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IDG Publications (223)

Publication Title Authors Journal Publication Date Page No PubMedID
TCRD and Pharos 2021: mining the human proteome for disease biology. Sheils TK; Mathias SL; Kelleher KJ; Siramshetty VB; Nguyen DT; Bologa CG; Jensen LJ; Vidović D; Koleti A; Schürer SC; Waller A; Yang JJ; Holmes J; Bocci G; Southall N; Dharkar P; Mathé E; Simeonov A; Oprea TI. Nucleic Acids Research. 2020 Nov; 33156327
DrugCentral 2021 supports drug discovery and repositioning. Patel, Nilkanth; Huang, Xi Ping Nucleic Acids Research. 2020 Mar 02; 33151287
Artificial intelligence, drug repurposing and peer review. Levin JM; Oprea TI; Davidovich S; Clozel T; Overington JP; Vanhaelen Q; Cantor CR; Bischof E; Zhavoronkov A. Nature Biotechnology. 2020 Oct; 32929264
Off-Patent Drug Repositioning. Avram S; Curpan R; Halip L; Bora A; Oprea TI. Journal of Chemical Information and Modeling. 2020 Sep 15; 32877182
KG-COVID-19: a framework to produce customized knowledge graphs for COVID-19 response. Reese, Justin; Unni, Deepak; Callahan, Tiffany J; Cappelletti, Luca; Ravanmehr, Vida; Carbon, Seth; Fontana, Tommaso; Blau, Hannah; Matentzoglu, Nicolas; Harris, Nomi L; Munoz-Torres, Monica C; Robinson, Peter N; Joachimiak, Marcin P; Mungall, Christopher J bioRxiv : the preprint server for biology. 2020 Aug 18; 32839776
The COVID-19 Drug and Gene Set Library. Kuleshov, Maxim V; Stein, Daniel J; Clarke, Daniel J B; Kropiwnicki, Eryk; Jagodnik, Kathleen M; Bartal, Alon; Evangelista, John E; Hom, Jason; Cheng, Minxuan; Bailey, Allison; Zhou, Abigail; Ferguson, Laura B; Lachmann, Alexander; Ma'ayan, Avi Patterns (New York, N.Y.). 2020 Sep 11; 32838343
Chemical Biology Toolkit for DCLK1 Reveals Connection to RNA Processing. Liu, Yan; Ferguson, Fleur M; Li, Lianbo; Kuljanin, Miljan; Mills, Caitlin E; Subramanian, Kartik; Harshbarger, Wayne; Gondi, Sudershan; Wang, Jinhua; Sorger, Peter K; Mancias, Joseph D; Gray, Nathanael S; Westover, Kenneth D Cell chemical biology. 2020 Aug 04; 32755567
The COVID-19 Gene and Drug Set Library. Kuleshov, Maxim V; Clarke, Daniel J B; Kropiwnicki, Eryk; Jagodnik, Kathleen M; Bartal, Alon; Evangelista, John E; Zhou, Abigail; Ferguson, Laura B; Lachmann, Alexander; Ma'ayan, Avi Research square. 2020 May 13; 32702729
Gain-of-function genetic screen of the kinome reveals BRSK2 as an inhibitor of the NRF2 transcription factor. Tamir, Tigist Y; Bowman, Brittany M; Agajanian, Megan J; Goldfarb, Dennis; Schrank, Travis P; Stohrer, Trent; Hale, Andrew E; Siesser, Priscila F; Weir, Seth J; Murphy, Ryan M; LaPak, Kyle M; Weissman, Bernard E; Moorman, Nathaniel J; Major, M Ben Journal of cell science. 2020 Jul 15; 32546533
Opposite regulation of conditioned place preference and intravenous drug self-administration in rodent models: Motivational and non-motivational examples. Green, Thomas A; Bardo, Michael T Neuroscience and biobehavioral reviews. 2020 Jun 12; 32534899
TMEM163 Regulates ATP-Gated P2X Receptor and Behavior. Salm, Elizabeth J; Dunn, Patrick J; Shan, Lili; Yamasaki, Miwako; Malewicz, Nathalie M; Miyazaki, Taisuke; Park, Joongkyu; Sumioka, Akio; Hamer, R Richard L; He, Wei-Wu; Morimoto-Tomita, Megumi; LaMotte, Robert H; Tomita, Susumu Cell reports. 2020 Jun 02; 32492420
Quantifying CDK inhibitor selectivity in live cells. Wells, Carrow I; Vasta, James D; Corona, Cesear R; Wilkinson, Jennifer; Zimprich, Chad A; Ingold, Morgan R; Pickett, Julie E; Drewry, David H; Pugh, Kathryn M; Schwinn, Marie K; Hwang, Byounghoon Brian; Zegzouti, Hicham; Huber, Kilian V M; Cong, Mei; Meisenheimer, Poncho L; Willson, Timothy M; Robers, Matthew B Nature communications. 2020 Jun 02; 32488087
Defining the Neural Kinome: Strategies and Opportunities for Small Molecule Drug Discovery to Target Neurodegenerative Diseases. Krahn, Andrea I; Wells, Carrow; Drewry, David H; Beitel, Lenore K; Durcan, Thomas M; Axtman, Alison D ACS chemical neuroscience. 2020 07 01; 32464049
Systematic Analysis of Environmental Chemicals That Dysregulate Critical Period Plasticity-Related Gene Expression Reveals Common Pathways That Mimic Immune Response to Pathogen. Smith, Milo R; Yevoo, Priscilla; Sadahiro, Masato; Readhead, Ben; Kidd, Brian; Dudley, Joel T; Morishita, Hirofumi Neural plasticity. 2020; 32454811
DCyFIR: a high-throughput CRISPR platform for multiplexed G protein-coupled receptor profiling and ligand discovery. Kapolka, N J; Taghon, G J; Rowe, J B; Morgan, W M; Enten, J F; Lambert, N A; Isom, D G Proceedings of the National Academy of Sciences of the United States of America. 2020 06 09; 32434907
Systems Analysis Implicates WAVE2 Complex in the Pathogenesis of Developmental Left-Sided Obstructive Heart Defects. Edwards, Jonathan J; Rouillard, Andrew D; Fernandez, Nicolas F; Wang, Zichen; Lachmann, Alexander; Shankaran, Sunita S; Bisgrove, Brent W; Demarest, Bradley; Turan, Nahid; Srivastava, Deepak; Bernstein, Daniel; Deanfield, John; Giardini, Alessandro; Porter, George; Kim, Richard; Roberts, Amy E; Newburger, Jane W; Goldmuntz, Elizabeth; Brueckner, Martina; Lifton, Richard P; Seidman, Christine E; Chung, Wendy K; Tristani-Firouzi, Martin; Yost, H Joseph; Ma'ayan, Avi; Gelb, Bruce D JACC. Basic to translational science. 2020 Apr; 32368696
TRUPATH, an open-source biosensor platform for interrogating the GPCR transducerome. Olsen, Reid H J; DiBerto, Jeffrey F; English, Justin G; Glaudin, Alexis M; Krumm, Brian E; Slocum, Samuel T; Che, Tao; Gavin, Ariana C; McCorvy, John D; Roth, Bryan L; Strachan, Ryan T Nature chemical biology. 2020 May 04; 32367019
Discovery and Structure-Activity Relationship Study of (Z)-5-Methylenethiazolidin-4-one Derivatives as Potent and Selective Pan-phosphatidylinositol 5-Phosphate 4-Kinase Inhibitors. Manz, Theresa D; Sivakumaren, Sindhu Carmen; Ferguson, Fleur M; Zhang, Tinghu; Yasgar, Adam; Seo, Hyuk-Soo; Ficarro, Scott B; Card, Joseph D; Shim, Hyeseok; Miduturu, Chandrasekhar V; Simeonov, Anton; Shen, Min; Marto, Jarrod A; Dhe-Paganon, Sirano; Hall, Matthew D; Cantley, Lewis C; Gray, Nathanael S Journal of medicinal chemistry. 2020 May 14; 32298120
EnrichrBot: Twitter bot tracking tweets about human genes. Bartal, Alon; Lachmann, Alexander; Clarke, Daniel J B; Seiden, Allison H; Jagodnik, Kathleen M; Ma'ayan, Avi Bioinformatics (Oxford, England). 2020 Jun 01; 32277816
Novel drug targets in 2019. Avram S; Halip L; Curpan R; Oprea TI. Nature reviews. Drug discovery. 2020 May; 32273590
Presynaptic calcium channels: specialized control of synaptic neurotransmitter release. Dolphin, Annette C; Lee, Amy Nature reviews. Neuroscience. 2020 04; 32161339
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
How many rare diseases are there? Haendel M; Vasilevsky N; Unni D; Bologa C; Harris N; Rehm H; Hamosh A; Baynam G; Groza T; McMurry J; Dawkins H; Rath A; Thaxon C; Bocci G; Joachimiak MP; Köhler S; Robinson PN; Mungall C; Oprea TI. Nature reviews. Drug discovery. 2020 Feb; 32020066
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 Mar; 32040955
Will Artificial Intelligence for Drug Discovery Impact Clinical Pharmacology? Zhavoronkov A; Vanhaelen Q; Oprea TI. Clinical Pharmacology and Therapeutics. 2020 Apr; 31957003
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
Machine and deep learning approaches for cancer drug repurposing. Issa, Naiem T; Stathias, Vasileios; Schürer, Stephan; Dakshanamurthy, Sivanesan Seminars in cancer biology. 2020 Jan 03; 31904426
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 Jan 10; 31857493
Research Techniques Made Simple: Molecular Docking in Dermatology - A Foray into In Silico Drug Discovery. Issa, Naiem T; Badiavas, Evangelos V; Schürer, Stephan The Journal of investigative dermatology. 2019 12; 31753122
LINCS Data Portal 2.0: next generation access point for perturbation-response signatures. Stathias, Vasileios; Turner, John; Koleti, Amar; Vidovic, Dusica; Cooper, Daniel; Fazel-Najafabadi, Mehdi; Pilarczyk, Marcin; Terryn, Raymond; Chung, Caty; Umeano, Afoma; Clarke, Daniel J B; Lachmann, Alexander; Evangelista, John Erol; Ma'ayan, Avi; Medvedovic, Mario; Schürer, Stephan C Nucleic acids research. 2020 01 08; 31701147
ADCK3/COQ8A: the choice target of the UbiB protein kinase-like family. Asquith, Christopher R M; Murray, Nathan H; Pagliarini, David J Nature reviews. Drug discovery. 2019 10; 31673128
Single-cell immune landscape of human atherosclerotic plaques. Fernandez, Dawn M; Rahman, Adeeb H; Fernandez, Nicolas F; Chudnovskiy, Aleksey; Amir, El-Ad David; Amadori, Letizia; Khan, Nayaab S; Wong, Christine K; Shamailova, Roza; Hill, Christopher A; Wang, Zichen; Remark, Romain; Li, Jennifer R; Pina, Christian; Faries, Christopher; Awad, Ahmed J; Moss, Noah; Bjorkegren, Johan L M; Kim-Schulze, Seunghee; Gnjatic, Sacha; Ma'ayan, Avi; Mocco, J; Faries, Peter; Merad, Miriam; Giannarelli, Chiara Nature medicine. 2019 10; 31591603
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 Sep 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
Integrative analysis of loss-of-function variants in clinical and genomic data reveals novel genes associated with cardiovascular traits. Glicksberg, Benjamin S; Amadori, Letizia; Akers, Nicholas K; Sukhavasi, Katyayani; Franzén, Oscar; Li, Li; Belbin, Gillian M; Ayers, Kristin L; Shameer, Khader; Badgeley, Marcus A; Johnson, Kipp W; Readhead, Ben; Darrow, Bruce J; Kenny, Eimear E; Betsholtz, Christer; Ermel, Raili; Skogsberg, Josefin; Ruusalepp, Arno; Schadt, Eric E; Dudley, Joel T; Ren, Hongxia; Kovacic, Jason C; Giannarelli, Chiara; Li, Shuyu D; Björkegren, Johan L M; Chen, Rong BMC medical genomics. 2019 07 25; 31345219
The crystal structure of the protein kinase HIPK2 reveals a unique architecture of its CMGC-insert region. Agnew, Christopher; Liu, Lijun; Liu, Shu; Xu, Wei; You, Liang; Yeung, Wayland; Kannan, Natarajan; Jablons, David; Jura, Natalia The Journal of biological chemistry. 2019 09 13; 31341017
Design, Synthesis, and Characterization of Ogerin-Based Positive Allosteric Modulators for G Protein-Coupled Receptor 68 (GPR68). Yu, Xufen; Huang, Xi-Ping; Kenakin, Terry P; Slocum, Samuel T; Chen, Xin; Martini, Michael L; Liu, Jing; Jin, Jian Journal of medicinal chemistry. 2019 08 22; 31298539
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
Discovery of Covalent CDK14 Inhibitors with Pan-TAIRE Family Specificity. Ferguson, Fleur M; Doctor, Zainab M; Ficarro, Scott B; Browne, Christopher M; Marto, Jarrod A; Johnson, Jared L; Yaron, Tomer M; Cantley, Lewis C; Kim, Nam Doo; Sim, Taebo; Berberich, Matthew J; Kalocsay, Marian; Sorger, Peter K; Gray, Nathanael S Cell chemical biology. 2019 Mar 11; 30930164
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
How structure informs and transforms chemogenetics. Roth, Bryan L Current opinion in structural biology. 2019 08; 30818201
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
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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
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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
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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