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The search results on this publication page are automated on a monthly schedule based on acknowledgement of NIH Common Fund award numbers and intramural awards. Therefore, this list is not an exhaustive or error-free account of the program’s publications.
Epigenomics (1260)
| Publication Title | Authors | Journal | Publication Date | Page No | PubMedID |
|---|---|---|---|---|---|
| Increased levels of endogenous retroviruses trigger fibroinflammation and play a role in kidney disease development. | Dhillon, Poonam; Mulholland, Kelly Ann; Hu, Hailong; Park, Jihwan; Sheng, Xin; Abedini, Amin; Liu, Hongbo; Vassalotti, Allison; Wu, Junnan; Susztak, Katalin | Nature communications | 2023 Feb 02 | 559 | 36732547 |
| Exploring genes for immunoglobulin A nephropathy: a summary data-based mendelian randomization and FUMA analysis. | Zhang, Qian; Zhang, Kang; Zhu, Yining; Yuan, Guangwei; Yang, Jingyun; Zhang, Minmin | BMC medical genomics | 2023 Jan 29 | 16 | 36709307 |
| Neuroimmune transcriptome changes in patient brains of psychiatric and neurological disorders. | Chen, Yu; Dai, Jiacheng; Tang, Longfei; Mikhailova, Tatiana; Liang, Qiuman; Li, Miao; Zhou, Jiaqi; Kopp, Richard F; Weickert, Cynthia; Chen, Chao; Liu, Chunyu | Molecular psychiatry | 2022 Nov 24 | 36424395 | |
| Differential Gene Expression and DNA Methylation in the Risk of Depression in LOAD Patients. | Upadhya, Suraj; Gingerich, Daniel; Lutz, Michael William; Chiba-Falek, Ornit | Biomolecules | 2022 Nov 12 | 36421693 | |
| Associations between accelerated parental biologic age, autism spectrum disorder, social traits, and developmental and cognitive outcomes in their children. | Song, Ashley Y; Bakulski, Kelly; Feinberg, Jason I; Newschaffer, Craig; Croen, Lisa A; Hertz-Picciotto, Irva; Schmidt, Rebecca J; Farzadegan, Homayoon; Lyall, Kristen; Fallin, M Daniele; Volk, Heather E; Ladd-Acosta, Christine | Autism research : official journal of the International Society for Autism Research | 2022 Dec | 36189953 | |
| Integrative Co-methylation Network Analysis Identifies Novel DNA Methylation Signatures and Their Target Genes in Alzheimer's Disease. | Kim, Jun Pyo; Kim, Bo-Hyun; Bice, Paula J; Seo, Sang Won; Bennett, David A; Saykin, Andrew J; Nho, Kwangsik | Biological psychiatry | 2022 Jun 24 | 36150909 | |
| Risperidone-induced changes in DNA methylation in peripheral blood from first-episode schizophrenia patients parallel changes in neuroimaging and cognitive phenotypes. | Hu, Maolin; Xia, Yan; Zong, Xiaofen; Sweeney, John A; Bishop, Jeffrey R; Liao, Yanhui; Giase, Gina; Li, Bingshan; Rubin, Leah H; Wang, Yunpeng; Li, Zongchang; He, Ying; Chen, Xiaogang; Liu, Chunyu; Chen, Chao; Tang, Jinsong | Psychiatry research | 2022 Nov | 36075150 | |
| Genome-wide meta-analyses reveal novel loci for verbal short-term memory and learning. | Lahti, Jari; Tuominen, Samuli; Yang, Qiong; Pergola, Giulio; Ahmad, Shahzad; Amin, Najaf; Armstrong, Nicola J; Beiser, Alexa; Bey, Katharina; Bis, Joshua C; Boerwinkle, Eric; Bressler, Jan; Campbell, Archie; Campbell, Harry; Chen, Qiang; Corley, Janie; Cox, Simon R; Davies, Gail; De Jager, Philip L; Derks, Eske M; Faul, Jessica D; Fitzpatrick, Annette L; Fohner, Alison E; Ford, Ian; Fornage, Myriam; Gerring, Zachary; Grabe, Hans J; Grodstein, Francine; Gudnason, Vilmundur; Simonsick, Eleanor; Holliday, Elizabeth G; Joshi, Peter K; Kajantie, Eero; Kaprio, Jaakko; Karell, Pauliina; Kleineidam, Luca; Knol, Maria J; Kochan, Nicole A; Kwok, John B; Leber, Markus; Lam, Max; Lee, Teresa; Li, Shuo; Loukola, Anu; Luck, Tobias; Marioni, Riccardo E; Mather, Karen A; Medland, Sarah; Mirza, Saira S; Nalls, Mike A; Nho, Kwangsik; O'Donnell, Adrienne; Oldmeadow, Christopher; Painter, Jodie; Pattie, Alison; Reppermund, Simone; Risacher, Shannon L; Rose, Richard J; Sadashivaiah, Vijay; Scholz, Markus; Satizabal, Claudia L; Schofield, Peter W; Schraut, Katharina E; Scott, Rodney J; Simino, Jeannette; Smith, Albert V; Smith, Jennifer A; Stott, David J; Surakka, Ida; Teumer, Alexander; Thalamuthu, Anbupalam; Trompet, Stella; Turner, Stephen T; van der Lee, Sven J; Villringer, Arno; Völker, Uwe; Wilson, Robert S; Wittfeld, Katharina; Vuoksimaa, Eero; Xia, Rui; Yaffe, Kristine; Yu, Lei; Zare, Habil; Zhao, Wei; Ames, David; Attia, John; Bennett, David A; Brodaty, Henry; Chasman, Daniel I; Goldman, Aaron L; Hayward, Caroline; Ikram, M Arfan; Jukema, J Wouter; Kardia, Sharon L R; Lencz, Todd; Loeffler, Markus; Mattay, Venkata S; Palotie, Aarno; Psaty, Bruce M; Ramirez, Alfredo; Ridker, Paul M; Riedel-Heller, Steffi G; Sachdev, Perminder S; Saykin, Andrew J; Scherer, Martin; Schofield, Peter R; Sidney, Stephen; Starr, John M; Trollor, Julian; Ulrich, William; Wagner, Michael; Weir, David R; Wilson, James F; Wright, Margaret J; Weinberger, Daniel R; Debette, Stephanie; Eriksson, Johan G; Mosley Jr, Thomas H; Launer, Lenore J; van Duijn, Cornelia M; Deary, Ian J; Seshadri, Sudha; Räikkönen, Katri | Molecular psychiatry | 2022 Nov | 35974141 | |
| RNASE6 is a novel modifier of APOE-ε4 effects on cognition. | Seto, Mabel; Weiner, Rebecca L; Dumitrescu, Logan; Mahoney, Emily R; Hansen, Shania L; Janve, Vaibhav; Khan, Omair A; Liu, Dandan; Wang, Yanling; Menon, Vilas; De Jager, Philip L; Schneider, Julie A; Bennett, David A; Gifford, Katherine A; Jefferson, Angela L; Hohman, Timothy J | Neurobiology of aging | 2022 10 | 35896049 | |
| Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stability. | de Mendoza, Alex; Nguyen, Trung Viet; Ford, Ethan; Poppe, Daniel; Buckberry, Sam; Pflueger, Jahnvi; Grimmer, Matthew R; Stolzenburg, Sabine; Bogdanovic, Ozren; Oshlack, Alicia; Farnham, Peggy J; Blancafort, Pilar; Lister, Ryan | Genome biology | 2022 07 26 | 35883107 | |
| [11C]Martinostat PET analysis reveals reduced HDAC I availability in Alzheimer's disease. | Pascoal, Tharick A; Chamoun, Mira; Lax, Elad; Wey, Hsiao-Ying; Shin, Monica; Ng, Kok Pin; Kang, Min Su; Mathotaarachchi, Sulantha; Benedet, Andrea L; Therriault, Joseph; Lussier, Firoza Z; Schroeder, Frederick A; DuBois, Jonathan M; Hightower, Baileigh G; Gilbert, Tonya M; Zürcher, Nicole R; Wang, Changning; Hopewell, Robert; Chakravarty, Mallar; Savard, Melissa; Thomas, Emilie; Mohaddes, Sara; Farzin, Sarah; Salaciak, Alyssa; Tullo, Stephanie; Cuello, A Claudio; Soucy, Jean-Paul; Massarweh, Gassan; Hwang, Heungsun; Kobayashi, Eliane; Hyman, Bradley T; Dickerson, Bradford C; Guiot, Marie-Christine; Szyf, Moshe; Gauthier, Serge; Hooker, Jacob M; Rosa-Neto, Pedro | Nature communications | 2022 07 19 | 35853847 | |
| Epigenetic and Transcriptomic Programming of HSC Quiescence Signaling in Large for Gestational Age Neonates. | Pelletier, Alexandre; Carrier, Arnaud; Zhao, Yongmei; Canouil, Mickaël; Derhourhi, Mehdi; Durand, Emmanuelle; Berberian-Ferrato, Lionel; Greally, John; Hughes, Francine; Froguel, Philippe; Bonnefond, Amélie; Delahaye, Fabien | International journal of molecular sciences | 2022 Jun 30 | 35806330 | |
| Keap1 moderates the transcription of virus induced genes through G9a-GLP and NFκB p50 recruitment. | Burns, Veronica Elizabeth; Kerppola, Tom Klaus | Immunology | 2022 Sep | 35751391 | |
| Epigenomic and transcriptomic analyses define core cell types, genes and targetable mechanisms for kidney disease. | Liu, Hongbo; Doke, Tomohito; Guo, Dong; Sheng, Xin; Ma, Ziyuan; Park, Joseph; Vy, Ha My T; Nadkarni, Girish N; Abedini, Amin; Miao, Zhen; Palmer, Matthew; Voight, Benjamin F; Li, Hongzhe; Brown, Christopher D; Ritchie, Marylyn D; Shu, Yan; Susztak, Katalin | Nature genetics | 2022 07 | 35710981 | |
| Developmental Pathways Are Epigenetically Reprogrammed during Lung Cancer Brain Metastasis. | Karlow, Jennifer A; Devarakonda, Siddhartha; Xing, Xiaoyun; Jang, Hyo Sik; Govindan, Ramaswamy; Watson, Mark; Wang, Ting | Cancer research | 2022 Aug 03 | 35706127 | |
| Single-cell analysis identifies the interaction of altered renal tubules with basophils orchestrating kidney fibrosis. | Doke, Tomohito; Abedini, Amin; Aldridge, Daniel L; Yang, Ya-Wen; Park, Jihwan; Hernandez, Christina M; Balzer, Michael S; Shrestra, Rojesh; Coppock, Gaia; Rico, Juan M Inclan; Han, Seung Yub; Kim, Junhyong; Xin, Sheng; Piliponsky, Adrian M; Angelozzi, Marco; Lefebvre, Veronique; Siracusa, Mark C; Hunter, Christopher A; Susztak, Katalin | Nature immunology | 2022 May 12 | 35552540 | |
| The multifaceted role of kidney tubule mitochondrial dysfunction in kidney disease development. | Doke, Tomohito; Susztak, Katalin | Trends in cell biology | 2022 Oct | 35473814 | |
| Antisense oligonucleotides ameliorate kidney dysfunction in podocyte-specific APOL1 risk variant mice. | Yang, Ya-Wen; Poudel, Bibek; Frederick, Julia; Dhillon, Poonam; Shrestha, Rojesh; Ma, Ziyuan; Wu, Junnan; Okamoto, Koji; Kopp, Jeffrey B; Booten, Sheri L; Gattis, Danielle; Watt, Andrew T; Palmer, Matthew; Aghajan, Mariam; Susztak, Katalin | Molecular therapy : the journal of the American Society of Gene Therapy | 2022 Jul 06 | 35450819 | |
| Distinct developmental phenotypes result from mutation of Set8/KMT5A and histone H4 lysine 20 in Drosophila melanogaster. | Crain, Aaron T; Klusza, Stephen; Armstrong, Robin L; Santa Rosa, Priscila; Temple, Brenda R S; Strahl, Brian D; McKay, Daniel J; Matera, A Gregory; Duronio, Robert J | Genetics | 2022 May 31 | 35404465 | |
| New insights into the genetic etiology of Alzheimer's disease and related dementias. | Bellenguez, Céline; Küçükali, Fahri; Jansen, Iris E; Kleineidam, Luca; Moreno-Grau, Sonia; Amin, Najaf; Naj, Adam C; Campos-Martin, Rafael; Grenier-Boley, Benjamin; Andrade, Victor; Holmans, Peter A; Boland, Anne; Damotte, Vincent; van der Lee, Sven J; Costa, Marcos R; Kuulasmaa, Teemu; Yang, Qiong; de Rojas, Itziar; Bis, Joshua C; Yaqub, Amber; Prokic, Ivana; Chapuis, Julien; Ahmad, Shahzad; Giedraitis, Vilmantas; Aarsland, Dag; Garcia-Gonzalez, Pablo; Abdelnour, Carla; Alarcón-Martín, Emilio; Alcolea, Daniel; Alegret, Montserrat; Alvarez, Ignacio; Álvarez, Victoria; Armstrong, Nicola J; Tsolaki, Anthoula; Antúnez, Carmen; Appollonio, Ildebrando; Arcaro, Marina; Archetti, Silvana; Pastor, Alfonso Arias; Arosio, Beatrice; Athanasiu, Lavinia; Bailly, Henri; Banaj, Nerisa; Baquero, Miquel; Barral, Sandra; Beiser, Alexa; Pastor, Ana Belén; Below, Jennifer E; Benchek, Penelope; Benussi, Luisa; Berr, Claudine; Besse, Céline; Bessi, Valentina; Binetti, Giuliano; Bizarro, Alessandra; Blesa, Rafael; Boada, Mercè; Boerwinkle, Eric; Borroni, Barbara; Boschi, Silvia; Bossù, Paola; Bråthen, Geir; Bressler, Jan; Bresner, Catherine; Brodaty, Henry; Brookes, Keeley J; Brusco, Luis Ignacio; Buiza-Rueda, Dolores; Bûrger, Katharina; Burholt, Vanessa; Bush, William S; Calero, Miguel; Cantwell, Laura B; Chene, Geneviève; Chung, Jaeyoon; Cuccaro, Michael L; Carracedo, Ángel; Cecchetti, Roberta; Cervera-Carles, Laura; Charbonnier, Camille; Chen, Hung-Hsin; Chillotti, Caterina; Ciccone, Simona; Claassen, Jurgen A H R; Clark, Christopher; Conti, Elisa; Corma-Gómez, Anaïs; Costantini, Emanuele; Custodero, Carlo; Daian, Delphine; Dalmasso, Maria Carolina; Daniele, Antonio; Dardiotis, Efthimios; Dartigues, Jean-François; de Deyn, Peter Paul; de Paiva Lopes, Katia; de Witte, Lot D; Debette, Stéphanie; Deckert, Jürgen; Del Ser, Teodoro; Denning, Nicola; DeStefano, Anita; Dichgans, Martin; Diehl-Schmid, Janine; Diez-Fairen, Mónica; Rossi, Paolo Dionigi; Djurovic, Srdjan; Duron, Emmanuelle; Düzel, Emrah; Dufouil, Carole; Eiriksdottir, Gudny; Engelborghs, Sebastiaan; Escott-Price, Valentina; Espinosa, Ana; Ewers, Michael; Faber, Kelley M; Fabrizio, Tagliavini; Nielsen, Sune Fallgaard; Fardo, David W; Farotti, Lucia; Fenoglio, Chiara; Fernández-Fuertes, Marta; Ferrari, Raffaele; Ferreira, Catarina B; Ferri, Evelyn; Fin, Bertrand; Fischer, Peter; Fladby, Tormod; Fließbach, Klaus; Fongang, Bernard; Fornage, Myriam; Fortea, Juan; Foroud, Tatiana M; Fostinelli, Silvia; Fox, Nick C; Franco-Macías, Emlio; Bullido, María J; Frank-García, Ana; Froelich, Lutz; Fulton-Howard, Brian; Galimberti, Daniela; García-Alberca, Jose Maria; García-González, Pablo; Garcia-Madrona, Sebastian; Garcia-Ribas, Guillermo; Ghidoni, Roberta; Giegling, Ina; Giorgio, Giaccone; Goate, Alison M; Goldhardt, Oliver; Gomez-Fonseca, Duber; González-Pérez, Antonio; Graff, Caroline; Grande, Giulia; Green, Emma; Grimmer, Timo; Grünblatt, Edna; Grunin, Michelle; Gudnason, Vilmundur; Guetta-Baranes, Tamar; Haapasalo, Annakaisa; Hadjigeorgiou, Georgios; Haines, Jonathan L; Hamilton-Nelson, Kara L; Hampel, Harald; Hanon, Olivier; Hardy, John; Hartmann, Annette M; Hausner, Lucrezia; Harwood, Janet; Heilmann-Heimbach, Stefanie; Helisalmi, Seppo; Heneka, Michael T; Hernández, Isabel; Herrmann, Martin J; Hoffmann, Per; Holmes, Clive; Holstege, Henne; Vilas, Raquel Huerto; Hulsman, Marc; Humphrey, Jack; Biessels, Geert Jan; Jian, Xueqiu; Johansson, Charlotte; Jun, Gyungah R; Kastumata, Yuriko; Kauwe, John; Kehoe, Patrick G; Kilander, Lena; Ståhlbom, Anne Kinhult; Kivipelto, Miia; Koivisto, Anne; Kornhuber, Johannes (see original citation for additional authors) | Nature genetics | 2022 04 | 35379992 | |
| Local connectivity and synaptic dynamics in mouse and human neocortex. | Campagnola, Luke; Seeman, Stephanie C; Chartrand, Thomas; Kim, Lisa; Hoggarth, Alex; Gamlin, Clare; Ito, Shinya; Trinh, Jessica; Davoudian, Pasha; Radaelli, Cristina; Kim, Mean-Hwan; Hage, Travis; Braun, Thomas; Alfiler, Lauren; Andrade, Julia; Bohn, Phillip; Dalley, Rachel; Henry, Alex; Kebede, Sara; Alice, Mukora; Sandman, David; Williams, Grace; Larsen, Rachael; Teeter, Corinne; Daigle, Tanya L; Berry, Kyla; Dotson, Nadia; Enstrom, Rachel; Gorham, Melissa; Hupp, Madie; Dingman Lee, Samuel; Ngo, Kiet; Nicovich, Philip R; Potekhina, Lydia; Ransford, Shea; Gary, Amanda; Goldy, Jeff; McMillen, Delissa; Pham, Trangthanh; Tieu, Michael; Siverts, La'Akea; Walker, Miranda; Farrell, Colin; Schroedter, Martin; Slaughterbeck, Cliff; Cobb, Charles; Ellenbogen, Richard; Gwinn, Ryder P; Keene, C Dirk; Ko, Andrew L; Ojemann, Jeffrey G; Silbergeld, Daniel L; Carey, Daniel; Casper, Tamara; Crichton, Kirsten; Clark, Michael; Dee, Nick; Ellingwood, Lauren; Gloe, Jessica; Kroll, Matthew; Sulc, Josef; Tung, Herman; Wadhwani, Katherine; Brouner, Krissy; Egdorf, Tom; Maxwell, Michelle; McGraw, Medea; Pom, Christina Alice; Ruiz, Augustin; Bomben, Jasmine; Feng, David; Hejazinia, Nika; Shi, Shu; Szafer, Aaron; Wakeman, Wayne; Phillips, John; Bernard, Amy; Esposito, Luke; D'Orazi, Florence D; Sunkin, Susan; Smith, Kimberly; Tasic, Bosiljka; Arkhipov, Anton; Sorensen, Staci; Lein, Ed; Koch, Christof; Murphy, Gabe; Zeng, Hongkui; Jarsky, Tim | Science (New York, N.Y.) | 2022 03 11 | 35271334 | |
| Multi-transcriptomic analysis points to early organelle dysfunction in human astrocytes in Alzheimer's disease. | Galea, Elena; Weinstock, Laura D; Larramona-Arcas, Raquel; Pybus, Alyssa F; Giménez-Llort, Lydia; Escartin, Carole; Wood, Levi B | Neurobiology of disease | 2022 05 | 35143967 | |
| Brain microRNAs are associated with variation in cognitive trajectory in advanced age. | Wingo, Aliza P; Wang, Mengli; Liu, Jiaqi; Breen, Michael S; Yang, Hyun-Sik; Tang, Beisha; Schneider, Julie A; Seyfried, Nicholas T; Lah, James J; Levey, Allan I; Bennett, David A; Jin, Peng; De Jager, Philip L; Wingo, Thomas S | Translational psychiatry | 2022 Feb 01 | 35105862 | |
| Monocyte miRNAs Are Associated With Type 2 Diabetes. | Parker, Daniel C; Wan, Ma; Lohman, Kurt; Hou, Li; Nguyen, Anh Tram; Ding, Jingzhong; Bertoni, Alain; Shea, Steve; Burke, Gregory L; Jacobs, David R; Post, Wendy; Corcoran, David; Hoeschele, Ina; Parks, John S; Liu, Yongmei | Diabetes | 2022 Apr 01 | 35073575 | |
| Integrated Genomic, Transcriptomic and Proteomic Analysis for Identifying Markers of Alzheimer's Disease. | Madrid, Laura; Labrador, Sandra C; González-Pérez, Antonio; Sáez, María E; The Alzheimer's Disease Neuroimaging Initiative Adni | Diagnostics (Basel, Switzerland) | 2021 Dec 08 | 34943540 | |
| AtheroSpectrum Reveals Novel Macrophage Foam Cell Gene Signatures Associated With Atherosclerotic Cardiovascular Disease Risk. | Li, Chuan; Qu, Lili; Matz, Alyssa J; Murphy, Patrick A; Liu, Yongmei; Manichaikul, Ani W; Aguiar, Derek; Rich, Stephen S; Herrington, David M; Vu, David; Johnson, W Craig; Rotter, Jerome I; Post, Wendy S; Vella, Anthony T; Rodriguez-Oquendo, Annabelle; Zhou, Beiyan | Circulation | 2022 Jan 18 | 34913723 | |
| Bayesian Sparse Mediation Analysis with Targeted Penalization of Natural Indirect Effects. | Song, Yanyi; Zhou, Xiang; Kang, Jian; Aung, Max T; Zhang, Min; Zhao, Wei; Needham, Belinda L; Kardia, Sharon L R; Liu, Yongmei; Meeker, John D; Smith, Jennifer A; Mukherjee, Bhramar | Journal of the Royal Statistical Society. Series C, Applied statistics | 2021 Nov | 34887595 | |
| Lifestyle and Genetic Factors Modify Parent-of-Origin Effects on the Human Methylome. | Zeng, Yanni; Amador, Carmen; Gao, Chenhao; Walker, Rosie M; Morris, Stewart W; Campbell, Archie; Frkatović, Azra; Madden, Rebecca A; Adams, Mark J; He, Shuai; Bretherick, Andrew D; Hayward, Caroline; Porteous, David J; Wilson, James F; Evans, Kathryn L; McIntosh, Andrew M; Navarro, Pau; Haley, Chris S | EBioMedicine | 2021 Dec | 34883445 | |
| Atlas of RNA editing events affecting protein expression in aged and Alzheimer's disease human brain tissue. | Ma, Yiyi; Dammer, Eric B; Felsky, Daniel; Duong, Duc M; Klein, Hans-Ulrich; White, Charles C; Zhou, Maotian; Logsdon, Benjamin A; McCabe, Cristin; Xu, Jishu; Wang, Minghui; Wingo, Thomas S; Lah, James J; Zhang, Bin; Schneider, Julie; Allen, Mariet; Wang, Xue; Ertekin-Taner, Nilüfer; Seyfried, Nicholas T; Levey, Allan I; Bennett, David A; De Jager, Philip L | Nature communications | 2021 12 02 | 34857756 | |
| How Many Cell Types Are in the Kidney and What Do They Do? | Balzer, Michael S; Rohacs, Tibor; Susztak, Katalin | Annual review of physiology | 2022 02 10 | 34843404 | |
| From mapping kidney function to mechanism and prediction. | Hirohama, Daigoro; Susztak, Katalin | Nature reviews. Nephrology | 2022 02 | 34819631 | |
| Genome-wide association studies identify the role of caspase-9 in kidney disease. | Doke, Tomohito; Huang, Shizheng; Qiu, Chengxiang; Sheng, Xin; Seasock, Matthew; Liu, Hongbo; Ma, Ziyuan; Palmer, Matthew; Susztak, Katalin | Science advances | 2021 Nov 05 | 34739325 | |
| APOL1 risk variants in individuals of African genetic ancestry drive endothelial cell defects that exacerbate sepsis. | Wu, Junnan; Ma, Ziyuan; Raman, Archana; Beckerman, Pazit; Dhillon, Poonam; Mukhi, Dhanunjay; Palmer, Matthew; Chen, Hua Chang; Cohen, Cassiane Robinson; Dunn, Thomas; Reilly, John; Meyer, Nuala; Shahaty, Michael; Arany, Zoltan; Haskó, György; Laudanski, Krzysztof; Hung, Adriana; Susztak, Katalin | Immunity | 2021 11 09 | 34715018 | |
| Systems Analysis Reveals Ageing-Related Perturbations in Retinoids and Sex Hormones in Alzheimer's and Parkinson's Diseases. | Lam, Simon; Hartmann, Nils; Benfeitas, Rui; Zhang, Cheng; Arif, Muhammad; Turkez, Hasan; Uhlén, Mathias; Englert, Christoph; Knight, Robert; Mardinoglu, Adil | Biomedicines | 2021 Sep 24 | 34680427 | |
| Comparative cellular analysis of motor cortex in human, marmoset and mouse. | Bakken, Trygve E; Jorstad, Nikolas L; Hu, Qiwen; Lake, Blue B; Tian, Wei; Kalmbach, Brian E; Crow, Megan; Hodge, Rebecca D; Krienen, Fenna M; Sorensen, Staci A; Eggermont, Jeroen; Yao, Zizhen; Aevermann, Brian D; Aldridge, Andrew I; Bartlett, Anna; Bertagnolli, Darren; Casper, Tamara; Castanon, Rosa G; Crichton, Kirsten; Daigle, Tanya L; Dalley, Rachel; Dee, Nick; Dembrow, Nikolai; Diep, Dinh; Ding, Song-Lin; Dong, Weixiu; Fang, Rongxin; Fischer, Stephan; Goldman, Melissa; Goldy, Jeff; Graybuck, Lucas T; Herb, Brian R; Hou, Xiaomeng; Kancherla, Jayaram; Kroll, Matthew; Lathia, Kanan; van Lew, Baldur; Li, Yang Eric; Liu, Christine S; Liu, Hanqing; Lucero, Jacinta D; Mahurkar, Anup; McMillen, Delissa; Miller, Jeremy A; Moussa, Marmar; Nery, Joseph R; Nicovich, Philip R; Niu, Sheng-Yong; Orvis, Joshua; Osteen, Julia K; Owen, Scott; Palmer, Carter R; Pham, Thanh; Plongthongkum, Nongluk; Poirion, Olivier; Reed, Nora M; Rimorin, Christine; Rivkin, Angeline; Romanow, William J; Sedeño-Cortés, Adriana E; Siletti, Kimberly; Somasundaram, Saroja; Sulc, Josef; Tieu, Michael; Torkelson, Amy; Tung, Herman; Wang, Xinxin; Xie, Fangming; Yanny, Anna Marie; Zhang, Renee; Ament, Seth A; Behrens, M Margarita; Bravo, Hector Corrada; Chun, Jerold; Dobin, Alexander; Gillis, Jesse; Hertzano, Ronna; Hof, Patrick R; Höllt, Thomas; Horwitz, Gregory D; Keene, C Dirk; Kharchenko, Peter V; Ko, Andrew L; Lelieveldt, Boudewijn P; Luo, Chongyuan; Mukamel, Eran A; Pinto-Duarte, António; Preissl, Sebastian; Regev, Aviv; Ren, Bing; Scheuermann, Richard H; Smith, Kimberly; Spain, William J; White, Owen R; Koch, Christof; Hawrylycz, Michael; Tasic, Bosiljka; Macosko, Evan Z; McCarroll, Steven A; Ting, Jonathan T; Zeng, Hongkui; Zhang, Kun; Feng, Guoping; Ecker, Joseph R; Linnarsson, Sten; Lein, Ed S | Nature | 2021 10 | 34616062 | |
| Longitudinal urinary biomarkers of immunological activation in covid-19 patients without clinically apparent kidney disease versus acute and chronic failure. | Laudanski, Krzysztof; Okeke, Tony; Jihane, Hajj; Siddiq, Kumal; Rader, Daniel J; Wu, Junnan; Susztak, Katalin | Scientific reports | 2021 10 04 | 34608231 | |
| Olfactory Bulb and Amygdala Gene Expression Changes in Subjects Dying with COVID-19. | Piras, Ignazio S; Huentelman, Matthew J; Walker, Jessica E; Arce, Richard; Glass, Michael J; Vargas, Daisy; Sue, Lucia I; Intorcia, Anthony J; Nelson, Courtney M; Suszczewicz, Katsuko E; Borja, Claryssa L; Desforges, Marc; Deture, Michael; Dickson, Dennis W; Beach, Thomas G; Serrano, Geidy E | medRxiv : the preprint server for health sciences | 2021 Sep 15 | 34545375 | |
| Signature morpho-electric, transcriptomic, and dendritic properties of human layer 5 neocortical pyramidal neurons. | Kalmbach, Brian E; Hodge, Rebecca D; Jorstad, Nikolas L; Owen, Scott; de Frates, Rebecca; Yanny, Anna Marie; Dalley, Rachel; Mallory, Matt; Graybuck, Lucas T; Radaelli, Cristina; Keene, C Dirk; Gwinn, Ryder P; Silbergeld, Daniel L; Cobbs, Charles; Ojemann, Jeffrey G; Ko, Andrew L; Patel, Anoop P; Ellenbogen, Richard G; Bakken, Trygve E; Daigle, Tanya L; Dee, Nick; Lee, Brian R; McGraw, Medea; Nicovich, Philip R; Smith, Kimberly; Sorensen, Staci A; Tasic, Bosiljka; Zeng, Hongkui; Koch, Christof; Lein, Ed S; Ting, Jonathan T | Neuron | 2021 09 15 | 34534454 | |
| Rare variants in the endocytic pathway are associated with Alzheimer's disease, its related phenotypes, and functional consequences. | Zhan, Lingyu; Li, Jiajin; Jew, Brandon; Sul, Jae Hoon | PLoS genetics | 2021 Sep | 34516545 | |
| Epigenomic features related to microglia are associated with attenuated effect of APOE ε4 on Alzheimer's disease risk in humans. | Ma, Yiyi; Yu, Lei; Olah, Marta; Smith, Rebecca; Oatman, Stephanie R; Allen, Mariet; Pishva, Ehsan; Zhang, Bin; Menon, Vilas; Ertekin-Taner, Nilüfer; Lunnon, Katie; Bennett, David A; Klein, Hans-Ulrich; De Jager, Philip L | Alzheimer's & dementia : the journal of the Alzheimer's Association | 2021 Sep 05 | 34482628 | |
| Novel DNA methylation loci and genes showing pleiotropic association with Alzheimer's dementia: a network Mendelian randomization analysis. | Liu, Di; Wang, Youxin; Jing, Huiquan; Meng, Qun; Yang, Jingyun | Epigenetics | 2022 Jun-Jul | 34461811 | |
| Manipulating the NKG2D Receptor-Ligand Axis Using CRISPR: Novel Technologies for Improved Host Immunity. | Alves, Eric; McLeish, Emily; Blancafort, Pilar; Coudert, Jerome D; Gaudieri, Silvana | Frontiers in immunology | 2021 | 34456921 | |
| A single genetic locus controls both expression of DPEP1/CHMP1A and kidney disease development via ferroptosis. | Guan, Yuting; Liang, Xiujie; Ma, Ziyuan; Hu, Hailong; Liu, Hongbo; Miao, Zhen; Linkermann, Andreas; Hellwege, Jacklyn N; Voight, Benjamin F; Susztak, Katalin | Nature communications | 2021 08 23 | 34426578 | |
| Bayesian hierarchical models for high-dimensional mediation analysis with coordinated selection of correlated mediators. | Song, Yanyi; Zhou, Xiang; Kang, Jian; Aung, Max T; Zhang, Min; Zhao, Wei; Needham, Belinda L; Kardia, Sharon L R; Liu, Yongmei; Meeker, John D; Smith, Jennifer A; Mukherjee, Bhramar | Statistics in medicine | 2021 11 30 | 34404112 | |
| Virus Infection Induces Keap1 Binding to Cytokine Genes, Which Recruits NF-κB p50 and G9a-GLP and Represses Cytokine Transcription. | Burns, Veronica Elizabeth; Kerppola, Tom Klaus | Journal of immunology (Baltimore, Md. : 1950) | 2021 09 01 | 34400522 | |
| EPIGENOMIC FEATURES RELATED TO MICROGLIA ARE ASSOCIATED WITH ATTENUATED EFFECT OF APOE ε4 ON ALZHEIMER'S DISEASE RISK IN HUMANS. | Ma, Yiyi; Yu, Lei; Olah, Marta; Smith, Rebecca; Oatman, Stephanie R; Allen, Mariet; Pishva, Ehsan; Zhang, Bin; Menon, Vilas; Ertekin-Taner, Nilüfer; Lunnon, Katie; Bennett, David A; Klein, Hans-Ulrich; De Jager, Philip L | Alzheimer's & dementia : the journal of the Alzheimer's Association | 2020 12 | 34393677 | |
| Mapping the genetic architecture of human traits to cell types in the kidney identifies mechanisms of disease and potential treatments. | Sheng, Xin; Guan, Yuting; Ma, Ziyuan; Wu, Junnan; Liu, Hongbo; Qiu, Chengxiang; Vitale, Steven; Miao, Zhen; Seasock, Matthew J; Palmer, Matthew; Shin, Myung K; Duffin, Kevin L; Pullen, Steven S; Edwards, Todd L; Hellwege, Jacklyn N; Hung, Adriana M; Li, Mingyao; Voight, Benjamin F; Coffman, Thomas M; Brown, Christopher D; Susztak, Katalin | Nature genetics | 2021 09 | 34385711 | |
| Transcriptome-Wide Association Study of Blood Cell Traits in African Ancestry and Hispanic/Latino Populations. | Wen, Jia; Xie, Munan; Rowland, Bryce; Rosen, Jonathan D; Sun, Quan; Chen, Jiawen; Tapia, Amanda L; Qian, Huijun; Kowalski, Madeline H; Shan, Yue; Young, Kristin L; Graff, Marielisa; Argos, Maria; Avery, Christy L; Bien, Stephanie A; Buyske, Steve; Yin, Jie; Choquet, Hélène; Fornage, Myriam; Hodonsky, Chani J; Jorgenson, Eric; Kooperberg, Charles; Loos, Ruth J F; Liu, Yongmei; Moon, Jee-Young; North, Kari E; Rich, Stephen S; Rotter, Jerome I; Smith, Jennifer A; Zhao, Wei; Shang, Lulu; Wang, Tao; Zhou, Xiang; Reiner, Alexander P; Raffield, Laura M; Li, Yun | Genes | 2021 Jul 08 | 34356065 | |
| Renal Histologic Analysis Provides Complementary Information to Kidney Function Measurement for Patients with Early Diabetic or Hypertensive Disease. | Quinn, Ghazal Z; Abedini, Amin; Liu, Hongbo; Ma, Ziyuan; Cucchiara, Andrew; Havasi, Andrea; Hill, Jon; Palmer, Matthew B; Susztak, Katalin | Journal of the American Society of Nephrology : JASN | 2021 Nov | 34348909 | |
| Isthmin-1 is an adipokine that promotes glucose uptake and improves glucose tolerance and hepatic steatosis. | Jiang, Zewen; Zhao, Meng; Voilquin, Laetitia; Jung, Yunshin; Aikio, Mari A; Sahai, Tanushi; Dou, Florence Y; Roche, Alexander M; Carcamo-Orive, Ivan; Knowles, Joshua W; Wabitsch, Martin; Appel, Eric A; Maikawa, Caitlin L; Camporez, Joao Paulo; Shulman, Gerald I; Tsai, Linus; Rosen, Evan D; Gardner, Christopher D; Spiegelman, Bruce M; Svensson, Katrin J | Cell metabolism | 2021 Sep 07 | 34348115 | |
| Transgenic mice for in vivo epigenome editing with CRISPR-based systems. | Gemberling, Matthew P; Siklenka, Keith; Rodriguez, Erica; Tonn-Eisinger, Katherine R; Barrera, Alejandro; Liu, Fang; Kantor, Ariel; Li, Liqing; Cigliola, Valentina; Hazlett, Mariah F; Williams, Courtney A; Bartelt, Luke C; Madigan, Victoria J; Bodle, Josephine C; Daniels, Heather; Rouse, Douglas C; Hilton, Isaac B; Asokan, Aravind; Ciofani, Maria; Poss, Kenneth D; Reddy, Timothy E; West, Anne E; Gersbach, Charles A | Nature methods | 2021 08 | 34341582 | |
| A machine learning approach to brain epigenetic analysis reveals kinases associated with Alzheimer's disease. | Huang, Yanting; Sun, Xiaobo; Jiang, Huige; Yu, Shaojun; Robins, Chloe; Armstrong, Matthew J; Li, Ronghua; Mei, Zhen; Shi, Xiaochuan; Gerasimov, Ekaterina Sergeevna; De Jager, Philip L; Bennett, David A; Wingo, Aliza P; Jin, Peng; Wingo, Thomas S; Qin, Zhaohui S | Nature communications | 2021 Jul 22 | 34294691 | |
| Association of Coding Variants in Hydroxysteroid 17-beta Dehydrogenase 14 (HSD17B14) with Reduced Progression to End Stage Kidney Disease in Type 1 Diabetes. | Mychaleckyj, Josyf C; Valo, Erkka; Ichimura, Takaharu; Ahluwalia, Tarunveer S; Dina, Christian; Miller, Rachel G; Shabalin, Ivan G; Gyorgy, Beata; Cao, JingJing; Onengut-Gumuscu, Suna; Satake, Eiichiro; Smiles, Adam M; Haukka, Jani K; Tregouet, David-Alexandre; Costacou, Tina; O'Neil, Kristina; Paterson, Andrew D; Forsblom, Carol; Keenan, Hillary A; Pezzolesi, Marcus G; Pragnell, Marlon; Galecki, Andrzej; Rich, Stephen S; Sandholm, Niina; Klein, Ronald; Klein, Barbara E; Susztak, Katalin; Orchard, Trevor J; Korstanje, Ron; King, George L; Hadjadj, Samy; Rossing, Peter; Bonventre, Joseph V; Groop, Per-Henrik; Warram, James H; Krolewski, Andrzej S | Journal of the American Society of Nephrology : JASN | 2021 10 | 34261756 | |
| The Socioeconomic Gradient in Epigenetic Ageing Clocks: Evidence from the Multi-Ethnic Study of Atherosclerosis and the Health and Retirement Study. | Schmitz, Lauren L; Zhao, Wei; Ratliff, Scott M; Goodwin, Julia; Miao, Jiacheng; Lu, Qiongshi; Guo, Xiuqing; Taylor, Kent D; Ding, Jingzhong; Liu, Yongmei; Levine, Morgan; Smith, Jennifer A | Epigenetics | 2022 Jun | 34227900 | |
| Unbiased Analysis of Temporal Changes in Immune Serum Markers in Acute COVID-19 Infection With Emphasis on Organ Failure, Anti-Viral Treatment, and Demographic Characteristics. | Laudanski, Krzysztof; Jihane, Hajj; Antalosky, Brook; Ghani, Danyal; Phan, Uyen; Hernandez, Ruth; Okeke, Tony; Wu, Junnan; Rader, Daniel; Susztak, Katalin | Frontiers in immunology | 2021 | 34177897 | |
| The association of epigenetic clocks in brain tissue with brain pathologies and common aging phenotypes. | Grodstein, Francine; Lemos, Bernardo; Yu, Lei; Klein, Hans-Ulrich; Iatrou, Artemis; Buchman, Aron S; Shireby, Gemma L; Mill, Jonathan; Schneider, Julie A; De Jager, Philip L; Bennett, David A | Neurobiology of disease | 2021 09 | 34153464 | |
| A meta-analysis of epigenome-wide association studies in Alzheimer's disease highlights novel differentially methylated loci across cortex. | Smith, Rebecca G; Pishva, Ehsan; Shireby, Gemma; Smith, Adam R; Roubroeks, Janou A Y; Hannon, Eilis; Wheildon, Gregory; Mastroeni, Diego; Gasparoni, Gilles; Riemenschneider, Matthias; Giese, Armin; Sharp, Andrew J; Schalkwyk, Leonard; Haroutunian, Vahram; Viechtbauer, Wolfgang; van den Hove, Daniel L A; Weedon, Michael; Brokaw, Danielle; Francis, Paul T; Thomas, Alan J; Love, Seth; Morgan, Kevin; Walter, Jörn; Coleman, Paul D; Bennett, David A; De Jager, Philip L; Mill, Jonathan; Lunnon, Katie | Nature communications | 2021 06 10 | 34112773 | |
| NEBULA is a fast negative binomial mixed model for differential or co-expression analysis of large-scale multi-subject single-cell data. | He, Liang; Davila-Velderrain, Jose; Sumida, Tomokazu S; Hafler, David A; Kellis, Manolis; Kulminski, Alexander M | Communications biology | 2021 May 26 | 34040149 | |
| Common DNA methylation dynamics in endometriod adenocarcinoma and glioblastoma suggest universal epigenomic alterations in tumorigenesis. | Karlow, Jennifer A; Miao, Benpeng; Xing, Xiaoyun; Wang, Ting; Zhang, Bo | Communications biology | 2021 May 21 | 34021236 | |
| Genome-wide analysis identifies a novel LINC-PINT splice variant associated with vascular amyloid pathology in Alzheimer's disease. | Reddy, Joseph S; Allen, Mariet; Ho, Charlotte C G; Oatman, Stephanie R; İş, Özkan; Quicksall, Zachary S; Wang, Xue; Jin, Jiangli; Patel, Tulsi A; Carnwath, Troy P; Nguyen, Thuy T; Malphrus, Kimberly G; Lincoln, Sarah J; Carrasquillo, Minerva M; Crook, Julia E; Kanekiyo, Takahisa; Murray, Melissa E; Bu, Guojun; Dickson, Dennis W; Ertekin-Taner, Nilüfer | Acta neuropathologica communications | 2021 05 21 | 34020725 | |
| Transcriptome-wide association analysis identifies DACH1 as a kidney disease risk gene that contributes to fibrosis. | Doke, Tomohito; Huang, Shizheng; Qiu, Chengxiang; Liu, Hongbo; Guan, Yuting; Hu, Hailong; Ma, Ziyuan; Wu, Junnan; Miao, Zhen; Sheng, Xin; Zhou, Jianfu; Cao, Aili; Li, Jianhua; Kaufman, Lewis; Hung, Adriana; Brown, Christopher D; Pestell, Richard; Susztak, Katalin | The Journal of clinical investigation | 2021 May 17 | 33998598 | |
| Transcriptome prediction performance across machine learning models and diverse ancestries. | Okoro, Paul C; Schubert, Ryan; Guo, Xiuqing; Johnson, W Craig; Rotter, Jerome I; Hoeschele, Ina; Liu, Yongmei; Im, Hae Kyung; Luke, Amy; Dugas, Lara R; Wheeler, Heather E | HGG advances | 2021 Apr 08 | 33937878 | |
| Identification of cell-type-specific marker genes from co-expression patterns in tissue samples. | Qiu, Yixuan; Wang, Jiebiao; Lei, Jing; Roeder, Kathryn | Bioinformatics (Oxford, England) | 2021 Apr 27 | 33904573 | |
| Human placental cytotrophoblast epigenome dynamics over gestation and alterations in placental disease. | Zhang, Bo; Kim, M Yvonne; Elliot, GiNell; Zhou, Yan; Zhao, Guangfeng; Li, Daofeng; Lowdon, Rebecca F; Gormley, Matthew; Kapidzic, Mirhan; Robinson, Joshua F; McMaster, Michael T; Hong, Chibo; Mazor, Tali; Hamilton, Emily; Sears, Renee L; Pehrsson, Erica C; Marra, Marco A; Jones, Steven J M; Bilenky, Misha; Hirst, Martin; Wang, Ting; Costello, Joseph F; Fisher, Susan J | Developmental cell | 2021 May 03 | 33891899 | |
| Brain DNA Methylation Patterns in CLDN5 Associated With Cognitive Decline. | Hüls, Anke; Robins, Chloe; Conneely, Karen N; Edgar, Rachel; De Jager, Philip L; Bennett, David A; Wingo, Aliza P; Epstein, Michael P; Wingo, Thomas S | Biological psychiatry | 2021 Feb 03 | 33838873 | |
| Bayesian estimation of cell type-specific gene expression with prior derived from single-cell data. | Wang, Jiebiao; Roeder, Kathryn; Devlin, Bernie | Genome research | 2021 10 | 33837133 | |
| Epigenome-wide analysis of long-term air pollution exposure and DNA methylation in monocytes: results from the Multi-Ethnic Study of Atherosclerosis. | C Chi, Gloria; Liu, Yongmei; MacDonald, James W; M Reynolds, Lindsay; Enquobahrie, Daniel A; L Fitzpatrick, Annette; Kerr, Kathleen F; J Budoff, Matthew; Lee, Su-In; Siscovick, David; D Kaufman, Joel | Epigenetics | 2022 03 | 33818294 | |
| The histone modification H3K4me3 is altered at the ANK1 locus in Alzheimer's disease brain. | Smith, Adam R; Smith, Rebecca G; Macdonald, Ruby; Marzi, Sarah J; Burrage, Joe; Troakes, Claire; Al-Sarraj, Safa; Mill, Jonathan; Lunnon, Katie | Future science OA | 2021 Feb 09 | 33815817 | |
| Maternal blood metal concentrations and whole blood DNA methylation during pregnancy in the Early Autism Risk Longitudinal Investigation (EARLI). | Aung, Max T; M Bakulski, Kelly; Feinberg, Jason I; F Dou, John; D Meeker, John; Mukherjee, Bhramar; Loch-Caruso, Rita; Ladd-Acosta, Christine; Volk, Heather E; Croen, Lisa A; Hertz-Picciotto, Irva; Newschaffer, Craig J; Fallin, M Daniele | Epigenetics | 2022 03 | 33794742 | |
| APOL1 at 10 years: progress and next steps. | Freedman, Barry I; Kopp, Jeffrey B; Sampson, Matthew G; Susztak, Katalin | Kidney international | 2021 06 | 33794228 | |
| Functional enhancer elements drive subclass-selective expression from mouse to primate neocortex. | Mich, John K; Graybuck, Lucas T; Hess, Erik E; Mahoney, Joseph T; Kojima, Yoshiko; Ding, Yi; Somasundaram, Saroja; Miller, Jeremy A; Kalmbach, Brian E; Radaelli, Cristina; Gore, Bryan B; Weed, Natalie; Omstead, Victoria; Bishaw, Yemeserach; Shapovalova, Nadiya V; Martinez, Refugio A; Fong, Olivia; Yao, Shenqin; Mortrud, Marty; Chong, Peter; Loftus, Luke; Bertagnolli, Darren; Goldy, Jeff; Casper, Tamara; Dee, Nick; Opitz-Araya, Ximena; Cetin, Ali; Smith, Kimberly A; Gwinn, Ryder P; Cobbs, Charles; Ko, Andrew L; Ojemann, Jeffrey G; Keene, C Dirk; Silbergeld, Daniel L; Sunkin, Susan M; Gradinaru, Viviana; Horwitz, Gregory D; Zeng, Hongkui; Tasic, Bosiljka; Lein, Ed S; Ting, Jonathan T; Levi, Boaz P | Cell reports | 2021 Mar 30 | 33789096 | |
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| The oncogene AAMDC links PI3K-AKT-mTOR signaling with metabolic reprograming in estrogen receptor-positive breast cancer. | Golden, Emily; Rashwan, Rabab; Woodward, Eleanor A; Sgro, Agustin; Wang, Edina; Sorolla, Anabel; Waryah, Charlene; Tie, Wan Jun; Cuyàs, Elisabet; Ratajska, Magdalena; Kardaś, Iwona; Kozlowski, Piotr; Johnstone, Elizabeth K M; See, Heng B; Duffy, Ciara; Parry, Jeremy; Lagerborg, Kim A; Czapiewski, Piotr; Menendez, Javier A; Gorczyński, Adam; Wasag, Bartosz; Pfleger, Kevin D G; Curtis, Christina; Lee, Bum-Kyu; Kim, Jonghwan; Cursons, Joseph; Pavlos, Nathan J; Biernat, Wojciech; Jain, Mohit; Woo, Andrew J; Redfern, Andrew; Blancafort, Pilar | Nature communications | 2021 03 26 | 33772001 | |
| Monitoring Recessions: A Bayesian Sequential Quickest Detection Method. | Li, Haixi; Sheng, Xuguang Simon; Yang, Jingyun | International journal of forecasting | 2021 Apr-Jun | 33716367 | |
| AP-1 subunits converge promiscuously at enhancers to potentiate transcription. | Seo, Jungkyun; Koçak, D Dewran; Bartelt, Luke C; Williams, Courtney A; Barrera, Alejandro; Gersbach, Charles A; Reddy, Timothy E | Genome research | 2021 04 | 33674350 | |
| Increased Alu RNA processing in Alzheimer brains is linked to gene expression changes. | Cheng, Yubo; Saville, Luke; Gollen, Babita; Veronesi, Ana Alvarez; Mohajerani, Majid; Joseph, Jeffrey T; Zovoilis, Athanasios | EMBO reports | 2021 05 05 | 33645898 | |
| Creatine kinase B controls futile creatine cycling in thermogenic fat. | Rahbani, Janane F; Roesler, Anna; Hussain, Mohammed F; Samborska, Bozena; Dykstra, Christien B; Tsai, Linus; Jedrychowski, Mark P; Vergnes, Laurent; Reue, Karen; Spiegelman, Bruce M; Kazak, Lawrence | Nature | 2021 02 | 33597756 | |
| Genetic control of the human brain proteome. | Robins, Chloe; Liu, Yue; Fan, Wen; Duong, Duc M; Meigs, Jacob; Harerimana, Nadia V; Gerasimov, Ekaterina S; Dammer, Eric B; Cutler, David J; Beach, Thomas G; Reiman, Eric M; De Jager, Philip L; Bennett, David A; Lah, James J; Wingo, Aliza P; Levey, Allan I; Seyfried, Nicholas T; Wingo, Thomas S | American journal of human genetics | 2021 03 04 | 33571421 | |
| Urinary Single-Cell Profiling Captures the Cellular Diversity of the Kidney. | Abedini, Amin; Zhu, Yuan O; Chatterjee, Shatakshee; Halasz, Gabor; Devalaraja-Narashimha, Kishor; Shrestha, Rojesh; S. Balzer, Michael; Park, Jihwan; Zhou, Tong; Ma, Ziyuan; Sullivan, Katie Marie; Hu, Hailong; Sheng, Xin; Liu, Hongbo; Wei, Yi; Boustany-Kari, Carine M; Patel, Uptal; Almaani, Salem; Palmer, Matthew; Townsend, Raymond; Blady, Shira; Hogan, Jonathan; TRIDENT Study Investigators,; Morton, Lori; Susztak, Katalin; TRIDENT Study Investigators | Journal of the American Society of Nephrology : JASN | 2021 03 | 33531352 | |
| FOS licenses early events in stem cell activation driving skeletal muscle regeneration. | Almada, Albert E; Horwitz, Naftali; Price, Feodor D; Gonzalez, Alfredo E; Ko, Michelle; Bolukbasi, Ozge Vargel; Messemer, Kathleen A; Chen, Sonia; Sinha, Manisha; Rubin, Lee L; Wagers, Amy J | Cell reports | 2021 01 26 | 33503437 | |
| Characteristics of Epigenetic Clocks Across Blood and Brain Tissue in Older Women and Men. | Grodstein, Francine; Lemos, Bernardo; Yu, Lei; Iatrou, Artemis; De Jager, Philip L; Bennett, David A | Frontiers in neuroscience | 2020 | 33488342 | |
| Single-cell lineages reveal the rates, routes, and drivers of metastasis in cancer xenografts. | Quinn, Jeffrey J; Jones, Matthew G; Okimoto, Ross A; Nanjo, Shigeki; Chan, Michelle M; Yosef, Nir; Bivona, Trever G; Weissman, Jonathan S | Science (New York, N.Y.) | 2021 02 26 | 33479121 | |
| Renal tubule Cpt1a overexpression protects from kidney fibrosis by restoring mitochondrial homeostasis. | Miguel, Verónica; Tituaña, Jessica; Herrero, J Ignacio; Herrero, Laura; Serra, Dolors; Cuevas, Paula; Barbas, Coral; Puyol, Diego Rodríguez; Márquez-Expósito, Laura; Ruiz-Ortega, Marta; Castillo, Carolina; Sheng, Xin; Susztak, Katalin; Ruiz-Canela, Miguel; Salas-Salvadó, Jordi; González, Miguel A Martínez; Ortega, Sagrario; Ramos, Ricardo; Lamas, Santiago | The Journal of clinical investigation | 2021 Mar 01 | 33465052 | |
| Kidney disease genetic risk variants alter lysosomal beta-mannosidase (MANBA) expression and disease severity. | Gu, Xiangchen; Yang, Hongliu; Sheng, Xin; Ko, Yi-An; Qiu, Chengxiang; Park, Jihwan; Huang, Shizheng; Kember, Rachel; Judy, Renae L; Park, Joseph; Damrauer, Scott M; Nadkarni, Girish; Loos, Ruth J F; My, Vy Thi Ha; Chaudhary, Kumardeep; Bottinger, Erwin P; Paranjpe, Ishan; Saha, Aparna; Brown, Christopher; Akilesh, Shreeram; Hung, Adriana M; Palmer, Matthew; Baras, Aris; Overton, John D; Reid, Jeffrey; Ritchie, Marylyn; Rader, Daniel J; Susztak, Katalin | Science translational medicine | 2021 Jan 13 | 33441424 | |
| The Nuclear Receptor ESRRA Protects from Kidney Disease by Coupling Metabolism and Differentiation. | Dhillon, Poonam; Park, Jihwan; Hurtado Del Pozo, Carmen; Li, Lingzhi; Doke, Tomohito; Huang, Shizheng; Zhao, Juanjuan; Kang, Hyun Mi; Shrestra, Rojesh; Balzer, Michael S; Chatterjee, Shatakshee; Prado, Patricia; Han, Seung Yub; Liu, Hongbo; Sheng, Xin; Dierickx, Pieterjan; Batmanov, Kirill; Romero, Juan P; Prósper, Felipe; Li, Mingyao; Pei, Liming; Kim, Junhyong; Montserrat, Nuria; Susztak, Katalin | Cell metabolism | 2021 Feb 02 | 33301705 | |
| 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, Jason | Nature 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 A | Cell 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, Lizhuo | The Journal of infection | 2021 01 | 33259846 | |
| 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, Pilar | Nucleic acids research | 2020 12 16 | 33196851 | |
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| The transcriptomic signature of the aging podocyte. | Mukhi, Dhanunjay; Susztak, Katalin | Kidney 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, Jingyun | Neurobiology 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 A | Cell 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 M | Genome medicine. | 2020 10 14; | 33054850 | |
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| Quantitative Kinetic Analyses of Histone Turnover Using Imaging and Flow Cytometry. | Sato, Hanae; Singer, Robert H; Greally, John M | Bio-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 D | Genome 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-Hong | Diabetes/metabolism research and reviews. | 2020 Oct 03; | 33010796 | |
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| 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 T | Nature 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, Jinying | Neurobiology of aging | 2019 Apr | 30660039 | |
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| 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, Katalin | PLoS biology. | 2018 09; | 30226866 | |
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| 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, Jing | International journal of cancer. | 2018 Nov 15; | 30183087 | |
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| A high-throughput screen of real-time ATP levels in individual cells reveals mechanisms of energy failure. | Mendelsohn, Bryce A; Bennett, Neal K; Darch, Maxwell A; Yu, Katharine; Nguyen, Mai K; Pucciarelli, Daniela; Nelson, Maxine; Horlbeck, Max A; Gilbert, Luke A; Hyun, William; Kampmann, Martin; Nakamura, Jean L; Nakamura, Ken | PLoS biology. | 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 A | Frontiers in genetics. | 2018; | 30140277 | |
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| Pre-established Chromatin Interactions Mediate the Genomic Response to Glucocorticoids. | D'Ippolito, Anthony M; McDowell, Ian C; Barrera, Alejandro; Hong, Linda K; Leichter, Sarah M; Bartelt, Luke C; Vockley, Christopher M; Majoros, William H; Safi, Alexias; Song, Lingyun; Gersbach, Charles A; Crawford, Gregory E; Reddy, Timothy E | Cell systems. | 2018 08 22; | 30031775 | |
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| Inhibition of the miR-192/215-Rab11-FIP2 axis suppresses human gastric cancer progression. | Zhang, Xiaojing; Peng, Yin; Huang, Yong; Deng, Shiqi; Feng, Xianling; Hou, Gangqiang; Lin, Huijuan; Wang, Jian; Yan, Ruibin; Zhao, Yanqiu; Fan, Xinmin; Meltzer, Stephen J; Li, Song; Jin, Zhe | Cell death & disease. | 2018 07 13; | 30006518 | |
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| A CRISPR-dCas Toolbox for Genetic Engineering and Synthetic Biology. | Xu, Xiaoshu; Qi, Lei S | Journal of molecular biology. | 2019 01 04; | 29958882 | |
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| Class I Histone Deacetylase Inhibition by Tianeptinaline Modulates Neuroplasticity and Enhances Memory. | Zhao, Wen-Ning; Ghosh, Balaram; Tyler, Marshall; Lalonde, Jasmin; Joseph, Nadine F; Kosaric, Nina; Fass, Daniel M; Tsai, Li-Huei; Mazitschek, Ralph; Haggarty, Stephen J | ACS chemical neuroscience. | 2018 09 19; | 29932631 | |
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| Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element. | Cho, Seung Woo; Xu, Jin; Sun, Ruping; Mumbach, Maxwell R; Carter, Ava C; Chen, Y Grace; Yost, Kathryn E; Kim, Jeewon; He, Jing; Nevins, Stephanie A; Chin, Suet-Feung; Caldas, Carlos; Liu, S John; Horlbeck, Max A; Lim, Daniel A; Weissman, Jonathan S; Curtis, Christina; Chang, Howard Y | Cell. | 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, Katalin | Kidney 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 A | Environmental 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 A | Nature communications. | 2018 Apr 26; | 29700298 | |
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| Cancer-Germline Antigen Expression Discriminates Clinical Outcome to CTLA-4 Blockade. | Shukla, Sachet A; Bachireddy, Pavan; Schilling, Bastian; Galonska, Christina; Zhan, Qian; Bango, Clyde; Langer, Rupert; Lee, Patrick C; Gusenleitner, Daniel; Keskin, Derin B; Babadi, Mehrtash; Mohammad, Arman; Gnirke, Andreas; Clement, Kendell; Cartun, Zachary J; Van Allen, Eliezer M; Miao, Diana; Huang, Ying; Snyder, Alexandra; Merghoub, Taha; Wolchok, Jedd D; Garraway, Levi A; Meissner, Alexander; Weber, Jeffrey S; Hacohen, Nir; Neuberg, Donna; Potts, Patrick R; Murphy, George F; Lian, Christine G; Schadendorf, Dirk; Hodi, F Stephen; Wu, Catherine J | Cell. | 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 Stafford | Nature communications | 2018 04 11 | 29643364 | |
| Single-cell transcriptomics of the mouse kidney reveals potential cellular targets of kidney disease. | Park, Jihwan; Shrestha, Rojesh; Qiu, Chengxiang; Kondo, Ayano; Huang, Shizheng; Werth, Max; Li, Mingyao; Barasch, Jonathan; Suszták, Katalin | Science (New York, N.Y.). | 2018 05 18; | 29622724 | |
| Introduction: Systems Biology of Kidney Disease. | Sharma, Kumar; Susztak, Katalin; Pennathur, Subramaniam | Seminars in nephrology. | 2018 03; | 29602402 | |
| The Role of Peroxisome Proliferator-Activated Receptor ? Coactivator 1? (PGC-1?) in Kidney Disease. | Li, Szu-Yuan; Susztak, Katalin | Seminars in nephrology. | 2018 03; | 29602395 | |
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| Dissecting the Functional Consequences of De Novo DNA Methylation Dynamics in Human Motor Neuron Differentiation and Physiology. | Ziller, Michael J; Ortega, Juan A; Quinlan, Katharina A; Santos, David P; Gu, Hongcang; Martin, Eric J; Galonska, Christina; Pop, Ramona; Maidl, Susanne; Di Pardo, Alba; Huang, Mei; Meltzer, Herbert Y; Gnirke, Andreas; Heckman, C J; Meissner, Alexander; Kiskinis, Evangelos | Cell stem cell. | 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, Katie | Alzheimer'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, Alexander | Nature structural & molecular biology. | 2018 Mar 12; | 29531288 | |
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| CRISPR-based methods for high-throughput annotation of regulatory DNA. | Klann, Tyler S; Black, Joshua B; Gersbach, Charles A | Current 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 P | Current biology : CB. | 2018 03 05; | 29478853 | |
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| Transcription start site profiling uncovers divergent transcription and enhancer-associated RNAs in Drosophila melanogaster. | Meers, Michael P; Adelman, Karen; Duronio, Robert J; Strahl, Brian D; McKay, Daniel J; Matera, A Gregory | BMC genomics. | 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, Brian | Chembiochem : a European journal of chemical biology. | ; | 29446199 | |
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| Zika Virus Alters DNA Methylation of Neural Genes in an Organoid Model of the Developing Human Brain. | Janssens, Sylvie; Schotsaert, Michael; Karnik, Rahul; Balasubramaniam, Vinod; Dejosez, Marion; Meissner, Alexander; García-Sastre, Adolfo; Zwaka, Thomas P | mSystems. | 2018 Jan-Feb; | 29435496 | |
| Hallmarks of cancer: The CRISPR generation. | Moses, Colette; Garcia-Bloj, Benjamin; Harvey, Alan R; Blancafort, Pilar | European journal of cancer (Oxford, England : 1990). | 2018 04; | 29433054 | |
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| SMG-1 inhibition by miR-192/-215 causes epithelial-mesenchymal transition in gastric carcinogenesis via activation of Wnt signaling. | Zhang, Xiaojing; Peng, Yin; Huang, Yong; Yang, Mengting; Yan, Ruibin; Zhao, Yanqiu; Cheng, Yulan; Liu, Xi; Deng, Shiqi; Feng, Xianling; Lin, Huijuan; Yu, Huimin; Chen, Si; Zhao, Zhenfu; Li, Shanni; Li, Kuan; Wang, Liang; Wei, Yanjie; He, Zhendan; Fan, Xinmin; Meltzer, Stephen J; Li, Song; Jin, Zhe | Cancer medicine. | 2018 01; | 29239144 | |
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| Transposable Element Mediated Innovation in Gene Regulatory Landscapes of Cells: Re-Visiting the ''Gene-Battery'' Model. | Sundaram, Vasavi; Wang, Ting | BioEssays : news and reviews in molecular, cellular and developmental biology. | 2018 Jan; | 29206283 | |
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| Association Between Brain Gene Expression, DNA Methylation, and Alteration of Ex Vivo Magnetic Resonance Imaging Transverse Relaxation in Late-Life Cognitive Decline. | Yu, Lei; Dawe, Robert J; Boyle, Patricia A; Gaiteri, Chris; Yang, Jingyun; Buchman, Aron S; Schneider, Julie A; Arfanakis, Konstantinos; De Jager, Philip L; Bennett, David A | JAMA neurology. | 2017 Dec 01; | 29084334 | |
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| Association of Bone Metabolic Markers With Diabetic Retinopathy and Diabetic Macular Edema in Elderly Chinese Individuals With Type 2 Diabetes Mellitus. | Zhang, Xiao; Yang, Jingyun; Zhong, Yong; Xu, Lingling; Wang, Ou; Huang, Ping; Li, Chunying; Qu, Bin; Wang, Jing; Zheng, Caixia; Niu, Meng; Yu, Weihong | The American journal of the medical sciences. | 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 A | Neurobiology 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 Daniele | Nature 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 J | International 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 S | Molecular 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 W | Nucleic 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, Katalin | EBioMedicine. | 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, Alexander | Nature. | 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 Z | ACS 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, Stavros | eLife. | 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 K | Experimental 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, Ting | BMC 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, Farshid | Trends 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 S | Cell stem cell. | 2017 Sep 07; | 28886366 | |
| Denoising genome-wide histone ChIP-seq with convolutional neural networks. | Koh, Pang Wei; Pierson, Emma; Kundaje, Anshul | Bioinformatics (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, Hanchuan | Scientific reports. | 2017 08 24; | 28839271 | |
| Electrophoretic stretching and imaging of single native chromatin fibers in nanoslits. | Yeh, Jia-Wei; Szeto, Kylan | Biomicrofluidics. | 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 A | ACS 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, H | Translational 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 K | Journal 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, Georg | Hypertension (Dallas, Tex. : 1979). | 2017 10; | 28784648 | |
| The Three-Dimensional Organization of Mammalian Genomes. | Yu, Miao; Ren, Bing | Annual 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 S | BMC 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 E | Journal 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, Katalin | Journal 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 J | Kidney & 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, Liangfu | American 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 Ari | PloS 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, Katalin | JCI 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 Klaus | British 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 V | Methods 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 L | Epigenetics. | 2017 08; | 28678593 | |
| The environment, epigenome, and asthma. | Yang, Ivana V; Lozupone, Catherine A; Schwartz, David A | The 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 L | Molecular neurodegeneration. | 2017 07 01; | 28668092 | |
| Genetic and epigenetic control of gene expression by CRISPR-Cas systems. | Lo, Albert; Qi, Lei | F1000Research. | 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, Yongmei | Immunity & ageing : I & A. | 2017; | 28642803 | |
| Repurposing CRISPR System for Transcriptional Activation. | Chen, Meng; Qi, Lei Stanley | Advances in experimental medicine and biology. | 2017; | 28639197 | |
| Mammalian Synthetic Biology: Engineering Biological Systems. | Black, Joshua B; Perez-Pinera, Pablo; Gersbach, Charles A | Annual 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, Benjamin | Genome 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 J | JCI 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 W | PLoS genetics | 2017 Jun | 28614350 | |
| EpiCompare: An online tool to define and explore genomic regions with tissue or cell type-specific epigenomic features. | He, Yu; Wang, Ting | Bioinformatics (Oxford, England). | 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, Ting | BMC 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 E | Molecular 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, Katalin | American 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, Liangfu | Molecular 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, Steve | Nature 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 Q | Bioinformatics (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 J | Nature 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, Kyunghee | The 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 H | Genome 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; S | Cell 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 L | Nucleic 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, Long | Biophysical 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, K | Journal 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 A | Nature biotechnology. | 2017 Jun; | 28369033 | |
| Population Epigenetics. | Greally, John M | Current opinion in systems biology. | 2017 Feb; | 28367533 | |
| Precision Medicine Approaches to Diabetic Kidney Disease: Tissue as an Issue. | Gluck, Caroline; Ko, Yi-An; Susztak, Katalin | Current 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 K | Environmental 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, Ting | Nature communications. | 2017 Mar 28; | 28348391 | |
| Histone gene replacement reveals a post-transcriptional role for H3K36 in maintaining metazoan transcriptome fidelity. | Meers, Michael P; Henriques, Telmo; Lavender, Christopher A; McKay, Daniel J; Strahl, Brian D; Duronio, Robert J; Adelman, Karen; Matera, A Gregory | eLife. | 2017 03 27; | 28346137 | |
| Visualization of the Genomic Loci That Are Bound by Specific Multiprotein Complexes by Bimolecular Fluorescence Complementation Analysis on Drosophila Polytene Chromosomes. | Deng, Huai; Kerppola, Tom K | Methods in enzymology. | 2017; | 28336073 | |
| Epigenomic annotation of noncoding mutations identifies mutated pathways in primary liver cancer. | Lowdon, Rebecca F; Wang, Ting | PloS 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 L | Molecular 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, Prashant | Nature 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 A | American 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, Shohei | Protein 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, Katalin | Nature 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 T | Proceedings 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, Viviane | Scientific 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 B | PloS 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 G | Nucleic acids research. | 2017 Jan 25; | 28123037 | |
| Layer-specific chromatin accessibility landscapes reveal regulatory networks in adult mouse visual cortex. | Gray, Lucas T; Yao, Zizhen; Nguyen, Thuc Nghi; Kim, Tae Kyung; Zeng, Hongkui; Tasic, Bosiljka | eLife. | 2017 Jan 23; | 28112643 | |
| Cooperative Binding of Transcription Factors Orchestrates Reprogramming. | Chronis, Constantinos; Fiziev, Petko; Papp, Bernadett; Butz, Stefan; Bonora, Giancarlo; Sabri, Shan; Ernst, Jason; Plath, Kathrin | Cell. | 2017 Jan 26; | 28111071 | |
| CRISPR-Based Epigenome Editing of Cytokine Receptors for the Promotion of Cell Survival and Tissue Deposition in Inflammatory Environments. | Farhang, Niloofar; Brunger, Jonathan M; Stover, Joshua D; Thakore, Pratiksha I; Lawrence, Brandon; Guilak, Farshid; Gersbach, Charles A; Setton, Lori A; Bowles, Robert D | Tissue engineering. Part A. | 2017 Jan 17; | 28095751 | |
| Epigenetic Research in Neuropsychiatric Disorders: the ''Tissue Issue''. | Bakulski, Kelly M; Halladay, Alycia; Hu, Valerie W; Mill, Jonathan; Fallin, M Daniele | Current behavioral neuroscience reports. | 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, Ting | Neoplasia (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 J | Cancer. | 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, Jonathan | Human 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 S | Bioinformatics (Oxford, England). | 2017 Apr 01; | 27993786 | |
| Developing Treatments for Chronic Kidney Disease in the 21st Century. | Breyer, Matthew D; Susztak, Katalin | Seminars 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 S | Cell. | 2016 Dec 15; | 27984733 | |
| Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens. | Dixit, Atray; Parnas, Oren; Li, Biyu; Chen, Jenny; Fulco, Charles P; Jerby-Arnon, Livnat; Marjanovic, Nemanja D; Dionne, Danielle; Burks, Tyler; Raychowdhury, Raktima; Adamson, Britt; Norman, Thomas M; Lander, Eric S; Weissman, Jonathan S; Friedman, Nir; Regev, Aviv | Cell. | 2016 Dec 15; | 27984732 | |
| ''Gap hunting'' to characterize clustered probe signals in Illumina methylation array data. | Andrews, Shan V; Ladd-Acosta, Christine; Feinberg, Andrew P; Hansen, Kasper D; Fallin, M Daniele | Epigenetics & chromatin. | 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 A | Science (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 K | ACS 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, Vineet | The Journal of biological chemistry | 2017 Jan 13 | 27913625 | |
| Trans-acting epigenetic effects of chromosomal aneuploidies: lessons from Down syndrome and mouse models. | Do, Catherine; Xing, Zhuo; Yu, Y Eugene; Tycko, Benjamin | Epigenomics. | 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, Katalin | The Journal of biological chemistry. | 2017 01 20; | 27909050 | |
| LOVTRAP: A Versatile Method to Control Protein Function with Light. | Wang, Hui; Hahn, Klaus M | Current protocols in cell biology. | ; | 27906450 | |
| Long-term outdoor air pollution and DNA methylation in circulating monocytes: results from the Multi-Ethnic Study of Atherosclerosis (MESA). | Chi, Gloria C; Liu, Yongmei; MacDonald, James W; Barr, R Graham; Donohue, Kathleen M; Hensley, Mark D; Hou, Lifang; McCall, Charles E; Reynolds, Lindsay M; Siscovick, David S; Kaufman, Joel D | Environmental health : a global access science source. | 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, Paula | Alzheimer'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 E | Nature reviews. Rheumatology | 2016 11 22 | 27872476 | |
| Soft X-Ray Tomography Reveals Gradual Chromatin Compaction and Reorganization during Neurogenesis In Vivo. | Le Gros, Mark A; Clowney, E Josephine; Magklara, Angeliki; Yen, Angela; Markenscoff-Papadimitriou, Eirene; Colquitt, Bradley; Myllys, Markko; Kellis, Manolis; Lomvardas, Stavros; Larabell, Carolyn A | Cell reports. | 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, Aleksandar | Cell 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, Bing | Cell 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, D | Molecular psychiatry. | 2016 Nov 15; | 27843151 | |
| Genetic engineering: Chemical control for CRISPR editing. | Hilton, Isaac B; Gersbach, Charles A | Nature 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 A | Molecular 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, Norbert | Nature 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 D | Alzheimer's & dementia : the journal of the Alzheimer's Association | 2017 May | 27793643 | |
| Complex transcriptional modulation with orthogonal and inducible dCas9 regulators. | Gao, Yuchen; Xiong, Xin; Wong, Spencer; Charles, Emeric J; Lim, Wendell A; Qi, Lei S | Nature methods. | 2016 Dec; | 27776111 | |
| Chromosome conformation elucidates regulatory relationships in developing human brain. | Won, Hyejung; de la Torre-Ubieta, Luis; Stein, Jason L; Parikshak, Neelroop N; Huang, Jerry; Opland, Carli K; Gandal, Michael J; Sutton, Gavin J; Hormozdiari, Farhad; Lu, Daning; Lee, Changhoon; Eskin, Eleazar; Voineagu, Irina; Ernst, Jason; Geschwind, Da | Nature. | 2016 Oct 19; | 27760116 | |
| The long noncoding RNA Tug1 connects metabolic changes with kidney disease in podocytes. | Li, Szu Yuan; Susztak, Katalin | The 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 A | The 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 Z | Gut. | 2018 Jan; | 27742763 | |
| Epigenomic and transcriptional control of insulin resistance. | Rosen, E D | Journal 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 K | Science (New York, N.Y.). | ; | 27738015 | |
| SOX2, OCT3/4 and NANOG expression and cellular plasticity in rare human somatic cells requires CD73. | Pan, Deng; Roy, Somdutta; Gascard, Philippe; Zhao, Jianxin; Chen-Tanyolac, Chira; Tlsty, Thea D | Cellular signalling. | 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, Manolis | Nature 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 A | Oncogene. | 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, Youxin | Medicine. | 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 Claudio | Scientific 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 S | eLife. | 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 A | Neurology | 2016 Oct 18 | 27655734 | |
| Epigenetic Signatures of Cigarette Smoking. | Joehanes, Roby; Just, Allan C; Marioni, Riccardo E; Pilling, Luke C; Reynolds, Lindsay M; Mandaviya, Pooja R; Guan, Weihua; Xu, Tao; Elks, Cathy E; Aslibekyan, Stella; Moreno-Macias, Hortensia; Smith, Jennifer A; Brody, Jennifer A; Dhingra, Radhika; Yousefi, Paul; Pankow, James S; Kunze, Sonja; Shah, Sonia H; McRae, Allan F; Lohman, Kurt; Sha, Jin; Absher, Devin M; Ferrucci, Luigi; Zhao, Wei; Demerath, Ellen W; Bressler, Jan; Grove, Megan L; Huan, Tianxiao; Liu, Chunyu; Mendelson, Michael M; Yao, Chen; Kiel, Douglas P; Peters, Annette; Wang-Sattler, Rui; Visscher, Peter M; Wray, Naomi R; Starr, John M; Ding, Jingzhong; Rodriguez, Carlos J; Wareham, Nicholas J; Irvin, Marguerite R; Zhi, Degui; Barrdahl, Myrto; Vineis, Paolo; Ambatipudi, Srikant; Uitterlinden, André G; Hofman, Albert; Schwartz, Joel; Colicino, Elena; Hou, Lifang; Vokonas, Pantel S; Hernandez, Dena G; Singleton, Andrew B; Bandinelli, Stefania; Turner, Stephen T; Ware, Erin B; Smith, Alicia K; Klengel, Torsten; Binder, Elisabeth B; Psaty, Bruce M; Taylor, Kent D; Gharib, Sina A; Swenson, Brenton R; Liang, Liming; DeMeo, Dawn L; O'Connor, George T; Herceg, Zdenko; Ressler, Kerry J; Conneely, Karen N; Sotoodehnia, Nona; Kardia, Sharon L R; Melzer, David; Baccarelli, Andrea A; van Meurs, Joyce B J; Romieu, Isabelle; Arnett, Donna K; Ong, Ken K; Liu, Yongmei; Waldenberger, Melanie; Deary, Ian J; Fornage, Myriam; Levy, Daniel; London, Stephanie J | Circulation. Cardiovascular genetics. | 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, Yongmei | Nicotine & 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, H | Methods in enzymology. | 2016; | 27586333 | |
| Genome-wide mapping and analysis of chromosome architecture. | Schmitt, Anthony D; Hu, Ming; Ren, Bing | Nature 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, Jonathan | Genome 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 J | Genes & development. | 2016 Aug 15; | 27566777 | |
| Female mice lacking Xist RNA show partial dosage compensation and survive to term. | Yang, Lin; Kirby, James E; Sunwoo, Hongjae; Lee, Jeannie T | Genes & development. | 2016 Aug 01; | 27542829 | |
| BatchQC: interactive software for evaluating sample and batch effects in genomic data. | Manimaran, Solaiappan; Selby, Heather Marie; Okrah, Kwame; Ruberman, Claire; Leek, Jeffrey T; Quackenbush, John; Haibe-Kains, Benjamin; Bravo, Hector Corrada; Johnson, W Evan | Bioinformatics (Oxford, England). | 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, Brian | Biochemistry. | 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, Pilar | Oncotarget. | 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 V | Journal 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 A | Cell 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, Katie | Neurobiology 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, Hiroko | Scientific 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 L | Genome 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 M | Science translational medicine. | 2016 08 10; | 27510902 | |
| Mechanisms of Nucleosome Dynamics In Vivo. | Henikoff, Steven | Cold 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 A | Neurology | 2016 Sep 06 | 27488597 | |
| 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, Dong | Human 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 G | Scientific 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 M | Nature methods. | 2016 Sep; | 27427858 | |
| Uncovering the Role of the Methylome in Dementia and Neurodegeneration. | Klein, Hans-Ulrich; De Jager, Philip L | Trends 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, Yingbin | Medicine. | 2016 Jul; | 27399073 | |
| Go in! Go out! Inducible control of nuclear localization. | Di Ventura, Barbara; Kuhlman, Brian | Current opinion in chemical biology. | 2016 Jun 30; | 27372352 | |
| Ligand-binding domains of nuclear receptors facilitate tight control of split CRISPR activity. | Nguyen, Duy P; Miyaoka, Yuichiro; Gilbert, Luke A; Mayerl, Steven J; Lee, Brian H; Weissman, Jonathan S; Conklin, Bruce R; Wells, James A | Nature communications. | 2016 Jul 01; | 27363581 | |
| Reference-free deconvolution of DNA methylation data and mediation by cell composition effects. | Houseman, E Andres; Kile, Molly L; Christiani, David C; Ince, Tan A; Kelsey, Karl T; Marsit, Carmen J | BMC bioinformatics. | 2016; | 27358049 | |
| An evaluation of processing methods for HumanMethylation450 BeadChip data. | Liu, Jie; Siegmund, Kimberly D | BMC 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 P | G3 (Bethesda, Md.). | 2016 Aug 09; | 27317773 | |
| Using genomic annotations increases statistical power to detect eGenes. | Duong, Dat; Zou, Jennifer; Hormozdiari, Farhad; Sul, Jae Hoon; Ernst, Jason; Han, Buhm; Eskin, Eleazar | Bioinformatics (Oxford, England). | 2016 Jun 15; | 27307612 | |
| Breast cancers from black women exhibit higher numbers of immunosuppressive macrophages with proliferative activity and of crown-like structures associated with lower survival compared to non-black Latinas and Caucasians. | Koru-Sengul, Tulay; Santander, Ana M; Miao, Feng; Sanchez, Lidia G; Jorda, Merce; Glück, Stefan; Ince, Tan A; Nadji, Mehrad; Chen, Zhibin; Penichet, Manuel L; Cleary, Margot P; Torroella-Kouri, Marta | Breast cancer research and treatment. | 2016 Jul; | 27283835 | |
| Genetic variants in Alzheimer disease - molecular and brain network approaches. | Gaiteri, Chris; Mostafavi, Sara; Honey, Christopher J; De Jager, Philip L; Bennett, David A | Nature reviews. Neurology. | 2016 Jul; | 27282653 | |
| Chromatin Domains: The Unit of Chromosome Organization. | Dixon, Jesse R; Gorkin, David U; Ren, Bing | Molecular 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, Kang | Oncotarget. | 2016 Jun 21; | 27246972 | |
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| Deletion of Lkb1 in Renal Tubular Epithelial Cells Leads to CKD by Altering Metabolism. | Han, Seung Hyeok; Malaga-Dieguez, Laura; Chinga, Frank; Kang, Hyun Mi; Tao, Jianling; Reidy, Kimberly; Susztak, Katalin | Journal of the American Society of Nephrology : JASN. | 2016 Feb; | 26054542 | |
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| Myogenin recruits the histone chaperone facilitates chromatin transcription (FACT) to promote nucleosome disassembly at muscle-specific genes. | Lolis, Alexandra A; Londhe, Priya; Beggs, Benjamin C; Byrum, Stephanie D; Tackett, Alan J; Davie, Judith K | The Journal of biological chemistry | 2013 Mar 15 | 7676-87 | 23364797 |
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| Broad ranges of affinity and specificity of anti-histone antibodies revealed by a quantitative peptide immunoprecipitation assay. | Nishikori, Shingo; Hattori, Takamitsu; Fuchs, Stephen M; Yasui, Norihisa; Wojcik, John; Koide, Akiko; Strahl, Brian D; Koide, Shohei | Journal of molecular biology | 2012 Dec 14 | 391-9 | 23041298 |
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