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by Leung, Wilson and Shaffer, Christopher D and Reed, Laura K and Smith, Sheryl T and Barshop, William and Dirkes, William and Dothager, Matthew and Lee, Paul and Wong, Jeannette and Xiong, David and Yuan, Han and Bedard, James E.J and Machone, Joshua F and Patterson, Seantay D and Price, Amber L and Turner, Bryce A and Robic, Srebrenka and Luippold, Erin K and McCartha, Shannon R and Walji, Tezin A and Walker, Chelsea A and Saville, Kenneth and Abrams, Marita K and Armstrong, Andrew R and Armstrong, William and Bailey, Robert J and Barberi, Chelsea R and Beck, Lauren R and Blaker, Amanda L and Blunden, Christopher E and Brand, Jordan P and Brock, Ethan J and Brooks, Dana W and Brown, Marie and Butzler, Sarah C and Clark, Eric M and Clark, Nicole B and Collins, Ashley A and Cotteleer, Rebecca J and Cullimore, Peterson R and Dawson, Seth G and Docking, Carter T and Dorsett, Sasha L and Dougherty, Grace A and Downey, Kaitlyn A and Drake, Andrew P and Earl, Erica K and Floyd, Trevor G and Forsyth, Joshua D and Foust, Jonathan D and Franchi, Spencer L and Geary, James F and Hanson, Cynthia K and Harding, Taylor S and Harris, Cameron B and Heckman, Jonathan M and Holderness, Heather L and Howey, Nicole A and Jacobs, Dontae A and Jewell, Elizabeth S and Kaisler, Maria and Karaska, Elizabeth A and Kehoe, James L and Koaches, Hannah C and Koehler, Jessica and Koenig, Dana and Kujawski, Alexander J and Kus, Jordan E and Lammers, Jennifer A and Leads, Rachel R and Leatherman, Emily C and Lippert, Rachel N and Messenger, Gregory S and Morrow, Adam T and NewcombVictoria, Haley J and Plasman, Plasman and Potocny, Stephanie J and Powers, Michelle K and Reem, Rachel M and Rennhack, Jonathan P and Reynolds, Katherine R and Reynolds, Lyndsey A and Rhee, Dong K and Rivard, Allyson B and Ronk, Adam J and Rooney, Meghan B and Rubin, Lainey S and Salbert, Luke R and Saluja, Rasleen K and Schauder, Taylor and Schneiter, Allison R and Schulz, Robert W and Smith, Karl E and Spencer, Sarah and Swanson, Bryant R and Tache, Melissa A and Tewilliager, Ashley A and Tilot, Amanda K and VanEck, Eve and Villerot, Matthew M and ... and Participating Students Fac Genomic
G3: Genes, Genomes, Genetics, ISSN 2160-1836, 2015, Volume 5, Issue 5, pp. 719 - 740
Journal Article
by Abeshouse, Adam and Adebamowo, Sally N and Adebamowo, Clement and Akbani, Rehan and Akeredolu, Teniola and Ally, Adrian and Anderson, Matthew L and Anur, Pavana and Appelbaum, Elizabeth L and Armenia, Joshua and Auman, J. Todd and Bailey, Matthew H and Baker, Laurence and Balasundaram, Miruna and Balu, Saianand and Barthel, Floris P and Bartlett, John and Baylin, Stephen B and Behera, Madhusmita and Belyaev, Dmitry and Bennett, Joesph and Benz, Christopher and Beroukhim, Rameen and Birrer, Michael and Bocklage, Thèrése and Bodenheimer, Tom and Boice, Lori and Bootwalla, Moiz S and Bowen, Jay and Bowlby, Reanne and Boyd, Jeff and Brohl, Andrew S and Brooks, Denise and Byers, Lauren and Carlsen, Rebecca and Castro, Patricia and Chen, Hsiao-Wei and Cherniack, Andrew D and Chibon, Fréderic and Chin, Lynda and Cho, Juok and Chuah, Eric and Chudamani, Sudha and Cibulskis, Carrie and Cooper, Lee A.D and Cope, Leslie and Cordes, Matthew G and Crain, Daniel and Curley, Erin and Danilova, Ludmila and Dao, Fanny and Davis, Ian J and Davis, Lara E and Defreitas, Timothy and Delman, Keith and Demchok, John A and Demetri, George D and Demicco, Elizabeth G and Dhalla, Noreen and Diao, Lixia and Ding, Li and DiSaia, Phil and Dottino, Peter and Doyle, Leona A and Drill, Esther and Dubina, Michael and Eschbacher, Jennifer and Fedosenko, Konstantin and Felau, Ina and Ferguson, Martin L and Frazer, Scott and Fronick, Catrina C and Fulidou, Victoria and Fulton, Lucinda A and Fulton, Robert S and Gabriel, Stacey B and Gao, Qingsong and Gao, Jianjiong and Gardner, Johanna and Gastier-Foster, Julie M and Gay, Carl M and Gehlenborg, Nils and Gerken, Mark and Getz, Gad and Godwin, Andrew K and Godwin, Eryn M and Gordienko, Elena and Grilley-Olson, Juneko E and Gutman, David A and Gutmann, David H and Hayes, D. Neil and Hegde, Apurva M and Heiman, David I and Heins, Zachary and Helsel, Carmen and Hepperla, Austin J and Higgins, Kelly and Hoadley, Katherine A and Hobensack, Shital and Holt, Robert A and ... and Canc Genome Atlas Res Network and Cancer Genome Atlas Research Network. Electronic address: elizabeth.demicco@sinaihealthsystem.ca and Cancer Genome Atlas Research Network
Cell, ISSN 0092-8674, 11/2017, Volume 171, Issue 4, pp. 950 - 965.e28
Journal Article
Journal of Computational Chemistry, ISSN 0192-8651, 01/2010, Volume 31, Issue 2, pp. 455 - 461
AutoDock Vina, a new program for molecular docking and virtual screening, is presented. AutoDock Vina achieves an approximately two orders of magnitude... 
Computer-aided drug design | Virtual screening | Scoring function | Multithreading | AutoDock | Molecular docking | molecular docking | virtual screening | LIGAND DOCKING | scoring function | BINDING AFFINITIES | COMPLEXES | PDBBIND DATABASE | multithreading | computer-aided drug design | CHEMISTRY, MULTIDISCIPLINARY | PREDICTION
Journal Article
Journal of Molecular Biology, ISSN 0022-2836, 10/2018, Volume 430, Issue 21, pp. 3997 - 4012
Visualization has been a key technology in the progress of structural molecular biology for as long as the field has existed. This perspective describes the... 
molecular graphics | visualization | structural molecular biology | molecular modeling | SYSTEM | PROTEIN STRUCTURES | MANIPULATION | MAPS | BIOCHEMISTRY & MOLECULAR BIOLOGY | MODEL | Analysis | Augmented Reality | Visualization (Computers) | Virtual reality | Models | Molecular biology | Artificial intelligence
Journal Article
by Browning, DJ and Glassman, AR and Aiello, LP and Beck, RW and Brown, DM and Fong, DS and Bressler, NM and Danis, RP and Kinyoun, JL and Nguyen, QD and Bhavsar, AR and Gottlieb, J and Pieramici, DJ and Rauser, ME and Apte, RS and Lim, JI and Miskala, PH and Solomon, SD and Bressler, S and Finkelstein, D and Gehlbach, PL and Sung, JU and Zimmer-Galler, I and Doll, W and Donohue, D and Jurao, R and Sheehan, SE and Belt, J and Sharuk, GS and Arrigg, PG and Schlossman, DK and Shah, ST and Kopple, A and Stockman, ME and Bestourous, L and Calderon, RM and Cavallerano, JD and Chau, T and Cavicchi, RW and Strong, J and Wells, JA and Clark, L and Bearden, RT and Taylor, MM and Spivey, R and Evans, MA and Stone, ML and Gardner, TW and Neely, KA and Chobanoff, SM and Frawley, ML and Ringenbach, KC and Rodriguez, E and Bennett, TJ and Kokame, GT and Shen, J and Chamian, SM and Yuen, A and Callanan, DG and Solley, WA and Elmore, GJ and Boleman, B and Creighton, J and Gray, K and Martinez, JA and Dooner, JW and Harper, CA and Montesclaros, CA and Odean, CE and Cadena, I and Sabo, RA and Berger, BB and Rodriguez, M and Rathman, J and Gallia, B and Ostrander, B and Elman, MJ and Raden, RZ and Sloan, MD and Starr, J and Salfer-Firestone, D and Cain, T and Sotirakos, P and Chew, EY and Coleman, HR and Lerner, R and Short, GL and Cunningham, D and Foster, GE and Kuehl, EM and Palmer, M and Antoszyk, AN and Helms, JV and Price, AK and Chatari, LB and Murphy, HL and Bowen, RM and Lutman, B and McOwen, MD and Gross, JG and ... and Diabet Retinopathy Clinical Res Ne and Diabetic Retinopathy Clinical Research Network
Ophthalmology, ISSN 0161-6420, 2007, Volume 114, Issue 3, pp. 525 - 536
Journal Article
JOURNAL OF CHEMICAL INFORMATION AND MODELING, ISSN 1549-9596, 08/2014, Volume 54, Issue 8, pp. 2371 - 2379
Zinc is present in a wide variety of proteins and is important in the metabolism of most organisms. Zinc metalloenzymes are therapeutically relevant targets in... 
BINDING MODES | CHEMISTRY, MEDICINAL | ATOMIC CHARGES | COMPUTER SCIENCE, INFORMATION SYSTEMS | COORDINATION | HYDROXAMATE | CHEMISTRY, MULTIDISCIPLINARY | BETA | COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS | LIGAND DOCKING | ENZYMES | INHIBITORS | SIMULATIONS | PROTEINS
Journal Article
by Li, Mingfeng and Santpere, Gabriel and Kawasawa, Yuka Imamura and Evgrafov, Oleg V and Gulden, Forrest O and Pochareddy, Sirisha and Sunkin, Susan M and Li, Zhen and Shin, Yurae and Zhu, Ying and Sousa, André M. M and Werling, Donna M and Kitchen, Robert R and Kang, Hyo Jung and Pletikos, Mihovil and Choi, Jinmyung and Muchnik, Sydney and Xu, Xuming and Wang, Daifeng and Lorente-Galdos, Belen and Liu, Shuang and Giusti-Rodríguez, Paola and Won, Hyejung and De Leeuw, Christiaan A and Pardiñas, Antonio F and Reimers, M.A and Willsey, A.J and Oldre, A and Szafer, A and Camarena, A and Cherskov, A and Charney, A.W and Abyzov, A and Kozlenkov, A and Safi, A and Jones, A.R and Ashley-Koch, AE and Ebbert, A and Price, A.J and Sekijima, A and Kefi, A and Bernard, A and Amiri, A and Sboner, A and Clark, A and Jaffe, A.E and Tebbenkamp, A.T.N and Sodt, A.J and Guillozet-Bongaarts, AL and Nairn, A.C and Carey, A and Huttner, A and Chervenak, A and Szekely, A and Shieh, A.W and Harmanci, A and Lipska, B.K and Carlyle, B.C and Gregor, B.W and Kassim, B.S and Sheppard, B and Bichsel, C and Hahn, C.G and Lee, C.K and Chen, C and Kuan, C.L and Dang, C and Lau, C and Cuhaciyan, C and Armoskus, C and Mason, C.E and Liu, C and Slaughterbeck, C.R and Bennet, C and Pinto, D and Polioudakis, D and Franjic, D and Miller, D.J and Bertagnolli, D and Lewis, D.A and Feng, D and Sandman, D and Clarke, D and Williams, D and DelValle, D and Fitzgerald, D and Shen, E.H and Flatow, E and Zharovsky, E and Burke, E.E and Olson, E and Fulfs, E and Mattei, E and Hadjimichael, E and Deelman, E and Navarro, F.C.P and Wu, F and Lee, F and Cheng, F and Goes, F.S and ... and PsychENCODE Dev Subgrp and BrainSpan Consortium and PsychENCODE Consortium and PsychENCODE Developmental Subgroup
Science, ISSN 0036-8075, 12/2018, Volume 362, Issue 6420, pp. 1264 - 1264
Journal Article
by Thorsson, Vesteinn and Thorsson, Vésteinn and Gibbs, Richard A and Gibbs, David L and Brown, Scott D and Wolf, Gregory and Wolf, Denise and Bortone, Dante S and Ou Yang, Tai-Hsien and Porta-Pardo, Eduard and Gao, Galen F and Gao, Jianjiong and Plaisier, Christopher L and Eddy, James A and Ziv, Elad and Culhane, Aedin C and Paull, Evan O and Sivakumar, I.K. Ashok and Gentles, Andrew J and Malhotra, Raunaq and Farshidfar, Farshad and Colaprico, Antonio and Parker, Joel S and Mose, Lisle E and Vo, Nam Sy and Liu, Wenbin and Liu, Jianfang and Liu, Jia and Liu, Yuexin and Liu, Xiuping and Rader, Janet and Dhankani, Varsha and Reynolds, Sheila and Reynolds, Sheila M and Bowlby, Reanne and Califano, Andrea and Cherniack, Andrew D and Anastassiou, Dimitris and Bedognetti, Davide and Mokrab, Younes and Newman, Aaron M and Rao, Arvind and Chen, Amy and Chen, Chu and Chen, Ken and Krasnitz, Alexander and Hu, Jianhong and Hu, Hai and Malta, Tathiane M and Noushmehr, Houtan and Pedamallu, Chandra Sekhar and Bullman, Susan and Ojesina, Akinyemi I and Lamb, Andrew and Zhou, Wanding and Shen, Hui and Choueiri, Toni K and Weinstein, John N and Guinney, Justin and Saltz, Joel and Holt, Robert and Holt, Robert A and Rabkin, Charles S and Caesar-Johnson, Samantha J and Demchok, John A and Felau, Ina and Kasapi, Melpomeni and Ferguson, Martin L and Hutter, Carolyn M and Sofia, Heidi J and Tarnuzzer, Roy and Wang, Jioajiao and Wang, Min and Wang, Linghua and Wang, Zhining and Wang, Timothy and Wang, Jing and Yang, Ju Dong and Yang, Hannah and Yang, Liming and Yang, Ian and Zenklusen, Jean C and Zhang, Jiashan (Julia) and Zhang, Jiexin and Zhang, Lizhi and Zhang, Wei and Zhang, Hongzheng and Zhang, Hailei and Zhang, Hongxin and Chudamani, Sudha and Lolla, Laxmi and Naresh, Rashi and Pihl, Todd and Sun, Yichao and Sun, Qiang and Wan, Yunhu and Wu, Ye and Cho, Juok and DeFreitas, Timothy and Frazer, Scott and ... and Canc Genome Atlas Res Network and Cancer Genome Atlas Research Network
Immunity, ISSN 1074-7613, 04/2018, Volume 48, Issue 4, pp. 812 - 830.e14
We performed an extensive immunogenomic analysis of more than 10,000 tumors comprising 33 diverse cancer types by utilizing data compiled by TCGA. Across... 
tumor immunology | immunotherapy | cancer genomics | integrative network analysis | immuno-oncology | tumor microenvironment | immune subtypes | immunomodulatory | GENOMIC ANALYSES | INFORMATION | T-CELL-RECEPTOR | REGULATORY NETWORK | CLASSIFICATION | IMMUNOLOGY | SEQUENCING DATA | SOMATIC MUTATIONS | COMPREHENSIVE ANALYSIS | PREDICTION | REVEALS | Transforming Growth Factor beta - immunology | Prognosis | Humans | Middle Aged | Th1-Th2 Balance - physiology | Male | Neoplasms - classification | Wound Healing - immunology | Young Adult | Transforming Growth Factor beta - genetics | Neoplasms - genetics | Neoplasms - immunology | Interferon-gamma - immunology | Adolescent | Aged, 80 and over | Adult | Female | Aged | Interferon-gamma - genetics | Wound Healing - genetics | Genomics - methods | Child | Macrophages - immunology | Cell proliferation | Cluster analysis | Transcription | Copy number | p53 Protein | Lung cancer | Genomics | Aneuploidy | Lymphocytes T | Genomes | Cell interactions | Macrophages | Immunotherapy | DNA methylation | Deoxyribonucleic acid--DNA | Immune system | Medical research | Wound healing | Immunomodulation | MiRNA | Stockholders | Inflammation | T cell receptors | Communications networks | Gene expression | White blood cells | Inventors | Medical prognosis | γ-Interferon | Mutation | Cancer | Tumors | Immune Subtypes | Integrative Network Analysis | Cancer Genomics | Immuno-oncology | Tumor immunology
Journal Article