| Structure-based discovery of potent and selective melatonin receptor agonists. | Patel, Nilkanth; Huang, Xi Ping; Grandner, Jessica M; Johansson, Linda C; Stauch, Benjamin; McCorvy, John D; Liu, Yongfeng; Roth, Bryan; Katritch, Vsevolod | eLife. | 2020 Mar 02; | | 32118583 |
| Virtual discovery of melatonin receptor ligands to modulate circadian rhythms. | Stein, Reed M; Kang, Hye Jin; McCorvy, John D; Glatfelter, Grant C; Jones, Anthony J; Che, Tao; Slocum, Samuel; Huang, Xi-Ping; Savych, Olena; Moroz, Yurii S; Stauch, Benjamin; Johansson, Linda C; Cherezov, Vadim; Kenakin, Terry; Irwin, John J; Shoichet, Brian K; Roth, Bryan L; Dubocovich, Margarita L | Nature. | 2020 03; | | 32040955 |
| Genetic deletion of gpr27 alters acylcarnitine metabolism, insulin sensitivity, and glucose homeostasis in zebrafish. | Nath, Anjali K; Ma, Junyan; Chen, Zsu-Zsu; Li, Zhuyun; Vitery, Maria Del Carmen; Kelley, Michelle L; Peterson, Randall T; Gerszten, Robert E; Yeh, Jing-Ruey J | FASEB journal : official publication of the Federation of American Societies for Experimental Biology. | 2020 Jan; | | 31914600 |
| How to Illuminate the Druggable Genome Using Pharos. | Sheils, Timothy; Mathias, Stephen L; Siramshetty, Vishal B; Bocci, Giovanni; Bologa, Cristian G; Yang, Jeremy J; Waller, Anna; Southall, Noel; Nguyen, Dac-Trung; Oprea, Tudor I | Current protocols in bioinformatics. | 2020 Mar; | | 31898878 |
| Dermal sheath contraction powers stem cell niche relocation during hair cycle regression. | Heitman, Nicholas; Sennett, Rachel; Mok, Ka-Wai; Saxena, Nivedita; Srivastava, Devika; Martino, Pieter; Grisanti, Laura; Wang, Zichen; Ma'ayan, Avi; Rompolas, Panteleimon; Rendl, Michael | Science (New York, N.Y.). | 2020 01 10; | | 31857493 |
| Can BDDCS illuminate targets in drug design? | Bocci, Giovanni; Benet, Leslie Z; Oprea, Tudor I | Drug discovery today. | 2019 Dec; | | 31585170 |
| PDBe-KB: a community-driven resource for structural and functional annotations. | PDBe-KB consortium | Nucleic acids research. | 2020 Jan 08; | | 31584092 |
| Recombination drives the evolution of mutational robustness. | Singhal, Sonia; Gomez, Shawn M; Burch, Christina L | Current opinion in systems biology. | 2019 Feb; | | 31572829 |
| Zebrafish behavioural profiling identifies GABA and serotonin receptor ligands related to sedation and paradoxical excitation. | McCarroll, Matthew N; Gendelev, Leo; Kinser, Reid; Taylor, Jack; Bruni, Giancarlo; Myers-Turnbull, Douglas; Helsell, Cole; Carbajal, Amanda; Rinaldi, Capria; Kang, Hye Jin; Gong, Jung Ho; Sello, Jason K; Tomita, Susumu; Peterson, Randall T; Keiser, Michae | Nature communications. | 2019 09 09; | | 31501447 |
| VEGAS as a Platform for Facile Directed Evolution in Mammalian Cells. | English, Justin G; Olsen, Reid H J; Lansu, Katherine; Patel, Michael; White, Karoline; Cockrell, Adam S; Singh, Darshan; Strachan, Ryan T; Wacker, Daniel; Roth, Bryan L | Cell. | 2019 Aug 08; | | 31398329 |
| Identification of hyper-rewired genomic stress non-oncogene addiction genes across 15 cancer types. | Hjaltelin, Jessica Xin; Izarzugaza, Jose M G; Jensen, Lars Juhl; Russo, Francesco; Westergaard, David; Brunak, Søren | NPJ systems biology and applications. | 2019; | | 31396397 |
| Visualization of drug target interactions in the contexts of pathways and networks with ReactomeFIViz. | Blucher, Aurora S; McWeeney, Shannon K; Stein, Lincoln; Wu, Guanming | F1000Research. | 2019; | | 31372215 |
| Kinome profiling of non-Hodgkin lymphoma identifies Tyro3 as a therapeutic target in primary effusion lymphoma. | Wong, Jason P; Stuhlmiller, Timothy J; Giffin, Louise C; Lin, Carolina; Bigi, Rachele; Zhao, Jichen; Zhang, Weihe; Bravo Cruz, Ariana G; Park, Steven I; Earp, H Shelton; Dittmer, Dirk P; Frye, Stephen V; Wang, Xiaodong; Johnson, Gary L; Damania, Blossom | Proceedings of the National Academy of Sciences of the United States of America. | 2019 Aug 13; | | 31346082 |
| VEGAS as a Platform for Facile Directed Evolution in Mammalian Cells. | English, Justin G; Olsen, Reid H J; Lansu, Katherine; Patel, Michael; White, Karoline; Cockrell, Adam S; Singh, Darshan; Strachan, Ryan T; Wacker, Daniel; Roth, Bryan L | Cell. | 2019 Jul 25; | | 31280962 |
| OSCI: standardized stem cell ontology representation and use cases for stem cell investigation. | He, Yongqun; Duncan, William D; Cooper, Daniel J; Hansen, Jens; Iyengar, Ravi; Ong, Edison; Walker, Kendal; Tibi, Omar; Smith, Sam; Serra, Lucas M; Zheng, Jie; Sarntivijai, Sirarat; Schürer, Stephan; O'Shea, K Sue; Diehl, Alexander D | BMC bioinformatics. | 2019 Apr 25; | | 31272389 |
| Exploring the dark genome: implications for precision medicine. | Oprea, Tudor I | Mammalian genome : official journal of the International Mammalian Genome Society. | 2019 Aug; | | 31270560 |
| Molecular pharmacology of metabotropic receptors targeted by neuropsychiatric drugs. | Roth, Bryan L | Nature structural & molecular biology. | 2019 Jul; | | 31270468 |
| The human endogenous metabolome as a pharmacology baseline for drug discovery. | Bofill, Andreu; Jalencas, Xavier; Oprea, Tudor I; Mestres, Jordi | Drug discovery today. | 2019 09; | | 31226432 |
| CoCoScore: context-aware co-occurrence scoring for text mining applications using distant supervision. | Junge, Alexander; Jensen, Lars Juhl | Bioinformatics (Oxford, England). | 2020 Jan 01; | | 31199464 |
| ChEA3: transcription factor enrichment analysis by orthogonal omics integration. | Keenan, Alexandra B; Torre, Denis; Lachmann, Alexander; Leong, Ariel K; Wojciechowicz, Megan L; Utti, Vivian; Jagodnik, Kathleen M; Kropiwnicki, Eryk; Wang, Zichen; Ma'ayan, Avi | Nucleic acids research. | 2019 Jul 02; | | 31114921 |
| Geneshot: search engine for ranking genes from arbitrary text queries. | Lachmann, Alexander; Schilder, Brian M; Wojciechowicz, Megan L; Torre, Denis; Kuleshov, Maxim V; Keenan, Alexandra B; Ma'ayan, Avi | Nucleic acids research. | 2019 Jul 02; | | 31114885 |
| modEnrichr: a suite of gene set enrichment analysis tools for model organisms. | Kuleshov, Maxim V; Diaz, Jennifer E L; Flamholz, Zachary N; Keenan, Alexandra B; Lachmann, Alexander; Wojciechowicz, Megan L; Cagan, Ross L; Ma'ayan, Avi | Nucleic acids research. | 2019 Jul 02; | | 31069376 |
| Publisher Correction: Structural basis of ligand recognition at the human MT1 melatonin receptor. | Stauch, Benjamin; Johansson, Linda C; McCorvy, John D; Patel, Nilkanth; Han, Gye Won; Huang, Xi-Ping; Gati, Cornelius; Batyuk, Alexander; Slocum, Samuel T; Ishchenko, Andrii; Brehm, Wolfgang; White, Thomas A; Michaelian, Nairie; Madsen, Caleb; Zhu, Lan; Grant, Thomas D; Grandner, Jessica M; Shiriaeva, Anna; Olsen, Reid H J; Tribo, Alexandra R; Yous, Saïd; Stevens, Raymond C; Weierstall, Uwe; Katritch, Vsevolod; Roth, Bryan L; Liu, Wei; Cherezov, Vadim | Nature. | 2019 May; | | 31048811 |
| A Perspective on Extreme Open Science: Companies Sharing Compounds without Restriction. | Drewry, David H; Wells, Carrow I; Zuercher, William J; Willson, Timothy M | SLAS discovery : advancing life sciences R & D. | 2019 Jun; | | 31034310 |
| Structural basis of ligand recognition at the human MT1 melatonin receptor. | Stauch, Benjamin; Johansson, Linda C; McCorvy, John D; Patel, Nilkanth; Han, Gye Won; Huang, Xi-Ping; Gati, Cornelius; Batyuk, Alexander; Slocum, Samuel T; Ishchenko, Andrii; Brehm, Wolfgang; White, Thomas A; Michaelian, Nairie; Madsen, Caleb; Zhu, Lan; Grant, Thomas D; Grandner, Jessica M; Shiriaeva, Anna; Olsen, Reid H J; Tribo, Alexandra R; Yous, Saïd; Stevens, Raymond C; Weierstall, Uwe; Katritch, Vsevolod; Roth, Bryan L; Liu, Wei; Cherezov, Vadim | Nature. | 2019 May; | | 31019306 |
| XFEL structures of the human MT2 melatonin receptor reveal the basis of subtype selectivity. | Johansson, Linda C; Stauch, Benjamin; McCorvy, John D; Han, Gye Won; Patel, Nilkanth; Huang, Xi-Ping; Batyuk, Alexander; Gati, Cornelius; Slocum, Samuel T; Li, Chufeng; Grandner, Jessica M; Hao, Shuming; Olsen, Reid H J; Tribo, Alexandra R; Zaare, Sahba; Zhu, Lan; Zatsepin, Nadia A; Weierstall, Uwe; Yous, Saïd; Stevens, Raymond C; Liu, Wei; Roth, Bryan L; Katritch, Vsevolod; Cherezov, Vadim | Nature. | 2019 May; | | 31019305 |
| Improving the Utility of the Tox21 Dataset by Deep Metadata Annotations and Constructing Reusable Benchmarked Chemical Reference Signatures. | Cooper, Daniel J; Schürer, Stephan | Molecules (Basel, Switzerland). | 2019 Apr 23; | | 31018579 |
| GSK2801, A BAZ2/BRD9 Bromodomain Inhibitor, Synergizes with BET Inhibitors to Induce Apoptosis in Triple-Negative Breast Cancer. | Bevill, Samantha M; Olivares-Quintero, Jose F; Sciaky, Noah; Golitz, Brian T; Singh, Darshan; Beltran, Adriana S; Rashid, Naim U; Stuhlmiller, Timothy J; Hale, Andrew; Moorman, Nathaniel J; Santos, Charlene M; Angus, Steven P; Zawistowski, Jon S; Johnson, Gary L | Molecular cancer research : MCR. | 2019 Apr 18; | | 31000582 |
| Engineering a haematopoietic stem cell niche by revitalizing mesenchymal stromal cells. | Nakahara, Fumio; Borger, Daniel K; Wei, Qiaozhi; Pinho, Sandra; Maryanovich, Maria; Zahalka, Ali H; Suzuki, Masako; Cruz, Cristian D; Wang, Zichen; Xu, Chunliang; Boulais, Philip E; Ma'ayan, Avi; Greally, John M; Frenette, Paul S | Nature cell biology. | 2019 Apr 15; | | 30988422 |
| D2 Dopamine Receptor G Protein-Biased Partial Agonists Based on Cariprazine. | Shen, Yudao; McCorvy, John D; Martini, Michael L; Rodriguiz, Ramona M; Pogorelov, Vladimir M; Ward, Karen M; Wetsel, William C; Liu, Jing; Roth, Bryan L; Jin, Jian | Journal of medicinal chemistry. | 2019 May 09; | | 30964661 |
| Cheminformatics Tools for Analyzing and Designing Optimized Small-Molecule Collections and Libraries. | Moret, Nienke; Clark, Nicholas A; Hafner, Marc; Wang, Yuan; Lounkine, Eugen; Medvedovic, Mario; Wang, Jinhua; Gray, Nathanael; Jenkins, Jeremy; Sorger, Peter K | Cell chemical biology. | 2019 Mar 12; | | 30956147 |
| Defining Structure-Functional Selectivity Relationships (SFSR) for a Class of Non-Catechol Dopamine D1 Receptor Agonists. | Martini, Michael L; Liu, Jing; Ray, Caroline; Yu, Xufen; Huang, Xi-Ping; Urs, Aarti; Urs, Nikhil; McCorvy, John D; Caron, Marc G; Roth, Bryan L; Jin, Jian | Journal of medicinal chemistry. | 2019 Apr 11; | | 30875219 |
| DREADD Agonist 21 Is an Effective Agonist for Muscarinic-Based DREADDs in Vitro and in Vivo. | Thompson, Karen J; Khajehali, Elham; Bradley, Sophie J; Navarrete, Jovana S; Huang, Xi Ping; Slocum, Samuel; Jin, Jian; Liu, Jing; Xiong, Yan; Olsen, Reid H J; Diberto, Jeffrey F; Boyt, Kristen M; Pina, Melanie M; Pati, Dipanwita; Molloy, Colin; Bundgaard | ACS pharmacology & translational science. | 2018 Sep 14; | | 30868140 |
| How to Prepare a Compound Collection Prior to Virtual Screening. | Bologa, Cristian G; Ursu, Oleg; Oprea, Tudor I | Methods in molecular biology (Clifton, N.J.). | 2019; | | 30848459 |
| Leveraging Big Data to Transform Drug Discovery. | Glicksberg, Benjamin S; Li, Li; Chen, Rong; Dudley, Joel; Chen, Bin | Methods in molecular biology (Clifton, N.J.). | 2019; | | 30848458 |
| How to Develop a Drug Target Ontology: KNowledge Acquisition and Representation Methodology (KNARM). | Küçük McGinty, Hande; Visser, Ubbo; Schürer, Stephan | Methods in molecular biology (Clifton, N.J.). | 2019; | | 30848456 |
| An African-specific haplotype in MRGPRX4 is associated with menthol cigarette smoking. | Kozlitina, Julia; Risso, Davide; Lansu, Katherine; Olsen, Reid Hans Johnson; Sainz, Eduardo; Luiselli, Donata; Barik, Arnab; Frigerio-Domingues, Carlos; Pagani, Luca; Wooding, Stephen; Kirchner, Thomas; Niaura, Ray; Roth, Bryan; Drayna, Dennis | PLoS genetics. | 2019 02; | | 30768591 |
| SGC-GAK-1: A Chemical Probe for Cyclin G Associated Kinase (GAK). | Asquith, Christopher R M; Berger, Benedict-Tilman; Wan, Jing; Bennett, James M; Capuzzi, Stephen J; Crona, Daniel J; Drewry, David H; East, Michael P; Elkins, Jonathan M; Fedorov, Oleg; Godoi, Paulo H; Hunter, Debra M; Knapp, Stefan; Müller, Susanne; Torrice, Chad D; Wells, Carrow I; Earp, H Shelton; Willson, Timothy M; Zuercher, William J | Journal of medicinal chemistry. | 2019 Mar 14; | | 30768268 |
| Predicting opioid dependence from electronic health records with machine learning. | Ellis, Randall J; Wang, Zichen; Genes, Nicholas; Ma'ayan, Avi | BioData mining. | 2019; | | 30728857 |
| Ultra-large library docking for discovering new chemotypes. | Lyu, Jiankun; Wang, Sheng; Balius, Trent E; Singh, Isha; Levit, Anat; Moroz, Yurii S; O'Meara, Matthew J; Che, Tao; Algaa, Enkhjargal; Tolmachova, Kateryna; Tolmachev, Andrey A; Shoichet, Brian K; Roth, Bryan L; Irwin, John J | Nature. | 2019 Feb; | | 30728502 |
| WNT Activates the AAK1 Kinase to Promote Clathrin-Mediated Endocytosis of LRP6 and Establish a Negative Feedback Loop. | Agajanian, Megan J; Walker, Matthew P; Axtman, Alison D; Ruela-de-Sousa, Roberta R; Serafin, D Stephen; Rabinowitz, Alex D; Graham, David M; Ryan, Meagan B; Tamir, Tigist; Nakamichi, Yuko; Gammons, Melissa V; Bennett, James M; Couñago, Rafael M; Drewry, David H; Elkins, Jonathan M; Gileadi, Carina; Gileadi, Opher; Godoi, Paulo H; Kapadia, Nirav; Müller, Susanne; Santiago, André S; Sorrell, Fiona J; Wells, Carrow I; Fedorov, Oleg; Willson, Timothy M; Zuercher, William J; Major, Michael B | Cell reports. | 2019 Jan 02; | | 30605688 |
| Dermal Condensate Niche Fate Specification Occurs Prior to Formation and Is Placode Progenitor Dependent. | Mok, Ka-Wai; Saxena, Nivedita; Heitman, Nicholas; Grisanti, Laura; Srivastava, Devika; Muraro, Mauro J; Jacob, Tina; Sennett, Rachel; Wang, Zichen; Su, Yutao; Yang, Lu M; Ma'ayan, Avi; Ornitz, David M; Kasper, Maria; Rendl, Michael | Developmental cell. | 2019 Jan 07; | | 30595537 |
| Mining data and metadata from the gene expression omnibus. | Wang, Zichen; Lachmann, Alexander; Ma'ayan, Avi | Biophysical reviews. | 2019 Feb; | | 30594974 |
| Drug and disease signature integration identifies synergistic combinations in glioblastoma. | Stathias, Vasileios; Jermakowicz, Anna M; Maloof, Marie E; Forlin, Michele; Walters, Winston; Suter, Robert K; Durante, Michael A; Williams, Sion L; Harbour, J William; Volmar, Claude-Henry; Lyons, Nicholas J; Wahlestedt, Claes; Graham, Regina M; Ivan, Michael E; Komotar, Ricardo J; Sarkaria, Jann N; Subramanian, Aravind; Golub, Todd R; Schürer, Stephan C; Ayad, Nagi G | Nature communications. | 2018 12 14; | | 30552330 |
| Far away from the lamppost. | Oprea, Tudor I; Jan, Lily; Johnson, Gary L; Roth, Bryan L; Ma'ayan, Avi; Schürer, Stephan; Shoichet, Brian K; Sklar, Larry A; McManus, Michael T | PLoS biology. | 2018 Dec; | | 30532236 |
| A Comparative Study of the Pharmacokinetics of Clozapine N-Oxide and Clozapine N-Oxide Hydrochloride Salt in Rhesus Macaques. | Allen, Daicia C; Carlson, Timothy L; Xiong, Yan; Jin, Jian; Grant, Kathleen A; Cuzon Carlson, Verginia C | The Journal of pharmacology and experimental therapeutics. | 2019 Feb; | | 30523062 |
| Temporal proteomic profiling of postnatal human cortical development. | Breen, Michael S; Ozcan, Sureyya; Ramsey, Jordan M; Wang, Zichen; Ma'ayan, Avi; Rustogi, Nitin; Gottschalk, Michael G; Webster, Maree J; Weickert, Cynthia Shannon; Buxbaum, Joseph D; Bahn, Sabine | Translational psychiatry. | 2018 Dec 05; | | 30518843 |
| BioJupies: Automated Generation of Interactive Notebooks for RNA-Seq Data Analysis in the Cloud. | Torre, Denis; Lachmann, Alexander; Ma'ayan, Avi | Cell systems. | 2018 Nov 08; | | 30447998 |
| Critical period plasticity-related transcriptional aberrations in schizophrenia and bipolar disorder. | Smith, Milo R; Readhead, Ben; Dudley, Joel T; Morishita, Hirofumi | Schizophrenia research. | 2019 05; | | 30442475 |
| Integrative bioinformatics identifies postnatal lead (Pb) exposure disrupts developmental cortical plasticity. | Smith, Milo R; Yevoo, Priscilla; Sadahiro, Masato; Austin, Christine; Amarasiriwardena, Chitra; Awawda, Mahmoud; Arora, Manish; Dudley, Joel T; Morishita, Hirofumi | Scientific reports. | 2018 11 06; | | 30401819 |
| DrugCentral 2018: an update. | Ursu, Oleg; Holmes, Jayme; Bologa, Cristian G; Yang, Jeremy J; Mathias, Stephen L; Stathias, Vasileios; Nguyen, Dac-Trung; Schürer, Stephan; Oprea, Tudor | Nucleic acids research. | 2018 Oct 29; | | 30371892 |
| Darkness in the Human Gene and Protein Function Space: Widely Modest or Absent Illumination by the Life Science Literature and the Trend for Fewer Protein Function Discoveries Since 2000. | Sinha, Swati; Eisenhaber, Birgit; Jensen, Lars Juhl; Kalbuaji, Bharata; Eisenhaber, Frank | Proteomics. | 2018 Nov; | | 30265449 |
| Covalent inhibitors of EGFR family protein kinases induce degradation of human Tribbles 2 (TRIB2) pseudokinase in cancer cells. | Foulkes, Daniel M; Byrne, Dominic P; Yeung, Wayland; Shrestha, Safal; Bailey, Fiona P; Ferries, Samantha; Eyers, Claire E; Keeshan, Karen; Wells, Carrow; Drewry, David H; Zuercher, William J; Kannan, Natarajan; Eyers, Patrick A | Science signaling. | 2018 Sep 25; | | 30254057 |
| Coral: Clear and Customizable Visualization of Human Kinome Data. | Metz, Kathleen S; Deoudes, Erika M; Berginski, Matthew E; Jimenez-Ruiz, Ivan; Aksoy, Bulent Arman; Hammerbacher, Jeff; Gomez, Shawn M; Phanstiel, Douglas H | Cell systems. | 2018 09 26; | | 30172842 |
| Drug Gene Budger (DGB): an application for ranking drugs to modulate a specific gene based on transcriptomic signatures. | Wang, Zichen; He, Edward; Sani, Kevin; Jagodnik, Kathleen M; Silverstein, Moshe C; Ma'ayan, Avi | Bioinformatics (Oxford, England). | 2019 Apr 01; | | 30169739 |
| Podocyte-Specific Induction of Krüppel-Like Factor 15 Restores Differentiation Markers and Attenuates Kidney Injury in Proteinuric Kidney Disease. | Guo, Yiqing; Pace, Jesse; Li, Zhengzhe; Ma'ayan, Avi; Wang, Zichen; Revelo, Monica P; Chen, Edward; Gu, Xiangchen; Attalah, Ahmed; Yang, Yaqi; Estrada, Chelsea; Yang, Vincent W; He, John C; Mallipattu, Sandeep K | Journal of the American Society of Nephrology : JASN. | 2018 Aug 24; | | 30143559 |
| Gut Microbial ?-Glucuronidase Inhibition via Catalytic Cycle Interception. | Pellock, Samuel J; Creekmore, Benjamin C; Walton, William G; Mehta, Naimee; Biernat, Kristen A; Cesmat, Andrew P; Ariyarathna, Yamuna; Dunn, Zachary D; Li, Bo; Jin, Jian; James, Lindsey I; Redinbo, Matthew R | ACS central science. | 2018 Jul 25; | | 30062115 |
| Artificial Intelligence in Cardiology. | Johnson, Kipp W; Torres Soto, Jessica; Glicksberg, Benjamin S; Shameer, Khader; Miotto, Riccardo; Ali, Mohsin; Ashley, Euan; Dudley, Joel T | Journal of the American College of Cardiology. | 2018 06 12; | | 29880128 |
| eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks. | Clarke, Daniel J B; Kuleshov, Maxim V; Schilder, Brian M; Torre, Denis; Duffy, Mary E; Keenan, Alexandra B; Lachmann, Alexander; Feldmann, Axel S; Gundersen, Gregory W; Silverstein, Moshe C; Wang, Zichen; Ma'ayan, Avi | Nucleic acids research. | 2018 Jul 02; | | 29800326 |
| Integration of protein phosphorylation, acetylation, and methylation data sets to outline lung cancer signaling networks. | Grimes, Mark; Hall, Benjamin; Foltz, Lauren; Levy, Tyler; Rikova, Klarisa; Gaiser, Jeremiah; Cook, William; Smirnova, Ekaterina; Wheeler, Travis; Clark, Neil R; Lachmann, Alexander; Zhang, Bin; Hornbeck, Peter; Ma'ayan, Avi; Comb, Michael | Science signaling. | 2018 05 22; | | 29789295 |
| Application of Integrated Drug Screening/Kinome Analysis to Identify Inhibitors of Gemcitabine-Resistant Pancreatic Cancer Cell Growth. | Krulikas, Linas J; McDonald, Ian M; Lee, Benjamin; Okumu, Denis O; East, Michael P; Gilbert, Thomas S K; Herring, Laura E; Golitz, Brian T; Wells, Carrow I; Axtman, Allison D; Zuercher, William J; Willson, Timothy M; Kireev, Dmitri; Yeh, Jen Jen; Johnson, Gary L; Baines, Antonio T; Graves, Lee M | SLAS discovery : advancing life sciences R & D. | 2018 09; | | 29742358 |
| A proteomics landscape of circadian clock in mouse liver. | Wang, Yunzhi; Song, Lei; Liu, Mingwei; Ge, Rui; Zhou, Quan; Liu, Wanlin; Li, Ruiyang; Qie, Jingbo; Zhen, Bei; Wang, Yi; He, Fuchu; Qin, Jun; Ding, Chen | Nature communications. | 2018 Apr 19; | | 29674717 |
| Proteomic analysis defines kinase taxonomies specific for subtypes of breast cancer. | Collins, Kyla A L; Stuhlmiller, Timothy J; Zawistowski, Jon S; East, Michael P; Pham, Trang T; Hall, Claire R; Goulet, Daniel R; Bevill, Samantha M; Angus, Steven P; Velarde, Sara H; Sciaky, Noah; Oprea, Tudor I; Graves, Lee M; Johnson, Gary L; Gomez, Shawn M | Oncotarget. | 2018 Mar 20; | | 29643987 |
| Massive mining of publicly available RNA-seq data from human and mouse. | Lachmann, Alexander; Torre, Denis; Keenan, Alexandra B; Jagodnik, Kathleen M; Lee, Hoyjin J; Wang, Lily; Silverstein, Moshe C; Ma'ayan, Avi | Nature communications. | ; | | 29636450 |
| Unexplored therapeutic opportunities in the human genome. | Oprea, Tudor I; Bologa, Cristian G; Brunak, Søren; Campbell, Allen; Gan, Gregory N; Gaulton, Anna; Gomez, Shawn M; Guha, Rajarshi; Hersey, Anne; Holmes, Jayme; Jadhav, Ajit; Jensen, Lars Juhl; Johnson, Gary L; Karlson, Anneli; Leach, Andrew R; Ma'ayan, Avi; Malovannaya, Anna; Mani, Subramani; Mathias, Steven L; McManus, Michael T; Meehan, Terrence F; von Mering, Christian; Muthas, Daniel; Nguyen, Dac-Trung; Overington, John P; Papadatos, George; Qin, Jun; Reich, Christian; Roth, Bryan L; Schürer, Stephan C; Simeonov, Anton; Sklar, Larry A; Southall, Noel; Tomita, Susumu; Tudose, Ilinca; Ursu, Oleg; Vidovic, Du?ica; Waller, Anna; Westergaard, David; Yang, Jeremy J; Zahoránszky-Köhalmi, Gergely | Nature reviews. Drug discovery. | 2018 May; | | 29567993 |
| A proteomic landscape of diffuse-type gastric cancer. | Ge, Sai; Xia, Xia; Ding, Chen; Zhen, Bei; Zhou, Quan; Feng, Jinwen; Yuan, Jiajia; Chen, Rui; Li, Yumei; Ge, Zhongqi; Ji, Jiafu; Zhang, Lianhai; Wang, Jiayuan; Li, Zhongwu; Lai, Yumei; Hu, Ying; Li, Yanyan; Li, Yilin; Gao, Jing; Chen, Lin; Xu, Jianming; Zh | Nature communications. | 2018 03 08; | | 29520031 |
| The Transcriptionally Permissive Chromatin State of Embryonic Stem Cells Is Acutely Tuned to Translational Output. | Bulut-Karslioglu, Aydan; Macrae, Trisha A; Oses-Prieto, Juan A; Covarrubias, Sergio; Percharde, Michelle; Ku, Gregory; Diaz, Aaron; McManus, Michael T; Burlingame, Alma L; Ramalho-Santos, Miguel | Cell stem cell. | 2018 03 01; | | 29499153 |
| Datasets2Tools, repository and search engine for bioinformatics datasets, tools and canned analyses. | Torre, Denis; Krawczuk, Patrycja; Jagodnik, Kathleen M; Lachmann, Alexander; Wang, Zichen; Wang, Lily; Kuleshov, Maxim V; Ma'ayan, Avi | Scientific data. | 2018 Feb 27; | | 29485625 |
| Unexplored therapeutic opportunities in the human genome. | Oprea, Tudor I; Bologa, Cristian G; Brunak, Søren; Campbell, Allen; Gan, Gregory N; Gaulton, Anna; Gomez, Shawn M; Guha, Rajarshi; Hersey, Anne; Holmes, Jayme; Jadhav, Ajit; Jensen, Lars Juhl; Johnson, Gary L; Karlson, Anneli; Leach, Andrew R; Ma'ayan, Avi; Malovannaya, Anna; Mani, Subramani; Mathias, Stephen L; McManus, Michael T; Meehan, Terrence F; von Mering, Christian; Muthas, Daniel; Nguyen, Dac-Trung; Overington, John P; Papadatos, George; Qin, Jun; Reich, Christian; Roth, Bryan L; Schürer, Stephan C; Simeonov, Anton; Sklar, Larry A; Southall, Noel; Tomita, Susumu; Tudose, Ilinca; Ursu, Oleg; Vidovic, Du?ica; Waller, Anna; Westergaard, David; Yang, Jeremy J; Zahoránszky-Köhalmi, Gergely | Nature reviews. Drug discovery. | 2018 May; | | 29472638 |
| Mass Spectrometry-Based Proteomics Reveals Potential Roles of NEK9 and MAP2K4 in Resistance to PI3K Inhibition in Triple-Negative Breast Cancers. | Mundt, Filip; Rajput, Sandeep; Li, Shunqiang; Ruggles, Kelly V; Mooradian, Arshag D; Mertins, Philipp; Gillette, Michael A; Krug, Karsten; Guo, Zhanfang; Hoog, Jeremy; Erdmann-Gilmore, Petra; Primeau, Tina; Huang, Shixia; Edwards, Dean P; Wang, Xiaowei; Wang, Xuya; Kawaler, Emily; Mani, D R; Clauser, Karl R; Gao, Feng; Luo, Jingqin; Davies, Sherri R; Johnson, Gary L; Huang, Kuan-Lin; Yoon, Christopher J; Ding, Li; Fenyö, David; Ellis, Matthew J; Townsend, R Reid; Held, Jason M; Carr, Steven A; Ma, Cynthia X | Cancer research. | 2018 05 15; | | 29472518 |
| L1000FWD: fireworks visualization of drug-induced transcriptomic signatures. | Wang, Zichen; Lachmann, Alexander; Keenan, Alexandra B; Ma'ayan, Avi | Bioinformatics (Oxford, England). | ; | | 29420694 |
| Machine learning in cardiovascular medicine: are we there yet? | Shameer, Khader; Johnson, Kipp W; Glicksberg, Benjamin S; Dudley, Joel T; Sengupta, Partho P | Heart (British Cardiac Society). | 2018 07; | | 29352006 |
| Dual gene activation and knockout screen reveals directional dependencies in genetic networks. | Boettcher, Michael; Tian, Ruilin; Blau, James A; Markegard, Evan; Wagner, Ryan T; Wu, David; Mo, Xiulei; Biton, Anne; Zaitlen, Noah; Fu, Haian; McCormick, Frank; Kampmann, Martin; McManus, Michael T | Nature biotechnology. | 2018 Feb; | | 29334369 |
| Integration of pan-cancer transcriptomics with RPPA proteomics reveals mechanisms of epithelial-mesenchymal transition. | Koplev, Simon; Lin, Katie; Dohlman, Anders B; Ma'ayan, Avi | PLoS computational biology. | 2018 01; | | 29293502 |
| Structure-inspired design of ?-arrestin-biased ligands for aminergic GPCRs. | McCorvy, John D; Butler, Kyle V; Kelly, Brendan; Rechsteiner, Katie; Karpiak, Joel; Betz, Robin M; Kormos, Bethany L; Shoichet, Brian K; Dror, Ron O; Jin, Jian; Roth, Bryan L | Nature chemical biology. | 2017 Dec 11; | | 29227473 |
| Cell-specific prediction and application of drug-induced gene expression profiles. | Hodos, Rachel; Zhang, Ping; Lee, Hao-Chih; Duan, Qiaonan; Wang, Zichen; Clark, Neil R; Ma'ayan, Avi; Wang, Fei; Kidd, Brian; Hu, Jianying; Sontag, David; Dudley, Joel | Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. | 2018; | | 29218867 |
| Quantitative, Wide-Spectrum Kinase Profiling in Live Cells for Assessing the Effect of Cellular ATP on Target Engagement. | Vasta, James D; Corona, Cesear R; Wilkinson, Jennifer; Zimprich, Chad A; Hartnett, James R; Ingold, Morgan R; Zimmerman, Kristopher; Machleidt, Thomas; Kirkland, Thomas A; Huwiler, Kristin G; Ohana, Rachel Friedman; Slater, Michael; Otto, Paul; Cong, Mei; | Cell chemical biology. | 2018 02 15; | | 29174542 |
| Drug target ontology to classify and integrate drug discovery data. | Lin, Yu; Mehta, Saurabh; Küçük-McGinty, Hande; Turner, John Paul; Vidovic, Dusica; Forlin, Michele; Koleti, Amar; Nguyen, Dac-Trung; Jensen, Lars Juhl; Guha, Rajarshi; Mathias, Stephen L; Ursu, Oleg; Stathias, Vasileios; Duan, Jianbin; Nabizadeh, Nooshin; | Journal of biomedical semantics. | 2017 Nov 09; | | 29122012 |
| Predicting age by mining electronic medical records with deep learning characterizes differences between chronological and physiological age. | Wang, Zichen; Li, Li; Glicksberg, Benjamin S; Israel, Ariel; Dudley, Joel T; Ma'ayan, Avi | Journal of biomedical informatics. | 2017 Dec; | | 29113935 |
| Common and cell-type specific responses to anti-cancer drugs revealed by high throughput transcript profiling. | Niepel, Mario; Hafner, Marc; Duan, Qiaonan; Wang, Zichen; Paull, Evan O; Chung, Mirra; Lu, Xiaodong; Stuart, Joshua M; Golub, Todd R; Subramanian, Aravind; Ma'ayan, Avi; Sorger, Peter K | Nature communications. | 2017 Oct 30; | | 29084964 |
| Identification and Optimization of 4-Anilinoquinolines as Inhibitors of Cyclin?G Associated Kinase. | Asquith, Christopher R M; Laitinen, Tuomo; Bennett, James M; Godoi, Paulo H; East, Michael P; Tizzard, Graham J; Graves, Lee M; Johnson, Gary L; Dornsife, Ronna E; Wells, Carrow I; Elkins, Jonathan M; Willson, Timothy M; Zuercher, William J | ChemMedChem. | 2018 Jan 08; | | 29072804 |
| D4dopamine receptor high-resolution structures enable the discovery of selective agonists. | Wang, Sheng; Wacker, Daniel; Levit, Anat; Che, Tao; Betz, Robin M; McCorvy, John D; Venkatakrishnan, A J; Huang, Xi-Ping; Dror, Ron O; Shoichet, Brian K; Roth, Bryan L | Science (New York, N.Y.). | 2017 10 20; | | 29051383 |
| Discovery of new GPCR ligands to illuminate new biology. | Roth, Bryan L; Irwin, John J; Shoichet, Brian K | Nature chemical biology. | 2017 Nov; | | 29045379 |
| Biased signaling of the proton-sensing receptor OGR1 by benzodiazepines. | Pera, Tonio; Deshpande, Deepak A; Ippolito, Michael; Wang, Bin; Gavrila, Adelina; Michael, James V; Nayak, Ajay P; Tompkins, Eric; Farrell, Eleni; Kroeze, Wesley K; Roth, Bryan L; Panettieri Jr, Reynold A; Benovic, Jeffrey L; An, Steven S; Dulin, Nickolai O; Penn, Raymond B | FASEB journal : official publication of the Federation of American Societies for Experimental Biology. | ; | | 29042451 |
| Report and Application of a Tool Compound Data Set. | Butler, Kyle V; MacDonald, Ian A; Hathaway, Nathaniel A; Jin, Jian | Journal of chemical information and modeling. | 2017 Nov 02; | | 29035535 |
| Formalizing drug indications on the road to therapeutic intent. | Nelson, Stuart J; Oprea, Tudor I; Ursu, Oleg; Bologa, Cristian G; Zaveri, Amrapali; Holmes, Jayme; Yang, Jeremy J; Mathias, Stephen L; Mani, Subramani; Tuttle, Mark S; Dumontier, Michel | Journal of the American Medical Informatics Association : JAMIA. | 2017 Nov 01; | | 29016968 |
| Clustergrammer, a web-based heatmap visualization and analysis tool for high-dimensional biological data. | Fernandez, Nicolas F; Gundersen, Gregory W; Rahman, Adeeb; Grimes, Mark L; Rikova, Klarisa; Hornbeck, Peter; Ma'ayan, Avi | Scientific data. | 2017 Oct 10; | | 28994825 |
| A Bioinformatic Algorithm for Analyzing Cell Signaling Using Temporal Proteomic Data. | Zhang, Chunchao; Chen, Yue; Mao, Xinfang; Huang, Yin; Jung, Sung Yun; Jain, Antrix; Qin, Jun; Wang, Yi | Proteomics. | 2017 Nov; | | 28940701 |
| Complex systems biology. | Ma'ayan, Avi | Journal of the Royal Society, Interface. | 2017 Sep; | | 28931638 |
| A high-conductance chemo-optogenetic system based on the vertebrate channel Trpa1b. | Lam, Pui-Ying; Mendu, Suresh K; Mills, Robert W; Zheng, Baohui; Padilla, Hugo; Milan, David J; Desai, Bimal N; Peterson, Randall T | Scientific reports. | 2017 Sep 19; | | 28928472 |
| Assembly rules for GABAA receptor complexes in the brain. | Martenson, James S;Yamasaki, Tokiwa;Chaudhury, Nashid H;Albrecht, David;Tomita, Susumu | eLife | | | 28816653 |
| Progress towards a public chemogenomic set for protein kinases and a call for contributions. | Drewry, David H; Wells, Carrow I; Andrews, David M; Angell, Richard; Al-Ali, Hassan; Axtman, Alison D; Capuzzi, Stephen J; Elkins, Jonathan M; Ettmayer, Peter; Frederiksen, Mathias; Gileadi, Opher; Gray, Nathanael; Hooper, Alice; Knapp, Stefan; Laufer, St | PloS one. | 2017; | | 28767711 |
| Intracoronary Imaging, Cholesterol Efflux, and Transcriptomics after Intensive Statin Treatment in Diabetes. | Chamaria, Surbhi; Johnson, Kipp W; Vengrenyuk, Yuliya; Baber, Usman; Shameer, Khader; Divaraniya, Aparna A; Glicksberg, Benjamin S; Li, Li; Bhatheja, Samit; Moreno, Pedro; Maehara, Akiko; Mehran, Roxana; Dudley, Joel T; Narula, Jagat; Sharma, Samin K; Kini, Annapoorna S | Scientific reports. | 2017 Aug 01; | | 28765529 |
| How Ligands Illuminate GPCR Molecular Pharmacology. | Wacker, Daniel; Stevens, Raymond C; Roth, Bryan L | Cell. | 2017 Jul 27; | | 28753422 |
| From flamingo dance to (desirable) drug discovery: a nature-inspired approach. | Sánchez-Rodríguez, Aminael; Pérez-Castillo, Yunierkis; Schürer, Stephan C; Nicolotti, Orazio; Mangiatordi, Giuseppe Felice; Borges, Fernanda; Cordeiro, M Natalia D S; Tejera, Eduardo; Medina-Franco, José L; Cruz-Monteagudo, Maykel | Drug discovery today. | 2017 Jun 15; | | 28624633 |
| Activation of tumor suppressor protein PP2A inhibits KRAS-driven tumor growth. | Sangodkar, Jaya; Perl, Abbey; Tohme, Rita; Kiselar, Janna; Kastrinsky, David B; Zaware, Nilesh; Izadmehr, Sudeh; Mazhar, Sahar; Wiredja, Danica D; O'Connor, Caitlin M; Hoon, Divya; Dhawan, Neil S; Schlatzer, Daniela; Yao, Shen; Leonard, Daniel; Borczuk, A | The Journal of clinical investigation. | 2017 Jun 01; | | 28504649 |
| Deep learning for healthcare: review, opportunities and challenges. | Miotto, Riccardo; Wang, Fei; Wang, Shuang; Jiang, Xiaoqian; Dudley, Joel T | Briefings in bioinformatics. | 2017 May 06; | | 28481991 |
| A mouse tissue transcription factor atlas. | Zhou, Quan; Liu, Mingwei; Xia, Xia; Gong, Tongqing; Feng, Jinwen; Liu, Wanlin; Liu, Yang; Zhen, Bei; Wang, Yi; Ding, Chen; Qin, Jun | Nature communications. | 2017 Apr 21; | | 28429721 |
| Reply: Deep Learning With Unsupervised Feature in Echocardiographic Imaging. | Narula, Sukrit; Shameer, Khader; Salem Omar, Alaa Mabrouk; Dudley, Joel T; Sengupta, Partho P | Journal of the American College of Cardiology. | 2017 04 25; | | 28427589 |
| L1000CDS(2): LINCS L1000 characteristic direction signatures search engine. | Duan, Qiaonan; Reid, St Patrick; Clark, Neil R; Wang, Zichen; Fernandez, Nicolas F; Rouillard, Andrew D; Readhead, Ben; Tritsch, Sarah R; Hodos, Rachel; Hafner, Marc; Niepel, Mario; Sorger, Peter K; Dudley, Joel T; Bavari, Sina; Panchal, Rekha G; Ma'ayan, Avi | NPJ systems biology and applications. | 2016; | | 28413689 |
| Dopaminergic control of anxiety in young and aged zebrafish. | Kacprzak, Victoria; Patel, Neil A; Riley, Elizabeth; Yu, Lili; Yeh, Jing-Ruey J; Zhdanova, Irina V | Pharmacology, biochemistry, and behavior. | 2017 06; | | 28408289 |
| TIN-X: target importance and novelty explorer. | Cannon, Daniel C; Yang, Jeremy J; Mathias, Stephen L; Ursu, Oleg; Mani, Subramani; Waller, Anna; Schürer, Stephan C; Jensen, Lars Juhl; Sklar, Larry A; Bologa, Cristian G; Oprea, Tudor I | Bioinformatics (Oxford, England). | 2017 Aug 15; | | 28398460 |
| In silico design of novel probes for the atypical opioid receptor MRGPRX2. | Lansu, Katherine; Karpiak, Joel; Liu, Jing; Huang, Xi-Ping; McCorvy, John D; Kroeze, Wesley K; Che, Tao; Nagase, Hiroshi; Carroll, Frank I; Jin, Jian; Shoichet, Brian K; Roth, Bryan L | Nature chemical biology. | 2017 May; | | 28288109 |
| GARLH Family Proteins Stabilize GABAA Receptors at Synapses. | Yamasaki, Tokiwa; Hoyos-Ramirez, Erika; Martenson, James S; Morimoto-Tomita, Megumi; Tomita, Susumu | Neuron. | 2017 Mar 08; | | 28279354 |
| Systemic QSAR and phenotypic virtual screening: chasing butterflies in drug discovery. | Cruz-Monteagudo, Maykel; Schürer, Stephan; Tejera, Eduardo; Pérez-Castillo, Yunierkis; Medina-Franco, José L; Sánchez-Rodríguez, Aminael; Borges, Fernanda | Drug discovery today. | 2017 Mar 06; | | 28274840 |
| A Whole-Genome RNA Interference Screen Reveals a Role for Spry2 in Insulin Transcription and the Unfolded Protein Response. | Pappalardo, Zachary; Gambhir Chopra, Deeksha; Hennings, Thomas G; Richards, Hunter; Choe, Justin; Yang, Katherine; Baeyens, Luc; Ang, Kenny; Chen, Steven; Arkin, Michelle; German, Michael S; McManus, Michael T; Ku, Gregory M | Diabetes. | 2017 Jun; | | 28246293 |
| Protamine is an antagonist of apelin receptor, and its activity is reversed by heparin. | Le Gonidec, Sophie; Chaves-Almagro, Carline; Bai, Yushi; Kang, Hye Jin; Smith, Allyson; Wanecq, Estelle; Huang, Xi-Ping; Prats, Hervé; Knibiehler, Bernard; Roth, Bryan L; Barak, Larry S; Caron, Marc G; Valet, Philippe; Audigier, Yves; Masri, Bernard | FASEB journal : official publication of the Federation of American Societies for Experimental Biology. | 2017 06; | | 28242772 |
| Differential cytokine contributions of perivascular haematopoietic stem cell niches. | Asada, Noboru; Kunisaki, Yuya; Pierce, Halley; Wang, Zichen; Fernandez, Nicolas F; Birbrair, Alexander; Ma'ayan, Avi; Frenette, Paul S | Nature cell biology. | 2017 Mar; | | 28218906 |
| Systematic analyses of drugs and disease indications in RepurposeDB reveal pharmacological, biological and epidemiological factors influencing drug repositioning. | Shameer, Khader; Glicksberg, Benjamin S; Hodos, Rachel; Johnson, Kipp W; Badgeley, Marcus A; Readhead, Ben; Tomlinson, Max S; O'Connor, Timothy; Miotto, Riccardo; Kidd, Brian A; Chen, Rong; Ma'ayan, Avi; Dudley, Joel T | Briefings in bioinformatics. | 2017 Feb 15; | | 28200013 |
| Transcription Factor Response Elements on Tip: A Sensitive Approach for Large-Scale Endogenous Transcription Factor Quantitative Identification. | Shi, Wenhao; Li, Kai; Song, Lei; Liu, Mingwei; Wang, Yunzhi; Liu, Wanlin; Xia, Xia; Qin, Zhaoyu; Zhen, Bei; Wang, Yi; He, Fuchu; Qin, Jun; Ding, Chen | Analytical chemistry. | 2016 12 20; | | 28193032 |
| Automated cell type discovery and classification through knowledge transfer. | Lee, Hao-Chih; Kosoy, Roman; Becker, Christine E; Dudley, Joel T; Kidd, Brian A | Bioinformatics (Oxford, England). | 2017 Jun 01; | | 28158442 |
| Protein biomarker druggability profiling. | Mani, Subramani; Cannon, Daniel; Ohls, Robin; Oprea, Tudor; Mathias, Stephen; Ballard, Karri; Ursu, Oleg; Bologa, Cristian | Journal of biomedical informatics. | 2017 Feb; | | 28131723 |
| Integrative Analysis of Disease Signatures Shows Inflammation Disrupts Juvenile Experience-Dependent Cortical Plasticity. | Smith, Milo R; Burman, Poromendro; Sadahiro, Masato; Kidd, Brian A; Dudley, Joel T; Morishita, Hirofumi | eNeuro. | 2016 Nov-Dec; | | 28101530 |
| Novel Therapeutics Identification for Fibrosis in Renal Allograft Using Integrative Informatics Approach. | Li, Li; Greene, Ilana; Readhead, Benjamin; Menon, Madhav C; Kidd, Brian A; Uzilov, Andrew V; Wei, Chengguo; Philippe, Nimrod; Schroppel, Bernd; He, John Cijiang; Chen, Rong; Dudley, Joel T; Murphy, Barbara | Scientific reports. | 2017 Jan 04; | | 28051114 |
| Nrf2 mitigates LRRK2- and α-synuclein-induced neurodegeneration by modulating proteostasis. | Gaia Skibinski, Vicky Hwang, Dale Michael Ando, Aaron Daub, Alicia K. Lee, Abinaya Ravisankar, Sara Modan, Mariel M. Finucane, Benjamin A. Shaby, and Steven Finkbeiner | Proceedings of the National Academy of Sciences of the United States of America. | 2017 Jan 31; | 1165–1170 | 28028237 |
| Genomic Analysis of Kidney Allograft Injury Identifies Hematopoietic Cell Kinase as a Key Driver of Renal Fibrosis. | Wei, Chengguo; Li, Li; Menon, Madhav C; Zhang, Weijia; Fu, Jia; Kidd, Brian; Keung, Karen L; Woytovich, Christopher; Greene, Ilana; Xiao, Wenzhen; Salem, Fadi; Yi, Zhengzi; He, John Cijiang; Dudley, Joel T; Murphy, Barbara | Journal of the American Society of Nephrology : JASN. | 2017 May; | | 27927780 |
| A comprehensive map of molecular drug targets. | Santos, Rita; Ursu, Oleg; Gaulton, Anna; Bento, A Patrícia; Donadi, Ramesh S; Bologa, Cristian G; Karlsson, Anneli; Al-Lazikani, Bissan; Hersey, Anne; Oprea, Tudor I; Overington, John P | Nature reviews. Drug discovery. | 2017 01; | | 27910877 |
| Pharos: Collating protein information to shed light on the druggable genome. | Nguyen, Dac-Trung; Mathias, Stephen; Bologa, Cristian; Brunak, Soren; Fernandez, Nicolas; Gaulton, Anna; Hersey, Anne; Holmes, Jayme; Jensen, Lars Juhl; Karlsson, Anneli; Liu, Guixia; Ma'ayan, Avi; Mandava, Geetha; Mani, Subramani; Mehta, Saurabh; Overington, John; Patel, Juhee; Rouillard, Andrew D; Schürer, Stephan; Sheils, Timothy; Simeonov, Anton; Sklar, Larry A; Southall, Noel; Ursu, Oleg; Vidovic, Dusica; Waller, Anna; Yang, Jeremy; Jadhav, Ajit; Oprea, Tudor I; Guha, Rajarshi | Nucleic acids research. | 2017 Jan 4; | | 27903890 |
| EXPLORING THE REPRODUCIBILITY OF PROBABILISTIC CAUSAL MOLECULAR NETWORK MODELS. | Cohain, Ariella; Divaraniya, Aparna A; Zhu, Kuixi; Scarpa, Joseph R; Kasarskis, Andrew; Zhu, Jun; Chang, Rui; Dudley, Joel T; Schadt, Eric E | Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. | 2016; | | 27896968 |
| EXPLORING BRAIN TRANSCRIPTOMIC PATTERNS: A TOPOLOGICAL ANALYSIS USING SPATIAL EXPRESSION NETWORKS. | Kuncheva, Zhana; Krishnan, Michelle L; Montana, Giovanni | Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. | 2016; | | 27896963 |
| GEN3VA: aggregation and analysis of gene expression signatures from related studies. | Gundersen, Gregory W; Jagodnik, Kathleen M; Woodland, Holly; Fernandez, Nicholas F; Sani, Kevin; Dohlman, Anders B; Ung, Peter Man-Un; Monteiro, Caroline D; Schlessinger, Avner; Ma'ayan, Avi | BMC bioinformatics. | 2016 Nov 15; | | 27846806 |
| DrugCentral: online drug compendium. | Ursu, Oleg; Holmes, Jayme; Knockel, Jeffrey; Bologa, Cristian G; Yang, Jeremy J; Mathias, Stephen L; Nelson, Stuart J; Oprea, Tudor I | Nucleic acids research. | 2017 Jan 4; | | 27789690 |
| Gold Nanoparticle Reprograms Pancreatic Tumor Microenvironment and Inhibits Tumor Growth. | Saha, Sounik; Xiong, Xunhao; Chakraborty, Prabir K; Shameer, Khader; Arvizo, Rochelle R; Kudgus, Rachel A; Dwivedi, Shailendra Kumar Dhar; Hossen, Md Nazir; Gillies, Elizabeth M; Robertson, J David; Dudley, Joel T; Urrutia, Raul A; Postier, Russell G; Bha | ACS nano. | 2016 12 27; | | 27758098 |
| Discovery and Characterization of Novel GPR39 Agonists Allosterically Modulated by Zinc. | Sato, Seiji; Huang, Xi-Ping; Kroeze, Wesley K; Roth, Bryan L | Molecular pharmacology. | 2016 Dec; | | 27754899 |
| Estimation of Maximum Recommended Therapeutic Dose Using Predicted Promiscuity and Potency. | Liu, T; Oprea, T; Ursu, O; Hasselgren, C; Altman, R B | Clinical and translational science. | 2016 12; | | 27736015 |
| Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd. | Wang, Zichen; Monteiro, Caroline D; Jagodnik, Kathleen M; Fernandez, Nicolas F; Gundersen, Gregory W; Rouillard, Andrew D; Jenkins, Sherry L; Feldmann, Axel S; Hu, Kevin S; McDermott, Michael G; Duan, Qiaonan; Clark, Neil R; Jones, Matthew R; Kou, Yan; Goff, Troy; Woodland, Holly; Amaral, Fabio M R; Szeto, Gregory L; Fuchs, Oliver; Schüssler-Fiorenza Rose, Sophia M; Sharma, Shvetank; Schwartz, Uwe; Bausela, Xabier Bengoetxea; Szymkiewicz, Maciej; Maroulis, Vasileios; Salykin, Anton; Barra, Carolina M; Kruth, Candice D; Bongio, Nicholas J; Mathur, Vaibhav; Todoric, Radmila D; Rubin, Udi E; Malatras, Apostolos; Fulp, Carl T; Galindo, John A; Motiejunaite, Ruta; Jüschke, Christoph; Dishuck, Philip C; Lahl, Katharina; Jafari, Mohieddin; Aibar, Sara; Zaravinos, Apostolos; Steenhuizen, Linda H; Allison, Lindsey R; Gamallo, Pablo; de Andres Segura, Fernando; Dae Devlin, Tyler; Pérez-García, Vicente; Ma'ayan, Avi | Nature communications. | 2016 Sep 26; | | 27667448 |
| Replicating Cardiovascular Condition-Birth Month Associations. | Li, Li; Boland, Mary Regina; Miotto, Riccardo; Tatonetti, Nicholas P; Dudley, Joel T | Scientific reports. | 2016 Sep 14; | | 27624541 |
| An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study. | Wang, Zichen; Ma'ayan, Avi | F1000Research. | 2016 Jul 5; | | 27583132 |
| Non-Substrate Based, Small Molecule Inhibitors of the Human Isoprenylcysteine Carboxyl Methyltransferase. | Butler, Kyle V; Bohn, Kelsey; Hrycyna, Christine A; Jin, Jian | MedChemComm. | 2016 May 1; | | 27547295 |
| Structure-based discovery of opioid analgesics with reduced side effects. | Manglik, Aashish; Lin, Henry; Aryal, Dipendra K; McCorvy, John D; Dengler, Daniela; Corder, Gregory; Levit, Anat; Kling, Ralf C; Bernat, Viachaslau; Hübner, Harald; Huang, Xi-Ping; Sassano, Maria F; Giguère, Patrick M; Löber, Stefan; Da Duan; Scherrer, Gr | Nature. | 2016 09 08; | | 27533032 |
| Polycomb repressive complex 2 (PRC2) silences genes responsible for neurodegeneration. | von Schimmelmann, Melanie; Feinberg, Philip A; Sullivan, Josefa M; Ku, Stacy M; Badimon, Ana; Duff, Mary Kaye; Wang, Zichen; Lachmann, Alexander; Dewell, Scott; Ma'ayan, Avi; Han, Ming-Hu; Tarakhovsky, Alexander; Schaefer, Anne | Nature neuroscience. | 2016 Oct; | | 27526204 |
| Identification of Novel Smoothened Ligands Using Structure-Based Docking. | Lacroix, Celine; Fish, Inbar; Torosyan, Hayarpi; Parathaman, Pranavan; Irwin, John J; Shoichet, Brian K; Angers, Stephane | PloS one. | 2016; | | 27490099 |
| The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. | Rouillard, Andrew D; Gundersen, Gregory W; Fernandez, Nicolas F; Wang, Zichen; Monteiro, Caroline D; McDermott, Michael G; Ma'ayan, Avi | Database : the journal of biological databases and curation. | 2016; | | 27374120 |
| Comparative analyses of population-scale phenomic data in electronic medical records reveal race-specific disease networks. | Glicksberg, Benjamin S; Li, Li; Badgeley, Marcus A; Shameer, Khader; Kosoy, Roman; Beckmann, Noam D; Pho, Nam; Hakenberg, Jörg; Ma, Meng; Ayers, Kristin L; Hoffman, Gabriel E; Dan Li, Shuyu; Schadt, Eric E; Patel, Chirag J; Chen, Rong; Dudley, Joel T | Bioinformatics (Oxford, England). | 2016 Jun 15; | | 27307606 |
| Krüppel-Like Factor 15 Mediates Glucocorticoid-Induced Restoration of Podocyte Differentiation Markers. | Mallipattu, Sandeep K; Guo, Yiqing; Revelo, Monica P; Roa-Peña, Lucia; Miller, Timothy; Ling, Jason; Shankland, Stuart J; Bialkowska, Agnieszka B; Ly, Victoria; Estrada, Chelsea; Jain, Mukesh K; Lu, Yuan; Ma'ayan, Avi; Mehrotra, Anita; Yacoub, Rabi; Nord, Edward P; Woroniecki, Robert P; Yang, Vincent W; He, John C | Journal of the American Society of Nephrology : JASN. | 2016 Jun 10; | | 27288011 |
| Cognitive Machine-Learning Algorithm for Cardiac Imaging: A Pilot Study for Differentiating Constrictive Pericarditis From Restrictive Cardiomyopathy. | Sengupta, Partho P; Huang, Yen-Min; Bansal, Manish; Ashrafi, Ali; Fisher, Matt; Shameer, Khader; Gall, Walt; Dudley, Joel T | Circulation. Cardiovascular imaging. | 2016 Jun; | | 27266599 |
| ?1 receptor ligands control a switch between passive and active threat responses. | Rennekamp, Andrew J; Huang, Xi-Ping; Wang, You; Patel, Samir; Lorello, Paul J; Cade, Lindsay; Gonzales, Andrew P W; Yeh, Jing-Ruey Joanna; Caldarone, Barbara J; Roth, Bryan L; Kokel, David; Peterson, Randall T | Nature chemical biology. | 2016 Jul; | | 27239788 |
| Zebrafish behavioral profiling identifies multitarget antipsychotic-like compounds. | Bruni, Giancarlo; Rennekamp, Andrew J; Velenich, Andrea; McCarroll, Matthew; Gendelev, Leo; Fertsch, Ethan; Taylor, Jack; Lakhani, Parth; Lensen, Dennis; Evron, Tama; Lorello, Paul J; Huang, Xi-Ping; Kolczewski, Sabine; Carey, Galen; Caldarone, Barbara J; Prinssen, Eric; Roth, Bryan L; Keiser, Michael J; Peterson, Randall T; Kokel, David | Nature chemical biology. | 2016 Jul; | | 27239787 |
| Badapple: promiscuity patterns from noisy evidence. | Yang, Jeremy J; Ursu, Oleg; Lipinski, Christopher A; Sklar, Larry A; Oprea, Tudor I; Bologa, Cristian G | Journal of cheminformatics. | 2016; | | 27239230 |
| Glucocorticoid receptor isoforms direct distinct mitochondrial programs to regulate ATP production. | Morgan, David J; Poolman, Toryn M; Williamson, Andrew J K; Wang, Zichen; Clark, Neil R; Ma'ayan, Avi; Whetton, Anthony D; Brass, Andrew; Matthews, Laura C; Ray, David W | Scientific reports. | 2016; | | 27226058 |
| Cre dependent DREADD (designer receptors exclusively activated by designer drugs) mice. | Zhu, Hu; Aryal, Dipendra K; Olsen, Reid H J; Urban, Daniel J; Swearingen, Amanda; Forbes, Stacy; Roth, Bryan L; Hochgeschwender, Ute | Genesis (New York, N.Y. : 2000). | 2016 May 19; | | 27194399 |
| Deep Patient: An Unsupervised Representation to Predict the Future of Patients from the Electronic Health Records. | Miotto, Riccardo; Li, Li; Kidd, Brian A; Dudley, Joel T | Scientific reports. | 2016 May 17; | | 27185194 |
| BDDCS, the Rule of 5 and drugability. | Benet, Leslie Z; Hosey, Chelsea M; Ursu, Oleg; Oprea, Tudor I | Advanced drug delivery reviews. | 2016 Jun 1; | | 27182629 |
| Systems Medicine Approaches to Improving Understanding, Treatment, and Clinical Management of Neuroendocrine Prostate Cancer. | Yadav, Kamlesh K; Shameer, Khader; Readhead, Ben; Yadav, Shalini S; Li, Li; Kasarskis, Andrew; Tewari, Ashutosh K; Dudley, Joel T | Current pharmaceutical design. | 2016; | | 27174811 |
| Drug-induced adverse events prediction with the LINCS L1000 data. | Wang, Zichen; Clark, Neil R; Ma'ayan, Avi | Bioinformatics (Oxford, England). | 2016 Aug 1; | | 27153606 |
| Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. | Kuleshov, Maxim V; Jones, Matthew R; Rouillard, Andrew D; Fernandez, Nicolas F; Duan, Qiaonan; Wang, Zichen; Koplev, Simon; Jenkins, Sherry L; Jagodnik, Kathleen M; Lachmann, Alexander; McDermott, Michael G; Monteiro, Caroline D; Gundersen, Gregory W; Ma'ayan, Avi | Nucleic acids research. | 2016 Jul 8; | | 27141961 |
| In silico methods for drug repurposing and pharmacology. | Hodos, Rachel A; Kidd, Brian A; Shameer, Khader; Readhead, Ben P; Dudley, Joel T | Wiley interdisciplinary reviews. Systems biology and medicine. | 2016 May; | | 27080087 |
| Discovery of a specific inhibitor of human GLUT5 by virtual screening and in vitro transport evaluation | George-Thompson AM, Ursu O, Babkin P, Iancu CV, Whang A, Oprea TI, Choe JY | Scientific Reports | Epub 2016 Apr 14. | | 27074918 |
| Integrative network modeling approaches to personalized cancer medicine | Kidd BA, Readhead BP, Eden C, Parekh S, Dudley JT | Personalized Medicine | 2015 Jun 1 | 12(3):245-257 | 27019658 |
| Integrative network modeling approaches to personalized cancer medicine. | Kidd BA, Readhead BP, Eden C, Parekh S, Dudley JT. | Personalized Medicine | 2015 Jun 1 | 12(3):245-257. | 27019658 |
| Evaluation of direct-to-consumer low-volume lab tests in healthy adults | Kidd BA, Hoffman G, Zimmerman N, Li L, Morgan JW, Glowe PK, Botwin GJ, Parekh S, Babic N, Doust MW, Stock GB, Schadt EE, Dudley JT | J Clin Invest | 2016 Mar 28 | pii: 86318. doi: 10.1172/JCI86318. [Epub ahead of print] | 27018593 |
| Signaling Networks among Stem Cell Precursors, Transit-Amplifying Progenitors, and their Niche in Developing Hair Follicles. | Rezza, Amélie; Wang, Zichen; Sennett, Rachel; Qiao, Wenlian; Wang, Dongmei; Heitman, Nicholas; Mok, Ka Wai; Clavel, Carlos; Yi, Rui; Zandstra, Peter; Ma'ayan, Avi; Rendl, Michael | Cell reports. | 2016 Mar 29; | | 27009580 |
| In Vitro and In Vivo Characterization of the Alkaloid Nuciferine. | Farrell, Martilias S; McCorvy, John D; Huang, Xi-Ping; Urban, Daniel J; White, Kate L; Giguere, Patrick M; Doak, Allison K; Bernstein, Alison I; Stout, Kristen A; Park, Su Mi; Rodriguiz, Ramona M; Gray, Bradley W; Hyatt, William S; Norwood, Andrew P; Webs | PloS one. | 2016; | | 26963248 |
| Polygenic overlap between schizophrenia risk and antipsychotic response: a genomic medicine approach. | Ruderfer, Douglas M; Charney, Alexander W; Readhead, Ben; Kidd, Brian A; Kähler, Anna K; Kenny, Paul J; Keiser, Michael J; Moran, Jennifer L; Hultman, Christina M; Scott, Stuart A; Sullivan, Patrick F; Purcell, Shaun M; Dudley, Joel T; Sklar, Pamela | The lancet. Psychiatry. | 2016 Apr; | | 26915512 |
| Docking Screens for Novel Ligands Conferring New Biology. | Irwin, John J; Shoichet, Brian K | Journal of medicinal chemistry. | 2016 05 12; | | 26913380 |
| Translational bioinformatics in the era of real-time biomedical, health care and wellness data streams | Shameer K, Badgeley MA, Miotto R, Glicksberg BS, Morgan JW, Dudley JT | Brief Bioinform | 2016 Feb 14 | pii: bbv118. [Epub ahead of print] | 26876889 |
| Integrative radiogenomic analysis for multicentric radiophenotype in glioblastoma | Kong DS, Kim J, Lee IH, Kim ST, Seol HJ, Lee JI, Park WY, Ryu G, Wang Z, Ma'ayan A, Nam DH | Oncotarget | 2016 Feb 1 | doi: 10.18632/oncotarget.7115. [Epub ahead of print] | 26863628 |
| Principal Angle Enrichment Analysis (PAEA): Dimensionally Reduced Multivariate Gene Set Enrichment Analysis Tool. | Clark, Neil R; Szymkiewicz, Maciej; Wang, Zichen; Monteiro, Caroline D; Jones, Matthew R; Ma'ayan, Avi | Proceedings. IEEE International Conference on Bioinformatics and Biomedicine. | 2015 Nov; | 256-262 | 26848405 |
| Leveraging Large-scale Behavioral Profiling in Zebrafish to Explore Neuroactive Polypharmacology. | McCarroll, Matthew N; Gendelev, Leo; Keiser, Michael J; Kokel, David | ACS chemical biology. | 2016 Apr 15; | | 26845413 |
| A three-groups model for high-throughput survival screens. | Shaby, Benjamin A; Skibinski, Gaia; Ando, Michael; LaDow, Eva S; Finkbeiner, Steven | Biometrics. | 2016 Jan 28; | | 26821783 |
| Fetal liver hematopoietic stem cell niches associate with portal vessels. | Khan, Jalal A; Mendelson, Avital; Kunisaki, Yuya; Birbrair, Alexander; Kou, Yan; Arnal-Estapé, Anna; Pinho, Sandra; Ciero, Paul; Nakahara, Fumio; Ma'ayan, Avi; Bergman, Aviv; Merad, Miriam; Frenette, Paul S | Science (New York, N.Y.). | 2016 Jan 8; | 176-80 | 26634440 |
| Mapping the effects of drugs on the immune system. | Kidd, Brian A; Wroblewska, Aleksandra; Boland, Mary R; Agudo, Judith; Merad, Miriam; Tatonetti, Nicholas P; Brown, Brian D; Dudley, Joel T | Nature biotechnology. | 2016 Jan; | 47-54 | 26619012 |
| Molecular systems evaluation of oligomerogenic APP(E693Q) and fibrillogenic APP(KM670/671NL)/PSEN1(?exon9) mouse models identifies shared features with human Alzheimer's brain molecular pathology. | Readhead, B; Haure-Mirande, J-V; Zhang, B; Haroutunian, V; Gandy, S; Schadt, E E; Dudley, J T; Ehrlich, M E | Molecular psychiatry. | 2015 Nov 10; | | 26552589 |
| Allosteric ligands for the pharmacologically dark receptors GPR68 and GPR65. | Huang, Xi-Ping; Karpiak, Joel; Kroeze, Wesley K; Zhu, Hu; Chen, Xin; Moy, Sheryl S; Saddoris, Kara A; Nikolova, Viktoriya D; Farrell, Martilias S; Wang, Sheng; Mangano, Thomas J; Deshpande, Deepak A; Jiang, Alice; Penn, Raymond B; Jin, Jian; Koller, Bever | Nature. | 2015 Nov 26; | 477-83 | 26550826 |
| Identification of type 2 diabetes subgroups through topological analysis of patient similarity. | Li, Li; Cheng, Wei-Yi; Glicksberg, Benjamin S; Gottesman, Omri; Tamler, Ronald; Chen, Rong; Bottinger, Erwin P; Dudley, Joel T | Science translational medicine. | 2015 Oct 28; | 311ra174 | 26511511 |
| Noribogaine is a G-protein biased ?-opioid receptor agonist. | Maillet, Emeline L; Milon, Nicolas; Heghinian, Mari D; Fishback, James; Schürer, Stephan C; Garamszegi, Nandor; Mash, Deborah C | Neuropharmacology. | 2015 Dec; | 675-88 | 26302653 |
| Reprint of ''Abstraction for data integration: Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction''. | Rouillard, Andrew D; Wang, Zichen; Ma'ayan, Avi | Computational biology and chemistry. | 2015 Dec; | 123-38 | 26297300 |
| An Integrated Transcriptome Atlas of Embryonic Hair Follicle Progenitors, Their Niche, and the Developing Skin. | Sennett, Rachel; Wang, Zichen; Rezza, Amélie; Grisanti, Laura; Roitershtein, Nataly; Sicchio, Cristina; Mok, Ka Wai; Heitman, Nicholas J; Clavel, Carlos; Ma'ayan, Avi; Rendl, Michael | Developmental cell. | 2015 Sep 14; | 577-91 | 26256211 |
| Computational and Practical Aspects of Drug Repositioning. | Oprea, Tudor I; Overington, John P | Assay and drug development technologies. | 2015 Jul-Aug; | 299-306 | 26241209 |
| Comprehensive comparison of large-scale tissue expression datasets | Santos A, Tsafou K, Stolte C, Pletscher-Frankild S, O'Donoghue SI, Jensen LJ. | Peer J | 2015 June 30 | | 26157623 |
| Morphine Regulated Synaptic Networks Revealed by Integrated Proteomics and Network Analysis. | Stockton Jr, Steven D; Gomes, Ivone; Liu, Tong; Moraje, Chandrakala; Hipólito, Lucia; Jones, Matthew R; Ma'ayan, Avi; Morón, Jose A; Li, Hong; Devi, Lakshmi A | Molecular & cellular proteomics : MCP. | 2015 Oct; | 2564-76 | 26149443 |
| Publisher?s Note:Abstraction for data integration:Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction. | Rouillard, Andrew D; Wang, Zichen; Ma'ayan, Avi | Computational biology and chemistry. | 2015 Oct; | 104-19 | 26101093 |
| Integrated Approaches for Genome-wide Interrogation of the Druggable Non-olfactory G Protein-coupled Receptor Superfamily. | Roth, Bryan L; Kroeze, Wesley K | The Journal of biological chemistry. | 2015 Aug 7; | 19471-7 | 26100629 |
| Dynamics of the discovery process of protein-protein interactions from low content studies. | Wang, Zichen; Clark, Neil R; Ma'ayan, Avi | BMC systems biology. | 2015; | 26 | 26048415 |
| Choosing the Right Tool for the Job: RNAi, TALEN, or CRISPR. | Boettcher, Michael; McManus, Michael T | Molecular cell. | 2015 May 21; | 575-85 | 26000843 |
| GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions. | Gundersen, Gregory W; Jones, Matthew R; Rouillard, Andrew D; Kou, Yan; Monteiro, Caroline D; Feldmann, Axel S; Hu, Kevin S; Ma'ayan, Avi | Bioinformatics (Oxford, England). | 2015 Sep 15; | 3060-2 | 25971742 |
| PRESTO-Tango as an open-source resource for interrogation of the druggable human GPCRome. | Kroeze, Wesley K; Sassano, Maria F; Huang, Xi-Ping; Lansu, Katherine; McCorvy, John D; Giguère, Patrick M; Sciaky, Noah; Roth, Bryan L | Nature structural & molecular biology. | 2015 May; | 362-9 | 25895059 |
| Inhibition of Lapatinib-Induced Kinome Reprogramming in ERBB2-Positive Breast Cancer by Targeting BET Family Bromodomains. | Stuhlmiller, Timothy J; Miller, Samantha M; Zawistowski, Jon S; Nakamura, Kazuhiro; Beltran, Adriana S; Duncan, James S; Angus, Steven P; Collins, Kyla A L; Granger, Deborah A; Reuther, Rachel A; Graves, Lee M; Gomez, Shawn M; Kuan, Pei-Fen; Parker, Joel | Cell reports. | 2015 Apr 21; | 390-404 | 25865888 |
| Cell-Based Screening: Extracting Meaning from Complex Data | Finkbeiner S., Frumkin M., Kassner PD | Neuron | 2015 Apr 8 | 86(1):160-174 | 25856492 |
| Genome-wide significant loci: how important are they? Systems genetics to understand heritability of coronary artery disease and other common complex disorders. | Björkegren, Johan L M; Kovacic, Jason C; Dudley, Joel T; Schadt, Eric E | Journal of the American College of Cardiology. | 2015 Mar 3; | 830-45 | 25720628 |
| Genomic and network patterns of schizophrenia genetic variation in human evolutionary accelerated regions. | Xu, Ke; Schadt, Eric E; Pollard, Katherine S; Roussos, Panos; Dudley, Joel T | Molecular biology and evolution. | 2015 May; | 1148-60 | 25681384 |
| Computational and experimental advances in drug repositioning for accelerated therapeutic stratification | Shameer K, Readhead B, Dudley JT. | Current Topics in Medicinal Chemistry | 2015 | | 25579574 |
| REDD1 functions at the crossroads between the therapeutic and adverse effects of topical glucocorticoids. | Baida, Gleb; Bhalla, Pankaj; Kirsanov, Kirill; Lesovaya, Ekaterina; Yakubovskaya, Marianna; Yuen, Kit; Guo, Shuchi; Lavker, Robert M; Readhead, Ben; Dudley, Joel T; Budunova, Irina | EMBO molecular medicine. | 2015 Jan; | 42-58 | 25504525 |
| The TLQP-21 peptide activates the G-protein-coupled receptor C3aR1 via a folding-upon-binding mechanism | Cero C, Vostrikov VV, Verardi R, Severini C, Gopinath T, Braun PD, Sassano MF, Gurney A, Roth BL, Vulchanova L, Possenti R, Veglia G, Bartolomucci A. | Structure | 2014 Dec 2 | 22(12):1744-53. | 25456411 |
| Lean Big Data integration in systems biology and systems pharmacology. | Ma'ayan, Avi; Rouillard, Andrew D; Clark, Neil R; Wang, Zichen; Duan, Qiaonan; Kou, Yan | Trends in pharmacological sciences | 2014 Sep | 450-460 | 25109570 |
| Drug/Cell-line Browser: interactive canvas visualization of cancer drug/cell-line viability assay datasets. | Duan, Qiaonan; Wang, Zichen; Fernandez, Nicolas F; Rouillard, Andrew D; Tan, Christopher M; Benes, Cyril H; Ma'ayan, Avi | Bioinformatics (Oxford, England). | 2014 Nov 15; | 3289-90 | 25100688 |
| Autophagy induction enhances TDP43 turnover and survival in neuronal ALS models. | Barmada, Sami J; Serio, Andrea; Arjun, Arpana; Bilican, Bilada; Daub, Aaron; Ando, D Michael; Tsvetkov, Andrey; Pleiss, Michael; Li, Xingli; Peisach, Daniel; Shaw, Christopher; Chandran, Siddharthan; Finkbeiner, Steven | Nature chemical biology. | 2014 Aug; | | 24974230 |
| LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures. | Duan, Qiaonan; Flynn, Corey; Niepel, Mario; Hafner, Marc; Muhlich, Jeremy L; Fernandez, Nicolas F; Rouillard, Andrew D; Tan, Christopher M; Chen, Edward Y; Golub, Todd R; Sorger, Peter K; Subramanian, Aravind; Ma'ayan, Avi | Nucleic acids research | 2014 Jul | W449-60 | 24906883 |
