Illuminating the Druggable Genome (349)
Publication TitleAuthorsJournalPublication DatePage NoPubMedID
RIOK3 and Its Alternatively Spliced Isoform Have Disparate Roles in the Innate Immune Response to Rift Valley Fever Virus (MP12) Infection.Bisom, Thomas C; White, Luke A; Lanchy, Jean-Marc; Lodmell, J StephenViruses2022 09 1736146870
Transforming L1000 profiles to RNA-seq-like profiles with deep learning.Jeon, Minji; Xie, Zhuorui; Evangelista, John E; Wojciechowicz, Megan L; Clarke, Daniel J B; Ma'ayan, AviBMC bioinformatics2022 Sep 1336100892
Magel2 knockdown in hypothalamic POMC neurons innervating the medial amygdala reduces susceptibility to diet-induced obesity.Choi, Yuna; Min, Hyeon-Young; Hwang, Jiyeon; Jo, Young-HwanLife science alliance2022 1136007929
Production of Eukaryotic Glycoproteins for Structural and Functional Studies Using Expi293F Cells.Greven, Jessica A; Brett, Tom JCurrent protocols2022 Aug35998009
A Superfolder Green Fluorescent Protein-Based Biosensor Allows Monitoring of Chloride in the Endoplasmic Reticulum.Shariati, Kaavian; Zhang, Yaohuan; Giubbolini, Simone; Parra, Riccardo; Liang, Steven; Edwards, Austin; Hejtmancik, J Fielding; Ratto, Gian Michele; Arosio, Daniele; Ku, GregoryACS sensors2022 Aug 2635951356
TRUPATH: An Open-Source Biosensor Platform for Interrogating the GPCR Transducerome.DiBerto, Jeffrey F; Olsen, Reid H J; Roth, Bryan LMethods in molecular biology (Clifton, N.J.)202235836068
Inactive and active state structures template selective tools for the human 5-HT5A receptor.Zhang, Shicheng; Chen, He; Zhang, Chengwei; Yang, Ying; Popov, Petr; Liu, Jing; Krumm, Brian E; Cao, Can; Kim, Kuglae; Xiong, Yan; Katritch, Vsevolod; Shoichet, Brian K; Jin, Jian; Fay, Jonathan F; Roth, Bryan LNature structural & molecular biology2022 0735835867
Overexpressing the hydroxycarboxylic acid receptor 1 in mouse brown adipose tissue restores glucose tolerance and insulin sensitivity in diet-induced obese mice.Min, Hyeon-Young; Hwang, Jiyeon; Choi, Yuna; Jo, Young-HwanAmerican journal of physiology. Endocrinology and metabolism2022 Sep 0135830691
The potassium channel auxiliary subunit Kvβ2 (Kcnab2) regulates Kv1 channels and dopamine neuron firing.Yee, Joshua X; Rastani, Ariana; Soden, Marta EJournal of neurophysiology2022 07 0135788155
CACHE (Critical Assessment of Computational Hit-finding Experiments): A public-private partnership benchmarking initiative to enable the development of computational methods for hit-finding.Ackloo, Suzanne; Al-Awar, Rima; Amaro, Rommie E; Arrowsmith, Cheryl H; Azevedo, Hatylas; Batey, Robert A; Bengio, Yoshua; Betz, Ulrich A K; Bologa, Cristian G; Chodera, John D; Cornell, Wendy D; Dunham, Ian; Ecker, Gerhard F; Edfeldt, Kristina; Edwards, Aled M; Gilson, Michael K; Gordijo, Claudia R; Hessler, Gerhard; Hillisch, Alexander; Hogner, Anders; Irwin, John J; Jansen, Johanna M; Kuhn, Daniel; Leach, Andrew R; Lee, Alpha A; Lessel, Uta; Morgan, Maxwell R; Moult, John; Muegge, Ingo; Oprea, Tudor I; Perry, Benjamin G; Riley, Patrick; Rousseaux, Sophie A L; Saikatendu, Kumar Singh; Santhakumar, Vijayaratnam; Schapira, Matthieu; Scholten, Cora; Todd, Matthew H; Vedadi, Masoud; Volkamer, Andrea; Willson, Timothy MNature reviews. Chemistry2022 Apr35783295
Numb-associated kinases are required for SARS-CoV-2 infection and are cellular targets for antiviral strategies.Karim, Marwah; Saul, Sirle; Ghita, Luca; Sahoo, Malaya Kumar; Ye, Chengjin; Bhalla, Nishank; Lo, Chieh-Wen; Jin, Jing; Park, Jun-Gyu; Martinez-Gualda, Belén; East, Michael Patrick; Johnson, Gary L; Pinsky, Benjamin A; Martinez-Sobrido, Luis; Asquith, Christopher R M; Narayanan, Aarthi; De Jonghe, Steven; Einav, ShiritAntiviral research2022 0835738348
Temozolomide-induced guanine mutations create exploitable vulnerabilities of guanine-rich DNA and RNA regions in drug-resistant gliomas.Tiek, Deanna M; Erdogdu, Beril; Razaghi, Roham; Jin, Lu; Sadowski, Norah; Alamillo-Ferrer, Carla; Hogg, J Robert; Haddad, Bassem R; Drewry, David H; Wells, Carrow I; Pickett, Julie E; Song, Xiao; Goenka, Anshika; Hu, Bo; Goldlust, Samuel A; Zuercher, William J; Pertea, Mihaela; Timp, Winston; Cheng, Shi-Yuan; Riggins, Rebecca BScience advances2022 06 2435731869
On-Chip Preconcentration Microchip Capillary Electrophoresis Based CE-PRM-LIVE for High-Throughput Selectivity Profiling of Deubiquitinase Inhibitors.Zhu, He; Mellors, J Scott; Chan, Wai Cheung; Thompson, J Will; Ficarro, Scott B; Tavares, Isidoro; Bratt, Ariana S; Decker, Jens; Krause, Michael; Kruppa, Gary; Buhrlage, Sara J; Marto, Jarrod AAnalytical chemistry2022 07 1235729701
Autophagy and Herpesvirus: A collaboration Contributing to Alzheimer's Disease.Nafchi, Amir R; Esmaeili, Mona; Myers, Orrin; Oprea, Tudor; Bearer, Elane LFASEB journal : official publication of the Federation of American Societies for Experimental Biology2022 0535723876
Calcium Channels in Retinal Function and Disease.Williams, Brittany; Maddox, J Wesley; Lee, AmyAnnual review of vision science2022 09 1535650675
Orphan G-Protein Coupled Receptor GPRC5B Is Critical for Lymphatic Development.Xu, Wenjing; Nelson-Maney, Nathan P; Bálint, László; Kwon, Hyouk-Bum; Davis, Reema B; Dy, Danielle C M; Dunleavey, James M; St Croix, Brad; Caron, Kathleen MInternational journal of molecular sciences2022 May 2035628521
Investigating the Therapeutic Potential of Cdk8 Small Molecule Inhibitors to Prevent Pathological Cardiac Remodeling and Heart Failure.Oppman, Alexis M; Gardner, Richard N; Martins, Ines; Minerath, Rachel A; Hall, Duane D; Grueter, Chad EFASEB journal : official publication of the Federation of American Societies for Experimental Biology2022 May35553110
Analysis of human Tribbles 2 (TRIB2) pseudokinase.Harris, John A; Fairweather, Emma; Byrne, Dominic P; Eyers, Patrick AMethods in enzymology202235525562
Computational tools and resources for pseudokinase research.O'Boyle, Brady; Shrestha, Safal; Kochut, Krzysztof; Eyers, Patrick A; Kannan, NatarajanMethods in enzymology202235525549
Open source fraction collector/MALDI spotter for proteomics.Ficarro, Scott B; Max Alexander, William; Tavares, Isidoro; Marto, Jarrod AHardwareX2022 Apr35518277
Protein proximity networks and functional evaluation of the casein kinase 1 gamma family reveal unique roles for CK1γ3 in WNT signaling.Agajanian, Megan J; Potjewyd, Frances M; Bowman, Brittany M; Solomon, Smaranda; LaPak, Kyle M; Bhatt, Dhaval P; Smith, Jeffery L; Goldfarb, Dennis; Axtman, Alison D; Major, Michael BThe Journal of biological chemistry2022 0635487243
Ectopic biomolecular phase transitions: fusion proteins in cancer pathologies.Davis, Richoo B; Moosa, Mahdi Muhammad; Banerjee, Priya RTrends in cell biology2022 Aug35484036
Cavβ1 regulates T cell expansion and apoptosis independently of voltage-gated Ca2+ channel function.Erdogmus, Serap; Concepcion, Axel R; Yamashita, Megumi; Sidhu, Ikjot; Tao, Anthony Y; Li, Wenyi; Rocha, Pedro P; Huang, Bonnie; Garippa, Ralph; Lee, Boram; Lee, Amy; Hell, Johannes W; Lewis, Richard S; Prakriya, Murali; Feske, StefanNature communications2022 04 1935440113
AlphaFold illuminates half of the dark human proteins.Binder, Jessica L; Berendzen, Joel; Stevens, Amy O; He, Yi; Wang, Jian; Dokholyan, Nikolay V; Oprea, Tudor ICurrent opinion in structural biology2022 0635439658
Identification of 4-Anilinoquin(az)oline as a Cell-Active Protein Kinase Novel 3 (PKN3) Inhibitor Chemotype.Asquith, Christopher R M; Temme, Louisa; East, Michael P; Laitinen, Tuomo; Pickett, Julie; Kwarcinski, Frank E; Sinha, Parvathi; Wells, Carrow I; Johnson, Gary L; Zutshi, Reena; Drewry, David HChemMedChem2022 06 2035403825
Agonist and antagonist TRUPATH assays for G protein-coupled receptors.DiBerto, Jeffrey F; Smart, Katie; Olsen, Reid H J; Roth, Bryan LSTAR protocols2022 06 1735403009
Gene and drug landing page aggregator.Clarke, Daniel J B; Kuleshov, Maxim V; Xie, Zhuorui; Evangelista, John E; Meyers, Marilyn R; Kropiwnicki, Eryk; Jenkins, Sherry L; Ma'ayan, AviBioinformatics advances202235368424
The voltage-gated Ca2+ channel subunit α2δ-4 regulates locomotor behavior and sensorimotor gating in mice.Klomp, Annette; Omichi, Ryotaro; Iwasa, Yoichiro; Smith, Richard J; Usachev, Yuriy M; Russo, Andrew F; Narayanan, Nandakumar S; Lee, AmyPloS one202235353835
Molecular recognition of formylpeptides and diverse agonists by the formylpeptide receptors FPR1 and FPR2.Zhuang, Youwen; Wang, Lei; Guo, Jia; Sun, Dapeng; Wang, Yue; Liu, Weiyi; Xu, H Eric; Zhang, ChengNature communications2022 Feb 2535217703
State of the Art and Uses for the Biopharmaceutics Drug Disposition Classification System (BDDCS): New Additions, Revisions, and Citation References.Bocci, Giovanni; Oprea, Tudor I; Benet, Leslie ZThe AAPS journal2022 02 2335199251
Structure-Based Design of a Chemical Probe Set for the 5-HT5A Serotonin Receptor.Levit Kaplan, Anat; Strachan, Ryan T; Braz, Joao M; Craik, Veronica; Slocum, Samuel; Mangano, Thomas; Amabo, Vanessa; O'Donnell, Henry; Lak, Parnian; Basbaum, Allan I; Roth, Bryan L; Shoichet, Brian KJournal of medicinal chemistry2022 03 1035195401
DrugShot: querying biomedical search terms to retrieve prioritized lists of small molecules.Kropiwnicki, Eryk; Lachmann, Alexander; Clarke, Daniel J B; Xie, Zhuorui; Jagodnik, Kathleen M; Ma'ayan, AviBMC bioinformatics2022 Feb 1935183110
EMBER: Multi-label prediction of kinase-substrate phosphorylation events through deep learning.Kirchoff, Kathryn E; Gomez, Shawn MBioinformatics (Oxford, England)2022 Feb 1435157015
Machine learning prediction and tau-based screening identifies potential Alzheimer's disease genes relevant to immunity.Binder, Jessica; Ursu, Oleg; Bologa, Cristian; Jiang, Shanya; Maphis, Nicole; Dadras, Somayeh; Chisholm, Devon; Weick, Jason; Myers, Orrin; Kumar, Praveen; Yang, Jeremy J; Bhaskar, Kiran; Oprea, Tudor ICommunications biology2022 02 1135149761
blitzGSEA: Efficient computation of Gene Set Enrichment Analysis through Gamma distribution approximation.Lachmann, Alexander; Xie, Zhuorui; Ma'ayan, AviBioinformatics (Oxford, England)2022 Feb 1035143610
Tousled-like kinase 2 targets ASF1 histone chaperones through client mimicry.Simon, Bertrand; Lou, Hua Jane; Huet-Calderwood, Clotilde; Shi, Guangda; Boggon, Titus J; Turk, Benjamin E; Calderwood, David ANature communications2022 02 0835136069
Tra2beta-Dependent Regulation of RIO Kinase 3 Splicing During Rift Valley Fever Virus Infection Underscores the Links Between Alternative Splicing and Innate Antiviral Immunity.White, Luke Adam; Bisom, Thomas C; Grimes, Hunter L; Hayashi, Miyuki; Lanchy, Jean-Marc; Lodmell, J StephenFrontiers in cellular and infection microbiology202135127560
Neuropeptide B/W receptor 1 peptidomimetic agonists: Structure-activity relationships and plasma stability.Nguyen, Thuy; Decker, Ann M; Snyder, Rodney W; Tonetti, Emma C; Gamage, Thomas F; Zhang, YananEuropean journal of medicinal chemistry2022 Mar 0535101647
A Learning Based Framework for Disease Prediction from Images of Human-Derived Pluripotent Stem Cells of Schizophrenia Patients.Fularczyk, Nickolas; Di Re, Jessica; Stertz, Laura; Walss-Bass, Consuelo; Laezza, Fernanda; Labate, DemetrioNeuroinformatics2022 Jan 2235064871
A Workflow of Integrated Resources to Catalyze Network Pharmacology Driven COVID-19 Research.Zahoránszky-Kőhalmi, Gergely; Siramshetty, Vishal B; Kumar, Praveen; Gurumurthy, Manideep; Grillo, Busola; Mathew, Biju; Metaxatos, Dimitrios; Backus, Mark; Mierzwa, Tim; Simon, Reid; Grishagin, Ivan; Brovold, Laura; Mathé, Ewy A; Hall, Matthew D; Michael, Samuel G; Godfrey, Alexander G; Mestres, Jordi; Jensen, Lars J; Oprea, Tudor IJournal of chemical information and modeling2022 02 1435057621
Host kinase CSNK2 is a target for inhibition of pathogenic β-coronaviruses including SARS-CoV-2.Yang, Xuan; Dickmander, Rebekah J; Bayati, Armin; Taft-Benz, Sharon A; Smith, Jeffery L; Wells, Carrow I; Madden, Emily A; Brown, Jason W; Lenarcic, Erik M; Yount Jr, Boyd L; Chang, Edcon; Axtman, Alison D; Baric, Ralph S; Heise, Mark T; McPherson, Peter S; Moorman, Nathaniel J; Willson, Timothy MbioRxiv : the preprint server for biology2022 Jan 2635018375
Systematic identification of ACE2 expression modulators reveals cardiomyopathy as a risk factor for mortality in COVID-19 patients.Kaur, Navchetan; Oskotsky, Boris; Butte, Atul J; Hu, ZichengGenome biology2022 01 1035012625
Intestinal Gpr17 deficiency improves glucose metabolism by promoting GLP-1 secretion.Yan, Shijun; Conley, Jason M; Reilly, Austin M; Stull, Natalie D; Abhyankar, Surabhi D; Ericsson, Aaron C; Kono, Tatsuyoshi; Molosh, Andrei I; Kubal, Chandrashekhar A; Evans-Molina, Carmella; Ren, HongxiaCell reports2022 01 0434986353
Adaptive chromatin remodeling and transcriptional changes of the functional kinome in tumor cells in response to targeted kinase inhibition.East, Michael P; Johnson, Gary LThe Journal of biological chemistry2022 Feb34958800
Identification of RIOK2 as a master regulator of human blood cell development.Ghosh, Shrestha; Raundhal, Mahesh; Myers, Samuel A; Carr, Steven A; Chen, Xi; Petsko, Gregory A; Glimcher, Laurie HNature immunology2022 0134937919
Supervised learning with word embeddings derived from PubMed captures latent knowledge about protein kinases and cancer.Ravanmehr, Vida; Blau, Hannah; Cappelletti, Luca; Fontana, Tommaso; Carmody, Leigh; Coleman, Ben; George, Joshy; Reese, Justin; Joachimiak, Marcin; Bocci, Giovanni; Hansen, Peter; Bult, Carol; Rueter, Jens; Casiraghi, Elena; Valentini, Giorgio; Mungall, Christopher; Oprea, Tudor I; Robinson, Peter NNAR genomics and bioinformatics2021 Dec34888523
A high-fat diet catalyzes progression to hyperglycemia in mice with selective impairment of insulin action in Glut4-expressing tissues.Reilly, Austin M; Yan, Shijun; Huang, Menghao; Abhyankar, Surabhi D; Conley, Jason M; Bone, Robert N; Stull, Natalie D; Horan, Daniel J; Roh, Hyun C; Robling, Alexander G; Ericsson, Aaron C; Dong, Xiaocheng C; Evans-Molina, Carmella; Ren, HongxiaThe Journal of biological chemistry2022 Jan34801552
Structure, function and pharmacology of human itch GPCRs.Cao, Can; Kang, Hye Jin; Singh, Isha; Chen, He; Zhang, Chengwei; Ye, Wenlei; Hayes, Byron W; Liu, Jing; Gumpper, Ryan H; Bender, Brian J; Slocum, Samuel T; Krumm, Brian E; Lansu, Katherine; McCorvy, John D; Kroeze, Wesley K; English, Justin G; DiBerto, Jeffrey F; Olsen, Reid H J; Huang, Xi-Ping; Zhang, Shicheng; Liu, Yongfeng; Kim, Kuglae; Karpiak, Joel; Jan, Lily Y; Abraham, Soman N; Jin, Jian; Shoichet, Brian K; Fay, Jonathan F; Roth, Bryan LNature2021 1234789874
The reactome pathway knowledgebase 2022.Gillespie, Marc; Jassal, Bijay; Stephan, Ralf; Milacic, Marija; Rothfels, Karen; Senff-Ribeiro, Andrea; Griss, Johannes; Sevilla, Cristoffer; Matthews, Lisa; Gong, Chuqiao; Deng, Chuan; Varusai, Thawfeek; Ragueneau, Eliot; Haider, Yusra; May, Bruce; Shamovsky, Veronica; Weiser, Joel; Brunson, Timothy; Sanati, Nasim; Beckman, Liam; Shao, Xiang; Fabregat, Antonio; Sidiropoulos, Konstantinos; Murillo, Julieth; Viteri, Guilherme; Cook, Justin; Shorser, Solomon; Bader, Gary; Demir, Emek; Sander, Chris; Haw, Robin; Wu, Guanming; Stein, Lincoln; Hermjakob, Henning; D'Eustachio, PeterNucleic acids research2022 01 0734788843
Structural basis of human ghrelin receptor signaling by ghrelin and the synthetic agonist ibutamoren.Liu, Heng; Sun, Dapeng; Myasnikov, Alexander; Damian, Marjorie; Baneres, Jean-Louis; Sun, Ji; Zhang, ChengNature communications2021 11 0434737341
Loss of proximal tubular transcription factor Krüppel-like factor 15 exacerbates kidney injury through loss of fatty acid oxidation.Piret, Sian E; Attallah, Ahmed A; Gu, Xiangchen; Guo, Yiqing; Gujarati, Nehaben A; Henein, Justina; Zollman, Amy; Hato, Takashi; Ma'ayan, Avi; Revelo, Monica P; Dickman, Kathleen G; Chen, Chung-Hsin; Shun, Chia-Tung; Rosenquist, Thomas A; He, John C; Mallipattu, Sandeep KKidney international2021 Dec34634362
PRM-LIVE with Trapped Ion Mobility Spectrometry and Its Application in Selectivity Profiling of Kinase Inhibitors.Zhu, He; Ficarro, Scott B; Alexander, William M; Fleming, Laura E; Adelmant, Guillaume; Zhang, Tinghu; Willetts, Matthew; Decker, Jens; Brehmer, Sven; Krause, Michael; East, Michael P; Gray, Nathanael S; Johnson, Gary L; Kruppa, Gary; Marto, Jarrod AAnalytical chemistry2021 10 1934606255
NeuriteNet: A convolutional neural network for assessing morphological parameters of neurite growth.Vecchi, Joseph T; Mullan, Sean; Lopez, Josue A; Hansen, Marlan R; Sonka, Milan; Lee, AmyJournal of neuroscience methods2021 11 0134480956
Non-canonical role of Hippo tumor suppressor serine/threonine kinase 3 STK3 in prostate cancer.Schirmer, Amelia U; Driver, Lucy M; Zhao, Megan T; Wells, Carrow I; Pickett, Julie E; O'Bryne, Sean N; Eduful, Benjamin J; Yang, Xuan; Howard, Lauren; You, Sungyong; Devi, Gayathri R; DiGiovanni, John; Freedland, Stephen J; Chi, Jen-Tsan; Drewry, David H; Macias, EverardoMolecular therapy : the journal of the American Society of Gene Therapy2022 01 0534450249
Adiponectin receptor fragmentation in mouse models of type 1 and type 2 diabetes.Frabutt, Dylan; Stull, Natalie; Pineros, Annie R; Tersey, Sarah A; Scheuner, Donalyn; Mastracci, Teresa L; Pugia, Michael JArchives of autoimmune diseases202034414399
Evaluation of Amide Bioisosteres Leading to 1,2,3-Triazole Containing Compounds as GPR88 Agonists: Design, Synthesis, and Structure-Activity Relationship Studies.Rahman, Md Toufiqur; Decker, Ann M; Laudermilk, Lucas; Maitra, Rangan; Ma, Weiya; Ben Hamida, Sami; Darcq, Emmanuel; Kieffer, Brigitte L; Jin, ChunyangJournal of medicinal chemistry2021 Aug 2634387471
Post-translational modification of RAS proteins.Campbell, Sharon L; Philips, Mark RCurrent opinion in structural biology2021 1234365229
Identification of Pyrimidine-Based Lead Compounds for Understudied Kinases Implicated in Driving Neurodegeneration.Drewry, David H; Annor-Gyamfi, Joel K; Wells, Carrow I; Pickett, Julie E; Dederer, Verena; Preuss, Franziska; Mathea, Sebastian; Axtman, Alison DJournal of medicinal chemistry2022 01 2734333981
The Tails of Protein Kinase A.Taylor, Susan S; Søberg, Kristoffer; Kobori, Evan; Wu, Jian; Pautz, Sabine; Herberg, Friedrich W; Skålhegg, Bjørn SteenMolecular pharmacology2022 0434330820
Hinge Binder Scaffold Hopping Identifies Potent Calcium/Calmodulin-Dependent Protein Kinase Kinase 2 (CAMKK2) Inhibitor Chemotypes.Eduful, Benjamin J; O'Byrne, Sean N; Temme, Louisa; Asquith, Christopher R M; Liang, Yi; Picado, Alfredo; Pilotte, Joseph R; Hossain, Mohammad Anwar; Wells, Carrow I; Zuercher, William J; Catta-Preta, Carolina M C; Zonzini Ramos, Priscila; Santiago, André de S; Couñago, Rafael M; Langendorf, Christopher G; Nay, Kévin; Oakhill, Jonathan S; Pulliam, Thomas L; Lin, Chenchu; Awad, Dominik; Willson, Timothy M; Frigo, Daniel E; Scott, John W; Drewry, David HJournal of medicinal chemistry2021 08 1234264658
A critical overview of computational approaches employed for COVID-19 drug discovery.Muratov , Eugene N; Amaro , Rommie; Andrade , Carolina H; Brown , Nathan; Ekins , Sean; Fourches , Denis; Isayev , Olexandr; Kozakov , Dima; Medina-Franco , José L; Merz , Kenneth M; Oprea , Tudor I; Poroikov , Vladimir; Schneider , Gisbert; Todd , Matthew H; Varnek , Alexandre; Winkler , David A; Zakharov , Alexey V; Cherkasov , Artem; Tropsha , AlexanderChemical Society reviews2021 Aug 2134212944
NEK5 activity regulates the mesenchymal and migratory phenotype in breast cancer cells.Matossian, Margarite D; Elliott, Steven; Van Hoang, T; Burks, Hope E; Wright, Maryl K; Alzoubi, Madlin S; Yan, Thomas; Chang, Tiffany; Wathieu, Henri; Windsor, Gabrielle O; Hartono, Alifiani Bo; Lee, Sean; Zuercher, William J; Drewry, David H; Wells, Carrow; Kapadia, Nirav; Buechlein, Aaron; Fang, Fang; Nephew, Kenneth P; Collins-Burow, Bridgette M; Burow, Matthew EBreast cancer research and treatment2021 Jul 0134196902
Chemoproteomic methods for covalent drug discovery.Chan, Wai Cheung; Sharifzadeh, Shabnam; Buhrlage, Sara J; Marto, Jarrod AChemical Society reviews2021 Aug 0234143170
TIGA: Target illumination GWAS analytics.Yang, Jeremy J; Grissa, Dhouha; Lambert, Christophe G; Bologa, Cristian G; Mathias, Stephen L; Waller, Anna; Wild, David J; Jensen, Lars Juhl; Oprea, Tudor IBioinformatics (Oxford, England)2021 Jun 0434086846
Crowdsourced mapping of unexplored target space of kinase inhibitors.Cichońska, Anna; Ravikumar, Balaguru; Allaway, Robert J; Wan, Fangping; Park, Sungjoon; Isayev, Olexandr; Li, Shuya; Mason, Michael; Lamb, Andrew; Tanoli, Ziaurrehman; Jeon, Minji; Kim, Sunkyu; Popova, Mariya; Capuzzi, Stephen; Zeng, Jianyang; Dang, Kristen; Koytiger, Gregory; Kang, Jaewoo; Wells, Carrow I; Willson, Timothy M; IDG-DREAM Drug-Kinase Binding Prediction Challenge Consortium; Oprea, Tudor I; Schlessinger, Avner; Drewry, David H; Stolovitzky, Gustavo; Wennerberg, Krister; Guinney, Justin; Aittokallio, TeroNature communications2021 06 0334083538
Krüppel-like factor 6-mediated loss of BCAA catabolism contributes to kidney injury in mice and humans.Piret, Sian E; Guo, Yiqing; Attallah, Ahmed A; Horne, Sylvia J; Zollman, Amy; Owusu, Daniel; Henein, Justina; Sidorenko, Viktoriya S; Revelo, Monica P; Hato, Takashi; Ma'ayan, Avi; He, John Cijiang; Mallipattu, Sandeep KProceedings of the National Academy of Sciences of the United States of America2021 06 0834074766
Regulation of Tissue Inflammation by 12-Lipoxygenases.Kulkarni, Abhishek; Nadler, Jerry L; Mirmira, Raghavendra G; Casimiro, IsabelBiomolecules2021 05 1134064822
KEA3: improved kinase enrichment analysis via data integration.Kuleshov, Maxim V; Xie, Zhuorui; London, Alexandra B K; Yang, Janice; Evangelista, John Erol; Lachmann, Alexander; Shu, Ingrid; Torre, Denis; Ma'ayan, AviNucleic acids research2021 07 0234019655
TMEM16C is involved in thermoregulation and protects rodent pups from febrile seizures.Wang, Tongfei A; Chen, Chao; Huang, Fen; Feng, Shengjie; Tien, Jason; Braz, João M; Basbaum, Allan I; Jan, Yuh Nung; Jan, Lily YehProceedings of the National Academy of Sciences of the United States of America2021 05 1833972431
mTORC2 controls the activity of PKC and Akt by phosphorylating a conserved TOR interaction motif.Baffi, Timothy R; Lordén, Gema; Wozniak, Jacob M; Feichtner, Andreas; Yeung, Wayland; Kornev, Alexandr P; King, Charles C; Del Rio, Jason C; Limaye, Ameya J; Bogomolovas, Julius; Gould, Christine M; Chen, Ju; Kennedy, Eileen J; Kannan, Natarajan; Gonzalez, David J; Stefan, Eduard; Taylor, Susan S; Newton, Alexandra CScience signaling2021 Apr 1333850054
An Esrrb and Nanog Cell Fate Regulatory Module Controlled by Feed Forward Loop Interactions.Sevilla, Ana; Papatsenko, Dimitri; Mazloom, Amin R; Xu, Huilei; Vasileva, Ana; Unwin, Richard D; LeRoy, Gary; Chen, Edward Y; Garrett-Bakelman, Francine E; Lee, Dung-Fang; Trinite, Benjamin; Webb, Ryan L; Wang, Zichen; Su, Jie; Gingold, Julian; Melnick, Ari; Garcia, Benjamin A; Whetton, Anthony D; MacArthur, Ben D; Ma'ayan, Avi; Lemischka, Ihor RFrontiers in cell and developmental biology202133816475
Drugmonizome and Drugmonizome-ML: integration and abstraction of small molecule attributes for drug enrichment analysis and machine learning.Kropiwnicki, Eryk; Evangelista, John E; Stein, Daniel J; Clarke, Daniel J B; Lachmann, Alexander; Kuleshov, Maxim V; Jeon, Minji; Jagodnik, Kathleen M; Ma'ayan, AviDatabase : the journal of biological databases and curation2021 03 3133787872
Gene Set Knowledge Discovery with Enrichr.Xie, Zhuorui; Bailey, Allison; Kuleshov, Maxim V; Clarke, Daniel J B; Evangelista, John E; Jenkins, Sherry L; Lachmann, Alexander; Wojciechowicz, Megan L; Kropiwnicki, Eryk; Jagodnik, Kathleen M; Jeon, Minji; Ma'ayan, AviCurrent protocols2021 Mar33780170
Predicting Lyme Disease From Patients' Peripheral Blood Mononuclear Cells Profiled With RNA-Sequencing.Clarke, Daniel J B; Rebman, Alison W; Bailey, Allison; Wojciechowicz, Megan L; Jenkins, Sherry L; Evangelista, John E; Danieletto, Matteo; Fan, Jinshui; Eshoo, Mark W; Mosel, Michael R; Robinson, William; Ramadoss, Nitya; Bobe, Jason; Soloski, Mark J; Aucott, John N; Ma'ayan, AviFrontiers in immunology202133763080
Blockade of IL-22 signaling reverses erythroid dysfunction in stress-induced anemias.Raundhal, Mahesh; Ghosh, Shrestha; Myers, Samuel A; Cuoco, Michael S; Singer, Meromit; Carr, Steven A; Waikar, Sushrut S; Bonventre, Joseph V; Ritz, Jerome; Stone, Richard M; Steensma, David P; Regev, Aviv; Glimcher, Laurie HNature immunology2021 0433753942
Discovery and resistance mechanism of a selective CDK12 degrader.Jiang, Baishan; Gao, Yang; Che, Jianwei; Lu, Wenchao; Kaltheuner, Ines H; Dries, Ruben; Kalocsay, Marian; Berberich, Matthew J; Jiang, Jie; You, Inchul; Kwiatkowski, Nicholas; Riching, Kristin M; Daniels, Danette L; Sorger, Peter K; Geyer, Matthias; Zhang, Tinghu; Gray, Nathanael SNature chemical biology2021 Mar 2233753926
Targeting Never-In-Mitosis-A Related Kinase 5 in Cancer: A Review.Matossian, Margarite D; Wells, Carrow I; Zuercher, William J; Collins-Burow, Bridgette M; Drewry, David H; Burow, Matthew ECurrent medicinal chemistry202133749548
Appyters: Turning Jupyter Notebooks into data-driven web apps.Clarke, Daniel J B; Jeon, Minji; Stein, Daniel J; Moiseyev, Nicole; Kropiwnicki, Eryk; Dai, Charles; Xie, Zhuorui; Wojciechowicz, Megan L; Litz, Skylar; Hom, Jason; Evangelista, John Erol; Goldman, Lucas; Zhang, Serena; Yoon, Christine; Ahamed, Tahmid; Bhuiyan, Samantha; Cheng, Minxuan; Karam, Julie; Jagodnik, Kathleen M; Shu, Ingrid; Lachmann, Alexander; Ayling, Sam; Jenkins, Sherry L; Ma'ayan, AviPatterns (New York, N.Y.)2021 Mar 1233748796
The Atypical Kinase RIOK3 Limits RVFV Propagation and Is Regulated by Alternative Splicing.Havranek, Katherine E; White, Luke Adam; Bisom, Thomas C; Lanchy, Jean-Marc; Lodmell, J StephenViruses2021 02 2633652597
Prioritizing Pain-Associated Targets with Machine Learning.Jeon, Minji; Jagodnik, Kathleen M; Kropiwnicki, Eryk; Stein, Daniel J; Ma'ayan, AviBiochemistry2021 05 1133606503
Machine learning identifies candidates for drug repurposing in Alzheimer's disease.Rodriguez, Steve; Hug, Clemens; Todorov, Petar; Moret, Nienke; Boswell, Sarah A; Evans, Kyle; Zhou, George; Johnson, Nathan T; Hyman, Bradley T; Sorger, Peter K; Albers, Mark W; Sokolov, ArtemNature communications2021 02 1533589615
InContext: curation of medical context for drug indications.Moodley, Kody; Rieswijk, Linda; Oprea, Tudor I; Dumontier, MichelJournal of biomedical semantics2021 02 1233579375
Development of a potent and selective chemical probe for the pleiotropic kinase CK2.Wells, Carrow I; Drewry, David H; Pickett, Julie E; Tjaden, Amelie; Krämer, Andreas; Müller, Susanne; Gyenis, Laszlo; Menyhart, Daniel; Litchfield, David W; Knapp, Stefan; Axtman, Alison DCell chemical biology2021 04 1533484635
SmartGraph: a network pharmacology investigation platform.Zahoránszky-Kőhalmi, Gergely; Sheils, Timothy; Oprea, Tudor IJournal of cheminformatics2020 Jan 2133430980
The Kinase Chemogenomic Set (KCGS): An Open Science Resource for Kinase Vulnerability Identification.Wells, Carrow I; Al-Ali, Hassan; Andrews, David M; Asquith, Christopher R M; Axtman, Alison D; Dikic, Ivan; Ebner, Daniel; Ettmayer, Peter; Fischer, Christian; Frederiksen, Mathias; Futrell, Robert E; Gray, Nathanael S; Hatch, Stephanie B; Knapp, Stefan; Lücking, Ulrich; Michaelides, Michael; Mills, Caitlin E; Müller, Susanne; Owen, Dafydd; Picado, Alfredo; Saikatendu, Kumar S; Schröder, Martin; Stolz, Alexandra; Tellechea, Mariana; Turunen, Brandon J; Vilar, Santiago; Wang, Jinhua; Zuercher, William J; Willson, Timothy M; Drewry, David HInternational journal of molecular sciences2021 Jan 0833429995
Virtual and In Vitro Antiviral Screening Revive Therapeutic Drugs for COVID-19.Bocci, Giovanni; Bradfute, Steven B; Ye, Chunyan; Garcia, Matthew J; Parvathareddy, Jyothi; Reichard, Walter; Surendranathan, Surekha; Bansal, Shruti; Bologa, Cristian G; Perkins, Douglas J; Jonsson, Colleen B; Sklar, Larry A; Oprea, Tudor IACS pharmacology & translational science2020 Dec 1133330842
Optogenetic stimulation of the liver-projecting melanocortinergic pathway promotes hepatic glucose production.Kwon, Eunjin; Joung, Hye-Young; Liu, Shun-Mei; Chua Jr, Streamson C; Schwartz, Gary J; Jo, Young-HwanNature communications.2020 12 08;33293550
Mapping the Degradable Kinome Provides a Resource for Expedited Degrader Development.Donovan, Katherine A; Ferguson, Fleur M; Bushman, Jonathan W; Eleuteri, Nicholas A; Bhunia, Debabrata; Ryu, SeongShick; Tan, Li; Shi, Kun; Yue, Hong; Liu, Xiaoxi; Dobrovolsky, Dennis; Jiang, Baishan; Wang, Jinhua; Hao, Mingfeng; You, Inchul; Teng, Mingxing; Liang, Yanke; Hatcher, John; Li, Zhengnian; Manz, Theresa D; Groendyke, Brian; Hu, Wanyi; Nam, Yunju; Sengupta, Sandip; Cho, Hanna; Shin, Injae; Agius, Michael P; Ghobrial, Irene M; Ma, Michelle W; Che, Jianwei; Buhrlage, Sara J; Sim, Taebo; Gray, Nathanael S; Fischer, Eric SCell2020 12 1033275901
Activation of the ARCPOMC?MeA Projection Reduces Food Intake.Kwon, Eunjin; Jo, Young-HwanFrontiers in neural circuits.2020;33250721
A Chemical Probe for Dark Kinase STK17B Derives Its Potency and High Selectivity through a Unique P-Loop Conformation.Picado, Alfredo; Chaikuad, Apirat; Wells, Carrow I; Shrestha, Safal; Zuercher, William J; Pickett, Julie E; Kwarcinski, Frank E; Sinha, Parvathi; de Silva, Chandi S; Zutshi, Reena; Liu, Shubin; Kannan, Natarajan; Knapp, Stefan; Drewry, David H; Willson, Timothy MJournal of medicinal chemistry2020 12 1033215924
The Clinical Kinase Index: A Method to Prioritize Understudied Kinases as Drug Targets for the Treatment of Cancer.Essegian, Derek; Khurana, Rimpi; Stathias, Vasileios; Schürer, Stephan CCell reports. Medicine.2020 Oct 20;33205077
REDIAL-2020: A Suite of Machine Learning Models to Estimate Anti-SARS-CoV-2 Activities.Kc, Govinda; Bocci, Giovanni; Verma, Srijan; Hassan, Mahmudulla; Holmes, Jayme; Yang, Jeremy; Sirimulla, Suman; Oprea, Tudor IChemRxiv : the preprint server for chemistry.2020 Sep 16;33200119
KG-COVID-19: a framework to produce customized knowledge graphs for COVID-19 response.Reese, Justin T; Unni, Deepak; Callahan, Tiffany J; Cappelletti, Luca; Ravanmehr, Vida; Carbon, Seth; Shefchek, Kent A; Good, Benjamin M; Balhoff, James P; Fontana, Tommaso; Blau, Hannah; Matentzoglu, Nicolas; Harris, Nomi L; Munoz-Torres, Monica C; HaendPatterns (New York, N.Y.).2020 Nov 09;33196056
Quantitative Structure-Mutation-Activity Relationship Tests (QSMART) model for protein kinase inhibitor response prediction.Huang, Liang-Chin; Yeung, Wayland; Wang, Ye; Cheng, Huimin; Venkat, Aarya; Li, Sheng; Ma, Ping; Rasheed, Khaled; Kannan, NatarajanBMC bioinformatics.2020 Nov 12;33183223
A Workflow of Integrated Resources to Catalyze Network Pharmacology Driven COVID-19 Research.Zahoránszky-K?halmi, Gergely; Siramshetty, Vishal B; Kumar, Praveen; Gurumurthy, Manideep; Grillo, Busola; Mathew, Biju; Metaxatos, Dimitrios; Backus, Mark; Mierzwa, Tim; Simon, Reid; Grishagin, Ivan; Brovold, Laura; Mathé, Ewy A; Hall, Matthew D; MichaelbioRxiv : the preprint server for biology.2020 Nov 05;33173863
Hypothesis: Unifying model of domain architecture for conventional and novel protein kinase C isozymes.Jones, Alexander C; Taylor, Susan S; Newton, Alexandra C; Kornev, Alexandr PIUBMB life2020 1233166426
TCRD and Pharos 2021: mining the human proteome for disease biology.Sheils, Timothy K; Mathias, Stephen L; Kelleher, Keith J; Siramshetty, Vishal B; Nguyen, Dac-Trung; Bologa, Cristian G; Jensen, Lars Juhl; Vidović, Dušica; Koleti, Amar; Schürer, Stephan C; Waller, Anna; Yang, Jeremy J; Holmes, Jayme; Bocci, Giovanni; Southall, Noel; Dharkar, Poorva; Mathé, Ewy; Simeonov, Anton; Oprea, Tudor INucleic acids research2021 01 0833156327
DrugCentral 2021 supports drug discovery and repositioning.Avram, Sorin; Bologa, Cristian G; Holmes, Jayme; Bocci, Giovanni; Wilson, Thomas B; Nguyen, Dac-Trung; Curpan, Ramona; Halip, Liliana; Bora, Alina; Yang, Jeremy J; Knockel, Jeffrey; Sirimulla, Suman; Ursu, Oleg; Oprea, Tudor INucleic acids research2021 01 0833151287
CALCIUM REGULATION OF T CELL METABOLISM.Wang, Yinhu; Tao, Anthony; Vaeth, Martin; Feske, StefanCurrent opinion in physiology.2020 Oct;33103016
The Dark Kinase Knowledgebase: an online compendium of knowledge and experimental results of understudied kinases.Berginski, Matthew E; Moret, Nienke; Liu, Changchang; Goldfarb, Dennis; Sorger, Peter K; Gomez, Shawn MNucleic acids research.2020 Oct 20;33079988
Connectivity Mapping Identifies BI-2536 as a Potential Drug to Treat Diabetic Kidney Disease.Zhang, Lu; Wang, Zichen; Liu, Ruijie; Li, Zhengzhe; Lin, Jennifer; Wojciechowicz, Megan L; Huang, Jiyi; Lee, Kyung; Ma'ayan, Avi; He, John CijiangDiabetes2021 Feb33067313
Unbiased proteomic screening identifies a novel role for the E3 ubiquitin ligase Nedd4-2 in translational suppression during ER stress.Eagleman, Daphne E; Zhu, Jiuhe; Liu, Dai-Chi; Seimetz, Joseph; Kalsotra, Auinash; Tsai, Nien-PeiJournal of neurochemistry.2020 Oct 16;33064840
Germline and Mosaic Variants in PRKACA and PRKACB Cause a Multiple Congenital Malformation Syndrome.Palencia-Campos, Adrian; Aoto, Phillip C; Machal, Erik M F; Rivera-Barahona, Ana; Soto-Bielicka, Patricia; Bertinetti, Daniela; Baker, Blaine; Vu, Lily; Piceci-Sparascio, Francesca; Torrente, Isabella; Boudin, Eveline; Peeters, Silke; Van Hul, Wim; Huber,American journal of human genetics.2020 11 05;33058759
Concise, gram-scale synthesis of furo[2,3-b]pyridines with functional handles for chemoselective cross-coupling.O'Byrne, Sean N; Eduful, Benjamin J; Willson, Timothy M; Drewry, David HTetrahedron letters2020 Sep 1733012852
HCAR3: an underexplored metabolite sensor.Kapolka, Nicholas J; Isom, Daniel GNature reviews. Drug discovery.2020 Nov;33009526
Chemokine Signatures of Pathogen-Specific T Cells I: Effector T Cells.Eberlein, Jens; Davenport, Bennett; Nguyen, Tom T; Victorino, Francisco; Jhun, Kevin; van der Heide, Verena; Kuleshov, Maxim; Ma'ayan, Avi; Kedl, Ross; Homann, DirkJournal of immunology (Baltimore, Md. : 1950).2020 Oct 15;32948687
Chemokine Signatures of Pathogen-Specific T Cells II: Memory T Cells in Acute and Chronic Infection.Davenport, Bennett; Eberlein, Jens; Nguyen, Tom T; Victorino, Francisco; van der Heide, Verena; Kuleshov, Maxim; Ma'ayan, Avi; Kedl, Ross; Homann, DirkJournal of immunology (Baltimore, Md. : 1950).2020 Oct 15;32948682
Artificial intelligence, drug repurposing and peer review.Levin, Jeremy M; Oprea, Tudor I; Davidovich, Sagie; Clozel, Thomas; Overington, John P; Vanhaelen, Quentin; Cantor, Charles R; Bischof, Evelyne; Zhavoronkov, AlexNature biotechnology.2020 10;32929264
Deciphering the Plasma Proteome of Type 2 Diabetes.Elhadad, Mohamed A; Jonasson, Christian; Huth, Cornelia; Wilson, Rory; Gieger, Christian; Matias, Pamela; Grallert, Harald; Graumann, Johannes; Gailus-Durner, Valerie; Rathmann, Wolfgang; von Toerne, Christine; Hauck, Stefanie M; Koenig, Wolfgang; Sinner,Diabetes.2020 Dec;32928870
A 12-lipoxygenase-Gpr31 signaling axis is required for pancreatic organogenesis in the zebrafish.Hernandez-Perez, Marimar; Kulkarni, Abhishek; Samala, Niharika; Sorrell, Cody; El, Kimberly; Haider, Isra; Mukhtar Aleem, Ansari; Holman, Theodore R; Rai, Ganesha; Tersey, Sarah A; Mirmira, Raghavendra G; Anderson, Ryan MFASEB journal : official publication of the Federation of American Societies for Experimental Biology.2020 Nov;32918516
Off-Patent Drug Repositioning.Avram, Sorin; Curpan, Ramona; Halip, Liliana; Bora, Alina; Oprea, Tudor IJournal of chemical information and modeling2020 12 2832877182
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 JbioRxiv : 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, AviPatterns (New York, N.Y.).2020 Sep 11;32838343
Nucleotide Binding, Evolutionary Insights, and Interaction Partners of the Pseudokinase Unc-51-like Kinase 4.Preuss, Franziska; Chatterjee, Deep; Mathea, Sebastian; Shrestha, Safal; St-Germain, Jonathan; Saha, Manipa; Kannan, Natarajan; Raught, Brian; Rottapel, Robert; Knapp, StefanStructure (London, England : 1993)2020 11 0332814032
A Semi-automated and Scalable 3D Spheroid Assay to Study Neuroblast Migration.Ducker, Martin; Millar, Valerie; Ebner, Daniel; Szele, Francis GStem cell reports.2020 09 08;32763162
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 DCell chemical biology.2020 Aug 04;32755567
Discrete Adaptive Responses to MEK Inhibitor in Subpopulations of Triple-Negative Breast Cancer.Goulet, Daniel R; Foster 2nd, Joseph P; Zawistowski, Jon S; Bevill, Samantha M; Noël, Mélodie P; Olivares-Quintero, José F; Sciaky, Noah; Singh, Darshan; Santos, Charlene; Pattenden, Samantha G; Davis, Ian J; Johnson, Gary LMolecular cancer research : MCR.2020 Nov;32753473
An acidic residue buried in the dimer interface of isocitrate dehydrogenase 1 (IDH1) helps regulate catalysis and pH sensitivity.Luna, Lucas A; Lesecq, Zachary; White, Katharine A; Hoang, An; Scott, David A; Zagnitko, Olga; Bobkov, Andrey A; Barber, Diane L; Schiffer, Jamie M; Isom, Daniel G; Sohl, Christal DThe Biochemical journal2020 08 2832729927
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, AviResearch square.2020 May 13;32702729
Deschloroclozapine, a potent and selective chemogenetic actuator enables rapid neuronal and behavioral modulations in mice and monkeys.Nagai, Yuji; Miyakawa, Naohisa; Takuwa, Hiroyuki; Hori, Yukiko; Oyama, Kei; Ji, Bin; Takahashi, Manami; Huang, Xi-Ping; Slocum, Samuel T; DiBerto, Jeffrey F; Xiong, Yan; Urushihata, Takuya; Hirabayashi, Toshiyuki; Fujimoto, Atsushi; Mimura, Koki; English,Nature neuroscience.2020 09;32632286
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 BenJournal 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 TNeuroscience and biobehavioral reviews.2020 Jun 12;32534899
GPR84: an immune response dial?Wojciechowicz, Megan L; Ma'ayan, AviNature reviews. Drug discovery2020 0632494048
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, SusumuCell 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 BNature 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 DACS 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, HirofumiNeural 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 GProceedings 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 DJACC. 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 TNature chemical biology.2020 May 04;32367019
CRISPR-addressable yeast strains with applications in human G protein-coupled receptor profiling and synthetic biology.Rowe, Jacob B; Taghon, Geoffrey J; Kapolka, Nicholas J; Morgan, William M; Isom, Daniel GThe Journal of biological chemistry.2020 Jun 12;32358068
QSAR without borders.Muratov, Eugene N; Bajorath, Jürgen; Sheridan, Robert P; Tetko, Igor V; Filimonov, Dmitry; Poroikov, Vladimir; Oprea, Tudor I; Baskin, Igor I; Varnek, Alexandre; Roitberg, Adrian; Isayev, Olexandr; Curtarolo, Stefano; Fourches, Denis; Cohen, Yoram; Aspuru-Guzik, Alan; Winkler, David A; Agrafiotis, Dimitris; Cherkasov, Artem; Tropsha, AlexanderChemical Society reviews2020 06 0732356548
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 SJournal 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, AviBioinformatics (Oxford, England).2020 Jun 01;32277816
Memory of Divisional History Directs the Continuous Process of Primitive Hematopoietic Lineage Commitment.Bernitz, Jeffrey M; Rapp, Katrina; Daniel, Michael G; Shcherbinin, Dmitrii; Yuan, Ye; Gomes, Andreia; Waghray, Avinash; Brosh, Ran; Lachmann, Alexander; Ma'ayan, Avi; Papatsenko, Dmitri; Moore, Kateri AStem cell reports.2020 04 14;32243840
Presynaptic calcium channels: specialized control of synaptic neurotransmitter release.Dolphin, Annette C; Lee, AmyNature reviews. Neuroscience.2020 04;32161339
Nanobody-enabled monitoring of kappa opioid receptor states.Che, Tao; English, Justin; Krumm, Brian E; Kim, Kuglae; Pardon, Els; Olsen, Reid H J; Wang, Sheng; Zhang, Shicheng; Diberto, Jeffrey F; Sciaky, Noah; Carroll, F Ivy; Steyaert, Jan; Wacker, Daniel; Roth, Bryan LNature communications.2020 03 02;32123179
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, VsevolodeLife.2020 Mar 02;32118583
Emerging roles of the αC-β4 loop in protein kinase structure, function, evolution, and disease.Yeung, Wayland; Ruan, Zheng; Kannan, NatarajanIUBMB life2020 0632101380
Cataloguing the dead: breathing new life into pseudokinase research.Shrestha, Safal; Byrne, Dominic P; Harris, John A; Kannan, Natarajan; Eyers, Patrick AThe FEBS journal.2020 Oct;32053275
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 LNature.2020 03;32040955
How many rare diseases are there?Haendel, Melissa; Vasilevsky, Nicole; Unni, Deepak; Bologa, Cristian; Harris, Nomi; Rehm, Heidi; Hamosh, Ada; Baynam, Gareth; Groza, Tudor; McMurry, Julie; Dawkins, Hugh; Rath, Ana; Thaxon, Courtney; Bocci, Giovanni; Joachimiak, Marcin P; Köhler, SebastiaNature reviews. Drug discovery.2020 02;32020066
ABC transporters control ATP release through cholesterol-dependent volume-regulated anion channel activity.Dunn, Patrick J; Salm, Elizabeth J; Tomita, SusumuThe Journal of biological chemistry.2020 Apr 17;31988241
Identification of DOT1L inhibitors by structure-based virtual screening adapted from a nucleoside-focused library.Gibbons, Garrett S; Chakraborty, Amarraj; Grigsby, Sierrah M; Umeano, Afoma C; Liao, Chenzhong; Moukha-Chafiq, Omar; Pathak, Vibha; Mathew, Bini; Lee, Young-Tae; Dou, Yali; Schürer, Stephan C; Reynolds, Robert C; Snowden, Timothy S; Nikolovska-Coleska, ZaEuropean journal of medicinal chemistry.2020 Mar 01;31978781
Will Artificial Intelligence for Drug Discovery Impact Clinical Pharmacology?Zhavoronkov, Alex; Vanhaelen, Quentin; Oprea, Tudor IClinical pharmacology and therapeutics2020 0431957003
In Depth Analysis of Kinase Cross Screening Data to Identify CAMKK2 Inhibitory Scaffolds.O'Byrne, Sean N; Scott, John W; Pilotte, Joseph R; Santiago, André da S; Langendorf, Christopher G; Oakhill, Jonathan S; Eduful, Benjamin J; Couñago, Rafael M; Wells, Carrow I; Zuercher, William J; Willson, Timothy M; Drewry, David HMolecules (Basel, Switzerland)2020 Jan 1331941153
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 JFASEB 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, SivanesanSeminars 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 ICurrent 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, MichaelScience (New York, N.Y.).2020 01 10;31857493
Research Techniques Made Simple: Molecular Docking in Dermatology - A Foray into In Silico Drug Discovery.Issa, Naiem T; Badiavas, Evangelos V; Schürer, StephanThe 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 CNucleic acids research.2020 01 08;31701147
The reactome pathway knowledgebase.Jassal, Bijay; Matthews, Lisa; Viteri, Guilherme; Gong, Chuqiao; Lorente, Pascual; Fabregat, Antonio; Sidiropoulos, Konstantinos; Cook, Justin; Gillespie, Marc; Haw, Robin; Loney, Fred; May, Bruce; Milacic, Marija; Rothfels, Karen; Sevilla, Cristoffer; Shamovsky, Veronica; Shorser, Solomon; Varusai, Thawfeek; Weiser, Joel; Wu, Guanming; Stein, Lincoln; Hermjakob, Henning; D'Eustachio, PeterNucleic acids research2020 01 0831691815
ADCK3/COQ8A: the choice target of the UbiB protein kinase-like family.Asquith, Christopher R M; Murray, Nathan H; Pagliarini, David JNature 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, ChiaraNature medicine.2019 10;31591603
Can BDDCS illuminate targets in drug design?Bocci, Giovanni; Benet, Leslie Z; Oprea, Tudor IDrug discovery today.2019 Dec;31585170
PDBe-KB: a community-driven resource for structural and functional annotations.PDBe-KB consortiumNucleic acids research.2020 Jan 08;31584092
Recombination drives the evolution of mutational robustness.Singhal, Sonia; Gomez, Shawn M; Burch, Christina LCurrent 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, MichaeNature 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 LCell.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, SørenNPJ 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, GuanmingF1000Research.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, BlossomProceedings 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, RongBMC 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, NataliaThe 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, JianJournal 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 LCell.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 DBMC bioinformatics.2019 Apr 25;31272389
Exploring the dark genome: implications for precision medicine.Oprea, Tudor IMammalian genome : official journal of the International Mammalian Genome Society.2019 Aug;31270560
Molecular pharmacology of metabotropic receptors targeted by neuropsychiatric drugs.Roth, Bryan LNature 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, JordiDrug discovery today.2019 09;31226432
CoCoScore: context-aware co-occurrence scoring for text mining applications using distant supervision.Junge, Alexander; Jensen, Lars JuhlBioinformatics (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, AviNucleic 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, AviNucleic 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, AviNucleic 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, VadimNature.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 MSLAS 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, VadimNature.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, VadimNature.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, StephanMolecules (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 LMolecular 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 SNature 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, JianJournal 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 KCell 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 SCell 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, JianJournal 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; BundgaardACS pharmacology & translational science.2018 Sep 14;30868140
How to Prepare a Compound Collection Prior to Virtual Screening.Bologa, Cristian G; Ursu, Oleg; Oprea, Tudor IMethods 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, BinMethods 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, StephanMethods in molecular biology (Clifton, N.J.).2019;30848456
How structure informs and transforms chemogenetics.Roth, Bryan LCurrent 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, DennisPLoS 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 JJournal 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, AviBioData 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 JNature.2019 Feb;30728502
Tracing cellular heterogeneity in pooled genetic screens via multi-level barcoding.Boettcher, Michael; Covarrubias, Sergio; Biton, Anne; Blau, James; Wang, Haopeng; Zaitlen, Noah; McManus, Michael TBMC genomics2019 Feb 0630727954
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 BCell 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, MichaelDevelopmental cell.2019 Jan 07;30595537
Mining data and metadata from the gene expression omnibus.Wang, Zichen; Lachmann, Alexander; Ma'ayan, AviBiophysical 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 GNature 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 TPLoS 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 CThe 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, SabineTranslational 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, AviCell 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, HirofumiSchizophrenia 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, HirofumiScientific 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, TudorNucleic 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, FrankProteomics.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 AScience 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 HCell 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, AviBioinformatics (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 KJournal 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 RACS 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 TJournal 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, AviNucleic 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, MichaelScience 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 MSLAS 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, ChenNature 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 MOncotarget.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, AviNature 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, GergelyNature 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; ZhNature 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, MiguelCell 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, AviScientific 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, GergelyNature 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 XCancer research.2018 05 15;29472518
L1000FWD: fireworks visualization of drug-induced transcriptomic signatures.Wang, Zichen; Lachmann, Alexander; Keenan, Alexandra B; Ma'ayan, AviBioinformatics (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 PHeart (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 TNature 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, AviPLoS computational biology.2018 01;29293502
Coordinated regulation of intracellular pH by two glucose-sensing pathways in yeast.Isom, Daniel G; Page, Stephani C; Collins, Leonard B; Kapolka, Nicholas J; Taghon, Geoffrey J; Dohlman, Henrik GThe Journal of biological chemistry.2018 02 16;29284676
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 LNature 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, JoelPacific 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
Competitive Kinase Enrichment Proteomics Reveals that Abemaciclib Inhibits GSK3β and Activates WNT Signaling.Cousins, Emily M; Goldfarb, Dennis; Yan, Feng; Roques, Jose; Darr, David; Johnson, Gary L; Major, Michael BMolecular cancer research : MCR2018 0229133594
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, AviJournal 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 KNature 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 JChemMedChem.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 LScience (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 KNature 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 BFASEB 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, JianJournal 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, MichelJournal 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, AviScientific 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, YiProteomics.2017 Nov;28940701
Complex systems biology.Ma'ayan, AviJournal 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 TScientific 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, SusumueLife28816653
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, StPloS 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 SScientific reports.2017 Aug 01;28765529
How Ligands Illuminate GPCR Molecular Pharmacology.Wacker, Daniel; Stevens, Raymond C; Roth, Bryan LCell.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, MaykelDrug 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, AThe 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 TBriefings 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, JunNature 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 PJournal 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, AviNPJ 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 VPharmacology, 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 IBioinformatics (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 LNature 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, SusumuNeuron.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, FernandaDrug 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 MDiabetes.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, BernardFASEB 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 SNature 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 TBriefings 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, ChenAnalytical 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 ABioinformatics (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, CristianJournal 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, HirofumieNeuro.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, BarbaraScientific 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 FinkbeinerProceedings of the National Academy of Sciences of the United States of America.2017 Jan 31;1165–117028028237
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, BarbaraJournal 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 PNature 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, RajarshiNucleic acids research.2017 Jan 4;27903890
The ChEMBL database in 2017.Gaulton, Anna; Hersey, Anne; Nowotka, Michał; Bento, A Patrícia; Chambers, Jon; Mendez, David; Mutowo, Prudence; Atkinson, Francis; Bellis, Louisa J; Cibrián-Uhalte, Elena; Davies, Mark; Dedman, Nathan; Karlsson, Anneli; Magariños, María Paula; Overington, John P; Papadatos, George; Smit, Ines; Leach, Andrew RNucleic acids research2017 01 0427899562
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 EPacific 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, GiovanniPacific 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, AviBMC 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 INucleic 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; BhaACS 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 LMolecular 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 BClinical 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, AviNature communications.2016 Sep 26;27667448
Replicating Cardiovascular Condition-Birth Month Associations.Li, Li; Boland, Mary Regina; Miotto, Riccardo; Tatonetti, Nicholas P; Dudley, Joel TScientific 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, AviF1000Research.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, JianMedChemComm.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, GrNature.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, AnneNature 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, StephanePloS one.2016;27490099
High quality, small molecule-activity datasets for kinase research.Sharma, Rajan; Schürer, Stephan C; Muskal, Steven MF1000Research.2016;27429748
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, AviDatabase : 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 TBioinformatics (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 CJournal 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 TCirculation. 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 TNature 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, DavidNature 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 GJournal 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 WScientific 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, UteGenesis (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 TScientific reports.2016 May 17;27185194
BDDCS, the Rule of 5 and drugability.Benet, Leslie Z; Hosey, Chelsea M; Ursu, Oleg; Oprea, Tudor IAdvanced 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 TCurrent pharmaceutical design.2016;27174811
Drug-induced adverse events prediction with the LINCS L1000 data.Wang, Zichen; Clark, Neil R; Ma'ayan, AviBioinformatics (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, AviNucleic 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 TWiley interdisciplinary reviews. Systems biology and medicine.2016 May;27080087
Discovery of a specific inhibitor of human GLUT5 by virtual screening and in vitro transport evaluationGeorge-Thompson AM, Ursu O, Babkin P, Iancu CV, Whang A, Oprea TI, Choe JYScientific ReportsEpub 2016 Apr 14.27074918
Integrative network modeling approaches to personalized cancer medicineKidd BA, Readhead BP, Eden C, Parekh S, Dudley JTPersonalized Medicine2015 Jun 112(3):245-25727019658
Integrative network modeling approaches to personalized cancer medicine.Kidd BA, Readhead BP, Eden C, Parekh S, Dudley JT.Personalized Medicine2015 Jun 112(3):245-257.27019658
Evaluation of direct-to-consumer low-volume lab tests in healthy adultsKidd BA, Hoffman G, Zimmerman N, Li L, Morgan JW, Glowe PK, Botwin GJ, Parekh S, Babic N, Doust MW, Stock GB, Schadt EE, Dudley JTJ Clin Invest2016 Mar 28pii: 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, MichaelCell 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; WebsPloS 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, PamelaThe lancet. Psychiatry.2016 Apr;26915512
Docking Screens for Novel Ligands Conferring New Biology.Irwin, John J; Shoichet, Brian KJournal of medicinal chemistry.2016 05 12;26913380
Translational bioinformatics in the era of real-time biomedical, health care and wellness data streamsShameer K, Badgeley MA, Miotto R, Glicksberg BS, Morgan JW, Dudley JTBrief Bioinform2016 Feb 14pii: bbv118. [Epub ahead of print]26876889
Integrative radiogenomic analysis for multicentric radiophenotype in glioblastomaKong DS, Kim J, Lee IH, Kim ST, Seol HJ, Lee JI, Park WY, Ryu G, Wang Z, Ma'ayan A, Nam DHOncotarget2016 Feb 1doi: 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, AviProceedings. IEEE International Conference on Bioinformatics and Biomedicine.2015 Nov;256-26226848405
Leveraging Large-scale Behavioral Profiling in Zebrafish to Explore Neuroactive Polypharmacology.McCarroll, Matthew N; Gendelev, Leo; Keiser, Michael J; Kokel, DavidACS 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, StevenBiometrics.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 SScience (New York, N.Y.).2016 Jan 8;176-8026634440
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 TNature biotechnology.2016 Jan;47-5426619012
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 EMolecular 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, BeverNature.2015 Nov 26;477-8326550826
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 TScience translational medicine.2015 Oct 28;311ra17426511511
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 CNeuropharmacology.2015 Dec;675-8826302653
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, AviComputational biology and chemistry.2015 Dec;123-3826297300
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, MichaelDevelopmental cell.2015 Sep 14;577-9126256211
Computational and Practical Aspects of Drug Repositioning.Oprea, Tudor I; Overington, John PAssay and drug development technologies.2015 Jul-Aug;299-30626241209
HOODS: finding context-specific neighborhoods of proteins, chemicals and diseases.Palleja, Albert; Jensen, Lars JPeerJ.2015;26157625
Comprehensive comparison of large-scale tissue expression datasetsSantos A, Tsafou K, Stolte C, Pletscher-Frankild S, O'Donoghue SI, Jensen LJ.Peer J2015 June 3026157623
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 AMolecular & cellular proteomics : MCP.2015 Oct;2564-7626149443
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, AviComputational biology and chemistry.2015 Oct;104-1926101093
Integrated Approaches for Genome-wide Interrogation of the Druggable Non-olfactory G Protein-coupled Receptor Superfamily.Roth, Bryan L; Kroeze, Wesley KThe Journal of biological chemistry.2015 Aug 7;19471-726100629
Dynamics of the discovery process of protein-protein interactions from low content studies.Wang, Zichen; Clark, Neil R; Ma'ayan, AviBMC systems biology.2015;2626048415
Choosing the Right Tool for the Job: RNAi, TALEN, or CRISPR.Boettcher, Michael; McManus, Michael TMolecular cell.2015 May 21;575-8526000843
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, AviBioinformatics (Oxford, England).2015 Sep 15;3060-225971742
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 LNature structural & molecular biology.2015 May;362-925895059
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;390-40425865888
Cell-Based Screening: Extracting Meaning from Complex DataFinkbeiner S., Frumkin M., Kassner PDNeuron 2015 Apr 886(1):160-17425856492
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 EJournal of the American College of Cardiology.2015 Mar 3;830-4525720628
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 TMolecular biology and evolution.2015 May;1148-6025681384
Computational and experimental advances in drug repositioning for accelerated therapeutic stratificationShameer K, Readhead B, Dudley JT. Current Topics in Medicinal Chemistry201525579574
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, IrinaEMBO molecular medicine.2015 Jan;42-5825504525
The TLQP-21 peptide activates the G-protein-coupled receptor C3aR1 via a folding-upon-binding mechanismCero 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.Structure2014 Dec 222(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, YanTrends in pharmacological sciences2014 Sep450-46025109570
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, AviBioinformatics (Oxford, England).2014 Nov 15;3289-9025100688
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, StevenNature 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, AviNucleic acids research2014 JulW449-6024906883