medea; Pom, Christina Alice; Ruiz, Augustin; Bomben, Jasmine; Feng, David; Hejazinia, Nika; Shi, Shu; Szafer, Aaron; Wakeman, Wayne; Phillips, John; Bernard, Amy; Esposito, Luke; D'Orazi, Florence D; Sunkin, Susan; Smith, Kimberly; Tasic, Bosiljka; Arkhipov, Anton; Sorensen, Staci; Lein, Ed; Koch, Christof; Murphy, Gabe; Zeng, Hongkui; Jarsky, Tim | Science (New York, N.Y.) | 35271334 | 2022 03 11 |
MOMA: a multi-task attention learning algorithm for multi-omics data interpretation and classification. | Moon, Sehwan; Lee, Hyunju | Bioinformatics (Oxford, England) | 35157023 | 2022 Apr 12 |
Multi-transcriptomic analysis points to early organelle dysfunction in human astrocytes in Alzheimer's disease. | Galea, Elena; Weinstock, Laura D; Larramona-Arcas, Raquel; Pybus, Alyssa F; Giménez-Llort, Lydia; Escartin, Carole; Wood, Levi B | Neurobiology of disease | 35143967 | 2022 05 |
Brain microRNAs are associated with variation in cognitive trajectory in advanced age. | Wingo, Aliza P; Wang, Mengli; Liu, Jiaqi; Breen, Michael S; Yang, Hyun-Sik; Tang, Beisha; Schneider, Julie A; Seyfried, Nicholas T; Lah, James J; Levey, Allan I; Bennett, David A; Jin, Peng; De Jager, Philip L; Wingo, Thomas S | Translational psychiatry | 35105862 | 2022 Feb 01 |
Monocyte miRNAs Are Associated With Type 2 Diabetes. | Parker, Daniel C; Wan, Ma; Lohman, Kurt; Hou, Li; Nguyen, Anh Tram; Ding, Jingzhong; Bertoni, Alain; Shea, Steve; Burke, Gregory L; Jacobs, David R; Post, Wendy; Corcoran, David; Hoeschele, Ina; Parks, John S; Liu, Yongmei | Diabetes | 35073575 | 2022 Apr 01 |
Integrated Genomic, Transcriptomic and Proteomic Analysis for Identifying Markers of Alzheimer's Disease. | Madrid, Laura; Labrador, Sandra C; González-Pérez, Antonio; Sáez, María E; The Alzheimer's Disease Neuroimaging Initiative Adni | Diagnostics (Basel, Switzerland) | 34943540 | 2021 Dec 08 |
AtheroSpectrum Reveals Novel Macrophage Foam Cell Gene Signatures Associated With Atherosclerotic Cardiovascular Disease Risk. | Li, Chuan; Qu, Lili; Matz, Alyssa J; Murphy, Patrick A; Liu, Yongmei; Manichaikul, Ani W; Aguiar, Derek; Rich, Stephen S; Herrington, David M; Vu, David; Johnson, W Craig; Rotter, Jerome I; Post, Wendy S; Vella, Anthony T; Rodriguez-Oquendo, Annabelle; Zhou, Beiyan | Circulation | 34913723 | 2022 Jan 18 |
Bayesian Sparse Mediation Analysis with Targeted Penalization of Natural Indirect Effects. | Song, Yanyi; Zhou, Xiang; Kang, Jian; Aung, Max T; Zhang, Min; Zhao, Wei; Needham, Belinda L; Kardia, Sharon L R; Liu, Yongmei; Meeker, John D; Smith, Jennifer A; Mukherjee, Bhramar | Journal of the Royal Statistical Society. Series C, Applied statistics | 34887595 | 2021 Nov |
Lifestyle and Genetic Factors Modify Parent-of-Origin Effects on the Human Methylome. | Zeng, Yanni; Amador, Carmen; Gao, Chenhao; Walker, Rosie M; Morris, Stewart W; Campbell, Archie; Frkatović, Azra; Madden, Rebecca A; Adams, Mark J; He, Shuai; Bretherick, Andrew D; Hayward, Caroline; Porteous, David J; Wilson, James F; Evans, Kathryn L; McIntosh, Andrew M; Navarro, Pau; Haley, Chris S | EBioMedicine | 34883445 | 2021 Dec |
Atlas of RNA editing events affecting protein expression in aged and Alzheimer's disease human brain tissue. | Ma, Yiyi; Dammer, Eric B; Felsky, Daniel; Duong, Duc M; Klein, Hans-Ulrich; White, Charles C; Zhou, Maotian; Logsdon, Benjamin A; McCabe, Cristin; Xu, Jishu; Wang, Minghui; Wingo, Thomas S; Lah, James J; Zhang, Bin; Schneider, Julie; Allen, Mariet; Wang, Xue; Ertekin-Taner, Nilüfer; Seyfried, Nicholas T; Levey, Allan I; Bennett, David A; De Jager, Philip L | Nature communications | 34857756 | 2021 12 02 |
How Many Cell Types Are in the Kidney and What Do They Do? | Balzer, Michael S; Rohacs, Tibor; Susztak, Katalin | Annual review of physiology | 34843404 | 2022 02 10 |
From mapping kidney function to mechanism and prediction. | Hirohama, Daigoro; Susztak, Katalin | Nature reviews. Nephrology | 34819631 | 2022 02 |
Genome-wide association studies identify the role of caspase-9 in kidney disease. | Doke, Tomohito; Huang, Shizheng; Qiu, Chengxiang; Sheng, Xin; Seasock, Matthew; Liu, Hongbo; Ma, Ziyuan; Palmer, Matthew; Susztak, Katalin | Science advances | 34739325 | 2021 Nov 05 |
APOL1 risk variants in individuals of African genetic ancestry drive endothelial cell defects that exacerbate sepsis. | Wu, Junnan; Ma, Ziyuan; Raman, Archana; Beckerman, Pazit; Dhillon, Poonam; Mukhi, Dhanunjay; Palmer, Matthew; Chen, Hua Chang; Cohen, Cassiane Robinson; Dunn, Thomas; Reilly, John; Meyer, Nuala; Shahaty, Michael; Arany, Zoltan; Haskó, György; Laudanski, Krzysztof; Hung, Adriana; Susztak, Katalin | Immunity | 34715018 | 2021 11 09 |
Systems Analysis Reveals Ageing-Related Perturbations in Retinoids and Sex Hormones in Alzheimer's and Parkinson's Diseases. | Lam, Simon; Hartmann, Nils; Benfeitas, Rui; Zhang, Cheng; Arif, Muhammad; Turkez, Hasan; Uhlén, Mathias; Englert, Christoph; Knight, Robert; Mardinoglu, Adil | Biomedicines | 34680427 | 2021 Sep 24 |
Research Priorities for Kidney-Related Research-An Agenda to Advance Kidney Care: A Position Statement From the National Kidney Foundation. | National Kidney Foundation Research Roundtable Work Group on behalf of the National Kidney Foundation | American journal of kidney diseases : the official journal of the National Kidney Foundation | 34627932 | 2022 Feb |
Comparative cellular analysis of motor cortex in human, marmoset and mouse. | Bakken, Trygve E; Jorstad, Nikolas L; Hu, Qiwen; Lake, Blue B; Tian, Wei; Kalmbach, Brian E; Crow, Megan; Hodge, Rebecca D; Krienen, Fenna M; Sorensen, Staci A; Eggermont, Jeroen; Yao, Zizhen; Aevermann, Brian D; Aldridge, Andrew I; Bartlett, Anna; Bertagnolli, Darren; Casper, Tamara; Castanon, Rosa G; Crichton, Kirsten; Daigle, Tanya L; Dalley, Rachel; Dee, Nick; Dembrow, Nikolai; Diep, Dinh; Ding, Song-Lin; Dong, Weixiu; Fang, Rongxin; Fischer, Stephan; Goldman, Melissa; Goldy, Jeff; Graybuck, Lucas T; Herb, Brian R; Hou, Xiaomeng; Kancherla, Jayaram; Kroll, Matthew; Lathia, Kanan; van Lew, Baldur; Li, Yang Eric; Liu, Christine S; Liu, Hanqing; Lucero, Jacinta D; Mahurkar, Anup; McMillen, Delissa; Miller, Jeremy A; Moussa, Marmar; Nery, Joseph R; Nicovich, Philip R; Niu, Sheng-Yong; Orvis, Joshua; Osteen, Julia K; Owen, Scott; Palmer, Carter R; Pham, Thanh; Plongthongkum, Nongluk; Poirion, Olivier; Reed, Nora M; Rimorin, Christine; Rivkin, Angeline; Romanow, William J; Sedeño-Cortés, Adriana E; Siletti, Kimberly; Somasundaram, Saroja; Sulc, Josef; Tieu, Michael; Torkelson, Amy; Tung, Herman; Wang, Xinxin; Xie, Fangming; Yanny, Anna Marie; Zhang, Renee; Ament, Seth A; Behrens, M Margarita; Bravo, Hector Corrada; Chun, Jerold; Dobin, Alexander; Gillis, Jesse; Hertzano, Ronna; Hof, Patrick R; Höllt, Thomas; Horwitz, Gregory D; Keene, C Dirk; Kharchenko, Peter V; Ko, Andrew L; Lelieveldt, Boudewijn P; Luo, Chongyuan; Mukamel, Eran A; Pinto-Duarte, António; Preissl, Sebastian; Regev, Aviv; Ren, Bing; Scheuermann, Richard H; Smith, Kimberly; Spain, William J; White, Owen R; Koch, Christof; Hawrylycz, Michael; Tasic, Bosiljka; Macosko, Evan Z; McCarroll, Steven A; Ting, Jonathan T; Zeng, Hongkui; Zhang, Kun; Feng, Guoping; Ecker, Joseph R; Linnarsson, Sten; Lein, Ed S | Nature | 34616062 | 2021 10 |
Longitudinal urinary biomarkers of immunological activation in covid-19 patients without clinically apparent kidney disease versus acute and chronic failure. | Laudanski, Krzysztof; Okeke, Tony; Jihane, Hajj; Siddiq, Kumal; Rader, Daniel J; Wu, Junnan; Susztak, Katalin | Scientific reports | 34608231 | 2021 10 04 |
Olfactory Bulb and Amygdala Gene Expression Changes in Subjects Dying with COVID-19. | Piras, Ignazio S; Huentelman, Matthew J; Walker, Jessica E; Arce, Richard; Glass, Michael J; Vargas, Daisy; Sue, Lucia I; Intorcia, Anthony J; Nelson, Courtney M; Suszczewicz, Katsuko E; Borja, Claryssa L; Desforges, Marc; Deture, Michael; Dickson, Dennis W; Beach, Thomas G; Serrano, Geidy E | medRxiv : the preprint server for health sciences | 34545375 | 2021 Sep 15 |
Signature morpho-electric, transcriptomic, and dendritic properties of human layer 5 neocortical pyramidal neurons. | Kalmbach, Brian E; Hodge, Rebecca D; Jorstad, Nikolas L; Owen, Scott; de Frates, Rebecca; Yanny, Anna Marie; Dalley, Rachel; Mallory, Matt; Graybuck, Lucas T; Radaelli, Cristina; Keene, C Dirk; Gwinn, Ryder P; Silbergeld, Daniel L; Cobbs, Charles; Ojemann, Jeffrey G; Ko, Andrew L; Patel, Anoop P; Ellenbogen, Richard G; Bakken, Trygve E; Daigle, Tanya L; Dee, Nick; Lee, Brian R; McGraw, Medea; Nicovich, Philip R; Smith, Kimberly; Sorensen, Staci A; Tasic, Bosiljka; Zeng, Hongkui; Koch, Christof; Lein, Ed S; Ting, Jonathan T | Neuron | 34534454 | 2021 09 15 |
Rare variants in the endocytic pathway are associated with Alzheimer's disease, its related phenotypes, and functional consequences. | Zhan, Lingyu; Li, Jiajin; Jew, Brandon; Sul, Jae Hoon | PLoS genetics | 34516545 | 2021 Sep |
Epigenomic features related to microglia are associated with attenuated effect of APOE ε4 on Alzheimer's disease risk in humans. | Ma, Yiyi; Yu, Lei; Olah, Marta; Smith, Rebecca; Oatman, Stephanie R; Allen, Mariet; Pishva, Ehsan; Zhang, Bin; Menon, Vilas; Ertekin-Taner, Nilüfer; Lunnon, Katie; Bennett, David A; Klein, Hans-Ulrich; De Jager, Philip L | Alzheimer's & dementia : the journal of the Alzheimer's Association | 34482628 | 2021 Sep 05 |
Novel DNA methylation loci and genes showing pleiotropic association with Alzheimer's dementia: a network Mendelian randomization analysis. | Liu, Di; Wang, Youxin; Jing, Huiquan; Meng, Qun; Yang, Jingyun | Epigenetics | 34461811 | 2022 Jun-Jul |
Manipulating the NKG2D Receptor-Ligand Axis Using CRISPR: Novel Technologies for Improved Host Immunity. | Alves, Eric; McLeish, Emily; Blancafort, Pilar; Coudert, Jerome D; Gaudieri, Silvana | Frontiers in immunology | 34456921 | 2021 |
A single genetic locus controls both expression of DPEP1/CHMP1A and kidney disease development via ferroptosis. | Guan, Yuting; Liang, Xiujie; Ma, Ziyuan; Hu, Hailong; Liu, Hongbo; Miao, Zhen; Linkermann, Andreas; Hellwege, Jacklyn N; Voight, Benjamin F; Susztak, Katalin | Nature communications | 34426578 | 2021 08 23 |
Bayesian hierarchical models for high-dimensional mediation analysis with coordinated selection of correlated mediators. | Song, Yanyi; Zhou, Xiang; Kang, Jian; Aung, Max T; Zhang, Min; Zhao, Wei; Needham, Belinda L; Kardia, Sharon L R; Liu, Yongmei; Meeker, John D; Smith, Jennifer A; Mukherjee, Bhramar | Statistics in medicine | 34404112 | 2021 11 30 |
Virus Infection Induces Keap1 Binding to Cytokine Genes, Which Recruits NF-κB p50 and G9a-GLP and Represses Cytokine Transcription. | Burns, Veronica Elizabeth; Kerppola, Tom Klaus | Journal of immunology (Baltimore, Md. : 1950) | 34400522 | 2021 09 01 |
EPIGENOMIC FEATURES RELATED TO MICROGLIA ARE ASSOCIATED WITH ATTENUATED EFFECT OF APOE ε4 ON ALZHEIMER'S DISEASE RISK IN HUMANS. | Ma, Yiyi; Yu, Lei; Olah, Marta; Smith, Rebecca; Oatman, Stephanie R; Allen, Mariet; Pishva, Ehsan; Zhang, Bin; Menon, Vilas; Ertekin-Taner, Nilüfer; Lunnon, Katie; Bennett, David A; Klein, Hans-Ulrich; De Jager, Philip L | Alzheimer's & dementia : the journal of the Alzheimer's Association | 34393677 | 2020 12 |
Mapping the genetic architecture of human traits to cell types in the kidney identifies mechanisms of disease and potential treatments. | Sheng, Xin; Guan, Yuting; Ma, Ziyuan; Wu, Junnan; Liu, Hongbo; Qiu, Chengxiang; Vitale, Steven; Miao, Zhen; Seasock, Matthew J; Palmer, Matthew; Shin, Myung K; Duffin, Kevin L; Pullen, Steven S; Edwards, Todd L; Hellwege, Jacklyn N; Hung, Adriana M; Li, Mingyao; Voight, Benjamin F; Coffman, Thomas M; Brown, Christopher D; Susztak, Katalin | Nature genetics | 34385711 | 2021 09 |
Transcriptome-Wide Association Study of Blood Cell Traits in African Ancestry and Hispanic/Latino Populations. | Wen, Jia; Xie, Munan; Rowland, Bryce; Rosen, Jonathan D; Sun, Quan; Chen, Jiawen; Tapia, Amanda L; Qian, Huijun; Kowalski, Madeline H; Shan, Yue; Young, Kristin L; Graff, Marielisa; Argos, Maria; Avery, Christy L; Bien, Stephanie A; Buyske, Steve; Yin, Jie; Choquet, Hélène; Fornage, Myriam; Hodonsky, Chani J; Jorgenson, Eric; Kooperberg, Charles; Loos, Ruth J F; Liu, Yongmei; Moon, Jee-Young; North, Kari E; Rich, Stephen S; Rotter, Jerome I; Smith, Jennifer A; Zhao, Wei; Shang, Lulu; Wang, Tao; Zhou, Xiang; Reiner, Alexander P; Raffield, Laura M; Li, Yun | Genes | 34356065 | 2021 Jul 08 |
Renal Histologic Analysis Provides Complementary Information to Kidney Function Measurement for Patients with Early Diabetic or Hypertensive Disease. | Quinn, Ghazal Z; Abedini, Amin; Liu, Hongbo; Ma, Ziyuan; Cucchiara, Andrew; Havasi, Andrea; Hill, Jon; Palmer, Matthew B; Susztak, Katalin | Journal of the American Society of Nephrology : JASN | 34348909 | 2021 Nov |
Isthmin-1 is an adipokine that promotes glucose uptake and improves glucose tolerance and hepatic steatosis. | Jiang, Zewen; Zhao, Meng; Voilquin, Laetitia; Jung, Yunshin; Aikio, Mari A; Sahai, Tanushi; Dou, Florence Y; Roche, Alexander M; Carcamo-Orive, Ivan; Knowles, Joshua W; Wabitsch, Martin; Appel, Eric A; Maikawa, Caitlin L; Camporez, Joao Paulo; Shulman, Gerald I; Tsai, Linus; Rosen, Evan D; Gardner, Christopher D; Spiegelman, Bruce M; Svensson, Katrin J | Cell metabolism | 34348115 | 2021 Sep 07 |
Transgenic mice for in vivo epigenome editing with CRISPR-based systems. | Gemberling, Matthew P; Siklenka, Keith; Rodriguez, Erica; Tonn-Eisinger, Katherine R; Barrera, Alejandro; Liu, Fang; Kantor, Ariel; Li, Liqing; Cigliola, Valentina; Hazlett, Mariah F; Williams, Courtney A; Bartelt, Luke C; Madigan, Victoria J; Bodle, Josephine C; Daniels, Heather; Rouse, Douglas C; Hilton, Isaac B; Asokan, Aravind; Ciofani, Maria; Poss, Kenneth D; Reddy, Timothy E; West, Anne E; Gersbach, Charles A | Nature methods | 34341582 | 2021 08 |
A machine learning approach to brain epigenetic analysis reveals kinases associated with Alzheimer's disease. | Huang, Yanting; Sun, Xiaobo; Jiang, Huige; Yu, Shaojun; Robins, Chloe; Armstrong, Matthew J; Li, Ronghua; Mei, Zhen; Shi, Xiaochuan; Gerasimov, Ekaterina Sergeevna; De Jager, Philip L; Bennett, David A; Wingo, Aliza P; Jin, Peng; Wingo, Thomas S; Qin, Zhaohui S | Nature communications | 34294691 | 2021 Jul 22 |
Association of Coding Variants in Hydroxysteroid 17-beta Dehydrogenase 14 (HSD17B14) with Reduced Progression to End Stage Kidney Disease in Type 1 Diabetes. | Mychaleckyj, Josyf C; Valo, Erkka; Ichimura, Takaharu; Ahluwalia, Tarunveer S; Dina, Christian; Miller, Rachel G; Shabalin, Ivan G; Gyorgy, Beata; Cao, JingJing; Onengut-Gumuscu, Suna; Satake, Eiichiro; Smiles, Adam M; Haukka, Jani K; Tregouet, David-Alexandre; Costacou, Tina; O'Neil, Kristina; Paterson, Andrew D; Forsblom, Carol; Keenan, Hillary A; Pezzolesi, Marcus G; Pragnell, Marlon; Galecki, Andrzej; Rich, Stephen S; Sandholm, Niina; Klein, Ronald; Klein, Barbara E; Susztak, Katalin; Orchard, Trevor J; Korstanje, Ron; King, George L; Hadjadj, Samy; Rossing, Peter; Bonventre, Joseph V; Groop, Per-Henrik; Warram, James H; Krolewski, Andrzej S | Journal of the American Society of Nephrology : JASN | 34261756 | 2021 10 |
The Socioeconomic Gradient in Epigenetic Ageing Clocks: Evidence from the Multi-Ethnic Study of Atherosclerosis and the Health and Retirement Study. | Schmitz, Lauren L; Zhao, Wei; Ratliff, Scott M; Goodwin, Julia; Miao, Jiacheng; Lu, Qiongshi; Guo, Xiuqing; Taylor, Kent D; Ding, Jingzhong; Liu, Yongmei; Levine, Morgan; Smith, Jennifer A | Epigenetics | 34227900 | 2022 Jun |
Unbiased Analysis of Temporal Changes in Immune Serum Markers in Acute COVID-19 Infection With Emphasis on Organ Failure, Anti-Viral Treatment, and Demographic Characteristics. | Laudanski, Krzysztof; Jihane, Hajj; Antalosky, Brook; Ghani, Danyal; Phan, Uyen; Hernandez, Ruth; Okeke, Tony; Wu, Junnan; Rader, Daniel; Susztak, Katalin | Frontiers in immunology | 34177897 | 2021 |
The association of epigenetic clocks in brain tissue with brain pathologies and common aging phenotypes. | Grodstein, Francine; Lemos, Bernardo; Yu, Lei; Klein, Hans-Ulrich; Iatrou, Artemis; Buchman, Aron S; Shireby, Gemma L; Mill, Jonathan; Schneider, Julie A; De Jager, Philip L; Bennett, David A | Neurobiology of disease | 34153464 | 2021 09 |
A meta-analysis of epigenome-wide association studies in Alzheimer's disease highlights novel differentially methylated loci across cortex. | Smith, Rebecca G; Pishva, Ehsan; Shireby, Gemma; Smith, Adam R; Roubroeks, Janou A Y; Hannon, Eilis; Wheildon, Gregory; Mastroeni, Diego; Gasparoni, Gilles; Riemenschneider, Matthias; Giese, Armin; Sharp, Andrew J; Schalkwyk, Leonard; Haroutunian, Vahram; Viechtbauer, Wolfgang; van den Hove, Daniel L A; Weedon, Michael; Brokaw, Danielle; Francis, Paul T; Thomas, Alan J; Love, Seth; Morgan, Kevin; Walter, Jörn; Coleman, Paul D; Bennett, David A; De Jager, Philip L; Mill, Jonathan; Lunnon, Katie | Nature communications | 34112773 | 2021 06 10 |
NEBULA is a fast negative binomial mixed model for differential or co-expression analysis of large-scale multi-subject single-cell data. | He, Liang; Davila-Velderrain, Jose; Sumida, Tomokazu S; Hafler, David A; Kellis, Manolis; Kulminski, Alexander M | Communications biology | 34040149 | 2021 May 26 |
Common DNA methylation dynamics in endometriod adenocarcinoma and glioblastoma suggest universal epigenomic alterations in tumorigenesis. | Karlow, Jennifer A; Miao, Benpeng; Xing, Xiaoyun; Wang, Ting; Zhang, Bo | Communications biology | 34021236 | 2021 May 21 |
Genome-wide analysis identifies a novel LINC-PINT splice variant associated with vascular amyloid pathology in Alzheimer's disease. | Reddy, Joseph S; Allen, Mariet; Ho, Charlotte C G; Oatman, Stephanie R; İş, Özkan; Quicksall, Zachary S; Wang, Xue; Jin, Jiangli; Patel, Tulsi A; Carnwath, Troy P; Nguyen, Thuy T; Malphrus, Kimberly G; Lincoln, Sarah J; Carrasquillo, Minerva M; Crook, Julia E; Kanekiyo, Takahisa; Murray, Melissa E; Bu, Guojun; Dickson, Dennis W; Ertekin-Taner, Nilüfer | Acta neuropathologica communications | 34020725 | 2021 05 21 |
Transcriptome-wide association analysis identifies DACH1 as a kidney disease risk gene that contributes to fibrosis. | Doke, Tomohito; Huang, Shizheng; Qiu, Chengxiang; Liu, Hongbo; Guan, Yuting; Hu, Hailong; Ma, Ziyuan; Wu, Junnan; Miao, Zhen; Sheng, Xin; Zhou, Jianfu; Cao, Aili; Li, Jianhua; Kaufman, Lewis; Hung, Adriana; Brown, Christopher D; Pestell, Richard; Susztak, Katalin | The Journal of clinical investigation | 33998598 | 2021 May 17 |
Transcriptome prediction performance across machine learning models and diverse ancestries. | Okoro, Paul C; Schubert, Ryan; Guo, Xiuqing; Johnson, W Craig; Rotter, Jerome I; Hoeschele, Ina; Liu, Yongmei; Im, Hae Kyung; Luke, Amy; Dugas, Lara R; Wheeler, Heather E | HGG advances | 33937878 | 2021 Apr 08 |
Identification of cell-type-specific marker genes from co-expression patterns in tissue samples. | Qiu, Yixuan; Wang, Jiebiao; Lei, Jing; Roeder, Kathryn | Bioinformatics (Oxford, England) | 33904573 | 2021 Apr 27 |
Human placental cytotrophoblast epigenome dynamics over gestation and alterations in placental disease. | Zhang, Bo; Kim, M Yvonne; Elliot, GiNell; Zhou, Yan; Zhao, Guangfeng; Li, Daofeng; Lowdon, Rebecca F; Gormley, Matthew; Kapidzic, Mirhan; Robinson, Joshua F; McMaster, Michael T; Hong, Chibo; Mazor, Tali; Hamilton, Emily; Sears, Renee L; Pehrsson, Erica C; Marra, Marco A; Jones, Steven J M; Bilenky, Misha; Hirst, Martin; Wang, Ting; Costello, Joseph F; Fisher, Susan J | Developmental cell | 33891899 | 2021 May 03 |
Brain DNA Methylation Patterns in CLDN5 Associated With Cognitive Decline. | Hüls, Anke; Robins, Chloe; Conneely, Karen N; Edgar, Rachel; De Jager, Philip L; Bennett, David A; Wingo, Aliza P; Epstein, Michael P; Wingo, Thomas S | Biological psychiatry | 33838873 | 2021 Feb 03 |
Bayesian estimation of cell type-specific gene expression with prior derived from single-cell data. | Wang, Jiebiao; Roeder, Kathryn; Devlin, Bernie | Genome research | 33837133 | 2021 10 |
Epigenome-wide analysis of long-term air pollution exposure and DNA methylation in monocytes: results from the Multi-Ethnic Study of Atherosclerosis. | C Chi, Gloria; Liu, Yongmei; MacDonald, James W; M Reynolds, Lindsay; Enquobahrie, Daniel A; L Fitzpatrick, Annette; Kerr, Kathleen F; J Budoff, Matthew; Lee, Su-In; Siscovick, David; D Kaufman, Joel | Epigenetics | 33818294 | 2022 03 |
The histone modification H3K4me3 is altered at the ANK1 locus in Alzheimer's disease brain. | Smith, Adam R; Smith, Rebecca G; Macdonald, Ruby; Marzi, Sarah J; Burrage, Joe; Troakes, Claire; Al-Sarraj, Safa; Mill, Jonathan; Lunnon, Katie | Future science OA | 33815817 | 2021 Feb 09 |
Maternal blood metal concentrations and whole blood DNA methylation during pregnancy in the Early Autism Risk Longitudinal Investigation (EARLI). | Aung, Max T; M Bakulski, Kelly; Feinberg, Jason I; F Dou, John; D Meeker, John; Mukherjee, Bhramar; Loch-Caruso, Rita; Ladd-Acosta, Christine; Volk, Heather E; Croen, Lisa A; Hertz-Picciotto, Irva; Newschaffer, Craig J; Fallin, M Daniele | Epigenetics | 33794742 | 2022 03 |
APOL1 at 10 years: progress and next steps. | Freedman, Barry I; Kopp, Jeffrey B; Sampson, Matthew G; Susztak, Katalin | Kidney international | 33794228 | 2021 06 |
Functional enhancer elements drive subclass-selective expression from mouse to primate neocortex. | Mich, John K; Graybuck, Lucas T; Hess, Erik E; Mahoney, Joseph T; Kojima, Yoshiko; Ding, Yi; Somasundaram, Saroja; Miller, Jeremy A; Kalmbach, Brian E; Radaelli, Cristina; Gore, Bryan B; Weed, Natalie; Omstead, Victoria; Bishaw, Yemeserach; Shapovalova, Nadiya V; Martinez, Refugio A; Fong, Olivia; Yao, Shenqin; Mortrud, Marty; Chong, Peter; Loftus, Luke; Bertagnolli, Darren; Goldy, Jeff; Casper, Tamara; Dee, Nick; Opitz-Araya, Ximena; Cetin, Ali; Smith, Kimberly A; Gwinn, Ryder P; Cobbs, Charles; Ko, Andrew L; Ojemann, Jeffrey G; Keene, C Dirk; Silbergeld, Daniel L; Sunkin, Susan M; Gradinaru, Viviana; Horwitz, Gregory D; Zeng, Hongkui; Tasic, Bosiljka; Lein, Ed S; Ting, Jonathan T; Levi, Boaz P | Cell reports | 33789096 | 2021 Mar 30 |
Enhancer viruses for combinatorial cell-subclass-specific labeling. | Graybuck, Lucas T; Daigle, Tanya L; Sedeño-Cortés, Adriana E; Walker, Miranda; Kalmbach, Brian; Lenz, Garreck H; Morin, Elyse; Nguyen, Thuc Nghi; Garren, Emma; Bendrick, Jacqueline L; Kim, Tae Kyung; Zhou, Thomas; Mortrud, Marty; Yao, Shenqin; Siverts, La' Akea; Larsen, Rachael; Gore, Bryan B; Szelenyi, Eric R; Trader, Cameron; Balaram, Pooja; van Velthoven, Cindy T J; Chiang, Megan; Mich, John K; Dee, Nick; Goldy, Jeff; Cetin, Ali H; Smith, Kimberly; Way, Sharon W; Esposito, Luke; Yao, Zizhen; Gradinaru, Viviana; Sunkin, Susan M; Lein, Ed; Levi, Boaz P; Ting, Jonathan T; Zeng, Hongkui; Tasic, Bosiljka | Neuron | 33789083 | 2021 May 05 |
The oncogene AAMDC links PI3K-AKT-mTOR signaling with metabolic reprograming in estrogen receptor-positive breast cancer. | Golden, Emily; Rashwan, Rabab; Woodward, Eleanor A; Sgro, Agustin; Wang, Edina; Sorolla, Anabel; Waryah, Charlene; Tie, Wan Jun; Cuyàs, Elisabet; Ratajska, Magdalena; Kardaś, Iwona; Kozlowski, Piotr; Johnstone, Elizabeth K M; See, Heng B; Duffy, Ciara; Parry, Jeremy; Lagerborg, Kim A; Czapiewski, Piotr; Menendez, Javier A; Gorczyński, Adam; Wasag, Bartosz; Pfleger, Kevin D G; Curtis, Christina; Lee, Bum-Kyu; Kim, Jonghwan; Cursons, Joseph; Pavlos, Nathan J; Biernat, Wojciech; Jain, Mohit; Woo, Andrew J; Redfern, Andrew; Blancafort, Pilar | Nature communications | 33772001 | 2021 03 26 |
Monitoring Recessions: A Bayesian Sequential Quickest Detection Method. | Li, Haixi; Sheng, Xuguang Simon; Yang, Jingyun | International journal of forecasting | 33716367 | 2021 Apr-Jun |
AP-1 subunits converge promiscuously at enhancers to potentiate transcription. | Seo, Jungkyun; Koçak, D Dewran; Bartelt, Luke C; Williams, Courtney A; Barrera, Alejandro; Gersbach, Charles A; Reddy, Timothy E | Genome research | 33674350 | 2021 04 |
Increased Alu RNA processing in Alzheimer brains is linked to gene expression changes. | Cheng, Yubo; Saville, Luke; Gollen, Babita; Veronesi, Ana Alvarez; Mohajerani, Majid; Joseph, Jeffrey T; Zovoilis, Athanasios | EMBO reports | 33645898 | 2021 05 05 |
Creatine kinase B controls futile creatine cycling in thermogenic fat. | Rahbani, Janane F; Roesler, Anna; Hussain, Mohammed F; Samborska, Bozena; Dykstra, Christien B; Tsai, Linus; Jedrychowski, Mark P; Vergnes, Laurent; Reue, Karen; Spiegelman, Bruce M; Kazak, Lawrence | Nature | 33597756 | 2021 02 |
Genetic control of the human brain proteome. | Robins, Chloe; Liu, Yue; Fan, Wen; Duong, Duc M; Meigs, Jacob; Harerimana, Nadia V; Gerasimov, Ekaterina S; Dammer, Eric B; Cutler, David J; Beach, Thomas G; Reiman, Eric M; De Jager, Philip L; Bennett, David A; Lah, James J; Wingo, Aliza P; Levey, Allan I; Seyfried, Nicholas T; Wingo, Thomas S | American journal of human genetics | 33571421 | 2021 03 04 |
Urinary Single-Cell Profiling Captures the Cellular Diversity of the Kidney. | Abedini, Amin; Zhu, Yuan O; Chatterjee, Shatakshee; Halasz, Gabor; Devalaraja-Narashimha, Kishor; Shrestha, Rojesh; S. Balzer, Michael; Park, Jihwan; Zhou, Tong; Ma, Ziyuan; Sullivan, Katie Marie; Hu, Hailong; Sheng, Xin; Liu, Hongbo; Wei, Yi; Boustany-Kari, Carine M; Patel, Uptal; Almaani, Salem; Palmer, Matthew; Townsend, Raymond; Blady, Shira; Hogan, Jonathan; TRIDENT Study Investigators,; Morton, Lori; Susztak, Katalin; TRIDENT Study Investigators | Journal of the American Society of Nephrology : JASN | 33531352 | 2021 03 |
FOS licenses early events in stem cell activation driving skeletal muscle regeneration. | Almada, Albert E; Horwitz, Naftali; Price, Feodor D; Gonzalez, Alfredo E; Ko, Michelle; Bolukbasi, Ozge Vargel; Messemer, Kathleen A; Chen, Sonia; Sinha, Manisha; Rubin, Lee L; Wagers, Amy J | Cell reports | 33503437 | 2021 01 26 |
Characteristics of Epigenetic Clocks Across Blood and Brain Tissue in Older Women and Men. | Grodstein, Francine; Lemos, Bernardo; Yu, Lei; Iatrou, Artemis; De Jager, Philip L; Bennett, David A | Frontiers in neuroscience | 33488342 | 2020 |
Single-cell lineages reveal the rates, routes, and drivers of metastasis in cancer xenografts. | Quinn, Jeffrey J; Jones, Matthew G; Okimoto, Ross A; Nanjo, Shigeki; Chan, Michelle M; Yosef, Nir; Bivona, Trever G; Weissman, Jonathan S | Science (New York, N.Y.) | 33479121 | 2021 02 26 |
Renal tubule Cpt1a overexpression protects from kidney fibrosis by restoring mitochondrial homeostasis. | Miguel, Verónica; Tituaña, Jessica; Herrero, J Ignacio; Herrero, Laura; Serra, Dolors; Cuevas, Paula; Barbas, Coral; Puyol, Diego Rodríguez; Márquez-Expósito, Laura; Ruiz-Ortega, Marta; Castillo, Carolina; Sheng, Xin; Susztak, Katalin; Ruiz-Canela, Miguel; Salas-Salvadó, Jordi; González, Miguel A Martínez; Ortega, Sagrario; Ramos, Ricardo; Lamas, Santiago | The Journal of clinical investigation | 33465052 | 2021 Mar 01 |
Kidney disease genetic risk variants alter lysosomal beta-mannosidase (MANBA) expression and disease severity. | Gu, Xiangchen; Yang, Hongliu; Sheng, Xin; Ko, Yi-An; Qiu, Chengxiang; Park, Jihwan; Huang, Shizheng; Kember, Rachel; Judy, Renae L; Park, Joseph; Damrauer, Scott M; Nadkarni, Girish; Loos, Ruth J F; My, Vy Thi Ha; Chaudhary, Kumardeep; Bottinger, Erwin P; Paranjpe, Ishan; Saha, Aparna; Brown, Christopher; Akilesh, Shreeram; Hung, Adriana M; Palmer, Matthew; Baras, Aris; Overton, John D; Reid, Jeffrey; Ritchie, Marylyn; Rader, Daniel J; Susztak, Katalin | Science translational medicine | 33441424 | 2021 Jan 13 |
The Nuclear Receptor ESRRA Protects from Kidney Disease by Coupling Metabolism and Differentiation. | Dhillon, Poonam; Park, Jihwan; Hurtado Del Pozo, Carmen; Li, Lingzhi; Doke, Tomohito; Huang, Shizheng; Zhao, Juanjuan; Kang, Hyun Mi; Shrestra, Rojesh; Balzer, Michael S; Chatterjee, Shatakshee; Prado, Patricia; Han, Seung Yub; Liu, Hongbo; Sheng, Xin; Dierickx, Pieterjan; Batmanov, Kirill; Romero, Juan P; Prósper, Felipe; Li, Mingyao; Pei, Liming; Kim, Junhyong; Montserrat, Nuria; Susztak, Katalin | Cell metabolism | 33301705 | 2021 Feb 02 |
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A high-fat diet alters genome-wide DNA methylation and gene expression in SM/J mice. | Keleher, Madeline Rose; Zaidi, Rabab; Hicks, Lauren; Shah, Shyam; Xing, Xiaoyun; Li, Daofeng; Wang, Ting; Cheverud, James M | BMC genomics. | 30526554 | 2018 Dec 07; |
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Step-Wise Chondrogenesis of Human Induced Pluripotent Stem Cells and Purification Via a Reporter Allele Generated by CRISPR-Cas9 Genome Editing. | Adkar, Shaunak S; Wu, Chia-Lung; Willard, Vincent P; Dicks, Amanda; Ettyreddy, Adarsh; Steward, Nancy; Bhutani, Nidhi; Gersbach, Charles A; Guilak, Farshid | Stem cells (Dayton, Ohio). | 30378731 | 2019 Jan; |
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Transposable element dysregulation in systemic lupus erythematosus and regulation by histone conformation and Hsp90. | Kelly, Maurer; Lihua, Shi; Zhe, Zhang; Li, Song; Yoselin, Paucar; Michelle, Petri; Sullivan Kathleen, E | Clinical immunology (Orlando, Fla.). | 30149120 | 2018 12; |
A high-throughput screen of real-time ATP levels in individual cells reveals mechanisms of energy failure. | Mendelsohn, Bryce A; Bennett, Neal K; Darch, Maxwell A; Yu, Katharine; Nguyen, Mai K; Pucciarelli, Daniela; Nelson, Maxine; Horlbeck, Max A; Gilbert, Luke A; Hyun, William; Kampmann, Martin; Nakamura, Jean L; Nakamura, Ken | PLoS biology. | 30148842 | 2018 Aug; |
Multi-omic Directed Networks Describe Features of Gene Regulation in Aged Brains and Expand the Set of Genes Driving Cognitive Decline. | Tasaki, Shinya; Gaiteri, Chris; Mostafavi, Sara; Yu, Lei; Wang, Yanling; De Jager, Philip L; Bennett, David A | Frontiers in genetics. | 30140277 | 2018; |
Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci. | Onuchic, Vitor; Lurie, Eugene; Carrero, Ivenise; Pawliczek, Piotr; Patel, Ronak Y; Rozowsky, Joel; Galeev, Timur; Huang, Zhuoyi; Altshuler, Robert C; Zhang, Zhizhuo; Harris, R Alan; Coarfa, Cristian; Ashmore, Lillian; Bertol, Jessica W; Fakhouri, Walid D; Yu, Fuli; Kellis, Manolis; Gerstein, Mark; Milosavljevic, Aleksandar | Science (New York, N.Y.). | 30139913 | 2018 Aug 23; |
Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding. | McDowell, Ian C; Barrera, Alejandro; D'Ippolito, Anthony M; Vockley, Christopher M; Hong, Linda K; Leichter, Sarah M; Bartelt, Luke C; Majoros, William H; Song, Lingyun; Safi, Alexias; Koçak, D Dewran; Gersbach, Charles A; Hartemink, Alexander J; Crawford, Gregory E; Engelhardt, Barbara E; Reddy, Timothy E | Genome research. | 30097539 | 2018 09; |
ChromTime: modeling spatio-temporal dynamics of chromatin marks. | Fiziev, Petko; Ernst, Jason | Genome biology. | 30097049 | 2018 08 10; |
A multi-omic atlas of the human frontal cortex for aging and Alzheimer's disease research. | De Jager, Philip L; Ma, Yiyi; McCabe, Cristin; Xu, Jishu; Vardarajan, Badri N; Felsky, Daniel; Klein, Hans-Ulrich; White, Charles C; Peters, Mette A; Lodgson, Ben; Nejad, Parham; Tang, Anna; Mangravite, Lara M; Yu, Lei; Gaiteri, Chris; Mostafavi, Sara; Schneider, Julie A; Bennett, David A | Scientific data. | 30084846 | 2018 08 07; |
Tumor penetrating peptides inhibiting MYC as a potent targeted therapeutic strategy for triple-negative breast cancers. | Wang, Edina; Sorolla, Anabel; Cunningham, Paula T; Bogdawa, Heique M; Beck, Samuel; Golden, Emily; Dewhurst, Robert E; Florez, Laura; Cruickshank, Mark N; Hoffmann, Katrin; Hopkins, Richard M; Kim, Jonghwan; Woo, Andrew J; Watt, Paul M; Blancafort, Pilar | Oncogene. | 30076412 | 2019 01; |
An Animal Model for Genetic Analysis of Multi-Gene Families: Cloning and Transgenesis of Large Tandemly Repeated Histone Gene Clusters. | Meers, Michael P; Leatham-Jensen, Mary; Penke, Taylor J R; McKay, Daniel J; Duronio, Robert J; Matera, A Gregory | Methods in molecular biology (Clifton, N.J.). | 30073535 | 2018; |
Reproductive period and epigenetic modifications of the oxidative phosphorylation pathway in the human prefrontal cortex. | Bove, Riley M; Patrick, Ellis; Aubin, Cristin McCabe; Srivastava, Gyan; Schneider, Julie A; Bennett, David A; De Jager, Philip L; Chibnik, Lori B | PloS one. | 30052629 | 2018; |
Molecular Imaging of Sirtuin1 Expression-Activity in Rat Brain Using Positron-Emission Tomography-Magnetic-Resonance Imaging with [18F]-2-Fluorobenzoylaminohexanoicanilide. | Bonomi, Robin; Popov, Vadim; Laws, Maxwell T; Gelovani, David; Majhi, Anjoy; Shavrin, Aleksandr; Lu, Xin; Muzik, Otto; Turkman, Nashaat; Liu, Renshyan; Mangner, Thomas; Gelovani, Juri G | Journal of medicinal chemistry. | 30052441 | 2018 08 23; |
Tsix-Mecp2 female mouse model for Rett syndrome reveals that low-level MECP2 expression extends life and improves neuromotor function. | Carrette, Lieselot L G; Blum, Roy; Ma, Weiyuan; Kelleher 3rd, Raymond J; Lee, Jeannie T | Proceedings of the National Academy of Sciences of the United States of America. | 30038001 | 2018 08 07; |
Mapping the Genetic Landscape of Human Cells. | Horlbeck, Max A; Xu, Albert; Wang, Min; Bennett, Neal K; Park, Chong Y; Bogdanoff, Derek; Adamson, Britt; Chow, Eric D; Kampmann, Martin; Peterson, Tim R; Nakamura, Ken; Fischbach, Michael A; Weissman, Jonathan S; Gilbert, Luke A | Cell. | 30033366 | 2018 Aug 09; |
Pre-established Chromatin Interactions Mediate the Genomic Response to Glucocorticoids. | D'Ippolito, Anthony M; McDowell, Ian C; Barrera, Alejandro; Hong, Linda K; Leichter, Sarah M; Bartelt, Luke C; Vockley, Christopher M; Majoros, William H; Safi, Alexias; Song, Lingyun; Gersbach, Charles A; Crawford, Gregory E; Reddy, Timothy E | Cell systems. | 30031775 | 2018 08 22; |
Facile target validation in an animal model with intracellularly expressed monobodies. | Gupta, Ankit; Xu, Jing; Lee, Shirley; Tsai, Steven T; Zhou, Bo; Kurosawa, Kohei; Werner, Michael S; Koide, Akiko; Ruthenburg, Alexander J; Dou, Yali; Koide, Shohei | Nature chemical biology. | 30013062 | 2018 Sep; |
A Suite of Transgenic Driver and Reporter Mouse Lines with Enhanced Brain-Cell-Type Targeting and Functionality. | Daigle, Tanya L; Madisen, Linda; Hage, Travis A; Valley, Matthew T; Knoblich, Ulf; Larsen, Rylan S; Takeno, Marc M; Huang, Lawrence; Gu, Hong; Larsen, Rachael; Mills, Maya; Bosma-Moody, Alice; Siverts, La' Akea; Walker, Miranda; Graybuck, Lucas T; Yao, Zizhen; Fong, Olivia; Nguyen, Thuc Nghi; Garren, Emma; Lenz, Garreck H; Chavarha, Mariya; Pendergraft, Julie; Harrington, James; Hirokawa, Karla E; Harris, Julie A; Nicovich, Philip R; McGraw, Medea J; Ollerenshaw, Douglas R; Smith, Kimberly A; Baker, Christopher A; Ting, Jonathan T; Sunkin, Susan M; Lecoq, Jérôme; Lin, Michael Z; Boyden, Edward S; Murphy, Gabe J; da Costa, Nuno M; Waters, Jack; Li, Lu; Tasic, Bosiljka; Zeng, Hongkui | Cell. | 30007418 | 2018 07 12; |
Inhibition of the miR-192/215-Rab11-FIP2 axis suppresses human gastric cancer progression. | Zhang, Xiaojing; Peng, Yin; Huang, Yong; Deng, Shiqi; Feng, Xianling; Hou, Gangqiang; Lin, Huijuan; Wang, Jian; Yan, Ruibin; Zhao, Yanqiu; Fan, Xinmin; Meltzer, Stephen J; Li, Song; Jin, Zhe | Cell death & disease. | 30006518 | 2018 07 13; |
Alternative empirical Bayes models for adjusting for batch effects in genomic studies. | Zhang, Yuqing; Jenkins, David F; Manimaran, Solaiappan; Johnson, W Evan | BMC bioinformatics. | 30001694 | 2018 07 13; |
Case-control meta-analysis of blood DNA methylation and autism spectrum disorder. | Andrews, Shan V; Sheppard, Brooke; Windham, Gayle C; Schieve, Laura A; Schendel, Diana E; Croen, Lisa A; Chopra, Pankaj; Alisch, Reid S; Newschaffer, Craig J; Warren, Stephen T; Feinberg, Andrew P; Fallin, M Daniele; Ladd-Acosta, Christine | Molecular autism. | 29988321 | 2018; |
BrainEXP: a database featuring with spatiotemporal expression variations and co-expression organizations in human brains. | Jiao, Chuan; Yan, Pengpeng; Xia, Cuihua; Shen, Zhaoming; Tan, Zexi; Tan, Yanyan; Wang, Kangli; Jiang, Yi; Huang, Lingling; Dai, Rujia; Wei, Yu; Xia, Yan; Meng, Qingtuan; Ouyang, Yanmei; Yi, Liu; Duan, Fangyuan; Dai, Jiacheng; Zhao, Shunan; Liu, Chunyu; Chen, Chao | Bioinformatics (Oxford, England). | 29985970 | 2019 01 01; |
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A CRISPR-dCas Toolbox for Genetic Engineering and Synthetic Biology. | Xu, Xiaoshu; Qi, Lei S | Journal of molecular biology. | 29958882 | 2019 01 04; |
A decade in psychiatric GWAS research. | Horwitz, Tanya; Lam, Katie; Chen, Yu; Xia, Yan; Liu, Chunyu | Molecular psychiatry. | 29942042 | 2019 03; |
Gene expression and DNA methylation are extensively coordinated with MRI-based brain microstructural characteristics. | Gaiteri, Chris; Dawe, Robert; Mostafavi, Sara; Blizinsky, Katherine D; Tasaki, Shinya; Komashko, Vitalina; Yu, Lei; Wang, Yanling; Schneider, Julie A; Arfanakis, Konstantinos; De Jager, Philip L; Bennett, David A | Brain imaging and behavior. | 29934819 | 2019 Aug; |
Class I Histone Deacetylase Inhibition by Tianeptinaline Modulates Neuroplasticity and Enhances Memory. | Zhao, Wen-Ning; Ghosh, Balaram; Tyler, Marshall; Lalonde, Jasmin; Joseph, Nadine F; Kosaric, Nina; Fass, Daniel M; Tsai, Li-Huei; Mazitschek, Ralph; Haggarty, Stephen J | ACS chemical neuroscience. | 29932631 | 2018 09 19; |
Microscopes and Mass Spectrometers. | Shields, Bradley; Shalin, Sara C; Tackett, Alan J | Journal of proteomics & bioinformatics. | 29910559 | 2016; |
A modular dCas9-SunTag DNMT3A epigenome editing system overcomes pervasive off-target activity of direct fusion dCas9-DNMT3A constructs. | Pflueger, Christian; Tan, Dennis; Swain, Tessa; Nguyen, Trung; Pflueger, Jahnvi; Nefzger, Christian; Polo, Jose M; Ford, Ethan; Lister, Ryan | Genome research. | 29907613 | 2018 08; |
APOL1: The Balance Imposed by Infection, Selection, and Kidney Disease. | Beckerman, Pazit; Susztak, Katalin | Trends in molecular medicine. | 29886044 | 2018 08; |
Tau Activates Transposable Elements in Alzheimer's Disease. | Guo, Caiwei; Jeong, Hyun-Hwan; Hsieh, Yi-Chen; Klein, Hans-Ulrich; Bennett, David A; De Jager, Philip L; Liu, Zhandong; Shulman, Joshua M | Cell reports. | 29874575 | 2018 06 05; |
Religious Orders Study and Rush Memory and Aging Project. | Bennett, David A; Buchman, Aron S; Boyle, Patricia A; Barnes, Lisa L; Wilson, Robert S; Schneider, Julie A | Journal of Alzheimer's disease : JAD. | 29865057 | 2018; |
Atomistic molecular dynamics simulations of bioactive engrailed 1 interference peptides (EN1-iPeps). | Gandhi, Neha S; Blancafort, Pilar; Mancera, Ricardo L | Oncotarget. | 29854286 | 2018 Apr 27; |
Editing the Epigenome: Reshaping the Genomic Landscape. | Holtzman, Liad; Gersbach, Charles A | Annual review of genomics and human genetics. | 29852072 | 2018 08 31; |
Synthetic transcription factors for cell fate reprogramming. | Black, Joshua B; Gersbach, Charles A | Current opinion in genetics & development. | 29803990 | 2018 10; |
Soluble inflammatory mediators induce transcriptional re-organization that is independent of dna methylation changes in cultured human chorionic villous trophoblasts. | Jiang, Kaiyu; Wong, Laiping; Chen, Yanmin; Xing, Xiaoyun; Li, Daofeng; Wang, Ting; Jarvis, James N | Journal of reproductive immunology. | 29800761 | 2018 Aug; |
Next-generation antibodies for post-translational modifications. | Hattori, Takamitsu; Koide, Shohei | Current opinion in structural biology. | 29753204 | 2018 08; |
Direct Reprogramming of Mouse Fibroblasts into Functional Skeletal Muscle Progenitors. | Bar-Nur, Ori; Gerli, Mattia F M; Di Stefano, Bruno; Almada, Albert E; Galvin, Amy; Coffey, Amy; Huebner, Aaron J; Feige, Peter; Verheul, Cassandra; Cheung, Priscilla; Payzin-Dogru, Duygu; Paisant, Sylvain; Anselmo, Anthony; Sadreyev, Ruslan I; Ott, Harald C; Tajbakhsh, Shahragim; Rudnicki, Michael A; Wagers, Amy J; Hochedlinger, Konrad | Stem cell reports. | 29742392 | 2018 05 08; |
Genomic integration of ERR?-HNF1? regulates renal bioenergetics and prevents chronic kidney disease. | Zhao, Juanjuan; Lupino, Katherine; Wilkins, Benjamin J; Qiu, Chengxiang; Liu, Jian; Omura, Yasuhiro; Allred, Amanda L; McDonald, Caitlin; Susztak, Katalin; Barish, Grant D; Pei, Liming | Proceedings of the National Academy of Sciences of the United States of America. | 29735694 | 2018 05 22; |
Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element. | Cho, Seung Woo; Xu, Jin; Sun, Ruping; Mumbach, Maxwell R; Carter, Ava C; Chen, Y Grace; Yost, Kathryn E; Kim, Jeewon; He, Jing; Nevins, Stephanie A; Chin, Suet-Feung; Caldas, Carlos; Liu, S John; Horlbeck, Max A; Lim, Daniel A; Weissman, Jonathan S; Curtis, Christina; Chang, Howard Y | Cell. | 29731168 | 2018 05 31; |
Cytosine methylation predicts renal function decline in American Indians. | Qiu, Chengxiang; Hanson, Robert L; Fufaa, Gudeta; Kobes, Sayuko; Gluck, Caroline; Huang, Jing; Chen, Yong; Raj, Dominic; Nelson, Robert G; Knowler, William C; Susztak, Katalin | Kidney international. | 29709239 | 2018 06; |
Identification of Smoking-Associated Differentially Methylated Regions Using Reduced Representation Bisulfite Sequencing and Cell type-Specific Enhancer Activation and Gene Expression. | Wan, Ma; Bennett, Brian D; Pittman, Gary S; Campbell, Michelle R; Reynolds, Lindsay M; Porter, Devin K; Crowl, Christopher L; Wang, Xuting; Su, Dan; Englert, Neal A; Thompson, Isabel J; Liu, Yongmei; Bell, Douglas A | Environmental health perspectives. | 29706059 | 2018 04 27; |
RNA-guided transcriptional silencing in vivo with S. aureus CRISPR-Cas9 repressors. | Thakore, Pratiksha I; Kwon, Jennifer B; Nelson, Christopher E; Rouse, Douglas C; Gemberling, Matthew P; Oliver, Matthew L; Gersbach, Charles A | Nature communications. | 29700298 | 2018 Apr 26; |
An epigenetic biomarker of aging for lifespan and healthspan. | Levine, Morgan E; Lu, Ake T; Quach, Austin; Chen, Brian H; Assimes, Themistocles L; Bandinelli, Stefania; Hou, Lifang; Baccarelli, Andrea A; Stewart, James D; Li, Yun; Whitsel, Eric A; Wilson, James G; Reiner, Alex P; Aviv, Abraham; Lohman, Kurt; Liu, Yongmei; Ferrucci, Luigi; Horvath, Steve | Aging. | 29676998 | 2018 04 18; |
Cancer-Germline Antigen Expression Discriminates Clinical Outcome to CTLA-4 Blockade. | Shukla, Sachet A; Bachireddy, Pavan; Schilling, Bastian; Galonska, Christina; Zhan, Qian; Bango, Clyde; Langer, Rupert; Lee, Patrick C; Gusenleitner, Daniel; Keskin, Derin B; Babadi, Mehrtash; Mohammad, Arman; Gnirke, Andreas; Clement, Kendell; Cartun, Zachary J; Van Allen, Eliezer M; Miao, Diana; Huang, Ying; Snyder, Alexandra; Merghoub, Taha; Wolchok, Jedd D; Garraway, Levi A; Meissner, Alexander; Weber, Jeffrey S; Hacohen, Nir; Neuberg, Donna; Potts, Patrick R; Murphy, George F; Lian, Christine G; Schadendorf, Dirk; Hodi, F Stephen; Wu, Catherine J | Cell. | 29656892 | 2018 04 19; |
PREDICTD PaRallel Epigenomics Data Imputation with Cloud-based Tensor Decomposition. | Durham, Timothy J; Libbrecht, Maxwell W; Howbert, J Jeffry; Bilmes, Jeff; Noble, William Stafford | Nature communications | 29643364 | 2018 04 11 |
Single-cell transcriptomics of the mouse kidney reveals potential cellular targets of kidney disease. | Park, Jihwan; Shrestha, Rojesh; Qiu, Chengxiang; Kondo, Ayano; Huang, Shizheng; Werth, Max; Li, Mingyao; Barasch, Jonathan; Suszták, Katalin | Science (New York, N.Y.). | 29622724 | 2018 05 18; |
Introduction: Systems Biology of Kidney Disease. | Sharma, Kumar; Susztak, Katalin; Pennathur, Subramaniam | Seminars in nephrology. | 29602402 | 2018 03; |
The Role of Peroxisome Proliferator-Activated Receptor ? Coactivator 1? (PGC-1?) in Kidney Disease. | Li, Szu-Yuan; Susztak, Katalin | Seminars in nephrology. | 29602395 | 2018 03; |
Pulling the genome in opposite directions to dissect gene networks. | Gersbach, Charles A; Barrangou, Rodolphe | Genome biology. | 29580291 | 2018 Mar 26; |
Dissecting the Functional Consequences of De Novo DNA Methylation Dynamics in Human Motor Neuron Differentiation and Physiology. | Ziller, Michael J; Ortega, Juan A; Quinlan, Katharina A; Santos, David P; Gu, Hongcang; Martin, Eric J; Galonska, Christina; Pop, Ramona; Maidl, Susanne; Di Pardo, Alba; Huang, Mei; Meltzer, Herbert Y; Gnirke, Andreas; Heckman, C J; Meissner, Alexander; Kiskinis, Evangelos | Cell stem cell. | 29551301 | 2018 04 05; |
Elevated DNA methylation across a 48-kb region spanning the HOXA gene cluster is associated with Alzheimer's disease neuropathology. | Smith, Rebecca G; Hannon, Eilis; De Jager, Philip L; Chibnik, Lori; Lott, Simon J; Condliffe, Daniel; Smith, Adam R; Haroutunian, Vahram; Troakes, Claire; Al-Sarraj, Safa; Bennett, David A; Powell, John; Lovestone, Simon; Schalkwyk, Leonard; Mill, Jonathan; Lunnon, Katie | Alzheimer's & dementia : the journal of the Alzheimer's Association. | 29550519 | 2018 Dec; |
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, Alexander | Nature structural & molecular biology. | 29531288 | 2018 Mar 12; |
Screening Regulatory Element Function with CRISPR/Cas9-based Epigenome Editing. | Klann, Tyler S; Crawford, Gregory E; Reddy, Timothy E; Gersbach, Charles A | Methods in molecular biology (Clifton, N.J.). | 29524151 | 2018; |
Zinc Fingers, TALEs, and CRISPR Systems: A Comparison of Tools for Epigenome Editing. | Waryah, Charlene Babra; Moses, Colette; Arooj, Mahira; Blancafort, Pilar | Methods in molecular biology (Clifton, N.J.). | 29524128 | 2018; |
The NIEHS TaRGET II Consortium and environmental epigenomics. | Wang, Ting; Pehrsson, Erica C; Purushotham, Deepak; Li, Daofeng; Zhuo, Xiaoyu; Zhang, Bo; Lawson, Heather A; Province, Michael A; Krapp, Christopher; Lan, Yemin; Coarfa, Cristian; Katz, Tiffany A; Tang, Wan Yee; Wang, Zhibin; Biswal, Shyam; Rajagopalan, Sanjay; Colacino, Justin A; Tsai, Zing Tsung-Yeh; Sartor, Maureen A; Neier, Kari; Dolinoy, Dana C; Pinto, Jayant; Hamanaka, Robert B; Mutlu, Gokhan M; Patisaul, Heather B; Aylor, David L; Crawford, Gregory E; Wiltshire, Tim; Chadwick, Lisa H; Duncan, Christopher G; Garton, Amanda E; McAllister, Kimberly A; TaRGET II Consortium; Bartolomei, Marisa S; Walker, Cheryl L; Tyson, Frederick L | Nature biotechnology. | 29509741 | 2018 Mar 06; |
CRISPR-based methods for high-throughput annotation of regulatory DNA. | Klann, Tyler S; Black, Joshua B; Gersbach, Charles A | Current opinion in biotechnology. | 29500989 | 2018 Feb 28; |
Remodeling the Specificity of an Endosomal CORVET Tether Underlies Formation of Regulated Secretory Vesicles in the Ciliate Tetrahymena thermophila. | Sparvoli, Daniela; Richardson, Elisabeth; Osakada, Hiroko; Lan, Xun; Iwamoto, Masaaki; Bowman, Grant R; Kontur, Cassandra; Bourland, William A; Lynn, Denis H; Pritchard, Jonathan K; Haraguchi, Tokuko; Dacks, Joel B; Turkewitz, Aaron P | Current biology : CB. | 29478853 | 2018 03 05; |
Positional effects revealed in Illumina methylation array and the impact on analysis. | Jiao, Chuan; Zhang, Chunling; Dai, Rujia; Xia, Yan; Wang, Kangli; Giase, Gina; Chen, Chao; Liu, Chunyu | Epigenomics. | 29469594 | 2018 05; |
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 Gregory | BMC genomics. | 29466941 | 2018 02 21; |
Light-Dependent Cytoplasmic Recruitment Enhances the Dynamic Range of a Nuclear Import Photoswitch. | Yumerefendi, Hayretin; Wang, Hui; Dickinson, Daniel J; Lerner, Andrew M; Malkus, Per; Goldstein, Bob; Hahn, Klaus; Kuhlman, Brian | Chembiochem : a European journal of chemical biology. | 29446199 | ; |
Shared molecular neuropathology across major psychiatric disorders parallels polygenic overlap. | Gandal, Michael J; Haney, Jillian R; Parikshak, Neelroop N; Leppa, Virpi; Ramaswami, Gokul; Hartl, Chris; Schork, Andrew J; Appadurai, Vivek; Buil, Alfonso; Werge, Thomas M; Liu, Chunyu; White, Kevin P; CommonMind Consortium; PsychENCODE Consortium; iPSYCH-BROAD Working Group; Horvath, Steve; Geschwind, Daniel H | Science (New York, N.Y.). | 29439242 | 2018 02 09; |
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 P | mSystems. | 29435496 | 2018 Jan-Feb; |
Hallmarks of cancer: The CRISPR generation. | Moses, Colette; Garcia-Bloj, Benjamin; Harvey, Alan R; Blancafort, Pilar | European journal of cancer (Oxford, England : 1990). | 29433054 | 2018 04; |
Genome-wide tracking of dCas9-methyltransferase footprints. | Galonska, Christina; Charlton, Jocelyn; Mattei, Alexandra L; Donaghey, Julie; Clement, Kendell; Gu, Hongcang; Mohammad, Arman W; Stamenova, Elena K; Cacchiarelli, Davide; Klages, Sven; Timmermann, Bernd; Cantz, Tobias; Schöler, Hans R; Gnirke, Andreas; Ziller, Michael J; Meissner, Alexander | Nature communications. | 29426832 | 2018 02 09; |
A Novel Substrate Radiotracer for Molecular Imaging of SIRT2 Expression and Activity with Positron Emission Tomography. | Bonomi, Robin E; Laws, Maxwell; Popov, Vadim; Kamal, Swatabdi; Potukutchi, Shreya; Shavrin, Aleksandr; Lu, Xin; Turkman, Nashaat; Liu, Ren-Shyan; Mangner, Thomas; Gelovani, Juri G | Molecular imaging and biology. | 29423902 | 2018 08; |
Role of epigenetics in the development of childhood asthma. | Davidson, Elizabeth J; Yang, Ivana V | Current opinion in allergy and clinical immunology. | 29389731 | 2018 04; |
Methylene-tetrahydrofolate reductase contributes to allergic airway disease. | Eyring, Kenneth R; Pedersen, Brent S; Maclean, Kenneth N; Stabler, Sally P; Yang, Ivana V; Schwartz, David A | PloS one. | 29329322 | 2018; |
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 T | Proceedings of the National Academy of Sciences of the United States of America. | 29282321 | 2018 Jan 23; |
Engineering cell sensing and responses using a GPCR-coupled CRISPR-Cas system. | Kipniss, Nathan H; Dingal, P C Dave P; Abbott, Timothy R; Gao, Yuchen; Wang, Haifeng; Dominguez, Antonia A; Labanieh, Louai; Qi, Lei S | Nature communications. | 29263378 | 2017 12 20; |
CRISPR Approaches to Small Molecule Target Identification. | Jost, Marco; Weissman, Jonathan S | ACS chemical biology. | 29261286 | 2018 Feb 16; |
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 C | The Journal of cell biology. | 29259096 | 2018 Feb 05; |
Sophisticated lessons from simple organisms: appreciating the value of curiosity-driven research. | Duronio, Robert J; O'Farrell, Patrick H; Sluder, Greenfield; Su, Tin Tin | Disease models & mechanisms. | 29259023 | 2017 12 19; |
SMG-1 inhibition by miR-192/-215 causes epithelial-mesenchymal transition in gastric carcinogenesis via activation of Wnt signaling. | Zhang, Xiaojing; Peng, Yin; Huang, Yong; Yang, Mengting; Yan, Ruibin; Zhao, Yanqiu; Cheng, Yulan; Liu, Xi; Deng, Shiqi; Feng, Xianling; Lin, Huijuan; Yu, Huimin; Chen, Si; Zhao, Zhenfu; Li, Shanni; Li, Kuan; Wang, Liang; Wei, Yanjie; He, Zhendan; Fan, Xinmin; Meltzer, Stephen J; Li, Song; Jin, Zhe | Cancer medicine. | 29239144 | 2018 01; |
Comprehensive Whole DNA Methylome Analysis by Integrating MeDIP-seq and MRE-seq. | Xing, Xiaoyun; Zhang, Bo; Li, Daofeng; Wang, Ting | Methods in molecular biology (Clifton, N.J.). | 29224147 | 2018; |
Transposable Element Mediated Innovation in Gene Regulatory Landscapes of Cells: Re-Visiting the ''Gene-Battery'' Model. | Sundaram, Vasavi; Wang, Ting | BioEssays : news and reviews in molecular, cellular and developmental biology. | 29206283 | 2018 Jan; |
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Tobacco exposure-related alterations in DNA methylation and gene expression in human monocytes: the Multi-Ethnic Study of Atherosclerosis (MESA). | Reynolds, Lindsay M; Lohman, Kurt; Pittman, Gary S; Barr, R Graham; Chi, Gloria C; Kaufman, Joel; Wan, Ma; Bell, Douglas A; Blaha, Michael J; Rodriguez, Carlos J; Liu, Yongmei | Epigenetics. | 29166816 | 2017; |
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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 A | JAMA neurology. | 29084334 | 2017 Dec 01; |
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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, Weihong | The American journal of the medical sciences. | 29078839 | 2017 Oct; |
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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 S | Molecular cell. | 28985505 | 2017 Oct 05; |
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 W | Nucleic acids research. | 28981717 | 2017 Dec 01; |
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, Katalin | EBioMedicine. | 28970079 | 2017 Oct; |
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, Alexander | Nature. | 28959968 | 2017 09 28; |
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 Z | ACS chemical biology. | 28938067 | 2018 Feb 16; |
Cooperative interactions enable singular olfactory receptor expression in mouse olfactory neurons. | Monahan, Kevin; Schieren, Ira; Cheung, Jonah; Mumbey-Wafula, Alice; Monuki, Edwin S; Lomvardas, Stavros | eLife. | 28933695 | 2017 Sep 21; |
Differentially conserved transcriptomic response to adversity related to self-rated health in the multi-ethnic study of atherosclerosis. | Riestra, Pia; Gebreab, Samson Y; Liu, Yongmei; Diez Roux, Ana V; Khan, Rumana R; Gaye, Amadou; Xu, Ruihua; Davis, S K | Experimental biology and medicine (Maywood, N.J.). | 28927291 | 2017 Dec; |
In Utero Exposure to a High-Fat Diet Programs Hepatic Hypermethylation and Gene Dysregulation and Development of Metabolic Syndrome in Male Mice. | Seki, Yoshinori; Suzuki, Masako; Guo, Xingyi; Glenn, Alan Scott; Vuguin, Patricia M; Fiallo, Ariana; Du, Quan; Ko, Yi-An; Yu, Yiting; Susztak, Katalin; Zheng, Deyou; Greally, John M; Katz, Ellen B; Charron, Maureen J | Endocrinology | 28911167 | 2017 Sep 01 |
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Genome Engineering for Personalized Arthritis Therapeutics. | Adkar, Shaunak S; Brunger, Jonathan M; Willard, Vincent P; Wu, Chia-Lung; Gersbach, Charles A; Guilak, Farshid | Trends in molecular medicine. | 28887050 | 2017 Oct; |
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 S | Cell stem cell. | 28886366 | 2017 Sep 07; |
Denoising genome-wide histone ChIP-seq with convolutional neural networks. | Koh, Pang Wei; Pierson, Emma; Kundaje, Anshul | Bioinformatics (Oxford, England). | 28881977 | 2017 Jul 15; |
SmartScope2: Simultaneous Imaging and Reconstruction of Neuronal Morphology. | Long, Brian; Zhou, Zhi; Cetin, Ali; Ting, Jonathan; Gwinn, Ryder; Tasic, Bosiljka; Daigle, Tanya; Lein, Ed; Zeng, Hongkui; Saggau, Peter; Hawrylycz, Michael; Peng, Hanchuan | Scientific reports. | 28839271 | 2017 08 24; |
APOL1 and Cardiovascular Disease: A Story in Evolution. | Bajaj, Archna; Susztak, Katalin; Damrauer, Scott M | Arteriosclerosis, thrombosis, and vascular biology | 28835482 | 2017 Sep |
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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 A | ACS synthetic biology. | 28793186 | 2017 Nov 17; |
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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 K | Journal of clinical immunology. | 28786026 | 2017 Oct; |
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The Three-Dimensional Organization of Mammalian Genomes. | Yu, Miao; Ren, Bing | Annual review of cell and developmental biology. | 28783961 | 2017 Oct 06; |
Correcting nucleotide-specific biases in high-throughput sequencing data. | Wang, Jeremy R; Quach, Bryan; Furey, Terrence S | BMC bioinformatics. | 28764645 | 2017 Aug 01; |
Cells lay their own tracks - optogenetic Cdc42 activation stimulates fibronectin deposition supporting directed migration. | Zimmerman, Seth P; Asokan, Sreeja B; Kuhlman, Brian; Bear, James E | Journal of cell science. | 28754687 | 2017 Sep 15; |
PGC-1? Protects from Notch-Induced Kidney Fibrosis Development. | Han, Seung Hyeok; Wu, Mei-Yan; Nam, Bo Young; Park, Jung Tak; Yoo, Tae-Hyun; Kang, Shin-Wook; Park, Jihwan; Chinga, Frank; Li, Szu-Yuan; Susztak, Katalin | Journal of the American Society of Nephrology : JASN. | 28751525 | 2017 Nov; |
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 J | Kidney & blood pressure research. | 28750406 | 2017; |
Whole exome sequencing identified genetic variations in Chinese hemangioblastoma patients. | Ma, Dexuan; Yang, Jingyun; Wang, Ying; Huang, Xiang; Du, Guhong; Zhou, Liangfu | American journal of medical genetics. Part A. | 28742274 | 2017 Oct; |
Benign and tumor parenchyma metabolomic profiles affect compensatory renal growth in renal cell carcinoma surgical patients. | Rosenzweig, Barak; Rubinstein, Nimrod D; Reznik, Ed; Shingarev, Roman; Juluru, Krishna; Akin, Oguz; Hsieh, James J; Jaimes, Edgar A; Russo, Paul; Susztak, Katalin; Coleman, Jonathan A; Hakimi, A Ari | PloS one. | 28727768 | 2017; |
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, Katalin | JCI insight. | 28724797 | 2017 Jul 20; |
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 Klaus | British journal of pharmacology. | 28710789 | 2017 Oct; |
High-Throughput Colorimetric Assay for Identifying PARP-1 Inhibitors Using a Large Small-Molecule Collection. | Kotova, Elena; Tulin, Alexei V | Methods in molecular biology (Clifton, N.J.). | 28695517 | 2017; |
Neighborhood characteristics influence DNA methylation of genes involved in stress response and inflammation: The Multi-Ethnic Study of Atherosclerosis. | Smith, Jennifer A; Zhao, Wei; Wang, Xu; Ratliff, Scott M; Mukherjee, Bhramar; Kardia, Sharon L R; Liu, Yongmei; Roux, Ava V Diez; Needham, Belinda L | Epigenetics. | 28678593 | 2017 08; |
The environment, epigenome, and asthma. | Yang, Ivana V; Lozupone, Catherine A; Schwartz, David A | The Journal of allergy and clinical immunology. | 28673400 | 2017 Jul; |
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 L | Molecular neurodegeneration. | 28668092 | 2017 07 01; |
Genetic and epigenetic control of gene expression by CRISPR-Cas systems. | Lo, Albert; Qi, Lei | F1000Research. | 28649363 | 2017; |
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, Yongmei | Immunity & ageing : I & A. | 28642803 | 2017; |
Repurposing CRISPR System for Transcriptional Activation. | Chen, Meng; Qi, Lei Stanley | Advances in experimental medicine and biology. | 28639197 | 2017; |
Mammalian Synthetic Biology: Engineering Biological Systems. | Black, Joshua B; Perez-Pinera, Pablo; Gersbach, Charles A | Annual review of biomedical engineering. | 28633563 | 2017 06 21; |
Genetic-epigenetic interactions in cis: a major focus in the post-GWAS era. | Do, Catherine; Shearer, Alyssa; Suzuki, Masako; Terry, Mary Beth; Gelernter, Joel; Greally, John M; Tycko, Benjamin | Genome biology. | 28629478 | 2017 06 19; |
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 J | JCI insight. | 28614801 | 2017 Jun 15; |
Ranking and characterization of established BMI and lipid associated loci as candidates for gene-environment interactions. | Shungin, Dmitry; Deng, Wei Q; Varga, Tibor V; Luan, Jian'an; Mihailov, Evelin; Metspalu, Andres; GIANT Consortium; Morris, Andrew P; Forouhi, Nita G; Lindgren, Cecilia; Magnusson, Patrik K E; Pedersen, Nancy L; Hallmans, Göran; Chu, Audrey Y; Justice, Anne E; Graff, Mariaelisa; Winkler, Thomas W; Rose, Lynda M; Langenberg, Claudia; Cupples, L Adrienne; Ridker, Paul M; Wareham, Nicholas J; Ong, Ken K; Loos, Ruth J F; Chasman, Daniel I; Ingelsson, Erik; Kilpeläinen, Tuomas O; Scott, Robert A; Mägi, Reedik; Paré, Guillaume; Franks, Paul W | PLoS genetics | 28614350 | 2017 Jun |
EpiCompare: An online tool to define and explore genomic regions with tissue or cell type-specific epigenomic features. | He, Yu; Wang, Ting | Bioinformatics (Oxford, England). | 28605501 | 2017 Jun 09; |
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. | 28604729 | 2017 Jul; |
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, Ting | BMC genomics. | 28583088 | 2017 Jun 05; |
SERPINB2 is regulated by dynamic interactions with pause-release proteins and enhancer RNAs. | Shii, Lihua; Song, Li; Maurer, Kelly; Zhang, Zhe; Sullivan, Kathleen E | Molecular immunology. | 28578223 | 2017 Aug; |
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, Katalin | American journal of human genetics. | 28575649 | 2017 Jun 01; |
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, Liangfu | Molecular carcinogenesis. | 28574654 | 2017 Oct; |
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, Steve | Nature communications. | 28516910 | 2017 May 18; |
DIRECTION: a machine learning framework for predicting and characterizing DNA methylation and hydroxymethylation in mammalian genomes. | Pavlovic, Milos; Ray, Pradipta; Pavlovic, Kristina; Kotamarti, Aaron; Chen, Min; Zhang, Michael Q | Bioinformatics (Oxford, England). | 28505334 | 2017 Oct 01; |
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 J | Nature methods. | 28481362 | 2017 Jun; |
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. | 28461595 | 2017 May 01; |
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 H | Genome medicine. | 28446242 | 2017 04 26; |
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; S | Cell reports. | 28445736 | 2017 Apr 25; |
Bidirectional approaches for optogenetic regulation of gene expression in mammalian cells using Arabidopsis cryptochrome 2. | Pathak, Gopal P; Spiltoir, Jessica I; Höglund, Camilla; Polstein, Lauren R; Heine-Koskinen, Sari; Gersbach, Charles A; Rossi, Jari; Tucker, Chandra L | Nucleic acids research. | 28431041 | 2017 Nov 16; |
Multiplexed Dynamic Imaging of Genomic Loci by Combined CRISPR Imaging and DNA Sequential FISH. | Takei, Yodai; Shah, Sheel; Harvey, Sho; Qi, Lei S; Cai, Long | Biophysical journal. | 28427715 | 2017 May 09; |
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, K | Journal of lipid research. | 28404638 | 2017 Jun; |
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 A | Nature biotechnology. | 28369033 | 2017 Jun; |
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Precision Medicine Approaches to Diabetic Kidney Disease: Tissue as an Issue. | Gluck, Caroline; Ko, Yi-An; Susztak, Katalin | Current diabetes reports. | 28364354 | 2017 05; |
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 K | Environmental health perspectives. | 28362264 | 2017 Apr; |
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. | 28348391 | 2017 Mar 28; |
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. | 28346137 | 2017 03 27; |
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 K | Methods in enzymology. | 28336073 | 2017; |
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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 L | Molecular psychiatry. | 28322283 | 2017 Mar 21; |
Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions. | Shen, John Paul; Zhao, Dongxin; Sasik, Roman; Luebeck, Jens; Birmingham, Amanda; Bojorquez-Gomez, Ana; Licon, Katherine; Klepper, Kristin; Pekin, Daniel; Beckett, Alex N; Sanchez, Kyle Salinas; Thomas, Alex; Kuo, Chih-Chung; Du, Dan; Roguev, Assen; Lewis, Nathan E; Chang, Aaron N; Kreisberg, Jason F; Krogan, Nevan; Qi, Lei; Ideker, Trey; Mali, Prashant | Nature methods. | 28319113 | 2017 Jun; |
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 A | American journal of respiratory and critical care medicine. | 28294656 | 2017 03 15; |
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. | 28249355 | 2017 May; |
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, Katalin | Nature medicine. | 28218918 | 2017 Apr; |
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 T | Proceedings of the National Academy of Sciences of the United States of America. | 28182563 | 2016 Dec 13; |
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, Viviane | Scientific reports. | 28139744 | 2017 Jan 31; |
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 B | PloS one. | 28135296 | 2017; |
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. | 28123037 | 2017 Jan 25; |
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. | 28112643 | 2017 Jan 23; |
Cooperative Binding of Transcription Factors Orchestrates Reprogramming. | Chronis, Constantinos; Fiziev, Petko; Papp, Bernadett; Butz, Stefan; Bonora, Giancarlo; Sabri, Shan; Ernst, Jason; Plath, Kathrin | Cell. | 28111071 | 2017 Jan 26; |
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. | 28095751 | 2017 Jan 17; |
Epigenetic Research in Neuropsychiatric Disorders: the ''Tissue Issue''. | Bakulski, Kelly M; Halladay, Alycia; Hu, Valerie W; Mill, Jonathan; Fallin, M Daniele | Current behavioral neuroscience reports. | 28093577 | 2016 Sep; |
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.). | 28088687 | 2017 Feb; |
The novel fusion transcript NR5A2-KLHL29FT is generated by an insertion at the KLHL29 locus. | Sun, Zhenguo; Ke, Xiquan; Salzberg, Steven L; Kim, Daehwan; Antonescu, Valentin; Cheng, Yulan; Huang, Binbin; Song, Jee Hoon; Abraham, John M; Ibrahim, Sariat; Tian, Hui; Meltzer, Stephen J | Cancer. | 28081303 | 2017 05 01; |
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, Jonathan | Human molecular genetics. | 28011714 | 2017 01 01; |
DeFCoM: analysis and modeling of transcription factor binding sites using a motif-centric genomic footprinter. | Quach, Bryan; Furey, Terrence S | Bioinformatics (Oxford, England). | 27993786 | 2017 Apr 01; |
Developing Treatments for Chronic Kidney Disease in the 21st Century. | Breyer, Matthew D; Susztak, Katalin | Seminars in nephrology. | 27987541 | 2016 Nov; |
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. | 27984733 | 2016 Dec 15; |
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. | 27984732 | 2016 Dec 15; |
''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 Daniele | Epigenetics & chromatin. | 27980682 | 2016; |
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.). | 27980086 | 2017 Jan 06; |
Expression of HDAC2 but Not HDAC1 Transcript Is Reduced in Dorsolateral Prefrontal Cortex of Patients with Schizophrenia. | Schroeder, Frederick A; Gilbert, Tonya M; Feng, Ningping; Taillon, Brendan D; Volkow, Nora D; Innis, Robert B; Hooker, Jacob M; Lipska, Barbara K | ACS chemical neuroscience. | 27959513 | 2017 03 15; |
Absence of miR-146a in Podocytes Increases Risk of Diabetic Glomerulopathy via Up-regulation of ErbB4 and Notch-1. | Lee, Ha Won; Khan, Samia Q; Khaliqdina, Shehryar; Altintas, Mehmet M; Grahammer, Florian; Zhao, Jimmy L; Koh, Kwi Hye; Tardi, Nicholas J; Faridi, Mohd Hafeez; Geraghty, Terese; Cimbaluk, David J; Susztak, Katalin; Moita, Luis F; Baltimore, David; Tharaux, Pierre-Louis; Huber, Tobias B; Kretzler, Matthias; Bitzer, Markus; Reiser, Jochen; Gupta, Vineet | The Journal of biological chemistry | 27913625 | 2017 Jan 13 |
Trans-acting epigenetic effects of chromosomal aneuploidies: lessons from Down syndrome and mouse models. | Do, Catherine; Xing, Zhuo; Yu, Y Eugene; Tycko, Benjamin | Epigenomics. | 27911079 | 2017 Feb; |
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, Katalin | The Journal of biological chemistry. | 27909050 | 2017 01 20; |
LOVTRAP: A Versatile Method to Control Protein Function with Light. | Wang, Hui; Hahn, Klaus M | Current 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 D | Environmental health : a global access science source. | 27903268 | 2016 12 01; |
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, Paula | Alzheimer's & dementia : the journal of the Alzheimer's Association. | 27883893 | 2017 Jun; |
New insights into the immunopathogenesis of systemic lupus erythematosus. | Tsokos, George C; Lo, Mindy S; Costa Reis, Patricia; Sullivan, Kathleen E | Nature reviews. Rheumatology | 27872476 | 2016 11 22 |
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 A | Cell reports. | 27851973 | 2016 Nov 15; |
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, Aleksandar | Cell reports. | 27851969 | 2016 11 15; |
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. | 27851967 | 2016 Nov 15; |
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, D | Molecular psychiatry. | 27843151 | 2016 Nov 15; |
Genetic engineering: Chemical control for CRISPR editing. | Hilton, Isaac B; Gersbach, Charles A | Nature chemical biology. | 27820804 | 2017 Jan; |
Differential transcriptome expression in human nucleus accumbens as a function of loneliness. | Canli, T; Wen, R; Wang, X; Mikhailik, A; Yu, L; Fleischman, D; Wilson, R S; Bennett, D A | Molecular psychiatry. | 27801889 | 2017 07; |
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. | 27795562 | 2017 01; |
Nuclear but not mitochondrial-encoded oxidative phosphorylation genes are altered in aging, mild cognitive impairment, and Alzheimer's disease. | Mastroeni, Diego; Khdour, Omar M; Delvaux, Elaine; Nolz, Jennifer; Olsen, Gary; Berchtold, Nicole; Cotman, Carl; Hecht, Sidney M; Coleman, Paul D | Alzheimer's & dementia : the journal of the Alzheimer's Association | 27793643 | 2017 May |
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. | 27776111 | 2016 Dec; |
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. | 27760116 | 2016 Oct 19; |
The long noncoding RNA Tug1 connects metabolic changes with kidney disease in podocytes. | Li, Szu Yuan; Susztak, Katalin | The Journal of clinical investigation. | 27760046 | 2016 Nov 01; |
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 A | The Journal of allergy and clinical immunology. | 27745942 | 2016 Oct 13; |
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 Z | Gut. | 27742763 | 2018 Jan; |
Epigenomic and transcriptional control of insulin resistance. | Rosen, E D | Journal of internal medicine. | 27739225 | 2016 Nov; |
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 | ; |
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 D | Cellular signalling. | 27705752 | 2016 Dec; |
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. | 27701403 | 2016 Nov; |
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 A | Oncogene. | 27694895 | 2017 Mar 23; |
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, Youxin | Medicine. | 27684793 | 2016 Sep; |
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 Claudio | Scientific reports. | 27681803 | 2016 Sep 29; |
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. | 27661255 | 2016 Sep 23; |
Cognitive decline following incident and preexisting diabetes mellitus in a population sample. | Rajan, Kumar B; Arvanitakis, Zoe; Lynch, Elizabeth B; McAninch, Elizabeth A; Wilson, Robert S; Weuve, Jennifer; Barnes, Lisa L; Bianco, Antonio C; Evans, Denis A | Neurology | 27655734 | 2016 Oct 18 |
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 J | Circulation. Cardiovascular genetics. | 27651444 | 2016 Oct; |
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, Yongmei | Nicotine & tobacco research : official journal of the Society for Research on Nicotine and Tobacco. | 27613907 | 2017 Apr 01; |
Engineering and Application of LOV2-Based Photoswitches. | Zimmerman, S P; Kuhlman, B; Yumerefendi, H | Methods in enzymology. | 27586333 | 2016; |
Genome-wide mapping and analysis of chromosome architecture. | Schmitt, Anthony D; Hu, Ming; Ren, Bing | Nature reviews. Molecular cell biology. | 27580841 | 2016 12; |
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, Jonathan | Genome biology. | 27572077 | 2016 Aug 30; |
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. | 27566777 | 2016 Aug 15; |
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. | 27542829 | 2016 Aug 01; |
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 Evan | Bioinformatics (Oxford, England). | 27540268 | 2016 Dec 15; |
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. | 27529180 | 2016 Sep 20; |
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, Pilar | Oncotarget. | 27528034 | 2016 Sep 13; |
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 V | Journal of immunology (Baltimore, Md. : 1950). | 27527593 | 2016 Sep 15; |
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. | 27524438 | 2016 Sep 1; |
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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, Jingyun | Medicine. | 27175669 | 2016 May; |
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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, Arturas | American journal of human genetics. | 27087318 | 2016 May 05; |
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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. | 26876208 | 2016 Feb 15; |
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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 J | Bioorganic & medicinal chemistry letters. | 26804233 | 2016 Feb 15; |
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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. | 26776520 | 2016 Feb 2; |
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. | 26740581 | 2016 Jan 5; |
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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. | 26702833 | 2015 Dec 21; |
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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. | 26684672 | 2015 Dec; |
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 M | ACS chemical neuroscience. | 26675505 | 2016 05 18; |
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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, Yingbin | Medicine. | 26656369 | 2015 Dec; |
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 A | PloS one. | 26642056 | 2015; |
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, Anna | Diabetes. | 26631737 | 2016 Mar; |
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. | 26619357 | 2016 Jan; |
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. | 26607552 | 2015; |
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. | 26603904 | 2015 Nov 10; |
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. | 26595473 | 2015 Nov; |
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. | 26579811 | 2015 Nov; |
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 A | Human molecular genetics. | 26566671 | 2016 Jan 15; |
Identification of differentially methylated loci using wavelet-based functional mixed models. | Lee, Wonyul; Morris, Jeffrey S | Bioinformatics (Oxford, England). | 26559505 | 2016 Mar 01; |
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. | 26553823 | 2015 Dec; |
Complete haplotype phasing of the MHC and KIR loci with targeted HaploSeq. | Selvaraj, Siddarth; Schmitt, Anthony D; Dixon, Jesse R; Ren, Bing | BMC genomics. | 26541200 | 2015; |
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. | 26523391 | 2015; |
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. | 26508642 | 2015 Nov 10; |
Validation and genomic interrogation of the MET variant rs11762213 as a predictor of adverse outcomes in clear cell renal cell carcinoma. | Hakimi, A Ari; Ostrovnaya, Irina; Jacobsen, Anders; Susztak, Katalin; Coleman, Jonathan A; Russo, Paul; Winer, Andrew G; Mano, Roy; Sankin, Alexander I; Motzer, Robert J; Voss, Martin H; Offit, Kenneth; Purdue, Mark; Pomerantz, Mark; Freedman, Matthew; Choueiri, Toni K; Hsieh, James J; Klein, Robert J | Cancer. | 26505625 | 2016 Feb 01; |
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 A | Nature genetics. | 26502339 | 2015 Dec; |
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. | 26501517 | 2015 Dec; |
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. | 26490019 | 2015; |
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. | 26481319 | 2016 Jan; |
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, Jonathan | Epigenetics. | 26479702 | 2015; |
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. | 26474029 | 2016 Jan 15; |
Ribosome profiling reveals the what, when, where and how of protein synthesis. | Brar, Gloria A; Weissman, Jonathan S | Nature reviews. Molecular cell biology. | 26465719 | 2015 Nov; |
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. | 26460735 | 2015 Oct 20; |
Interindividual methylomic variation across blood, cortex, and cerebellum: implications for epigenetic studies of neurological and neuropsychiatric phenotypes. | Hannon, Eilis; Lunnon, Katie; Schalkwyk, Leonard; Mill, Jonathan | Epigenetics. | 26457534 | 2015; |
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. | 26451733 | 2015 Oct; |
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. | 26450788 | 2015 Dec; |
Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes. | Yao, Lijing; Berman, Benjamin P; Farnham, Peggy J | Critical reviews in biochemistry and molecular biology. | 26446758 | 2015; |
Design, Assembly, and Characterization of TALE-Based Transcriptional Activators and Repressors. | Thakore, Pratiksha I; Gersbach, Charles A | Methods in molecular biology (Clifton, N.J.). | 26443215 | 2016; |
The Development of TALE Nucleases for Biotechnology. | Ousterout, David G; Gersbach, Charles A | Methods in molecular biology (Clifton, N.J.). | 26443211 | 2016; |
Monocyte enhancers are highly altered in systemic lupus erythematosus. | Shi, Lihua; Zhang, Zhe; Song, Li; Leung, Yiu Tak; Petri, Michelle A; Sullivan, Kathleen E | Epigenomics. | 26442457 | 2015; |
Animal Models of Chemical Carcinogenesis: Driving Breakthroughs in Cancer Research for 100 Years. | Kemp, Christopher J | Cold Spring Harbor protocols. | 26430259 | 2015 Oct; |
Enabling functional genomics with genome engineering. | Hilton, Isaac B; Gersbach, Charles A | Genome research. | 26430154 | 2015 Oct; |
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, Shuixiang | Oncotarget. | 26416455 | 2015 Oct 20; |
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, Mattia | BMC bioinformatics. | 26415965 | 2015; |
The long noncoding RNA landscape in hypoxic and inflammatory renal epithelial injury. | Lin, Jennie; Zhang, Xuan; Xue, Chenyi; Zhang, Hanrui; Shashaty, Michael G S; Gosai, Sager J; Meyer, Nuala; Grazioli, Alison; Hinkle, Christine; Caughey, Jennifer; Li, Wenjun; Susztak, Katalin; Gregory, Brian D; Li, Mingyao; Reilly, Muredach P | American journal of physiology. Renal physiology. | 26400545 | 2015 Dec 01; |
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 E | Nucleic acids research. | 26384421 | 2015 Oct 15; |
The New State of the Art: Cas9 for Gene Activation and Repression. | La Russa, Marie F; Qi, Lei S | Molecular and cellular biology. | 26370509 | 2015 Nov; |
The CRISPR road: from bench to bedside on an RNA-guided path. | Garcia-Bloj, Benjamin; Moses, Colette; Blancafort, Pilar | Annals of translational medicine. | 26366391 | 2015 Aug; |
Bacterial CRISPR: accomplishments and prospects. | Peters, Jason M; Silvis, Melanie R; Zhao, Dehua; Hawkins, John S; Gross, Carol A; Qi, Lei S | Current opinion in microbiology. | 26363124 | 2015 Oct; |
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, Haruo | Nature. | 26352471 | 2015 Sep 17; |
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, Yue | Scientific reports. | 26350498 | 2015; |
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, Bing | The British journal of psychiatry : the journal of mental science. | 26338991 | 2016 Feb; |
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; J | Circulation. Cardiovascular genetics. | 26307030 | 2015 Oct; |
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; Busta | Cell. | 26300125 | 2015 Aug 27; |
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-M | Oncogene. | 26300005 | 2016 05 05; |
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 V | Epigenetics. | 26295359 | 2015; |
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, Katalin | Diabetes. | 26293507 | 2015 Dec; |
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 H | Proceedings of the National Academy of Sciences of the United States of America. | 26283398 | 2015 Sep 1; |
Systematic chromatin state comparison of epigenomes associated with diverse properties including sex and tissue type. | Yen, Angela; Kellis, Manolis | Nature communications. | 26282110 | 2015; |
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, Ale | Genome biology. | 26268681 | 2015; |
Role of DNA Methylation in Modulating Transcription Factor Occupancy. | Maurano, Matthew T; Wang, Hao; John, Sam; Shafer, Anthony; Canfield, Theresa; Lee, Kristen; Stamatoyannopoulos, John A | Cell reports. | 26257180 | 2015 Aug 18; |
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 W | Molecular psychiatry. | 26239289 | 2015 Aug 4; |
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 J | Laboratory investigation; a journal of technical methods and pathology. | 26237271 | 2016 Feb; |
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, Huidong | Journal of genetics and genomics = Yi chuan xue bao. | 26233891 | 2015 Jul 20; |
Epigenetic Signatures as Biomarkers of Exposure. | Ladd-Acosta, Christine | Current environmental health reports. | 26231361 | 2015 Jun; |
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 A | Breast cancer research and treatment. | 26223813 | 2015 Aug; |
Synthetic biology approaches to engineer T cells. | Wu, Chia-Yung; Rupp, Levi J; Roybal, Kole T; Lim, Wendell A | Current opinion in immunology. | 26218616 | 2015 Aug; |
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 S | Bioinformatics (Oxford, England). | 26209430 | 2015 Nov 15; |
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 R | Bioinformatics (Oxford, England). | 26209429 | 2015 Nov 15; |
Endotoxin tolerance in monocytes can be mitigated by ?2-interferon. | Shi, Lihua; Song, Li; Maurer, Kelly; Sharp, James; Zhang, Zhe; Sullivan, Kathleen E | Journal of leukocyte biology. | 26206900 | 2015 Oct; |
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 J | Human molecular genetics. | 26206884 | 2015 Oct 1; |
Role of DNA methylation in renal cell carcinoma. | Shenoy, Niraj; Vallumsetla, Nishanth; Zou, Yiyu; Galeas, Jose Nahun; Shrivastava, Makardhwaj; Hu, Caroline; Susztak, Katalin; Verma, Amit | Journal of hematology & oncology. | 26198328 | 2015 Jul 22; |
Diet-Induced Podocyte Dysfunction in Drosophila and Mammals. | Na, Jianbo; Sweetwyne, Mariya T; Park, Ae Seo Deok; Susztak, Katalin; Cagan, Ross L | Cell reports. | 26190114 | 2015 Jul 28; |
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 T | Nature protocols. | 26182240 | 2015 Aug; |
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; Sethupath | Inflammatory bowel diseases. | 26164662 | 2015 Sep; |
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; Good | Diabetes. | 26153245 | 2015 Oct; |
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 L | Annals of clinical and translational neurology. | 26125039 | 2015 Jun; |
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 T | Science (New York, N.Y.). | 26089354 | 2015 Jul 17; |
Population dynamics of cancer cells with cell state conversions. | Zhou, Da; Wu, Dingming; Li, Zhe; Qian, Minping; Zhang, Michael Q | Quantitative biology. | 26085954 | 2013 Sep; |
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, Brian | PloS one. | 26083500 | 2015; |
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. | 26080861 | 2015; |
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, Arturas | Schizophrenia bulletin. | 26078387 | 2016 Jan; |
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 L | Epigenetics. | 26067391 | 2015; |
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 P | Chronobiology international. | 26061588 | 2015; |
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, Katalin | Journal of the American Society of Nephrology : JASN. | 26054542 | 2016 Feb; |
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 M | PloS one. | 26030880 | 2015; |
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 R | Nature. | 26030523 | 2015 Jul 9; |
GATA factors in endocrine neoplasia. | Pihlajoki, Marjut; Färkkilä, Anniina; Soini, Tea; Heikinheimo, Markku; Wilson, David B | Molecular and cellular endocrinology. | 26027919 | 2016 Feb 05; |
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 A | Genome research. | 26025803 | 2015 Aug; |
The Role of MicroRNAs and Human Epidermal Growth Factor Receptor 2 in Proliferative Lupus Nephritis. | Costa-Reis, Patrícia; Russo, Pierre A; Zhang, Zhe; Colonna, Lucrezia; Maurer, Kelly; Gallucci, Stefania; Schulz, Steffan W; Kiani, Adnan N; Petri, Michelle; Sullivan, Kathleen E | Arthritis & rheumatology (Hoboken, N.J.) | 26016809 | 2015 Sep |
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 A | The international journal of biochemistry & cell biology. | 26003740 | 2015 May 21; |
Inferring regulatory element landscapes and transcription factor networks from cancer methylomes. | Yao, Lijing; Shen, Hui; Laird, Peter W; Farnham, Peggy J; Berman, Benjamin P | Genome biology. | 25994056 | 2015; |
Targeted Transcriptional Repression in Bacteria Using CRISPR Interference (CRISPRi). | Hawkins, John S; Wong, Spencer; Peters, Jason M; Almeida, Ricardo; Qi, Lei S | Methods in molecular biology (Clifton, N.J.). | 25981485 | 2015; |
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 P | Nucleic acids research. | 25977295 | 2015 Sep 3; |
Cognitive aging in older Black and White persons. | Wilson, Robert S; Capuano, Ana W; Sytsma, Joel; Bennett, David A; Barnes, Lisa L | Psychology and aging. | 25961876 | 2015 Jun; |
The evolving understanding of the contribution of lipid metabolism to diabetic kidney disease. | Stadler, Krisztian; Goldberg, Ira J; Susztak, Katalin | Current diabetes reports. | 25957525 | 2015 Jul; |
Chemosensory receptor specificity and regulation. | Dalton, Ryan P; Lomvardas, Stavros | Annual review of neuroscience. | 25938729 | 2015 Jul 8; |
A unique chromatin complex occupies young ?-satellite arrays of human centromeres. | Henikoff, Jorja G; Thakur, Jitendra; Kasinathan, Sivakanthan; Henikoff, Steven | Science advances. | 25927077 | 2015 Feb 12; |
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 R | International journal of epidemiology. | 25906783 | 2015 Aug; |
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, Yongmei | BMC genomics. | 25898983 | 2015; |
MIRA-seq for DNA methylation analysis of CpG islands. | Jung, Marc; Kadam, Swati; Xiong, Wenying; Rauch, Tibor A; Jin, Seung-Gi; Pfeifer, Gerd P | Epigenomics. | 25881900 | 2015 Apr 17; |
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 P | International journal of epidemiology. | 25878217 | 2015 Aug; |
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 E | Nature neuroscience. | 25849986 | 2015 May; |
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 A | Nature biotechnology. | 25849900 | 2015 May; |
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, Jinyu | Molecular psychiatry. | 25849321 | 2016 Feb; |
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 S | The Journal of experimental medicine. | 25847946 | 2015 May 4; |
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, Maike | Cell stem cell. | 25842977 | 2015 Apr 2; |
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 L | Journal of bacteriology. | 25825433 | 2015 Jun; |
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, Alexander | Nature genetics. | 25822089 | 2015 May; |
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, Kyunghee | EMBO reports. | 25802403 | 2015 May; |
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. | 25769910 | 2015 Jul; |
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 M | ACS chemical neuroscience. | 25768025 | 2015 May 20; |
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 S | Neurology. | 25762710 | 2015 Mar 31; |
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 M | Nature. | 25707804 | 2015 Apr 30; |
Epigenome engineering in cancer: fairytale or a realistic path to the clinic? | Falahi, Fahimeh; Sgro, Agustin; Blancafort, Pilar | Frontiers in oncology. | 25705610 | 2015; |
Anthracyclines induce double-strand DNA breaks at active gene promoters. | Yang, Fan; Kemp, Christopher J; Henikoffa, Steven | Mutation research. | 25705119 | 2015 Mar; |
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, Ting | Nature communications. | 25697895 | 2015 Feb 20; |
PRIMEGENSw3: a web-based tool for high-throughput primer and probe design. | Kushwaha, Garima; Srivastava, Gyan Prakash; Xu, Dong | Methods in molecular biology (Clifton, N.J.). | 25697661 | 2015; |
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 R | Nature. | 25693567 | 2015 Feb 19; |
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, Bing | Nature. | 25693566 | 2015 Feb 19; |
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, Alexander | Nature. | 25693565 | 2015 Feb 19; |
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, Bing | Nature. | 25693564 | 2015 Feb 19; |
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, Manolis | Nature. | 25693563 | 2015 Feb 19; |
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, Aleksandar | Nature communications. | 25691256 | 2015; |
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 F | Nature communications. | 25691127 | 2015; |
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, Martin | Nature communications. | 25690954 | 2015; |
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, Ting | Nature biotechnology. | 25690851 | 2015 Apr; |
Quantitative proteomic analysis of histone modifications. | Huang, He; Lin, Shu; Garcia, Benjamin A; Zhao, Yingming | Chemical reviews. | 25688442 | 2015 Mar 25; |
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, P | Oncogene. | 25684141 | 2015 Feb 16; |
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 T | Molecular & cellular proteomics : MCP. | 25680957 | 2015 Jun; |
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 Stafford | Genome research. | 25677182 | 2015 Apr; |
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 Gregory | Developmental cell. | 25669886 | 2015 Feb 9; |
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 D | ACS chemical neuroscience. | 25668062 | 2015 Apr 15; |
A light-inducible CRISPR-Cas9 system for control of endogenous gene activation. | Polstein, Lauren R; Gersbach, Charles A | Nature chemical biology. | 25664691 | 2015 Mar; |
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 S | Cell stem cell. | 25658371 | 2015 Feb 5; |
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 A | Neurology. | 25653292 | 2015 Mar 3; |
Genetics and epigenetics of circadian rhythms and their potential roles in neuropsychiatric disorders. | Liu, Chunyu; Chung, Michael | Neuroscience bulletin. | 25652815 | 2015 Feb; |
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 A | PloS one. | 25642713 | 2015; |
Aging and DNA methylation. | Jung, Marc; Pfeifer, Gerd P | BMC biology. | 25637097 | 2015; |
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 E | Epigenetics : official journal of the DNA Methylation Society. | 25611806 | 2015; |
(Epi)genomics approaches and their applications. | Meissner, Alexander | Methods (San Diego, Calif.). | 25597875 | 2015 Jan 15; |
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 A | Cell research. | 25591927 | 2015 Mar; |
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 Schnaider | Neurobiology of aging. | 25585531 | 2015 Mar; |
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, George | Nature biotechnology. | 25580597 | 2015 Feb; |
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 A | Cancer informatics. | 25574126 | 2014; |
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, Alexander | Nucleic acids research. | 25541195 | 2015 Jan; |
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, Alexander | Nature. | 25533951 | 2015 Feb 19; |
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 A | Cell. | 25533786 | 2015 Jan 15; |
The mitochondrial epigenome: a role in Alzheimer's disease? | Devall, Matthew; Mill, Jonathan; Lunnon, Katie | Epigenomics. | 25531259 | 2014; |
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 John | Nucleic acids research. | 25505163 | 2015 Jan; |
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 D | Nature cell biology. | 25503565 | 2015 Jan; |
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 B | Molecular and cellular endocrinology. | 25498963 | 2015 Jun 15; |
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 A | ACS synthetic biology. | 25494287 | 2015 Jun 19; |
Locally disordered methylation forms the basis of intratumor methylome variation in chronic lymphocytic leukemia. | Landau, Dan A; Clement, Kendell; Ziller, Michael J; Boyle, Patrick; Fan, Jean; Gu, Hongcang; Stevenson, Kristen; Sougnez, Carrie; Wang, Lili; Li, Shuqiang; Kotliar, Dylan; Zhang, Wandi; Ghandi, Mahmoud; Garraway, Levi; Fernandes, Stacey M; Livak, Kenneth J; Gabriel, Stacey; Gnirke, Andreas; Lander, Eric S; Brown, Jennifer R; Neuberg, Donna; Kharchenko, Peter V; Hacohen, Nir; Getz, Gad; Meissner, Alexander; Wu, Catherine J | Cancer cell. | 25490447 | 2014 Dec 8; |
rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data. | Shen, Shihao; Park, Juw Won; Lu, Zhi-xiang; Lin, Lan; Henry, Michael D; Wu, Ying Nian; Zhou, Qing; Xing, Yi | Proceedings of the National Academy of Sciences of the United States of America. | 25480548 | 2014 Dec 23; |
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, Samy | Diabetologia. | 25476525 | 2015 Mar; |
TEMPORARY REMOVAL: 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 Schnaider | Neurobiology of aging. | 25475537 | 2014 Nov 8; |
Computational schemes for the prediction and annotation of enhancers from epigenomic assays. | Whitaker, John W; Nguyen, Tung T; Zhu, Yun; Wildberg, Andre; Wang, Wei | Methods (San Diego, Calif.). | 25461775 | 2015 Jan 15; |
Building the Connectivity Map of epigenetics: chromatin profiling by quantitative targeted mass spectrometry. | Creech, Amanda L; Taylor, Jordan E; Maier, Verena K; Wu, Xiaoyun; Feeney, Caitlin M; Udeshi, Namrata D; Peach, Sally E; Boehm, Jesse S; Lee, Jeannie T; Carr, Steven A; Jaffe, Jacob D | Methods (San Diego, Calif.). | 25448295 | 2015 Jan 15; |
Combining MeDIP-seq and MRE-seq to investigate genome-wide CpG methylation. | Li, Daofeng; Zhang, Bo; Xing, Xiaoyun; Wang, Ting | Methods (San Diego, Calif.). | 25448294 | 2015 Jan 15; |
A CRISPR/Cas9-based system for reprogramming cell lineage specification. | Chakraborty, Syandan; Ji, HaYeun; Kabadi, Ami M; Gersbach, Charles A; Christoforou, Nicolas; Leong, Kam W | Stem cell reports. | 25448066 | 2014 Dec 9; |
Epigenomics in translational research. | Replogle, Joseph M; De Jager, Philip L | Translational research : the journal of laboratory and clinical medicine. | 25445204 | 2015 Jan; |
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Building a pipeline to discover and validate novel therapeutic targets and lead compounds for Alzheimer's disease. | Bennett, David A; Yu, Lei; De Jager, Philip L | Biochemical pharmacology | 24508835 | 2014 Apr 15 |
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 | 24508391 | 2014 Mar 6 |
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TBX2 blocks myogenesis and promotes proliferation in rhabdomyosarcoma cells. | Zhu, Bo; Zhang, Meiling; Byrum, Stephanie D; Tackett, Alan J; Davie, Judith K | International journal of cancer. Journal international du cancer | 24470334 | 2014 Aug 15 |
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Effects of vitamin D3 stimulation of thioredoxin-interacting protein in hepatocellular carcinoma. | Hamilton, James P; Potter, James J; Koganti, Lahari; Meltzer, Stephen J; Mezey, Esteban | Hepatology research : the official journal of the Japan Society of Hepatology. | 24451003 | 2014 Dec; |
Epigenetic epidemiology: promises for public health research. | Bakulski, Kelly M; Fallin, M Daniele | Environmental and molecular mutagenesis | 24449392 | 2014 Apr |
What we talk about when we talk about fat. | Rosen, Evan D; Spiegelman, Bruce M | Cell | 24439368 | 2014 Jan 16 |
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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 | 24399446 | 2014 May 15 |
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 | 24391148 | 2014 Apr |
MYC and transcription elongation. | Rahl, Peter B; Young, Richard A | Cold Spring Harbor perspectives in medicine | 24384817 | 2014 Jan |
Design, synthesis, and evaluation of hydroxamic acid-based molecular probes for in vivo imaging of histone deacetylase (HDAC) in brain. | Wang, Changning; Eessalu, Thomas E; Barth, Vanessa N; Mitch, Charles H; Wagner, Florence F; Hong, Yijia; Neelamegam, Ramesh; Schroeder, Frederick A; Holson, Edward B; Haggarty, Stephen J; Hooker, Jacob M | American journal of nuclear medicine and molecular imaging. | 24380043 | 2013; |
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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 | 24373284 | 2013 Dec 26 |
Doxorubicin, DNA torsion, and chromatin dynamics. | Yang, Fan; Teves, Sheila S; Kemp, Christopher J; Henikoff, Steven | Biochimica et biophysica acta | 24361676 | 2014 Jan |
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 | 24360272 | 2013 Dec 19 |
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 | 24343027 | 2014 Mar |
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 | 24336359 | 2013 Dec 15 |
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 | 24336317 | 2014 Jan |
SILAC Peptide Ratio Calculator: A Tool for SILAC Quantitation of Peptides and Post-Translational Modifications. | Guan, Xiaoyan; Rastogi, Neha; Parthun, Mark R; Freitas, Michael A | Journal of proteome research | 24328097 | 2014 Feb 7 |
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 | 24303006 | 2013 |
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 | 24285438 | 2013 Jun 15 |
Inferring the perturbed microRNA regulatory networks in cancer using hierarchical gene co-expression signatures. | Gu, Jin; Xuan, Zhenyu | PloS one | 24278370 | 2013 |
ADCK4 ''reenergizes'' nephrotic syndrome. | Malaga-Dieguez, Laura; Susztak, Katalin | The Journal of clinical investigation. | 24270414 | 2013 Dec; |
Mechanisms of cohesin-mediated gene regulation and lessons learned from cohesinopathies. | Ball Jr, Alexander R; Chen, Yen-Yun; Yokomori, Kyoko | Biochimica et biophysica acta | 24269489 | 2013 Nov 22 |
Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser. | Raney, Brian J; Dreszer, Timothy R; Barber, Galt P; Clawson, Hiram; Fujita, Pauline A; Wang, Ting; Nguyen, Ngan; Paten, Benedict; Zweig, Ann S; Karolchik, Donna; Kent, W James | Bioinformatics (Oxford, England) | 24227676 | 2014 Apr 1 |
Aberrant methylation of the Ras-related associated with diabetes gene in human primary esophageal cancer. | Jin, Zhe; Feng, Xianling; Jian, Qianhe; Cheng, Yulan; Gao, Yan; Zhang, Xiaojing; Wang, Liang; Zhang, Yuan; Huang, Weiling; Fan, Xinmin; Chen, Si; Yu, Huimin; Zhao, Zhenfu; Dong, Ming; Liu, Jie; Mori, Yuriko; Meltzer, Stephen J | Anticancer research | 24222170 | 2013 Nov |
Radionuclide labeling and evaluation of candidate radioligands for PET imaging of histone deacetylase in the brain. | Seo, Young Jun; Muench, Lisa; Reid, Alicia; Chen, Jinzhu; Kang, Yeona; Hooker, Jacob M; Volkow, Nora D; Fowler, Joanna S; Kim, Sung Won | Bioorganic & medicinal chemistry letters | 24210501 | 2013 Dec 15 |
The human protein PRR14 tethers heterochromatin to the nuclear lamina during interphase and mitotic exit. | Poleshko, Andrey; Mansfield, Katelyn M; Burlingame, Caroline C; Andrake, Mark D; Shah, Neil R; Katz, Richard A | Cell reports | 24209742 | 2013 Oct 31 |
Exomic analysis of myxoid liposarcomas, synovial sarcomas, and osteosarcomas. | Joseph, Christine G; Hwang, Heejung; Jiao, Yuchen; Wood, Laura D; Kinde, Isaac; Wu, Jian; Mandahl, Nils; Luo, Jinyong; Hruban, Ralph H; Diaz Jr, Luis A; He, Tong-Chuan; Vogelstein, Bert; Kinzler, Kenneth W; Mertens, Fredrik; Papadopoulos, Nickolas | Genes, chromosomes & cancer | 24190505 | 2014 Jan |
Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing. | Selvaraj, Siddarth; R Dixon, Jesse; Bansal, Vikas; Ren, Bing | Nature biotechnology | 24185094 | 2013 Dec |
Understanding the epigenetic syntax for the genetic alphabet in the kidney. | Susztak, Katalin | Journal of the American Society of Nephrology : JASN | 24179169 | 2014 Jan |
Mot1 redistributes TBP from TATA-containing to TATA-less promoters. | Zentner, Gabriel E; Henikoff, Steven | Molecular and cellular biology | 24144978 | 2013 Dec |
A high-resolution map of the three-dimensional chromatin interactome in human cells. | Jin, Fulai; Li, Yan; Dixon, Jesse R; Selvaraj, Siddarth; Ye, Zhen; Lee, Ah Young; Yen, Chia-An; Schmitt, Anthony D; Espinoza, Celso A; Ren, Bing | Nature | 24141950 | 2013 Nov 14 |
CRISPR interference (CRISPRi) for sequence-specific control of gene expression. | Larson, Matthew H; Gilbert, Luke A; Wang, Xiaowo; Lim, Wendell A; Weissman, Jonathan S; Qi, Lei S | Nature protocols | 24136345 | 2013 Nov |
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.) | 24129635 | 2013 Dec |
Super-enhancers in the control of cell identity and disease. | Hnisz, Denes; Abraham, Brian J; Lee, Tong Ihn; Lau, Ashley; Saint-Andre, Violaine; Sigova, Alla A; Hoke, Heather A; Young, Richard A | Cell | 24119843 | 2013 Nov 7 |
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 | 24098934 | 2013 |
Micro- and nanoscale devices for the investigation of epigenetics and chromatin dynamics. | Aguilar, Carlos A; Craighead, Harold G | Nature nanotechnology | 24091454 | 2013 Oct |
MAL hypermethylation is a tissue-specific event that correlates with MAL mRNA expression in esophageal carcinoma. | Jin, Zhe; Wang, Liang; Zhang, Yuan; Cheng, Yulan; Gao, Yan; Feng, Xianling; Dong, Ming; Cao, Ziyi; Chen, Si; Yu, Huimin; Zhao, Zhenfu; Zhang, Xiaojing; Liu, Jie; Mori, Yuriko; Fan, Xinmin; Meltzer, Stephen J | Scientific reports | 24088706 | 2013 |
STAR: an integrated solution to management and visualization of sequencing data. | Wang, Tao; Liu, Jie; Shen, Li; Tonti-Filippini, Julian; Zhu, Yun; Jia, Haiyang; Lister, Ryan; Whitaker, John W; Ecker, Joseph R; Millar, A Harvey; Ren, Bing; Wang, Wei | Bioinformatics (Oxford, England) | 24078702 | 2013 Dec 15 |
CDKN2A/p16 inactivation mechanisms and their relationship to smoke exposure and molecular features in non-small-cell lung cancer. | Tam, Kit W; Zhang, Wei; Soh, Junichi; Stastny, Victor; Chen, Min; Sun, Han; Thu, Kelsie; Rios, Jonathan J; Yang, Chenchen; Marconett, Crystal N; Selamat, Suhaida A; Laird-Offringa, Ite A; Taguchi, Ayumu; Hanash, Samir; Shames, David; Ma, Xiaotu; Zhang, Mi | Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer | 24077454 | 2013 Nov |
Recommendations for the design and analysis of epigenome-wide association studies. | Michels, Karin B; Binder, Alexandra M; Dedeurwaerder, Sarah; Epstein, Charles B; Greally, John M; Gut, Ivo; Houseman, E Andres; Izzi, Benedetta; Kelsey, Karl T; Meissner, Alexander; Milosavljevic, Aleksandar; Siegmund, Kimberly D; Bock, Christoph; Irizarry, Rafael A | Nature methods. | 24076989 | 2013 Oct; |
Mapping human epigenomes. | Rivera, Chloe M; Ren, Bing | Cell | 24074860 | 2013 Sep 26 |
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. | 24052944 | 2013; |
Visualizing epigenetics: Current advances and advantages in HDAC PET imaging techniques. | Wang, C; Schroeder, F A; Hooker, J M | Neuroscience | 24051365 | 2013 Sep 17 |
Epigenetic studies in Alzheimer's disease: Current findings, caveats, and considerations for future studies. | Lunnon, Katie; Mill, Jonathan | American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics | 24038819 | 2013 Sep 13 |
Locus-specific editing of histone modifications at endogenous enhancers. | Mendenhall, Eric M; Williamson, Kaylyn E; Reyon, Deepak; Zou, James Y; Ram, Oren; Joung, J Keith; Bernstein, Bradley E | Nature biotechnology | 24013198 | 2013 Dec |
Epigenomics: The Science of No-Longer-Junk DNA. Why Study it in Chronic Kidney Disease? | Ko, Yi-An; Susztak, Katalin | Seminars in nephrology | 24011577 | 2013 Jul |
Comparative anatomy of chromosomal domains with imprinted and non-imprinted allele-specific DNA methylation. | Paliwal, Anupam; Temkin, Alexis M; Kerkel, Kristi; Yale, Alexander; Yotova, Iveta; Drost, Natalia; Lax, Simon; Nhan-Chang, Chia-Ling; Powell, Charles; Borczuk, Alain; Aviv, Abraham; Wapner, Ronald; Chen, Xiaowei; Nagy, Peter L; Schork, Nicholas; Do, Cathe | PLoS genetics | 24009515 | 2013 Aug |
Total daily activity declines more rapidly with increasing age in older adults. | Buchman, Aron S; Wilson, Robert S; Yu, Lei; James, Bryan D; Boyle, Patricia A; Bennett, David A | Archives of gerontology and geriatrics. | 24007938 | 2014 Jan-Feb; |
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 | 24000294 | 2014 Jun |
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 | 23995138 | 2013 Oct |
A universal DNA-based protein detection system. | Tran, Thua N N; Cui, Jinhui; Hartman, Mark R; Peng, Songming; Funabashi, Hisakage; Duan, Faping; Yang, Dayong; March, John C; Lis, John T; Cui, Haixin; Luo, Dan | Journal of the American Chemical Society | 23978265 | 2013 Sep 25 |
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 | 23976835 | 2013 Mar 1 |
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 | 23967191 | 2013 |
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 | 23955773 | 2013 Oct |
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 | 23953118 | 2013 Aug 15 |
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 | 23948299 | 2013 Aug 12 |
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 | 23948298 | 2013 Aug 12 |
H1 histones: current perspectives and challenges. | Harshman, Sean W; Young, Nicolas L; Parthun, Mark R; Freitas, Michael A | Nucleic acids research | 23945933 | 2013 Nov |
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 | 23940299 | 2013 Oct 1 |
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 | 23925113 | 2013 Aug 22 |
Bimolecular fluorescence complementation (BiFC) analysis of protein interactions in live cells. | Kerppola, Tom K | Cold Spring Harbor protocols | 23906917 | 2013 Aug |
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 | 23906667 | 2013 Jul 29 |
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 | 23900278 | 2013 |
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 | 23900078 | 2013 Dec 15 |
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 | 23893879 | 2013 Jul 24 |
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 | 23877302 | 2013 |
An epigenetic trap stabilizes singular olfactory receptor expression. | Lyons, David B; Allen, William E; Goh, Tracie; Tsai, Lulu; Barnea, Gilad; Lomvardas, Stavros | Cell | 23870122 | 2013 Jul 18 |
Developmental biology. Enhancing pluripotency and lineage specification. | Xie, Wei; Ren, Bing | Science (New York, N.Y.) | 23869010 | 2013 Jul 19 |
Browsing (Epi)genomes: a guide to data resources and epigenome browsers for stem cell researchers. | Karnik, Rahul; Meissner, Alexander | Cell stem cell | 23827707 | 2013 Jul 3 |
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 | 23827675 | 2013 Jul 3 |
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 | 23818866 | 2013 Jun |
From promises to practical strategies in epigenetic epidemiology. | Mill, Jonathan; Heijmans, Bastiaan T | Nature reviews. Genetics | 23817309 | 2013 Aug |
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 | 23810801 | 2013 Jun 25 |
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 | 23804401 | 2013 Sep |
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 | 23804400 | 2013 Sep |
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 | 23803584 | 2013 Jun 11 |
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 | 23791644 | 2013 Jun 27 |
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 | 23788618 | 2013 Sep |
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 | 23775118 | 2013 Aug |
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 | 23752194 | 2013 Jun 10 |
DNA methylation data analysis and its application to cancer research. | Ma, Xiaotu; Wang, Yi-Wei; Zhang, Michael Q; Gazdar, Adi F | Epigenomics | 23750645 | 2013 Jun |
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 | 23737446 | 2013 Jun 3 |
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 | 23737446 | 2013 Aug |
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 | 23708189 | 2013 Jul |
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 | 23708142 | 2013 May 23 |
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 | 23707066 | 2013 May 30 |
Stochastic gene expression in mammals: lessons from olfaction. | Magklara, Angeliki; Lomvardas, Stavros | Trends in cell biology | 23689023 | 2013 May 17 |
Role of Macrophage Receptor with Collagenous Structure in Innate Immune Tolerance. | Jing, Jian; Yang, Ivana V; Hui, Lucy; Patel, Jay A; Evans, Christopher M; Prikeris, Rytis; Kobzik, Lester; O'Connor, Brian P; Schwartz, David A | Journal of immunology (Baltimore, Md. : 1950) | 23667110 | 2013 May 10 |
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 | 23664764 | 2013 May 23 |
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 | 23664763 | 2013 May 23 |
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 | 23631413 | 2013 |
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 | 23630576 | 2013 |
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 | 23629413 | 2013 May |
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 | 23621218 | 2013 |
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 | 23610441 | 2013 May 7 |
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 | 23606611 | 2013 Apr |
Doxorubicin Enhances Nucleosome Turnover around Promoters. | Yang, Fan; Kemp, Christopher J; Henikoff, Steven | Current biology : CB | 23602475 | 2013 May 6 |
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 | 23592332 | 2013 Aug |
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 | 23589626 | 2013 Jun |
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 | 23582657 | 2013 Sep |
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 | 23582323 | 2013 Apr 11 |
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 | 23582322 | 2013 Apr 11 |
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 | 23571780 | 2013 Apr 9 |
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 | 23571587 | 2013 Apr 10 |
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 | 23568951 | 2013 Aug |
Endocardial to myocardial notch-wnt-bmp axis regulates early heart valve development. | Wang, Yidong; Wu, Bingruo; Chamberlain, Alyssa A; Lui, Wendy; Koirala, Pratistha; Susztak, Katalin; Klein, Diana; Taylor, Verdon; Zhou, Bin | PloS one. | 23560082 | 2013; |
Interplay between the cancer genome and epigenome. | Shen, Hui; Laird, Peter W | Cell | 23540689 | 2013 Mar 28 |
Epigenetic reprogramming in cancer. | Suva, Mario L; Riggi, Nicolo; Bernstein, Bradley E | Science (New York, N.Y.) | 23539597 | 2013 Mar 29 |
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 | 23526891 | 2013 Mar |
Transcriptional regulation and its misregulation in disease. | Lee, Tong Ihn; Young, Richard A | Cell | 23498934 | 2013 Mar 14 |
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 | 23487770 | 2013 Mar 19 |
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 | 23482655 | 2013 Mar |
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 | 23482391 | 2013 Apr |
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 | 23468659 | 2013 Feb |
ISWI and CHD chromatin remodelers bind promoters but act in gene bodies. | Zentner, Gabriel E; Tsukiyama, Toshio; Henikoff, Steven | PLoS genetics | 23468649 | 2013 |
Genome organization and long-range regulation of gene expression by enhancers. | Smallwood, Andrea; Ren, Bing | Current opinion in cell biology | 23465541 | 2013 Jun |
Regulation of nucleosome dynamics by histone modifications. | Zentner, Gabriel E; Henikoff, Steven | Nature structural & molecular biology | 23463310 | 2013 Mar |
Tet-mediated covalent labelling of 5-methylcytosine for its genome-wide detection and sequencing. | Zhang, Liang; Szulwach, Keith E; Hon, Gary C; Song, Chun-Xiao; Park, Beomseok; Yu, Miao; Lu, Xingyu; Dai, Qing; Wang, Xiao; Street, Craig R; Tan, Huiping; Min, Jung-Hyun; Ren, Bing; Jin, Peng; He, Chuan | Nature communications | 23443545 | 2013 |
Aberrant regulation of the integrin very late antigen-4 in systemic lupus erythematosus. | Rahimi, H; Maurer, K; Song, L; Akhter, E; Petri, M; Sullivan, K E | Lupus. | 23439470 | 2013 Mar; |
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 E | BMC genomics | 23414147 | 2013 |
Epigenomics: sequencing the methylome. | Hirst, Martin | Methods in molecular biology (Clifton, N.J.) | 23412782 | 2013 |
Regulation of Drosophila metamorphosis by xenobiotic response regulators. | Deng, Huai; Kerppola, Tom K | PLoS genetics | 23408904 | 2013 Feb |
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, Qin | The Journal of biological chemistry | 23408432 | 2013 Mar 29 |
DNA methylation: roles in mammalian development. | Smith, Zachary D; Meissner, Alexander | Nature reviews. Genetics | 23400093 | 2013 Mar |
Multiplexed microcolumn-based process for efficient selection of RNA aptamers. | Latulippe, David R; Szeto, Kylan; Ozer, Abdullah; Duarte, Fabiana M; Kelly, Christopher V; Pagano, John M; White, Brian S; Shalloway, David; Lis, John T; Craighead, Harold G | Analytical chemistry | 23398198 | 2013 Mar 19 |
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, Stephen | Molecular carcinogenesis | 23390063 | 2013 Nov |
Separation and purification of multiply acetylated proteins using cation-exchange chromatography. | Papazyan, Romeo; Taverna, Sean D | Methods in molecular biology (Clifton, N.J.) | 23381856 | 2013 |
Genome-wide analysis uncovers high frequency, strong differential chromosomal interactions and their associated epigenetic patterns in E2-mediated gene regulation. | Wang, Junbai; Lan, Xun; Hsu, Pei-Yin; Hsu, Hang-Kai; Huang, Kun; Parvin, Jeffrey; Huang, Tim H-M; Jin, Victor X | BMC genomics | 23368971 | 2013 |
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 K | The Journal of biological chemistry | 23364797 | 2013 Mar 15 |
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, Zdenko | Stem cells (Dayton, Ohio). | 23362228 | 2013 May; |
Bookmarking by specific and nonspecific binding of FoxA1 pioneer factor to mitotic chromosomes. | Caravaca, Juan Manuel; Donahue, Greg; Becker, Justin S; He, Ximiao; Vinson, Charles; Zaret, Kenneth S | Genes & development | 23355396 | 2013 Feb 1 |
Holocarboxylase synthetase interacts physically with euchromatic histone-lysine N-methyltransferase, linking histone biotinylation with methylation events. | Li, Yong; Hassan, Yousef I; Moriyama, Hideaki; Zempleni, Janos | The Journal of nutritional biochemistry | 23337344 | 2013 Aug |
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, | Gastroenterology | 23333711 | 2013 May |
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, | Cell | 23333102 | 2013 Jan 31 |
Reduced RAN expression and disrupted transport between cytoplasm and nucleus; a key event in Alzheimer's disease pathophysiology. | Mastroeni, Diego; Chouliaras, Leonidas; Grover, Andrew; Liang, Winnie S; Hauns, Kevin; Rogers, Joseph; Coleman, Paul D | PloS one | 23308199 | 2013 |
Identification and assessment of markers of biotin status in healthy adults. | Eng, Wei Kay; Giraud, David; Schlegel, Vicki L; Wang, Dong; Lee, Bo Hyun; Zempleni, Janos | The British journal of nutrition | 23302490 | 2013 Jul 28 |
The simplest explanation: passive DNA demethylation in PGCs. | Smith, Zachary D; Meissner, Alexander | The EMBO journal | 23299938 | 2013 Feb 6 |
Differential processing of amyloid precursor protein in brain and in peripheral blood leukocytes. | Delvaux, Elaine; Bentley, Karen; Stubbs, Victoria; Sabbagh, Marwan; Coleman, Paul D | Neurobiology of aging | 23298733 | 2013 Jun |
Major chromosomal breakpoint intervals in breast cancer co-localize with differentially methylated regions. | Tang, Man-Hung; Varadan, Vinay; Kamalakaran, Sitharthan; Zhang, Michael Q; Dimitrova, Nevenka; Hicks, James | Frontiers in oncology. | 23293768 | 2012; |
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 W | Neurobiology of aging | 23273601 | 2013 Jun |
A novel Bayesian change-point algorithm for genome-wide analysis of diverse ChIPseq data types. | Xing, Haipeng; Liao, Willey; Mo, Yifan; Zhang, Michael Q | Journal of visualized experiments : JoVE | 23271069 | 2012 |
Enrichment of meiotic recombination hotspot sequences by avidin capture technology. | Camara Teixeira, Daniel; Malkaram, Sridhar A; Zempleni, Janos | Gene | 23270922 | 2013 Mar 1 |
Using the Wash U Epigenome Browser to examine genome-wide sequencing data. | Zhou, Xin; Wang, Ting | Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] | 23255151 | 2012 Dec |
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 L | Proceedings of the National Academy of Sciences of the United States of America | 23248290 | 2013 Jan 2 |
Defined, serum-free conditions for in vitro culture of primary human T-ALL blasts. | Yost, A J; Shevchuk, O O; Gooch, R; Gusscott, S; You, M J; Ince, T A; Aster, J C; Weng, A P | Leukemia | 23246990 | 2013 Jun |
Analyzing the cancer methylome through targeted bisulfite sequencing. | Lee, Eun-Joon; Luo, Junfeng; Wilson, James M; Shi, Huidong | Cancer letters | 23200671 | 2012 Nov 28 |
Tet-assisted bisulfite sequencing of 5-hydroxymethylcytosine. | Yu, Miao; Hon, Gary C; Szulwach, Keith E; Song, Chun-Xiao; Jin, Peng; Ren, Bing; He, Chuan | Nature protocols | 23196972 | 2012 Dec |
Physical and functional interaction between yeast Pif1 helicase and Rim1 single-stranded DNA binding protein. | Ramanagoudr-Bhojappa, Ramanagouda; Blair, Lauren P; Tackett, Alan J; Raney, Kevin D | Nucleic acids research | 23175612 | 2013 Jan |
Hierarchical modularity in ERýý transcriptional network is associated with distinct functions and implicates clinical outcomes. | Tang, Binhua; Hsu, Hang-Kai; Hsu, Pei-Yin; Bonneville, Russell; Chen, Su-Shing; Huang, Tim H-M; Jin, Victor X | Scientific reports | 23166858 | 2012 |
Genetic analysis of DNA methylation and gene expression levels in whole blood of healthy human subjects. | van Eijk, Kristel R; de Jong, Simone; Boks, Marco P M; Langeveld, Terry; Colas, Fabrice; Veldink, Jan H; de Kovel, Carolien G F; Janson, Esther; Strengman, Eric; Langfelder, Peter; Kahn, Rene S; van den Berg, Leonard H; Horvath, Steve; Ophoff, Roel A | BMC genomics | 23157493 | 2012 |
The UCSC Genome Browser database: extensions and updates 2013. | Meyer, Laurence R; Zweig, Ann S; Hinrichs, Angie S; Karolchik, Donna; Kuhn, Robert M; Wong, Matthew; Sloan, Cricket A; Rosenbloom, Kate R; Roe, Greg; Rhead, Brooke; Raney, Brian J; Pohl, Andy; Malladi, Venkat S; Li, Chin H; Lee, Brian T; Learned, Katrina; | Nucleic acids research | 23155063 | 2013 Jan |
Nuclear aggregation of olfactory receptor genes governs their monogenic expression. | Clowney, E Josephine; LeGros, Mark A; Mosley, Colleen P; Clowney, Fiona G; Markenskoff-Papadimitriou, Eirene C; Myllys, Markko; Barnea, Gilad; Larabell, Carolyn A; Lomvardas, Stavros | Cell | 23141535 | 2012 Nov 9 |
A modulator based regulatory network for ERýý signaling pathway. | Wu, Heng-Yi; Zheng, Pengyue; Jiang, Guanglong; Liu, Yunlong; Nephew, Kenneth P; Huang, Tim H M; Li, Lang | BMC genomics | 23134758 | 2012 |
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, Fuli | BMC genomics | 23134663 | 2012 |
'Leveling' the playing field for analyses of single-base resolution DNA methylomes. | Schultz, Matthew D; Schmitz, Robert J; Ecker, Joseph R | Trends in genetics : TIG | 23131467 | 2012 Dec |
Revisiting global gene expression analysis. | Loven, Jakob; Orlando, David A; Sigova, Alla A; Lin, Charles Y; Rahl, Peter B; Burge, Christopher B; Levens, David L; Lee, Tong Ihn; Young, Richard A | Cell | 23101621 | 2012 Oct 26 |
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, Guokai | Nature protocols | 23099485 | 2012 Nov |
Surveying the epigenomic landscape, one base at a time. | Zentner, Gabriel E; Henikoff, Steven | Genome biology | 23088423 | 2012 Oct 22 |
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; Th | Nature | 23075850 | 2012 Nov 22 |
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 S | Molecular microbiology | 23075270 | 2012 Dec |
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, Shohei | Journal of molecular biology | 23041298 | 2012 Dec 14 |
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, Alexander | Genome biology. | 23034176 | 2012; |
Aging effects on DNA methylation modules in human brain and blood tissue. | Horvath, Steve; Zhang, Yafeng; Langfelder, Peter; Kahn, Rene S; Boks, Marco Pm; van Eijk, Kristel; van den Berg, Leonard H; Ophoff, Roel A | Genome biology | 23034122 | 2012 Oct 3 |
Combination therapy: histone deacetylase inhibitors and platinum-based chemotherapeutics for cancer. | Diyabalanage, Himashinie V K; Granda, Michael L; Hooker, Jacob M | Cancer letters | 23032720 | 2013 Feb 1 |
Epigenetic mechanisms and the development of asthma. | Yang, Ivana V; Schwartz, David A | The Journal of allergy and clinical immunology | 23026498 | 2012 Dec |
Transcriptional amplification in tumor cells with elevated c-Myc. | Lin, Charles Y; Loven, Jakob; Rahl, Peter B; Paranal, Ronald M; Burge, Christopher B; Bradner, James E; Lee, Tong Ihn; Young, Richard A | Cell | 23021215 | 2012 Sep 28 |
Microfluidic extraction, stretching and analysis of human chromosomal DNA from single cells. | Benítez, Jaime J; Topolancik, Juraj; Tian, Harvey C; Wallin, Christopher B; Latulippe, David R; Szeto, Kylan; Murphy, Patrick J; Cipriany, Benjamin R; Levy, Stephen L; Soloway, Paul D; Craighead, Harold G | Lab on a chip. | 23018789 | 2012 Nov 21; |
Online tools for bioinformatics analyses in nutrition sciences. | Malkaram, Sridhar A; Hassan, Yousef I; Zempleni, Janos | Advances in nutrition (Bethesda, Md.) | 22983844 | 2012 |
A maternal high-fat diet modulates fetal SIRT1 histone and protein deacetylase activity in nonhuman primates. | Suter, Melissa A; Chen, Aishe; Burdine, Marie S; Choudhury, Mahua; Harris, R Alan; Lane, Robert H; Friedman, Jacob E; Grove, Kevin L; Tackett, Alan J; Aagaard, Kjersti M | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 22982377 | 2012 Dec |
High-fat or ethinyl-oestradiol intake during pregnancy increases mammary cancer risk in several generations of offspring. | de Assis, Sonia; Warri, Anni; Cruz, M Idalia; Laja, Olusola; Tian, Ye; Zhang, Bai; Wang, Yue; Huang, Tim Hui-Ming; Hilakivi-Clarke, Leena | Nature communications | 22968699 | 2012 |
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, Arturas | Nature structural & molecular biology | 22961382 | 2012 Oct |
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Library-free methylation sequencing with bisulfite padlock probes. | Diep, Dinh; Plongthongkum, Nongluk; Gore, Athurva; Fung, Ho-Lim; Shoemaker, Robert; Zhang, Kun | Nature methods | 22306810 | 2012 Mar |
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. | 22297167 | 2012 Jul 15; |
Retrotransposon profiling of RNA polymerase III initiation sites. | Qi, Xiaojie; Daily, Kenneth; Nguyen, Kim; Wang, Haoyi; Mayhew, David; Rigor, Paul; Forouzan, Sholeh; Johnston, Mark; Mitra, Robi David; Baldi, Pierre; Sandmeyer, Suzanne | Genome research | 22287102 | 2012 Apr |
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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) | 22213113 | 2012 Apr |
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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 J | Endocrine-related cancer | 22194443 | 2012 Feb |
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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 | 22099308 | 2011 Nov 18 |
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Heat shock reduces stalled RNA polymerase II and nucleosome turnover genome-wide. | Teves, Sheila S; Henikoff, Steven | Genes & development | 22085965 | 2011 Nov 15 |
Epigenomic insights into common disease. | Revill, Kate; Tycko, Benjamin | Genome medicine. | 22085423 | 2011 Nov 23; |
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 | 22073196 | 2011 |
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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) | 21732495 | 2011 Sep |
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Opposing roles of FoxP1 and Nfat3 in transcriptional control of cardiomyocyte hypertrophy. | Bai, Shoumei; Kerppola, Tom K | Molecular and cellular biology | 21606195 | 2011 Jul |
Epigenetic control of gene expression in the lung. | Yang, Ivana V; Schwartz, David A | American journal of respiratory and critical care medicine | 21596832 | 2011 May 15 |
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; Lau | Cell stem cell | 21596650 | 2011 Jun 3 |
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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, Stavros | Cell | 21529909 | 2011 May 13 |
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Toward an integrated genetic and epigenetic approach to Alzheimer's disease. | Mill, Jonathan | Neurobiology of aging | 21497948 | 2011 Jul |
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Monocyte polarization: the relationship of genome-wide changes in H4 acetylation with polarization. | Zhang, Z; Song, L; Maurer, K; Bagashev, A; Sullivan, K E | Genes and immunity | 21451557 | 2011 Sep |
Tracing the footsteps of glomerular insulin signaling in diabetic kidney disease. | Chang, Gene-Yuan; Park, Ae Seo Deok; Susztak, Katalin | Kidney international | 21451535 | 2011 Apr |
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The histone methyltransferase SETDB1 is recurrently amplified in melanoma and accelerates its onset. | Ceol CJ, Houvras Y, Jane-Valbuena J, Bilodeau S, Orlando DA, Battisti V, Fritsch L, Lin WM, Hollmann TJ, Ferré F, Bourque C, Burke CJ, Turner L, Uong A, Johnson LA, Beroukhim R, Mermel CH, Loda M, Ait-Si-Ali S, Garraway LA, Young RA, Zon LI. | Nature | 21430779 | 2011 Mar 24 |
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Characterization of the contradictory chromatin signatures at the 3' exons of zinc finger genes. | Blahnik, Kimberly R; Dou, Lei; Echipare, Lorigail; Iyengar, Sushma; O'Geen, Henriette; Sanchez, Erica; Zhao, Yongjun; Marra, Marco A; Hirst, Martin; Costello, Joseph F; Korf, Ian; Farnham, Peggy J | PloS one | 21347206 | 2011 |
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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 E | Proceedings of the National Academy of Sciences of the United States of America | 21321204 | 2011 Mar 1 |
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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-M | Carcinogenesis | 21304052 | 2011 Jun |
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, Janos | Analytical biochemistry | 21303649 | 2011 Jun 1 |
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 L | PloS one | 21298003 | 2011 |
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Contribution of inherited mutations in the BRCA2-interacting protein PALB2 to familial breast cancer. | Casadei, Silvia; Norquist, Barbara M; Walsh, Tom; Stray, Sunday; Mandell, Jessica B; Lee, Ming K; Stamatoyannopoulos, John A; King, Mary-Claire | Cancer research | 21285249 | 2011 Mar 15 |
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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, Xiaodong | Proteins | 19434754 | 2009 Aug 15 |
Epigenetic alterations in the breast: Implications for breast cancer detection, prognosis and treatment. | Dworkin, Amy M; Huang, Tim H-M; Toland, Amanda Ewart | Seminars in cancer biology | 19429480 | 2009 Jun |
K12-biotinylated histone H4 is enriched in telomeric repeats from human lung IMR-90 fibroblasts. | Wijeratne, Subhashinee S K; Camporeale, Gabriela; Zempleni, Janos | The Journal of nutritional biochemistry | 19369050 | 2010 Apr |
Mascot-derived false positive peptide identifications revealed by manual analysis of tandem mass spectra. | Chen, Yue; Zhang, Junmei; Xing, Gang; Zhao, Yingming | Journal of proteome research | 19368407 | 2009 Jun |
Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming. | Deng, Jie; Shoemaker, Robert; Xie, Bin; Gore, Athurva; LeProust, Emily M; Antosiewicz-Bourget, Jessica; Egli, Dieter; Maherali, Nimet; Park, In-Hyun; Yu, Junying; Daley, George Q; Eggan, Kevin; Hochedlinger, Konrad; Thomson, James; Wang, Wei; Gao, Yuan; Z | Nature biotechnology | 19330000 | 2009 Apr |
The importance of being tyrosine: lessons in molecular recognition from minimalist synthetic binding proteins. | Koide, Shohei; Sidhu, Sachdev S | ACS chemical biology | 19298050 | 2009 May 15 |
Human and murine kidneys show gender- and species-specific gene expression differences in response to injury. | Si, Han; Banga, Ramandeep S; Kapitsinou, Pinelopi; Ramaiah, Manjunath; Lawrence, Janis; Kambhampati, Ganesh; Gruenwald, Antje; Bottinger, Erwin; Glicklich, Daniel; Tellis, Vivian; Greenstein, Stuart; Thomas, David B; Pullman, James; Fazzari, Melissa; Susztak, Katalin | PloS one. | 19277126 | 2009; |
Seed in soil, with an epigenetic view. | Lin, Huey-Jen L; Zuo, Tao; Chao, Jennifer R; Peng, Zhengang; Asamoto, Lisa K; Yamashita, Sonya S; Huang, Tim H-M | Biochimica et biophysica acta | 19162126 | 2009 Sep |
Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond. | Lister, Ryan; Gregory, Brian D; Ecker, Joseph R | Current opinion in plant biology | 19157957 | 2009 Apr |
Epigenetic changes in Alzheimer's disease: decrements in DNA methylation. | Mastroeni, Diego; Grover, Andrew; Delvaux, Elaine; Whiteside, Charisse; Coleman, Paul D; Rogers, Joseph | Neurobiology of aging | 19117641 | 2010 Dec |
Identification and verification of lysine propionylation and butyrylation in yeast core histones using PTMap software. | Zhang, Kai; Chen, Yue; Zhang, Zhihong; Zhao, Yingming | Journal of proteome research | 19113941 | 2009 Feb |
Smad1 as a biomarker for diabetic nephropathy. | Kato, Hideki; Si, Han; Hostetter, Thomas; Susztak, Katalin | Diabetes. | 18511448 | 2008 Jun; |
Acetylation is indispensable for p53 activation. | Tang, Yi; Zhao, Wenhui; Chen, Yue; Zhao, Yingming; Gu, Wei | Cell | 18485870 | 2008 May 16 |
The role of osteopontin in the development of albuminuria. | Lorenzen, Johan; Shah, Rajshree; Biser, Alisha; Staicu, Serban A; Niranjan, Thiruvur; Garcia, Ana Maria; Gruenwald, Antje; Thomas, David B; Shatat, Ibrahim F; Supe, Katarine; Woroniecki, Robert P; Susztak, Katalin | Journal of the American Society of Nephrology : JASN. | 18443355 | 2008 May; |
Epigenomic profiling reveals DNA-methylation changes associated with major psychosis. | Mill, Jonathan; Tang, Thomas; Kaminsky, Zachary; Khare, Tarang; Yazdanpanah, Simin; Bouchard, Luigi; Jia, Peixin; Assadzadeh, Abbas; Flanagan, James; Schumacher, Axel; Wang, Sun-Chong; Petronis, Arturas | American journal of human genetics | 18319075 | 2008 Mar |
Changes in the distributions and dynamics of polycomb repressive complexes during embryonic stem cell differentiation. | Ren, Xiaojun; Vincenz, Claudius; Kerppola, Tom K | Molecular and cellular biology | 18316406 | 2008 May |
Age-at-onset linkage analysis in Caribbean Hispanics with familial late-onset Alzheimer's disease. | Lee, Joseph H; Barral, Sandra; Cheng, Rong; Chacon, Inara; Santana, Vincent; Williamson, Jennifer; Lantigua, Rafael; Medrano, Martin; Jimenez-Velazquez, Ivonne Z; Stern, Yaakov; Tycko, Benjamin; Rogaeva, Ekaterina; Wakutani, Yosuke; Kawarai, Toshitaka; St George-Hyslop, Peter; Mayeux, Richard | Neurogenetics. | 17940814 | 2008 Feb; |
Lysine propionylation and butyrylation are novel post-translational modifications in histones. | Chen, Yue; Sprung, Robert; Tang, Yi; Ball, Haydn; Sangras, Bhavani; Kim, Sung Chan; Falck, John R; Peng, Junmin; Gu, Wei; Zhao, Yingming | Molecular & cellular proteomics : MCP | 17267393 | 2007 May |
Painting a truer picture of US socioeconomic and racial/ethnic health inequalities: the Public Health Disparities Geocoding Project. | Krieger, Nancy; Chen, Jarvis T; Waterman, Pamela D; Rehkopf, David H; Subramanian, S V | American journal of public health | 15671470 | 2005 Feb |
Race/ethnicity, gender, and monitoring socioeconomic gradients in health: a comparison of area-based socioeconomic measures--the public health disparities geocoding project. | Krieger, Nancy; Chen, Jarvis T; Waterman, Pamela D; Rehkopf, David H; Subramanian, S V | American journal of public health. | 14534218 | 2003 Oct; |