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The search results on this publication page are automated on a monthly schedule based on acknowledgment of NIH Common Fund award numbers and intramural awards. Therefore, this list is not an exhaustive or error-free account of the program’s publications.
Illuminating the Druggable Genome (378)
| Publication Title | Authors | Journal | Publication Date | Page No | PubMedID |
|---|---|---|---|---|---|
| Modulation of tau tubulin kinases (TTBK1 and TTBK2) impacts ciliogenesis. | Bashore, Frances M; Marquez, Ariana B; Chaikuad, Apirat; Howell, Stefanie; Dunn, Andrea S; Beltran, Alvaro A; Smith, Jeffery L; Drewry, David H; Beltran, Adriana S; Axtman, Alison D | Scientific reports | 2023 Apr 14 | 6118 | 37059819 |
| Using the Reactome Database. | Rothfels, Karen; Milacic, Marija; Matthews, Lisa; Haw, Robin; Sevilla, Cristoffer; Gillespie, Marc; Stephan, Ralf; Gong, Chuqiao; Ragueneau, Eliot; May, Bruce; Shamovsky, Veronica; Wright, Adam; Weiser, Joel; Beavers, Deidre; Conley, Patrick; Tiwari, Krishna; Jassal, Bijay; Griss, Johannes; Senff-Ribeiro, Andrea; Brunson, Timothy; Petryszak, Robert; Hermjakob, Henning; D'Eustachio, Peter; Wu, Guanming; Stein, Lincoln | Current protocols | 2023 Apr | e722 | 37053306 |
| Development of Cell Permeable NanoBRET Probes for the Measurement of PLK1 Target Engagement in Live Cells. | Yang, Xuan; Smith, Jeffery L; Beck, Michael T; Wilkinson, Jennifer M; Michaud, Ani; Vasta, James D; Robers, Matthew B; Willson, Timothy M | Molecules (Basel, Switzerland) | 2023 Mar 25 | 37049713 | |
| PrismEXP: gene annotation prediction from stratified gene-gene co-expression matrices. | Lachmann, Alexander; Rizzo, Kaeli A; Bartal, Alon; Jeon, Minji; Clarke, Daniel J B; Ma'ayan, Avi | PeerJ | 2023 | e14927 | 36874981 |
| lncHUB2: aggregated and inferred knowledge about human and mouse lncRNAs. | Marino, Giacomo B; Wojciechowicz, Megan L; Clarke, Daniel J B; Kuleshov, Maxim V; Xie, Zhuorui; Jeon, Minji; Lachmann, Alexander; Ma'ayan, Avi | Database : the journal of biological databases and curation | 2023 Mar 04 | 36869839 | |
| Accelerating inhibitor discovery for deubiquitinating enzymes. | Chan, Wai Cheung; Liu, Xiaoxi; Magin, Robert S; Girardi, Nicholas M; Ficarro, Scott B; Hu, Wanyi; Tarazona Guzman, Maria I; Starnbach, Cara A; Felix, Alejandra; Adelmant, Guillaume; Varca, Anthony C; Hu, Bin; Bratt, Ariana S; DaSilva, Ethan; Schauer, Nathan J; Jaen Maisonet, Isabella; Dolen, Emma K; Ayala, Anthony X; Marto, Jarrod A; Buhrlage, Sara J | Nature communications | 2023 Feb 08 | 686 | 36754960 |
| Multiplexed kinase interactome profiling quantifies cellular network activity and plasticity. | Golkowski, Martin; Lius, Andrea; Sapre, Tanmay; Lau, Ho-Tak; Moreno, Taylor; Maly, Dustin J; Ong, Shao-En | Molecular cell | 2023 Mar 02 | 803-818.e8 | 36736316 |
| SGC-CAMKK2-1: A Chemical Probe for CAMKK2. | Wells, Carrow; Liang, Yi; Pulliam, Thomas L; Lin, Chenchu; Awad, Dominik; Eduful, Benjamin; O'Byrne, Sean; Hossain, Mohammad Anwar; Catta-Preta, Carolina Moura Costa; Ramos, Priscila Zonzini; Gileadi, Opher; Gileadi, Carina; Couñago, Rafael M; Stork, Brittany; Langendorf, Christopher G; Nay, Kevin; Oakhill, Jonathan S; Mukherjee, Debarati; Racioppi, Luigi; Means, Anthony R; York, Brian; McDonnell, Donald P; Scott, John W; Frigo, Daniel E; Drewry, David H | Cells | 2023 Jan 11 | 36672221 | |
| An atlas of substrate specificities for the human serine/threonine kinome. | Johnson, Jared L; Yaron, Tomer M; Huntsman, Emily M; Kerelsky, Alexander; Song, Junho; Regev, Amit; Lin, Ting-Yu; Liberatore, Katarina; Cizin, Daniel M; Cohen, Benjamin M; Vasan, Neil; Ma, Yilun; Krismer, Konstantin; Robles, Jaylissa Torres; van de Kooij, Bert; van Vlimmeren, Anne E; Andrée-Busch, Nicole; Käufer, Norbert F; Dorovkov, Maxim V; Ryazanov, Alexey G; Takagi, Yuichiro; Kastenhuber, Edward R; Goncalves, Marcus D; Hopkins, Benjamin D; Elemento, Olivier; Taatjes, Dylan J; Maucuer, Alexandre; Yamashita, Akio; Degterev, Alexei; Uduman, Mohamed; Lu, Jingyi; Landry, Sean D; Zhang, Bin; Cossentino, Ian; Linding, Rune; Blenis, John; Hornbeck, Peter V; Turk, Benjamin E; Yaffe, Michael B; Cantley, Lewis C | Nature | 2023 Jan | 759-766 | 36631611 |
| Pharos 2023: an integrated resource for the understudied human proteome. | Kelleher, Keith J; Sheils, Timothy K; Mathias, Stephen L; Yang, Jeremy J; Metzger, Vincent T; Siramshetty, Vishal B; Nguyen, Dac-Trung; Jensen, Lars Juhl; Vidović, Dušica; Schürer, Stephan C; Holmes, Jayme; Sharma, Karlie R; Pillai, Ajay; Bologa, Cristian G; Edwards, Jeremy S; Mathé, Ewy A; Oprea, Tudor I | Nucleic acids research | 2023 Jan 06 | D1405-D1416 | 36624666 |
| Synthesis and pharmacological validation of a novel radioligand for the orphan GPR88 receptor. | Decker, Ann M; Rahman, Md Toufiqur; Kormos, Chad M; Hesk, David; Darcq, Emmanuel; Kieffer, Brigitte L; Jin, Chunyang | Bioorganic & medicinal chemistry letters | 2023 Jan 15 | 129120 | 36587872 |
| SARS-CoV-2 replication in airway epithelia requires motile cilia and microvillar reprogramming. | Wu, Chien-Ting; Lidsky, Peter V; Xiao, Yinghong; Cheng, Ran; Lee, Ivan T; Nakayama, Tsuguhisa; Jiang, Sizun; He, Wei; Demeter, Janos; Knight, Miguel G; Turn, Rachel E; Rojas-Hernandez, Laura S; Ye, Chengjin; Chiem, Kevin; Shon, Judy; Martinez-Sobrido, Luis; Bertozzi, Carolyn R; Nolan, Garry P; Nayak, Jayakar V; Milla, Carlos; Andino, Raul; Jackson, Peter K | Cell | 2023 Jan 05 | 112-130.e20 | 36580912 |
| Activation of amygdala prokineticin receptor 2 neurons drives the anorexigenic activity of the neuropeptide PK2. | Yin, Terry C; Mittal, Ayushi; Buscaglia, Paul; Li, Wenxian; Sebag, Julien A | The Journal of biological chemistry | 2023 Jan | 102814 | 36539034 |
| Centering on synaptic vesicle release. | Young Jr, Samuel M | Cell calcium | 2023 Jan | 102686 | 36527762 |
| Seeing spermine blocking of K+ ion movement through inward rectifier Kir2.2 channels. | Lee, Sun-Joo; Nichols, Colin G | The Journal of general physiology | 2023 Feb 06 | 36524992 | |
| DrugCentral 2023 extends human clinical data and integrates veterinary drugs. | Avram, Sorin; Wilson, Thomas B; Curpan, Ramona; Halip, Liliana; Borota, Ana; Bora, Alina; Bologa, Cristian G; Holmes, Jayme; Knockel, Jeffrey; Yang, Jeremy J; Oprea, Tudor I | Nucleic acids research | 2022 Dec 09 | 36484092 | |
| Protein kinase inhibitor selectivity "hinges" on evolution. | Shrestha, Safal; Bendzunas, George; Kannan, Natarajan | Structure (London, England : 1993) | 2022 Dec 01 | 36459973 | |
| Molecular basis for selective activation of DREADD-based chemogenetics. | Zhang, Shicheng; Gumpper, Ryan H; Huang, Xi-Ping; Liu, Yongfeng; Krumm, Brian E; Cao, Can; Fay, Jonathan F; Roth, Bryan L | Nature | 2022 Dec | 354-362 | 36450989 |
| Beyond PI3Ks: targeting phosphoinositide kinases in disease. | Burke, John E; Triscott, Joanna; Emerling, Brooke M; Hammond, Gerald R V | Nature reviews. Drug discovery | 2022 Nov 14 | 1-30 | 36376561 |
| Multiplexed and reproducible high content screening of live and fixed cells using Dye Drop. | Mills, Caitlin E; Subramanian, Kartik; Hafner, Marc; Niepel, Mario; Gerosa, Luca; Chung, Mirra; Victor, Chiara; Gaudio, Benjamin; Yapp, Clarence; Nirmal, Ajit J; Clark, Nicholas; Sorger, Peter K | Nature communications | 2022 Nov 14 | 36376301 | |
| TTBK2 controls cilium stability by regulating distinct modules of centrosomal proteins. | Nguyen, Abraham; Goetz, Sarah C | Molecular biology of the cell | 2023 Jan 01 | ar8 | 36322399 |
| CLIC4 localizes to mitochondrial-associated membranes and mediates cardioprotection. | Ponnalagu, Devasena; Hamilton, Shanna; Sanghvi, Shridhar; Antelo, Diego; Schwieterman, Neill; Hansra, Inderjot; Xu, Xianyao; Gao, Erhe; Edwards, John C; Bansal, Shyam S; Wold, Loren E; Terentyev, Dmitry; Janssen, Paul M L; Hund, Thomas J; Khan, Mahmood; Kohut, Andrew R; Koch, Walter J; Singh, Harpreet | Science advances | 2022 Oct 21 | 36269835 | |
| A PKA inhibitor motif within SMOOTHENED controls Hedgehog signal transduction. | Happ, John T; Arveseth, Corvin D; Bruystens, Jessica; Bertinetti, Daniela; Nelson, Isaac B; Olivieri, Cristina; Zhang, Jingyi; Hedeen, Danielle S; Zhu, Ju-Fen; Capener, Jacob L; Bröckel, Jan W; Vu, Lily; King, C C; Ruiz-Perez, Victor L; Ge, Xuecai; Veglia, Gianluigi; Herberg, Friedrich W; Taylor, Susan S; Myers, Benjamin R | Nature structural & molecular biology | 2022 Oct | 36202993 | |
| Agent-based modeling predicts RAC1 is critical for ovarian cancer metastasis. | Rivera, Melanie; Toledo-Jacobo, Leslie; Romero, Elsa; Oprea, Tudor I; Moses, Melanie E; Hudson, Laurie G; Wandinger-Ness, Angela; Grimes, Martha M | Molecular biology of the cell | 2022 Dec 01 | 36200848 | |
| 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 Stephen | Viruses | 2022 09 17 | 36146870 | |
| Identification and Utilization of a Chemical Probe to Interrogate the Roles of PIKfyve in the Lifecycle of β-Coronaviruses. | Drewry, David H; Potjewyd, Frances M; Bayati, Armin; Smith, Jeffery L; Dickmander, Rebekah J; Howell, Stefanie; Taft-Benz, Sharon; Min, Sophia M; Hossain, Mohammad Anwar; Heise, Mark; McPherson, Peter S; Moorman, Nathaniel J; Axtman, Alison D | Journal of medicinal chemistry | 2022 10 13 | 36111834 | |
| 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, Avi | BMC bioinformatics | 2022 Sep 13 | 36100892 | |
| 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-Hwan | Life science alliance | 2022 11 | 36007929 | |
| Production of Eukaryotic Glycoproteins for Structural and Functional Studies Using Expi293F Cells. | Greven, Jessica A; Brett, Tom J | Current protocols | 2022 Aug | 35998009 | |
| 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, Gregory | ACS sensors | 2022 Aug 26 | 35951356 | |
| Getting Started with LINCS Datasets and Tools. | Xie, Zhuorui; Kropiwnicki, Eryk; Wojciechowicz, Megan L; Jagodnik, Kathleen M; Shu, Ingrid; Bailey, Allison; Clarke, Daniel J B; Jeon, Minji; Evangelista, John Erol; V Kuleshov, Maxim; Lachmann, Alexander; Parigi, Abhijna A; Sanchez, Jose M; Jenkins, Sherry L; Ma'ayan, Avi | Current protocols | 2022 Jul | 35876555 | |
| TRUPATH: An Open-Source Biosensor Platform for Interrogating the GPCR Transducerome. | DiBerto, Jeffrey F; Olsen, Reid H J; Roth, Bryan L | Methods in molecular biology (Clifton, N.J.) | 2022 | 35836068 | |
| 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 L | Nature structural & molecular biology | 2022 07 | 35835867 | |
| 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-Hwan | American journal of physiology. Endocrinology and metabolism | 2022 Sep 01 | 35830691 | |
| The potassium channel auxiliary subunit Kvβ2 (Kcnab2) regulates Kv1 channels and dopamine neuron firing. | Yee, Joshua X; Rastani, Ariana; Soden, Marta E | Journal of neurophysiology | 2022 07 01 | 35788155 | |
| 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 M | Nature reviews. Chemistry | 2022 Apr | 35783295 | |
| 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, Shirit | Antiviral research | 2022 08 | 35738348 | |
| 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 B | Science advances | 2022 06 24 | 35731869 | |
| 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 A | Analytical chemistry | 2022 07 12 | 35729701 | |
| Autophagy and Herpesvirus: A collaboration Contributing to Alzheimer's Disease. | Nafchi, Amir R; Esmaeili, Mona; Myers, Orrin; Oprea, Tudor; Bearer, Elane L | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 2022 05 | 35723876 | |
| Host Kinase CSNK2 is a Target for Inhibition of Pathogenic SARS-like β-Coronaviruses. | 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 M | ACS chemical biology | 2022 Jul 15 | 35723434 | |
| Calcium Channels in Retinal Function and Disease. | Williams, Brittany; Maddox, J Wesley; Lee, Amy | Annual review of vision science | 2022 09 15 | 35650675 | |
| 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 M | International journal of molecular sciences | 2022 May 20 | 35628521 | |
| 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 E | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 2022 May | 35553110 | |
| Analysis of human Tribbles 2 (TRIB2) pseudokinase. | Harris, John A; Fairweather, Emma; Byrne, Dominic P; Eyers, Patrick A | Methods in enzymology | 2022 | 35525562 | |
| Computational tools and resources for pseudokinase research. | O'Boyle, Brady; Shrestha, Safal; Kochut, Krzysztof; Eyers, Patrick A; Kannan, Natarajan | Methods in enzymology | 2022 | 35525549 | |
| SigCom LINCS: data and metadata search engine for a million gene expression signatures. | Evangelista, John Erol; Clarke, Daniel J B; Xie, Zhuorui; Lachmann, Alexander; Jeon, Minji; Chen, Kerwin; Jagodnik, Kathleen M; Jenkins, Sherry L; Kuleshov, Maxim V; Wojciechowicz, Megan L; Schürer, Stephan C; Medvedovic, Mario; Ma'ayan, Avi | Nucleic acids research | 2022 May 07 | 35524556 | |
| Open source fraction collector/MALDI spotter for proteomics. | Ficarro, Scott B; Max Alexander, William; Tavares, Isidoro; Marto, Jarrod A | HardwareX | 2022 Apr | 35518277 | |
| 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 B | The Journal of biological chemistry | 2022 06 | 35487243 | |
| Ectopic biomolecular phase transitions: fusion proteins in cancer pathologies. | Davis, Richoo B; Moosa, Mahdi Muhammad; Banerjee, Priya R | Trends in cell biology | 2022 Aug | 35484036 | |
| 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, Stefan | Nature communications | 2022 04 19 | 35440113 | |
| 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 I | Current opinion in structural biology | 2022 06 | 35439658 | |
| 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 H | ChemMedChem | 2022 06 20 | 35403825 | |
| Agonist and antagonist TRUPATH assays for G protein-coupled receptors. | DiBerto, Jeffrey F; Smart, Katie; Olsen, Reid H J; Roth, Bryan L | STAR protocols | 2022 06 17 | 35403009 | |
| 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, Avi | Bioinformatics advances | 2022 | 35368424 | |
| 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, Amy | PloS one | 2022 | 35353835 | |
| 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, Cheng | Nature communications | 2022 Feb 25 | 35217703 | |
| 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 Z | The AAPS journal | 2022 02 23 | 35199251 | |
| 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 K | Journal of medicinal chemistry | 2022 03 10 | 35195401 | |
| 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, Avi | BMC bioinformatics | 2022 Feb 19 | 35183110 | |
| EMBER: Multi-label prediction of kinase-substrate phosphorylation events through deep learning. | Kirchoff, Kathryn E; Gomez, Shawn M | Bioinformatics (Oxford, England) | 2022 Feb 14 | 35157015 | |
| 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 I | Communications biology | 2022 02 11 | 35149761 | |
| blitzGSEA: Efficient computation of Gene Set Enrichment Analysis through Gamma distribution approximation. | Lachmann, Alexander; Xie, Zhuorui; Ma'ayan, Avi | Bioinformatics (Oxford, England) | 2022 Feb 10 | 35143610 | |
| 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 A | Nature communications | 2022 02 08 | 35136069 | |
| 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 Stephen | Frontiers in cellular and infection microbiology | 2021 | 35127560 | |
| 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, Yanan | European journal of medicinal chemistry | 2022 Mar 05 | 35101647 | |
| 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, Demetrio | Neuroinformatics | 2022 Jan 22 | 35064871 | |
| 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 I | Journal of chemical information and modeling | 2022 02 14 | 35057621 | |
| 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 M | bioRxiv : the preprint server for biology | 2022 Jan 26 | 35018375 | |
| 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, Zicheng | Genome biology | 2022 01 10 | 35012625 | |
| 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, Hongxia | Cell reports | 2022 01 04 | 34986353 | |
| Adaptive chromatin remodeling and transcriptional changes of the functional kinome in tumor cells in response to targeted kinase inhibition. | East, Michael P; Johnson, Gary L | The Journal of biological chemistry | 2022 Feb | 34958800 | |
| 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 H | Nature immunology | 2022 01 | 34937919 | |
| 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 N | NAR genomics and bioinformatics | 2021 Dec | 34888523 | |
| 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, Hongxia | The Journal of biological chemistry | 2022 Jan | 34801552 | |
| 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 L | Nature | 2021 12 | 34789874 | |
| 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, Peter | Nucleic acids research | 2022 01 07 | 34788843 | |
| 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, Cheng | Nature communications | 2021 11 04 | 34737341 | |
| 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 K | Kidney international | 2021 Dec | 34634362 | |
| 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 A | Analytical chemistry | 2021 10 19 | 34606255 | |
| 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, Amy | Journal of neuroscience methods | 2021 11 01 | 34480956 | |
| 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, Everardo | Molecular therapy : the journal of the American Society of Gene Therapy | 2022 01 05 | 34450249 | |
| 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 J | Archives of autoimmune diseases | 2020 | 34414399 | |
| 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, Chunyang | Journal of medicinal chemistry | 2021 Aug 26 | 34387471 | |
| Post-translational modification of RAS proteins. | Campbell, Sharon L; Philips, Mark R | Current opinion in structural biology | 2021 12 | 34365229 | |
| 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 D | Journal of medicinal chemistry | 2022 01 27 | 34333981 | |
| The Tails of Protein Kinase A. | Taylor, Susan S; Søberg, Kristoffer; Kobori, Evan; Wu, Jian; Pautz, Sabine; Herberg, Friedrich W; Skålhegg, Bjørn Steen | Molecular pharmacology | 2022 04 | 34330820 | |
| 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 H | Journal of medicinal chemistry | 2021 08 12 | 34264658 | |
| 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 , Alexander | Chemical Society reviews | 2021 Aug 21 | 34212944 | |
| 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 E | Breast cancer research and treatment | 2021 Jul 01 | 34196902 | |
| Chemoproteomic methods for covalent drug discovery. | Chan, Wai Cheung; Sharifzadeh, Shabnam; Buhrlage, Sara J; Marto, Jarrod A | Chemical Society reviews | 2021 Aug 02 | 34143170 | |
| 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 I | Bioinformatics (Oxford, England) | 2021 Jun 04 | 34086846 | |
| 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, Tero | Nature communications | 2021 06 03 | 34083538 | |
| 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 K | Proceedings of the National Academy of Sciences of the United States of America | 2021 06 08 | 34074766 | |
| Regulation of Tissue Inflammation by 12-Lipoxygenases. | Kulkarni, Abhishek; Nadler, Jerry L; Mirmira, Raghavendra G; Casimiro, Isabel | Biomolecules | 2021 05 11 | 34064822 | |
| 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, Avi | Nucleic acids research | 2021 07 02 | 34019655 | |
| 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 Yeh | Proceedings of the National Academy of Sciences of the United States of America | 2021 05 18 | 33972431 | |
| 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 C | Science signaling | 2021 Apr 13 | 33850054 | |
| 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 R | Frontiers in cell and developmental biology | 2021 | 33816475 | |
| 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, Avi | Database : the journal of biological databases and curation | 2021 03 31 | 33787872 | |
| 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, Avi | Current protocols | 2021 Mar | 33780170 | |
| 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, Avi | Frontiers in immunology | 2021 | 33763080 | |
| 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 H | Nature immunology | 2021 04 | 33753942 | |
| 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 S | Nature chemical biology | 2021 Mar 22 | 33753926 | |
| 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 E | Current medicinal chemistry | 2021 | 33749548 | |
| 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, Avi | Patterns (New York, N.Y.) | 2021 Mar 12 | 33748796 | |
| 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 Stephen | Viruses | 2021 02 26 | 33652597 | |
| Prioritizing Pain-Associated Targets with Machine Learning. | Jeon, Minji; Jagodnik, Kathleen M; Kropiwnicki, Eryk; Stein, Daniel J; Ma'ayan, Avi | Biochemistry | 2021 05 11 | 33606503 | |
| 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, Artem | Nature communications | 2021 02 15 | 33589615 | |
| InContext: curation of medical context for drug indications. | Moodley, Kody; Rieswijk, Linda; Oprea, Tudor I; Dumontier, Michel | Journal of biomedical semantics | 2021 02 12 | 33579375 | |
| 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 D | Cell chemical biology | 2021 04 15 | 33484635 | |
| SmartGraph: a network pharmacology investigation platform. | Zahoránszky-Kőhalmi, Gergely; Sheils, Timothy; Oprea, Tudor I | Journal of cheminformatics | 2020 Jan 21 | 33430980 | |
| 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 H | International journal of molecular sciences | 2021 Jan 08 | 33429995 | |
| 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 I | ACS pharmacology & translational science | 2020 Dec 11 | 33330842 | |
| 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-Hwan | Nature 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 S | Cell | 2020 12 10 | 33275901 | |
| Activation of the ARCPOMC?MeA Projection Reduces Food Intake. | Kwon, Eunjin; Jo, Young-Hwan | Frontiers 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 M | Journal of medicinal chemistry | 2020 12 10 | 33215924 | |
| 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 C | Cell 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 I | ChemRxiv : 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; Haend | Patterns (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, Natarajan | BMC 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; Michael | bioRxiv : 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 P | IUBMB life | 2020 12 | 33166426 | |
| 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 I | Nucleic acids research | 2021 01 08 | 33156327 | |
| 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 I | Nucleic acids research | 2021 01 08 | 33151287 | |
| CALCIUM REGULATION OF T CELL METABOLISM. | Wang, Yinhu; Tao, Anthony; Vaeth, Martin; Feske, Stefan | Current 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 M | Nucleic 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 Cijiang | Diabetes | 2021 Feb | 33067313 | |
| 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-Pei | Journal 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 H | Tetrahedron letters | 2020 Sep 17 | 33012852 | |
| HCAR3: an underexplored metabolite sensor. | Kapolka, Nicholas J; Isom, Daniel G | Nature 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, Dirk | Journal 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, Dirk | Journal 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, Alex | Nature 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 M | FASEB 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 I | Journal of chemical information and modeling | 2020 12 28 | 32877182 | |
| KG-COVID-19: a framework to produce customized knowledge graphs for COVID-19 response. | Reese, Justin; Unni, Deepak; Callahan, Tiffany J; Cappelletti, Luca; Ravanmehr, Vida; Carbon, Seth; Fontana, Tommaso; Blau, Hannah; Matentzoglu, Nicolas; Harris, Nomi L; Munoz-Torres, Monica C; Robinson, Peter N; Joachimiak, Marcin P; Mungall, Christopher J | bioRxiv : the preprint server for biology. | 2020 Aug 18; | 32839776 | |
| The COVID-19 Drug and Gene Set Library. | Kuleshov, Maxim V; Stein, Daniel J; Clarke, Daniel J B; Kropiwnicki, Eryk; Jagodnik, Kathleen M; Bartal, Alon; Evangelista, John E; Hom, Jason; Cheng, Minxuan; Bailey, Allison; Zhou, Abigail; Ferguson, Laura B; Lachmann, Alexander; Ma'ayan, Avi | Patterns (New York, N.Y.). | 2020 Sep 11; | 32838343 | |
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| A Comparative Study of the Pharmacokinetics of Clozapine N-Oxide and Clozapine N-Oxide Hydrochloride Salt in Rhesus Macaques. | Allen, Daicia C; Carlson, Timothy L; Xiong, Yan; Jin, Jian; Grant, Kathleen A; Cuzon Carlson, Verginia C | The Journal of pharmacology and experimental therapeutics. | 2019 Feb; | 30523062 | |
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| Integrative bioinformatics identifies postnatal lead (Pb) exposure disrupts developmental cortical plasticity. | Smith, Milo R; Yevoo, Priscilla; Sadahiro, Masato; Austin, Christine; Amarasiriwardena, Chitra; Awawda, Mahmoud; Arora, Manish; Dudley, Joel T; Morishita, Hirofumi | Scientific reports. | 2018 11 06; | 30401819 | |
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| Darkness in the Human Gene and Protein Function Space: Widely Modest or Absent Illumination by the Life Science Literature and the Trend for Fewer Protein Function Discoveries Since 2000. | Sinha, Swati; Eisenhaber, Birgit; Jensen, Lars Juhl; Kalbuaji, Bharata; Eisenhaber, Frank | Proteomics. | 2018 Nov; | 30265449 | |
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| Podocyte-Specific Induction of Krüppel-Like Factor 15 Restores Differentiation Markers and Attenuates Kidney Injury in Proteinuric Kidney Disease. | Guo, Yiqing; Pace, Jesse; Li, Zhengzhe; Ma'ayan, Avi; Wang, Zichen; Revelo, Monica P; Chen, Edward; Gu, Xiangchen; Attalah, Ahmed; Yang, Yaqi; Estrada, Chelsea; Yang, Vincent W; He, John C; Mallipattu, Sandeep K | Journal of the American Society of Nephrology : JASN. | 2018 Aug 24; | 30143559 | |
| Gut Microbial ?-Glucuronidase Inhibition via Catalytic Cycle Interception. | Pellock, Samuel J; Creekmore, Benjamin C; Walton, William G; Mehta, Naimee; Biernat, Kristen A; Cesmat, Andrew P; Ariyarathna, Yamuna; Dunn, Zachary D; Li, Bo; Jin, Jian; James, Lindsey I; Redinbo, Matthew R | ACS central science. | 2018 Jul 25; | 30062115 | |
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| eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks. | Clarke, Daniel J B; Kuleshov, Maxim V; Schilder, Brian M; Torre, Denis; Duffy, Mary E; Keenan, Alexandra B; Lachmann, Alexander; Feldmann, Axel S; Gundersen, Gregory W; Silverstein, Moshe C; Wang, Zichen; Ma'ayan, Avi | Nucleic acids research. | 2018 Jul 02; | 29800326 | |
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| Application of Integrated Drug Screening/Kinome Analysis to Identify Inhibitors of Gemcitabine-Resistant Pancreatic Cancer Cell Growth. | Krulikas, Linas J; McDonald, Ian M; Lee, Benjamin; Okumu, Denis O; East, Michael P; Gilbert, Thomas S K; Herring, Laura E; Golitz, Brian T; Wells, Carrow I; Axtman, Allison D; Zuercher, William J; Willson, Timothy M; Kireev, Dmitri; Yeh, Jen Jen; Johnson, Gary L; Baines, Antonio T; Graves, Lee M | SLAS discovery : advancing life sciences R & D. | 2018 09; | 29742358 | |
| A proteomics landscape of circadian clock in mouse liver. | Wang, Yunzhi; Song, Lei; Liu, Mingwei; Ge, Rui; Zhou, Quan; Liu, Wanlin; Li, Ruiyang; Qie, Jingbo; Zhen, Bei; Wang, Yi; He, Fuchu; Qin, Jun; Ding, Chen | Nature communications. | 2018 Apr 19; | 29674717 | |
| Proteomic analysis defines kinase taxonomies specific for subtypes of breast cancer. | Collins, Kyla A L; Stuhlmiller, Timothy J; Zawistowski, Jon S; East, Michael P; Pham, Trang T; Hall, Claire R; Goulet, Daniel R; Bevill, Samantha M; Angus, Steven P; Velarde, Sara H; Sciaky, Noah; Oprea, Tudor I; Graves, Lee M; Johnson, Gary L; Gomez, Shawn M | Oncotarget. | 2018 Mar 20; | 29643987 | |
| Massive mining of publicly available RNA-seq data from human and mouse. | Lachmann, Alexander; Torre, Denis; Keenan, Alexandra B; Jagodnik, Kathleen M; Lee, Hoyjin J; Wang, Lily; Silverstein, Moshe C; Ma'ayan, Avi | Nature communications. | ; | 29636450 | |
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| A proteomic landscape of diffuse-type gastric cancer. | Ge, Sai; Xia, Xia; Ding, Chen; Zhen, Bei; Zhou, Quan; Feng, Jinwen; Yuan, Jiajia; Chen, Rui; Li, Yumei; Ge, Zhongqi; Ji, Jiafu; Zhang, Lianhai; Wang, Jiayuan; Li, Zhongwu; Lai, Yumei; Hu, Ying; Li, Yanyan; Li, Yilin; Gao, Jing; Chen, Lin; Xu, Jianming; Zh | Nature communications. | 2018 03 08; | 29520031 | |
| The Transcriptionally Permissive Chromatin State of Embryonic Stem Cells Is Acutely Tuned to Translational Output. | Bulut-Karslioglu, Aydan; Macrae, Trisha A; Oses-Prieto, Juan A; Covarrubias, Sergio; Percharde, Michelle; Ku, Gregory; Diaz, Aaron; McManus, Michael T; Burlingame, Alma L; Ramalho-Santos, Miguel | Cell stem cell. | 2018 03 01; | 29499153 | |
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| Mass Spectrometry-Based Proteomics Reveals Potential Roles of NEK9 and MAP2K4 in Resistance to PI3K Inhibition in Triple-Negative Breast Cancers. | Mundt, Filip; Rajput, Sandeep; Li, Shunqiang; Ruggles, Kelly V; Mooradian, Arshag D; Mertins, Philipp; Gillette, Michael A; Krug, Karsten; Guo, Zhanfang; Hoog, Jeremy; Erdmann-Gilmore, Petra; Primeau, Tina; Huang, Shixia; Edwards, Dean P; Wang, Xiaowei; Wang, Xuya; Kawaler, Emily; Mani, D R; Clauser, Karl R; Gao, Feng; Luo, Jingqin; Davies, Sherri R; Johnson, Gary L; Huang, Kuan-Lin; Yoon, Christopher J; Ding, Li; Fenyö, David; Ellis, Matthew J; Townsend, R Reid; Held, Jason M; Carr, Steven A; Ma, Cynthia X | Cancer research. | 2018 05 15; | 29472518 | |
| L1000FWD: fireworks visualization of drug-induced transcriptomic signatures. | Wang, Zichen; Lachmann, Alexander; Keenan, Alexandra B; Ma'ayan, Avi | Bioinformatics (Oxford, England). | ; | 29420694 | |
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| Dual gene activation and knockout screen reveals directional dependencies in genetic networks. | Boettcher, Michael; Tian, Ruilin; Blau, James A; Markegard, Evan; Wagner, Ryan T; Wu, David; Mo, Xiulei; Biton, Anne; Zaitlen, Noah; Fu, Haian; McCormick, Frank; Kampmann, Martin; McManus, Michael T | Nature biotechnology. | 2018 Feb; | 29334369 | |
| Integration of pan-cancer transcriptomics with RPPA proteomics reveals mechanisms of epithelial-mesenchymal transition. | Koplev, Simon; Lin, Katie; Dohlman, Anders B; Ma'ayan, Avi | PLoS computational biology. | 2018 01; | 29293502 | |
| 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 G | The 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 L | Nature chemical biology. | 2017 Dec 11; | 29227473 | |
| Cell-specific prediction and application of drug-induced gene expression profiles. | Hodos, Rachel; Zhang, Ping; Lee, Hao-Chih; Duan, Qiaonan; Wang, Zichen; Clark, Neil R; Ma'ayan, Avi; Wang, Fei; Kidd, Brian; Hu, Jianying; Sontag, David; Dudley, Joel | Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. | 2018; | 29218867 | |
| Quantitative, Wide-Spectrum Kinase Profiling in Live Cells for Assessing the Effect of Cellular ATP on Target Engagement. | Vasta, James D; Corona, Cesear R; Wilkinson, Jennifer; Zimprich, Chad A; Hartnett, James R; Ingold, Morgan R; Zimmerman, Kristopher; Machleidt, Thomas; Kirkland, Thomas A; Huwiler, Kristin G; Ohana, Rachel Friedman; Slater, Michael; Otto, Paul; Cong, Mei; | Cell chemical biology. | 2018 02 15; | 29174542 | |
| 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 B | Molecular cancer research : MCR | 2018 02 | 29133594 | |
| Drug target ontology to classify and integrate drug discovery data. | Lin, Yu; Mehta, Saurabh; Küçük-McGinty, Hande; Turner, John Paul; Vidovic, Dusica; Forlin, Michele; Koleti, Amar; Nguyen, Dac-Trung; Jensen, Lars Juhl; Guha, Rajarshi; Mathias, Stephen L; Ursu, Oleg; Stathias, Vasileios; Duan, Jianbin; Nabizadeh, Nooshin; | Journal of biomedical semantics. | 2017 Nov 09; | 29122012 | |
| Predicting age by mining electronic medical records with deep learning characterizes differences between chronological and physiological age. | Wang, Zichen; Li, Li; Glicksberg, Benjamin S; Israel, Ariel; Dudley, Joel T; Ma'ayan, Avi | Journal of biomedical informatics. | 2017 Dec; | 29113935 | |
| Common and cell-type specific responses to anti-cancer drugs revealed by high throughput transcript profiling. | Niepel, Mario; Hafner, Marc; Duan, Qiaonan; Wang, Zichen; Paull, Evan O; Chung, Mirra; Lu, Xiaodong; Stuart, Joshua M; Golub, Todd R; Subramanian, Aravind; Ma'ayan, Avi; Sorger, Peter K | Nature communications. | 2017 Oct 30; | 29084964 | |
| Identification and Optimization of 4-Anilinoquinolines as Inhibitors of Cyclin?G Associated Kinase. | Asquith, Christopher R M; Laitinen, Tuomo; Bennett, James M; Godoi, Paulo H; East, Michael P; Tizzard, Graham J; Graves, Lee M; Johnson, Gary L; Dornsife, Ronna E; Wells, Carrow I; Elkins, Jonathan M; Willson, Timothy M; Zuercher, William J | ChemMedChem. | 2018 Jan 08; | 29072804 | |
| D4dopamine receptor high-resolution structures enable the discovery of selective agonists. | Wang, Sheng; Wacker, Daniel; Levit, Anat; Che, Tao; Betz, Robin M; McCorvy, John D; Venkatakrishnan, A J; Huang, Xi-Ping; Dror, Ron O; Shoichet, Brian K; Roth, Bryan L | Science (New York, N.Y.). | 2017 10 20; | 29051383 | |
| Discovery of new GPCR ligands to illuminate new biology. | Roth, Bryan L; Irwin, John J; Shoichet, Brian K | Nature chemical biology. | 2017 Nov; | 29045379 | |
| Biased signaling of the proton-sensing receptor OGR1 by benzodiazepines. | Pera, Tonio; Deshpande, Deepak A; Ippolito, Michael; Wang, Bin; Gavrila, Adelina; Michael, James V; Nayak, Ajay P; Tompkins, Eric; Farrell, Eleni; Kroeze, Wesley K; Roth, Bryan L; Panettieri Jr, Reynold A; Benovic, Jeffrey L; An, Steven S; Dulin, Nickolai O; Penn, Raymond B | FASEB journal : official publication of the Federation of American Societies for Experimental Biology. | ; | 29042451 | |
| Report and Application of a Tool Compound Data Set. | Butler, Kyle V; MacDonald, Ian A; Hathaway, Nathaniel A; Jin, Jian | Journal of chemical information and modeling. | 2017 Nov 02; | 29035535 | |
| Formalizing drug indications on the road to therapeutic intent. | Nelson, Stuart J; Oprea, Tudor I; Ursu, Oleg; Bologa, Cristian G; Zaveri, Amrapali; Holmes, Jayme; Yang, Jeremy J; Mathias, Stephen L; Mani, Subramani; Tuttle, Mark S; Dumontier, Michel | Journal of the American Medical Informatics Association : JAMIA. | 2017 Nov 01; | 29016968 | |
| Clustergrammer, a web-based heatmap visualization and analysis tool for high-dimensional biological data. | Fernandez, Nicolas F; Gundersen, Gregory W; Rahman, Adeeb; Grimes, Mark L; Rikova, Klarisa; Hornbeck, Peter; Ma'ayan, Avi | Scientific data. | 2017 Oct 10; | 28994825 | |
| A Bioinformatic Algorithm for Analyzing Cell Signaling Using Temporal Proteomic Data. | Zhang, Chunchao; Chen, Yue; Mao, Xinfang; Huang, Yin; Jung, Sung Yun; Jain, Antrix; Qin, Jun; Wang, Yi | Proteomics. | 2017 Nov; | 28940701 | |
| Complex systems biology. | Ma'ayan, Avi | Journal of the Royal Society, Interface. | 2017 Sep; | 28931638 | |
| A high-conductance chemo-optogenetic system based on the vertebrate channel Trpa1b. | Lam, Pui-Ying; Mendu, Suresh K; Mills, Robert W; Zheng, Baohui; Padilla, Hugo; Milan, David J; Desai, Bimal N; Peterson, Randall T | Scientific reports. | 2017 Sep 19; | 28928472 | |
| Assembly rules for GABAA receptor complexes in the brain. | Martenson, James S;Yamasaki, Tokiwa;Chaudhury, Nashid H;Albrecht, David;Tomita, Susumu | eLife | 28816653 | ||
| Progress towards a public chemogenomic set for protein kinases and a call for contributions. | Drewry, David H; Wells, Carrow I; Andrews, David M; Angell, Richard; Al-Ali, Hassan; Axtman, Alison D; Capuzzi, Stephen J; Elkins, Jonathan M; Ettmayer, Peter; Frederiksen, Mathias; Gileadi, Opher; Gray, Nathanael; Hooper, Alice; Knapp, Stefan; Laufer, St | PloS one. | 2017; | 28767711 | |
| Intracoronary Imaging, Cholesterol Efflux, and Transcriptomics after Intensive Statin Treatment in Diabetes. | Chamaria, Surbhi; Johnson, Kipp W; Vengrenyuk, Yuliya; Baber, Usman; Shameer, Khader; Divaraniya, Aparna A; Glicksberg, Benjamin S; Li, Li; Bhatheja, Samit; Moreno, Pedro; Maehara, Akiko; Mehran, Roxana; Dudley, Joel T; Narula, Jagat; Sharma, Samin K; Kini, Annapoorna S | Scientific reports. | 2017 Aug 01; | 28765529 | |
| How Ligands Illuminate GPCR Molecular Pharmacology. | Wacker, Daniel; Stevens, Raymond C; Roth, Bryan L | Cell. | 2017 Jul 27; | 28753422 | |
| From flamingo dance to (desirable) drug discovery: a nature-inspired approach. | Sánchez-Rodríguez, Aminael; Pérez-Castillo, Yunierkis; Schürer, Stephan C; Nicolotti, Orazio; Mangiatordi, Giuseppe Felice; Borges, Fernanda; Cordeiro, M Natalia D S; Tejera, Eduardo; Medina-Franco, José L; Cruz-Monteagudo, Maykel | Drug discovery today. | 2017 Jun 15; | 28624633 | |
| Activation of tumor suppressor protein PP2A inhibits KRAS-driven tumor growth. | Sangodkar, Jaya; Perl, Abbey; Tohme, Rita; Kiselar, Janna; Kastrinsky, David B; Zaware, Nilesh; Izadmehr, Sudeh; Mazhar, Sahar; Wiredja, Danica D; O'Connor, Caitlin M; Hoon, Divya; Dhawan, Neil S; Schlatzer, Daniela; Yao, Shen; Leonard, Daniel; Borczuk, A | The Journal of clinical investigation. | 2017 Jun 01; | 28504649 | |
| Deep learning for healthcare: review, opportunities and challenges. | Miotto, Riccardo; Wang, Fei; Wang, Shuang; Jiang, Xiaoqian; Dudley, Joel T | Briefings in bioinformatics. | 2017 May 06; | 28481991 | |
| A mouse tissue transcription factor atlas. | Zhou, Quan; Liu, Mingwei; Xia, Xia; Gong, Tongqing; Feng, Jinwen; Liu, Wanlin; Liu, Yang; Zhen, Bei; Wang, Yi; Ding, Chen; Qin, Jun | Nature communications. | 2017 Apr 21; | 28429721 | |
| Reply: Deep Learning With Unsupervised Feature in Echocardiographic Imaging. | Narula, Sukrit; Shameer, Khader; Salem Omar, Alaa Mabrouk; Dudley, Joel T; Sengupta, Partho P | Journal of the American College of Cardiology. | 2017 04 25; | 28427589 | |
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| In silico design of novel probes for the atypical opioid receptor MRGPRX2. | Lansu, Katherine; Karpiak, Joel; Liu, Jing; Huang, Xi-Ping; McCorvy, John D; Kroeze, Wesley K; Che, Tao; Nagase, Hiroshi; Carroll, Frank I; Jin, Jian; Shoichet, Brian K; Roth, Bryan L | Nature chemical biology. | 2017 May; | 28288109 | |
| GARLH Family Proteins Stabilize GABAA Receptors at Synapses. | Yamasaki, Tokiwa; Hoyos-Ramirez, Erika; Martenson, James S; Morimoto-Tomita, Megumi; Tomita, Susumu | Neuron. | 2017 Mar 08; | 28279354 | |
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| A Whole-Genome RNA Interference Screen Reveals a Role for Spry2 in Insulin Transcription and the Unfolded Protein Response. | Pappalardo, Zachary; Gambhir Chopra, Deeksha; Hennings, Thomas G; Richards, Hunter; Choe, Justin; Yang, Katherine; Baeyens, Luc; Ang, Kenny; Chen, Steven; Arkin, Michelle; German, Michael S; McManus, Michael T; Ku, Gregory M | Diabetes. | 2017 Jun; | 28246293 | |
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| Integrative Analysis of Disease Signatures Shows Inflammation Disrupts Juvenile Experience-Dependent Cortical Plasticity. | Smith, Milo R; Burman, Poromendro; Sadahiro, Masato; Kidd, Brian A; Dudley, Joel T; Morishita, Hirofumi | eNeuro. | 2016 Nov-Dec; | 28101530 | |
| Novel Therapeutics Identification for Fibrosis in Renal Allograft Using Integrative Informatics Approach. | Li, Li; Greene, Ilana; Readhead, Benjamin; Menon, Madhav C; Kidd, Brian A; Uzilov, Andrew V; Wei, Chengguo; Philippe, Nimrod; Schroppel, Bernd; He, John Cijiang; Chen, Rong; Dudley, Joel T; Murphy, Barbara | Scientific reports. | 2017 Jan 04; | 28051114 | |
| Nrf2 mitigates LRRK2- and α-synuclein-induced neurodegeneration by modulating proteostasis. | Gaia Skibinski, Vicky Hwang, Dale Michael Ando, Aaron Daub, Alicia K. Lee, Abinaya Ravisankar, Sara Modan, Mariel M. Finucane, Benjamin A. Shaby, and Steven Finkbeiner | Proceedings of the National Academy of Sciences of the United States of America. | 2017 Jan 31; | 1165–1170 | 28028237 |
| Genomic Analysis of Kidney Allograft Injury Identifies Hematopoietic Cell Kinase as a Key Driver of Renal Fibrosis. | Wei, Chengguo; Li, Li; Menon, Madhav C; Zhang, Weijia; Fu, Jia; Kidd, Brian; Keung, Karen L; Woytovich, Christopher; Greene, Ilana; Xiao, Wenzhen; Salem, Fadi; Yi, Zhengzi; He, John Cijiang; Dudley, Joel T; Murphy, Barbara | Journal of the American Society of Nephrology : JASN. | 2017 May; | 27927780 | |
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| EXPLORING THE REPRODUCIBILITY OF PROBABILISTIC CAUSAL MOLECULAR NETWORK MODELS. | Cohain, Ariella; Divaraniya, Aparna A; Zhu, Kuixi; Scarpa, Joseph R; Kasarskis, Andrew; Zhu, Jun; Chang, Rui; Dudley, Joel T; Schadt, Eric E | Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. | 2016; | 27896968 | |
| EXPLORING BRAIN TRANSCRIPTOMIC PATTERNS: A TOPOLOGICAL ANALYSIS USING SPATIAL EXPRESSION NETWORKS. | Kuncheva, Zhana; Krishnan, Michelle L; Montana, Giovanni | Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. | 2016; | 27896963 | |
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| Gold Nanoparticle Reprograms Pancreatic Tumor Microenvironment and Inhibits Tumor Growth. | Saha, Sounik; Xiong, Xunhao; Chakraborty, Prabir K; Shameer, Khader; Arvizo, Rochelle R; Kudgus, Rachel A; Dwivedi, Shailendra Kumar Dhar; Hossen, Md Nazir; Gillies, Elizabeth M; Robertson, J David; Dudley, Joel T; Urrutia, Raul A; Postier, Russell G; Bha | ACS nano. | 2016 12 27; | 27758098 | |
| Discovery and Characterization of Novel GPR39 Agonists Allosterically Modulated by Zinc. | Sato, Seiji; Huang, Xi-Ping; Kroeze, Wesley K; Roth, Bryan L | Molecular pharmacology. | 2016 Dec; | 27754899 | |
| Estimation of Maximum Recommended Therapeutic Dose Using Predicted Promiscuity and Potency. | Liu, T; Oprea, T; Ursu, O; Hasselgren, C; Altman, R B | Clinical and translational science. | 2016 12; | 27736015 | |
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| Polycomb repressive complex 2 (PRC2) silences genes responsible for neurodegeneration. | von Schimmelmann, Melanie; Feinberg, Philip A; Sullivan, Josefa M; Ku, Stacy M; Badimon, Ana; Duff, Mary Kaye; Wang, Zichen; Lachmann, Alexander; Dewell, Scott; Ma'ayan, Avi; Han, Ming-Hu; Tarakhovsky, Alexander; Schaefer, Anne | Nature neuroscience. | 2016 Oct; | 27526204 | |
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| Integrative network modeling approaches to personalized cancer medicine | Kidd BA, Readhead BP, Eden C, Parekh S, Dudley JT | Personalized Medicine | 2015 Jun 1 | 12(3):245-257 | 27019658 |
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| Evaluation of direct-to-consumer low-volume lab tests in healthy adults | Kidd BA, Hoffman G, Zimmerman N, Li L, Morgan JW, Glowe PK, Botwin GJ, Parekh S, Babic N, Doust MW, Stock GB, Schadt EE, Dudley JT | J Clin Invest | 2016 Mar 28 | pii: 86318. doi: 10.1172/JCI86318. [Epub ahead of print] | 27018593 |
| Signaling Networks among Stem Cell Precursors, Transit-Amplifying Progenitors, and their Niche in Developing Hair Follicles. | Rezza, Amélie; Wang, Zichen; Sennett, Rachel; Qiao, Wenlian; Wang, Dongmei; Heitman, Nicholas; Mok, Ka Wai; Clavel, Carlos; Yi, Rui; Zandstra, Peter; Ma'ayan, Avi; Rendl, Michael | Cell reports. | 2016 Mar 29; | 27009580 | |
| In Vitro and In Vivo Characterization of the Alkaloid Nuciferine. | Farrell, Martilias S; McCorvy, John D; Huang, Xi-Ping; Urban, Daniel J; White, Kate L; Giguere, Patrick M; Doak, Allison K; Bernstein, Alison I; Stout, Kristen A; Park, Su Mi; Rodriguiz, Ramona M; Gray, Bradley W; Hyatt, William S; Norwood, Andrew P; Webs | PloS one. | 2016; | 26963248 | |
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| Mapping the effects of drugs on the immune system. | Kidd, Brian A; Wroblewska, Aleksandra; Boland, Mary R; Agudo, Judith; Merad, Miriam; Tatonetti, Nicholas P; Brown, Brian D; Dudley, Joel T | Nature biotechnology. | 2016 Jan; | 47-54 | 26619012 |
| Molecular systems evaluation of oligomerogenic APP(E693Q) and fibrillogenic APP(KM670/671NL)/PSEN1(?exon9) mouse models identifies shared features with human Alzheimer's brain molecular pathology. | Readhead, B; Haure-Mirande, J-V; Zhang, B; Haroutunian, V; Gandy, S; Schadt, E E; Dudley, J T; Ehrlich, M E | Molecular psychiatry. | 2015 Nov 10; | 26552589 | |
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| Identification of type 2 diabetes subgroups through topological analysis of patient similarity. | Li, Li; Cheng, Wei-Yi; Glicksberg, Benjamin S; Gottesman, Omri; Tamler, Ronald; Chen, Rong; Bottinger, Erwin P; Dudley, Joel T | Science translational medicine. | 2015 Oct 28; | 311ra174 | 26511511 |
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