Epigenomics (1260)
Publication TitleAuthorsJournalPublication DatePage NoPubMedID
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, KatalinNature communications2023 Feb 0255936732547
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, MinminBMC medical genomics2023 Jan 291636709307
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, ChunyuMolecular psychiatry2022 Nov 2436424395
Differential Gene Expression and DNA Methylation in the Risk of Depression in LOAD Patients.Upadhya, Suraj; Gingerich, Daniel; Lutz, Michael William; Chiba-Falek, OrnitBiomolecules2022 Nov 1236421693
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, ChristineAutism research : official journal of the International Society for Autism Research2022 Dec36189953
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, KwangsikBiological psychiatry2022 Jun 2436150909
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, JinsongPsychiatry research2022 Nov36075150
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, KatriMolecular psychiatry2022 Nov35974141
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 JNeurobiology of aging2022 1035896049
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, RyanGenome biology2022 07 2635883107
[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, PedroNature communications2022 07 1935853847
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, FabienInternational journal of molecular sciences2022 Jun 3035806330
Keap1 moderates the transcription of virus induced genes through G9a-GLP and NFκB p50 recruitment.Burns, Veronica Elizabeth; Kerppola, Tom KlausImmunology2022 Sep35751391
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, KatalinNature genetics2022 0735710981
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, TingCancer research2022 Aug 0335706127
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, KatalinNature immunology2022 May 1235552540
The multifaceted role of kidney tubule mitochondrial dysfunction in kidney disease development.Doke, Tomohito; Susztak, KatalinTrends in cell biology2022 Oct35473814
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, KatalinMolecular therapy : the journal of the American Society of Gene Therapy2022 Jul 0635450819
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 JGenetics2022 May 3135404465
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 genetics2022 0435379992
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, TimScience (New York, N.Y.)2022 03 1135271334
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 BNeurobiology of disease2022 0535143967
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 STranslational psychiatry2022 Feb 0135105862
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, YongmeiDiabetes2022 Apr 0135073575
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 AdniDiagnostics (Basel, Switzerland)2021 Dec 0834943540
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, BeiyanCirculation2022 Jan 1834913723
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, BhramarJournal of the Royal Statistical Society. Series C, Applied statistics2021 Nov34887595
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 SEBioMedicine2021 Dec34883445
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 LNature communications2021 12 0234857756
How Many Cell Types Are in the Kidney and What Do They Do?Balzer, Michael S; Rohacs, Tibor; Susztak, KatalinAnnual review of physiology2022 02 1034843404
From mapping kidney function to mechanism and prediction.Hirohama, Daigoro; Susztak, KatalinNature reviews. Nephrology2022 0234819631
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, KatalinScience advances2021 Nov 0534739325
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, KatalinImmunity2021 11 0934715018
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, AdilBiomedicines2021 Sep 2434680427
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 SNature2021 1034616062
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, KatalinScientific reports2021 10 0434608231
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 EmedRxiv : the preprint server for health sciences2021 Sep 1534545375
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 TNeuron2021 09 1534534454
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 HoonPLoS genetics2021 Sep34516545
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 LAlzheimer's & dementia : the journal of the Alzheimer's Association2021 Sep 0534482628
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, JingyunEpigenetics2022 Jun-Jul34461811
Manipulating the NKG2D Receptor-Ligand Axis Using CRISPR: Novel Technologies for Improved Host Immunity.Alves, Eric; McLeish, Emily; Blancafort, Pilar; Coudert, Jerome D; Gaudieri, SilvanaFrontiers in immunology202134456921
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, KatalinNature communications2021 08 2334426578
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, BhramarStatistics in medicine2021 11 3034404112
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 KlausJournal of immunology (Baltimore, Md. : 1950)2021 09 0134400522
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 LAlzheimer's & dementia : the journal of the Alzheimer's Association2020 1234393677
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, KatalinNature genetics2021 0934385711
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, YunGenes2021 Jul 0834356065
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, KatalinJournal of the American Society of Nephrology : JASN2021 Nov34348909
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 JCell metabolism2021 Sep 0734348115
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 ANature methods2021 0834341582
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 SNature communications2021 Jul 2234294691
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 SJournal of the American Society of Nephrology : JASN2021 1034261756
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 AEpigenetics2022 Jun34227900
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, KatalinFrontiers in immunology202134177897
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 ANeurobiology of disease2021 0934153464
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, KatieNature communications2021 06 1034112773
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 MCommunications biology2021 May 2634040149
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, BoCommunications biology2021 May 2134021236
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, NilüferActa neuropathologica communications2021 05 2134020725
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, KatalinThe Journal of clinical investigation2021 May 1733998598
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 EHGG advances2021 Apr 0833937878
Identification of cell-type-specific marker genes from co-expression patterns in tissue samples.Qiu, Yixuan; Wang, Jiebiao; Lei, Jing; Roeder, KathrynBioinformatics (Oxford, England)2021 Apr 2733904573
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 JDevelopmental cell2021 May 0333891899
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 SBiological psychiatry2021 Feb 0333838873
Bayesian estimation of cell type-specific gene expression with prior derived from single-cell data.Wang, Jiebiao; Roeder, Kathryn; Devlin, BernieGenome research2021 1033837133
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, JoelEpigenetics2022 0333818294
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, KatieFuture science OA2021 Feb 0933815817
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 DanieleEpigenetics2022 0333794742
APOL1 at 10 years: progress and next steps.Freedman, Barry I; Kopp, Jeffrey B; Sampson, Matthew G; Susztak, KatalinKidney international2021 0633794228
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 PCell reports2021 Mar 3033789096
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, BosiljkaNeuron2021 May 0533789083
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, PilarNature communications2021 03 2633772001
Monitoring Recessions: A Bayesian Sequential Quickest Detection Method.Li, Haixi; Sheng, Xuguang Simon; Yang, JingyunInternational journal of forecasting2021 Apr-Jun33716367
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 EGenome research2021 0433674350
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, AthanasiosEMBO reports2021 05 0533645898
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, LawrenceNature2021 0233597756
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 SAmerican journal of human genetics2021 03 0433571421
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 InvestigatorsJournal of the American Society of Nephrology : JASN2021 0333531352
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 JCell reports2021 01 2633503437
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 AFrontiers in neuroscience202033488342
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 SScience (New York, N.Y.)2021 02 2633479121
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, SantiagoThe Journal of clinical investigation2021 Mar 0133465052
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, KatalinScience translational medicine2021 Jan 1333441424
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, KatalinCell metabolism2021 Feb 0233301705
Identification and characterization of constrained non-exonic bases lacking predictive epigenomic and transcription factor binding annotations.Grujic, Olivera; Phung, Tanya N; Kwon, Soo Bin; Arneson, Adriana; Lee, Yuju; Lohmueller, Kirk E; Ernst, JasonNature communications.2020 12 02;33268804
Master Regulators and Cofactors of Human Neuronal Cell Fate Specification Identified by CRISPR Gene Activation Screens.Black, Joshua B; McCutcheon, Sean R; Dube, Shataakshi; Barrera, Alejandro; Klann, Tyler S; Rice, Grayson A; Adkar, Shaunak S; Soderling, Scott H; Reddy, Timothy E; Gersbach, Charles ACell reports.2020 Dec 01;33264623
Mendelian randomization analysis identified genes pleiotropically associated with the risk and prognosis of COVID-19.Liu, Di; Yang, Jingyun; Feng, Bowen; Lu, Wenjin; Zhao, Chuntao; Li, LizhuoThe Journal of infection2021 0133259846
A map of cis-regulatory elements and 3D genome structures in zebrafish.Yang, Hongbo; Luan, Yu; Liu, Tingting; Lee, Hyung Joo; Fang, Li; Wang, Yanli; Wang, Xiaotao; Zhang, Bo; Jin, Qiushi; Ang, Khai Chung; Xing, Xiaoyun; Wang, Juan; Xu, Jie; Song, Fan; Sriranga, Iyyanki; Khunsriraksakul, Chachrit; Salameh, Tarik; Li, Daofeng;Nature.2020 Dec;33239788
Epigenome engineering: new technologies for precision medicine.Sgro, Agustin; Blancafort, PilarNucleic acids research2020 12 1633196851
Systematic integrated analysis of genetic and epigenetic variation in diabetic kidney disease.Sheng, Xin; Qiu, Chengxiang; Liu, Hongbo; Gluck, Caroline; Hsu, Jesse Y; He, Jiang; Hsu, Chi-Yuan; Sha, Daohang; Weir, Matthew R; Isakova, Tamara; Raj, Dominic; Rincon-Choles, Hernan; Feldman, Harold I; Townsend, Raymond; Li, Hongzhe; Susztak, KatalinProceedings of the National Academy of Sciences of the United States of America.2020 Nov 17;33144501
The transcriptomic signature of the aging podocyte.Mukhi, Dhanunjay; Susztak, KatalinKidney international.2020 11;33126968
Mendelian randomization integrating GWAS and mQTL data identified novel pleiotropic DNA methylation loci for neuropathology of Alzheimer's disease.Liu, Di; Wang, Youxin; Jing, Huiquan; Meng, Qun; Yang, JingyunNeurobiology of aging.2021 Jan;33120085
Mismatch-CRISPRi Reveals the Co-varying Expression-Fitness Relationships of Essential Genes in Escherichia coli and Bacillus subtilis.Hawkins, John S; Silvis, Melanie R; Koo, Byoung-Mo; Peters, Jason M; Osadnik, Hendrik; Jost, Marco; Hearne, Cameron C; Weissman, Jonathan S; Todor, Horia; Gross, Carol ACell systems.2020 Nov 18;33080209
Cord blood DNA methylome in newborns later diagnosed with autism spectrum disorder reflects early dysregulation of neurodevelopmental and X-linked genes.Mordaunt, Charles E; Jianu, Julia M; Laufer, Benjamin I; Zhu, Yihui; Hwang, Hyeyeon; Dunaway, Keith W; Bakulski, Kelly M; Feinberg, Jason I; Volk, Heather E; Lyall, Kristen; Croen, Lisa A; Newschaffer, Craig J; Ozonoff, Sally; Hertz-Picciotto, Irva; Fallin, M Daniele; Schmidt, Rebecca J; LaSalle, Janine MGenome medicine.2020 10 14;33054850
Insulin-sensitizing effects of vitamin D repletion mediated by adipocyte vitamin D receptor: Studies in humans and mice.Lontchi-Yimagou, Eric; Kang, Sona; Goyal, Akankasha; Zhang, Kehao; You, Jee Y; Carey, Michelle; Jain, Swati; Bhansali, Shobhit; Kehlenbrink, Sylvia; Guo, Peng; Rosen, Evan D; Kishore, Preeti; Hawkins, MeredithMolecular metabolism.2020 Dec;33045433
Quantitative Kinetic Analyses of Histone Turnover Using Imaging and Flow Cytometry.Sato, Hanae; Singer, Robert H; Greally, John MBio-protocol.2020 Sep 05;33043098
An optogenetic switch for the Set2 methyltransferase provides evidence for transcription-dependent and -independent dynamics of H3K36 methylation.Lerner, Andrew M; Hepperla, Austin J; Keele, Gregory R; Meriesh, Hashem A; Yumerefendi, Hayretin; Restrepo, David; Zimmerman, Seth; Bear, James E; Kuhlman, Brian; Davis, Ian J; Strahl, Brian DGenome research.2020 Nov;33020206
Progress of artificial intelligence in diabetic retinopathy screening.Wang, Yue-Lin; Yang, Jing-Yun; Yang, Jing-Yuan; Zhao, Xin-Yu; Chen, You-Xin; Yu, Wei-HongDiabetes/metabolism research and reviews.2020 Oct 03;33010796
The qBED track: a novel genome browser visualization for point processes.Moudgil, Arnav; Li, Daofeng; Hsu, Silas; Purushotham, Deepak; Wang, Ting; Mitra, Robi DBioinformatics (Oxford, England).2020 Sep 17;32941613
DeepH&M: Estimating single-CpG hydroxymethylation and methylation levels from enrichment and restriction enzyme sequencing methods.He, Yu; Jang, Hyo Sik; Xing, Xiaoyun; Li, Daofeng; Vasek, Michael J; Dougherty, Joseph D; Wang, TingScience advances.2020 Jul;32937429
Underlying features of epigenetic aging clocks in vivo and in vitro.Liu, Zuyun; Leung, Diana; Thrush, Kyra; Zhao, Wei; Ratliff, Scott; Tanaka, Toshiko; Schmitz, Lauren L; Smith, Jennifer A; Ferrucci, Luigi; Levine, Morgan EAging cell.2020 Oct;32930491
Stoichiometric analysis of protein complexes by cell fusion and single molecule imaging.Singh, Avtar; Van Slyke, Alexander L; Sirenko, Maria; Song, Alexander; Kammermeier, Paul J; Zipfel, Warren RScientific reports.2020 09 10;32913201
Cross-Species Analyses Identify Dlgap2 as a Regulator of Age-Related Cognitive Decline and Alzheimer's Dementia.Ouellette, Andrew R; Neuner, Sarah M; Dumitrescu, Logan; Anderson, Laura C; Gatti, Daniel M; Mahoney, Emily R; Bubier, Jason A; Churchill, Gary; Peters, Luanne; Huentelman, Matthew J; Herskowitz, Jeremy H; Yang, Hyun-Sik; Smith, Alexandra N; Reitz, Christiane; Kunkle, Brian W; White, Charles C; De Jager, Philip L; Schneider, Julie A; Bennett, David A; Seyfried, Nicholas T; Alzheimer?s Disease Genetics Consortium; Chesler, Elissa J; Hadad, Niran; Hohman, Timothy J; Kaczorowski, Catherine CCell reports.2020 Sep 01;32877673
Integration of postmortem amygdala expression profiling, GWAS, and functional cell culture assays: neuroticism-associated synaptic vesicle glycoprotein 2A (SV2A) gene is regulated by miR-133a and miR-218.Jurkiewicz, Magdalena; Moser, Dirk; Koller, Antonius; Yu, Lei; Chen, Emily I; Bennett, David A; Canli, TurhanTranslational psychiatry.2020 08 24;32839459
Integrative analyses prioritize GNL3 as a risk gene for bipolar disorder.Meng, Qingtuan; Wang, Le; Dai, Rujia; Wang, Jiawen; Ren, Zongyao; Liu, Sihan; Xia, Yan; Jiang, Yi; Duan, Fangyuan; Wang, Kangli; Liu, Chunyu; Chen, ChaoMolecular psychiatry.2020 11;32826963
Enhancer RNAs predict enhancer-gene regulatory links and are critical for enhancer function in neuronal systems.Carullo, Nancy V N; Phillips Iii, Robert A; Simon, Rhiana C; Soto, Salomon A Roman; Hinds, Jenna E; Salisbury, Aaron J; Revanna, Jasmin S; Bunner, Kendra D; Ianov, Lara; Sultan, Faraz A; Savell, Katherine E; Gersbach, Charles A; Day, Jeremy JNucleic acids research.2020 09 25;32810208
Podocytopathies.Kopp, Jeffrey B; Anders, Hans-Joachim; Susztak, Katalin; Podestà, Manuel A; Remuzzi, Giuseppe; Hildebrandt, Friedhelm; Romagnani, PaolaNature reviews. Disease primers.2020 08 13;32792490
An epigenome-wide association study of Alzheimer's disease blood highlights robust DNA hypermethylation in the HOXB6 gene.Roubroeks, Janou A Y; Smith, Adam R; Smith, Rebecca G; Pishva, Ehsan; Ibrahim, Zina; Sattlecker, Martina; Hannon, Eilis J; K?oszewska, Iwona; Mecocci, Patrizia; Soininen, Hilkka; Tsolaki, Magda; Vellas, Bruno; Wahlund, Lars-Olof; Aarsland, Dag; Proitsi, Petroula; Hodges, Angela; Lovestone, Simon; Newhouse, Stephen J; Dobson, Richard J B; Mill, Jonathan; van den Hove, Daniël L A; Lunnon, KatieNeurobiology of aging.2020 Nov;32745807
Cell death and survival pathways in Alzheimer's disease: an integrative hypothesis testing approach utilizing -omic data sets.Brokaw, Danielle L; Piras, Ignazio S; Mastroeni, Diego; Weisenberger, Daniel J; Nolz, Jennifer; Delvaux, Elaine; Serrano, Geidy E; Beach, Thomas G; Huentelman, Matthew J; Coleman, Paul DNeurobiology of aging.2020 Nov;32745806
Association between DNA methylation levels in brain tissue and late-life depression in community-based participants.Hüls, Anke; Robins, Chloe; Conneely, Karen N; De Jager, Philip L; Bennett, David A; Epstein, Michael P; Wingo, Thomas S; Wingo, Aliza PTranslational psychiatry.2020 07 30;32733030
Epigenomic programming in early fetal brain development.Li, Luolan; Maire, Cecile L; Bilenky, Misha; Carles, Annaïck; Heravi-Moussavi, Alireza; Hong, Chibo; Tam, Angela; Kamoh, Baljit; Cho, Stephanie; Cheung, Dorothy; Li, Irene; Wong, Tina; Nagarajan, Raman P; Mungall, Andrew J; Moore, Richard; Wang, Ting; Kleinman, Claudia L; Jabado, Nada; Jones, Steven Jm; Marra, Marco A; Ligon, Keith L; Costello, Joseph F; Hirst, MartinEpigenomics2020 0632677466
Deciphering cellular transcriptional alterations in Alzheimer's disease brains.Wang, Xue; Allen, Mariet; Li, Shaoyu; Quicksall, Zachary S; Patel, Tulsi A; Carnwath, Troy P; Reddy, Joseph S; Carrasquillo, Minerva M; Lincoln, Sarah J; Nguyen, Thuy T; Malphrus, Kimberly G; Dickson, Dennis W; Crook, Julia E; Asmann, Yan W; Ertekin-Taner, NilüferMolecular neurodegeneration.2020 07 13;32660529
Transcriptional repression of PTEN in neural cells using CRISPR/dCas9 epigenetic editing.Moses, C; Hodgetts, S I; Nugent, F; Ben-Ary, G; Park, K K; Blancafort, P; Harvey, A RScientific reports2020 07 0932647121
Clinical validation of the novel HDAC6 radiotracer [18F]EKZ-001 in the human brain.Koole, Michel; Van Weehaeghe, Donatienne; Serdons, Kim; Herbots, Marissa; Cawthorne, Christopher; Celen, Sofie; Schroeder, Frederick A; Hooker, Jacob M; Bormans, Guy; de Hoon, Jan; Kranz, Janice E; Van Laere, Koen; Gilbert, Tonya MEuropean journal of nuclear medicine and molecular imaging2021 Feb32638097
Pharmaceutical-Grade Rigosertib Is a Microtubule-Destabilizing Agent.Jost, Marco; Chen, Yuwen; Gilbert, Luke A; Horlbeck, Max A; Krenning, Lenno; Menchon, Grégory; Rai, Ankit; Cho, Min Y; Stern, Jacob J; Prota, Andrea E; Kampmann, Martin; Akhmanova, Anna; Steinmetz, Michel O; Tanenbaum, Marvin E; Weissman, Jonathan SMolecular cell.2020 07 02;32619469
Discovery of 318 new risk loci for type 2 diabetes and related vascular outcomes among 1.4 million participants in a multi-ancestry meta-analysis.Vujkovic, Marijana; Keaton, Jacob M; Lynch, Julie A; Miller, Donald R; Zhou, Jin; Tcheandjieu, Catherine; Huffman, Jennifer E; Assimes, Themistocles L; Lorenz, Kimberly; Zhu, Xiang; Hilliard, Austin T; Judy, Renae L; Huang, Jie; Lee, Kyung M; Klarin, Derek; Pyarajan, Saiju; Danesh, John; Melander, Olle; Rasheed, Asif; Mallick, Nadeem H; Hameed, Shahid; Qureshi, Irshad H; Afzal, Muhammad Naeem; Malik, Uzma; Jalal, Anjum; Abbas, Shahid; Sheng, Xin; Gao, Long; Kaestner, Klaus H; Susztak, Katalin; Sun, Yan V; DuVall, Scott L; Cho, Kelly; Lee, Jennifer S; Gaziano, J Michael; Phillips, Lawrence S; Meigs, James B; Reaven, Peter D; Wilson, Peter W; Edwards, Todd L; Rader, Daniel J; Damrauer, Scott M; O'Donnell, Christopher J; Tsao, Philip S; HPAP Consortium; Regeneron Genetics Center; VA Million Veteran Program; Chang, Kyong-Mi; Voight, Benjamin F; Saleheen, DanishNature genetics.2020 07;32541925
Whole Blood DNA Methylation Signatures of Diet Are Associated With Cardiovascular Disease Risk Factors and All-Cause Mortality.Ma, Jiantao; Rebholz, Casey M; Braun, Kim V E; Reynolds, Lindsay M; Aslibekyan, Stella; Xia, Rui; Biligowda, Niranjan G; Huan, Tianxiao; Liu, Chunyu; Mendelson, Michael M; Joehanes, Roby; Hu, Emily A; Vitolins, Mara Z; Wood, Alexis C; Lohman, Kurt; Ochoa-Rosales, Carolina; van Meurs, Joyce; Uitterlinden, Andre; Liu, Yongmei; Elhadad, Mohamed A; Heier, Margit; Waldenberger, Melanie; Peters, Annette; Colicino, Elena; Whitsel, Eric A; Baldassari, Antoine; Gharib, Sina A; Sotoodehnia, Nona; Brody, Jennifer A; Sitlani, Colleen M; Tanaka, Toshiko; Hill, W David; Corley, Janie; Deary, Ian J; Zhang, Yan; Schöttker, Ben; Brenner, Hermann; Walker, Maura E; Ye, Shumao; Nguyen, Steve; Pankow, Jim; Demerath, Ellen W; Zheng, Yinan; Hou, Lifang; Liang, Liming; Lichtenstein, Alice H; Hu, Frank B; Fornage, Myriam; Voortman, Trudy; Levy, DanielCirculation. Genomic and precision medicine.2020 Aug;32525743
Loss of IL-27Rα Results in Enhanced Tubulointerstitial Fibrosis Associated with Elevated Th17 Responses.Coppock, Gaia M; Aronson, Lillian R; Park, Jihwan; Qiu, Chengxiang; Park, Jeongho; DeLong, Jonathan H; Radaelli, Enrico; Suszták, Katalin; Hunter, Christopher AJournal of immunology (Baltimore, Md. : 1950)2020 07 1532522836
The interdependence of renal epithelial and endothelial metabolism and cell state.Balzer, Michael S; Susztak, KatalinScience signaling2020 06 0932518144
Unravelling the complex genetics of common kidney diseases: from variants to mechanisms.Sullivan, Katie Marie; Susztak, KatalinNature reviews. Nephrology.2020 11;32514149
Low oxygen saturation during sleep reduces CD1D and RAB20 expressions that are reversed by CPAP therapy.Sofer, Tamar; Li, Ruitong; Joehanes, Roby; Lin, Honghuang; Gower, Adam C; Wang, Heming; Kurniansyah, Nuzulul; Cade, Brian E; Lee, Jiwon; Williams, Stephanie; Mehra, Reena; Patel, Sanjay R; Quan, Stuart F; Liu, Yongmei; Rotter, Jerome I; Rich, Stephen S; Spira, Avrum; Levy, Daniel; Gharib, Sina A; Redline, Susan; Gottlieb, Daniel JEBioMedicine2020 Jun32512511
The association between genetic variants in lactotransferrin and dental caries: a meta- and gene-based analysis.Li, Xueyan; Su, Yi; Liu, Di; Yang, JingyunBMC medical genetics.2020 May 27;32460726
ASEP: Gene-based detection of allele-specific expression across individuals in a population by RNA sequencing.Fan, Jiaxin; Hu, Jian; Xue, Chenyi; Zhang, Hanrui; Susztak, Katalin; Reilly, Muredach P; Xiao, Rui; Li, MingyaoPLoS genetics.2020 05;32392242
Social regulation of inflammation related gene expression in the multi-ethnic study of atherosclerosis.Brown, Kristen M; Diez-Roux, Ana V; Smith, Jennifer A; Needham, Belinda L; Mukherjee, Bhramar; Ware, Erin B; Liu, Yongmei; Cole, Steven W; Seeman, Teresa E; Kardia, Sharon L RPsychoneuroendocrinology.2020 07;32387875
It Takes Two to Tango: The Role of Dysregulated Metabolism and Inflammation in Kidney Disease Development.Quinn, Ghazal Z; Dhillon, Poonam; Susztak, KatalinSeminars in nephrology.2020 03;32303282
Inference of single-cell phylogenies from lineage tracing data using Cassiopeia.Jones, Matthew G; Khodaverdian, Alex; Quinn, Jeffrey J; Chan, Michelle M; Hussmann, Jeffrey A; Wang, Robert; Xu, Chenling; Weissman, Jonathan S; Yosef, NirGenome biology.2020 04 14;32290857
DRAMS: A tool to detect and re-align mixed-up samples for integrative studies of multi-omics data.Jiang, Yi; Giase, Gina; Grennan, Kay; Shieh, Annie W; Xia, Yan; Han, Lide; Wang, Quan; Wei, Qiang; Chen, Rui; Liu, Sihan; White, Kevin P; Chen, Chao; Li, Bingshan; Liu, ChunyuPLoS computational biology.2020 04;32282793
Bayesian integrative analysis of epigenomic and transcriptomic data identifies Alzheimer's disease candidate genes and networks.Klein, Hans-Ulrich; Schäfer, Martin; Bennett, David A; Schwender, Holger; De Jager, Philip LPLoS computational biology.2020 04;32255787
Phenome-wide association analysis suggests the APOL1 linked disease spectrum primarily drives kidney-specific pathways.Bajaj, Archna; Ihegword, Andrea; Qiu, Chengxiang; Small, Aeron M; Wei, Wei-Qi; Bastarache, Lisa; Feng, QiPing; Kember, Rachel L; Risman, Marjorie; Bloom, Roy D; Birtwell, David L; Williams, Heather; Shaffer, Christian M; Chen, Jinbo; Center, Regeneron Genetics; Denny, Joshua C; Rader, Daniel J; Stein, C Michael; Damrauer, Scott M; Susztak, KatalinKidney international.2020 May;32247630
Combinatorial single-cell CRISPR screens by direct guide RNA capture and targeted sequencing.Replogle, Joseph M; Norman, Thomas M; Xu, Albert; Hussmann, Jeffrey A; Chen, Jin; Cogan, J Zachery; Meer, Elliott J; Terry, Jessica M; Riordan, Daniel P; Srinivas, Niranjan; Fiddes, Ian T; Arthur, Joseph G; Alvarado, Luigi J; Pfeiffer, Katherine A; Mikkelsen, Tarjei S; Weissman, Jonathan S; Adamson, BrittNature biotechnology.2020 Mar 30;32231336
RecV recombinase system for in vivo targeted optogenomic modifications of single cells or cell populations.Yao, Shenqin; Yuan, Peng; Ouellette, Ben; Zhou, Thomas; Mortrud, Marty; Balaram, Pooja; Chatterjee, Soumya; Wang, Yun; Daigle, Tanya L; Tasic, Bosiljka; Kuang, Xiuli; Gong, Hui; Luo, Qingming; Zeng, Shaoqun; Curtright, Andrew; Dhaka, Ajay; Kahan, Anat; Gradinaru, Viviana; Chrapkiewicz, Rados?aw; Schnitzer, Mark; Zeng, Hongkui; Cetin, AliNature methods.2020 04;32203389
Translation of HDAC6 PET Imaging Using [18F]EKZ-001-cGMP Production and Measurement of HDAC6 Target Occupancy in Nonhuman Primates.Celen, Sofie; Rokka, Johanna; Gilbert, Tonya M; Koole, Michel; Vermeulen, Isabeau; Serdons, Kim; Schroeder, Frederick A; Wagner, Florence F; Bleeser, Tom; Hightower, Baileigh G; Hu, Jiyun; Rahal, Dania; Beyzavi, M Hassan; Vanduffel, Wim; Van Laere, Koen; Kranz, Janice E; Hooker, Jacob M; Bormans, Guy; Cawthorne, Christopher JACS chemical neuroscience2020 04 0132159328
Shared Causal Paths underlying Alzheimer's dementia and Type 2 Diabetes.Hu, Zixin; Jiao, Rong; Wang, Panpan; Zhu, Yun; Zhao, Jinying; De Jager, Phil; Bennett, David A; Jin, Li; Xiong, MomiaoScientific reports2020 Mar 0532139775
Dnmt3a and Dnmt3b-Decommissioned Fetal Enhancers are Linked to Kidney Disease.Guan, Yuting; Liu, Hongbo; Ma, Ziyuan; Li, Szu-Yuan; Park, Jihwan; Sheng, Xin; Susztak, KatalinJournal of the American Society of Nephrology : JASN.2020 04;32127410
Fitness effects of CRISPR/Cas9-targeting of long noncoding RNA genes.Horlbeck, Max A; Liu, S John; Chang, Howard Y; Lim, Daniel A; Weissman, Jonathan SNature biotechnology2020 0532094656
Brain microRNAs associated with late-life depressive symptoms are also associated with cognitive trajectory and dementia.Wingo, Thomas S; Yang, Jingjing; Fan, Wen; Min Canon, Se; Gerasimov, Ekaterina Sergeevna; Lori, Adriana; Logsdon, Benjamin; Yao, Bing; Seyfried, Nicholas T; Lah, James J; Levey, Allan I; Boyle, Patricia A; Schneider, Julia A; De Jager, Philip L; Bennett, David A; Wingo, Aliza PNPJ genomic medicine.2020;32047652
Psychosis-associated DNA methylomic variation in Alzheimer's disease cortex.Pishva, Ehsan; Creese, Byron; Smith, Adam R; Viechtbauer, Wolfgang; Proitsi, Petroula; van den Hove, Daniel L A; Ballard, Clive; Mill, Jonathan; Lunnon, KatieNeurobiology of aging.2020 05;32007278
Co-opted transposons help perpetuate conserved higher-order chromosomal structures.Choudhary, Mayank Nk; Friedman, Ryan Z; Wang, Julia T; Jang, Hyo Sik; Zhuo, Xiaoyu; Wang, TingGenome biology.2020 01 24;31973766
IL-1 Transcriptional Responses to Lipopolysaccharides Are Regulated by a Complex of RNA Binding Proteins.Shi, Lihua; Song, Li; Maurer, Kelly; Dou, Ying; Patel, Vishesh R; Su, Chun; Leonard, Michelle E; Lu, Sumei; Hodge, Kenyaita M; Torres, Annabel; Chesi, Alessandra; Grant, Struan F A; Wells, Andrew D; Zhang, Zhe; Petri, Michelle A; Sullivan, Kathleen EJournal of immunology (Baltimore, Md. : 1950).2020 Mar 01;31953354
Loss of ELK1 has differential effects on age-dependent organ fibrosis.Cairns, Jennifer T; Habgood, Anthony; Edwards-Pritchard, Rochelle C; Joseph, Chitra; John, Alison E; Wilkinson, Chloe; Stewart, Iain D; Leslie, Jack; Blaxall, Burns C; Susztak, Katalin; Alberti, Siegfried; Nordheim, Alfred; Oakley, Fiona; Jenkins, Gisli; Tatler, Amanda LThe international journal of biochemistry & cell biology2020 0331877385
Systematic underestimation of the epigenetic clock and age acceleration in older subjects.El Khoury, Louis Y; Gorrie-Stone, Tyler; Smart, Melissa; Hughes, Amanda; Bao, Yanchun; Andrayas, Alexandria; Burrage, Joe; Hannon, Eilis; Kumari, Meena; Mill, Jonathan; Schalkwyk, Leonard CGenome biology2019 12 1731847916
Leveraging allelic imbalance to refine fine-mapping for eQTL studies.Zou, Jennifer; Hormozdiari, Farhad; Jew, Brandon; Castel, Stephane E; Lappalainen, Tuuli; Ernst, Jason; Sul, Jae Hoon; Eskin, EleazarPLoS genetics.2019 12;31834882
The epigenomic landscape of transposable elements across normal human development and anatomy.Pehrsson, Erica C; Choudhary, Mayank N K; Sundaram, Vasavi; Wang, TingNature communications.2019 Dec 10;31822674
An integrative approach for fine-mapping chromatin interactions.Jaroszewicz, Artur; Ernst, JasonBioinformatics (Oxford, England).2020 03 01;31742318
Bayesian shrinkage estimation of high dimensional causal mediation effects in omics studies.Song, Yanyi; Zhou, Xiang; Zhang, Min; Zhao, Wei; Liu, Yongmei; Kardia, Sharon L R; Roux, Ana V Diez; Needham, Belinda L; Smith, Jennifer A; Mukherjee, BhramarBiometrics.2019 Nov 16;31733066
Recapitulation and Reversal of Schizophrenia-Related Phenotypes in Setd1a-Deficient Mice.Mukai, Jun; Cannavò, Enrico; Crabtree, Gregg W; Sun, Ziyi; Diamantopoulou, Anastasia; Thakur, Pratibha; Chang, Chia-Yuan; Cai, Yifei; Lomvardas, Stavros; Takata, Atsushi; Xu, Bin; Gogos, Joseph ANeuron2019 11 0631606247
Targeted transcriptional modulation with type I CRISPR-Cas systems in human cells.Pickar-Oliver, Adrian; Black, Joshua B; Lewis, Mae M; Mutchnick, Kevin J; Klann, Tyler S; Gilcrest, Kylie A; Sitton, Madeleine J; Nelson, Christopher E; Barrera, Alejandro; Bartelt, Luke C; Reddy, Timothy E; Beisel, Chase L; Barrangou, Rodolphe; Gersbach, Charles ANature biotechnology.2019 Sep 23;31548729
A compendium of promoter-centered long-range chromatin interactions in the human genome.Jung, Inkyung; Schmitt, Anthony; Diao, Yarui; Lee, Andrew J; Liu, Tristin; Yang, Dongchan; Tan, Catherine; Eom, Junghyun; Chan, Marilynn; Chee, Sora; Chiang, Zachary; Kim, Changyoun; Masliah, Eliezer; Barr, Cathy L; Li, Bin; Kuan, Samantha; Kim, Dongsup; Ren, BingNature genetics.2019 Oct;31501517
Understanding the kidney one cell at a time.Park, Jihwan; Liu, Chang Linda; Kim, Junhyong; Susztak, KatalinKidney international.2019 Oct;31492507
Epigenetic signatures of methylated DNA cytosine in Alzheimer's disease.Fetahu, Irfete S; Ma, Dingailu; Rabidou, Kimberlie; Argueta, Christian; Smith, Michael; Liu, Hang; Wu, Feizhen; Shi, Yujiang GScience advances.2019 Aug;31489368
Mitochondrial Damage and Activation of the STING Pathway Lead to Renal Inflammation and Fibrosis.Chung, Ki Wung; Dhillon, Poonam; Huang, Shizheng; Sheng, Xin; Shrestha, Rojesh; Qiu, Chengxiang; Kaufman, Brett A; Park, Jihwan; Pei, Liming; Baur, Joseph; Palmer, Matthew; Susztak, KatalinCell metabolism.2019 Oct 01;31474566
Using Transcriptomic Hidden Variables to Infer Context-Specific Genotype Effects in the Brain.Ng, Bernard; Casazza, William; Patrick, Ellis; Tasaki, Shinya; Novakovsky, Gherman; Felsky, Daniel; Ma, Yiyi; Bennett, David A; Gaiteri, Chris; De Jager, Philip L; Mostafavi, SaraAmerican journal of human genetics2019 Sep 0531447098
cindr, the Drosophila Homolog of the CD2AP Alzheimer's Disease Risk Gene, Is Required for Synaptic Transmission and Proteostasis.Ojelade, Shamsideen A; Lee, Tom V; Giagtzoglou, Nikolaos; Yu, Lei; Ugur, Berrak; Li, Yarong; Duraine, Lita; Zuo, Zhongyuan; Petyuk, Vlad; De Jager, Philip L; Bennett, David A; Arenkiel, Benjamin R; Bellen, Hugo J; Shulman, Joshua MCell reports.2019 Aug 13;31412248
Exploring genetic interaction manifolds constructed from rich single-cell phenotypes.Norman, Thomas M; Horlbeck, Max A; Replogle, Joseph M; Ge, Alex Y; Xu, Albert; Jost, Marco; Gilbert, Luke A; Weissman, Jonathan SScience (New York, N.Y.).2019 08 23;31395745
Systematic discovery of conservation states for single-nucleotide annotation of the human genome.Arneson, Adriana; Ernst, JasonCommunications biology.2019;31286065
Neuroepigenetic signatures of age and sex in the living human brain.Gilbert, Tonya M; Zürcher, Nicole R; Catanese, Mary C; Tseng, Chieh-En J; Di Biase, Maria A; Lyall, Amanda E; Hightower, Baileigh G; Parmar, Anjali J; Bhanot, Anisha; Wu, Christine J; Hibert, Matthew L; Kim, Minhae; Mahmood, Umar; Stufflebeam, Steven M; Schroeder, Frederick A; Wang, Changning; Roffman, Joshua L; Holt, Daphne J; Greve, Douglas N; Pasternak, Ofer; Kubicki, Marek; Wey, Hsiao-Ying; Hooker, Jacob MNature communications.2019 07 03;31270332
NUCLIZE for quantifying epigenome: generating histone modification data at single-nucleosome resolution using genuine nucleosome positions.Zheng, Daoshan; Trynda, Justyna; Sun, Zhifu; Li, ZhaoyuBMC genomics.2019 Jul 02;31266464
The association between apolipoprotein E and gallstone disease: an updated meta-analysis.Li, Lizhuo; Qiao, Xin; Wang, Xia; Liu, Di; Xue, Qingmu; Han, Lu; Dai, Fei; Ma, Guomin; Yang, Zhipeng; Zhang, Tao; Yang, Shuo; Cai, Shikang; Gao, Mingyue; Yang, JingyunBMC medical genetics.2019 Jun 14;31200656
Functional methylome analysis of human diabetic kidney disease.Park, Jihwan; Guan, Yuting; Sheng, Xin; Gluck, Caroline; Seasock, Matthew J; Hakimi, A. Ari; Qiu, Chengxiang; Pullman, James; Verma, Amit; Li, Hongzhe; Palmer, Matthew; Susztak, KatalinJCI insight.2019 06 06;31167971
WashU Epigenome Browser update 2019.Li, Daofeng; Hsu, Silas; Purushotham, Deepak; Sears, Renee L; Wang, TingNucleic acids research.2019 Jul 02;31165883
Kidney cytosine methylation changes improve renal function decline estimation in patients with diabetic kidney disease.Gluck, Caroline; Qiu, Chengxiang; Han, Sang Youb; Palmer, Matthew; Park, Jihwan; Ko, Yi-An; Guan, Yuting; Sheng, Xin; Hanson, Robert L; Huang, Jing; Chen, Yong; Park, Ae Seo Deok; Izquierdo, Maria Concepcion; Mantzaris, Ioannis; Verma, Amit; Pullman, James; Li, Hongzhe; Susztak, KatalinNature communications.2019 06 05;31165727
Ablation of adipocyte creatine transport impairs thermogenesis and causes diet-induced obesity.Kazak, Lawrence; Rahbani, Janane F; Samborska, Bozena; Lu, Gina Z; Jedrychowski, Mark P; Lajoie, Mathieu; Zhang, Song; Ramsay, LeeAnn C; Dou, Florence Y; Tenen, Danielle; Chouchani, Edward T; Dzeja, Petras; Watson, Ian R; Tsai, Linus; Rosen, Evan D; Spiegelman, Bruce MNature metabolism.2019;31161155
The next generation of CRISPR-Cas technologies and applications.Pickar-Oliver, Adrian; Gersbach, Charles ANature reviews. Molecular cell biology.2019 08;31147612
CpG-related SNPs in the MS4A region have a dose-dependent effect on risk of late-onset Alzheimer disease.Ma, Yiyi; Jun, Gyungah R; Chung, Jaeyoon; Zhang, Xiaoling; Kunkle, Brian W; Naj, Adam C; White, Charles C; Bennett, David A; De Jager, Philip L; Alzheimer?s Disease Genetics Consortium; Mayeux, Richard; Haines, Jonathan L; Pericak-Vance, Margaret A; Schellenberg, Gerard D; Farrer, Lindsay A; Lunetta, Kathryn LAging cell.2019 Aug;31144443
Epigenome-wide association analysis of daytime sleepiness in the Multi-Ethnic Study of Atherosclerosis reveals African-American-specific associations.Barfield, Richard; Wang, Heming; Liu, Yongmei; Brody, Jennifer A; Swenson, Brenton; Li, Ruitong; Bartz, Traci M; Sotoodehnia, Nona; Chen, Yii-der I; Cade, Brian E; Chen, Han; Patel, Sanjay R; Zhu, Xiaofeng; Gharib, Sina A; Johnson, W Craig; Rotter, Jerome I; Saxena, Richa; Purcell, Shaun; Lin, Xihong; Redline, Susan; Sofer, TamarSleep.2019 08 01;31139831
Epigenetic dysregulation of enhancers in neurons is associated with Alzheimer's disease pathology and cognitive symptoms.Li, Peipei; Marshall, Lee; Oh, Gabriel; Jakubowski, Jennifer L; Groot, Daniel; He, Yu; Wang, Ting; Petronis, Arturas; Labrie, VivianeNature communications.2019 05 21;31113950
Retargeting of macroH2A following mitosis to cytogenetic-scale heterochromatic domains.Sato, Hanae; Wu, Bin; Delahaye, Fabien; Singer, Robert H; Greally, John MThe Journal of cell biology.2019 Jun 03;31110057
Molecular recording of mammalian embryogenesis.Chan, Michelle M; Smith, Zachary D; Grosswendt, Stefanie; Kretzmer, Helene; Norman, Thomas M; Adamson, Britt; Jost, Marco; Quinn, Jeffrey J; Yang, Dian; Jones, Matthew G; Khodaverdian, Alex; Yosef, Nir; Meissner, Alexander; Weissman, Jonathan SNature.2019 06;31086336
Next-generation characterization of the Cancer Cell Line Encyclopedia.Ghandi, Mahmoud; Huang, Franklin W; Jané-Valbuena, Judit; Kryukov, Gregory V; Lo, Christopher C; McDonald 3rd, E Robert; Barretina, Jordi; Gelfand, Ellen T; Bielski, Craig M; Li, Haoxin; Hu, Kevin; Andreev-Drakhlin, Alexander Y; Kim, Jaegil; Hess, Julian M; Haas, Brian J; Aguet, François; Weir, Barbara A; Rothberg, Michael V; Paolella, Brenton R; Lawrence, Michael S; Akbani, Rehan; Lu, Yiling; Tiv, Hong L; Gokhale, Prafulla C; de Weck, Antoine; Mansour, Ali Amin; Oh, Coyin; Shih, Juliann; Hadi, Kevin; Rosen, Yanay; Bistline, Jonathan; Venkatesan, Kavitha; Reddy, Anupama; Sonkin, Dmitriy; Liu, Manway; Lehar, Joseph; Korn, Joshua M; Porter, Dale A; Jones, Michael D; Golji, Javad; Caponigro, Giordano; Taylor, Jordan E; Dunning, Caitlin M; Creech, Amanda L; Warren, Allison C; McFarland, James M; Zamanighomi, Mahdi; Kauffmann, Audrey; Stransky, Nicolas; Imielinski, Marcin; Maruvka, Yosef E; Cherniack, Andrew D; Tsherniak, Aviad; Vazquez, Francisca; Jaffe, Jacob D; Lane, Andrew A; Weinstock, David M; Johannessen, Cory M; Morrissey, Michael P; Stegmeier, Frank; Schlegel, Robert; Hahn, William C; Getz, Gad; Mills, Gordon B; Boehm, Jesse S; Golub, Todd R; Garraway, Levi A; Sellers, William RNature.2019 May;31068700
Going from acute to chronic kidney injury with FoxO3.Gu, Xiangchen; Raman, Archana; Susztak, KatalinThe Journal of clinical investigation.2019 05 06;31063992
DNA methylation signatures as biomarkers of prior environmental exposures.Ladd-Acosta, Christine; Fallin, M DanieleCurrent epidemiology reports.2019 Mar;31032172
A signature of circulating inflammatory proteins and development of end-stage renal disease in diabetes.Niewczas, Monika A; Pavkov, Meda E; Skupien, Jan; Smiles, Adam; Md Dom, Zaipul I; Wilson, Jonathan M; Park, Jihwan; Nair, Viji; Schlafly, Andrew; Saulnier, Pierre-Jean; Satake, Eiichiro; Simeone, Christopher A; Shah, Hetal; Qiu, Chengxiang; Looker, Helen C; Fiorina, Paolo; Ware, Carl F; Sun, Jennifer K; Doria, Alessandro; Kretzler, Matthias; Susztak, Katalin; Duffin, Kevin L; Nelson, Robert G; Krolewski, Andrzej SNature medicine.2019 05;31011203
Increasing the specificity of CRISPR systems with engineered RNA secondary structures.Kocak, D Dewran; Josephs, Eric A; Bhandarkar, Vidit; Adkar, Shaunak S; Kwon, Jennifer B; Gersbach, Charles ANature biotechnology.2019 06;30988504
In vivo Application of the REMOTE-control System for the Manipulation of Endogenous Gene Expression.Vander Schaaf, Nicole A; Oghamian, Shirley; Park, Jin-A; Kang, Liang; Laird, Peter W; Lee, Kwang-HoJournal of visualized experiments : JoVE.2019 Mar 29;30985765
Sex-differential DNA methylation and associated regulation networks in human brain implicated in the sex-biased risks of psychiatric disorders.Xia, Yan; Dai, Rujia; Wang, Kangli; Jiao, Chuan; Zhang, Chunling; Xu, Yuchen; Li, Honglei; Jing, Xi; Chen, Yu; Jiang, Yi; Kopp, Richard F; Giase, Gina; Chen, Chao; Liu, ChunyuMolecular psychiatry.2019 Apr 11;30976086
Expression of socially sensitive genes: The multi-ethnic study of atherosclerosis.Brown, Kristen M; Diez-Roux, Ana V; Smith, Jennifer A; Needham, Belinda L; Mukherjee, Bhramar; Ware, Erin B; Liu, Yongmei; Cole, Steven W; Seeman, Teresa E; Kardia, Sharon L RPloS one.2019;30973896
A Peripheral Blood DNA Methylation Signature of Hepatic Fat Reveals a Potential Causal Pathway for Nonalcoholic Fatty Liver Disease.Ma, Jiantao; Nano, Jana; Ding, Jingzhong; Zheng, Yinan; Hennein, Rachel; Liu, Chunyu; Speliotes, Elizabeth K; Huan, Tianxiao; Song, Ci; Mendelson, Michael M; Joehanes, Roby; Long, Michelle T; Liang, Liming; Smith, Jennifer A; Reynolds, Lindsay M; Ghanbari, Mohsen; Muka, Taulant; van Meurs, Joyce B J; Alferink, Louise J M; Franco, Oscar H; Dehghan, Abbas; Ratliff, Scott; Zhao, Wei; Bielak, Lawrence; Kardia, Sharon L R; Peyser, Patricia A; Ning, Hongyan; VanWagner, Lisa B; Lloyd-Jones, Donald M; Carr, John Jeffrey; Greenland, Philip; Lichtenstein, Alice H; Hu, Frank B; Liu, Yongmei; Hou, Lifang; Darwish Murad, Sarwa; Levy, DanielDiabetes.2019 May;30936141
Novel methods for integration and visualization of genomics and genetics data in Alzheimer's disease.Bihlmeyer, Nathan A; Merrill, Emily; Lambert, Yann; Srivastava, Gyan P; Clark, Timothy W; Hyman, Bradley T; Das, SudeshnaAlzheimer's & dementia : the journal of the Alzheimer's Association.2019 Jun;30935898
Transposable elements drive widespread expression of oncogenes in human cancers.Jang, Hyo Sik; Shah, Nakul M; Du, Alan Y; Dailey, Zea Z; Pehrsson, Erica C; Godoy, Paula M; Zhang, David; Li, Daofeng; Xing, Xiaoyun; Kim, Sungsu; O'Donnell, David; Gordon, Jeffrey I; Wang, TingNature genetics.2019 04;30926969
Measuring the reproducibility and quality of Hi-C data.Yard?mc?, Galip Gürkan; Ozadam, Hakan; Sauria, Michael E G; Ursu, Oana; Yan, Koon-Kiu; Yang, Tao; Chakraborty, Abhijit; Kaul, Arya; Lajoie, Bryan R; Song, Fan; Zhan, Ye; Ay, Ferhat; Gerstein, Mark; Kundaje, Anshul; Li, Qunhua; Taylor, James; Yue, Feng; Dekker, Job; Noble, William SGenome biology.2019 03 19;30890172
Cellular response to small molecules that selectively stall protein synthesis by the ribosome.Liaud, Nadège; Horlbeck, Max A; Gilbert, Luke A; Gjoni, Ketrin; Weissman, Jonathan S; Cate, Jamie H DPLoS genetics.2019 03;30875366
DNMT1 in Six2 Progenitor Cells Is Essential for Transposable Element Silencing and Kidney Development.Li, Szu-Yuan; Park, Jihwan; Guan, Yuting; Chung, Kiwung; Shrestha, Rojesh; Palmer, Matthew B; Susztak, KatalinJournal of the American Society of Nephrology : JASN.2019 Apr;30850438
The kidney transcriptome, from single cells to whole organs and back.Huang, Shizheng; Sheng, Xin; Susztak, KatalinCurrent opinion in nephrology and hypertension.2019 May;30844884
Molecular imaging HDACs class IIa expression-activity and pharmacologic inhibition in intracerebral glioma models in rats using PET/CT/(MRI) with [18F]TFAHA.Laws, Maxwell T; Bonomi, Robin E; Kamal, Swatabdi; Gelovani, David J; Llaniguez, Jeremy; Potukutchi, Shreya; Lu, Xin; Mangner, Thomas; Gelovani, Juri GScientific reports.2019 Mar 05;30837601
Epigenetic marks of prenatal air pollution exposure found in multiple tissues relevant for child health.Ladd-Acosta, Christine; Feinberg, Jason I; Brown, Shannon C; Lurmann, Frederick W; Croen, Lisa A; Hertz-Picciotto, Irva; Newschaffer, Craig J; Feinberg, Andrew P; Fallin, M Daniele; Volk, Heather EEnvironment international.2019 05;30826615
Prioritizing Parkinson's disease genes using population-scale transcriptomic data.Li, Yang I; Wong, Garrett; Humphrey, Jack; Raj, TowfiqueNature communications2019 Mar 0130824768
Long-Range Chromatin Interactions in the Kidney.Guan, Yuting; Liu, Hongbo; Susztak, KatalinJournal of the American Society of Nephrology : JASN.2019 Feb 13;30760498
Ascorbic acid-induced TET activation mitigates adverse hydroxymethylcytosine loss in renal cell carcinoma.Shenoy, Niraj; Bhagat, Tushar D; Cheville, John; Lohse, Christine; Bhattacharyya, Sanchari; Tischer, Alexander; Machha, Venkata; Gordon-Mitchell, Shanisha; Choudhary, Gaurav; Wong, Li-Fan; Gross, LouAnn; Ressigue, Emily; Leibovich, Bradley; Boorjian, Stephen A; Steidl, Ulrich; Wu, Xiaosheng; Pradhan, Kith; Gartrell, Benjamin; Agarwal, Beamon; Pagliaro, Lance; Suzuki, Masako; Greally, John M; Rakheja, Dinesh; Thompson, R Houston; Susztak, Katalin; Witzig, Thomas; Zou, Yiyu; Verma, AmitThe Journal of clinical investigation.2019 Mar 04;30702441
Enhancer Histone Acetylation Modulates Transcriptional Bursting Dynamics of Neuronal Activity-Inducible Genes.Chen, Liang-Fu; Lin, Yen Ting; Gallegos, David A; Hazlett, Mariah F; Gómez-Schiavon, Mariana; Yang, Marty G; Kalmeta, Breanna; Zhou, Allen S; Holtzman, Liad; Gersbach, Charles A; Grandl, Jörg; Buchler, Nicolas E; West, Anne ECell reports.2019 01 29;30699347
Lysine 27 of replication-independent histone H3.3 is required for Polycomb target gene silencing but not for gene activation.Leatham-Jensen, Mary; Uyehara, Christopher M; Strahl, Brian D; Matera, A Gregory; Duronio, Robert J; McKay, Daniel JPLoS genetics.2019 01;30699116
Genetic risk variants for brain disorders are enriched in cortical H3K27ac domains.Hannon, Eilis; Marzi, Sarah J; Schalkwyk, Leonard S; Mill, JonathanMolecular brain.2019 01 28;30691483
Bulk tissue cell type deconvolution with multi-subject single-cell expression reference.Wang, Xuran; Park, Jihwan; Susztak, Katalin; Zhang, Nancy R; Li, MingyaoNature communications.2019 01 22;30670690
Xist RNA antagonizes the SWI/SNF chromatin remodeler BRG1 on the inactive X chromosome.Jégu, Teddy; Blum, Roy; Cochrane, Jesse C; Yang, Lin; Wang, Chen-Yu; Gilles, Maud-Emmanuelle; Colognori, David; Szanto, Attila; Marr, Sharon K; Kingston, Robert E; Lee, Jeannie TNature structural & molecular biology.2019 Feb;30664740
DNA methylation variability in Alzheimer's disease.Huo, Zhiguang; Zhu, Yun; Yu, Lei; Yang, Jingyun; De Jager, Philip; Bennett, David A; Zhao, JinyingNeurobiology of aging2019 Apr30660039
Activating PTEN Tumor Suppressor Expression with the CRISPR/dCas9 System.Moses, Colette; Nugent, Fiona; Waryah, Charlene Babra; Garcia-Bloj, Benjamin; Harvey, Alan R; Blancafort, PilarMolecular therapy. Nucleic acids.2019 Mar 01;30654190
Allele-specific RNA imaging shows that allelic imbalances can arise in tissues through transcriptional bursting.Symmons, Orsolya; Chang, Marcello; Mellis, Ian A; Kalish, Jennifer M; Park, Jihwan; Suszták, Katalin; Bartolomei, Marisa S; Raj, ArjunPLoS genetics.2019 01;30625149
Associations of Fenofibrate Therapy With Incidence and Progression of CKD in Patients With Type 2 Diabetes.Frazier, Rebecca; Mehta, Rupal; Cai, Xuan; Lee, Jungwha; Napoli, Sara; Craven, Timothy; Tuazon, Jennifer; Safdi, Adam; Scialla, Julia; Susztak, Katalin; Isakova, TamaraKidney international reports.2019 Jan;30596172
Trans-ethnic association study of blood pressure determinants in over 750,000 individuals.Giri, Ayush; Hellwege, Jacklyn N; Keaton, Jacob M; Park, Jihwan; Qiu, Chengxiang; Warren, Helen R; Torstenson, Eric S; Kovesdy, Csaba P; Sun, Yan V; Wilson, Otis D; Robinson-Cohen, Cassianne; Roumie, Christianne L; Chung, Cecilia P; Birdwell, Kelly A; Damrauer, Scott M; DuVall, Scott L; Klarin, Derek; Cho, Kelly; Wang, Yu; Evangelou, Evangelos; Cabrera, Claudia P; Wain, Louise V; Shrestha, Rojesh; Mautz, Brian S; Akwo, Elvis A; Sargurupremraj, Muralidharan; Debette, Stéphanie; Boehnke, Michael; Scott, Laura J; Luan, Jian'an; Zhao, Jing-Hua; Willems, Sara M; Thériault, Sébastien; Shah, Nabi; Oldmeadow, Christopher; Almgren, Peter; Li-Gao, Ruifang; Verweij, Niek; Boutin, Thibaud S; Mangino, Massimo; Ntalla, Ioanna; Feofanova, Elena; Surendran, Praveen; Cook, James P; Karthikeyan, Savita; Lahrouchi, Najim; Liu, Chunyu; Sepúlveda, Nuno; Richardson, Tom G; Kraja, Aldi; Amouyel, Philippe; Farrall, Martin; Poulter, Neil R; Understanding Society Scientific Group; International Consortium for Blood Pressure; Blood Pressure-International Consortium of Exome Chip Studies; Laakso, Markku; Zeggini, Eleftheria; Sever, Peter; Scott, Robert A; Langenberg, Claudia; Wareham, Nicholas J; Conen, David; Palmer, Colin Neil Alexander; Attia, John; Chasman, Daniel I; Ridker, Paul M; Melander, Olle; Mook-Kanamori, Dennis Owen; Harst, Pim van der; Cucca, Francesco; Schlessinger, David; Hayward, Caroline; Spector, Tim D; Jarvelin, Marjo-Riitta; Hennig, Branwen J; Timpson, Nicholas J; Wei, Wei-Qi; Smith, Joshua C; Xu, Yaomin; Matheny, Michael E; Siew, Edward E; Lindgren, Cecilia; Herzig, Karl-Heinz; Dedoussis, George; Denny, Joshua C; Psaty, Bruce M; Howson, Joanna M M; Munroe, Patricia B; Newton-Cheh, Christopher; Caulfield, Mark J; Elliott, Paul; Gaziano, J Michael; Concato, John; Wilson, Peter W F; Tsao, Philip S; Velez Edwards, Digna R; Susztak, Katalin; Million Veteran Program; O'Donnell, Christopher J; Hung, Adriana M; Edwards, Todd LNature genetics.2019 01;30578418
Epigenome-wide study uncovers large-scale changes in histone acetylation driven by tau pathology in aging and Alzheimer's human brains.Klein, Hans-Ulrich; McCabe, Cristin; Gjoneska, Elizabeta; Sullivan, Sarah E; Kaskow, Belinda J; Tang, Anna; Smith, Robert V; Xu, Jishu; Pfenning, Andreas R; Bernstein, Bradley E; Meissner, Alexander; Schneider, Julie A; Mostafavi, Sara; Tsai, Li-Huei; Young-Pearse, Tracy L; Bennett, David A; De Jager, Philip LNature neuroscience2019 Jan30559478
The DGCR5 long noncoding RNA may regulate expression of several schizophrenia-related genes.Meng, Qingtuan; Wang, Kangli; Brunetti, Tonya; Xia, Yan; Jiao, Chuan; Dai, Rujia; Fitzgerald, Dominic; Thomas, Amber; Jay, Lindsey; Eckart, Heather; Grennan, Kay; Imamura-Kawasawa, Yuka; Li, Mingfeng; Sestan, Nenad; White, Kevin P; Chen, Chao; Liu, ChunyuScience translational medicine.2018 12 19;30545965
The transcription factor POU3F2 regulates a gene coexpression network in brain tissue from patients with psychiatric disorders.Chen, Chao; Meng, Qingtuan; Xia, Yan; Ding, Chaodong; Wang, Le; Dai, Rujia; Cheng, Lijun; Gunaratne, Preethi; Gibbs, Richard A; Min, Shishi; Coarfa, Cristian; Reid, Jeffrey G; Zhang, Chunling; Jiao, Chuan; Jiang, Yi; Giase, Gina; Thomas, Amber; Fitzgerald, Dominic; Brunetti, Tonya; Shieh, Annie; Xia, Cuihua; Wang, Yongjun; Wang, Yunpeng; Badner, Judith A; Gershon, Elliot S; White, Kevin P; Liu, ChunyuScience translational medicine.2018 12 19;30545964
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 MBMC genomics.2018 Dec 07;30526554
Targets and genomic constraints of ectopic Dnmt3b expression.Zhang, Yingying; Charlton, Jocelyn; Karnik, Rahul; Beerman, Isabel; Smith, Zachary D; Gu, Hongcang; Boyle, Patrick; Mi, Xiaoli; Clement, Kendell; Pop, Ramona; Gnirke, Andreas; Rossi, Derrick J; Meissner, AlexandereLife.2018 11 23;30468428
Engineering Improved Photoswitches for the Control of Nucleocytoplasmic Distribution.Lerner, Andrew M; Yumerefendi, Hayretin; Goudy, Odessa J; Strahl, Brian D; Kuhlman, BrianACS synthetic biology.2018 Nov 29;30441907
Characterization of a Mouse Model of Börjeson-Forssman-Lehmann Syndrome.Cheng, Cheng; Deng, Pan-Yue; Ikeuchi, Yoshiho; Yuede, Carla; Li, Daofeng; Rensing, Nicholas; Huang, Ju; Baldridge, Dustin; Maloney, Susan E; Dougherty, Joseph D; Constantino, John; Jahani-Asl, Arezu; Wong, Michael; Wozniak, David F; Wang, Ting; Klyachko, Vitaly A; Bonni, AzadCell reports.2018 Nov 06;30403997
A non-randomized procedure for large-scale heterogeneous multiple discrete testing based on randomized tests.Dai, Xiaoyu; Lin, Nan; Li, Daofeng; Wang, TingBiometrics.2018 Nov 02;30387496
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, FarshidStem cells (Dayton, Ohio).2019 Jan;30378731
Enhancer RNA and NF?B-dependent P300 regulation of ADAMDEC1.Shi, Lihua; Li, Song; Maurer, Kelly; Zhang, Zhe; Petri, Michelle; Sullivan, Kathleen EMolecular immunology.2018 11;30352365
The Molecular and Neuropathological Consequences of Genetic Risk for Alzheimer's Dementia.Tasaki, Shinya; Gaiteri, Chris; Mostafavi, Sara; De Jager, Philip L; Bennett, David AFrontiers in neuroscience.2018;30349450
Fate mapping during regeneration: Cells that undergo compensatory proliferation in damaged Drosophila eye imaginal discs differentiate into multiple retinal accessory cell types.Meserve, Joy H; Duronio, Robert JDevelopmental biology.2018 12 15;30347187
Comparative genomic analysis of embryonic, lineage-converted and stem cell-derived motor neurons.Ichida, Justin K; Staats, Kim A; Davis-Dusenbery, Brandi N; Clement, Kendell; Galloway, Kate E; Babos, Kimberly N; Shi, Yingxiao; Son, Esther Y; Kiskinis, Evangelos; Atwater, Nicholas; Gu, Hongcang; Gnirke, Andreas; Meissner, Alexander; Eggan, KevinDevelopment (Cambridge, England).2018 11 21;30337375
Long-Term In Vitro Expansion of Epithelial Stem Cells Enabled by Pharmacological Inhibition of PAK1-ROCK-Myosin II and TGF-? Signaling.Zhang, Chengkang; Lee, Hyung Joo; Shrivastava, Anura; Wang, Ruipeng; McQuiston, Travis J; Challberg, Sharon S; Pollok, Brian A; Wang, TingCell reports.2018 Oct 16;30332641
CRISPhieRmix: a hierarchical mixture model for CRISPR pooled screens.Daley, Timothy P; Lin, Zhixiang; Lin, Xueqiu; Liu, Yanxia; Wong, Wing Hung; Qi, Lei SGenome biology.2018 10 08;30296940
The 3D Genome Browser: a web-based browser for visualizing 3D genome organization and long-range chromatin interactions.Wang, Yanli; Song, Fan; Zhang, Bo; Zhang, Lijun; Xu, Jie; Kuang, Da; Li, Daofeng; Choudhary, Mayank N K; Li, Yun; Hu, Ming; Hardison, Ross; Wang, Ting; Yue, FengGenome biology.2018 10 04;30286773
Colonic epithelial miR-31 associates with the development of Crohn's phenotypes.Keith, Benjamin P; Barrow, Jasmine B; Toyonaga, Takahiko; Kazgan, Nevzat; O'Connor, Michelle Hoffner; Shah, Neil D; Schaner, Matthew S; Wolber, Elisabeth A; Trad, Omar K; Gipson, Greg R; Pitman, Wendy A; Kanke, Matthew; Saxena, Shruti J; Chaumont, Nicole; Sadiq, Timothy S; Koruda, Mark J; Cotney, Paul A; Allbritton, Nancy; Trembath, Dimitri G; Sylvester, Francisco; Furey, Terrence S; Sethupathy, Praveen; Sheikh, Shehzad ZJCI insight.2018 10 04;30282822
Renal compartment-specific genetic variation analyses identify new pathways in chronic kidney disease.Qiu, Chengxiang; Huang, Shizheng; Park, Jihwan; Park, YoSon; Ko, Yi-An; Seasock, Matthew J; Bryer, Joshua S; Xu, Xiang-Xi; Song, Wen-Chao; Palmer, Matthew; Hill, Jon; Guarnieri, Paolo; Hawkins, Julie; Boustany-Kari, Carine M; Pullen, Steven S; Brown, Christopher D; Susztak, KatalinNature medicine.2018 11;30275566
Mathematical modeling identifies potential gene structure determinants of co-transcriptional control of alternative pre-mRNA splicing.Davis-Turak, Jeremy; Johnson, Tracy L; Hoffmann, AlexanderNucleic acids research.2018 11 16;30272246
Deconstructing and targeting the genomic architecture of human neurodegeneration.De Jager, Philip L; Yang, Hyun-Sik; Bennett, David ANature neuroscience2018 Oct30258235
Epigenetics and Epigenomics: Implications for Diabetes and Obesity.Rosen, Evan D; Kaestner, Klaus H; Natarajan, Rama; Patti, Mary-Elizabeth; Sallari, Richard; Sander, Maike; Susztak, KatalinDiabetes.2018 10;30237160
Jagged1/Notch2 controls kidney fibrosis via Tfam-mediated metabolic reprogramming.Huang, Shizheng; Park, Jihwan; Qiu, Chengxiang; Chung, Ki Wung; Li, Szu-Yuan; Sirin, Yasemin; Han, Seung Hyeok; Taylor, Verdon; Zimber-Strobl, Ursula; Susztak, KatalinPLoS biology.2018 09;30226866
Proteomics and melanoma: a current perspective.Shields, Bradley D; Tackett, Alan J; Shalin, Sara CGlobal dermatology.2016 Aug;30214824
Genome-wide DNA methylation profiling of primary colorectal laterally spreading tumors identifies disease-specific epimutations on common pathways.Zhu, Liangliang; Yan, Feihu; Wang, Zhen; Dong, Haiyan; Bian, Chengling; Wang, Ting; Yu, Enda; Li, JingInternational journal of cancer.2018 Nov 15;30183087
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, EClinical immunology (Orlando, Fla.).2018 12;30149120
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, KenPLoS biology.2018 Aug;30148842
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 AFrontiers in genetics.2018;30140277
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, AleksandarScience (New York, N.Y.).2018 Aug 23;30139913
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 EGenome research.2018 09;30097539
ChromTime: modeling spatio-temporal dynamics of chromatin marks.Fiziev, Petko; Ernst, JasonGenome biology.2018 08 10;30097049
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 AScientific data.2018 08 07;30084846
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, PilarOncogene.2019 01;30076412
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 GregoryMethods in molecular biology (Clifton, N.J.).2018;30073535
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 BPloS one.2018;30052629
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 GJournal of medicinal chemistry.2018 08 23;30052441
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 TProceedings of the National Academy of Sciences of the United States of America.2018 08 07;30038001
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 ACell.2018 Aug 09;30033366
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 ECell systems.2018 08 22;30031775
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, ShoheiNature chemical biology.2018 Sep;30013062
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, HongkuiCell.2018 07 12;30007418
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, ZheCell death & disease.2018 07 13;30006518
Alternative empirical Bayes models for adjusting for batch effects in genomic studies.Zhang, Yuqing; Jenkins, David F; Manimaran, Solaiappan; Johnson, W EvanBMC bioinformatics.2018 07 13;30001694
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, ChristineMolecular autism.2018;29988321
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, ChaoBioinformatics (Oxford, England).2019 01 01;29985970
A CRISPR-dCas Toolbox for Genetic Engineering and Synthetic Biology.Xu, Xiaoshu; Qi, Lei SJournal of molecular biology.2019 01 04;29958882
A decade in psychiatric GWAS research.Horwitz, Tanya; Lam, Katie; Chen, Yu; Xia, Yan; Liu, ChunyuMolecular psychiatry.2019 03;29942042
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 ABrain imaging and behavior.2019 Aug;29934819
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 JACS chemical neuroscience.2018 09 19;29932631
Microscopes and Mass Spectrometers.Shields, Bradley; Shalin, Sara C; Tackett, Alan JJournal of proteomics & bioinformatics.2016;29910559
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, RyanGenome research.2018 08;29907613
APOL1: The Balance Imposed by Infection, Selection, and Kidney Disease.Beckerman, Pazit; Susztak, KatalinTrends in molecular medicine.2018 08;29886044
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 MCell reports.2018 06 05;29874575
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 AJournal of Alzheimer's disease : JAD.2018;29865057
Atomistic molecular dynamics simulations of bioactive engrailed 1 interference peptides (EN1-iPeps).Gandhi, Neha S; Blancafort, Pilar; Mancera, Ricardo LOncotarget.2018 Apr 27;29854286
Editing the Epigenome: Reshaping the Genomic Landscape.Holtzman, Liad; Gersbach, Charles AAnnual review of genomics and human genetics.2018 08 31;29852072
Synthetic transcription factors for cell fate reprogramming.Black, Joshua B; Gersbach, Charles ACurrent opinion in genetics & development.2018 10;29803990
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 NJournal of reproductive immunology.2018 Aug;29800761
Next-generation antibodies for post-translational modifications.Hattori, Takamitsu; Koide, ShoheiCurrent opinion in structural biology.2018 08;29753204
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, KonradStem cell reports.2018 05 08;29742392
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, LimingProceedings of the National Academy of Sciences of the United States of America.2018 05 22;29735694
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 YCell.2018 05 31;29731168
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, KatalinKidney international.2018 06;29709239
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 AEnvironmental health perspectives.2018 04 27;29706059
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 ANature communications.2018 Apr 26;29700298
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, SteveAging.2018 04 18;29676998
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 JCell.2018 04 19;29656892
PREDICTD PaRallel Epigenomics Data Imputation with Cloud-based Tensor Decomposition.Durham, Timothy J; Libbrecht, Maxwell W; Howbert, J Jeffry; Bilmes, Jeff; Noble, William StaffordNature communications2018 04 1129643364
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, KatalinScience (New York, N.Y.).2018 05 18;29622724
Introduction: Systems Biology of Kidney Disease.Sharma, Kumar; Susztak, Katalin; Pennathur, SubramaniamSeminars in nephrology.2018 03;29602402
The Role of Peroxisome Proliferator-Activated Receptor ? Coactivator 1? (PGC-1?) in Kidney Disease.Li, Szu-Yuan; Susztak, KatalinSeminars in nephrology.2018 03;29602395
Pulling the genome in opposite directions to dissect gene networks.Gersbach, Charles A; Barrangou, RodolpheGenome biology.2018 Mar 26;29580291
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, EvangelosCell stem cell.2018 04 05;29551301
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, KatieAlzheimer's & dementia : the journal of the Alzheimer's Association.2018 Dec;29550519
Global delay in nascent strand DNA methylation.Charlton, Jocelyn; Downing, Timothy L; Smith, Zachary D; Gu, Hongcang; Clement, Kendell; Pop, Ramona; Akopian, Veronika; Klages, Sven; Santos, David P; Tsankov, Alexander M; Timmermann, Bernd; Ziller, Michael J; Kiskinis, Evangelos; Gnirke, Andreas; Meissner, AlexanderNature structural & molecular biology.2018 Mar 12;29531288
Screening Regulatory Element Function with CRISPR/Cas9-based Epigenome Editing.Klann, Tyler S; Crawford, Gregory E; Reddy, Timothy E; Gersbach, Charles AMethods in molecular biology (Clifton, N.J.).2018;29524151
Zinc Fingers, TALEs, and CRISPR Systems: A Comparison of Tools for Epigenome Editing.Waryah, Charlene Babra; Moses, Colette; Arooj, Mahira; Blancafort, PilarMethods in molecular biology (Clifton, N.J.).2018;29524128
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 LNature biotechnology.2018 Mar 06;29509741
CRISPR-based methods for high-throughput annotation of regulatory DNA.Klann, Tyler S; Black, Joshua B; Gersbach, Charles ACurrent opinion in biotechnology.2018 Feb 28;29500989
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 PCurrent biology : CB.2018 03 05;29478853
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, ChunyuEpigenomics.2018 05;29469594
Transcription start site profiling uncovers divergent transcription and enhancer-associated RNAs in Drosophila melanogaster.Meers, Michael P; Adelman, Karen; Duronio, Robert J; Strahl, Brian D; McKay, Daniel J; Matera, A GregoryBMC genomics.2018 02 21;29466941
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, BrianChembiochem : 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 HScience (New York, N.Y.).2018 02 09;29439242
Zika Virus Alters DNA Methylation of Neural Genes in an Organoid Model of the Developing Human Brain.Janssens, Sylvie; Schotsaert, Michael; Karnik, Rahul; Balasubramaniam, Vinod; Dejosez, Marion; Meissner, Alexander; García-Sastre, Adolfo; Zwaka, Thomas PmSystems.2018 Jan-Feb;29435496
Hallmarks of cancer: The CRISPR generation.Moses, Colette; Garcia-Bloj, Benjamin; Harvey, Alan R; Blancafort, PilarEuropean journal of cancer (Oxford, England : 1990).2018 04;29433054
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, AlexanderNature communications.2018 02 09;29426832
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 GMolecular imaging and biology.2018 08;29423902
Role of epigenetics in the development of childhood asthma.Davidson, Elizabeth J; Yang, Ivana VCurrent opinion in allergy and clinical immunology.2018 04;29389731
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 APloS one.2018;29329322
A mixed modality approach towards Xi reactivation for Rett syndrome and other X-linked disorders.Carrette, Lieselot L G; Wang, Chen-Yu; Wei, Chunyao; Press, William; Ma, Weiyuan; Kelleher 3rd, Raymond J; Lee, Jeannie TProceedings of the National Academy of Sciences of the United States of America.2018 Jan 23;29282321
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 SNature communications.2017 12 20;29263378
CRISPR Approaches to Small Molecule Target Identification.Jost, Marco; Weissman, Jonathan SACS chemical biology.2018 Feb 16;29261286
Control of microtubule dynamics using an optogenetic microtubule plus end-F-actin cross-linker.Adikes, Rebecca C; Hallett, Ryan A; Saway, Brian F; Kuhlman, Brian; Slep, Kevin CThe Journal of cell biology.2018 Feb 05;29259096
Sophisticated lessons from simple organisms: appreciating the value of curiosity-driven research.Duronio, Robert J; O'Farrell, Patrick H; Sluder, Greenfield; Su, Tin TinDisease models & mechanisms.2017 12 19;29259023
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, ZheCancer medicine.2018 01;29239144
Comprehensive Whole DNA Methylome Analysis by Integrating MeDIP-seq and MRE-seq.Xing, Xiaoyun; Zhang, Bo; Li, Daofeng; Wang, TingMethods in molecular biology (Clifton, N.J.).2018;29224147
Transposable Element Mediated Innovation in Gene Regulatory Landscapes of Cells: Re-Visiting the ''Gene-Battery'' Model.Sundaram, Vasavi; Wang, TingBioEssays : news and reviews in molecular, cellular and developmental biology.2018 Jan;29206283
Landscape of the regulatory elements for lysine 2-hydroxyisobutyrylation pathway.Huang, He; Luo, Zhouqing; Qi, Shankang; Huang, Jing; Xu, Peng; Wang, Xiuxuan; Gao, Li; Li, Fangyi; Wang, Jian; Zhao, Wenhui; Gu, Wei; Chen, Zhucheng; Dai, Lunzhi; Dai, Junbiao; Zhao, YingmingCell research.2018 Jan;29192674
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, YongmeiEpigenetics.2017;29166816
Corrigendum: High-throughput discovery of novel developmental phenotypes.Dickinson, Mary E; Flenniken, Ann M; Ji, Xiao; Teboul, Lydia; Wong, Michael D; White, Jacqueline K; Meehan, Terrence F; Weninger, Wolfgang J; Westerberg, Henrik; Adissu, Hibret; Baker, Candice N; Bower, Lynette; Brown, James M; Caddle, L Brianna; Chiani, Francesco; Clary, Dave; Cleak, James; Daly, Mark J; Denegre, James M; Doe, Brendan; Dolan, Mary E; Edie Helmut Fuchs, Sarah M; Gailus-Durner, Valerie; Galli, Antonella; Gambadoro, Alessia; Gallegos, Juan; Guo, Shiying; Horner, Neil R; Hsu, Chih-Wei; Johnson, Sara J; Kalaga, Sowmya; Keith, Lance C; Lanoue, Louise; Lawson, Thomas N; Lek, Monkol; Mark, Manuel; Marschall, Susan; Mason, Jeremy; McElwee, Melissa L; Nutter, Susan Newbigging Lauryl M J; Peterson, Kevin A; Ramirez-Solis, Ramiro; Rowland, Douglas J; Ryder, Edward; Samocha, Kaitlin E; Seavitt, John R; Selloum, Mohammed; Szoke-Kovacs, Zsombor; Tamura, Masaru; Trainor, Amanda G; Tudose, Ilinca; Wakana, Shigeharu; Warren, Jonathan; Wendling, Olivia; West, David B; Wong, Leeyean; Yoshiki, Atsushi; International Mouse Phenotyping Consortium; Wurst, Wolfgang; MacArthur, Daniel G; Tocchini-Valentini, Glauco P; Gao, Xiang; Flicek, Paul; Bradley, Allan; Skarnes, William C; Justice, Monica J; Parkinson, Helen E; Moore, Mark; Wells, Sara; Braun, Robert E; Svenson, Karen L; de Angelis, Martin Hrabe; Herault, Yann; Mohun, Tim; Mallon, Ann-Marie; Henkelman, R Mark; Brown, Steve D M; Adams, David J; Lloyd, K C Kent; McKerlie, Colin; Beaudet, Arthur L; Murray, Maja Bu?an Stephen ANature.2017 Nov 16;29144450
Functional Redundancy of Variant and Canonical Histone H3 Lysine 9 Modification in Drosophila.Penke, Taylor J R; McKay, Daniel J; Strahl, Brian D; Matera, A Gregory; Duronio, Robert JGenetics.2018 Jan;29133298
Chromatin-state discovery and genome annotation with ChromHMM.Ernst, Jason; Kellis, ManolisNature protocols.2017 Dec;29120462
Genome-wide association study identifies a novel locus for cannabis dependence.Agrawal, A; Chou, Y-L; Carey, C E; Baranger, D A A; Zhang, B; Sherva, R; Wetherill, L; Kapoor, M; Wang, J-C; Bertelsen, S; Anokhin, A P; Hesselbrock, V; Kramer, J; Lynskey, M T; Meyers, J L; Nurnberger, J I; Rice, J P; Tischfield, J; Bierut, L J; Degenhardt, L; Farrer, L A; Gelernter, J; Hariri, A R; Heath, A C; Kranzler, H R; Madden, P A F; Martin, N G; Montgomery, G W; Porjesz, B; Wang, T; Whitfield, J B; Edenberg, H J; Foroud, T; Goate, A M; Bogdan, R; Nelson, E CMolecular psychiatry.2017 Nov 07;29112194
Epigenome-wide association studies identify DNA methylation associated with kidney function.Chu, Audrey Y; Tin, Adrienne; Schlosser, Pascal; Ko, Yi-An; Qiu, Chengxiang; Yao, Chen; Joehanes, Roby; Grams, Morgan E; Liang, Liming; Gluck, Caroline A; Liu, Chunyu; Coresh, Josef; Hwang, Shih-Jen; Levy, Daniel; Boerwinkle, Eric; Pankow, James S; Yang, Qiong; Fornage, Myriam; Fox, Caroline S; Susztak, Katalin; Köttgen, AnnaNature communications.2017 Nov 03;29097680
Combinatorial genetics in liver repopulation and carcinogenesis with a in vivo CRISPR activation platform.Wangensteen, Kirk J; Wang, Yue J; Dou, Zhixun; Wang, Amber W; Mosleh-Shirazi, Elham; Horlbeck, Max A; Gilbert, Luke A; Weissman, Jonathan S; Berger, Shelley L; Kaestner, Klaus HHepatology (Baltimore, Md.).2018 08;29091290
Association Between Brain Gene Expression, DNA Methylation, and Alteration of Ex Vivo Magnetic Resonance Imaging Transverse Relaxation in Late-Life Cognitive Decline.Yu, Lei; Dawe, Robert J; Boyle, Patricia A; Gaiteri, Chris; Yang, Jingyun; Buchman, Aron S; Schneider, Julie A; Arfanakis, Konstantinos; De Jager, Philip L; Bennett, David AJAMA neurology.2017 Dec 01;29084334
Inducible and multiplex gene regulation using CRISPR-Cpf1-based transcription factors.Tak, Y Esther; Kleinstiver, Benjamin P; Nuñez, James K; Hsu, Jonathan Y; Horng, Joy E; Gong, Jingyi; Weissman, Jonathan S; Joung, J KeithNature methods.2017 Dec;29083402
Association of Bone Metabolic Markers With Diabetic Retinopathy and Diabetic Macular Edema in Elderly Chinese Individuals With Type 2 Diabetes Mellitus.Zhang, Xiao; Yang, Jingyun; Zhong, Yong; Xu, Lingling; Wang, Ou; Huang, Ping; Li, Chunying; Qu, Bin; Wang, Jing; Zheng, Caixia; Niu, Meng; Yu, WeihongThe American journal of the medical sciences.2017 Oct;29078839
Age and the association of dementia-related pathology with trajectories of cognitive decline.Jansen, Willemijn J; Wilson, Robert S; Visser, Pieter Jelle; Nag, Sukriti; Schneider, Julie A; James, Bryan D; Leurgans, Sue E; Capuano, Ana W; Bennett, David A; Boyle, Patricia ANeurobiology of aging.2018 01;29078129
Cross-tissue integration of genetic and epigenetic data offers insight into autism spectrum disorder.Andrews, Shan V; Ellis, Shannon E; Bakulski, Kelly M; Sheppard, Brooke; Croen, Lisa A; Hertz-Picciotto, Irva; Newschaffer, Craig J; Feinberg, Andrew P; Arking, Dan E; Ladd-Acosta, Christine; Fallin, M DanieleNature communications.2017 10 24;29066808
Cohort Profile: Pregnancy And Childhood Epigenetics (PACE) Consortium.Felix, Janine F; Joubert, Bonnie R; Baccarelli, Andrea A; Sharp, Gemma C; Almqvist, Catarina; Annesi-Maesano, Isabella; Arshad, Hasan; Baïz, Nour; Bakermans-Kranenburg, Marian J; Bakulski, Kelly M; Binder, Elisabeth B; Bouchard, Luigi; Breton, Carrie V; Brunekreef, Bert; Brunst, Kelly J; Burchard, Esteban G; Bustamante, Mariona; Chatzi, Leda; Cheng Munthe-Kaas, Monica; Corpeleijn, Eva; Czamara, Darina; Dabelea, Dana; Davey Smith, George; De Boever, Patrick; Duijts, Liesbeth; Dwyer, Terence; Eng, Celeste; Eskenazi, Brenda; Everson, Todd M; Falahi, Fahimeh; Fallin, M Daniele; Farchi, Sara; Fernandez, Mariana F; Gao, Lu; Gaunt, Tom R; Ghantous, Akram; Gillman, Matthew W; Gonseth, Semira; Grote, Veit; Gruzieva, Olena; Håberg, Siri E; Herceg, Zdenko; Hivert, Marie-France; Holland, Nina; Holloway, John W; Hoyo, Cathrine; Hu, Donglei; Huang, Rae-Chi; Huen, Karen; Järvelin, Marjo-Riitta; Jima, Dereje D; Just, Allan C; Karagas, Margaret R; Karlsson, Robert; Karmaus, Wilfried; Kechris, Katerina J; Kere, Juha; Kogevinas, Manolis; Koletzko, Berthold; Koppelman, Gerard H; Küpers, Leanne K; Ladd-Acosta, Christine; Lahti, Jari; Lambrechts, Nathalie; Langie, Sabine A S; Lie, Rolv T; Liu, Andrew H; Magnus, Maria C; Magnus, Per; Maguire, Rachel L; Marsit, Carmen J; McArdle, Wendy; Melén, Erik; Melton, Phillip; Murphy, Susan K; Nawrot, Tim S; Nisticò, Lorenza; Nohr, Ellen A; Nordlund, Björn; Nystad, Wenche; Oh, Sam S; Oken, Emily; Page, Christian M; Perron, Patrice; Pershagen, Göran; Pizzi, Costanza; Plusquin, Michelle; Raikkonen, Katri; Reese, Sarah E; Reischl, Eva; Richiardi, Lorenzo; Ring, Susan; Roy, Ritu P; Rzehak, Peter; Schoeters, Greet; Schwartz, David A; Sebert, Sylvain; Snieder, Harold; Sørensen, Thorkild I A; Starling, Anne P; Sunyer, Jordi; Taylor, Jack A; Tiemeier, Henning; Ullemar, Vilhelmina; Vafeiadi, Marina; Van Ijzendoorn, Marinus H; Vonk, Judith M; Vriens, Annette; Vrijheid, Martine; Wang, Pei; Wiemels, Joseph L; Wilcox, Allen J; Wright, Rosalind J; Xu, Cheng-Jian; Xu, Zongli; Yang, Ivana V; Yousefi, Paul; Zhang, Hongmei; Zhang, Weiming; Zhao, Shanshan; Agha, Golareh; Relton, Caroline L; Jaddoe, Vincent W V; London, Stephanie JInternational journal of epidemiology.2018 02 01;29025028
Combined CRISPRi/a-Based Chemical Genetic Screens Reveal that Rigosertib Is a Microtubule-Destabilizing Agent.Jost, Marco; Chen, Yuwen; Gilbert, Luke A; Horlbeck, Max A; Krenning, Lenno; Menchon, Grégory; Rai, Ankit; Cho, Min Y; Stern, Jacob J; Prota, Andrea E; Kampmann, Martin; Akhmanova, Anna; Steinmetz, Michel O; Tanenbaum, Marvin E; Weissman, Jonathan SMolecular cell.2017 Oct 05;28985505
The REMOTE-control system: a system for reversible and tunable control of endogenous gene expression in mice.Lee, Kwang-Ho; Oghamian, Shirley; Park, Jin-A; Kang, Liang; Laird, Peter WNucleic acids research.2017 Dec 01;28981717
Human Kidney Tubule-Specific Gene Expression Based Dissection of Chronic Kidney Disease Traits.Beckerman, Pazit; Qiu, Chengxiang; Park, Jihwan; Ledo, Nora; Ko, Yi-An; Park, Ae-Seo Deok; Han, Sang-Youb; Choi, Peter; Palmer, Matthew; Susztak, KatalinEBioMedicine.2017 Oct;28970079
Epigenetic restriction of extraembryonic lineages mirrors the somatic transition to cancer.Smith, Zachary D; Shi, Jiantao; Gu, Hongcang; Donaghey, Julie; Clement, Kendell; Cacchiarelli, Davide; Gnirke, Andreas; Michor, Franziska; Meissner, AlexanderNature.2017 09 28;28959968
A Single-Chain Photoswitchable CRISPR-Cas9 Architecture for Light-Inducible Gene Editing and Transcription.Zhou, Xin X; Zou, Xinzhi; Chung, Hokyung K; Gao, Yuchen; Liu, Yanxia; Qi, Lei S; Lin, Michael ZACS chemical biology.2018 Feb 16;28938067
Cooperative interactions enable singular olfactory receptor expression in mouse olfactory neurons.Monahan, Kevin; Schieren, Ira; Cheung, Jonah; Mumbey-Wafula, Alice; Monuki, Edwin S; Lomvardas, StavroseLife.2017 Sep 21;28933695
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 KExperimental biology and medicine (Maywood, N.J.).2017 Dec;28927291
Tissue-specific DNA methylation is conserved across human, mouse, and rat, and driven by primary sequence conservation.Zhou, Jia; Sears, Renee L; Xing, Xiaoyun; Zhang, Bo; Li, Daofeng; Rockweiler, Nicole B; Jang, Hyo Sik; Choudhary, Mayank N K; Lee, Hyung Joo; Lowdon, Rebecca F; Arand, Jason; Tabers, Brianne; Gu, C Charles; Cicero, Theodore J; Wang, TingBMC genomics.2017 Sep 12;28899353
Genome Engineering for Personalized Arthritis Therapeutics.Adkar, Shaunak S; Brunger, Jonathan M; Willard, Vincent P; Wu, Chia-Lung; Gersbach, Charles A; Guilak, FarshidTrends in molecular medicine.2017 Oct;28887050
MicroRNAs Induce a Permissive Chromatin Environment that Enables Neuronal Subtype-Specific Reprogramming of Adult Human Fibroblasts.Abernathy, Daniel G; Kim, Woo Kyung; McCoy, Matthew J; Lake, Allison M; Ouwenga, Rebecca; Lee, Seong Won; Xing, Xiaoyun; Li, Daofeng; Lee, Hyung Joo; Heuckeroth, Robert O; Dougherty, Joseph D; Wang, Ting; Yoo, Andrew SCell stem cell.2017 Sep 07;28886366
Denoising genome-wide histone ChIP-seq with convolutional neural networks.Koh, Pang Wei; Pierson, Emma; Kundaje, AnshulBioinformatics (Oxford, England).2017 Jul 15;28881977
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, HanchuanScientific reports.2017 08 24;28839271
Electrophoretic stretching and imaging of single native chromatin fibers in nanoslits.Yeh, Jia-Wei; Szeto, KylanBiomicrofluidics.2017 Jul;28794818
An Engineered Optogenetic Switch for Spatiotemporal Control of Gene Expression, Cell Differentiation, and Tissue Morphogenesis.Polstein, Lauren R; Juhas, Mark; Hanna, Gabi; Bursac, Nenad; Gersbach, Charles AACS synthetic biology.2017 Nov 17;28793186
Neuronal-expressed microRNA-targeted pseudogenes compete with coding genes in the human brain.Barbash, S; Simchovitz, A; Buchman, A S; Bennett, D A; Shifman, S; Soreq, HTranslational psychiatry.2017 Aug 08;28786976
Emerging Infections and Pertinent Infections Related to Travel for Patients with Primary Immunodeficiencies.Sullivan, Kathleen E; Bassiri, Hamid; Bousfiha, Ahmed A; Costa-Carvalho, Beatriz T; Freeman, Alexandra F; Hagin, David; Lau, Yu L; Lionakis, Michail S; Moreira, Ileana; Pinto, Jorge A; de Moraes-Pinto, M Isabel; Rawat, Amit; Reda, Shereen M; Reyes, Saul Oswaldo Lugo; Seppänen, Mikko; Tang, Mimi L KJournal of clinical immunology.2017 Oct;28786026
Transcriptome-Wide Analysis Identifies Novel Associations With Blood Pressure.Zeller, Tanja; Schurmann, Claudia; Schramm, Katharina; Müller, Christian; Kwon, Soonil; Wild, Philipp S; Teumer, Alexander; Herrington, David; Schillert, Arne; Iacoviello, Licia; Kratzer, Adelheid; Jagodzinski, Annika; Karakas, Mahir; Ding, Jingzhong; Neumann, Johannes T; Kuulasmaa, Kari; Gieger, Christian; Kacprowski, Tim; Schnabel, Renate B; Roden, Michael; Wahl, Simone; Rotter, Jerome I; Ojeda, Francisco; Carstensen-Kirberg, Maren; Tregouet, David-Alexandre; Dörr, Marcus; Meitinger, Thomas; Lackner, Karl J; Wolf, Petra; Felix, Stephan B; Landmesser, Ulf; Costanzo, Simona; Ziegler, Andreas; Liu, Yongmei; Völker, Uwe; Palmas, Walter; Prokisch, Holger; Guo, Xiuqing; Herder, Christian; Blankenberg, Stefan; Homuth, GeorgHypertension (Dallas, Tex. : 1979).2017 10;28784648
The Three-Dimensional Organization of Mammalian Genomes.Yu, Miao; Ren, BingAnnual review of cell and developmental biology.2017 Oct 06;28783961
Correcting nucleotide-specific biases in high-throughput sequencing data.Wang, Jeremy R; Quach, Bryan; Furey, Terrence SBMC bioinformatics.2017 Aug 01;28764645
Cells lay their own tracks - optogenetic Cdc42 activation stimulates fibronectin deposition supporting directed migration.Zimmerman, Seth P; Asokan, Sreeja B; Kuhlman, Brian; Bear, James EJournal of cell science.2017 Sep 15;28754687
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, KatalinJournal of the American Society of Nephrology : JASN.2017 Nov;28751525
A High Fat Diet During Pregnancy and Lactation Induces Cardiac and Renal Abnormalities in GLUT4 +/- Male Mice.Kruse, Michael; Fiallo, Ariana; Tao, Jianling; Susztak, Katalin; Amann, Kerstin; Katz, Ellen B; Charron, Maureen JKidney & blood pressure research.2017;28750406
Whole exome sequencing identified genetic variations in Chinese hemangioblastoma patients.Ma, Dexuan; Yang, Jingyun; Wang, Ying; Huang, Xiang; Du, Guhong; Zhou, LiangfuAmerican journal of medical genetics. Part A.2017 Oct;28742274
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 AriPloS one.2017;28727768
Increasing the level of peroxisome proliferator-activated receptor ? coactivator-1? in podocytes results in collapsing glomerulopathy.Li, Szu-Yuan; Park, Jihwan; Qiu, Chengxiang; Han, Seung Hyeok; Palmer, Matthew B; Arany, Zoltan; Susztak, KatalinJCI insight.2017 Jul 20;28724797
ATR-101 inhibits cholesterol efflux and cortisol secretion by ATP-binding cassette transporters, causing cytotoxic cholesterol accumulation in adrenocortical carcinoma cells.Burns, Veronica Elizabeth; Kerppola, Tom KlausBritish journal of pharmacology.2017 Oct;28710789
High-Throughput Colorimetric Assay for Identifying PARP-1 Inhibitors Using a Large Small-Molecule Collection.Kotova, Elena; Tulin, Alexei VMethods in molecular biology (Clifton, N.J.).2017;28695517
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 LEpigenetics.2017 08;28678593
The environment, epigenome, and asthma.Yang, Ivana V; Lozupone, Catherine A; Schwartz, David AThe Journal of allergy and clinical immunology.2017 Jul;28673400
Dissecting the role of non-coding RNAs in the accumulation of amyloid and tau neuropathologies in Alzheimer's disease.Patrick, Ellis; Rajagopal, Sathyapriya; Wong, Hon-Kit Andus; McCabe, Cristin; Xu, Jishu; Tang, Anna; Imboywa, Selina H; Schneider, Julie A; Pochet, Nathalie; Krichevsky, Anna M; Chibnik, Lori B; Bennett, David A; De Jager, Philip LMolecular neurodegeneration.2017 07 01;28668092
Genetic and epigenetic control of gene expression by CRISPR-Cas systems.Lo, Albert; Qi, LeiF1000Research.2017;28649363
Transcriptomic profiles of aging in naïve and memory CD4+ cells from mice.Taylor, Jackson; Reynolds, Lindsay; Hou, Li; Lohman, Kurt; Cui, Wei; Kritchevsky, Stephen; McCall, Charles; Liu, YongmeiImmunity & ageing : I & A.2017;28642803
Repurposing CRISPR System for Transcriptional Activation.Chen, Meng; Qi, Lei StanleyAdvances in experimental medicine and biology.2017;28639197
Mammalian Synthetic Biology: Engineering Biological Systems.Black, Joshua B; Perez-Pinera, Pablo; Gersbach, Charles AAnnual review of biomedical engineering.2017 06 21;28633563
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, BenjaminGenome biology.2017 06 19;28629478
DNA methyltransferase 3b regulates articular cartilage homeostasis by altering metabolism.Shen, Jie; Wang, Cuicui; Li, Daofeng; Xu, Taotao; Myers, Jason; Ashton, John M; Wang, Ting; Zuscik, Michael J; McAlinden, Audrey; O'Keefe, Regis JJCI insight.2017 Jun 15;28614801
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 WPLoS genetics2017 Jun28614350
EpiCompare: An online tool to define and explore genomic regions with tissue or cell type-specific epigenomic features.He, Yu; Wang, TingBioinformatics (Oxford, England).2017 Jun 09;28605501
DNMT and HDAC inhibitors induce cryptic transcription start sites encoded in long terminal repeats.Brocks, David; Schmidt, Christopher R; Daskalakis, Michael; Jang, Hyo Sik; Shah, Nakul M; Li, Daofeng; Li, Jing; Zhang, Bo; Hou, Yiran; Laudato, Sara; Lipka, Daniel B; Schott, Johanna; Bierhoff, Holger; Assenov, Yassen; Helf, Monika; Ressnerova, Alzbeta; Nature genetics.2017 Jul;28604729
Uncovering the transcriptomic and epigenomic landscape of nicotinic receptor genes in non-neuronal tissues.Zhang, Bo; Madden, Pamela; Gu, Junchen; Xing, Xiaoyun; Sankar, Savita; Flynn, Jennifer; Kroll, Kristen; Wang, TingBMC genomics.2017 Jun 05;28583088
SERPINB2 is regulated by dynamic interactions with pause-release proteins and enhancer RNAs.Shii, Lihua; Song, Li; Maurer, Kelly; Zhang, Zhe; Sullivan, Kathleen EMolecular immunology.2017 Aug;28578223
Genetic-Variation-Driven Gene-Expression Changes Highlight Genes with Important Functions for Kidney Disease.Ko, Yi-An; Yi, Huiguang; Qiu, Chengxiang; Huang, Shizheng; Park, Jihwan; Ledo, Nora; Köttgen, Anna; Li, Hongzhe; Rader, Daniel J; Pack, Michael A; Brown, Christopher D; Susztak, KatalinAmerican journal of human genetics.2017 Jun 01;28575649
Neuroprotective effects respond to cerebral ischemia without susceptibility to HB-tumorigenesis in VHL heterozygous knockout mice.Wang, Ying; Yang, Jingyun; Du, Guhong; Ma, Dexuan; Zhou, LiangfuMolecular carcinogenesis.2017 Oct;28574654
Genetic architecture of epigenetic and neuronal ageing rates in human brain regions.Lu, Ake T; Hannon, Eilis; Levine, Morgan E; Crimmins, Eileen M; Lunnon, Katie; Mill, Jonathan; Geschwind, Daniel H; Horvath, SteveNature communications.2017 May 18;28516910
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 QBioinformatics (Oxford, England).2017 Oct 01;28505334
Genetic interaction mapping in mammalian cells using CRISPR interference.Du, Dan; Roguev, Assen; Gordon, David E; Chen, Meng; Chen, Si-Han; Shales, Michael; Shen, John Paul; Ideker, Trey; Mali, Prashant; Qi, Lei S; Krogan, Nevan JNature methods.2017 Jun;28481362
ETV2/ER71 regulates hematopoietic regeneration by promoting hematopoietic stem cell proliferation.Xu, Can-Xin; Lee, Tae-Jin; Sakurai, Nagisa; Krchma, Karen; Liu, Fang; Li, Daofeng; Wang, Ting; Choi, KyungheeThe Journal of experimental medicine.2017 May 01;28461595
Activity of distinct growth factor receptor network components in breast tumors uncovers two biologically relevant subtypes.Rahman, Mumtahena; MacNeil, Shelley M; Jenkins, David F; Shrestha, Gajendra; Wyatt, Sydney R; McQuerry, Jasmine A; Piccolo, Stephen R; Heiser, Laura M; Gray, Joe W; Johnson, W Evan; Bild, Andrea HGenome medicine.2017 04 26;28446242
Systematic Epigenomic Analysis Reveals Chromatin States Associated with Melanoma Progression.Fiziev, Petko; Akdemir, Kadir C; Miller, John P; Keung, Emily Z; Samant, Neha S; Sharma, Sneha; Natale, Christopher A; Terranova, Christopher J; Maitituoheti, Mayinuer; Amin, Samirkumar B; Martinez-Ledesma, Emmanuel; Dhamdhere, Mayura; Axelrad, Jacob B; SCell reports.2017 Apr 25;28445736
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 LNucleic acids research.2017 Nov 16;28431041
Multiplexed Dynamic Imaging of Genomic Loci by Combined CRISPR Imaging and DNA Sequential FISH.Takei, Yodai; Shah, Sheel; Harvey, Sho; Qi, Lei S; Cai, LongBiophysical journal.2017 May 09;28427715
Kidney triglyceride accumulation in the fasted mouse is dependent upon serum free fatty acids.Scerbo, Diego; Son, Ni-Huiping; Sirwi, Alaa; Zeng, Lixia; Sas, Kelli M; Cifarelli, Vincenza; Schoiswohl, Gabriele; Huggins, Lesley-Ann; Gumaste, Namrata; Hu, Yunying; Pennathur, Subramaniam; Abumrad, Nada A; Kershaw, Erin E; Hussain, M Mahmood; Susztak, KJournal of lipid research.2017 Jun;28404638
CRISPR-Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome.Klann, Tyler S; Black, Joshua B; Chellappan, Malathi; Safi, Alexias; Song, Lingyun; Hilton, Isaac B; Crawford, Gregory E; Reddy, Timothy E; Gersbach, Charles ANature biotechnology.2017 Jun;28369033
Population Epigenetics.Greally, John MCurrent opinion in systems biology.2017 Feb;28367533
Precision Medicine Approaches to Diabetic Kidney Disease: Tissue as an Issue.Gluck, Caroline; Ko, Yi-An; Susztak, KatalinCurrent diabetes reports.2017 05;28364354
Small-Magnitude Effect Sizes in Epigenetic End Points are Important in Children's Environmental Health Studies: The Children's Environmental Health and Disease Prevention Research Center's Epigenetics Working Group.Breton, Carrie V; Marsit, Carmen J; Faustman, Elaine; Nadeau, Kari; Goodrich, Jaclyn M; Dolinoy, Dana C; Herbstman, Julie; Holland, Nina; LaSalle, Janine M; Schmidt, Rebecca; Yousefi, Paul; Perera, Frederica; Joubert, Bonnie R; Wiemels, Joseph; Taylor, Michele; Yang, Ivana V; Chen, Rui; Hew, Kinjal M; Freeland, Deborah M Hussey; Miller, Rachel; Murphy, Susan KEnvironmental health perspectives.2017 Apr;28362264
Functional cis-regulatory modules encoded by mouse-specific endogenous retrovirus.Sundaram, Vasavi; Choudhary, Mayank N K; Pehrsson, Erica; Xing, Xiaoyun; Fiore, Christopher; Pandey, Manishi; Maricque, Brett; Udawatta, Methma; Ngo, Duc; Chen, Yujie; Paguntalan, Asia; Ray, Tammy; Hughes, Ava; Cohen, Barak A; Wang, TingNature communications.2017 Mar 28;28348391
Histone gene replacement reveals a post-transcriptional role for H3K36 in maintaining metazoan transcriptome fidelity.Meers, Michael P; Henriques, Telmo; Lavender, Christopher A; McKay, Daniel J; Strahl, Brian D; Duronio, Robert J; Adelman, Karen; Matera, A GregoryeLife.2017 03 27;28346137
Visualization of the Genomic Loci That Are Bound by Specific Multiprotein Complexes by Bimolecular Fluorescence Complementation Analysis on Drosophila Polytene Chromosomes.Deng, Huai; Kerppola, Tom KMethods in enzymology.2017;28336073
Epigenomic annotation of noncoding mutations identifies mutated pathways in primary liver cancer.Lowdon, Rebecca F; Wang, TingPloS one.2017;28333948
Susceptibility to neurofibrillary tangles: role of the PTPRD locus and limited pleiotropy with other neuropathologies.Chibnik, L B; White, C C; Mukherjee, S; Raj, T; Yu, L; Larson, E B; Montine, T J; Keene, C D; Sonnen, J; Schneider, J A; Crane, P K; Shulman, J M; Bennett, D A; De Jager, P LMolecular psychiatry.2017 Mar 21;28322283
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, PrashantNature methods.2017 Jun;28319113
The Nasal Methylome: A Key to Understanding Allergic Asthma.Yang, Ivana V; Richards, Adam; Davidson, Elizabeth J; Stevens, Allen D; Kolakowski, Christena A; Martin, Richard J; Schwartz, David AAmerican journal of respiratory and critical care medicine.2017 03 15;28294656
Monobodies and other synthetic binding proteins for expanding protein science.Sha, Fern; Salzman, Gabriel; Gupta, Ankit; Koide, ShoheiProtein science : a publication of the Protein Society.2017 May;28249355
Transgenic expression of human APOL1 risk variants in podocytes induces kidney disease in mice.Beckerman, Pazit; Bi-Karchin, Jing; Park, Ae Seo Deok; Qiu, Chengxiang; Dummer, Patrick D; Soomro, Irfana; Boustany-Kari, Carine M; Pullen, Steven S; Miner, Jeffrey H; Hu, Chien-An A; Rohacs, Tibor; Inoue, Kazunori; Ishibe, Shuta; Saleem, Moin A; Palmer, Matthew B; Cuervo, Ana Maria; Kopp, Jeffrey B; Susztak, KatalinNature medicine.2017 Apr;28218918
A high-throughput small molecule screen identifies synergism between DNA methylation and Aurora kinase pathways for X reactivation.Lessing, Derek; Dial, Thomas O; Wei, Chunyao; Payer, Bernhard; Carrette, Lieselot L G; Kesner, Barry; Szanto, Attila; Jadhav, Ajit; Maloney, David J; Simeonov, Anton; Theriault, Jimmy; Hasaka, Thomas; Bedalov, Antonio; Bartolomei, Marisa S; Lee, Jeannie TProceedings of the National Academy of Sciences of the United States of America.2016 Dec 13;28182563
Transcriptional heterogeneity in the lactase gene within cell-type is linked to the epigenome.Oh, Edward; Jeremian, Richie; Oh, Gabriel; Groot, Daniel; Susic, Miki; Lee, KwangHo; Foy, Kelly; Laird, Peter W; Petronis, Arturas; Labrie, VivianeScientific reports.2017 Jan 31;28139744
Genome-Wide Association of Copy Number Polymorphisms and Kidney Function.Li, Man; Carey, Jacob; Cristiano, Stephen; Susztak, Katalin; Coresh, Josef; Boerwinkle, Eric; Kao, Wen Hong L; Beaty, Terri H; Köttgen, Anna; Scharpf, Robert BPloS one.2017;28135296
sNASP and ASF1A function through both competitive and compatible modes of histone binding.Bowman, Andrew; Koide, Akiko; Goodman, Jay S; Colling, Meaghan E; Zinne, Daria; Koide, Shohei; Ladurner, Andreas GNucleic acids research.2017 Jan 25;28123037
Layer-specific chromatin accessibility landscapes reveal regulatory networks in adult mouse visual cortex.Gray, Lucas T; Yao, Zizhen; Nguyen, Thuc Nghi; Kim, Tae Kyung; Zeng, Hongkui; Tasic, BosiljkaeLife.2017 Jan 23;28112643
Cooperative Binding of Transcription Factors Orchestrates Reprogramming.Chronis, Constantinos; Fiziev, Petko; Papp, Bernadett; Butz, Stefan; Bonora, Giancarlo; Sabri, Shan; Ernst, Jason; Plath, KathrinCell.2017 Jan 26;28111071
CRISPR-Based Epigenome Editing of Cytokine Receptors for the Promotion of Cell Survival and Tissue Deposition in Inflammatory Environments.Farhang, Niloofar; Brunger, Jonathan M; Stover, Joshua D; Thakore, Pratiksha I; Lawrence, Brandon; Guilak, Farshid; Gersbach, Charles A; Setton, Lori A; Bowles, Robert DTissue engineering. Part A.2017 Jan 17;28095751
Epigenetic Research in Neuropsychiatric Disorders: the ''Tissue Issue''.Bakulski, Kelly M; Halladay, Alycia; Hu, Valerie W; Mill, Jonathan; Fallin, M DanieleCurrent behavioral neuroscience reports.2016 Sep;28093577
Whole-Genome DNA Methylation Profiling Identifies Epigenetic Signatures of Uterine Carcinosarcoma.Li, Jing; Xing, Xiaoyun; Li, Daofeng; Zhang, Bo; Mutch, David G; Hagemann, Ian S; Wang, TingNeoplasia (New York, N.Y.).2017 Feb;28088687
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 JCancer.2017 05 01;28081303
Schizophrenia-associated methylomic variation: molecular signatures of disease and polygenic risk burden across multiple brain regions.Viana, Joana; Hannon, Eilis; Dempster, Emma; Pidsley, Ruth; Macdonald, Ruby; Knox, Olivia; Spiers, Helen; Troakes, Claire; Al-Saraj, Safa; Turecki, Gustavo; Schalkwyk, Leonard C; Mill, JonathanHuman molecular genetics.2017 01 01;28011714
DeFCoM: analysis and modeling of transcription factor binding sites using a motif-centric genomic footprinter.Quach, Bryan; Furey, Terrence SBioinformatics (Oxford, England).2017 Apr 01;27993786
Developing Treatments for Chronic Kidney Disease in the 21st Century.Breyer, Matthew D; Susztak, KatalinSeminars in nephrology.2016 Nov;27987541
A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response.Adamson, Britt; Norman, Thomas M; Jost, Marco; Cho, Min Y; Nuñez, James K; Chen, Yuwen; Villalta, Jacqueline E; Gilbert, Luke A; Horlbeck, Max A; Hein, Marco Y; Pak, Ryan A; Gray, Andrew N; Gross, Carol A; Dixit, Atray; Parnas, Oren; Regev, Aviv; Weissman, Jonathan SCell.2016 Dec 15;27984733
Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens.Dixit, Atray; Parnas, Oren; Li, Biyu; Chen, Jenny; Fulco, Charles P; Jerby-Arnon, Livnat; Marjanovic, Nemanja D; Dionne, Danielle; Burks, Tyler; Raychowdhury, Raktima; Adamson, Britt; Norman, Thomas M; Lander, Eric S; Weissman, Jonathan S; Friedman, Nir; Regev, AvivCell.2016 Dec 15;27984732
''Gap hunting'' to characterize clustered probe signals in Illumina methylation array data.Andrews, Shan V; Ladd-Acosta, Christine; Feinberg, Andrew P; Hansen, Kasper D; Fallin, M DanieleEpigenetics & chromatin.2016;27980682
CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells.Liu, S John; Horlbeck, Max A; Cho, Seung Woo; Birk, Harjus S; Malatesta, Martina; He, Daniel; Attenello, Frank J; Villalta, Jacqueline E; Cho, Min Y; Chen, Yuwen; Mandegar, Mohammad A; Olvera, Michael P; Gilbert, Luke A; Conklin, Bruce R; Chang, Howard Y; Weissman, Jonathan S; Lim, Daniel AScience (New York, N.Y.).2017 Jan 06;27980086
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 KACS chemical neuroscience.2017 03 15;27959513
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, VineetThe Journal of biological chemistry2017 Jan 1327913625
Trans-acting epigenetic effects of chromosomal aneuploidies: lessons from Down syndrome and mouse models.Do, Catherine; Xing, Zhuo; Yu, Y Eugene; Tycko, BenjaminEpigenomics.2017 Feb;27911079
Notch Pathway Is Activated via Genetic and Epigenetic Alterations and Is a Therapeutic Target in Clear Cell Renal Cancer.Bhagat, Tushar D; Zou, Yiyu; Huang, Shizheng; Park, Jihwan; Palmer, Matthew B; Hu, Caroline; Li, Weijuan; Shenoy, Niraj; Giricz, Orsolya; Choudhary, Gaurav; Yu, Yiting; Ko, Yi-An; Izquierdo, María C; Park, Ae Seo Deok; Vallumsetla, Nishanth; Laurence, Remi; Lopez, Robert; Suzuki, Masako; Pullman, James; Kaner, Justin; Gartrell, Benjamin; Hakimi, A Ari; Greally, John M; Patel, Bharvin; Benhadji, Karim; Pradhan, Kith; Verma, Amit; Susztak, KatalinThe Journal of biological chemistry.2017 01 20;27909050
LOVTRAP: A Versatile Method to Control Protein Function with Light.Wang, Hui; Hahn, Klaus MCurrent protocols in cell biology.;27906450
Long-term outdoor air pollution and DNA methylation in circulating monocytes: results from the Multi-Ethnic Study of Atherosclerosis (MESA).Chi, Gloria C; Liu, Yongmei; MacDonald, James W; Barr, R Graham; Donohue, Kathleen M; Hensley, Mark D; Hou, Lifang; McCall, Charles E; Reynolds, Lindsay M; Siscovick, David S; Kaufman, Joel DEnvironmental health : a global access science source.2016 12 01;27903268
Circadian alterations during early stages of Alzheimer's disease are associated with aberrant cycles of DNA methylation in BMAL1.Cronin, Peter; McCarthy, Michael J; Lim, Andrew S P; Salmon, David P; Galasko, Douglas; Masliah, Eliezer; De Jager, Philip L; Bennett, David A; Desplats, PaulaAlzheimer's & dementia : the journal of the Alzheimer's Association.2017 Jun;27883893
New insights into the immunopathogenesis of systemic lupus erythematosus.Tsokos, George C; Lo, Mindy S; Costa Reis, Patricia; Sullivan, Kathleen ENature reviews. Rheumatology2016 11 2227872476
Soft X-Ray Tomography Reveals Gradual Chromatin Compaction and Reorganization during Neurogenesis In Vivo.Le Gros, Mark A; Clowney, E Josephine; Magklara, Angeliki; Yen, Angela; Markenscoff-Papadimitriou, Eirene; Colquitt, Bradley; Myllys, Markko; Kellis, Manolis; Lomvardas, Stavros; Larabell, Carolyn ACell reports.2016 Nov 15;27851973
Epigenomic Deconvolution of Breast Tumors Reveals Metabolic Coupling between Constituent Cell Types.Onuchic, Vitor; Hartmaier, Ryan J; Boone, David N; Samuels, Michael L; Patel, Ronak Y; White, Wendy M; Garovic, Vesna D; Oesterreich, Steffi; Roth, Matt E; Lee, Adrian V; Milosavljevic, AleksandarCell reports.2016 11 15;27851969
A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome.Schmitt, Anthony D; Hu, Ming; Jung, Inkyung; Xu, Zheng; Qiu, Yunjiang; Tan, Catherine L; Li, Yun; Lin, Shin; Lin, Yiing; Barr, Cathy L; Ren, BingCell reports.2016 Nov 15;27851967
A DNA methylation biomarker of alcohol consumption.Liu, C; Marioni, R E; Hedman, Å K; Pfeiffer, L; Tsai, P-C; Reynolds, L M; Just, A C; Duan, Q; Boer, C G; Tanaka, T; Elks, C E; Aslibekyan, S; Brody, J A; Kühnel, B; Herder, C; Almli, L M; Zhi, D; Wang, Y; Huan, T; Yao, C; Mendelson, M M; Joehanes, R; Liang, L; Love, S-A; Guan, W; Shah, S; McRae, A F; Kretschmer, A; Prokisch, H; Strauch, K; Peters, A; Visscher, P M; Wray, N R; Guo, X; Wiggins, K L; Smith, A K; Binder, E B; Ressler, K J; Irvin, M R; Absher, D M; Hernandez, D; Ferrucci, L; Bandinelli, S; Lohman, K; Ding, J; Trevisi, L; Gustafsson, S; Sandling, J H; Stolk, L; Uitterlinden, A G; Yet, I; Castillo-Fernandez, J E; Spector, T D; Schwartz, J D; Vokonas, P; Lind, L; Li, Y; Fornage, M; Arnett, D K; Wareham, N J; Sotoodehnia, N; Ong, K K; van Meurs, J B J; Conneely, K N; Baccarelli, A A; Deary, I J; Bell, J T; North, K E; Liu, Y; Waldenberger, M; London, S J; Ingelsson, E; Levy, DMolecular psychiatry.2016 Nov 15;27843151
Genetic engineering: Chemical control for CRISPR editing.Hilton, Isaac B; Gersbach, Charles ANature chemical biology.2017 Jan;27820804
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 AMolecular psychiatry.2017 07;27801889
Loss-of-function genetic tools for animal models: cross-species and cross-platform differences.Housden, Benjamin E; Muhar, Matthias; Gemberling, Matthew; Gersbach, Charles A; Stainier, Didier Y R; Seydoux, Geraldine; Mohr, Stephanie E; Zuber, Johannes; Perrimon, NorbertNature reviews. Genetics.2017 01;27795562
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 DAlzheimer's & dementia : the journal of the Alzheimer's Association2017 May27793643
Complex transcriptional modulation with orthogonal and inducible dCas9 regulators.Gao, Yuchen; Xiong, Xin; Wong, Spencer; Charles, Emeric J; Lim, Wendell A; Qi, Lei SNature methods.2016 Dec;27776111
Chromosome conformation elucidates regulatory relationships in developing human brain.Won, Hyejung; de la Torre-Ubieta, Luis; Stein, Jason L; Parikshak, Neelroop N; Huang, Jerry; Opland, Carli K; Gandal, Michael J; Sutton, Gavin J; Hormozdiari, Farhad; Lu, Daning; Lee, Changhoon; Eskin, Eleazar; Voineagu, Irina; Ernst, Jason; Geschwind, DaNature.2016 Oct 19;27760116
The long noncoding RNA Tug1 connects metabolic changes with kidney disease in podocytes.Li, Szu Yuan; Susztak, KatalinThe Journal of clinical investigation.2016 Nov 01;27760046
The nasal methylome and childhood atopic asthma.Yang, Ivana V; Pedersen, Brent S; Liu, Andrew H; O'Connor, George T; Pillai, Dinesh; Kattan, Meyer; Misiak, Rana Tawil; Gruchalla, Rebecca; Szefler, Stanley J; Khurana Hershey, Gurjit K; Kercsmar, Carolyn; Richards, Adam; Stevens, Allen D; Kolakowski, Christena A; Makhija, Melanie; Sorkness, Christine A; Krouse, Rebecca Z; Visness, Cynthia; Davidson, Elizabeth J; Hennessy, Corinne E; Martin, Richard J; Togias, Alkis; Busse, William W; Schwartz, David AThe Journal of allergy and clinical immunology.2016 Oct 13;27745942
Molecular classification of Crohn's disease reveals two clinically relevant subtypes.Weiser, Matthew; Simon, Jeremy M; Kochar, Bharati; Tovar, Adelaide; Israel, Jennifer W; Robinson, Adam; Gipson, Gregory R; Schaner, Matthew S; Herfarth, Hans H; Sartor, R Balfour; McGovern, Dermot P B; Rahbar, Reza; Sadiq, Timothy S; Koruda, Mark J; Furey, Terrence S; Sheikh, Shehzad ZGut.2018 Jan;27742763
Epigenomic and transcriptional control of insulin resistance.Rosen, E DJournal of internal medicine.2016 Nov;27739225
Detection of human adaptation during the past 2000 years.Field, Yair; Boyle, Evan A; Telis, Natalie; Gao, Ziyue; Gaulton, Kyle J; Golan, David; Yengo, Loic; Rocheleau, Ghislain; Froguel, Philippe; McCarthy, Mark I; Pritchard, Jonathan KScience (New York, N.Y.).;27738015
SOX2, OCT3/4 and NANOG expression and cellular plasticity in rare human somatic cells requires CD73.Pan, Deng; Roy, Somdutta; Gascard, Philippe; Zhao, Jianxin; Chen-Tanyolac, Chira; Tlsty, Thea DCellular signalling.2016 Dec;27705752
Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions.Ernst, Jason; Melnikov, Alexandre; Zhang, Xiaolan; Wang, Li; Rogov, Peter; Mikkelsen, Tarjei S; Kellis, ManolisNature biotechnology.2016 Nov;27701403
Identification of a cancer stem cell-specific function for the histone deacetylases, HDAC1 and HDAC7, in breast and ovarian cancer.Witt, A E; Lee, C-W; Lee, T I; Azzam, D J; Wang, B; Caslini, C; Petrocca, F; Grosso, J; Jones, M; Cohick, E B; Gropper, A B; Wahlestedt, C; Richardson, A L; Shiekhattar, R; Young, R A; Ince, T AOncogene.2017 Mar 23;27694895
Association of genetic variants in the receptor for advanced glycation end products gene with diabetic retinopathy: A meta-analysis.Yu, Weihong; Yang, Jingyun; Sui, Wenda; Qu, Bin; Huang, Ping; Chen, YouxinMedicine.2016 Sep;27684793
Rescue of Early bace-1 and Global DNA Demethylation by S-Adenosylmethionine Reduces Amyloid Pathology and Improves Cognition in an Alzheimer's Model.Do Carmo, Sonia; Hanzel, Cecilia E; Jacobs, Marie L; Machnes, Ziv; Iulita, M Florencia; Yang, Jingyun; Yu, Lei; Ducatenzeiler, Adriana; Danik, Marc; Breuillaud, Lionel S; Bennett, David A; Szyf, Moshe; Cuello, A ClaudioScientific reports.2016 Sep 29;27681803
Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation.Horlbeck, Max A; Gilbert, Luke A; Villalta, Jacqueline E; Adamson, Britt; Pak, Ryan A; Chen, Yuwen; Fields, Alexander P; Park, Chong Yon; Corn, Jacob E; Kampmann, Martin; Weissman, Jonathan SeLife.2016 Sep 23;27661255
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 ANeurology2016 Oct 1827655734
Epigenetic Signatures of Cigarette Smoking.Joehanes, Roby; Just, Allan C; Marioni, Riccardo E; Pilling, Luke C; Reynolds, Lindsay M; Mandaviya, Pooja R; Guan, Weihua; Xu, Tao; Elks, Cathy E; Aslibekyan, Stella; Moreno-Macias, Hortensia; Smith, Jennifer A; Brody, Jennifer A; Dhingra, Radhika; Yousefi, Paul; Pankow, James S; Kunze, Sonja; Shah, Sonia H; McRae, Allan F; Lohman, Kurt; Sha, Jin; Absher, Devin M; Ferrucci, Luigi; Zhao, Wei; Demerath, Ellen W; Bressler, Jan; Grove, Megan L; Huan, Tianxiao; Liu, Chunyu; Mendelson, Michael M; Yao, Chen; Kiel, Douglas P; Peters, Annette; Wang-Sattler, Rui; Visscher, Peter M; Wray, Naomi R; Starr, John M; Ding, Jingzhong; Rodriguez, Carlos J; Wareham, Nicholas J; Irvin, Marguerite R; Zhi, Degui; Barrdahl, Myrto; Vineis, Paolo; Ambatipudi, Srikant; Uitterlinden, André G; Hofman, Albert; Schwartz, Joel; Colicino, Elena; Hou, Lifang; Vokonas, Pantel S; Hernandez, Dena G; Singleton, Andrew B; Bandinelli, Stefania; Turner, Stephen T; Ware, Erin B; Smith, Alicia K; Klengel, Torsten; Binder, Elisabeth B; Psaty, Bruce M; Taylor, Kent D; Gharib, Sina A; Swenson, Brenton R; Liang, Liming; DeMeo, Dawn L; O'Connor, George T; Herceg, Zdenko; Ressler, Kerry J; Conneely, Karen N; Sotoodehnia, Nona; Kardia, Sharon L R; Melzer, David; Baccarelli, Andrea A; van Meurs, Joyce B J; Romieu, Isabelle; Arnett, Donna K; Ong, Ken K; Liu, Yongmei; Waldenberger, Melanie; Deary, Ian J; Fornage, Myriam; Levy, Daniel; London, Stephanie JCirculation. Cardiovascular genetics.2016 Oct;27651444
Secondhand Tobacco Smoke Exposure Associations With DNA Methylation of the Aryl Hydrocarbon Receptor Repressor.Reynolds, Lindsay M; Magid, Hoda S; Chi, Gloria C; Lohman, Kurt; Barr, R Graham; Kaufman, Joel D; Hoeschele, Ina; Blaha, Michael J; Navas-Acien, Ana; Liu, YongmeiNicotine & tobacco research : official journal of the Society for Research on Nicotine and Tobacco.2017 Apr 01;27613907
Engineering and Application of LOV2-Based Photoswitches.Zimmerman, S P; Kuhlman, B; Yumerefendi, HMethods in enzymology.2016;27586333
Genome-wide mapping and analysis of chromosome architecture.Schmitt, Anthony D; Hu, Ming; Ren, BingNature reviews. Molecular cell biology.2016 12;27580841
An integrated genetic-epigenetic analysis of schizophrenia: evidence for co-localization of genetic associations and differential DNA methylation.Hannon, Eilis; Dempster, Emma; Viana, Joana; Burrage, Joe; Smith, Adam R; Macdonald, Ruby; St Clair, David; Mustard, Colette; Breen, Gerome; Therman, Sebastian; Kaprio, Jaakko; Toulopoulou, Timothea; Hulshoff Pol, Hilleke E; Bohlken, Marc M; Kahn, Rene S; Nenadic, Igor; Hultman, Christina M; Murray, Robin M; Collier, David A; Bass, Nick; Gurling, Hugh; McQuillin, Andrew; Schalkwyk, Leonard; Mill, JonathanGenome biology.2016 Aug 30;27572077
Direct interrogation of the role of H3K9 in metazoan heterochromatin function.Penke, Taylor J R; McKay, Daniel J; Strahl, Brian D; Matera, A Gregory; Duronio, Robert JGenes & development.2016 Aug 15;27566777
Female mice lacking Xist RNA show partial dosage compensation and survive to term.Yang, Lin; Kirby, James E; Sunwoo, Hongjae; Lee, Jeannie TGenes & development.2016 Aug 01;27542829
BatchQC: interactive software for evaluating sample and batch effects in genomic data.Manimaran, Solaiappan; Selby, Heather Marie; Okrah, Kwame; Ruberman, Claire; Leek, Jeffrey T; Quackenbush, John; Haibe-Kains, Benjamin; Bravo, Hector Corrada; Johnson, W EvanBioinformatics (Oxford, England).2016 Dec 15;27540268
Tuning the Binding Affinities and Reversion Kinetics of a Light Inducible Dimer Allows Control of Transmembrane Protein Localization.Zimmerman, Seth P; Hallett, Ryan A; Bourke, Ashley M; Bear, James E; Kennedy, Matthew J; Kuhlman, BrianBiochemistry.2016 Sep 20;27529180
Waking up dormant tumor suppressor genes with zinc fingers, TALEs and the CRISPR/dCas9 system.Garcia-Bloj, Benjamin; Moses, Colette; Sgro, Agustin; Plani-Lam, Janice; Arooj, Mahira; Duffy, Ciara; Thiruvengadam, Shreyas; Sorolla, Anabel; Rashwan, Rabab; Mancera, Ricardo L; Leisewitz, Andrea; Swift-Scanlan, Theresa; Corvalan, Alejandro H; Blancafort, PilarOncotarget.2016 Sep 13;27528034
Charon Mediates Immune Deficiency-Driven PARP-1-Dependent Immune Responses in Drosophila.Ji, Yingbiao; Thomas, Colin; Tulin, Nikita; Lodhi, Niraj; Boamah, Ernest; Kolenko, Vladimir; Tulin, Alexei VJournal of immunology (Baltimore, Md. : 1950).2016 Sep 15;27527593
Targeted Epigenetic Remodeling of Endogenous Loci by CRISPR/Cas9-Based Transcriptional Activators Directly Converts Fibroblasts to Neuronal Cells.Black, Joshua B; Adler, Andrew F; Wang, Hong-Gang; D'Ippolito, Anthony M; Hutchinson, Hunter A; Reddy, Timothy E; Pitt, Geoffrey S; Leong, Kam W; Gersbach, Charles ACell stem cell.2016 Sep 1;27524438
Increased DNA methylation near TREM2 is consistently seen in the superior temporal gyrus in Alzheimer's disease brain.Smith, Adam R; Smith, Rebecca G; Condliffe, Daniel; Hannon, Eilis; Schalkwyk, Leonard; Mill, Jonathan; Lunnon, KatieNeurobiology of aging.2016 Nov;27522519
Inhibition of DNA Methyltransferases Blocks Mutant Huntingtin-Induced Neurotoxicity.Pan, Yanchun; Daito, Takuji; Sasaki, Yo; Chung, Yong Hee; Xing, Xiaoyun; Pondugula, Santhi; Swamidass, S Joshua; Wang, Ting; Kim, Albert H; Yano, HirokoScientific reports.2016 Aug 12;27516062
An epigenetic clock analysis of race/ethnicity, sex, and coronary heart disease.Horvath, Steve; Gurven, Michael; Levine, Morgan E; Trumble, Benjamin C; Kaplan, Hillard; Allayee, Hooman; Ritz, Beate R; Chen, Brian; Lu, Ake T; Rickabaugh, Tammy M; Jamieson, Beth D; Sun, Dianjianyi; Li, Shengxu; Chen, Wei; Quintana-Murci, Lluis; Fagny, Maud; Kobor, Michael S; Tsao, Philip S; Reiner, Alexander P; Edlefsen, Kerstin L; Absher, Devin; Assimes, Themistocles LGenome biology.2016 Aug 11;27511193
Insights into neuroepigenetics through human histone deacetylase PET imaging.Wey, Hsiao-Ying; Gilbert, Tonya M; Zürcher, Nicole R; She, Angela; Bhanot, Anisha; Taillon, Brendan D; Schroeder, Fredrick A; Wang, Changing; Haggarty, Stephen J; Hooker, Jacob MScience translational medicine.2016 08 10;27510902
Mechanisms of Nucleosome Dynamics In Vivo.Henikoff, StevenCold Spring Harbor perspectives in medicine.2016 Sep 01;27503998
Incident parkinsonism in older adults without Parkinson disease.Buchman, Aron S; Leurgans, Sue E; Yu, Lei; Wilson, Robert S; Lim, Andrew S; James, Bryan D; Shulman, Joshua M; Bennett, David ANeurology2016 Sep 0627488597
Hypomethylation coordinates antagonistically with hypermethylation in cancer development: a case study of leukemia.Kushwaha, Garima; Dozmorov, Mikhail; Wren, Jonathan D; Qiu, Jing; Shi, Huidong; Xu, DongHuman genomics.2016 Jul 25;27461342
Highly Multiplexed RNA Aptamer Selection using a Microplate-based Microcolumn Device.Reinholt, Sarah J; Ozer, Abdullah; Lis, John T; Craighead, Harold GScientific reports.2016 Jul 19;27432610
LOVTRAP: an optogenetic system for photoinduced protein dissociation.Wang, Hui; Vilela, Marco; Winkler, Andreas; Tarnawski, Miroslaw; Schlichting, Ilme; Yumerefendi, Hayretin; Kuhlman, Brian; Liu, Rihe; Danuser, Gaudenz; Hahn, Klaus MNature methods.2016 Sep;27427858
Uncovering the Role of the Methylome in Dementia and Neurodegeneration.Klein, Hans-Ulrich; De Jager, Philip LTrends in molecular medicine.2016 08;27423266
Long-term clinical outcomes of laparoscopy-assisted distal gastrectomy versus open distal gastrectomy for early gastric cancer: A comprehensive systematic review and meta-analysis of randomized control trials.Lu, Wei; Gao, Jian; Yang, Jingyun; Zhang, Yijian; Lv, Wenjie; Mu, Jiasheng; Dong, Ping; Liu, YingbinMedicine.2016 Jul;27399073
Go in! Go out! Inducible control of nuclear localization.Di Ventura, Barbara; Kuhlman, BrianCurrent opinion in chemical biology.2016 Jun 30;27372352
Ligand-binding domains of nuclear receptors facilitate tight control of split CRISPR activity.Nguyen, Duy P; Miyaoka, Yuichiro; Gilbert, Luke A; Mayerl, Steven J; Lee, Brian H; Weissman, Jonathan S; Conklin, Bruce R; Wells, James ANature communications.2016 Jul 01;27363581
Reference-free deconvolution of DNA methylation data and mediation by cell composition effects.Houseman, E Andres; Kile, Molly L; Christiani, David C; Ince, Tan A; Kelsey, Karl T; Marsit, Carmen JBMC bioinformatics.2016;27358049
An evaluation of processing methods for HumanMethylation450 BeadChip data.Liu, Jie; Siegmund, Kimberly DBMC genomics.2016 06 22;27334613
Whole Genome Sequencing Identifies a Novel Factor Required for Secretory Granule Maturation in Tetrahymena thermophila.Kontur, Cassandra; Kumar, Santosh; Lan, Xun; Pritchard, Jonathan K; Turkewitz, Aaron PG3 (Bethesda, Md.).2016 Aug 09;27317773
Using genomic annotations increases statistical power to detect eGenes.Duong, Dat; Zou, Jennifer; Hormozdiari, Farhad; Sul, Jae Hoon; Ernst, Jason; Han, Buhm; Eskin, EleazarBioinformatics (Oxford, England).2016 Jun 15;27307612
Breast cancers from black women exhibit higher numbers of immunosuppressive macrophages with proliferative activity and of crown-like structures associated with lower survival compared to non-black Latinas and Caucasians.Koru-Sengul, Tulay; Santander, Ana M; Miao, Feng; Sanchez, Lidia G; Jorda, Merce; Glück, Stefan; Ince, Tan A; Nadji, Mehrad; Chen, Zhibin; Penichet, Manuel L; Cleary, Margot P; Torroella-Kouri, MartaBreast cancer research and treatment.2016 Jul;27283835
Genetic variants in Alzheimer disease - molecular and brain network approaches.Gaiteri, Chris; Mostafavi, Sara; Honey, Christopher J; De Jager, Philip L; Bennett, David ANature reviews. Neurology.2016 Jul;27282653
Chromatin Domains: The Unit of Chromosome Organization.Dixon, Jesse R; Gorkin, David U; Ren, BingMolecular cell.2016 Jun 2;27259200
Paf15 expression correlates with rectal cancer prognosis, cell proliferation and radiation response.Yan, Rong; Zhu, Kun; Dang, Chengxue; Lan, Ke; Wang, Haonan; Yuan, Dawei; Chen, Wei; Meltzer, Stephen J; Li, KangOncotarget.2016 Jun 21;27246972
Pediatric Obesity-Related Asthma: The Role of Metabolic Dysregulation.Vijayakanthi, Nandini; Greally, John M; Rastogi, DeepaPediatrics.2016 May;27244776
A Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria.Peters, Jason M; Colavin, Alexandre; Shi, Handuo; Czarny, Tomasz L; Larson, Matthew H; Wong, Spencer; Hawkins, John S; Lu, Candy H S; Koo, Byoung-Mo; Marta, Elizabeth; Shiver, Anthony L; Whitehead, Evan H; Weissman, Jonathan S; Brown, Eric D; Qi, Lei S; Huang, Kerwyn Casey; Gross, Carol ACell.2016 Jun 2;27238023
The next generation of therapeutics for chronic kidney disease.Breyer, Matthew D; Susztak, KatalinNature reviews. Drug discovery.2016 08;27230798
CRISPR/Cas9 for Human Genome Engineering and Disease Research.Xiong, Xin; Chen, Meng; Lim, Wendell A; Zhao, Dehua; Qi, Lei SAnnual review of genomics and human genetics.2016 Aug 31;27216776
Coregulation of tandem duplicate genes slows evolution of subfunctionalization in mammals.Lan, Xun; Pritchard, Jonathan KScience (New York, N.Y.).2016 May 20;27199432
All Things in Moderation: Prevention of Intestinal Adenomas by DNA Hypomethylation.Lee, Kwang-Ho; Laird, Peter WCancer prevention research (Philadelphia, Pa.).2016 Jul;27190044
Diabetic kidney disease.Thomas, Merlin C; Brownlee, Michael; Susztak, Katalin; Sharma, Kumar; Jandeleit-Dahm, Karin A M; Zoungas, Sophia; Rossing, Peter; Groop, Per-Henrik; Cooper, Mark ENature reviews. Disease primers.2015 07 30;27188921
Activation of the pluripotency factor OCT4 in smooth muscle cells is atheroprotective.Cherepanova, Olga A; Gomez, Delphine; Shankman, Laura S; Swiatlowska, Pamela; Williams, Jason; Sarmento, Olga F; Alencar, Gabriel F; Hess, Daniel L; Bevard, Melissa H; Greene, Elizabeth S; Murgai, Meera; Turner, Stephen D; Geng, Yong-Jian; Bekiranov, Stefan; Connelly, Jessica J; Tomilin, Alexey; Owens, Gary KNature medicine.2016 06;27183216
The Association Between Genetic Polymorphism rs703842 in CYP27B1 and Multiple Sclerosis: A Meta-Analysis.Jiang, Tao; Li, Lizhuo; Wang, Ying; Zhao, Chuntao; Yang, Jundong; Ma, Dexuan; Guan, Yanlei; Zhao, Dan; Bao, Yijun; Wang, Yunjie; Yang, JingyunMedicine.2016 May;27175669
Lamellipodia are crucial for haptotactic sensing and response.King, Samantha J; Asokan, Sreeja B; Haynes, Elizabeth M; Zimmerman, Seth P; Rotty, Jeremy D; Alb Jr, James G; Tagliatela, Alicia; Blake, Devon R; Lebedeva, Irina P; Marston, Daniel; Johnson, Heath E; Parsons, Maddy; Sharpless, Norman E; Kuhlman, Brian; Haugh, Jason M; Bear, James EJournal of cell science.2016 Jun 15;27173494
Lactase nonpersistence is directed by DNA-variation-dependent epigenetic aging.Labrie, Viviane; Buske, Orion J; Oh, Edward; Jeremian, Richie; Ptak, Carolyn; Gasi?nas, Giedrius; Maleckas, Almantas; Petereit, R?ta; ?virbliene, Aida; Adamonis, K?stutis; Kriukien?, Edita; Koncevi?ius, Karolis; Gordevi?ius, Juozas; Nair, Akhil; Zhang, Aiping; Ebrahimi, Sasha; Oh, Gabriel; ?ik?nys, Virginijus; Kup?inskas, Limas; Brudno, Michael; Petronis, ArturasNature structural & molecular biology.2016 06;27159559
Alterations to chromatin in intestinal macrophages link IL-10 deficiency to inappropriate inflammatory responses.Simon, Jeremy M; Davis, James P; Lee, Saangyoung E; Schaner, Matthew R; Gipson, Gregory R; Weiser, Matthew; Sartor, R Balfour; Herfarth, Hans H; Rahbar, Reza; Sadiq, Timothy S; Koruda, Mark J; McGovern, Dermot P; Lieb, Jason D; Mohlke, Karen L; Furey, Terrence S; Sheikh, Shehzad ZEuropean journal of immunology.2016 08;27159132
Novel method to ascertain chromatin accessibility at specific genomic loci from frozen brain homogenates and laser capture microdissected defined cells.Delvaux, Elaine; Mastroeni, Diego; Nolz, Jennifer; Coleman, Paul DNeuroepigenetics.2016 Jun;27158594
Mechanisms and Disease Associations of Haplotype-Dependent Allele-Specific DNA Methylation.Do, Catherine; Lang, Charles F; Lin, John; Darbary, Huferesh; Krupska, Izabela; Gaba, Aulona; Petukhova, Lynn; Vonsattel, Jean-Paul; Gallagher, Mary P; Goland, Robin S; Clynes, Raphael A; Dwork, Andrew; Kral, John G; Monk, Catherine; Christiano, Angela M; Tycko, BenjaminAmerican journal of human genetics.2016 May 05;27153397
Developmental signalling pathways in renal fibrosis: the roles of Notch, Wnt and Hedgehog.Edeling, Maria; Ragi, Grace; Huang, Shizheng; Pavenstädt, Hermann; Susztak, KatalinNature reviews. Nephrology.2016 07;27140856
Taking Stock of Regulatory Variation.Maurano, Matthew T; Stamatoyannopoulos, John ACell systems.2015 Jul 29;27135686
Methylation of histone H4 lysine 20 by PR-Set7 ensures the integrity of late replicating sequence domains in Drosophila.Li, Yulong; Armstrong, Robin L; Duronio, Robert J; MacAlpine, David MNucleic acids research.2016 Sep 06;27131378
Nucleosome breathing and remodeling constrain CRISPR-Cas9 function.Isaac, R Stefan; Jiang, Fuguo; Doudna, Jennifer A; Lim, Wendell A; Narlikar, Geeta J; Almeida, RicardoeLife.2016 Apr 28;27130520
Epigenetic assimilation in the aging human brain.Oh, Gabriel; Ebrahimi, Sasha; Wang, Sun-Chong; Cortese, Rene; Kaminsky, Zachary A; Gottesman, Irving I; Burke, James R; Plassman, Brenda L; Petronis, ArtGenome biology.2016 Apr 28;27122015
Vitamin D and androgen receptor-targeted therapy for triple-negative breast cancer.Thakkar, A; Wang, B; Picon-Ruiz, M; Buchwald, P; Ince, Tan ABreast cancer research and treatment.2016 May;27120467
Metabolic Regulation of Gene Expression by Histone Lysine ?-Hydroxybutyrylation.Xie, Zhongyu; Zhang, Di; Chung, Dongjun; Tang, Zhanyun; Huang, He; Dai, Lunzhi; Qi, Shankang; Li, Jingya; Colak, Gozde; Chen, Yue; Xia, Chunmei; Peng, Chao; Ruan, Haibin; Kirkey, Matt; Wang, Danli; Jensen, Lindy M; Kwon, Oh Kwang; Lee, Sangkyu; Pletcher, Scott D; Tan, Minjia; Lombard, David B; White, Kevin P; Zhao, Hongyu; Li, Jia; Roeder, Robert G; Yang, Xiaoyong; Zhao, YingmingMolecular cell.2016 04 21;27105115
Light-induced nuclear export reveals rapid dynamics of epigenetic modifications.Yumerefendi, Hayretin; Lerner, Andrew Michael; Zimmerman, Seth Parker; Hahn, Klaus; Bear, James E; Strahl, Brian D; Kuhlman, BrianNature chemical biology.2016 Jun;27089030
Allele-Skewed DNA Modification in the Brain: Relevance to a Schizophrenia GWAS.Gagliano, Sarah A; Ptak, Carolyn; Mak, Denise Y F; Shamsi, Mehrdad; Oh, Gabriel; Knight, Joanne; Boutros, Paul C; Petronis, ArturasAmerican journal of human genetics.2016 May 05;27087318
Evolution of Epigenetic Regulation in Vertebrate Genomes.Lowdon, Rebecca F; Jang, Hyo Sik; Wang, TingTrends Genet2016 MayP:269-8327080453
Podocytes: the Weakest Link in Diabetic Kidney Disease?Lin, Jamie S; Susztak, KatalinCurrent diabetes reports.2016 May;27053072
Mitotic bookmarking: maintaining post-mitotic reprogramming of transcription reactivation.Lodhi, Niraj; Ji, Yingbiao; Tulin, AlexeiCurrent molecular biology reports.2016 Mar;27042400
Methylation profiles in peripheral blood CD4+ lymphocytes versus brain: The relation to Alzheimer's disease pathology.Yu, Lei; Chibnik, Lori B; Yang, Jingyun; McCabe, Cristin; Xu, Jishu; Schneider, Julie A; De Jager, Philip L; Bennett, David AAlzheimer's & dementia : the journal of the Alzheimer's Association.2016 Mar 24;27016692
Versatile protein tagging in cells with split fluorescent protein.Kamiyama, Daichi; Sekine, Sayaka; Barsi-Rhyne, Benjamin; Hu, Jeffrey; Chen, Baohui; Gilbert, Luke A; Ishikawa, Hiroaki; Leonetti, Manuel D; Marshall, Wallace F; Weissman, Jonathan S; Huang, BoNature communications.2016;26988139
Nucleosomes impede Cas9 access to DNA in vivo and in vitro.Horlbeck, Max A; Witkowsky, Lea B; Guglielmi, Benjamin; Replogle, Joseph M; Gilbert, Luke A; Villalta, Jacqueline E; Torigoe, Sharon E; Tjian, Robert; Weissman, Jonathan SeLife.2016;26987018
The Association Between Genetic Variants in the Dopaminergic System and Posttraumatic Stress Disorder: A Meta-Analysis.Li, Lizhuo; Bao, Yijun; He, Songbai; Wang, Gang; Guan, Yanlei; Ma, Dexuan; Wang, Pengfei; Huang, Xiaolong; Tao, Shanwei; Zhang, Dewei; Liu, Qiwen; Wang, Yunjie; Yang, JingyunMedicine.2016 Mar;26986136
Occupational cognitive requirements and late-life cognitive aging.Pool, Lindsay R; Weuve, Jennifer; Wilson, Robert S; Bültmann, Ute; Evans, Denis A; Mendes de Leon, Carlos FNeurology.2016 04 12;26984944
CRISPR Interference Efficiently Induces Specific and Reversible Gene Silencing in Human iPSCs.Mandegar, Mohammad A; Huebsch, Nathaniel; Frolov, Ekaterina B; Shin, Edward; Truong, Annie; Olvera, Michael P; Chan, Amanda H; Miyaoka, Yuichiro; Holmes, Kristin; Spencer, C Ian; Judge, Luke M; Gordon, David E; Eskildsen, Tilde V; Villalta, Jacqueline E; Horlbeck, Max A; Gilbert, Luke A; Krogan, Nevan J; Sheikh, Søren P; Weissman, Jonathan S; Qi, Lei S; So, Po-Lin; Conklin, Bruce RCell stem cell.2016 Apr 7;26971820
Constructing 3D interaction maps from 1D epigenomes.Zhu, Yun; Chen, Zhao; Zhang, Kai; Wang, Mengchi; Medovoy, David; Whitaker, John W; Ding, Bo; Li, Nan; Zheng, Lina; Wang, WeiNature communications.2016;26960733
Molecular circuitry of stem cell fate in skeletal muscle regeneration, ageing and disease.Almada, Albert E; Wagers, Amy JNature reviews. Molecular cell biology.2016 May;26956195
YAP Induces Human Naive Pluripotency.Qin, Han; Hejna, Miroslav; Liu, Yanxia; Percharde, Michelle; Wossidlo, Mark; Blouin, Laure; Durruthy-Durruthy, Jens; Wong, Priscilla; Qi, Zhongxia; Yu, Jingwei; Qi, Lei S; Sebastiano, Vittorio; Song, Jun S; Ramalho-Santos, MiguelCell reports.2016 Mar 15;26947063
Mapping of Variable DNA Methylation Across Multiple Cell Types Defines a Dynamic Regulatory Landscape of the Human Genome.Gu, Junchen; Stevens, Michael; Xing, Xiaoyun; Li, Daofeng; Zhang, Bo; Payton, Jacqueline E; Oltz, Eugene M; Jarvis, James N; Jiang, Kaiyu; Cicero, Theodore; Costello, Joseph F; Wang, TingG3 (Bethesda)2016P:973-8626888867
Variation in 5-hydroxymethylcytosine across human cortex and cerebellum.Lunnon, Katie; Hannon, Eilis; Smith, Rebecca G; Dempster, Emma; Wong, Chloe; Burrage, Joe; Troakes, Claire; Al-Sarraj, Safa; Kepa, Agnieszka; Schalkwyk, Leonard; Mill, JonathanGenome biology.2016 Feb 16;26883014
Epigenetic regulation of mitochondrial function in neurodegenerative disease: New insights from advances in genomic technologies.Devall, Matthew; Roubroeks, Janou; Mill, Jonathan; Weedon, Michael; Lunnon, KatieNeuroscience letters.2016 Jun 20;26876477
Long non-coding antisense RNA KRT7-AS is activated in gastric cancers and supports cancer cell progression by increasing KRT7 expression.Huang, B; Song, J H; Cheng, Y; Abraham, J M; Ibrahim, S; Sun, Z; Ke, X; Meltzer, S JOncogene.2016 Feb 15;26876208
Antigen clasping by two antigen-binding sites of an exceptionally specific antibody for histone methylation.Hattori, Takamitsu; Lai, Darson; Dementieva, Irina S; Montaño, Sherwin P; Kurosawa, Kohei; Zheng, Yupeng; Akin, Louesa R; ?wist-Rosowska, Kalina M; Grzybowski, Adrian T; Koide, Akiko; Krajewski, Krzysztof; Strahl, Brian D; Kelleher, Neil L; Ruthenburg, Alexander J; Koide, ShoheiProceedings of the National Academy of Sciences of the United States of America.2016 Feb 23;26862167
ATR-101 disrupts mitochondrial functions in adrenocortical carcinoma cells and in vivo.Cheng, Yunhui; Kerppola, Raili Emilia; Kerppola, Tom KlausEndocrine-related cancer.2016 Apr;26843528
H3K4 tri-methylation breadth at transcription start sites impacts the transcriptome of systemic lupus erythematosus.Zhang, Zhe; Shi, Lihua; Dawany, Noor; Kelsen, Judith; Petri, Michelle A; Sullivan, Kathleen EClinical epigenetics.2016;26839600
Genetic associations at 53 loci highlight cell types and biological pathways relevant for kidney function.Pattaro, Cristian (see original citation for additional authors)Nature communications.2016 Jan 21;26831199
Editing the epigenome: technologies for programmable transcription and epigenetic modulation.Thakore, Pratiksha I; Black, Joshua B; Hilton, Isaac B; Gersbach, Charles ANature methods.2016 Feb;26820547
A full Bayesian partition model for identifying hypo- and hyper-methylated loci from single nucleotide resolution sequencing data.Wang, Henan; He, Chong; Kushwaha, Garima; Xu, Dong; Qiu, JingBMC bioinformatics.2016;26818685
Dissecting structure-activity-relationships of crebinostat: Brain penetrant HDAC inhibitors for neuroepigenetic regulation.Ghosh, Balaram; Zhao, Wen-Ning; Reis, Surya A; Patnaik, Debasis; Fass, Daniel M; Tsai, Li-Huei; Mazitschek, Ralph; Haggarty, Stephen JBioorganic & medicinal chemistry letters.2016 Feb 15;26804233
Interaction of methylation-related genetic variants with circulating fatty acids on plasma lipids: a meta-analysis of 7 studies and methylation analysis of 3 studies in the Cohorts for Heart and Aging Research in Genomic Epidemiology consortium.Ma, Yiyi; Follis, Jack L; Smith, Caren E; Tanaka, Toshiko; Manichaikul, Ani W; Chu, Audrey Y; Samieri, Cecilia; Zhou, Xia; Guan, Weihua; Wang, Lu; Biggs, Mary L; Chen, Yii-Der I; Hernandez, Dena G; Borecki, Ingrid; Chasman, Daniel I; Rich, Stephen S; Ferrucci, Luigi; Irvin, Marguerite Ryan; Aslibekyan, Stella; Zhi, Degui; Tiwari, Hemant K; Claas, Steven A; Sha, Jin; Kabagambe, Edmond K; Lai, Chao-Qiang; Parnell, Laurence D; Lee, Yu-Chi; Amouyel, Philippe; Lambert, Jean-Charles; Psaty, Bruce M; King, Irena B; Mozaffarian, Dariush; McKnight, Barbara; Bandinelli, Stefania; Tsai, Michael Y; Ridker, Paul M; Ding, Jingzhong; Mstat, Kurt Lohmant; Liu, Yongmei; Sotoodehnia, Nona; Barberger-Gateau, Pascale; Steffen, Lyn M; Siscovick, David S; Absher, Devin; Arnett, Donna K; Ordovás, José M; Lemaitre, Rozenn NThe American journal of clinical nutrition.2016 Feb;26791180
Tissue-specific patterns of allelically-skewed DNA methylation.Marzi, Sarah J; Meaburn, Emma L; Dempster, Emma L; Lunnon, Katie; Paya-Cano, Jose L; Smith, Rebecca G; Volta, Manuela; Troakes, Claire; Schalkwyk, Leonard C; Mill, JonathanEpigenetics.2016;26786711
Sox9-Positive Progenitor Cells Play a Key Role in Renal Tubule Epithelial Regeneration in Mice.Kang, Hyun Mi; Huang, Shizheng; Reidy, Kimberly; Han, Seung Hyeok; Chinga, Frank; Susztak, KatalinCell reports.2016 Feb 2;861-7126776520
Expanding the CRISPR imaging toolset with Staphylococcus aureus Cas9 for simultaneous imaging of multiple genomic loci.Chen, Baohui; Hu, Jeffrey; Almeida, Ricardo; Liu, Harrison; Balakrishnan, Sanjeev; Covill-Cooke, Christian; Lim, Wendell A; Huang, BoNucleic acids research.2016 Jan 5;26740581
Mathematical modelling of transcriptional heterogeneity identifies novel markers and subpopulations in complex tissues.Wang, Niya; Hoffman, Eric P; Chen, Lulu; Chen, Li; Zhang, Zhen; Liu, Chunyu; Yu, Guoqiang; Herrington, David M; Clarke, Robert; Wang, YueScientific reports.2016;26739359
Genetic and Epigenetic Variation, but Not Diet, Shape the Sperm Methylome.Shea, Jeremy M; Serra, Ryan W; Carone, Benjamin R; Shulha, Hennady P; Kucukural, Alper; Ziller, Michael J; Vallaster, Markus P; Gu, Hongcang; Tapper, Andrew R; Gardner, Paul D; Meissner, Alexander; Garber, Manuel; Rando, Oliver JDevelopmental cell.2015 Dec 21;26702833
Epithelial Plasticity versus EMT in Kidney Fibrosis.Huang, Shizheng; Susztak, KatalinTrends in molecular medicine.2016 Jan;26700490
Genome editing: the end of the beginning.Doudna, Jennifer A; Gersbach, Charles AGenome biology.2015;29226700220
PET Neurochemical Imaging Modes.Placzek, Michael S; Zhao, Wenjun; Wey, Hsiao-Ying; Morin, Thomas M; Hooker, Jacob MSeminars in nuclear medicine.2016 Jan;20-726687854
Epigenetic age of the pre-frontal cortex is associated with neuritic plaques, amyloid load, and Alzheimer's disease related cognitive functioning.Levine, Morgan E; Lu, Ake T; Bennett, David A; Horvath, SteveAging.2015 Dec;26684672
Development of a Fluorinated Class-I HDAC Radiotracer Reveals Key Chemical Determinants of Brain Penetrance.Strebl, Martin G; Wang, Changning; Schroeder, Frederick A; Placzek, Michael S; Wey, Hsiao-Ying; Van de Bittner, Genevieve C; Neelamegam, Ramesh; Hooker, Jacob MACS chemical neuroscience.2016 05 18;26675505
Beyond editing: repurposing CRISPR-Cas9 for precision genome regulation and interrogation.Dominguez, Antonia A; Lim, Wendell A; Qi, Lei SNature reviews. Molecular cell biology.2016 Jan;26670017
Down-Regulated Phosphoglycerate Kinase 1 Expression Is Associated With Poor Prognosis in Patients With Gallbladder Cancer.Lu, Wei; Gao, Jian; Yang, Jingyun; Cao, Yang; Jiang, Lin; Li, Maolan; Zhang, Yijian; Zhou, Jian; Liu, YingbinMedicine.2015 Dec;26656369
In Utero Cigarette Smoke Affects Allergic Airway Disease But Does Not Alter the Lung Methylome.Eyring, Kenneth R; Pedersen, Brent S; Yang, Ivana V; Schwartz, David APloS one.2015;26642056
Genome-wide Association Studies Identify Genetic Loci Associated With Albuminuria in Diabetes.Teumer, Alexander; Tin, Adrienne; Sorice, Rossella; Gorski, Mathias; Yeo, Nan Cher; Chu, Audrey Y; Li, Man; Li, Yong; Mijatovic, Vladan; Ko, Yi-An; Taliun, Daniel; Luciani, Alessandro; Chen, Ming-Huei; Yang, Qiong; Foster, Meredith C; Olden, Matthias; Hiraki, Linda T; Tayo, Bamidele O; Fuchsberger, Christian; Dieffenbach, Aida Karina; Shuldiner, Alan R; Smith, Albert V; Zappa, Allison M; Lupo, Antonio; Kollerits, Barbara; Ponte, Belen; Stengel, Bénédicte; Krämer, Bernhard K; Paulweber, Bernhard; Mitchell, Braxton D; Hayward, Caroline; Helmer, Catherine; Meisinger, Christa; Gieger, Christian; Shaffer, Christian M; Müller, Christian; Langenberg, Claudia; Ackermann, Daniel; Siscovick, David; DCCT/EDIC; Boerwinkle, Eric; Kronenberg, Florian; Ehret, Georg B; Homuth, Georg; Waeber, Gerard; Navis, Gerjan; Gambaro, Giovanni; Malerba, Giovanni; Eiriksdottir, Gudny; Li, Guo; Wichmann, H Erich; Grallert, Harald; Wallaschofski, Henri; Völzke, Henry; Brenner, Herrmann; Kramer, Holly; Mateo Leach, I; Rudan, Igor; Hillege, Hans L; Beckmann, Jacques S; Lambert, Jean Charles; Luan, Jian'an; Zhao, Jing Hua; Chalmers, John; Coresh, Josef; Denny, Joshua C; Butterbach, Katja; Launer, Lenore J; Ferrucci, Luigi; Kedenko, Lyudmyla; Haun, Margot; Metzger, Marie; Woodward, Mark; Hoffman, Matthew J; Nauck, Matthias; Waldenberger, Melanie; Pruijm, Menno; Bochud, Murielle; Rheinberger, Myriam; Verweij, Niek; Wareham, Nicholas J; Endlich, Nicole; Soranzo, Nicole; Polasek, Ozren; van der Harst, Pim; Pramstaller, Peter Paul; Vollenweider, Peter; Wild, Philipp S; Gansevoort, Ron T; Rettig, Rainer; Biffar, Reiner; Carroll, Robert J; Katz, Ronit; Loos, Ruth J F; Hwang, Shih-Jen; Coassin, Stefan; Bergmann, Sven; Rosas, Sylvia E; Stracke, Sylvia; Harris, Tamara B; Corre, Tanguy; Zeller, Tanja; Illig, Thomas; Aspelund, Thor; Tanaka, Toshiko; Lendeckel, Uwe; Völker, Uwe; Gudnason, Vilmundur; Chouraki, Vincent; Koenig, Wolfgang; Kutalik, Zoltan; O'Connell, Jeffrey R; Parsa, Afshin; Heid, Iris M; Paterson, Andrew D; de Boer, Ian H; Devuyst, Olivier; Lazar, Jozef; Endlich, Karlhans; Susztak, Katalin; Tremblay, Johanne; Hamet, Pavel; Jacob, Howard J; Böger, Carsten A; Fox, Caroline S; Pattaro, Cristian; Köttgen, AnnaDiabetes.2016 Mar;26631737
Methylation QTLs in the developing brain and their enrichment in schizophrenia risk loci.Hannon, Eilis; Spiers, Helen; Viana, Joana; Pidsley, Ruth; Burrage, Joe; Murphy, Therese M; Troakes, Claire; Turecki, Gustavo; O'Donovan, Michael C; Schalkwyk, Leonard C; Bray, Nicholas J; Mill, JonathanNature neuroscience.2016 Jan;48-5426619357
Trans effects of chromosome aneuploidies on DNA methylation patterns in human Down syndrome and mouse models.Mendioroz, Maite; Do, Catherine; Jiang, Xiaoling; Liu, Chunhong; Darbary, Huferesh K; Lang, Charles F; Lin, John; Thomas, Anna; Abu-Amero, Sayeda; Stanier, Philip; Temkin, Alexis; Yale, Alexander; Liu, Meng-Min; Li, Yang; Salas, Martha; Kerkel, Kristi; CaGenome biology.2015;26326607552
A Systematic Approach to Identify Candidate Transcription Factors that Control Cell Identity.D'Alessio, Ana C; Fan, Zi Peng; Wert, Katherine J; Baranov, Petr; Cohen, Malkiel A; Saini, Janmeet S; Cohick, Evan; Charniga, Carol; Dadon, Daniel; Hannett, Nancy M; Young, Michael J; Temple, Sally; Jaenisch, Rudoff; Lee, Tong Ihn; Young, Richard AStem cell reports.2015 Nov 10;763-7526603904
Monoacylglycerol lipase (MGLL) polymorphism rs604300 interacts with childhood adversity to predict cannabis dependence symptoms and amygdala habituation: Evidence from an endocannabinoid system-level analysis.Carey, Caitlin E; Agrawal, Arpana; Zhang, Bo; Conley, Emily D; Degenhardt, Louisa; Heath, Andrew C; Li, Daofeng; Lynskey, Michael T; Martin, Nicholas G; Montgomery, Grant W; Wang, Ting; Bierut, Laura J; Hariri, Ahmad R; Nelson, Elliot C; Bogdan, RyanJournal of abnormal psychology.2015 Nov;860-7726595473
The Association Between Apolipoprotein E and Functional Outcome After Traumatic Brain Injury: A Meta-Analysis.Li, Lizhuo; Bao, Yijun; He, Songbai; Wang, Gang; Guan, Yanlei; Ma, Dexuan; Wu, Rile; Wang, Pengfei; Huang, Xiaolong; Tao, Shanwei; Liu, Qiwen; Wang, Yunjie; Yang, JingyunMedicine.2015 Nov;e202826579811
CpG methylation differences between neurons and glia are highly conserved from mouse to human.Kessler, Noah J; Van Baak, Timothy E; Baker, Maria S; Laritsky, Eleonora; Coarfa, Cristian; Waterland, Robert AHuman molecular genetics.2016 Jan 15;26566671
Identification of differentially methylated loci using wavelet-based functional mixed models.Lee, Wonyul; Morris, Jeffrey SBioinformatics (Oxford, England).2016 Mar 01;26559505
Aberrant intracellular localization of H3k4me3 demonstrates an early epigenetic phenomenon in Alzheimer's disease.Mastroeni, Diego; Delvaux, Elaine; Nolz, Jennifer; Tan, Yuyan; Grover, Andrew; Oddo, Salvatore; Coleman, Paul DNeurobiology of aging.2015 Dec;3121-926553823
Complete haplotype phasing of the MHC and KIR loci with targeted HaploSeq.Selvaraj, Siddarth; Schmitt, Anthony D; Dixon, Jesse R; Ren, BingBMC genomics.2015;90026541200
ETO family protein Mtgr1 mediates Prdm14 functions in stem cell maintenance and primordial germ cell formation.Nady, Nataliya; Gupta, Ankit; Ma, Ziyang; Swigut, Tomek; Koide, Akiko; Koide, Shohei; Wysocka, JoannaeLife.2015;26523391
Perinatal deiodinase 2 expression in hepatocytes defines epigenetic susceptibility to liver steatosis and obesity.Fonseca, Tatiana L; Fernandes, Gustavo W; McAninch, Elizabeth A; Bocco, Barbara M L C; Abdalla, Sherine M; Ribeiro, Miriam O; Mohácsik, Petra; Fekete, Csaba; Li, Daofeng; Xing, Xiaoyun; Wang, Ting; Gereben, Balázs; Bianco, Antonio CProceedings of the National Academy of Sciences of the United States of America.2015 Nov 10;14018-2326508642
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 JCancer.2016 Feb 01;26505625
Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo.Maurano, Matthew T; Haugen, Eric; Sandstrom, Richard; Vierstra, Jeff; Shafer, Anthony; Kaul, Rajinder; Stamatoyannopoulos, John ANature genetics.2015 Dec;26502339
Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements.Thakore, Pratiksha I; D'Ippolito, Anthony M; Song, Lingyun; Safi, Alexias; Shivakumar, Nishkala K; Kabadi, Ami M; Reddy, Timothy E; Crawford, Gregory E; Gersbach, Charles ANature methods.2015 Dec;1143-926501517
ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo.Zentner, Gabriel E; Kasinathan, Sivakanthan; Xin, Beibei; Rohs, Remo; Henikoff, StevenNature communications.2015;873326490019
Psychiatric genetics in China: achievements and challenges.Liu, C; Saffen, D; Schulze, T G; Burmeister, M; Sham, P C; Yao, Y-G; Kuo, P-H; Chen, C; An, Y; Dai, J; Yue, W; Li, M X; Xue, H; Su, B; Chen, L; Shi, Y; Qiao, M; Liu, T; Xia, K; Chan, R C KMolecular psychiatry.2016 Jan;26481319
Methylomic analysis of monozygotic twins discordant for childhood psychotic symptoms.Fisher, Helen L; Murphy, Therese M; Arseneault, Louise; Caspi, Avshalom; Moffitt, Terrie E; Viana, Joana; Hannon, Eilis; Pidsley, Ruth; Burrage, Joe; Dempster, Emma L; Wong, Chloe C Y; Pariante, Carmine M; Mill, JonathanEpigenetics.2015;26479702
Correlating in Vitro and in Vivo Activities of Light-Inducible Dimers: A Cellular Optogenetics Guide.Hallett, Ryan A; Zimmerman, Seth P; Yumerefendi, Hayretin; Bear, James E; Kuhlman, BrianACS synthetic biology.2016 Jan 15;53-6426474029
Ribosome profiling reveals the what, when, where and how of protein synthesis.Brar, Gloria A; Weissman, Jonathan SNature reviews. Molecular cell biology.2015 Nov;26465719
Integrated miRNA profiling and bioinformatics analyses reveal potential causative miRNAs in gastric adenocarcinoma.Zhang, Xiaojing; Peng, Yin; Jin, Zhe; Huang, Weiling; Cheng, Yulan; Liu, Yudan; Feng, Xianling; Yang, Mengting; Huang, Yong; Zhao, Zhenfu; Wang, Liang; Wei, Yanjie; Fan, Xinmin; Zheng, Duo; Meltzer, Stephen JOncotarget.2015 Oct 20;32878-8926460735
Interindividual methylomic variation across blood, cortex, and cerebellum: implications for epigenetic studies of neurological and neuropsychiatric phenotypes.Hannon, Eilis; Lunnon, Katie; Schalkwyk, Leonard; Mill, JonathanEpigenetics.2015;26457534
Parent-of-Origin Effects of the APOB Gene on Adiposity in Young Adults.Hochner, Hagit; Allard, Catherine; Granot-Hershkovitz, Einat; Chen, Jinbo; Sitlani, Colleen M; Sazdovska, Sandra; Lumley, Thomas; McKnight, Barbara; Rice, Kenneth; Enquobahrie, Daniel A; Meigs, James B; Kwok, Pui; Hivert, Marie-France; Borecki, Ingrid B; Gomez, Felicia; Wang, Ting; van Duijn, Cornelia; Amin, Najaf; Rotter, Jerome I; Stamatoyannopoulos, John; Meiner, Vardiella; Manor, Orly; Dupuis, Josée; Friedlander, Yechiel; Siscovick, David SPLoS genetics.2015 Oct;e100557326451733
Dual Roles of RNF2 in Melanoma Progression.Rai, Kunal; Akdemir, Kadir C; Kwong, Lawrence N; Fiziev, Petko; Wu, Chang-Jiun; Keung, Emily Z; Sharma, Sneha; Samant, Neha S; Williams, Maura; Axelrad, Jacob B; Shah, Amiksha; Yang, Dong; Grimm, Elizabeth A; Barton, Michelle C; Milton, Denai R; Heffernan, Timothy P; Horner, James W; Ekmekcioglu, Suhendan; Lazar, Alexander J; Ernst, Jason; Chin, LyndaCancer discovery.2015 Dec;26450788
Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes.Yao, Lijing; Berman, Benjamin P; Farnham, Peggy JCritical reviews in biochemistry and molecular biology.2015;550-7326446758
Design, Assembly, and Characterization of TALE-Based Transcriptional Activators and Repressors.Thakore, Pratiksha I; Gersbach, Charles AMethods in molecular biology (Clifton, N.J.).2016;71-8826443215
The Development of TALE Nucleases for Biotechnology.Ousterout, David G; Gersbach, Charles AMethods in molecular biology (Clifton, N.J.).2016;27-4226443211
Monocyte enhancers are highly altered in systemic lupus erythematosus.Shi, Lihua; Zhang, Zhe; Song, Li; Leung, Yiu Tak; Petri, Michelle A; Sullivan, Kathleen EEpigenomics.2015;921-3526442457
Animal Models of Chemical Carcinogenesis: Driving Breakthroughs in Cancer Research for 100 Years.Kemp, Christopher JCold Spring Harbor protocols.2015 Oct;865-7426430259
Enabling functional genomics with genome engineering.Hilton, Isaac B; Gersbach, Charles AGenome research.2015 Oct;1442-5526430154
TQ inhibits hepatocellular carcinoma growth in vitro and in vivo via repression of Notch signaling.Ke, Xiquan; Zhao, Yan; Lu, Xinlan; Wang, Zhe; Liu, Yuanyuan; Ren, Mudan; Lu, Guifang; Zhang, Dan; Sun, Zhenguo; Xu, Zhipeng; Song, Jee Hoon; Cheng, Yulan; Meltzer, Stephen J; He, ShuixiangOncotarget.2015 Oct 20;32610-2126416455
methylPipe and compEpiTools: a suite of R packages for the integrative analysis of epigenomics data.Kishore, Kamal; de Pretis, Stefano; Lister, Ryan; Morelli, Marco J; Bianchi, Valerio; Amati, Bruno; Ecker, Joseph R; Pelizzola, MattiaBMC bioinformatics.2015;31326415965
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 PAmerican journal of physiology. Renal physiology.2015 Dec 01;26400545
Structure and specificity of the RNA-guided endonuclease Cas9 during DNA interrogation, target binding and cleavage.Josephs, Eric A; Kocak, D Dewran; Fitzgibbon, Christopher J; McMenemy, Joshua; Gersbach, Charles A; Marszalek, Piotr ENucleic acids research.2015 Oct 15;8924-4126384421
The New State of the Art: Cas9 for Gene Activation and Repression.La Russa, Marie F; Qi, Lei SMolecular and cellular biology.2015 Nov;3800-926370509
The CRISPR road: from bench to bedside on an RNA-guided path.Garcia-Bloj, Benjamin; Moses, Colette; Blancafort, PilarAnnals of translational medicine.2015 Aug;26366391
Bacterial CRISPR: accomplishments and prospects.Peters, Jason M; Silvis, Melanie R; Zhao, Dehua; Hawkins, John S; Gross, Carol A; Qi, Lei SCurrent opinion in microbiology.2015 Oct;121-626363124
Labelling and optical erasure of synaptic memory traces in the motor cortex.Hayashi-Takagi, Akiko; Yagishita, Sho; Nakamura, Mayumi; Shirai, Fukutoshi; Wu, Yi I; Loshbaugh, Amanda L; Kuhlman, Brian; Hahn, Klaus M; Kasai, HaruoNature.2015 Sep 17;26352471
BACOM2.0 facilitates absolute normalization and quantification of somatic copy number alterations in heterogeneous tumor.Fu, Yi; Yu, Guoqiang; Levine, Douglas A; Wang, Niya; Shih, Ie-Ming; Zhang, Zhen; Clarke, Robert; Wang, YueScientific reports.2015;1395526350498
Impact of a cis-associated gene expression SNP on chromosome 20q11.22 on bipolar disorder susceptibility, hippocampal structure and cognitive performance.Li, Ming; Luo, Xiong-Jian; Landén, Mikael; Bergen, Sarah E; Hultman, Christina M; Li, Xiao; Zhang, Wen; Yao, Yong-Gang; Zhang, Chen; Liu, Jiewei; Mattheisen, Manuel; Cichon, Sven; Mühleisen, Thomas W; Degenhardt, Franziska A; Nöthen, Markus M; Schulze, Thomas G; Grigoroiu-Serbanescu, Maria; Li, Hao; Fuller, Chris K; Chen, Chunhui; Dong, Qi; Chen, Chuansheng; Jamain, Stéphane; Leboyer, Marion; Bellivier, Frank; Etain, Bruno; Kahn, Jean-Pierre; Henry, Chantal; Preisig, Martin; Kutalik, Zoltán; Castelao, Enrique; Wright, Adam; Mitchell, Philip B; Fullerton, Janice M; Schofield, Peter R; Montgomery, Grant W; Medland, Sarah E; Gordon, Scott D; Martin, Nicholas G; MooDS Consortium; Swedish Bipolar Study Group; Rietschel, Marcella; Liu, Chunyu; Kleinman, Joel E; Hyde, Thomas M; Weinberger, Daniel R; Su, BingThe British journal of psychiatry : the journal of mental science.2016 Feb;26338991
DNA Methylation of the Aryl Hydrocarbon Receptor Repressor Associations With Cigarette Smoking and Subclinical Atherosclerosis.Reynolds, Lindsay M; Wan, Ma; Ding, Jingzhong; Taylor, Jackson R; Lohman, Kurt; Su, Dan; Bennett, Brian D; Porter, Devin K; Gimple, Ryan; Pittman, Gary S; Wang, Xuting; Howard, Timothy D; Siscovick, David; Psaty, Bruce M; Shea, Steven; Burke, Gregory L; JCirculation. Cardiovascular genetics.2015 Oct;707-1626307030
Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions.Grubert, Fabian; Zaugg, Judith B; Kasowski, Maya; Ursu, Oana; Spacek, Damek V; Martin, Alicia R; Greenside, Peyton; Srivas, Rohith; Phanstiel, Doug H; Pekowska, Aleksandra; Heidari, Nastaran; Euskirchen, Ghia; Huber, Wolfgang; Pritchard, Jonathan K; BustaCell.2015 Aug 27;1051-6526300125
Spatiotemporal control of estrogen-responsive transcription in ER?-positive breast cancer cells.Hsu, P-Y; Hsu, H-K; Hsiao, T-H; Ye, Z; Wang, E; Profit, A L; Jatoi, I; Chen, Y; Kirma, N B; Jin, V X; Sharp, Z D; Huang, T H-MOncogene.2016 05 05;26300005
Life course socioeconomic status and DNA methylation in genes related to stress reactivity and inflammation: The multi-ethnic study of atherosclerosis.Needham, Belinda L; Smith, Jennifer A; Zhao, Wei; Wang, Xu; Mukherjee, Bhramar; Kardia, Sharon L R; Shively, Carol A; Seeman, Teresa E; Liu, Yongmei; Diez Roux, Ava VEpigenetics.2015;958-6926295359
Notch1 and Notch2 in Podocytes Play Differential Roles During Diabetic Nephropathy Development.Sweetwyne, Mariya T; Gruenwald, Antje; Niranjan, Thiruvur; Nishinakamura, Ryuichi; Strobl, Lothar J; Susztak, KatalinDiabetes.2015 Dec;26293507
LINE-1 expression and retrotransposition in Barrett's esophagus and esophageal carcinoma.Doucet-O'Hare, Tara T; Rodi?, Nemanja; Sharma, Reema; Darbari, Isha; Abril, Gabriela; Choi, Jungbin A; Young Ahn, Ji; Cheng, Yulan; Anders, Robert A; Burns, Kathleen H; Meltzer, Stephen J; Kazazian Jr, Haig HProceedings of the National Academy of Sciences of the United States of America.2015 Sep 1;E4894-90026283398
Systematic chromatin state comparison of epigenomes associated with diverse properties including sex and tissue type.Yen, Angela; Kellis, ManolisNature communications.2015;797326282110
Comparative analyses of CTCF and BORIS occupancies uncover two distinct classes of CTCF binding genomic regions.Pugacheva, Elena M; Rivero-Hinojosa, Samuel; Espinoza, Celso A; Méndez-Catalá, Claudia Fabiola; Kang, Sungyun; Suzuki, Teruhiko; Kosaka-Suzuki, Natsuki; Robinson, Susan; Nagarajan, Vijayaraj; Ye, Zhen; Boukaba, Abdelhalim; Rasko, John E J; Strunnikov, AleGenome biology.2015;16126268681
Role of DNA Methylation in Modulating Transcription Factor Occupancy.Maurano, Matthew T; Wang, Hao; John, Sam; Shafer, Anthony; Canfield, Theresa; Lee, Kristen; Stamatoyannopoulos, John ACell reports.2015 Aug 18;1184-9526257180
Evidence of CNIH3 involvement in opioid dependence.Nelson, E C; Agrawal, A; Heath, A C; Bogdan, R; Sherva, R; Zhang, B; Al-Hasani, R; Bruchas, M R; Chou, Y-L; Demers, C H; Carey, C E; Conley, E D; Fakira, A K; Farrer, L A; Goate, A; Gordon, S; Henders, A K; Hesselbrock, V; Kapoor, M; Lynskey, M T; Madden, P A F; Moron, J A; Rice, J P; Saccone, N L; Schwab, S G; Shand, F L; Todorov, A A; Wallace, L; Wang, T; Wray, N R; Zhou, X; Degenhardt, L; Martin, N G; Hariri, A R; Kranzler, H R; Gelernter, J; Bierut, L J; Clark, D J; Montgomery, G WMolecular psychiatry.2015 Aug 4;26239289
Klotho: a tumor suppressor and modulator of the Wnt/?-catenin pathway in human hepatocellular carcinoma.Tang, Xiaowei; Wang, Yun; Fan, Zhining; Ji, Guozhong; Wang, Min; Lin, Jie; Huang, Shu; Meltzer, Stephen JLaboratory investigation; a journal of technical methods and pathology.2016 Feb;26237271
Identification of Global DNA Methylation Signatures in Glioblastoma-Derived Cancer Stem Cells.Lee, Eun-Joon; Rath, Prakash; Liu, Jimei; Ryu, Dungsung; Pei, Lirong; Noonepalle, Satish K; Shull, Austin Y; Feng, Qi; Litofsky, N Scott; Miller, Douglas C; Anthony, Douglas C; Kirk, Mark D; Laterra, John; Deng, Libin; Xin, Hong-Bo; Wang, Xinguo; Choi, Jeong-Hyeon; Shi, HuidongJournal of genetics and genomics = Yi chuan xue bao.2015 Jul 20;355-7126233891
Epigenetic Signatures as Biomarkers of Exposure.Ladd-Acosta, ChristineCurrent environmental health reports.2015 Jun;117-2526231361
Heat shock factor 1 induces cancer stem cell phenotype in breast cancer cell lines.Wang, Bin; Lee, Chung-Wei; Witt, Abigail; Thakkar, Ankita; Ince, Tan ABreast cancer research and treatment.2015 Aug;57-6626223813
Synthetic biology approaches to engineer T cells.Wu, Chia-Yung; Rupp, Levi J; Roybal, Kole T; Lim, Wendell ACurrent opinion in immunology.2015 Aug;123-3026218616
CRISPR-ERA: a comprehensive design tool for CRISPR-mediated gene editing, repression and activation.Liu, Honglei; Wei, Zheng; Dominguez, Antonia; Li, Yanda; Wang, Xiaowo; Qi, Lei SBioinformatics (Oxford, England).2015 Nov 15;3676-826209430
Alternative preprocessing of RNA-Sequencing data in The Cancer Genome Atlas leads to improved analysis results.Rahman, Mumtahena; Jackson, Laurie K; Johnson, W Evan; Li, Dean Y; Bild, Andrea H; Piccolo, Stephen RBioinformatics (Oxford, England).2015 Nov 15;3666-7226209429
Endotoxin tolerance in monocytes can be mitigated by ?2-interferon.Shi, Lihua; Song, Li; Maurer, Kelly; Sharp, James; Zhang, Zhe; Sullivan, Kathleen EJournal of leukocyte biology.2015 Oct;651-926206900
Genomic analysis reveals distinct mechanisms and functional classes of SOX10-regulated genes in melanocytes.Fufa, Temesgen D; Harris, Melissa L; Watkins-Chow, Dawn E; Levy, Denise; Gorkin, David U; Gildea, Derek E; Song, Lingyun; Safi, Alexias; Crawford, Gregory E; Sviderskaya, Elena V; Bennett, Dorothy C; Mccallion, Andrew S; Loftus, Stacie K; Pavan, William JHuman molecular genetics.2015 Oct 1;5433-5026206884
Role of DNA methylation in renal cell carcinoma.Shenoy, Niraj; Vallumsetla, Nishanth; Zou, Yiyu; Galeas, Jose Nahun; Shrivastava, Makardhwaj; Hu, Caroline; Susztak, Katalin; Verma, AmitJournal of hematology & oncology.2015 Jul 22;26198328
Diet-Induced Podocyte Dysfunction in Drosophila and Mammals.Na, Jianbo; Sweetwyne, Mariya T; Park, Ae Seo Deok; Susztak, Katalin; Cagan, Ross LCell reports.2015 Jul 28;26190114
Quantitative assessment of RNA-protein interactions with high-throughput sequencing-RNA affinity profiling.Ozer, Abdullah; Tome, Jacob M; Friedman, Robin C; Gheba, Dan; Schroth, Gary P; Lis, John TNature protocols.2015 Aug;1212-3326182240
MicroRNAs Classify Different Disease Behavior Phenotypes of Crohn's Disease and May Have Prognostic Utility.Peck, Bailey C E; Weiser, Matthew; Lee, Saangyoung E; Gipson, Gregory R; Iyer, Vishal B; Sartor, Ryan B; Herfarth, Hans H; Long, Millie D; Hansen, Jonathan J; Isaacs, Kim L; Trembath, Dimitri G; Rahbar, Reza; Sadiq, Timothy S; Furey, Terrence S; SethupathInflammatory bowel diseases.2015 Sep;2178-8726164662
Alterations of a Cellular Cholesterol Metabolism Network Are a Molecular Feature of Obesity-Related Type 2 Diabetes and Cardiovascular Disease.Ding, Jingzhong; Reynolds, Lindsay M; Zeller, Tanja; Müller, Christian; Lohman, Kurt; Nicklas, Barbara J; Kritchevsky, Stephen B; Huang, Zhiqing; de la Fuente, Alberto; Soranzo, Nicola; Settlage, Robert E; Chuang, Chia-Chi; Howard, Timothy; Xu, Ning; GoodDiabetes.2015 Oct;3464-7426153245
Alzheimer's loci: epigenetic associations and interaction with genetic factors.Chibnik, Lori B; Yu, Lei; Eaton, Matthew L; Srivastava, Gyan; Schneider, Julie A; Kellis, Manolis; Bennett, David A; De Jager, Philip LAnnals of clinical and translational neurology.2015 Jun;636-4726125039
Chromosomes. A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation.Minajigi, Anand; Froberg, John E; Wei, Chunyao; Sunwoo, Hongjae; Kesner, Barry; Colognori, David; Lessing, Derek; Payer, Bernhard; Boukhali, Myriam; Haas, Wilhelm; Lee, Jeannie TScience (New York, N.Y.).2015 Jul 17;26089354
Population dynamics of cancer cells with cell state conversions.Zhou, Da; Wu, Dingming; Li, Zhe; Qian, Minping; Zhang, Michael QQuantitative biology.2013 Sep;201-20826085954
Control of Protein Activity and Cell Fate Specification via Light-Mediated Nuclear Translocation.Yumerefendi, Hayretin; Dickinson, Daniel J; Wang, Hui; Zimmerman, Seth P; Bear, James E; Goldstein, Bob; Hahn, Klaus; Kuhlman, BrianPloS one.2015;e012844326083500
Characterization of twenty-five ovarian tumour cell lines that phenocopy primary tumours.Ince, Tan A; Sousa, Aurea D; Jones, Michelle A; Harrell, J Chuck; Agoston, Elin S; Krohn, Marit; Selfors, Laura M; Liu, Wenbin; Chen, Ken; Yong, Mao; Buchwald, Peter; Wang, Bin; Hale, Katherine S; Cohick, Evan; Sergent, Petra; Witt, Abigail; Kozhekbaeva, Nature communications.2015;741926080861
High Precision DNA Modification Analysis of HCG9 in Major Psychosis.Pal, Mrinal; Ebrahimi, Sasha; Oh, Gabriel; Khare, Tarang; Zhang, Aiping; Kaminsky, Zachary A; Wang, Sun-Chong; Petronis, ArturasSchizophrenia bulletin.2016 Jan;26078387
Differential DNA methylation identified in the blood and retina of AMD patients.Oliver, Verity F; Jaffe, Andrew E; Song, Jin; Wang, Guohua; Zhang, Pingwu; Branham, Kari E; Swaroop, Anand; Eberhart, Charles G; Zack, Donald J; Qian, Jiang; Merbs, Shannath LEpigenetics.2015;698-70726067391
Irregular 24-hour activity rhythms and the metabolic syndrome in older adults.Sohail, Shahmir; Yu, Lei; Bennett, David A; Buchman, Aron S; Lim, Andrew S PChronobiology international.2015;802-1326061588
Deletion of Lkb1 in Renal Tubular Epithelial Cells Leads to CKD by Altering Metabolism.Han, Seung Hyeok; Malaga-Dieguez, Laura; Chinga, Frank; Kang, Hyun Mi; Tao, Jianling; Reidy, Kimberly; Susztak, KatalinJournal of the American Society of Nephrology : JASN.2016 Feb;26054542
Phosphorus-32, a clinically available drug, inhibits cancer growth by inducing DNA double-strand breakage.Cheng, Yulan; Kiess, Ana P; Herman, Joseph M; Pomper, Martin G; Meltzer, Stephen J; Abraham, John MPloS one.2015;e012815226030880
Human body epigenome maps reveal noncanonical DNA methylation variation.Schultz, Matthew D; He, Yupeng; Whitaker, John W; Hariharan, Manoj; Mukamel, Eran A; Leung, Danny; Rajagopal, Nisha; Nery, Joseph R; Urich, Mark A; Chen, Huaming; Lin, Shin; Lin, Yiing; Jung, Inkyung; Schmitt, Anthony D; Selvaraj, Siddarth; Ren, Bing; Sejnowski, Terrence J; Wang, Wei; Ecker, Joseph RNature.2015 Jul 9;212-626030523
GATA factors in endocrine neoplasia.Pihlajoki, Marjut; Färkkilä, Anniina; Soini, Tea; Heikinheimo, Markku; Wilson, David BMolecular and cellular endocrinology.2016 Feb 05;26027919
Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators.Polstein, Lauren R; Perez-Pinera, Pablo; Kocak, D Dewran; Vockley, Christopher M; Bledsoe, Peggy; Song, Lingyun; Safi, Alexias; Crawford, Gregory E; Reddy, Timothy E; Gersbach, Charles AGenome research.2015 Aug;1158-6926025803
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 EArthritis & rheumatology (Hoboken, N.J.)2015 Sep26016809
Association of DNA methylation in the brain with age in older persons is confounded by common neuropathologies.Yang, Jingyun; Yu, Lei; Gaiteri, Christopher; Srivastava, Gyan P; Chibnik, Lori B; Leurgans, Sue E; Schneider, Julie A; Meissner, Alexander; De Jager, Philip L; Bennett, David AThe international journal of biochemistry & cell biology.2015 May 21;26003740
Inferring regulatory element landscapes and transcription factor networks from cancer methylomes.Yao, Lijing; Shen, Hui; Laird, Peter W; Farnham, Peggy J; Berman, Benjamin PGenome biology.2015;10525994056
Targeted Transcriptional Repression in Bacteria Using CRISPR Interference (CRISPRi).Hawkins, John S; Wong, Spencer; Peters, Jason M; Almeida, Ricardo; Qi, Lei SMethods in molecular biology (Clifton, N.J.).2015;349-6225981485
Longitudinal epigenetic and gene expression profiles analyzed by three-component analysis reveal down-regulation of genes involved in protein translation in human aging.Jung, Marc; Jin, Seung-Gi; Zhang, Xiaoying; Xiong, Wenying; Gogoshin, Grigoriy; Rodin, Andrei S; Pfeifer, Gerd PNucleic acids research.2015 Sep 3;e10025977295
Cognitive aging in older Black and White persons.Wilson, Robert S; Capuano, Ana W; Sytsma, Joel; Bennett, David A; Barnes, Lisa LPsychology and aging.2015 Jun;279-8525961876
The evolving understanding of the contribution of lipid metabolism to diabetic kidney disease.Stadler, Krisztian; Goldberg, Ira J; Susztak, KatalinCurrent diabetes reports.2015 Jul;4025957525
Chemosensory receptor specificity and regulation.Dalton, Ryan P; Lomvardas, StavrosAnnual review of neuroscience.2015 Jul 8;331-4925938729
A unique chromatin complex occupies young ?-satellite arrays of human centromeres.Henikoff, Jorja G; Thakur, Jitendra; Kasinathan, Sivakanthan; Henikoff, StevenScience advances.2015 Feb 12;25927077
Prenatal mercury concentration is associated with changes in DNA methylation at TCEANC2 in newborns.Bakulski, Kelly M; Lee, HwaJin; Feinberg, Jason I; Wells, Ellen M; Brown, Shannon; Herbstman, Julie B; Witter, Frank R; Halden, Rolf U; Caldwell, Kathleen; Mortensen, Mary Ellen; Jaffe, Andrew E; Moye Jr, John; Caulfield, Laura E; Pan, Yi; Goldman, Lynn RInternational journal of epidemiology.2015 Aug;1249-6225906783
Transcriptomic profiles of aging in purified human immune cells.Reynolds, Lindsay M; Ding, Jingzhong; Taylor, Jackson R; Lohman, Kurt; Soranzo, Nicola; de la Fuente, Alberto; Liu, Tie Fu; Johnson, Craig; Barr, R Graham; Register, Thomas C; Donohue, Kathleen M; Talor, Monica V; Cihakova, Daniela; Gu, Charles; Divers, Jasmin; Siscovick, David; Burke, Gregory; Post, Wendy; Shea, Steven; Jacobs Jr, David R; Hoeschele, Ina; McCall, Charles E; Kritchevsky, Stephen B; Herrington, David; Tracy, Russell P; Liu, YongmeiBMC genomics.2015;33325898983
MIRA-seq for DNA methylation analysis of CpG islands.Jung, Marc; Kadam, Swati; Xiong, Wenying; Rauch, Tibor A; Jin, Seung-Gi; Pfeifer, Gerd PEpigenomics.2015 Apr 17;12-Jan25881900
Paternal sperm DNA methylation associated with early signs of autism risk in an autism-enriched cohort.Feinberg, Jason I; Bakulski, Kelly M; Jaffe, Andrew E; Tryggvadottir, Rakel; Brown, Shannon C; Goldman, Lynn R; Croen, Lisa A; Hertz-Picciotto, Irva; Newschaffer, Craig J; Daniele Fallin, M; Feinberg, Andrew PInternational journal of epidemiology.2015 Aug;1199-21025878217
Regulation of chromatin accessibility and Zic binding at enhancers in the developing cerebellum.Frank, Christopher L; Liu, Fang; Wijayatunge, Ranjula; Song, Lingyun; Biegler, Matthew T; Yang, Marty G; Vockley, Christopher M; Safi, Alexias; Gersbach, Charles A; Crawford, Gregory E; West, Anne ENature neuroscience.2015 May;647-5625849986
Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers.Hilton, Isaac B; D'Ippolito, Anthony M; Vockley, Christopher M; Thakore, Pratiksha I; Crawford, Gregory E; Reddy, Timothy E; Gersbach, Charles ANature biotechnology.2015 May;510-725849900
Genes with de novo mutations are shared by four neuropsychiatric disorders discovered from NPdenovo database.Li, Jinchen; Cai, Tao; Jiang, Yi; Chen, Huiqian; He, Xin; Chen, Chao; Li, Xianfeng; Shao, Qianzhi; Ran, Xia; Li, Zhongshan; Xia, Kun; Liu, Chunyu; Sun, Zhong Sheng; Wu, JinyuMolecular psychiatry.2016 Feb;25849321
An anti-silencer- and SATB1-dependent chromatin hub regulates Rag1 and Rag2 gene expression during thymocyte development.Hao, Bingtao; Naik, Abani Kanta; Watanabe, Akiko; Tanaka, Hirokazu; Chen, Liang; Richards, Hunter W; Kondo, Motonari; Taniuchi, Ichiro; Kohwi, Yoshinori; Kohwi-Shigematsu, Terumi; Krangel, Michael SThe Journal of experimental medicine.2015 May 4;809-2425847946
Epigenetic priming of enhancers predicts developmental competence of hESC-derived endodermal lineage intermediates.Wang, Allen; Yue, Feng; Li, Yan; Xie, Ruiyu; Harper, Thomas; Patel, Nisha A; Muth, Kayla; Palmer, Jeffrey; Qiu, Yunjiang; Wang, Jinzhao; Lam, Dieter K; Raum, Jeffrey C; Stoffers, Doris A; Ren, Bing; Sander, MaikeCell stem cell.2015 Apr 2;386-9925842977
Genome Modification in Enterococcus faecalis OG1RF Assessed by Bisulfite Sequencing and Single-Molecule Real-Time Sequencing.Huo, Wenwen; Adams, Hannah M; Zhang, Michael Q; Palmer, Kelli LJournal of bacteriology.2015 Jun;1939-5125825433
Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells.Liao, Jing; Karnik, Rahul; Gu, Hongcang; Ziller, Michael J; Clement, Kendell; Tsankov, Alexander M; Akopian, Veronika; Gifford, Casey A; Donaghey, Julie; Galonska, Christina; Pop, Ramona; Reyon, Deepak; Tsai, Shengdar Q; Mallard, William; Joung, J Keith; Rinn, John L; Gnirke, Andreas; Meissner, AlexanderNature genetics.2015 May;469-7825822089
Induction of hematopoietic and endothelial cell program orchestrated by ETS transcription factor ER71/ETV2.Liu, Fang; Li, Daofeng; Yu, Yik Yeung Lawrence; Kang, Inyoung; Cha, Min-Ji; Kim, Ju Young; Park, Changwon; Watson, Dennis K; Wang, Ting; Choi, KyungheeEMBO reports.2015 May;654-6925802403
DNA methylation and childhood asthma in the inner city.Yang, Ivana V; Pedersen, Brent S; Liu, Andrew; O'Connor, George T; Teach, Stephen J; Kattan, Meyer; Misiak, Rana Tawil; Gruchalla, Rebecca; Steinbach, Suzanne F; Szefler, Stanley J; Gill, Michelle A; Calatroni, Agustin; David, Gloria; Hennessy, Corinne E;The Journal of allergy and clinical immunology.2015 Jul;69-8025769910
Kinetic Analysis and Quantification of [¹¹C]Martinostat for in Vivo HDAC Imaging of the Brain.Wey, Hsiao-Ying; Wang, Changning; Schroeder, Frederick A; Logan, Jean; Price, Julie C; Hooker, Jacob MACS chemical neuroscience.2015 May 20;708-1525768025
Physical activity, motor function, and white matter hyperintensity burden in healthy older adults.Fleischman, Debra A; Yang, Jingyun; Arfanakis, Konstantinos; Arvanitakis, Zoe; Leurgans, Sue E; Turner, Arlener D; Barnes, Lisa L; Bennett, David A; Buchman, Aron SNeurology.2015 Mar 31;1294-30025762710
An epigenome-wide association study of total serum immunoglobulin E concentration.Liang, Liming; Willis-Owen, Saffron A G; Laprise, Catherine; Wong, Kenny C C; Davies, Gwyneth A; Hudson, Thomas J; Binia, Aristea; Hopkin, Julian M; Yang, Ivana V; Grundberg, Elin; Busche, Stephan; Hudson, Marie; Ronnblom, Lars; Pastinen, Tomi M; Schwartz, David A; Lathrop, G Mark; Moffatt, Miriam F; Cookson, William O C MNature.2015 Apr 30;670-425707804
Epigenome engineering in cancer: fairytale or a realistic path to the clinic?Falahi, Fahimeh; Sgro, Agustin; Blancafort, PilarFrontiers in oncology.2015;25705610
Anthracyclines induce double-strand DNA breaks at active gene promoters.Yang, Fan; Kemp, Christopher J; Henikoffa, StevenMutation research.2015 Mar;15-Sep25705119
Developmental enhancers revealed by extensive DNA methylome maps of zebrafish early embryos.Lee, Hyung Joo; Lowdon, Rebecca F; Maricque, Brett; Zhang, Bo; Stevens, Michael; Li, Daofeng; Johnson, Stephen L; Wang, TingNature communications.2015 Feb 20;631525697895
PRIMEGENSw3: a web-based tool for high-throughput primer and probe design.Kushwaha, Garima; Srivastava, Gyan Prakash; Xu, DongMethods in molecular biology (Clifton, N.J.).2015;181-9925697661
Cell-of-origin chromatin organization shapes the mutational landscape of cancer.Polak, Paz; Karli?, Rosa; Koren, Amnon; Thurman, Robert; Sandstrom, Richard; Lawrence, Michael S; Reynolds, Alex; Rynes, Eric; Vlahovi?ek, Kristian; Stamatoyannopoulos, John A; Sunyaev, Shamil RNature.2015 Feb 19;360-425693567
Integrative analysis of haplotype-resolved epigenomes across human tissues.Leung, Danny; Jung, Inkyung; Rajagopal, Nisha; Schmitt, Anthony; Selvaraj, Siddarth; Lee, Ah Young; Yen, Chia-An; Lin, Shin; Lin, Yiing; Qiu, Yunjiang; Xie, Wei; Yue, Feng; Hariharan, Manoj; Ray, Pradipta; Kuan, Samantha; Edsall, Lee; Yang, Hongbo; Chi, Neil C; Zhang, Michael Q; Ecker, Joseph R; Ren, BingNature.2015 Feb 19;350-425693566
Transcription factor binding dynamics during human ES cell differentiation.Tsankov, Alexander M; Gu, Hongcang; Akopian, Veronika; Ziller, Michael J; Donaghey, Julie; Amit, Ido; Gnirke, Andreas; Meissner, AlexanderNature.2015 Feb 19;344-925693565
Chromatin architecture reorganization during stem cell differentiation.Dixon, Jesse R; Jung, Inkyung; Selvaraj, Siddarth; Shen, Yin; Antosiewicz-Bourget, Jessica E; Lee, Ah Young; Ye, Zhen; Kim, Audrey; Rajagopal, Nisha; Xie, Wei; Diao, Yarui; Liang, Jing; Zhao, Huimin; Lobanenkov, Victor V; Ecker, Joseph R; Thomson, James A; Ren, BingNature.2015 Feb 19;331-625693564
Integrative analysis of 111 reference human epigenomes.Roadmap Epigenomics Consortium; Kundaje, Anshul; Meuleman, Wouter; Ernst, Jason; Bilenky, Misha; Yen, Angela; Heravi-Moussavi, Alireza; Kheradpour, Pouya; Zhang, Zhizhuo; Wang, Jianrong; Ziller, Michael J; Amin, Viren; Whitaker, John W; Schultz, Matthew D; Ward, Lucas D; Sarkar, Abhishek; Quon, Gerald; Sandstrom, Richard S; Eaton, Matthew L; Wu, Yi-Chieh; Pfenning, Andreas R; Wang, Xinchen; Claussnitzer, Melina; Liu, Yaping; Coarfa, Cristian; Harris, R Alan; Shoresh, Noam; Epstein, Charles B; Gjoneska, Elizabeta; Leung, Danny; Xie, Wei; Hawkins, R David; Lister, Ryan; Hong, Chibo; Gascard, Philippe; Mungall, Andrew J; Moore, Richard; Chuah, Eric; Tam, Angela; Canfield, Theresa K; Hansen, R Scott; Kaul, Rajinder; Sabo, Peter J; Bansal, Mukul S; Carles, Annaick; Dixon, Jesse R; Farh, Kai-How; Feizi, Soheil; Karlic, Rosa; Kim, Ah-Ram; Kulkarni, Ashwinikumar; Li, Daofeng; Lowdon, Rebecca; Elliott, GiNell; Mercer, Tim R; Neph, Shane J; Onuchic, Vitor; Polak, Paz; Rajagopal, Nisha; Ray, Pradipta; Sallari, Richard C; Siebenthall, Kyle T; Sinnott-Armstrong, Nicholas A; Stevens, Michael; Thurman, Robert E; Wu, Jie; Zhang, Bo; Zhou, Xin; Beaudet, Arthur E; Boyer, Laurie A; De Jager, Philip L; Farnham, Peggy J; Fisher, Susan J; Haussler, David; Jones, Steven J M; Li, Wei; Marra, Marco A; McManus, Michael T; Sunyaev, Shamil; Thomson, James A; Tlsty, Thea D; Tsai, Li-Huei; Wang, Wei; Waterland, Robert A; Zhang, Michael Q; Chadwick, Lisa H; Bernstein, Bradley E; Costello, Joseph F; Ecker, Joseph R; Hirst, Martin; Meissner, Alexander; Milosavljevic, Aleksandar; Ren, Bing; Stamatoyannopoulos, John A; Wang, Ting; Kellis, ManolisNature.2015 Feb 19;317-3025693563
Epigenomic footprints across 111 reference epigenomes reveal tissue-specific epigenetic regulation of lincRNAs.Amin, Viren; Harris, R Alan; Onuchic, Vitor; Jackson, Andrew R; Charnecki, Tim; Paithankar, Sameer; Lakshmi Subramanian, Sai; Riehle, Kevin; Coarfa, Cristian; Milosavljevic, AleksandarNature communications.2015;637025691256
Intermediate DNA methylation is a conserved signature of genome regulation.Elliott, GiNell; Hong, Chibo; Xing, Xiaoyun; Zhou, Xin; Li, Daofeng; Coarfa, Cristian; Bell, Robert J A; Maire, Cecile L; Ligon, Keith L; Sigaroudinia, Mahvash; Gascard, Philippe; Tlsty, Thea D; Harris, R Alan; Schalkwyk, Leonard C; Bilenky, Misha; Mill, Jonathan; Farnham, Peggy J; Kellis, Manolis; Marra, Marco A; Milosavljevic, Aleksandar; Hirst, Martin; Stormo, Gary D; Wang, Ting; Costello, Joseph FNature communications.2015;636325691127
Epigenetic and transcriptional determinants of the human breast.Gascard, Philippe; Bilenky, Misha; Sigaroudinia, Mahvash; Zhao, Jianxin; Li, Luolan; Carles, Annaick; Delaney, Allen; Tam, Angela; Kamoh, Baljit; Cho, Stephanie; Griffith, Malachi; Chu, Andy; Robertson, Gordon; Cheung, Dorothy; Li, Irene; Heravi-Moussavi, Alireza; Moksa, Michelle; Mingay, Matthew; Hussainkhel, Angela; Davis, Brad; Nagarajan, Raman P; Hong, Chibo; Echipare, Lorigail; O'Geen, Henriette; Hangauer, Matthew J; Cheng, Jeffrey B; Neel, Dana; Hu, Donglei; McManus, Michael T; Moore, Richard; Mungall, Andrew; Ma, Yussanne; Plettner, Patrick; Ziv, Elad; Wang, Ting; Farnham, Peggy J; Jones, Steven J M; Marra, Marco A; Tlsty, Thea D; Costello, Joseph F; Hirst, MartinNature communications.2015;635125690954
Epigenomic annotation of genetic variants using the Roadmap Epigenome Browser.Zhou, Xin; Li, Daofeng; Zhang, Bo; Lowdon, Rebecca F; Rockweiler, Nicole B; Sears, Renee L; Madden, Pamela A F; Smirnov, Ivan; Costello, Joseph F; Wang, TingNature biotechnology.2015 Apr;345-625690851
Quantitative proteomic analysis of histone modifications.Huang, He; Lin, Shu; Garcia, Benjamin A; Zhao, YingmingChemical reviews.2015 Mar 25;2376-41825688442
Stable oncogenic silencing in vivo by programmable and targeted de novo DNA methylation in breast cancer.Stolzenburg, S; Beltran, A S; Swift-Scanlan, T; Rivenbark, A G; Rashwan, R; Blancafort, POncogene.2015 Feb 16;25684141
Functional Proteomic Analysis of Repressive Histone Methyltransferase Complexes Reveals ZNF518B as a G9A Regulator.Maier, Verena K; Feeney, Caitlin M; Taylor, Jordan E; Creech, Amanda L; Qiao, Jana W; Szanto, Attila; Das, Partha P; Chevrier, Nicholas; Cifuentes-Rojas, Catherine; Orkin, Stuart H; Carr, Steven A; Jaffe, Jacob D; Mertins, Philipp; Lee, Jeannie TMolecular & cellular proteomics : MCP.2015 Jun;1435-4625680957
Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression.Libbrecht, Maxwell W; Ay, Ferhat; Hoffman, Michael M; Gilbert, David M; Bilmes, Jeffrey A; Noble, William StaffordGenome research.2015 Apr;544-5725677182
Interrogating the function of metazoan histones using engineered gene clusters.McKay, Daniel J; Klusza, Stephen; Penke, Taylor J R; Meers, Michael P; Curry, Kaitlin P; McDaniel, Stephen L; Malek, Pamela Y; Cooper, Stephen W; Tatomer, Deirdre C; Lieb, Jason D; Strahl, Brian D; Duronio, Robert J; Matera, A GregoryDevelopmental cell.2015 Feb 9;373-8625669886
Novel antioxidants protect mitochondria from the effects of oligomeric amyloid beta and contribute to the maintenance of epigenome function.Mastroeni, Diego; Khdour, Omar M; Arce, Pablo M; Hecht, Sidney M; Coleman, Paul DACS chemical neuroscience.2015 Apr 15;588-9825668062
A light-inducible CRISPR-Cas9 system for control of endogenous gene activation.Polstein, Lauren R; Gersbach, Charles ANature chemical biology.2015 Mar;198-20025664691
Small molecules enhance CRISPR genome editing in pluripotent stem cells.Yu, Chen; Liu, Yanxia; Ma, Tianhua; Liu, Kai; Xu, Shaohua; Zhang, Yu; Liu, Honglei; La Russa, Marie; Xie, Min; Ding, Sheng; Qi, Lei SCell stem cell.2015 Feb 5;142-725658371
The TMEM106B locus and TDP-43 pathology in older persons without FTLD.Yu, Lei; De Jager, Philip L; Yang, Jingyun; Trojanowski, John Q; Bennett, David A; Schneider, Julie ANeurology.2015 Mar 3;927-3425653292
Genetics and epigenetics of circadian rhythms and their potential roles in neuropsychiatric disorders.Liu, Chunyu; Chung, MichaelNeuroscience bulletin.2015 Feb;141-5925652815
Inhibitor of DNA Binding 4 (ID4) is highly expressed in human melanoma tissues and may function to restrict normal differentiation of melanoma cells.Peretz, Yuval; Wu, Hong; Patel, Shayan; Bellacosa, Alfonso; Katz, Richard APloS one.2015;e011683925642713
Aging and DNA methylation.Jung, Marc; Pfeifer, Gerd PBMC biology.2015;725637097
Interferon regulatory factor 1 and histone H4 acetylation in systemic lupus erythematosus.Leung, Yiu Tak; Shi, Lihua; Maurer, Kelly; Song, Li; Zhang, Zhe; Petri, Michelle; Sullivan, Kathleen EEpigenetics : official journal of the DNA Methylation Society.2015;191-925611806
(Epi)genomics approaches and their applications.Meissner, AlexanderMethods (San Diego, Calif.).2015 Jan 15;2-Jan25597875
Characterization and target identification of a DNA aptamer that labels pluripotent stem cells.Hou, Zhonggang; Meyer, Susanne; Propson, Nicholas E; Nie, Jeff; Jiang, Peng; Stewart, Ron; Thomson, James ACell research.2015 Mar;390-325591927
Blood methylomic signatures of presymptomatic dementia in elderly subjects with type 2 diabetes mellitus.Lunnon, Katie; Smith, Rebecca G; Cooper, Itzik; Greenbaum, Lior; Mill, Jonathan; Beeri, Michal SchnaiderNeurobiology of aging.2015 Mar;1600.e1-425585531
Genomic discovery of potent chromatin insulators for human gene therapy.Liu, Mingdong; Maurano, Matthew T; Wang, Hao; Qi, Heyuan; Song, Chao-Zhong; Navas, Patrick A; Emery, David W; Stamatoyannopoulos, John A; Stamatoyannopoulos, GeorgeNature biotechnology.2015 Feb;198-20325580597
Normal cell-type epigenetics and breast cancer classification: a case study of cell mixture-adjusted analysis of DNA methylation data from tumors.Houseman, Eugene Andrés; Ince, Tan ACancer informatics.2014;25574126
Considering the kinetics of mRNA synthesis in the analysis of the genome and epigenome reveals determinants of co-transcriptional splicing.Davis-Turak, Jeremy C; Allison, Karmel; Shokhirev, Maxim N; Ponomarenko, Petr; Tsimring, Lev S; Glass, Christopher K; Johnson, Tracy L; Hoffmann, AlexanderNucleic acids research.2015 Jan;699-70725541195
Dissecting neural differentiation regulatory networks through epigenetic footprinting.Ziller, Michael J; Edri, Reuven; Yaffe, Yakey; Donaghey, Julie; Pop, Ramona; Mallard, William; Issner, Robbyn; Gifford, Casey A; Goren, Alon; Xing, Jeffrey; Gu, Hongcang; Cacchiarelli, Davide; Tsankov, Alexander M; Epstein, Charles; Rinn, John L; Mikkelsen, Tarjei S; Kohlbacher, Oliver; Gnirke, Andreas; Bernstein, Bradley E; Elkabetz, Yechiel; Meissner, AlexanderNature.2015 Feb 19;355-925533951
Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds.Zalatan, Jesse G; Lee, Michael E; Almeida, Ricardo; Gilbert, Luke A; Whitehead, Evan H; La Russa, Marie; Tsai, Jordan C; Weissman, Jonathan S; Dueber, John E; Qi, Lei S; Lim, Wendell ACell.2015 Jan 15;339-5025533786
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Defective fatty acid oxidation in renal tubular epithelial cells has a key role in kidney fibrosis development.Kang, Hyun Mi; Ahn, Seon Ho; Choi, Peter; Ko, Yi-An; Han, Seung Hyeok; Chinga, Frank; Park, Ae Seo Deok; Tao, Jianling; Sharma, Kumar; Pullman, James; Bottinger, Erwin P; Goldberg, Ira J; Susztak, KatalinNature medicine.2015 Jan;25419705
Proteomics-Based Identification of Differentially Abundant Proteins from Human Keratinocytes Exposed to Arsenic Trioxide.Udensi, Udensi K; Tackett, Alan J; Byrum, Stephanie; Avaritt, Nathan L; Sengupta, Deepanwita; Moreland, Linley W; Tchounwou, Paul B; Isokpehi, Raphael DJournal of proteomics & bioinformatics.2014 Jul;166-17825419056
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Normal cell phenotypes of breast epithelial cells provide the foundation of a breast cancer taxonomy.Santagata, Sandro; Ince, Tan AExpert review of anticancer therapy.2014 Dec;1385-925263303
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Functional genomic annotation of genetic risk loci highlights inflammation and epithelial biology networks in CKD.Ledo, Nora; Ko, Yi-An; Park, Ae-Seo Deok; Kang, Hyun-Mi; Han, Sang-Youb; Choi, Peter; Susztak, KatalinJournal of the American Society of Nephrology : JASN.2015 Mar;692-71425231882
Relation of DASH- and Mediterranean-like dietary patterns to cognitive decline in older persons.Tangney, Christy C; Li, Hong; Wang, Yamin; Barnes, Lisa; Schneider, Julie A; Bennett, David A; Morris, Martha CNeurology.2014 Oct 14;1410-625230996
In vivo imaging of histone deacetylases (HDACs) in the central nervous system and major peripheral organs.Wang, Changning; Schroeder, Frederick A; Wey, Hsiao-Ying; Borra, Ronald; Wagner, Florence F; Reis, Surya; Kim, Sung Won; Holson, Edward B; Haggarty, Stephen J; Hooker, Jacob MJournal of medicinal chemistry.2014 Oct 9;7999-800925203558
PET imaging demonstrates histone deacetylase target engagement and clarifies brain penetrance of known and novel small molecule inhibitors in rat.Schroeder, F A; Wang, C; Van de Bittner, G C; Neelamegam, R; Takakura, W R; Karunakaran, A; Wey, H Y; Reis, S A; Gale, J; Zhang, Y L; Holson, E B; Haggarty, S J; Hooker, J MACS chemical neuroscience.2014 Oct 15;1055-6225188794
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Methylomic profiling implicates cortical deregulation of ANK1 in Alzheimer's disease.Lunnon, Katie; Smith, Rebecca; Hannon, Eilis; De Jager, Philip L; Srivastava, Gyan; Volta, Manuela; Troakes, Claire; Al-Sarraj, Safa; Burrage, Joe; Macdonald, Ruby; Condliffe, Daniel; Harries, Lorna W; Katsel, Pavel; Haroutunian, Vahram; Kaminsky, ZacharyNature neuroscience2014 Sep1164-117025129077
Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci.De Jager, Philip L; Srivastava, Gyan; Lunnon, Katie; Burgess, Jeremy; Schalkwyk, Leonard C; Yu, Lei; Eaton, Matthew L; Keenan, Brendan T; Ernst, Jason; McCabe, Cristin; Tang, Anna; Raj, Towfique; Replogle, Joseph; Brodeur, Wendy; Gabriel, Stacey; Chai, High S; Younkin, Curtis; Younkin, Steven G; Zou, Fanggeng; Szyf, Moshe; Epstein, Charles B; Schneider, Julie A; Bernstein, Bradley E; Meissner, Alex; Ertekin-Taner, Nilufer; Chibnik, Lori B; Kellis, Manolis; Mill, Jonathan; Bennett, David ANature neuroscience.2014 Sep;1156-6325129075
Functional kinomics identifies candidate therapeutic targets in head and neck cancer.Moser, Russell; Xu, Chang; Kao, Michael; Annis, James; Lerma, Luisa Angelica; Schaupp, Christopher M; Gurley, Kay E; Jang, In Sock; Biktasova, Asel; Yarbrough, Wendell G; Margolin, Adam A; Grandori, Carla; Kemp, Christopher J; Mendez, EduardoClinical cancer research : an official journal of the American Association for Cancer Research2014 Aug 154274-8825125259
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A PWWP domain-containing protein targets the NuA3 acetyltransferase complex via histone H3 lysine 36 trimethylation to coordinate transcriptional elongation at coding regions.Gilbert, Tonya M; McDaniel, Stephen L; Byrum, Stephanie D; Cades, Jessica A; Dancy, Blair C R; Wade, Herschel; Tackett, Alan J; Strahl, Brian D; Taverna, Sean DMolecular & cellular proteomics : MCP.2014 Nov;2883-9525104842
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Analysis of interactions between the epigenome and structural mutability of the genome using Genboree Workbench tools.Coarfa, Cristian; Pichot, Christina; Jackson, Andrew; Tandon, Arpit; Amin, Viren; Raghuraman, Sriram; Paithankar, Sameer; Lee, Adrian V; McGuire, Sean E; Milosavljevic, AleksandarBMC bioinformatics.2014;S225080362
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Visualization of the Drosophila dKeap1-CncC interaction on chromatin illumines cooperative, xenobiotic-specific gene activation.Deng, Huai; Kerppola, Tom KDevelopment (Cambridge, England).2014 Aug;3277-8825063457
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Characterization of genome-methylome interactions in 22 nuclear pedigrees.Plongthongkum, Nongluk; van Eijk, Kristel R; de Jong, Simone; Wang, Tina; Sul, Jae Hoon; Boks, Marco P M; Kahn, Rene S; Fung, Ho-Lim; Ophoff, Roel A; Zhang, KunPloS one2014e9931325019935
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Kidney cancer is characterized by aberrant methylation of tissue-specific enhancers that are prognostic for overall survival.Hu, Caroline Y; Mohtat, Davoud; Yu, Yiting; Ko, Yi-An; Shenoy, Niraj; Bhattacharya, Sanchari; Izquierdo, Maria C; Park, Ae Seo Deok; Giricz, Orsolya; Vallumsetla, Nishanth; Gundabolu, Krishna; Ware, Kristin; Bhagat, Tushar D; Suzuki, Masako; Pullman, James; Liu, X Shirley; Greally, John M; Susztak, Katalin; Verma, AmitClinical cancer research : an official journal of the American Association for Cancer Research.2014 Aug 15;4349-6024916699
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Developmental biology. Enhancing pluripotency and lineage specification.Xie, Wei; Ren, BingScience (New York, N.Y.)2013 Jul 19245-723869010
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FDG-PET imaging reveals local brain glucose utilization is altered by class I histone deacetylase inhibitors.Schroeder, Frederick A; Chonde, Daniel B; Riley, Misha M; Moseley, Christian K; Granda, Michael L; Wilson, Colin M; Wagner, Florence F; Zhang, Yan-Ling; Gale, Jennifer; Holson, Edward B; Haggarty, Stephen J; Hooker, Jacob MNeuroscience letters2013 Jun 25NULL23810801
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Global chromatin state analysis reveals lineage-specific enhancers during the initiation of human T helper 1 and T helper 2 cell polarization.Hawkins, R David; Larjo, Antti; Tripathi, Subhash K; Wagner, Ulrich; Luu, Ying; Lonnberg, Tapio; Raghav, Sunil K; Lee, Leonard K; Lund, Riikka; Ren, Bing; Lahdesmaki, Harri; Lahesmaa, RiittaImmunity2013 Jun 271271-8423791644
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Epigenomic analysis of multilineage differentiation of human embryonic stem cells.Xie, Wei; Schultz, Matthew D; Lister, Ryan; Hou, Zhonggang; Rajagopal, Nisha; Ray, Pradipta; Whitaker, John W; Tian, Shulan; Hawkins, R David; Leung, Danny; Yang, Hongbo; Wang, Tao; Lee, Ah Young; Swanson, Scott A; Zhang, Jiuchun; Zhu, Yun; Kim, Audrey; NCell2013 May 231134-4823664764
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Evidence for enhanced telomerase activity in Barrett's esophagus with dysplasia and adenocarcinoma.Merchant, Nipun B; Dutta, Sudhir K; Girotra, Mohit; Arora, Manish; Meltzer, Stephen JAsian Pacific journal of cancer prevention : APJCP2013679-8323621218
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Laser capture microdissection-reduced representation bisulfite sequencing (LCM-RRBS) maps changes in DNA methylation associated with gonadectomy-induced adrenocortical neoplasia in the mouse.Schillebeeckx, Maximiliaan; Schrade, Anja; Lobs, Ann-Kathrin; Pihlajoki, Marjut; Wilson, David B; Mitra, Robi DNucleic acids research2013 June11623589626
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Variants in the ATP-binding cassette transporter (ABCA7), apolipoprotein E ýý4,and the risk of late-onset Alzheimer disease in African Americans.Reitz, Christiane; Jun, Gyungah; Naj, Adam; Rajbhandary, Ruchita; Vardarajan, Badri Narayan; Wang, Li-San; Valladares, Otto; Lin, Chiao-Feng; Larson, Eric B; Graff-Radford, Neill R; Evans, Denis; De Jager, Philip L; Crane, Paul K; Buxbaum, Joseph D; MurreJAMA : the journal of the American Medical Association2013 Apr 101483-9223571587
Epigenetic deregulation of the anaplastic lymphoma kinase gene modulates mesenchymal characteristics of oral squamous cell carcinomas.Huang, Tze-Ta; Gonzales, Cara B; Gu, Fei; Hsu, Ya-Ting; Jadhav, Rohit R; Wang, Chiou-Miin; Redding, Spencer W; Tseng, Chih-En; Lee, Ching-Chih; Thompson, Ian M; Chen, Hau-Ren; Huang, Tim Hui-Ming; Kirma, Nameer BCarcinogenesis2013 Aug1717-2723568951
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Genome-wide map of quantified epigenetic changes during in vitro chondrogenic differentiation of primary human mesenchymal stem cells.Herlofsen, Sarah R; Bryne, Jan Christian; Hoiby, Torill; Wang, Li; Issner, Robbyn; Zhang, Xiaolan; Coyne, Michael J; Boyle, Patrick; Gu, Hongcang; Meza-Zepeda, Leonardo A; Collas, Philippe; Mikkelsen, Tarjei S; Brinchmann, Jan EBMC genomics201310523414147
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Identification of small molecule inhibitors of Jumonji AT-rich interactive domain 1B (JARID1B) histone demethylase by a sensitive high throughput screen.Sayegh, Joyce; Cao, Jian; Zou, Mike Ran; Morales, Alfonso; Blair, Lauren P; Norcia, Michael; Hoyer, Denton; Tackett, Alan J; Merkel, Jane S; Yan, QinThe Journal of biological chemistry2013 Mar 299408-1723408432
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A sequence variant in the phospholipase C epsilon C2 domain is associated with esophageal carcinoma and esophagitis.Wang, Li-Dong; Bi, Xiuli; Song, Xin; Pohl, Nicole M; Cheng, Yulan; Zhou, Yixing; Shears, Stephen; Ansong, Emmanuel; Xing, Mengtao; Wang, Shaomeng; Xu, Xiao-Chun; Huang, Peng; Xu, Liyan; Wang, Liang; Fan, Zongmin; Zhao, Xueke; Dong, Huali; Meltzer, StephenMolecular carcinogenesis2013 NovE80-623390063
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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 XBMC genomics20137023368971
Myogenin recruits the histone chaperone facilitates chromatin transcription (FACT) to promote nucleosome disassembly at muscle-specific genes.Lolis, Alexandra A; Londhe, Priya; Beggs, Benjamin C; Byrum, Stephanie D; Tackett, Alan J; Davie, Judith KThe Journal of biological chemistry2013 Mar 157676-8723364797
Histone acetyltransferase cofactor Trrap maintains self-renewal and restricts differentiation of embryonic stem cells.Sawan, Carla; Hernandez-Vargas, Hector; Murr, Rabih; Lopez, Fabrice; Vaissiere, Thomas; Ghantous, Akram Y; Cuenin, Cyrille; Imbert, Jean; Wang, Zhao-Qi; Ren, Bing; Herceg, ZdenkoStem cells (Dayton, Ohio).2013 May;979-9123362228
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Holocarboxylase synthetase interacts physically with euchromatic histone-lysine N-methyltransferase, linking histone biotinylation with methylation events.Li, Yong; Hassan, Yousef I; Moriyama, Hideaki; Zempleni, JanosThe Journal of nutritional biochemistry2013 Aug1446-5223337344
Hypomethylation of noncoding DNA regions and overexpression of the long noncoding RNA, AFAP1-AS1, in Barrett's esophagus and esophageal adenocarcinoma.Wu, Wenjing; Bhagat, Tushar D; Yang, Xue; Song, Jee Hoon; Cheng, Yulan; Agarwal, Rachana; Abraham, John M; Ibrahim, Sariat; Bartenstein, Matthias; Hussain, Zulfiqar; Suzuki, Masako; Yu, Yiting; Chen, Wei; Eng, Charis; Greally, John; Verma, Amit; Meltzer, Gastroenterology2013 May956-966.e423333711
Genome-wide chromatin state transitions associated with developmental and environmental cues.Zhu, Jiang; Adli, Mazhar; Zou, James Y; Verstappen, Griet; Coyne, Michael; Zhang, Xiaolan; Durham, Timothy; Miri, Mohammad; Deshpande, Vikram; De Jager, Philip L; Bennett, David A; Houmard, Joseph A; Muoio, Deborah M; Onder, Tamer T; Camahort, Ray; Cowan,Cell2013 Jan 31642-5423333102
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The simplest explanation: passive DNA demethylation in PGCs.Smith, Zachary D; Meissner, AlexanderThe EMBO journal2013 Feb 6318-2123299938
Differential processing of amyloid precursor protein in brain and in peripheral blood leukocytes.Delvaux, Elaine; Bentley, Karen; Stubbs, Victoria; Sabbagh, Marwan; Coleman, Paul DNeurobiology of aging2013 Jun1680-623298733
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Functional characterization of piggyBat from the bat Myotis lucifugus unveils an active mammalian DNA transposon.Mitra, Rupak; Li, Xianghong; Kapusta, Aurelie; Mayhew, David; Mitra, Robi D; Feschotte, Cedric; Craig, Nancy LProceedings of the National Academy of Sciences of the United States of America2013 Jan 2234-923248290
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Analyzing the cancer methylome through targeted bisulfite sequencing.Lee, Eun-Joon; Luo, Junfeng; Wilson, James M; Shi, HuidongCancer letters2012 Nov 2823200671
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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, OrMolecular cell2011 Nov 18609-2022099308
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Heat shock reduces stalled RNA polymerase II and nucleosome turnover genome-wide.Teves, Sheila S; Henikoff, StevenGenes & development2011 Nov 152387-9722085965
Epigenomic insights into common disease.Revill, Kate; Tycko, BenjaminGenome medicine.2011 Nov 23;22085423
Methylation of the CpG sites only on the sense strand of the APC gene is specific for hepatocellular carcinoma.Jain, Surbhi; Chang, Ting-Tsung; Hamilton, James P; Lin, Selena Y; Lin, Yih-Jyh; Evans, Alison A; Selaru, Florin M; Lin, Pin-Wen; Chen, Shun-Hua; Block, Timothy M; Hu, Chi-Tan; Song, Wei; Meltzer, Stephen J; Su, Ying-HsiuPloS one2011e2679922073196
Pioneer transcription factors: establishing competence for gene expression.Zaret, Kenneth S; Carroll, Jason SGenes & development2011 Nov 12227-4122056668
5-Hydroxymethylcytosine is strongly depleted in human cancers but its levels do not correlate with IDH1 mutations.Jin, Seung-Gi; Jiang, Yong; Qiu, Runxiang; Rauch, Tibor A; Wang, Yinsheng; Schackert, Gabriele; Krex, Dietmar; Lu, Qiang; Pfeifer, Gerd PCancer research2011 Dec 157360-522052461
High levels of nuclear heat-shock factor 1 (HSF1) are associated with poor prognosis in breast cancer.Santagata, Sandro; Hu, Rong; Lin, Nancy U; Mendillo, Marc L; Collins, Laura C; Hankinson, Susan E; Schnitt, Stuart J; Whitesell, Luke; Tamimi, Rulla M; Lindquist, Susan; Ince, Tan AProceedings of the National Academy of Sciences of the United States of America2011 Nov 818378-8322042860
Sensitive single-molecule protein quantification and protein complex detection in a microarray format.Tessler, Lee A; Mitra, Robi DProteomics2011 Dec4731-522038904
Effects of single-nucleotide polymorphisms in the human holocarboxylase synthetase gene on enzyme catalysis.Esaki, Shingo; Malkaram, Sridhar A; Zempleni, JanosEuropean journal of human genetics : EJHG2012 Apr428-3322027809
MicroRNA involvement in esophageal carcinogenesis.David, Stefan; Meltzer, Stephen JCurrent opinion in pharmacology2011 Dec612-621992930
Single DNA molecule patterning for high-throughput epigenetic mapping.Cerf, Aline; Cipriany, Benjamin R; Benitez, Jaime J; Craighead, Harold GAnalytical chemistry2011 Nov 18073-721981444
Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seq.Adli, Mazhar; Bernstein, Bradley ENature protocols.2011 Oct;1656-6821959244
Biotinylation is a natural, albeit rare, modification of human histones.Kuroishi, Toshinobu; Rios-Avila, Luisa; Pestinger, Valerie; Wijeratne, Subhashinee S K; Zempleni, JanosMolecular genetics and metabolism2011 Dec537-4521930408
Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification.Tan, Minjia; Luo, Hao; Lee, Sangkyu; Jin, Fulai; Yang, Jeong Soo; Montellier, Emilie; Buchou, Thierry; Cheng, Zhongyi; Rousseaux, Sophie; Rajagopal, Nisha; Lu, Zhike; Ye, Zhen; Zhu, Qin; Wysocka, Joanna; Ye, Yang; Khochbin, Saadi; Ren, Bing; Zhao, YingminCell2011 Sep 161016-2821925322
Transfer-printing of single DNA molecule arrays on graphene for high-resolution electron imaging and analysis.Cerf, Aline; Alava, Thomas; Barton, Robert A; Craighead, Harold GNano letters2011 Oct 124232-821919532
Identification of the putative intestinal stem cell marker doublecortin and CaM kinase-like-1 in Barrett's esophagus and esophageal adenocarcinoma.Vega, Kenneth J; May, Randal; Sureban, Sripathi M; Lightfoot, Stan A; Qu, Dongfeng; Reed, Alessandra; Weygant, Nathaniel; Ramanujam, Rama; Souza, Rhonda; Madhoun, Mohammad; Whorton, Joshua; Anant, Shrikant; Meltzer, Stephen J; Houchen, Courtney WJournal of gastroenterology and hepatology2012 Apr773-8021916995
Using ChIP-seq technology to generate high-resolution profiles of histone modifications.O'Geen, Henriette; Echipare, Lorigail; Farnham, Peggy JMethods in molecular biology (Clifton, N.J.)2011265-8621913086
The first identification of lysine malonylation substrates and its regulatory enzyme.Peng C, Lu Z, Xie Z, Cheng Z, Chen Y, Tan M, Luo H, Zhang Y, He W, Yang K, Zwaans BM, Tishkoff D, Ho L, Lombard D, He TC, Dai J, Verdin E, Ye Y, Zhao Y.Mol Cell Proteomics2011 DecM111.01265821908771
Disease-associated epigenetic changes in monozygotic twins discordant for schizophrenia and bipolar disorder.Dempster, Emma L; Pidsley, Ruth; Schalkwyk, Leonard C; Owens, Sheena; Georgiades, Anna; Kane, Fergus; Kalidindi, Sridevi; Picchioni, Marco; Kravariti, Eugenia; Toulopoulou, Timothea; Murray, Robin M; Mill, JonathanHuman molecular genetics2011 Dec 154786-9621908516
Quantitative analysis of histone exchange for transcriptionally active chromatin.Byrum, Stephanie D; Taverna, Sean D; Tackett, Alan JJournal of clinical bioinformatics2011 Jul 071721884633
A quantitative proteomic analysis of FFPE melanoma.Byrum, Stephanie; Avaritt, Nathan L; Mackintosh, Samuel G; Munkberg, Josie M; Badgwell, Brian D; Cheung, Wang L; Tackett, Alan JJournal of cutaneous pathology2011 Nov933-621883366
Dynamic chromatin states in human ES cells reveal potential regulatory sequences and genes involved in pluripotency.Hawkins, R David; Hon, Gary C; Yang, Chuhu; Antosiewicz-Bourget, Jessica E; Lee, Leonard K; Ngo, Que-Minh; Klugman, Sarit; Ching, Keith A; Edsall, Lee E; Ye, Zhen; Kuan, Samantha; Yu, Pengzhi; Liu, Hui; Zhang, Xinmin; Green, Roland D; Lobanenkov, Victor VCell research2011 Oct1393-40921876557
Neuronal activity modifies the DNA methylation landscape in the adult brain.Guo, Junjie U; Ma, Dengke K; Mo, Huan; Ball, Madeleine P; Jang, Mi-Hyeon; Bonaguidi, Michael A; Balazer, Jacob A; Eaves, Hugh L; Xie, Bin; Ford, Eric; Zhang, Kun; Ming, Guo-li; Gao, Yuan; Song, HongjunNature neuroscience.2011 Oct;1345-5121874013
Biotin requirements for DNA damage prevention.Zempleni J, Teixeira DC, Kuroishi T, Cordonier EL, Baier S.Mutat Res2012 May 158-6021871906
Biotin requirements for DNA damage prevention.Zempleni, Janos; Teixeira, Daniel Camara; Kuroishi, Toshinobu; Cordonier, Elizabeth L; Baier, ScottMutation research2012 May 158-6021871906
Small-molecule collection and high-throughput colorimetric assay to identify PARP1 inhibitors.Kotova, Elena; Pinnola, Aaron D; Tulin, Alexei VMethods in molecular biology (Clifton, N.J.)2011491-51621870279
PARP1 genomics: chromatin immunoprecipitation approach using anti-PARP1 antibody (ChIP and ChIP-seq).Lodhi, Niraj; Tulin, Alexei VMethods in molecular biology (Clifton, N.J.)2011191-20821870262
Cohesin: a critical chromatin organizer in mammalian gene regulation.Chien, Richard; Zeng, Weihua; Ball, Alexander R; Yokomori, KyokoBiochemistry and cell biology = Biochimie et biologie cellulaire2011 Oct445-5821851156
Long noncoding RNA, polycomb, and the ghosts haunting INK4b-ARF-INK4a expression.Aguilo F, Zhou MM, Walsh MJ.Cancer Res2011 Aug 155365-921828241
Perinephric and epididymal fat affect hepatic metabolism in rats.Ben-Shlomo, Shani; Einstein, Francine H; Zvibel, Isabel; Atias, Dikla; Shlomai, Amir; Halpern, Zamir; Barzilai, Nir; Fishman, SigalObesity (Silver Spring, Md.)2012 Jan151-621818154
Genome-wide analysis of interferon regulatory factor I binding in primary human monocytes.Shi, Lihua; Perin, Juan C; Leipzig, Jeremy; Zhang, Zhe; Sullivan, Kathleen EGene2011 Nov 121-821803131
Human holocarboxylase synthetase with a start site at methionine-58 is the predominant nuclear variant of this protein and has catalytic activity.Bao, Baolong; Wijeratne, Subhashinee S K; Rodriguez-Melendez, Rocio; Zempleni, JanosBiochemical and biophysical research communications2011 Aug 19115-2021802411
Selection of proteins with desired properties from natural proteome libraries using mRNA display.Cotten, Steven W; Zou, Jianwei; Valencia, C Alexander; Liu, RiheNature protocols2011 Aug1163-8221799486
Regulation of embryonic stem cell self-renewal and pluripotency by leukaemia inhibitory factor.Hirai, Hiroyuki; Karian, Peter; Kikyo, NobuakiThe Biochemical journal2011 Aug 1511-2321793804
Germline mutations in MSR1, ASCC1, and CTHRC1 in patients with Barrett esophagus and esophageal adenocarcinoma.Orloff, Mohammed; Peterson, Charissa; He, Xin; Ganapathi, Shireen; Heald, Brandie; Yang, Yi-ran; Bebek, Gurkan; Romigh, Todd; Song, Jee Hoon; Wu, Wenjing; David, Stefan; Cheng, Yulan; Meltzer, Stephen J; Eng, CharisJAMA : the journal of the American Medical Association2011 Jul 27410-921791690
Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing.Lee, Eun-Joon; Pei, Lirong; Srivastava, Gyan; Joshi, Trupti; Kushwaha, Garima; Choi, Jeong-Hyeon; Robertson, Keith D; Wang, Xinguo; Colbourne, John K; Zhang, Lu; Schroth, Gary P; Xu, Dong; Zhang, Kun; Shi, HuidongNucleic acids research2011 Octe12721785137
Cytosine methylation in miR-153 gene promoters increases the expression of holocarboxylase synthetase, thereby increasing the abundance of histone H4 biotinylation marks in HEK-293 human kidney cells.Bao, Baolong; Rodriguez-Melendez, Rocio; Zempleni, JanosThe Journal of nutritional biochemistry2012 Jun635-921764280
Transcriptome analysis of human diabetic kidney disease.Woroniecka, Karolina I; Park, Ae Seo Deok; Mohtat, Davoud; Thomas, David B; Pullman, James M; Susztak, KatalinDiabetes2011 Sep2354-6921752957
Epstein-Barr virus exploits intrinsic B-lymphocyte transcription programs to achieve immortal cell growth.Zhao, Bo; Zou, James; Wang, Hongfang; Johannsen, Eric; Peng, Chih-wen; Quackenbush, John; Mar, Jessica C; Morton, Cynthia Casson; Freedman, Matthew L; Blacklow, Stephen C; Aster, Jon C; Bernstein, Bradley E; Kieff, ElliottProceedings of the National Academy of Sciences of the United States of America2011 Sep 614902-721746931
A chemical probe selectively inhibits G9a and GLP methyltransferase activity in cells.Vedadi, Masoud; Barsyte-Lovejoy, Dalia; Liu, Feng; Rival-Gervier, Sylvie; Allali-Hassani, Abdellah; Labrie, Viviane; Wigle, Tim J; Dimaggio, Peter A; Wasney, Gregory A; Siarheyeva, Alena; Dong, Aiping; Tempel, Wolfram; Wang, Sun-Chong; Chen, Xin; Chau, IrNature chemical biology2011 Aug566-7421743462
Genome-wide analysis reveals conserved and divergent features of Notch1/RBPJ binding in human and murine T-lymphoblastic leukemia cells.Wang, Hongfang; Zou, James; Zhao, Bo; Johannsen, Eric; Ashworth, Todd; Wong, Hoifung; Pear, Warren S; Schug, Jonathan; Blacklow, Stephen C; Arnett, Kelly L; Bernstein, Bradley E; Kieff, Elliott; Aster, Jon CProceedings of the National Academy of Sciences of the United States of America2011 Sep 614908-1321737748
Radical acceleration of nuclear reprogramming by chromatin remodeling with the transactivation domain of MyoD.Hirai, Hiroyuki; Tani, Tetsuya; Katoku-Kikyo, Nobuko; Kellner, Steven; Karian, Peter; Firpo, Meri; Kikyo, NobuakiStem cells (Dayton, Ohio)2011 Sep1349-6121732495
Analysis of Histone Exchange during Chromatin Purification.Byrum, Stephanie; Mackintosh, Samuel G; Edmondson, Ricky D; Cheung, Wang L; Taverna, Sean D; Tackett, Alan JJournal of integrated OMICS2011 Feb 161-6521709819
Increased methylation variation in epigenetic domains across cancer types.Hansen, Kasper Daniel; Timp, Winston; Bravo, Hector Corrada; Sabunciyan, Sarven; Langmead, Benjamin; McDonald, Oliver G; Wen, Bo; Wu, Hao; Liu, Yun; Diep, Dinh; Briem, Eirikur; Zhang, Kun; Irizarry, Rafael A; Feinberg, Andrew PNature genetics2011 Aug768-7521706001
Advantages of mRNA display selections over other selection techniques for investigation of protein-protein interactions.Wang, Hui; Liu, RiheExpert review of proteomics2011 Jun335-4621679115
Characterization of single-nucleotide variation in Indian-origin rhesus macaques (Macaca mulatta).Fawcett, Gloria L; Raveendran, Muthuswamy; Deiros, David Rio; Chen, David; Yu, Fuli; Harris, Ronald Alan; Ren, Yanru; Muzny, Donna M; Reid, Jeffrey G; Wheeler, David A; Worley, Kimberly C; Shelton, Steven E; Kalin, Ned H; Milosavljevic, Aleksandar; Gibbs,BMC genomics201131121668978
A multi-tissue analysis identifies HLA complex group 9 gene methylation differences in bipolar disorder.Kaminsky, Z; Tochigi, M; Jia, P; Pal, M; Mill, J; Kwan, A; Ioshikhes, I; Vincent, J B; Kennedy, J L; Strauss, J; Pai, S; Wang, S-C; Petronis, AMolecular psychiatry2012 Jul728-4021647149
Opposing roles of FoxP1 and Nfat3 in transcriptional control of cardiomyocyte hypertrophy.Bai, Shoumei; Kerppola, Tom KMolecular and cellular biology2011 Jul3068-8021606195
Epigenetic control of gene expression in the lung.Yang, Ivana V; Schwartz, David AAmerican journal of respiratory and critical care medicine2011 May 151295-30121596832
Targeted gene correction of laminopathy-associated LMNA mutations in patient-specific iPSCs.Liu, Guang-Hui; Suzuki, Keiichiro; Qu, Jing; Sancho-Martinez, Ignacio; Yi, Fei; Li, Mo; Kumar, Sachin; Nivet, Emmanuel; Kim, Jessica; Soligalla, Rupa Devi; Dubova, Ilir; Goebl, April; Plongthongkum, Nongluk; Fung, Ho-Lim; Zhang, Kun; Loring, Jeanne F; LauCell stem cell2011 Jun 3688-9421596650
The role of holocarboxylase synthetase in genome stability is mediated partly by epigenomic synergies between methylation and biotinylation events.Zempleni, Janos; Li, Yong; Xue, Jing; Cordonier, Elizabeth LEpigenetics : official journal of the DNA Methylation Society2011 Jul892-421555910
Probing the role of HDACs and mechanisms of chromatin-mediated neuroplasticity.Haggarty, Stephen J; Tsai, Li-HueiNeurobiology of learning and memory2011 Jul41-5221545841
An epigenetic signature for monoallelic olfactory receptor expression.Magklara, Angeliki; Yen, Angela; Colquitt, Bradley M; Clowney, E Josephine; Allen, William; Markenscoff-Papadimitriou, Eirene; Evans, Zoe A; Kheradpour, Pouya; Mountoufaris, George; Carey, Catriona; Barnea, Gilad; Kellis, Manolis; Lomvardas, StavrosCell2011 May 13555-7021529909
Relationship between gene body DNA methylation and intragenic H3K9me3 and H3K36me3 chromatin marks.Hahn, Maria A; Wu, Xiwei; Li, Arthur X; Hahn, Torsten; Pfeifer, Gerd PPloS one2011e1884421526191
Structural basis of SETD6-mediated regulation of the NF-kB network via methyl-lysine signaling.Chang, Yanqi; Levy, Dan; Horton, John R; Peng, Junmin; Zhang, Xing; Gozani, Or; Cheng, XiaodongNucleic acids research2011 Aug6380-921515635
Genome-wide regulation of 5hmC, 5mC, and gene expression by Tet1 hydroxylase in mouse embryonic stem cells.Xu, Yufei; Wu, Feizhen; Tan, Li; Kong, Lingchun; Xiong, Lijun; Deng, Jie; Barbera, Andrew J; Zheng, Lijuan; Zhang, Haikuo; Huang, Stephen; Min, Jinrong; Nicholson, Thomas; Chen, Taiping; Xu, Guoliang; Shi, Yang; Zhang, Kun; Shi, Yujiang GenoMolecular cell2011 May 20451-6421514197
Emerging patterns of epigenomic variation.Milosavljevic, AleksandarTrends in genetics : TIG2011 Jun242-5021507501
Nuclear mobility and mitotic chromosome binding: similarities between pioneer transcription factor FoxA and linker histone H1.Zaret, K S; Caravaca, J M; Tulin, A; Sekiya, TCold Spring Harbor symposia on quantitative biology2010219-2621502411
The epigenetics of Alzheimer's disease--additional considerations.Rogers, Joseph; Mastroeni, Diego; Grover, Andrew; Delvaux, Elaine; Whiteside, Charisse; Coleman, Paul DNeurobiology of aging2011 Jul1196-721497949
Toward an integrated genetic and epigenetic approach to Alzheimer's disease.Mill, JonathanNeurobiology of aging2011 Jul1188-9121497948
Widespread hypomethylation occurs early and synergizes with gene amplification during esophageal carcinogenesis.Alvarez, Hector; Opalinska, Joanna; Zhou, Li; Sohal, Davendra; Fazzari, Melissa J; Yu, Yiting; Montagna, Christina; Montgomery, Elizabeth A; Canto, Marcia; Dunbar, Kerry B; Wang, Jean; Roa, Juan Carlos; Mo, Yongkai; Bhagat, Tushar; Ramesh, K H; CannizzaroPLoS genetics2011 Mare100135621483804
Epigenetic mechanisms in Alzheimer's disease.Mastroeni, Diego; Grover, Andrew; Delvaux, Elaine; Whiteside, Charisse; Coleman, Paul D; Rogers, JosephNeurobiology of aging2011 Jul1161-8021482442
Chemically defined conditions for human iPSC derivation and culture.Chen, Guokai; Gulbranson, Daniel R; Hou, Zhonggang; Bolin, Jennifer M; Ruotti, Victor; Probasco, Mitchell D; Smuga-Otto, Kimberly; Howden, Sara E; Diol, Nicole R; Propson, Nicholas E; Wagner, Ryan; Lee, Garrett O; Antosiewicz-Bourget, Jessica; Teng, JoyceNature methods2011 May424-921478862
Calling Cards enable multiplexed identification of the genomic targets of DNA-binding proteins.Wang, Haoyi; Mayhew, David; Chen, Xuhua; Johnston, Mark; Mitra, Robi DavidGenome research2011 May748-5521471402
Cohesin mediates chromatin interactions that regulate mammalian ýý-globin expression.Chien, Richard; Zeng, Weihua; Kawauchi, Shimako; Bender, M A; Santos, Rosaysela; Gregson, Heather C; Schmiesing, John A; Newkirk, Daniel A; Kong, Xiangduo; Ball Jr, Alexander R; Calof, Anne L; Lander, Arthur D; Groudine, Mark T; Yokomori, KyokoThe Journal of biological chemistry2011 May 2017870-821454523
Monocyte polarization: the relationship of genome-wide changes in H4 acetylation with polarization.Zhang, Z; Song, L; Maurer, K; Bagashev, A; Sullivan, K EGenes and immunity2011 Sep445-5621451557
Tracing the footsteps of glomerular insulin signaling in diabetic kidney disease.Chang, Gene-Yuan; Park, Ae Seo Deok; Susztak, KatalinKidney international2011 Apr802-421451535
Drosophila histone H2A variant (H2Av) controls poly(ADP-ribose) polymerase 1 (PARP1) activation in chromatin.Kotova, Elena; Lodhi, Niraj; Jarnik, Michael; Pinnola, Aaron D; Ji, Yingbiao; Tulin, Alexei VProceedings of the National Academy of Sciences of the United States of America2011 Apr 126205-1021444826
The histone methyltransferase SETDB1 is recurrently amplified in melanoma and accelerates its onset.Ceol CJ, Houvras Y, Jane-Valbuena J, Bilodeau S, Orlando DA, Battisti V, Fritsch L, Lin WM, Hollmann TJ, Ferré F, Bourque C, Burke CJ, Turner L, Uong A, Johnson LA, Beroukhim R, Mermel CH, Loda M, Ait-Si-Ali S, Garraway LA, Young RA, Zon LI.Nature2011 Mar 24513-721430779
Biophysical probes reveal a compromise" nature of the methyl-lysine binding pocket in L3MBTL1."Gao C, Herold JM, Kireev D, Wigle T, Norris JL, Frye S.J Am Chem Soc2011 Apr 135357-6221428286
The ATRX-ADD domain binds to H3 tail peptides and reads the combined methylation state of K4 and K9.Dhayalan A, Tamas R, Bock I, Tattermusch A, Dimitrova E, Kudithipudi S, Ragozin S, Jeltsch A.Hum Mol Genet2011 Jun 12195-20321421568
Small-molecule ligands of methyl-lysine binding proteins.Herold JM, Wigle TJ, Norris JL, Lam R, Korboukh VK, Gao C, Ingerman LA, Kireev DB, Senisterra G, Vedadi M, Tripathy A, Brown PJ, Arrowsmith CH, Jin J, Janzen WP, Frye SV.J Med Chem2011 Apr 142504-1121417280
Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling.Gu, Hongcang; Smith, Zachary D; Bock, Christoph; Boyle, Patrick; Gnirke, Andreas; Meissner, AlexanderNature protocols2011 Apr468-8121412275
Structure and functions of powerful transactivators: VP16, MyoD and FoxA.Hirai, Hiroyuki; Tani, Tetsuya; Kikyo, NobuakiThe International journal of developmental biology20101589-9621404180
REST interacts with Cbx proteins and regulates polycomb repressive complex 1 occupancy at RE1 elements.Ren, Xiaojun; Kerppola, Tom KMolecular and cellular biology2011 May2100-1021402785
Genomic mapping of 5-hydroxymethylcytosine in the human brain.Jin, Seung-Gi; Wu, Xiwei; Li, Arthur X; Pfeifer, Gerd PNucleic acids research2011 Jul5015-2421378125
Nucleosome fragility reveals novel functional states of chromatin and poises genes for activation.Xi, Yuanxin; Yao, Jianhui; Chen, Rui; Li, Wei; He, XiangweiGenome research2011 May718-2421363969
Development of an internet based system for modeling biotin metabolism using Bayesian networks.Zhou, Jinglei; Wang, Dong; Schlegel, Vicki; Zempleni, JanosComputer methods and programs in biomedicine2011 Nov254-921356565
Characterization of the contradictory chromatin signatures at the 3' exons of zinc finger genes.Blahnik, Kimberly R; Dou, Lei; Echipare, Lorigail; Iyengar, Sushma; O'Geen, Henriette; Sanchez, Erica; Zhao, Yongjun; Marra, Marco A; Hirst, Martin; Costello, Joseph F; Korf, Ian; Farnham, Peggy JPloS one2011e1712121347206
Recapitulation of premature ageing with iPSCs from Hutchinson-Gilford progeria syndrome.Liu, Guang-Hui; Barkho, Basam Z; Ruiz, Sergio; Diep, Dinh; Qu, Jing; Yang, Sheng-Lian; Panopoulos, Athanasia D; Suzuki, Keiichiro; Kurian, Leo; Walsh, Christopher; Thompson, James; Boue, Stephanie; Fung, Ho Lim; Sancho-Martinez, Ignacio; Zhang, Kun; YatesNature2011 Apr 14221-521346760
Diabetes in pregnancy: glycemia control guidelines and rationale.Karakash, Scarlett D; Einstein, Francine HCurrent opinion in endocrinology, diabetes, and obesity2011 Apr99-10321330917
Nanogel surface coatings for improved single-molecule imaging substrates.Tessler, Lee A; Donahoe, Casey D; Garcia, Daniel J; Jun, Young-Shin; Elbert, Donald L; Mitra, Robi DJournal of the Royal Society, Interface / the Royal Society2011 Oct 71400-821325313
Reprogramming of the paternal genome upon fertilization involves genome-wide oxidation of 5-methylcytosine.Iqbal, Khursheed; Jin, Seung-Gi; Pfeifer, Gerd P; Szabo, Piroska EProceedings of the National Academy of Sciences of the United States of America2011 Mar 13642-721321204
ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads.Miller, Christopher A; Hampton, Oliver; Coarfa, Cristian; Milosavljevic, AleksandarPloS one2011e1632721305028
Estrogen-mediated epigenetic repression of the imprinted gene cyclin-dependent kinase inhibitor 1C in breast cancer cells.Rodriguez, Benjamin A T; Weng, Yu-I; Liu, Ta-Ming; Zuo, Tao; Hsu, Pei-Yin; Lin, Ching-Hung; Cheng, Ann-Lii; Cui, Hengmi; Yan, Pearlly S; Huang, Tim H-MCarcinogenesis2011 Jun812-2121304052
Identification of holocarboxylase synthetase chromatin binding sites in human mammary cell lines using the DNA adenine methyltransferase identification technology.Singh, Dipika; Pannier, Angela K; Zempleni, JanosAnalytical biochemistry2011 Jun 155-921303649
The role of histone H4 biotinylation in the structure of nucleosomes.Filenko, Nina A; Kolar, Carol; West, John T; Smith, S Abbie; Hassan, Yousef I; Borgstahl, Gloria E O; Zempleni, Janos; Lyubchenko, Yuri LPloS one2011e1629921298003
Reference Maps of human ES and iPS cell variation enable high-throughput characterization of pluripotent cell lines.Bock, Christoph; Kiskinis, Evangelos; Verstappen, Griet; Gu, Hongcang; Boulting, Gabriella; Smith, Zachary D; Ziller, Michael; Croft, Gist F; Amoroso, Mackenzie W; Oakley, Derek H; Gnirke, Andreas; Eggan, Kevin; Meissner, AlexanderCell2011 Feb 4439-5221295703
Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells.Lister, Ryan; Pelizzola, Mattia; Kida, Yasuyuki S; Hawkins, R David; Nery, Joseph R; Hon, Gary; Antosiewicz-Bourget, Jessica; O'Malley, Ronan; Castanon, Rosa; Klugman, Sarit; Downes, Michael; Yu, Ruth; Stewart, Ron; Ren, Bing; Thomson, James A; Evans, RonNature2011 Mar 368-7321289626
Structure and mechanisms of lysine methylation recognition by the chromodomain in gene transcription.Yap KL, Zhou MM.Biochemistry2011 Mar 291966-8021288002
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-ClaireCancer research2011 Mar 152222-921285249
MassSQUIRM: An assay for quantitative measurement of lysine demethylase activity.Blair, Lauren P; Avaritt, Nathan L; Huang, Rong; Cole, Phillip A; Taverna, Sean D; Tackett, Alan JEpigenetics : official journal of the DNA Methylation Society2011 Apr490-921273814
Next generation sequencing based approaches to epigenomics.Hirst, Martin; Marra, Marco ABriefings in functional genomics2010 Dec455-6521266347
Identification of lysine 37 of histone H2B as a novel site of methylation.Gardner, Kathryn E; Zhou, Li; Parra, Michael A; Chen, Xian; Strahl, Brian DPloS one2011e1624421249157
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Epigenetic silencing mediated through activated PI3K/AKT signaling in breast cancer.Zuo, Tao; Liu, Ta-Ming; Lan, Xun; Weng, Yu-I; Shen, Rulong; Gu, Fei; Huang, Yi-Wen; Liyanarachchi, Sandya; Deatherage, Daniel E; Hsu, Pei-Yin; Taslim, Cenny; Ramaswamy, Bhuvaneswari; Shapiro, Charles L; Lin, Huey-Jen L; Cheng, Alfred S L; Jin, Victor X; HCancer research2011 Mar 11752-6221216892
A 96-well plate assay for high-throughput analysis of holocarboxylase synthetase activity.Rios-Avila, Luisa; Prince, Sara A; Wijeratne, Subhashinee S K; Zempleni, JanosClinica chimica acta; international journal of clinical chemistry2011 Apr 11735-921195703
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Epithelial Notch signaling regulates interstitial fibrosis development in the kidneys of mice and humans.Bielesz, Bernhard; Sirin, Yasemin; Si, Han; Niranjan, Thiruvur; Gruenwald, Antje; Ahn, Seonho; Kato, Hideki; Pullman, James; Gessler, Manfred; Haase, Volker H; Susztak, KatalinThe Journal of clinical investigation2010 Nov20978353
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The first global screening of protein substrates bearing protein-bound 3,4-Dihydroxyphenylalanine in Escherichia coli and human mitochondria.Lee, Sangkyu; Chen, Yue; Luo, Hao; Wu, Andrew A; Wilde, Michael; Schumacker, Paul T; Zhao, YingmingJournal of proteome research2010 Nov 55705-1420818827
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Holocarboxylase synthetase is a chromatin protein and interacts directly with histone H3 to mediate biotinylation of K9 and K18.Bao, Baolong; Pestinger, Valerie; Hassan, Yousef I; Borgstahl, Gloria E O; Kolar, Carol; Zempleni, JanosThe Journal of nutritional biochemistry2011 May470-520688500
SILAC-based quantitative proteomic approach to identify potential biomarkers from the esophageal squamous cell carcinoma secretome.Kashyap, Manoj Kumar; Harsha, H C; Renuse, Santosh; Pawar, Harsh; Sahasrabuddhe, Nandini A; Kim, Min-Sik; Marimuthu, Arivusudar; Keerthikumar, Shivakumar; Muthusamy, Babylakshmi; Kandasamy, Kumaran; Subbannayya, Yashwanth; Prasad, Thottethodi Subrahmanya Cancer biology & therapy2010 Oct 15796-81020686364
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Actin-myosin contractility is responsible for the reduced viability of dissociated human embryonic stem cells.Chen, Guokai; Hou, Zhonggang; Gulbranson, Daniel R; Thomson, James ACell stem cell2010 Aug 6240-820682449
Epigenetic influences of low-dose bisphenol A in primary human breast epithelial cells.Weng, Yu-I; Hsu, Pei-Yin; Liyanarachchi, Sandya; Liu, Joseph; Deatherage, Daniel E; Huang, Yi-Wen; Zuo, Tao; Rodriguez, Benjamin; Lin, Ching-Hung; Cheng, Ann-Lii; Huang, Tim H-MToxicology and applied pharmacology2010 Oct 15111-2120678512
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Protein lysine methyltransferase G9a inhibitors: design, synthesis, and structure activity relationships of 2,4-diamino-7-aminoalkoxy-quinazolines.Liu F, Chen X, Allali-Hassani A, Quinn AM, Wigle TJ, Wasney GA, Dong A, Senisterra G, Chau I, Siarheyeva A, Norris JL, Kireev DB, Jadhav A, Herold JM, Janzen WP, Arrowsmith CH, Frye SV, Brown PJ, Simeonov A, Vedadi M, Jin J.J Med Chem2010 Aug 125844-5720614940
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The polypeptide Syn67 interacts physically with human holocarboxylase synthetase, but is not a target for biotinylation.Hassan, Yousef I; Moriyama, Hideaki; Zempleni, JanosArchives of biochemistry and biophysics2010 Mar 135-4120026029
Parylene peel-off arrays to probe the role of cell-cell interactions in tumour angiogenesis.Tan CP, Seo BR, Brooks DJ, Chandler EM, Craighead HG, Fischbach C.Integr Biol (Camb)2009 Oct587-9420023775
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Epigenome microarray platform for proteome-wide dissection of chromatin-signaling networks.Bua, Dennis J; Kuo, Alex J; Cheung, Peggie; Liu, Chih Long; Migliori, Valentina; Espejo, Alexsandra; Casadio, Fabio; Bassi, Christian; Amati, Bruno; Bedford, Mark T; Guccione, Ernesto; Gozani, OrPloS one2009e678919956676
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A homogeneous method for investigation of methylation-dependent protein-protein interactions in epigenetics.Quinn, Amy M; Bedford, Mark T; Espejo, Alexsandra; Spannhoff, Astrid; Austin, Christopher P; Oppermann, Udo; Simeonov, AntonNucleic acids research2010 Jane1119897549
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Biotin tagging coupled with amino acid-coded mass tagging for efficient and precise screening of interaction proteome in mammalian cells.He, Yu-Fei; Bao, Hui-Min; Xiao, Xiao-Feng; Zuo, Shuai; Du, Ru-Yun; Tang, Si-Wei; Yang, Peng-Yuan; Chen, XianProteomics2009 Dec5414-2419834888
Human DNA methylomes at base resolution show widespread epigenomic differences.Lister, Ryan; Pelizzola, Mattia; Dowen, Robert H; Hawkins, R David; Hon, Gary; Tonti-Filippini, Julian; Nery, Joseph R; Lee, Leonard; Ye, Zhen; Ngo, Que-Minh; Edsall, Lee; Antosiewicz-Bourget, Jessica; Stewart, Ron; Ruotti, Victor; Millar, A Harvey; ThomsNature2009 Nov 19315-2219829295
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Epithelial-mesenchymal transition and podocyte loss in diabetic kidney disease.Reidy, Kimberly; Susztak, KatalinAmerican journal of kidney diseases : the official journal of the National Kidney Foundation2009 Oct590-319781451
HRTBLDb: an informative data resource for hormone receptors target binding loci.Kennedy, Brian A; Gao, Wenqing; Huang, Tim H-M; Jin, Victor XNucleic acids research2010 JanD676-8119773424
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Epigenetic differences in cortical neurons from a pair of monozygotic twins discordant for Alzheimer's disease.Mastroeni, Diego; McKee, Ann; Grover, Andrew; Rogers, Joseph; Coleman, Paul DPloS one2009e661719672297
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Structural basis for exquisite specificity of affinity clamps, synthetic binding proteins generated through directed domain-interface evolution.Huang, Jin; Makabe, Koki; Biancalana, Matthew; Koide, Akiko; Koide, ShoheiJournal of molecular biology2009 Oct 91221-3119646997
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High-throughput bisulfite sequencing in mammalian genomes.Smith, Zachary D; Gu, Hongcang; Bock, Christoph; Gnirke, Andreas; Meissner, AlexanderMethods (San Diego, Calif.)2009 Jul226-3219442738
A multicenter, double-blinded validation study of methylation biomarkers for progression prediction in Barrett's esophagus.Jin, Zhe; Cheng, Yulan; Gu, Wen; Zheng, Yingye; Sato, Fumiaki; Mori, Yuriko; Olaru, Alexandru V; Paun, Bogdan C; Yang, Jian; Kan, Takatsugu; Ito, Tetsuo; Hamilton, James P; Selaru, Florin M; Agarwal, Rachana; David, Stefan; Abraham, John M; Wolfsen, HerbeCancer research2009 May 154112-519435894
The ankyrin repeat domain of Huntingtin interacting protein 14 contains a surface aromatic cage, a potential site for methyl-lysine binding.Gao, Tiyu; Collins, Robert E; Horton, John R; Zhang, Xing; Zhang, Rongguang; Dhayalan, Arunkumar; Tamas, Raluca; Jeltsch, Albert; Cheng, XiaodongProteins2009 Aug 15772-719434754
Epigenetic alterations in the breast: Implications for breast cancer detection, prognosis and treatment.Dworkin, Amy M; Huang, Tim H-M; Toland, Amanda EwartSeminars in cancer biology2009 Jun165-7119429480
K12-biotinylated histone H4 is enriched in telomeric repeats from human lung IMR-90 fibroblasts.Wijeratne, Subhashinee S K; Camporeale, Gabriela; Zempleni, JanosThe Journal of nutritional biochemistry2010 Apr310-619369050
Mascot-derived false positive peptide identifications revealed by manual analysis of tandem mass spectra.Chen, Yue; Zhang, Junmei; Xing, Gang; Zhao, YingmingJournal of proteome research2009 Jun3141-719368407
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; ZNature biotechnology2009 Apr353-6019330000
The importance of being tyrosine: lessons in molecular recognition from minimalist synthetic binding proteins.Koide, Shohei; Sidhu, Sachdev SACS chemical biology2009 May 15325-3419298050
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, KatalinPloS one.2009;19277126
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-MBiochimica et biophysica acta2009 Sep920-419162126
Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond.Lister, Ryan; Gregory, Brian D; Ecker, Joseph RCurrent opinion in plant biology2009 Apr107-1819157957
Epigenetic changes in Alzheimer's disease: decrements in DNA methylation.Mastroeni, Diego; Grover, Andrew; Delvaux, Elaine; Whiteside, Charisse; Coleman, Paul D; Rogers, JosephNeurobiology of aging2010 Dec2025-3719117641
Identification and verification of lysine propionylation and butyrylation in yeast core histones using PTMap software.Zhang, Kai; Chen, Yue; Zhang, Zhihong; Zhao, YingmingJournal of proteome research2009 Feb900-619113941
Smad1 as a biomarker for diabetic nephropathy.Kato, Hideki; Si, Han; Hostetter, Thomas; Susztak, KatalinDiabetes.2008 Jun;1459-6018511448
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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, KatalinJournal of the American Society of Nephrology : JASN.2008 May;18443355
Epigenomic profiling reveals DNA-methylation changes associated with major psychosis.Mill, Jonathan; Tang, Thomas; Kaminsky, Zachary; Khare, Tarang; Yazdanpanah, Simin; Bouchard, Luigi; Jia, Peixin; Assadzadeh, Abbas; Flanagan, James; Schumacher, Axel; Wang, Sun-Chong; Petronis, ArturasAmerican journal of human genetics2008 Mar696-71118319075
Changes in the distributions and dynamics of polycomb repressive complexes during embryonic stem cell differentiation.Ren, Xiaojun; Vincenz, Claudius; Kerppola, Tom KMolecular and cellular biology2008 May18316406
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, RichardNeurogenetics.2008 Feb;17940814
Lysine propionylation and butyrylation are novel post-translational modifications in histones.Chen, Yue; Sprung, Robert; Tang, Yi; Ball, Haydn; Sangras, Bhavani; Kim, Sung Chan; Falck, John R; Peng, Junmin; Gu, Wei; Zhao, YingmingMolecular & cellular proteomics : MCP2007 May812-917267393
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 VAmerican journal of public health2005 Feb15671470
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 VAmerican journal of public health.2003 Oct;14534218