IDG Publications
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The Target Watch series in Nature Reviews Drug Discovery:
- "Novel drug targets in 2018" by O. Ursu, M. Glick, T. Oprea (Nature Reviews Drug Discovery 18, 328 (2019), doi: https://doi.org/10.1038/d41573-019-00052-5.)
- "CDK16: the pick of the understudied PCTAIRE kinases" by Alison Axtman, David Drewry & Carrow Wells (Nature Reviews Drug Discovery 2019 Jul;18(7):489. doi: https://doi.org/10.1038/d41573-019-00076-x.)
- "RIOK2: straddling the kinase/ATPase line" by Christopher R. M. Asquith, Michael P. East & William J. Zuercher (Nature Reviews Drug Discovery 18, 574 (2019). doi: https://doi.org/10.1038/d41573-019-00107-7)
- "TRIC-B: an under-explored druggable ion channel" by Zicheng Hu & Olga Gulyaeva (Nature Reviews Drug Discovery 18, 657 (2019). doi: https://doi.org/10.1038/d41573-019-00131-7
- "ADCK3/COQ8A: the choice target of the UbiB protein kinase-like family" by Christopher R. M. Asquith, Nathan H. Murray & David J. Pagliarini (Nature Reviews Drug Discovery 18, 815 (2019). doi: https://doi.org/10.1038/d41573-019-00158-w)
- "PKMYT1: a forgotten member of the WEE1 family" by Christopher R. M. Asquith, Tuomo Laitinen & Michael P. East (Nature Reviews Drug Discovery 19, 157 (2020) doi: https://doi.org/10.1038/d41573-019-00202-9)
- "GPR84: an immune response dial?" by Megan L. Wojciechowicz & Avi Ma’ayan (Nature Reviews Drug Discovery 19, 374 (2020) doi: https://doi.org/10.1038/d41573-020-00029-9)
- "Novel drug targets in 2019" by Sorin Avram, Liliana Halip, Ramona Curpan & Tudor I. Oprea (Nature Reviews Drug Discovery 19, 300 (2020) doi: https://doi.org/10.1038/d41573-020-00052-w)
- "PIP5K1A: a potential target for cancers with KRAS or TP53 mutations" by Michael P. East, Tuomo Laitinen & Christopher R. M. Asquith (Nature Reviews Drug Discovery 19, 436 (2020) doi: https://doi.org/10.1038/d41573-020-00067-3)
- "KNa1.1 channels as a target for treating early-onset epilepsy" by Zicheng Hu, Hannah N. Gruner, Jana Gagacheva & Olga Gulyaeva (Nature Reviews Drug Discovery 19, 502 (2020) doi: https://doi.org/10.1038/d41573-020-00092-2)
- "STK19: a new target for NRAS-driven cancer" by Christopher R. M. Asquith & Louisa Temme (Nature Reviews Drug Discovery 19, 579 (2020) doi: https://doi.org/10.1038/d41573-020-00116-x)
- "HCAR3: an underexplored metabolite sensor" by Nicholas J. Kapolka & Daniel G. Isom (Nature Reviews Drug Discovery 19, 745 (2020) doi: https://doi.org/10.1038/d41573-020-00173-2)
- "WNK kinases: an untapped opportunity to modulate ion transport" by Michael P. East, Tuomo Laitinen & Christopher R. M. Asquith (Nature Reviews Drug Discovery 19, 828 (2020) doi: https://doi.org/10.1038/d41573-020-00196-9)
- "CDC42BPA/MRCKα: a kinase target for brain, ovarian and skin cancers" by Michael P. East & Christopher R. M. Asquith (Nature Reviews Drug Discovery 20, 167 (2021) doi: https://doi.org/10.1038/d41573-021-00023-9)
- "Novel drug targets in 2020" by Sorin Avram , Liliana Halip , Ramona Curpan & Tudor I. Oprea (Nature Reviews Drug Discovery 20, 333 (2021) https://doi.org/10.1038/d41573-021-00057-z)
- "BCKDK: an emerging kinase target for metabolic diseases and cancer" by Michael P. East , Tuomo Laitinen & Christopher R. M. Asquith (Nature Reviews Drug Discovery 20, 498 (2021) https://doi.org/10.1038/d41573-021-00107-6)
- "PIKfyve: a lipid kinase target for COVID-19, cancer and neurodegenerative disorders" by Pei-Tzu Huang , Shirit Einav & Christopher R. M. Asquith (Nature Reviews Drug Discovery 20, 730 (2021) https://doi.org/10.1038/d41573-021-00158-9 )
- “eEF2K: an atypical kinase target for cancer” by Louisa Temme & Christopher R. M. Asquith (Nature Reviews Drug Discovery, 20, 577 (2021) https://doi.org/10.1038/d41573-021-00124-5
- "Novel drug targets in 2021" by Sorin Avram , Liliana Halip , Ramona Curpan & Tudor I. Oprea (Nature Reviews Drug Discovery, 21, 328 (2022)) https://doi.org/10.1038/d41573-022-00057-7
- "PKN3: a target in cancer metastasis" by Louisa Temme, Tuomo Laitinen & Christopher R. M. Asquith (Nature Reviews Drug Discovery, 21, 704 (2022)) https://doi.org/10.1038/d41573-022-00154-7
- "Novel drug targets in 2022" by Sorin Avram, Liliana Halip, Ramona Curpan & Tudor I. Oprea (Nature Reviews Drug Discovery, 22, 437 (2023)) https://doi.org/10.1038/d41573-023-00068-y
- "Novel drug targets in 2023" by Sorin Avram, Liliana Halip, Ramona Curpan & Tudor I. Oprea (Nature Reviews Drug Discovery, 2024) https://doi.org/10.1038/d41573-024-00057-9
| Publication Title | Authors | Journal | Publication Date | Page No | PubMedID |
|---|---|---|---|---|---|
| Bitter taste receptor activation by cholesterol and an intracellular tastant. | Kim Y, Gumpper RH, Liu Y, Kocak DD, Xiong Y, Cao C, Deng Z, Krumm BE, Jain MK, Zhang S, Jin J, Roth BL. | Nature. | 2024 Apr 10; | 38600377 | |
| Utilizing Low-Dimensional Molecular Embeddings for Rapid Chemical Similarity Search. | Kirchoff KE, Wellnitz J, Hochuli JE, Maxfield T, Popov KI, Gomez S, Tropsha A.. | Adv Inf Retr. | 2024 Mar; | 38585224 | |
| Synthesis of 5-Benzylamino and 5-Alkylamino-Substituted Pyrimido[4,5-c]quinoline Derivatives as CSNK2A Inhibitors with Antiviral Activity. | Asressu KH, Smith JL, Dickmander RJ, Moorman NJ, Wellnitz J, Popov KI, Axtman AD, Willson TM.. | Pharmaceuticals (Basel). | 2024 Feb 27; | 38543092 | |
| Kinome-Wide Virtual Screening by Multi-Task Deep Learning. | Hu J, Allen BK, Stathias V, Ayad NG, Schürer SC.. | Int J Mol Sci. | 2024 Feb 22; | 38473785 | |
| Bioinformatic analysis of human ZPR1 gene pathogenic exome mutations. | Abok JI, Garver WS, Edwards JS.. | bioRxiv. | 2024 Mar 1; | 38464185 | |
| Pan-cancer proteogenomics characterization of tumor immunity. | Petralia F, Ma W, Yaron TM, Caruso FP, Tignor N, Wang JM, Charytonowicz D, Johnson JL, Huntsman EM, Marino GB, Calinawan A, Evangelista JE, Selvan ME, Chowdhury S, Rykunov D, Krek A, Song X, Turhan B, Christianson KE, Lewis DA, Deng EZ, Clarke DJB, Whiteaker JR, Kennedy JJ, Zhao L, Segura RL, Batra H, Raso MG, Parra ER, Soundararajan R, Tang X, Li Y, Yi X, Satpathy S, Wang Y, Wiznerowicz M, González-Robles TJ, Iavarone A, Gosline SJC, Reva B, Robles AI, Nesvizhskii AI, Mani DR, Gillette MA, Klein RJ, Cieslik M, Zhang B, Paulovich AG, Sebra R, Gümüş ZH, Hostetter G, Fenyö D, Omenn GS, Cantley LC, Ma'ayan A, Lazar AJ, Ceccarelli M, Wang P; Clinical Proteomic Tumor Analysis Consortium.. | Cell. | 2024 Feb 29; | 38359819 | |
| Alternative splicing of latrophilin-3 controls synapse formation. | Wang S, DeLeon C, Sun W, Quake SR, Roth BL, Südhof TC.. | Nature. | 2024 Feb; | 38233523 | |
| Overview of the Knowledge Management Center for Illuminating the Druggable Genome. | Oprea TI, Bologa C, Holmes J, Mathias S, Metzger VT, Waller A, Yang JJ, Leach AR, Jensen LJ, Kelleher KJ, Sheils TK, Mathé E, Avram S, Edwards JS.. | Drug Discov Today. | 2024 Mar; | 38218214 | |
| Illuminating function of the understudied druggable kinome. | Gomez SM, Axtman AD, Willson TM, Major MB, Townsend RR, Sorger PK, Johnson GL.. | Drug Discov Today. | 2024 Mar; | 38218213 | |
| GRAPE for fast and scalable graph processing and random-walk-based embedding. | Cappelletti L, Fontana T, Casiraghi E, Ravanmehr V, Callahan TJ, Cano C, Joachimiak MP, Mungall CJ, Robinson PN, Reese J, Valentini G.. | Nat Comput Sci. | 2023 Jun; | 38177435 | |
| Detection of neoplastic-immune hybrid cells with metastatic properties in uveal melanoma. | Anderson AN, Conley P, Klocke CD, Sengupta SK, Pang A, Farley HC, Gillingham AR, Dawson AD, Fan Y, Jones JA, Gibbs SL, Skalet AH, Wu G, Wong MH.. | Res Sq. | 2023 Dec 6; | 38106024 | |
| Identification of 4-(6-((2-methoxyphenyl)amino)pyrazin-2-yl)benzoic acids as CSNK2A inhibitors with antiviral activity and improved selectivity over PIM3. | Galal KA, Krämer A, Strickland BG, Smith JL, Dickmander RJ, Moorman NJ, Willson TM.. | bioRxiv. | 2023 Dec 5; | 38106118 | |
| Dark kinase annotation, mining, and visualization using the Protein Kinase Ontology. | Soleymani S, Gravel N, Huang LC, Yeung W, Bozorgi E, Bendzunas NG, Kochut KJ, Kannan N.. | PeerJ. | 2023 Dec 5; | 38077442 | |
| Genome-wide prediction of pathogenic gain- and loss-of-function variants from ensemble learning of a diverse feature set. | Stein D, Kars ME, Wu Y, Bayrak ÇS, Stenson PD, Cooper DN, Schlessinger A, Itan Y.. | Genome Med. | 2023 Nov 30; | 38037155 | |
| Integrated single-dose kinome profiling data is predictive of cancer cell line sensitivity to kinase inhibitors. | Joisa CU, Chen KA, Berginski ME, Golitz BT, Jenner MR, Herrera Loeza G, Yeh JJ, Gomez SM.. | PeerJ. | 2023 Nov 16; | 38025707 | |
| Identification of Cellular Interactions in the Tumor Immune Microenvironment Underlying CD8 T Cell Exhaustion. | Klocke C, Moran A, Adey A, McWeeney S, Wu G.. | bioRxiv. | 2023 Nov 13; | 38014233 | |
| SGC-CLK-1: A chemical probe for the Cdc2-like kinases CLK1, CLK2, and CLK4. | Tiek D, Wells CI, Schröder M, Song X, Alamillo-Ferrer C, Goenka A, Iglesia R, Lu M, Hu B, Kwarcinski F, Sintha P, de Silva C, Hossain MA, Picado A, Zuercher W, Zutshi R, Knapp S, Riggins RB, Cheng SY, Drewry DH.. | Curr Res Chem Biol. | 2023; | 38009092 | |
| ChatGPT usage in the Reactome curation process. | Tiwari K, Matthews L, May B, Shamovsky V, Orlic-Milacic M, Rothfels K, Ragueneau E, Gong C, Stephan R, Li N, Wu G, Stein L, D'Eustachio P, Hermjakob H.. | bioRxiv. | 2023 Nov 8; | 37986970 | |
| A small molecule exerts selective antiviral activity by targeting the human cytomegalovirus nuclear egress complex. | Chen H, Lye MF, Gorgulla C, Ficarro SB, Cuny GD, Scott DA, Wu F, Rothlauf PW, Wang X, Fernandez R, Pesola JM, Draga S, Marto JA, Hogle JM, Arthanari H, Coen DM.. | PLoS Pathog. | 2023 Nov 17; | 37976321 | |
| Covalent Stapling of the Cereblon Sensor Loop Histidine Using Sulfur-Heterocycle Exchange. | Cruite JT, Nowak RP, Donovan KA, Ficarro SB, Huang H, Liu H, Liu Y, Marto JA, Metivier RJ, Fischer ES, Jones LH.. | ACS Med Chem Lett. | 2023 Oct 24; | 37974938 | |
| Dex-Benchmark: datasets and code to evaluate algorithms for transcriptomics data analysis. | Xie Z, Chen C, Ma'ayan A.. | PeerJ. | 2023 Nov 8; | 37953774 | |
| The Reactome Pathway Knowledgebase 2024. | Milacic M, Beavers D, Conley P, Gong C, Gillespie M, Griss J, Haw R, Jassal B, Matthews L, May B, Petryszak R, Ragueneau E, Rothfels K, Sevilla C, Shamovsky V, Stephan R, Tiwari K, Varusai T, Weiser J, Wright A, Wu G, Stein L, Hermjakob H, D'Eustachio P.. | Nucleic Acids Res. | 2024 Jan 5; | 37941124 | |
| Development of a covalent cereblon-based PROTAC employing a fluorosulfate warhead. | Nowak RP, Ragosta L, Huerta F, Liu H, Ficarro SB, Cruite JT, Metivier RJ, Donovan KA, Marto JA, Fischer ES, Zerfas BL, Jones LH.. | RSC Chem Biol. | 2023 Aug 31; | 37920397 | |
| Optimization of 3-Cyano-7-cyclopropylamino-pyrazolo[1,5-a]pyrimidines toward the Development of an In Vivo Chemical Probe for CSNK2A. | Yang X, Ong HW, Dickmander RJ, Smith JL, Brown JW, Tao W, Chang E, Moorman NJ, Axtman AD, Willson TM.. | ACS Omega. | 2023 Oct 10; | 37901516 | |
| Predicting protein and pathway associations for understudied dark kinases using pattern-constrained knowledge graph embedding. | Salcedo MV, Gravel N, Keshavarzi A, Huang LC, Kochut KJ, Kannan N.. | PeerJ. | 2023 Oct 18; | 37868056 | |
| KSFinder-a knowledge graph model for link prediction of novel phosphorylated substrates of kinases. | Anandakrishnan M, Ross KE, Chen C, Shanker V, Cowart J, Wu CH.. | PeerJ. | 2023 Oct 6; | 37818330 | |
| Targeted Proteomic Quantitation of NRF2 Signaling and Predictive Biomarkers in HNSCC. | Wamsley NT, Wilkerson EM, Guan L, LaPak KM, Schrank TP, Holmes BJ, Sprung RW, Gilmore PE, Gerndt SP, Jackson RS, Paniello RC, Pipkorn P, Puram SV, Rich JT, Townsend RR, Zevallos JP, Zolkind P, Le QT, Goldfarb D, Major MB.. | Mol Cell Proteomics. | 2023 Nov; | 37716475 | |
| Exploring DrugCentral: from molecular structures to clinical effects. | Halip L, Avram S, Curpan R, Borota A, Bora A, Bologa C, Oprea TI.. | J Comput Aided Mol Des. | 2023 Dec; | 37707619 | |
| Molecular Complexity: You Know It When You See It. | Oprea TI, Bologa C.. | J Med Chem. | 2023 Sep 28; | 37675804 | |
| How many kinases are druggable? A review of our current understanding. | Anderson B, Rosston P, Ong HW, Hossain MA, Davis-Gilbert ZW, Drewry DH.. | Biochem J. | 2023 Aug 30; | 37642371 | |
| Investigation of the Host Kinome Response to Coronavirus Infection Reveals PI3K/mTOR Inhibitors as Betacoronavirus Antivirals. | Fritch EJ, Mordant AL, Gilbert TSK, Wells CI, Yang X, Barker NK, Madden EA, Dinnon KH 3rd, Hou YJ, Tse LV, Castillo IN, Sims AC, Moorman NJ, Lakshmanane P, Willson TM, Herring LE, Graves LM, Baric RS.. | J Proteome Res. | 2023 Oct 6; | 37634194 | |
| A proteogenomics data-driven knowledge base of human cancer. | Liao Y, Savage SR, Dou Y, Shi Z, Yi X, Jiang W, Lei JT, Zhang B.. | Cell Syst. | 2023 Sep 20; | 37619559 | |
| A Hybrid Structure-Based Machine Learning Approach for Predicting Kinase Inhibition by Small Molecules. | Liu C, Kutchukian P, Nguyen ND, AlQuraishi M, Sorger PK.. | J Chem Inf Model. | 2023 Sep 11; | 37595065 | |
| Combined kinome inhibition states are predictive of cancer cell line sensitivity to kinase inhibitor combination therapies. | Joisa CU, Chen KA, Beville S, Stuhlmiller T, Berginski ME, Okumu D, Golitz BT, Johnson GL, Gomez SM.. | bioRxiv. | 2023 Aug 3; | 37577663 | |
| A peroxiredoxin-P38 MAPK scaffold increases MAPK activity by MAP3K-independent mechanisms. | Cao M, Day AM, Galler M, Latimer HR, Byrne DP, Foy TW, Dwyer E, Bennett E, Palmer J, Morgan BA, Eyers PA, Veal EA.. | Mol Cell. | 2023 Sep 7; | 37572670 | |
| Discovery and characterization of a specific inhibitor of serine-threonine kinase cyclin-dependent kinase-like 5 (CDKL5) demonstrates role in hippocampal CA1 physiology. | Castano A, Silvestre M, Wells CI, Sanderson JL, Ferrer CA, Ong HW, Lang Y, Richardson W, Silvaroli JA, Bashore FM, Smith JL, Genereux IM, Dempster K, Drewry DH, Pabla NS, Bullock AN, Benke TA, Ultanir SK, Axtman AD.. | Elife. | 2023 Jul 25; | 37490324 | |
| Illuminate the Functions of Dark Proteins Using the Reactome-IDG Web Portal. | Beavers D, Brunson T, Sanati N, Matthews L, Haw R, Shorser S, Sevilla C, Viteri G, Conley P, Rothfels K, Hermjakob H, Stein L, D'Eustachio P, Wu G.. | Curr Protoc. | 2023 Jul; | 37467006 | |
| Combined CDK4/6 and ERK1/2 Inhibition Enhances Antitumor Activity in NF1-Associated Plexiform Neurofibroma. | Flint AC, Mitchell DK, Angus SP, Smith AE, Bessler W, Jiang L, Mang H, Li X, Lu Q, Rodriguez B, Sandusky GE, Masters AR, Zhang C, Dang P, Koenig J, Johnson GL, Shen W, Liu J, Aggarwal A, Donoho GP, Willard MD, Bhagwat SV, Clapp DW, Rhodes SD.. | Clin Cancer Res. | 2023 Sep 1; | 37406085 | |
| KG-Hub-building and exchanging biological knowledge graphs. | Caufield JH, Putman T, Schaper K, Unni DR, Hegde H, Callahan TJ, Cappelletti L, Moxon SAT, Ravanmehr V, Carbon S, Chan LE, Cortes K, Shefchek KA, Elsarboukh G, Balhoff J, Fontana T, Matentzoglu N, Bruskiewich RM, Thessen AE, Harris NL, Munoz-Torres MC, Haendel MA, Robinson PN, Joachimiak MP, Mungall CJ, Reese JT.. | Bioinformatics. | 2023 Jul 1; | 37389415 | |
| Illuminating Dark Proteins using Reactome Pathways. | Brunson T, Sanati N, Matthews L, Haw R, Beavers D, Shorser S, Sevilla C, Viteri G, Conley P, Rothfels K, Hermjakob H, Stein L, D'Eustachio P, Wu G.. | bioRxiv. | 2023 Jun 5; | 37333417 | |
| Optimization of 3-Cyano-7-cyclopropylamino-pyrazolo[1,5-a]pyrimidines Toward the Development of an In Vivo Chemical Probe for CSNK2A. | Yang X, Ong HW, Dickmander RJ, Smith JL, Brown JW, Tao W, Chang E, Moorman NJ, Axtman AD, Willson TM.. | bioRxiv. | 2023 Jul 23; | 37292607 | |
| AI-Assisted chemical probe discovery for the understudied Calcium-Calmodulin Dependent Kinase, PNCK. | Essegian DJ, Chavez V, Khurshid R, Merchan JR, Schürer SC.. | PLoS Comput Biol. | 2023 May 26; | 37235579 | |
| VIGET: A web portal for study of vaccine-induced host responses based on Reactome pathways and ImmPort data. | Brunson T, Sanati N, Huffman A, Masci AM, Zheng J, Cooke MF, Conley P, He Y, Wu G.. | Front Immunol. | 2023 Mar 21; | 37180100 | |
| Enrichr-KG: bridging enrichment analysis across multiple libraries. | Evangelista JE, Xie Z, Marino GB, Nguyen N, Clarke DJB, Ma'ayan A.. | Nucleic Acids Res. | 2023 Jul 5; | 37166973 | |
| GeneRanger and TargetRanger: processed gene and protein expression levels across cells and tissues for target discovery. | Marino GB, Ngai M, Clarke DJB, Fleishman RH, Deng EZ, Xie Z, Ahmed N, Ma'ayan A.. | Nucleic Acids Res. | 2023 Jul 5; | 37166966 | |
| Editorial: The next generation of tools and technologies for studying human neurons in a dish. | Durcan TM, Axtman AD.. | Front Cell Neurosci. | 2023 Apr 14; | 37124399 | |
| Proteomic approaches to study ubiquitinomics. | Sahu I, Zhu H, Buhrlage SJ, Marto JA.. | Biochim Biophys Acta Gene Regul Mech. | 2023 Jun; | 37121501 | |
| Computational screen to identify potential targets for immunotherapeutic identification and removal of senescence cells. | Deng EZ, Fleishman RH, Xie Z, Marino GB, Clarke DJB, Ma'ayan A.. | Aging Cell. | 2023 Jun; | 37082798 | |
| Discovery of a Potent and Selective CDKL5/GSK3 Chemical Probe That Is Neuroprotective. | Ong HW, Liang Y, Richardson W, Lowry ER, Wells CI, Chen X, Silvestre M, Dempster K, Silvaroli JA, Smith JL, Wichterle H, Pabla NS, Ultanir SK, Bullock AN, Drewry DH, Axtman AD.. | ACS Chem Neurosci. | 2023 May 3; | 37084253 | |
| Discovery of a Potent and Selective Naphthyridine-Based Chemical Probe for Casein Kinase 2. | Davis-Gilbert ZW, Krämer A, Dunford JE, Howell S, Senbabaoglu F, Wells CI, Bashore FM, Havener TM, Smith JL, Hossain MA, Oppermann U, Drewry DH, Axtman AD.. | ACS Med Chem Lett. | 2023 Mar 14; | 37077385 | |
| Modulation of tau tubulin kinases (TTBK1 and TTBK2) impacts ciliogenesis. | Bashore FM, Marquez AB, Chaikuad A, Howell S, Dunn AS, Beltran AA, Smith JL, Drewry DH, Beltran AS, Axtman AD.. | Sci Rep. | 2023 Apr 14; | 37059819 | |
| Using the Reactome Database. | Rothfels K, Milacic M, Matthews L, Haw R, Sevilla C, Gillespie M, Stephan R, Gong C, Ragueneau E, May B, Shamovsky V, Wright A, Weiser J, Beavers D, Conley P, Tiwari K, Jassal B, Griss J, Senff-Ribeiro A, Brunson T, Petryszak R, Hermjakob H, D'Eustachio P, Wu G, Stein L.. | Curr Protoc. | 2023 Apr; | 37053306 | |
| Development of Cell Permeable NanoBRET Probes for the Measurement of PLK1 Target Engagement in Live Cells. | Yang X, Smith JL, Beck MT, Wilkinson JM, Michaud A, Vasta JD, Robers MB, Willson TM.. | Molecules. | 2023 Mar 25; | 37049713 | |
| SARS-CoV-2 ORF3A interacts with the Clic-like chloride channel-1 (CLCC1) and triggers an unfolded protein response. | Gruner HN, Zhang Y, Shariati K, Yiv N, Hu Z, Wang Y, Hejtmancik JF, McManus MT, Tharp K, Ku G.. | PeerJ. | 2023 Apr 3; | 37033725 | |
| Leveraging biochemical reactions to unravel functional impacts of cancer somatic variants affecting protein interaction interfaces. | Raimondi F, Burkhart JG, Betts MJ, Russell RB, Wu G.. | F1000Res. | 2021 Nov 3; | 36569594 | |
| PrismEXP: gene annotation prediction from stratified gene-gene co-expression matrices. | Lachmann A, Rizzo KA, Bartal A, Jeon M, Clarke DJB, Ma'ayan A.. | PeerJ. | 2023 Feb 27; | 36874981 | |
| lncHUB2: aggregated and inferred knowledge about human and mouse lncRNAs. | Marino GB, Wojciechowicz ML, Clarke DJB, Kuleshov MV, Xie Z, Jeon M, Lachmann A, Ma'ayan A.. | Database (Oxford). | 2023 Mar 4; | 36869839 | |
| The structure, function, and pharmacology of MRGPRs. | Cao C, Roth BL.. | Trends Pharmacol Sci. | 2023 Apr; | 36870785 | |
| Reversal of Lactate and PD-1-mediated Macrophage Immunosuppression Controls Growth of PTEN/p53-deficient Prostate Cancer. | Chaudagar K, Hieromnimon HM, Khurana R, Labadie B, Hirz T, Mei S, Hasan R, Shafran J, Kelley A, Apostolov E, Al-Eryani G, Harvey K, Rameshbabu S, Loyd M, Bynoe K, Drovetsky C, Solanki A, Markiewicz E, Zamora M, Fan X, Schürer S, Swarbrick A, Sykes DB, Patnaik A.. | Clin Cancer Res. | 2023 May 15; | 36862086 | |
| Kinome inhibition states and multiomics data enable prediction of cell viability in diverse cancer types. | Berginski ME, Joisa CU, Golitz BT, Gomez SM.. | PLoS Comput Biol. | 2023 Feb 21; | 36809237 | |
| A Potent and Selective CDKL5/GSK3 Chemical Probe is Neuroprotective. | Ong HW, Liang Y, Richardson W, Lowry ER, Wells CI, Chen X, Silvestre M, Dempster K, Silvaroli JA, Smith JL, Wichterle H, Pabla NS, Ultanir SK, Bullock AN, Drewry DH, Axtman AD.. | bioRxiv. | 2023 Feb 10; | 36798313 | |
| Accelerating inhibitor discovery for deubiquitinating enzymes. | Chan WC, Liu X, Magin RS, Girardi NM, Ficarro SB, Hu W, Tarazona Guzman MI, Starnbach CA, Felix A, Adelmant G, Varca AC, Hu B, Bratt AS, DaSilva E, Schauer NJ, Jaen Maisonet I, Dolen EK, Ayala AX, Marto JA, Buhrlage SJ.. | Nat Commun. | 2023 Feb 8; | 36754960 | |
| SGC-CAMKK2-1: A Chemical Probe for CAMKK2. | Wells C, Liang Y, Pulliam TL, Lin C, Awad D, Eduful B, O'Byrne S, Hossain MA, Catta-Preta CMC, Ramos PZ, Gileadi O, Gileadi C, Couñago RM, Stork B, Langendorf CG, Nay K, Oakhill JS, Mukherjee D, Racioppi L, Means AR, York B, McDonnell DP, Scott JW, Frigo DE, Drewry DH.. | Cells. | 2023 Jan 11; | 36672221 | |
| An atlas of substrate specificities for the human serine/threonine kinome. | Johnson JL, Yaron TM, Huntsman EM, Kerelsky A, Song J, Regev A, Lin TY, Liberatore K, Cizin DM, Cohen BM, Vasan N, Ma Y, Krismer K, Robles JT, van de Kooij B, van Vlimmeren AE, Andrée-Busch N, Käufer NF, Dorovkov MV, Ryazanov AG, Takagi Y, Kastenhuber ER, Goncalves MD, Hopkins BD, Elemento O, Taatjes DJ, Maucuer A, Yamashita A, Degterev A, Uduman M, Lu J, Landry SD, Zhang B, Cossentino I, Linding R, Blenis J, Hornbeck PV, Turk BE, Yaffe MB, Cantley LC.. | Nature. | 2023 Jan; | 36631611 | |
| Pharos 2023: an integrated resource for the understudied human proteome. | Kelleher KJ, Sheils TK, Mathias SL, Yang JJ, Metzger VT, Siramshetty VB, Nguyen DT, Jensen LJ, Vidović D, Schürer SC, Holmes J, Sharma KR, Pillai A, Bologa CG, Edwards JS, Mathé EA, Oprea TI.. | Nucleic Acids Res. | 2023 Jan 6; | 36624666 | |
| Evolutionary and cellular analysis of the 'dark' pseudokinase PSKH2. | Byrne DP, Shrestha S, Daly LA, Marensi V, Ramakrishnan K, Eyers CE, Kannan N, Eyers PA.. | Biochem J. | 2023 Jan 31; | 36520605 | |
| DrugCentral 2023 extends human clinical data and integrates veterinary drugs. | Avram S, Wilson TB, Curpan R, Halip L, Borota A, Bora A, Bologa CG, Holmes J, Knockel J, Yang JJ, Oprea TI.. | Nucleic Acids Res. | 2023 Jan 6; | 36484092 | |
| Cellular and molecular effects of PNCK, a non-canonical kinase target in renal cell carcinoma. | Essegian DJ, Chavez V, Bustamante F, Schürer SC, Merchan JR.. | iScience. | 2022 Nov 17; | 36465101 | |
| Protein kinase inhibitor selectivity "hinges" on evolution. | Shrestha S, Bendzunas G, Kannan N.. | Structure. | 2022 Dec 1; | 36459973 | |
| Molecular basis for selective activation of DREADD-based chemogenetics. | Zhang S, Gumpper RH, Huang XP, Liu Y, Krumm BE, Cao C, Fay JF, Roth BL.. | Nature. | 2022 Dec; | 36450989 | |
| Multiplexed and reproducible high content screening of live and fixed cells using Dye Drop. | Mills CE, Subramanian K, Hafner M, Niepel M, Gerosa L, Chung M, Victor C, Gaudio B, Yapp C, Nirmal AJ, Clark N, Sorger PK.. | Nat Commun. | 2022 Nov 14; | 36376301 | |
| Identification and Utilization of a Chemical Probe to Interrogate the Roles of PIKfyve in the Lifecycle of β-Coronaviruses. | Drewry DH, Potjewyd FM, Bayati A, Smith JL, Dickmander RJ, Howell S, Taft-Benz S, Min SM, Hossain MA, Heise M, McPherson PS, Moorman NJ, Axtman AD.. | J Med Chem. | 2022 Oct 13; | 36111834 | |
| Transforming L1000 profiles to RNA-seq-like profiles with deep learning. | Jeon M, Xie Z, Evangelista JE, Wojciechowicz ML, Clarke DJB, Ma'ayan A.. | BMC Bioinformatics. | 2022 Sep 13; | 36100892 | |
| Getting Started with LINCS Datasets and Tools. | Xie Z, Kropiwnicki E, Wojciechowicz ML, Jagodnik KM, Shu I, Bailey A, Clarke DJB, Jeon M, Evangelista JE, V Kuleshov M, Lachmann A, Parigi AA, Sanchez JM, Jenkins SL, Ma'ayan A.. | Curr Protoc. | 2022 Jul; | 35876555 | |
| Inactive and active state structures template selective tools for the human 5-HT(5A) receptor. | Zhang S, Chen H, Zhang C, Yang Y, Popov P, Liu J, Krumm BE, Cao C, Kim K, Xiong Y, Katritch V, Shoichet BK, Jin J, Fay JF, Roth BL.. | Nat Struct Mol Biol. | 2022 Jul; | 35835867 | |
| TRUPATH: An Open-Source Biosensor Platform for Interrogating the GPCR Transducerome. | DiBerto JF, Olsen RHJ, Roth BL.. | Methods Mol Biol. | 2022; | 35836068 | |
| 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 S, Al-Awar R, Amaro RE, Arrowsmith CH, Azevedo H, Batey RA, Bengio Y, Betz UAK, Bologa CG, Chodera JD, Cornell WD, Dunham I, Ecker GF, Edfeldt K, Edwards AM, Gilson MK, Gordijo CR, Hessler G, Hillisch A, Hogner A, Irwin JJ, Jansen JM, Kuhn D, Leach AR, Lee AA, Lessel U, Morgan MR, Moult J, Muegge I, Oprea TI, Perry BG, Riley P, Rousseaux SAL, Saikatendu KS, Santhakumar V, Schapira M, Scholten C, Todd MH, Vedadi M, Volkamer A, Willson TM.. | Nat Rev Chem. | 2022 Apr; | 35783295 | |
| Evaluation of a Selective Chemical Probe Validates That CK2 Mediates Neuroinflammation in a Human Induced Pluripotent Stem Cell-Derived Microglial Model. | Mishra S, Kinoshita C, Axtman AD, Young JE.. | Front Mol Neurosci. | 2022 Jun 14; | 35774866 | |
| Numb-associated kinases are required for SARS-CoV-2 infection and are cellular targets for antiviral strategies. | Karim M, Saul S, Ghita L, Sahoo MK, Ye C, Bhalla N, Lo CW, Jin J, Park JG, Martinez-Gualda B, East MP, Johnson GL, Pinsky BA, Martinez-Sobrido L, Asquith CRM, Narayanan A, De Jonghe S, Einav S.. | Antiviral Res. | 2022 Aug; | 35738348 | |
| Temozolomide-induced guanine mutations create exploitable vulnerabilities of guanine-rich DNA and RNA regions in drug-resistant gliomas. | Tiek DM, Erdogdu B, Razaghi R, Jin L, Sadowski N, Alamillo-Ferrer C, Hogg JR, Haddad BR, Drewry DH, Wells CI, Pickett JE, Song X, Goenka A, Hu B, Goldlust SA, Zuercher WJ, Pertea M, Timp W, Cheng SY, Riggins RB.. | Sci Adv. | 2022 Jun 24; | 35731869 | |
| On-Chip Preconcentration Microchip Capillary Electrophoresis Based CE-PRM-LIVE for High-Throughput Selectivity Profiling of Deubiquitinase Inhibitors. | Zhu H, Mellors JS, Chan WC, Thompson JW, Ficarro SB, Tavares I, Bratt AS, Decker J, Krause M, Kruppa G, Buhrlage SJ, Marto JA.. | Anal Chem. | 2022 Jul 12; | 35729701 | |
| Autophagy and Herpesvirus: A collaboration Contributing to Alzheimer's Disease. | Nafchi AR, Esmaeili M, Myers O, Oprea T, Bearer EL.. | FASEB J. | 2022 May; | 35723876 | |
| Host Kinase CSNK2 is a Target for Inhibition of Pathogenic SARS-like β-Coronaviruses. | Yang X, Dickmander RJ, Bayati A, Taft-Benz SA, Smith JL, Wells CI, Madden EA, Brown JW, Lenarcic EM, Yount BL Jr, Chang E, Axtman AD, Baric RS, Heise MT, McPherson PS, Moorman NJ, Willson TM.. | ACS Chem Biol. | 2022 Jul 15; | 35723434 | |
| SigCom LINCS: data and metadata search engine for a million gene expression signatures. | Evangelista JE, Clarke DJB, Xie Z, Lachmann A, Jeon M, Chen K, Jagodnik KM, Jenkins SL, Kuleshov MV, Wojciechowicz ML, Schürer SC, Medvedovic M, Ma'ayan A.. | Nucleic Acids Res. | 2022 Jul 5; | 35524556 | |
| Analysis of human Tribbles 2 (TRIB2) pseudokinase. | Harris JA, Fairweather E, Byrne DP, Eyers PA.. | Methods Enzymol. | 2022 Mar 25; | 35525562 | |
| Computational tools and resources for pseudokinase research. | O'Boyle B, Shrestha S, Kochut K, Eyers PA, Kannan N.. | Methods Enzymol. | 2022 Mar 4; | 35525549 | |
| Open source fraction collector/MALDI spotter for proteomics. | Ficarro SB, Max Alexander W, Tavares I, Marto JA.. | HardwareX. | 2022 Apr 18; | 35518277 | |
| Protein proximity networks and functional evaluation of the casein kinase 1 gamma family reveal unique roles for CK1γ3 in WNT signaling. | Agajanian MJ, Potjewyd FM, Bowman BM, Solomon S, LaPak KM, Bhatt DP, Smith JL, Goldfarb D, Axtman AD, Major MB.. | J Biol Chem. | 2022 Jun; | 35487243 | |
| AlphaFold illuminates half of the dark human proteins. | Binder JL, Berendzen J, Stevens AO, He Y, Wang J, Dokholyan NV, Oprea TI.. | Curr Opin Struct Biol. | 2022 Jun; | 35439658 | |
| Agonist and antagonist TRUPATH assays for G protein-coupled receptors. | DiBerto JF, Smart K, Olsen RHJ, Roth BL.. | STAR Protoc. | 2022 Apr 1; | 35403009 | |
| Identification of 4-Anilinoquin(az)oline as a Cell-Active Protein Kinase Novel 3 (PKN3) Inhibitor Chemotype. | Asquith CRM, Temme L, East MP, Laitinen T, Pickett J, Kwarcinski FE, Sinha P, Wells CI, Johnson GL, Zutshi R, Drewry DH.. | ChemMedChem. | 2022 Jun 20; | 35403825 | |
| Gene and drug landing page aggregator. | Clarke DJB, Kuleshov MV, Xie Z, Evangelista JE, Meyers MR, Kropiwnicki E, Jenkins SL, Ma'ayan A.. | Bioinform Adv. | 2022 Feb 28; | 35368424 | |
| State of the Art and Uses for the Biopharmaceutics Drug Disposition Classification System (BDDCS): New Additions, Revisions, and Citation References. | Bocci G, Oprea TI, Benet LZ.. | AAPS J. | 2022 Feb 23; | 35199251 | |
| Structure-Based Design of a Chemical Probe Set for the 5-HT(5A) Serotonin Receptor. | Levit Kaplan A, Strachan RT, Braz JM, Craik V, Slocum S, Mangano T, Amabo V, O'Donnell H, Lak P, Basbaum AI, Roth BL, Shoichet BK.. | J Med Chem. | 2022 Mar 10; | 35195401 | |
| DrugShot: querying biomedical search terms to retrieve prioritized lists of small molecules. | Kropiwnicki E, Lachmann A, Clarke DJB, Xie Z, Jagodnik KM, Ma'ayan A.. | BMC Bioinformatics. | 2022 Feb 19; | 35183110 | |
| EMBER: multi-label prediction of kinase-substrate phosphorylation events through deep learning. | Kirchoff KE, Gomez SM.. | Bioinformatics. | 2022 Apr 12; | 35157015 | |
| Machine learning prediction and tau-based screening identifies potential Alzheimer's disease genes relevant to immunity. | Binder J, Ursu O, Bologa C, Jiang S, Maphis N, Dadras S, Chisholm D, Weick J, Myers O, Kumar P, Yang JJ, Bhaskar K, Oprea TI.. | Commun Biol. | 2022 Feb 11; | 35149761 | |
| blitzGSEA: efficient computation of gene set enrichment analysis through gamma distribution approximation. | Lachmann A, Xie Z, Ma'ayan A.. | Bioinformatics. | 2022 Apr 12; | 35143610 | |
| Getting Started with the IDG KMC Datasets and Tools. | Kropiwnicki E, Binder JL, Yang JJ, Holmes J, Lachmann A, Clarke DJB, Sheils T, Kelleher KJ, Metzger VT, Bologa CG, Oprea TI, Ma'ayan A.. | Curr Protoc. | 2022 Jan; | 35085427 | |
| Host kinase CSNK2 is a target for inhibition of pathogenic β-coronaviruses including SARS-CoV-2. | Yang X, Dickmander RJ, Bayati A, Taft-Benz SA, Smith JL, Wells CI, Madden EA, Brown JW, Lenarcic EM, Yount BL Jr, Chang E, Axtman AD, Baric RS, Heise MT, McPherson PS, Moorman NJ, Willson TM.. | bioRxiv. | 2022 Jan 26; | 35018375 | |
| Systematic identification of ACE2 expression modulators reveals cardiomyopathy as a risk factor for mortality in COVID-19 patients. | Kaur N, Oskotsky B, Butte AJ, Hu Z.. | Genome Biol. | 2022 Jan 10; | 35012625 | |
| Adaptive chromatin remodeling and transcriptional changes of the functional kinome in tumor cells in response to targeted kinase inhibition. | East MP, Johnson GL.. | J Biol Chem. | 2022 Feb; | 34958800 | |
| Supervised learning with word embeddings derived from PubMed captures latent knowledge about protein kinases and cancer. | Ravanmehr V, Blau H, Cappelletti L, Fontana T, Carmody L, Coleman B, George J, Reese J, Joachimiak M, Bocci G, Hansen P, Bult C, Rueter J, Casiraghi E, Valentini G, Mungall C, Oprea TI, Robinson PN.. | NAR Genom Bioinform. | 2021 Dec 8; | 34888523 | |
| Structure, function and pharmacology of human itch GPCRs. | Cao C, Kang HJ, Singh I, Chen H, Zhang C, Ye W, Hayes BW, Liu J, Gumpper RH, Bender BJ, Slocum ST, Krumm BE, Lansu K, McCorvy JD, Kroeze WK, English JG, DiBerto JF, Olsen RHJ, Huang XP, Zhang S, Liu Y, Kim K, Karpiak J, Jan LY, Abraham SN, Jin J, Shoichet BK, Fay JF, Roth BL.. | Nature. | 2021 Dec; | 34789874 | |
| The reactome pathway knowledgebase 2022. | Gillespie M, Jassal B, Stephan R, Milacic M, Rothfels K, Senff-Ribeiro A, Griss J, Sevilla C, Matthews L, Gong C, Deng C, Varusai T, Ragueneau E, Haider Y, May B, Shamovsky V, Weiser J, Brunson T, Sanati N, Beckman L, Shao X, Fabregat A, Sidiropoulos K, Murillo J, Viteri G, Cook J, Shorser S, Bader G, Demir E, Sander C, Haw R, Wu G, Stein L, Hermjakob H, D'Eustachio P.. | Nucleic Acids Res. | 2022 Jan 7; | 34788843 | |
| Loss of proximal tubular transcription factor Krüppel-like factor 15 exacerbates kidney injury through loss of fatty acid oxidation. | Piret SE, Attallah AA, Gu X, Guo Y, Gujarati NA, Henein J, Zollman A, Hato T, Ma'ayan A, Revelo MP, Dickman KG, Chen CH, Shun CT, Rosenquist TA, He JC, Mallipattu SK.. | Kidney Int. | 2021 Dec; | 34634362 | |
| PRM-LIVE with Trapped Ion Mobility Spectrometry and Its Application in Selectivity Profiling of Kinase Inhibitors. | Zhu H, Ficarro SB, Alexander WM, Fleming LE, Adelmant G, Zhang T, Willetts M, Decker J, Brehmer S, Krause M, East MP, Gray NS, Johnson GL, Kruppa G, Marto JA.. | Anal Chem. | 2021 Oct 19; | 34606255 | |
| Characterizing the role of the dark kinome in neurodegenerative disease - A mini review. | Axtman AD.. | Biochim Biophys Acta Gen Subj. | 2021 Dec; | 34547390 | |
| KinOrtho: a method for mapping human kinase orthologs across the tree of life and illuminating understudied kinases. | Huang LC, Taujale R, Gravel N, Venkat A, Yeung W, Byrne DP, Eyers PA, Kannan N.. | BMC Bioinformatics. | 2021 Sep 18; | 34537014 | |
| Non-canonical role of Hippo tumor suppressor serine/threonine kinase 3 STK3 in prostate cancer. | Schirmer AU, Driver LM, Zhao MT, Wells CI, Pickett JE, O'Bryne SN, Eduful BJ, Yang X, Howard L, You S, Devi GR, DiGiovanni J, Freedland SJ, Chi JT, Drewry DH, Macias E.. | Mol Ther. | 2022 Jan 5; | 34450249 | |
| Identification of Pyrimidine-Based Lead Compounds for Understudied Kinases Implicated in Driving Neurodegeneration. | Drewry DH, Annor-Gyamfi JK, Wells CI, Pickett JE, Dederer V, Preuss F, Mathea S, Axtman AD.. | J Med Chem. | 2022 Jan 27; | 34333981 | |
| Hinge Binder Scaffold Hopping Identifies Potent Calcium/Calmodulin-Dependent Protein Kinase Kinase 2 (CAMKK2) Inhibitor Chemotypes. | Eduful BJ, O'Byrne SN, Temme L, Asquith CRM, Liang Y, Picado A, Pilotte JR, Hossain MA, Wells CI, Zuercher WJ, Catta-Preta CMC, Zonzini Ramos P, Santiago AS, Couñago RM, Langendorf CG, Nay K, Oakhill JS, Pulliam TL, Lin C, Awad D, Willson TM, Frigo DE, Scott JW, Drewry DH.. | J Med Chem. | 2021 Aug 12; | 34264658 | |
| A critical overview of computational approaches employed for COVID-19 drug discovery. | Muratov EN , Amaro R , Andrade CH , Brown N , Ekins S , Fourches D , Isayev O , Kozakov D , Medina-Franco JL , Merz KM , Oprea TI , Poroikov V , Schneider G , Todd MH , Varnek A , Winkler DA , Zakharov AV , Cherkasov A , Tropsha A .. | Chem Soc Rev. | 2021 Aug 21; | 34212944 | |
| TIGA: target illumination GWAS analytics. | Yang JJ, Grissa D, Lambert CG, Bologa CG, Mathias SL, Waller A, Wild DJ, Jensen LJ, Oprea TI.. | Bioinformatics. | 2021 Nov 5; | 34086846 | |
| Crowdsourced mapping of unexplored target space of kinase inhibitors. | Cichońska A, Ravikumar B, Allaway RJ, Wan F, Park S, Isayev O, Li S, Mason M, Lamb A, Tanoli Z, Jeon M, Kim S, Popova M, Capuzzi S, Zeng J, Dang K, Koytiger G, Kang J, Wells CI, Willson TM; IDG-DREAM Drug-Kinase Binding Prediction Challenge Consortium; Oprea TI, Schlessinger A, Drewry DH, Stolovitzky G, Wennerberg K, Guinney J, Aittokallio T.. | Nat Commun. | 2021 Jun 3; | 34083538 | |
| Krüppel-like factor 6-mediated loss of BCAA catabolism contributes to kidney injury in mice and humans. | Piret SE, Guo Y, Attallah AA, Horne SJ, Zollman A, Owusu D, Henein J, Sidorenko VS, Revelo MP, Hato T, Ma'ayan A, He JC, Mallipattu SK.. | Proc Natl Acad Sci U S A. | 2021 Jun 8; | 34074766 | |
| Towards a RIOK2 chemical probe: cellular potency improvement of a selective 2-(acylamino)pyridine series. | Wang CB, Lorente-Macías Á, Wells C, Pickett JE, Picado A, Zuercher WJ, Axtman AD.. | RSC Med Chem. | 2020 Nov 11; | 34046605 | |
| KEA3: improved kinase enrichment analysis via data integration. | Kuleshov MV, Xie Z, London ABK, Yang J, Evangelista JE, Lachmann A, Shu I, Torre D, Ma'ayan A.. | Nucleic Acids Res. | 2021 Jul 2; | 34019655 | |
| FOXA1 and adaptive response determinants to HER2 targeted therapy in TBCRC 036. | Angus SP, Stuhlmiller TJ, Mehta G, Bevill SM, Goulet DR, Olivares-Quintero JF, East MP, Tanioka M, Zawistowski JS, Singh D, Sciaky N, Chen X, He X, Rashid NU, Chollet-Hinton L, Fan C, Soloway MG, Spears PA, Jefferys S, Parker JS, Gallagher KK, Forero-Torres A, Krop IE, Thompson AM, Murthy R, Gatza ML, Perou CM, Earp HS, Carey LA, Johnson GL.. | NPJ Breast Cancer. | 2021 May 12; | 33980863 | |
| TMEM16C is involved in thermoregulation and protects rodent pups from febrile seizures. | Wang TA, Chen C, Huang F, Feng S, Tien J, Braz JM, Basbaum AI, Jan YN, Jan LY.. | Proc Natl Acad Sci U S A. | 2021 May 18; | 33972431 | |
| mTORC2 controls the activity of PKC and Akt by phosphorylating a conserved TOR interaction motif. | Baffi TR, Lordén G, Wozniak JM, Feichtner A, Yeung W, Kornev AP, King CC, Del Rio JC, Limaye AJ, Bogomolovas J, Gould CM, Chen J, Kennedy EJ, Kannan N, Gonzalez DJ, Stefan E, Taylor SS, Newton AC.. | Sci Signal. | 2021 Apr 13; | 33850054 | |
| Highly Accurate Chip-Based Resequencing of SARS-CoV-2 Clinical Samples. | Hoff K, Ding X, Carter L, Duque J, Lin JY, Dung S, Singh P, Sun J, Crnogorac F, Swaminathan R, Alden EN, Zhu X, Shimada R, Posavi M, Hull N, Dinwiddie D, Halasz AM, McGall G, Zhou W, Edwards JS.. | Langmuir. | 2021 Apr 27; | 33848173 | |
| An Esrrb and Nanog Cell Fate Regulatory Module Controlled by Feed Forward Loop Interactions. | Sevilla A, Papatsenko D, Mazloom AR, Xu H, Vasileva A, Unwin RD, LeRoy G, Chen EY, Garrett-Bakelman FE, Lee DF, Trinite B, Webb RL, Wang Z, Su J, Gingold J, Melnick A, Garcia BA, Whetton AD, MacArthur BD, Ma'ayan A, Lemischka IR.. | Front Cell Dev Biol. | 2021 Mar 19; | 33816475 | |
| Drugmonizome and Drugmonizome-ML: integration and abstraction of small molecule attributes for drug enrichment analysis and machine learning. | Kropiwnicki E, Evangelista JE, Stein DJ, Clarke DJB, Lachmann A, Kuleshov MV, Jeon M, Jagodnik KM, Ma'ayan A.. | Database (Oxford). | 2021 Mar 31; | 33787872 | |
| Gene Set Knowledge Discovery with Enrichr. | Xie Z, Bailey A, Kuleshov MV, Clarke DJB, Evangelista JE, Jenkins SL, Lachmann A, Wojciechowicz ML, Kropiwnicki E, Jagodnik KM, Jeon M, Ma'ayan A.. | Curr Protoc. | 2021 Mar; | 33780170 | |
| Predicting Lyme Disease From Patients' Peripheral Blood Mononuclear Cells Profiled With RNA-Sequencing. | Clarke DJB, Rebman AW, Bailey A, Wojciechowicz ML, Jenkins SL, Evangelista JE, Danieletto M, Fan J, Eshoo MW, Mosel MR, Robinson W, Ramadoss N, Bobe J, Soloski MJ, Aucott JN, Ma'ayan A.. | Front Immunol. | 2021 Mar 8; | 33763080 | |
| Discovery and resistance mechanism of a selective CDK12 degrader. | Jiang B, Gao Y, Che J, Lu W, Kaltheuner IH, Dries R, Kalocsay M, Berberich MJ, Jiang J, You I, Kwiatkowski N, Riching KM, Daniels DL, Sorger PK, Geyer M, Zhang T, Gray NS.. | Nat Chem Biol. | 2021 Jun; | 33753926 | |
| Appyters: Turning Jupyter Notebooks into data-driven web apps. | Clarke DJB, Jeon M, Stein DJ, Moiseyev N, Kropiwnicki E, Dai C, Xie Z, Wojciechowicz ML, Litz S, Hom J, Evangelista JE, Goldman L, Zhang S, Yoon C, Ahamed T, Bhuiyan S, Cheng M, Karam J, Jagodnik KM, Shu I, Lachmann A, Ayling S, Jenkins SL, Ma'ayan A.. | Patterns (N Y). | 2021 Mar 4; | 33748796 | |
| Prioritizing Pain-Associated Targets with Machine Learning. | Jeon M, Jagodnik KM, Kropiwnicki E, Stein DJ, Ma'ayan A.. | Biochemistry. | 2021 May 11; | 33606503 | |
| Machine learning identifies candidates for drug repurposing in Alzheimer's disease. | Rodriguez S, Hug C, Todorov P, Moret N, Boswell SA, Evans K, Zhou G, Johnson NT, Hyman BT, Sorger PK, Albers MW, Sokolov A.. | Nat Commun. | 2021 Feb 15; | 33589615 | |
| InContext: curation of medical context for drug indications. | Moodley K, Rieswijk L, Oprea TI, Dumontier M.. | J Biomed Semantics. | 2021 Feb 12; | 33579375 | |
| Development of a potent and selective chemical probe for the pleiotropic kinase CK2. | Wells CI, Drewry DH, Pickett JE, Tjaden A, Krämer A, Müller S, Gyenis L, Menyhart D, Litchfield DW, Knapp S, Axtman AD.. | Cell Chem Biol. | 2021 Apr 15; | 33484635 | |
| The Kinase Chemogenomic Set (KCGS): An Open Science Resource for Kinase Vulnerability Identification. | Wells CI, Al-Ali H, Andrews DM, Asquith CRM, Axtman AD, Dikic I, Ebner D, Ettmayer P, Fischer C, Frederiksen M, Futrell RE, Gray NS, Hatch SB, Knapp S, Lücking U, Michaelides M, Mills CE, Müller S, Owen D, Picado A, Saikatendu KS, Schröder M, Stolz A, Tellechea M, Turunen BJ, Vilar S, Wang J, Zuercher WJ, Willson TM, Drewry DH.. | Int J Mol Sci. | 2021 Jan 8; | 33429995 | |
| Virtual and In Vitro Antiviral Screening Revive Therapeutic Drugs for COVID-19. | Bocci G, Bradfute SB, Ye C, Garcia MJ, Parvathareddy J, Reichard W, Surendranathan S, Bansal S, Bologa CG, Perkins DJ, Jonsson CB, Sklar LA, Oprea TI.. | ACS Pharmacol Transl Sci. | 2020 Oct 14; | 33330842 | |
| Mapping the Degradable Kinome Provides a Resource for Expedited Degrader Development. | Donovan KA, Ferguson FM, Bushman JW, Eleuteri NA, Bhunia D, Ryu S, Tan L, Shi K, Yue H, Liu X, Dobrovolsky D, Jiang B, Wang J, Hao M, You I, Teng M, Liang Y, Hatcher J, Li Z, Manz TD, Groendyke B, Hu W, Nam Y, Sengupta S, Cho H, Shin I, Agius MP, Ghobrial IM, Ma MW, Che J, Buhrlage SJ, Sim T, Gray NS, Fischer ES.. | Cell. | 2020 Dec 10; | 33275901 | |
| A Chemical Probe for Dark Kinase STK17B Derives Its Potency and High Selectivity through a Unique P-Loop Conformation. | Picado A, Chaikuad A, Wells CI, Shrestha S, Zuercher WJ, Pickett JE, Kwarcinski FE, Sinha P, de Silva CS, Zutshi R, Liu S, Kannan N, Knapp S, Drewry DH, Willson TM.. | J Med Chem. | 2020 Dec 10; | 33215924 | |
| The Clinical Kinase Index: A Method to Prioritize Understudied Kinases as Drug Targets for the Treatment of Cancer. | Essegian D, Khurana R, Stathias V, Schürer SC.. | Cell Rep Med. | 2020 Oct 20; | 33205077 | |
| REDIAL-2020: A suite of machine learning models to estimate Anti-SARS-CoV-2 activities. | Govinda KC, Bocci G, Verma S, Hassan M, Holmes J, Yang JJ, Sirimulla S, Oprea TI.. | ChemRxiv. | 2020 Sep 16; | 33200119 | |
| KG-COVID-19: A Framework to Produce Customized Knowledge Graphs for COVID-19 Response. | Reese JT, Unni D, Callahan TJ, Cappelletti L, Ravanmehr V, Carbon S, Shefchek KA, Good BM, Balhoff JP, Fontana T, Blau H, Matentzoglu N, Harris NL, Munoz-Torres MC, Haendel MA, Robinson PN, Joachimiak MP, Mungall CJ.. | Patterns (N Y). | 2021 Jan 8; | 33196056 | |
| Quantitative Structure-Mutation-Activity Relationship Tests (QSMART) model for protein kinase inhibitor response prediction. | Huang LC, Yeung W, Wang Y, Cheng H, Venkat A, Li S, Ma P, Rasheed K, Kannan N.. | BMC Bioinformatics. | 2020 Nov 12; | 33183223 | |
| TCRD and Pharos 2021: mining the human proteome for disease biology. | Sheils TK, Mathias SL, Kelleher KJ, Siramshetty VB, Nguyen DT, Bologa CG, Jensen LJ, Vidović D, Koleti A, Schürer SC, Waller A, Yang JJ, Holmes J, Bocci G, Southall N, Dharkar P, Mathé E, Simeonov A, Oprea TI.. | Nucleic Acids Res. | 2021 Jan 8; | 33156327 | |
| DrugCentral 2021 supports drug discovery and repositioning. | Avram S, Bologa CG, Holmes J, Bocci G, Wilson TB, Nguyen DT, Curpan R, Halip L, Bora A, Yang JJ, Knockel J, Sirimulla S, Ursu O, Oprea TI.. | Nucleic Acids Res. | 2021 Jan 8; | 33151287 | |
| The Dark Kinase Knowledgebase: an online compendium of knowledge and experimental results of understudied kinases. | Berginski ME, Moret N, Liu C, Goldfarb D, Sorger PK, Gomez SM.. | Nucleic Acids Res. | 2021 Jan 8; | 33079988 | |
| Connectivity Mapping Identifies BI-2536 as a Potential Drug to Treat Diabetic Kidney Disease. | Zhang L, Wang Z, Liu R, Li Z, Lin J, Wojciechowicz ML, Huang J, Lee K, Ma'ayan A, He JC.. | Diabetes. | 2021 Feb; | 33067313 | |
| Concise, gram-scale synthesis of furo[2,3-b]pyridines with functional handles for chemoselective cross-coupling. | O'Byrne SN, Eduful BJ, Willson TM, Drewry DH.. | Tetrahedron Lett. | 2020 Sep 17; | 33012852 | |
| PKIS deep dive yields a chemical starting point for dark kinases and a cell active BRSK2 inhibitor. | Tamir TY, Drewry DH, Wells C, Major MB, Axtman AD.. | Sci Rep. | 2020 Sep 28; | 32985588 | |
| Chemokine Signatures of Pathogen-Specific T Cells I: Effector T Cells. | Eberlein J, Davenport B, Nguyen TT, Victorino F, Jhun K, van der Heide V, Kuleshov M, Ma'ayan A, Kedl R, Homann D.. | J Immunol. | 2020 Oct 15; | 32948687 | |
| Chemokine Signatures of Pathogen-Specific T Cells II: Memory T Cells in Acute and Chronic Infection. | Davenport B, Eberlein J, Nguyen TT, Victorino F, van der Heide V, Kuleshov M, Ma'ayan A, Kedl R, Homann D.. | J Immunol. | 2020 Oct 15; | 32948682 | |
| Deciphering the Plasma Proteome of Type 2 Diabetes. | Elhadad MA, Jonasson C, Huth C, Wilson R, Gieger C, Matias P, Grallert H, Graumann J, Gailus-Durner V, Rathmann W, von Toerne C, Hauck SM, Koenig W, Sinner MF, Oprea TI, Suhre K, Thorand B, Hveem K, Peters A, Waldenberger M.. | Diabetes. | 2020 Dec; | 32928870 | |
| Artificial intelligence, drug repurposing and peer review. | Levin JM, Oprea TI, Davidovich S, Clozel T, Overington JP, Vanhaelen Q, Cantor CR, Bischof E, Zhavoronkov A.. | Nat Biotechnol. | 2020 Oct; | 32929264 | |
| Off-Patent Drug Repositioning. | Avram S, Curpan R, Halip L, Bora A, Oprea TI.. | J Chem Inf Model. | 2020 Dec 28; | 32877182 | |
| KG-COVID-19: a framework to produce customized knowledge graphs for COVID-19 response. | Reese J, Unni D, Callahan TJ, Cappelletti L, Ravanmehr V, Carbon S, Fontana T, Blau H, Matentzoglu N, Harris NL, Munoz-Torres MC, Robinson PN, Joachimiak MP, Mungall CJ.. | bioRxiv. | 2020 Aug 18; | 32839776 | |
| The COVID-19 Drug and Gene Set Library. | Kuleshov MV, Stein DJ, Clarke DJB, Kropiwnicki E, Jagodnik KM, Bartal A, Evangelista JE, Hom J, Cheng M, Bailey A, Zhou A, Ferguson LB, Lachmann A, Ma'ayan A.. | Patterns (N Y). | 2020 Sep 11; | 32838343 | |
| A Semi-automated and Scalable 3D Spheroid Assay to Study Neuroblast Migration. | Ducker M, Millar V, Ebner D, Szele FG.. | Stem Cell Reports. | 2020 Sep 8; | 32763162 | |
| Chemical Biology Toolkit for DCLK1 Reveals Connection to RNA Processing. | Liu Y, Ferguson FM, Li L, Kuljanin M, Mills CE, Subramanian K, Harshbarger W, Gondi S, Wang J, Sorger PK, Mancias JD, Gray NS, Westover KD.. | Cell Chem Biol. | 2020 Oct 15; | 32755567 | |
| Discrete Adaptive Responses to MEK Inhibitor in Subpopulations of Triple-Negative Breast Cancer. | Goulet DR, Foster JP 2nd, Zawistowski JS, Bevill SM, Noël MP, Olivares-Quintero JF, Sciaky N, Singh D, Santos C, Pattenden SG, Davis IJ, Johnson GL.. | Mol Cancer Res. | 2020 Nov; | 32753473 | |
| The COVID-19 Gene and Drug Set Library. | Kuleshov MV, Clarke DJB, Kropiwnicki E, Jagodnik KM, Bartal A, Evangelista JE, Zhou A, Ferguson LB, Lachmann A, Ma'ayan A.. | Res Sq. | 2020 May 13; | 32702729 | |
| Deschloroclozapine, a potent and selective chemogenetic actuator enables rapid neuronal and behavioral modulations in mice and monkeys. | Nagai Y, Miyakawa N, Takuwa H, Hori Y, Oyama K, Ji B, Takahashi M, Huang XP, Slocum ST, DiBerto JF, Xiong Y, Urushihata T, Hirabayashi T, Fujimoto A, Mimura K, English JG, Liu J, Inoue KI, Kumata K, Seki C, Ono M, Shimojo M, Zhang MR, Tomita Y, Nakahara J, Suhara T, Takada M, Higuchi M, Jin J, Roth BL, Minamimoto T.. | Nat Neurosci. | 2020 Sep; | 32632286 | |
| Gain-of-function genetic screen of the kinome reveals BRSK2 as an inhibitor of the NRF2 transcription factor. | Tamir TY, Bowman BM, Agajanian MJ, Goldfarb D, Schrank TP, Stohrer T, Hale AE, Siesser PF, Weir SJ, Murphy RM, LaPak KM, Weissman BE, Moorman NJ, Major MB.. | J Cell Sci. | 2020 Jul 15; | 32546533 | |
| GPR84: an immune response dial?. | Wojciechowicz ML, Ma'ayan A.. | Nat Rev Drug Discov. | 2020 Jun; | 32494048 | |
| Quantifying CDK inhibitor selectivity in live cells. | Wells CI, Vasta JD, Corona CR, Wilkinson J, Zimprich CA, Ingold MR, Pickett JE, Drewry DH, Pugh KM, Schwinn MK, Hwang BB, Zegzouti H, Huber KVM, Cong M, Meisenheimer PL, Willson TM, Robers MB.. | Nat Commun. | 2020 Jun 2; | 32488087 | |
| Defining the Neural Kinome: Strategies and Opportunities for Small Molecule Drug Discovery to Target Neurodegenerative Diseases. | Krahn AI, Wells C, Drewry DH, Beitel LK, Durcan TM, Axtman AD.. | ACS Chem Neurosci. | 2020 Jul 1; | 32464049 | |
| Systems Analysis Implicates WAVE2 Complex in the Pathogenesis of Developmental Left-Sided Obstructive Heart Defects. | Edwards JJ, Rouillard AD, Fernandez NF, Wang Z, Lachmann A, Shankaran SS, Bisgrove BW, Demarest B, Turan N, Srivastava D, Bernstein D, Deanfield J, Giardini A, Porter G, Kim R, Roberts AE, Newburger JW, Goldmuntz E, Brueckner M, Lifton RP, Seidman CE, Chung WK, Tristani-Firouzi M, Yost HJ, Ma'ayan A, Gelb BD.. | JACC Basic Transl Sci. | 2020 Apr 8; | 32368696 | |
| TRUPATH, an open-source biosensor platform for interrogating the GPCR transducerome. | Olsen RHJ, DiBerto JF, English JG, Glaudin AM, Krumm BE, Slocum ST, Che T, Gavin AC, McCorvy JD, Roth BL, Strachan RT.. | Nat Chem Biol. | 2020 Aug; | 32367019 | |
| QSAR without borders. | Muratov EN, Bajorath J, Sheridan RP, Tetko IV, Filimonov D, Poroikov V, Oprea TI, Baskin II, Varnek A, Roitberg A, Isayev O, Curtarolo S, Fourches D, Cohen Y, Aspuru-Guzik A, Winkler DA, Agrafiotis D, Cherkasov A, Tropsha A.. | Chem Soc Rev. | 2020 Jun 7; | 32356548 | |
| EnrichrBot: Twitter bot tracking tweets about human genes. | Bartal A, Lachmann A, Clarke DJB, Seiden AH, Jagodnik KM, Ma'ayan A.. | Bioinformatics. | 2020 Jun 1; | 32277816 | |
| Memory of Divisional History Directs the Continuous Process of Primitive Hematopoietic Lineage Commitment. | Bernitz JM, Rapp K, Daniel MG, Shcherbinin D, Yuan Y, Gomes A, Waghray A, Brosh R, Lachmann A, Ma'ayan A, Papatsenko D, Moore KA.. | Stem Cell Reports. | 2020 Apr 14; | 32243840 | |
| Nanobody-enabled monitoring of kappa opioid receptor states. | Che T, English J, Krumm BE, Kim K, Pardon E, Olsen RHJ, Wang S, Zhang S, Diberto JF, Sciaky N, Carroll FI, Steyaert J, Wacker D, Roth BL.. | Nat Commun. | 2020 Mar 2; | 32123179 | |
| Structure-based discovery of potent and selective melatonin receptor agonists. | Patel N, Huang XP, Grandner JM, Johansson LC, Stauch B, McCorvy JD, Liu Y, Roth B, Katritch V.. | Elife. | 2020 Mar 2; | 32118583 | |
| Emerging roles of the αC-β4 loop in protein kinase structure, function, evolution, and disease. | Yeung W, Ruan Z, Kannan N.. | IUBMB Life. | 2020 Jun; | 32101380 | |
| Cataloguing the dead: breathing new life into pseudokinase research. | Shrestha S, Byrne DP, Harris JA, Kannan N, Eyers PA.. | FEBS J. | 2020 Oct; | 32053275 | |
| Virtual discovery of melatonin receptor ligands to modulate circadian rhythms. | Stein RM, Kang HJ, McCorvy JD, Glatfelter GC, Jones AJ, Che T, Slocum S, Huang XP, Savych O, Moroz YS, Stauch B, Johansson LC, Cherezov V, Kenakin T, Irwin JJ, Shoichet BK, Roth BL, Dubocovich ML.. | Nature. | 2020 Mar; | 32040955 | |
| How many rare diseases are there?. | Haendel M, Vasilevsky N, Unni D, Bologa C, Harris N, Rehm H, Hamosh A, Baynam G, Groza T, McMurry J, Dawkins H, Rath A, Thaxton C, Bocci G, Joachimiak MP, Köhler S, Robinson PN, Mungall C, Oprea TI.. | Nat Rev Drug Discov. | 2020 Feb; | 32020066 | |
| Identification of DOT1L inhibitors by structure-based virtual screening adapted from a nucleoside-focused library. | Gibbons GS, Chakraborty A, Grigsby SM, Umeano AC, Liao C, Moukha-Chafiq O, Pathak V, Mathew B, Lee YT, Dou Y, Schürer SC, Reynolds RC, Snowden TS, Nikolovska-Coleska Z.. | Eur J Med Chem. | 2020 Mar 1; | 31978781 | |
| Will Artificial Intelligence for Drug Discovery Impact Clinical Pharmacology?. | Zhavoronkov A, Vanhaelen Q, Oprea TI.. | Clin Pharmacol Ther. | 2020 Apr; | 31957003 | |
| In Depth Analysis of Kinase Cross Screening Data to Identify CAMKK2 Inhibitory Scaffolds. | O'Byrne SN, Scott JW, Pilotte JR, Santiago ADS, Langendorf CG, Oakhill JS, Eduful BJ, Couñago RM, Wells CI, Zuercher WJ, Willson TM, Drewry DH.. | Molecules. | 2020 Jan 13; | 31941153 | |
| Machine and deep learning approaches for cancer drug repurposing. | Issa NT, Stathias V, Schürer S, Dakshanamurthy S.. | Semin Cancer Biol. | 2021 Jan; | 31904426 | |
| How to Illuminate the Druggable Genome Using Pharos. | Sheils T, Mathias SL, Siramshetty VB, Bocci G, Bologa CG, Yang JJ, Waller A, Southall N, Nguyen DT, Oprea TI.. | Curr Protoc Bioinformatics. | 2020 Mar; | 31898878 | |
| Dermal sheath contraction powers stem cell niche relocation during hair cycle regression. | Heitman N, Sennett R, Mok KW, Saxena N, Srivastava D, Martino P, Grisanti L, Wang Z, Ma'ayan A, Rompolas P, Rendl M.. | Science. | 2020 Jan 10; | 31857493 | |
| Research Techniques Made Simple: Molecular Docking in Dermatology - A Foray into In Silico Drug Discovery. | Issa NT, Badiavas EV, Schürer S.. | J Invest Dermatol. | 2019 Dec; | 31753122 | |
| LINCS Data Portal 2.0: next generation access point for perturbation-response signatures. | Stathias V, Turner J, Koleti A, Vidovic D, Cooper D, Fazel-Najafabadi M, Pilarczyk M, Terryn R, Chung C, Umeano A, Clarke DJB, Lachmann A, Evangelista JE, Ma'ayan A, Medvedovic M, Schürer SC.. | Nucleic Acids Res. | 2020 Jan 8; | 31701147 | |
| ADCK3/COQ8A: the choice target of the UbiB protein kinase-like family. | Asquith CRM, Murray NH, Pagliarini DJ.. | Nat Rev Drug Discov. | 2019 Oct; | 31673128 | |
| Single-cell immune landscape of human atherosclerotic plaques. | Fernandez DM, Rahman AH, Fernandez NF, Chudnovskiy A, Amir ED, Amadori L, Khan NS, Wong CK, Shamailova R, Hill CA, Wang Z, Remark R, Li JR, Pina C, Faries C, Awad AJ, Moss N, Bjorkegren JLM, Kim-Schulze S, Gnjatic S, Ma'ayan A, Mocco J, Faries P, Merad M, Giannarelli C.. | Nat Med. | 2019 Oct; | 31591603 | |
| Can BDDCS illuminate targets in drug design?. | Bocci G, Benet LZ, Oprea TI.. | Drug Discov Today. | 2019 Dec; | 31585170 | |
| PDBe-KB: a community-driven resource for structural and functional annotations. | PDBe-KB consortium.. | Nucleic Acids Res. | 2020 Jan 8; | 31584092 | |
| TCRD and Pharos 2021: mining the human proteome for disease biology. | Sheils TK; Mathias SL; Kelleher KJ; Siramshetty VB; Nguyen DT; Bologa CG; Jensen LJ; Vidović D; Koleti A; Schürer SC; Waller A; Yang JJ; Holmes J; Bocci G; Southall N; Dharkar P; Mathé E; Simeonov A; Oprea TI. | Nucleic Acids Research. | 2020 Nov; | 33156327 | |
| DrugCentral 2021 supports drug discovery and repositioning. | Patel, Nilkanth; Huang, Xi Ping | Nucleic Acids Research. | 2020 Mar 02; | 33151287 | |
| Artificial intelligence, drug repurposing and peer review. | Levin JM; Oprea TI; Davidovich S; Clozel T; Overington JP; Vanhaelen Q; Cantor CR; Bischof E; Zhavoronkov A. | Nature Biotechnology. | 2020 Oct; | 32929264 | |
| Off-Patent Drug Repositioning. | Avram S; Curpan R; Halip L; Bora A; Oprea TI. | Journal of Chemical Information and Modeling. | 2020 Sep 15; | 32877182 | |
| KG-COVID-19: a framework to produce customized knowledge graphs for COVID-19 response. | Reese, Justin; Unni, Deepak; Callahan, Tiffany J; Cappelletti, Luca; Ravanmehr, Vida; Carbon, Seth; Fontana, Tommaso; Blau, Hannah; Matentzoglu, Nicolas; Harris, Nomi L; Munoz-Torres, Monica C; Robinson, Peter N; Joachimiak, Marcin P; Mungall, Christopher J | bioRxiv : the preprint server for biology. | 2020 Aug 18; | 32839776 | |
| The COVID-19 Drug and Gene Set Library. | Kuleshov, Maxim V; Stein, Daniel J; Clarke, Daniel J B; Kropiwnicki, Eryk; Jagodnik, Kathleen M; Bartal, Alon; Evangelista, John E; Hom, Jason; Cheng, Minxuan; Bailey, Allison; Zhou, Abigail; Ferguson, Laura B; Lachmann, Alexander; Ma'ayan, Avi | Patterns (New York, N.Y.). | 2020 Sep 11; | 32838343 | |
| Chemical Biology Toolkit for DCLK1 Reveals Connection to RNA Processing. | Liu, Yan; Ferguson, Fleur M; Li, Lianbo; Kuljanin, Miljan; Mills, Caitlin E; Subramanian, Kartik; Harshbarger, Wayne; Gondi, Sudershan; Wang, Jinhua; Sorger, Peter K; Mancias, Joseph D; Gray, Nathanael S; Westover, Kenneth D | Cell chemical biology. | 2020 Aug 04; | 32755567 | |
| The COVID-19 Gene and Drug Set Library. | Kuleshov, Maxim V; Clarke, Daniel J B; Kropiwnicki, Eryk; Jagodnik, Kathleen M; Bartal, Alon; Evangelista, John E; Zhou, Abigail; Ferguson, Laura B; Lachmann, Alexander; Ma'ayan, Avi | Research square. | 2020 May 13; | 32702729 | |
| Gain-of-function genetic screen of the kinome reveals BRSK2 as an inhibitor of the NRF2 transcription factor. | Tamir, Tigist Y; Bowman, Brittany M; Agajanian, Megan J; Goldfarb, Dennis; Schrank, Travis P; Stohrer, Trent; Hale, Andrew E; Siesser, Priscila F; Weir, Seth J; Murphy, Ryan M; LaPak, Kyle M; Weissman, Bernard E; Moorman, Nathaniel J; Major, M Ben | Journal of cell science. | 2020 Jul 15; | 32546533 | |
| Opposite regulation of conditioned place preference and intravenous drug self-administration in rodent models: Motivational and non-motivational examples. | Green, Thomas A; Bardo, Michael T | Neuroscience and biobehavioral reviews. | 2020 Jun 12; | 32534899 | |
| TMEM163 Regulates ATP-Gated P2X Receptor and Behavior. | Salm, Elizabeth J; Dunn, Patrick J; Shan, Lili; Yamasaki, Miwako; Malewicz, Nathalie M; Miyazaki, Taisuke; Park, Joongkyu; Sumioka, Akio; Hamer, R Richard L; He, Wei-Wu; Morimoto-Tomita, Megumi; LaMotte, Robert H; Tomita, Susumu | Cell reports. | 2020 Jun 02; | 32492420 | |
| Quantifying CDK inhibitor selectivity in live cells. | Wells, Carrow I; Vasta, James D; Corona, Cesear R; Wilkinson, Jennifer; Zimprich, Chad A; Ingold, Morgan R; Pickett, Julie E; Drewry, David H; Pugh, Kathryn M; Schwinn, Marie K; Hwang, Byounghoon Brian; Zegzouti, Hicham; Huber, Kilian V M; Cong, Mei; Meisenheimer, Poncho L; Willson, Timothy M; Robers, Matthew B | Nature communications. | 2020 Jun 02; | 32488087 | |
| Defining the Neural Kinome: Strategies and Opportunities for Small Molecule Drug Discovery to Target Neurodegenerative Diseases. | Krahn, Andrea I; Wells, Carrow; Drewry, David H; Beitel, Lenore K; Durcan, Thomas M; Axtman, Alison D | ACS chemical neuroscience. | 2020 07 01; | 32464049 | |
| Systematic Analysis of Environmental Chemicals That Dysregulate Critical Period Plasticity-Related Gene Expression Reveals Common Pathways That Mimic Immune Response to Pathogen. | Smith, Milo R; Yevoo, Priscilla; Sadahiro, Masato; Readhead, Ben; Kidd, Brian; Dudley, Joel T; Morishita, Hirofumi | Neural plasticity. | 2020; | 32454811 | |
| DCyFIR: a high-throughput CRISPR platform for multiplexed G protein-coupled receptor profiling and ligand discovery. | Kapolka, N J; Taghon, G J; Rowe, J B; Morgan, W M; Enten, J F; Lambert, N A; Isom, D G | Proceedings of the National Academy of Sciences of the United States of America. | 2020 06 09; | 32434907 | |
| Systems Analysis Implicates WAVE2 Complex in the Pathogenesis of Developmental Left-Sided Obstructive Heart Defects. | Edwards, Jonathan J; Rouillard, Andrew D; Fernandez, Nicolas F; Wang, Zichen; Lachmann, Alexander; Shankaran, Sunita S; Bisgrove, Brent W; Demarest, Bradley; Turan, Nahid; Srivastava, Deepak; Bernstein, Daniel; Deanfield, John; Giardini, Alessandro; Porter, George; Kim, Richard; Roberts, Amy E; Newburger, Jane W; Goldmuntz, Elizabeth; Brueckner, Martina; Lifton, Richard P; Seidman, Christine E; Chung, Wendy K; Tristani-Firouzi, Martin; Yost, H Joseph; Ma'ayan, Avi; Gelb, Bruce D | JACC. Basic to translational science. | 2020 Apr; | 32368696 | |
| TRUPATH, an open-source biosensor platform for interrogating the GPCR transducerome. | Olsen, Reid H J; DiBerto, Jeffrey F; English, Justin G; Glaudin, Alexis M; Krumm, Brian E; Slocum, Samuel T; Che, Tao; Gavin, Ariana C; McCorvy, John D; Roth, Bryan L; Strachan, Ryan T | Nature chemical biology. | 2020 May 04; | 32367019 | |
| Discovery and Structure-Activity Relationship Study of (Z)-5-Methylenethiazolidin-4-one Derivatives as Potent and Selective Pan-phosphatidylinositol 5-Phosphate 4-Kinase Inhibitors. | Manz, Theresa D; Sivakumaren, Sindhu Carmen; Ferguson, Fleur M; Zhang, Tinghu; Yasgar, Adam; Seo, Hyuk-Soo; Ficarro, Scott B; Card, Joseph D; Shim, Hyeseok; Miduturu, Chandrasekhar V; Simeonov, Anton; Shen, Min; Marto, Jarrod A; Dhe-Paganon, Sirano; Hall, Matthew D; Cantley, Lewis C; Gray, Nathanael S | Journal of medicinal chemistry. | 2020 May 14; | 32298120 | |
| EnrichrBot: Twitter bot tracking tweets about human genes. | Bartal, Alon; Lachmann, Alexander; Clarke, Daniel J B; Seiden, Allison H; Jagodnik, Kathleen M; Ma'ayan, Avi | Bioinformatics (Oxford, England). | 2020 Jun 01; | 32277816 | |
| Novel drug targets in 2019. | Avram S; Halip L; Curpan R; Oprea TI. | Nature reviews. Drug discovery. | 2020 May; | 32273590 | |
| Presynaptic calcium channels: specialized control of synaptic neurotransmitter release. | Dolphin, Annette C; Lee, Amy | Nature reviews. Neuroscience. | 2020 04; | 32161339 | |
| Structure-based discovery of potent and selective melatonin receptor agonists. | Patel, Nilkanth; Huang, Xi Ping; Grandner, Jessica M; Johansson, Linda C; Stauch, Benjamin; McCorvy, John D; Liu, Yongfeng; Roth, Bryan; Katritch, Vsevolod | eLife. | 2020 Mar 02; | 32118583 | |
| Virtual discovery of melatonin receptor ligands to modulate circadian rhythms. | Stein, Reed M; Kang, Hye Jin; McCorvy, John D; Glatfelter, Grant C; Jones, Anthony J; Che, Tao; Slocum, Samuel; Huang, Xi-Ping; Savych, Olena; Moroz, Yurii S; Stauch, Benjamin; Johansson, Linda C; Cherezov, Vadim; Kenakin, Terry; Irwin, John J; Shoichet, Brian K; Roth, Bryan L; Dubocovich, Margarita L | Nature. | 2020 03; | 32040955 | |
| How many rare diseases are there? | Haendel M; Vasilevsky N; Unni D; Bologa C; Harris N; Rehm H; Hamosh A; Baynam G; Groza T; McMurry J; Dawkins H; Rath A; Thaxon C; Bocci G; Joachimiak MP; Köhler S; Robinson PN; Mungall C; Oprea TI. | Nature reviews. Drug discovery. | 2020 Feb; | 32020066 | |
| Structure-based discovery of potent and selective melatonin receptor agonists. | Patel, Nilkanth; Huang, Xi Ping; Grandner, Jessica M; Johansson, Linda C; Stauch, Benjamin; McCorvy, John D; Liu, Yongfeng; Roth, Bryan; Katritch, Vsevolod | eLife. | 2020 Mar 02; | 32118583 | |
| Virtual discovery of melatonin receptor ligands to modulate circadian rhythms. | Stein, Reed M; Kang, Hye Jin; McCorvy, John D; Glatfelter, Grant C; Jones, Anthony J; Che, Tao; Slocum, Samuel; Huang, Xi-Ping; Savych, Olena; Moroz, Yurii S; Stauch, Benjamin; Johansson, Linda C; Cherezov, Vadim; Kenakin, Terry; Irwin, John J; Shoichet, Brian K; Roth, Bryan L; Dubocovich, Margarita L | Nature. | 2020 Mar; | 32040955 | |
| Will Artificial Intelligence for Drug Discovery Impact Clinical Pharmacology? | Zhavoronkov A; Vanhaelen Q; Oprea TI. | Clinical Pharmacology and Therapeutics. | 2020 Apr; | 31957003 | |
| Genetic deletion of gpr27 alters acylcarnitine metabolism, insulin sensitivity, and glucose homeostasis in zebrafish. | Nath, Anjali K; Ma, Junyan; Chen, Zsu-Zsu; Li, Zhuyun; Vitery, Maria Del Carmen; Kelley, Michelle L; Peterson, Randall T; Gerszten, Robert E; Yeh, Jing-Ruey J | FASEB journal : official publication of the Federation of American Societies for Experimental Biology. | 2020 Jan; | 31914600 | |
| Machine and deep learning approaches for cancer drug repurposing. | Issa, Naiem T; Stathias, Vasileios; Schürer, Stephan; Dakshanamurthy, Sivanesan | Seminars in cancer biology. | 2020 Jan 03; | 31904426 | |
| How to Illuminate the Druggable Genome Using Pharos. | Sheils, Timothy; Mathias, Stephen L; Siramshetty, Vishal B; Bocci, Giovanni; Bologa, Cristian G; Yang, Jeremy J; Waller, Anna; Southall, Noel; Nguyen, Dac-Trung; Oprea, Tudor I | Current protocols in bioinformatics. | 2020 Mar; | 31898878 | |
| Dermal sheath contraction powers stem cell niche relocation during hair cycle regression. | Heitman, Nicholas; Sennett, Rachel; Mok, Ka-Wai; Saxena, Nivedita; Srivastava, Devika; Martino, Pieter; Grisanti, Laura; Wang, Zichen; Ma'ayan, Avi; Rompolas, Panteleimon; Rendl, Michael | Science (New York, N.Y.). | 2020 Jan 10; | 31857493 | |
| Research Techniques Made Simple: Molecular Docking in Dermatology - A Foray into In Silico Drug Discovery. | Issa, Naiem T; Badiavas, Evangelos V; Schürer, Stephan | The Journal of investigative dermatology. | 2019 12; | 31753122 | |
| LINCS Data Portal 2.0: next generation access point for perturbation-response signatures. | Stathias, Vasileios; Turner, John; Koleti, Amar; Vidovic, Dusica; Cooper, Daniel; Fazel-Najafabadi, Mehdi; Pilarczyk, Marcin; Terryn, Raymond; Chung, Caty; Umeano, Afoma; Clarke, Daniel J B; Lachmann, Alexander; Evangelista, John Erol; Ma'ayan, Avi; Medvedovic, Mario; Schürer, Stephan C | Nucleic acids research. | 2020 01 08; | 31701147 | |
| ADCK3/COQ8A: the choice target of the UbiB protein kinase-like family. | Asquith, Christopher R M; Murray, Nathan H; Pagliarini, David J | Nature reviews. Drug discovery. | 2019 10; | 31673128 | |
| Single-cell immune landscape of human atherosclerotic plaques. | Fernandez, Dawn M; Rahman, Adeeb H; Fernandez, Nicolas F; Chudnovskiy, Aleksey; Amir, El-Ad David; Amadori, Letizia; Khan, Nayaab S; Wong, Christine K; Shamailova, Roza; Hill, Christopher A; Wang, Zichen; Remark, Romain; Li, Jennifer R; Pina, Christian; Faries, Christopher; Awad, Ahmed J; Moss, Noah; Bjorkegren, Johan L M; Kim-Schulze, Seunghee; Gnjatic, Sacha; Ma'ayan, Avi; Mocco, J; Faries, Peter; Merad, Miriam; Giannarelli, Chiara | Nature medicine. | 2019 10; | 31591603 | |
| Can BDDCS illuminate targets in drug design? | Bocci, Giovanni; Benet, Leslie Z; Oprea, Tudor I | Drug discovery today. | 2019 Dec; | 31585170 | |
| PDBe-KB: a community-driven resource for structural and functional annotations. | PDBe-KB consortium | Nucleic acids research. | 2020 Jan 08; | 31584092 | |
| Recombination drives the evolution of mutational robustness. | Singhal, Sonia; Gomez, Shawn M; Burch, Christina L | Current opinion in systems biology. | 2019 Feb; | 31572829 | |
| Zebrafish behavioural profiling identifies GABA and serotonin receptor ligands related to sedation and paradoxical excitation. | McCarroll, Matthew N; Gendelev, Leo; Kinser, Reid; Taylor, Jack; Bruni, Giancarlo; Myers-Turnbull, Douglas; Helsell, Cole; Carbajal, Amanda; Rinaldi, Capria; Kang, Hye Jin; Gong, Jung Ho; Sello, Jason K; Tomita, Susumu; Peterson, Randall T; Keiser, Michae | Nature communications. | 2019 Sep 09; | 31501447 | |
| VEGAS as a Platform for Facile Directed Evolution in Mammalian Cells. | English, Justin G; Olsen, Reid H J; Lansu, Katherine; Patel, Michael; White, Karoline; Cockrell, Adam S; Singh, Darshan; Strachan, Ryan T; Wacker, Daniel; Roth, Bryan L | Cell. | 2019 Aug 08; | 31398329 | |
| Identification of hyper-rewired genomic stress non-oncogene addiction genes across 15 cancer types. | Hjaltelin, Jessica Xin; Izarzugaza, Jose M G; Jensen, Lars Juhl; Russo, Francesco; Westergaard, David; Brunak, Søren | NPJ systems biology and applications. | 2019; | 31396397 | |
| Visualization of drug target interactions in the contexts of pathways and networks with ReactomeFIViz. | Blucher, Aurora S; McWeeney, Shannon K; Stein, Lincoln; Wu, Guanming | F1000Research. | 2019; | 31372215 | |
| Kinome profiling of non-Hodgkin lymphoma identifies Tyro3 as a therapeutic target in primary effusion lymphoma. | Wong, Jason P; Stuhlmiller, Timothy J; Giffin, Louise C; Lin, Carolina; Bigi, Rachele; Zhao, Jichen; Zhang, Weihe; Bravo Cruz, Ariana G; Park, Steven I; Earp, H Shelton; Dittmer, Dirk P; Frye, Stephen V; Wang, Xiaodong; Johnson, Gary L; Damania, Blossom | Proceedings of the National Academy of Sciences of the United States of America. | 2019 Aug 13; | 31346082 | |
| Integrative analysis of loss-of-function variants in clinical and genomic data reveals novel genes associated with cardiovascular traits. | Glicksberg, Benjamin S; Amadori, Letizia; Akers, Nicholas K; Sukhavasi, Katyayani; Franzén, Oscar; Li, Li; Belbin, Gillian M; Ayers, Kristin L; Shameer, Khader; Badgeley, Marcus A; Johnson, Kipp W; Readhead, Ben; Darrow, Bruce J; Kenny, Eimear E; Betsholtz, Christer; Ermel, Raili; Skogsberg, Josefin; Ruusalepp, Arno; Schadt, Eric E; Dudley, Joel T; Ren, Hongxia; Kovacic, Jason C; Giannarelli, Chiara; Li, Shuyu D; Björkegren, Johan L M; Chen, Rong | BMC medical genomics. | 2019 07 25; | 31345219 | |
| The crystal structure of the protein kinase HIPK2 reveals a unique architecture of its CMGC-insert region. | Agnew, Christopher; Liu, Lijun; Liu, Shu; Xu, Wei; You, Liang; Yeung, Wayland; Kannan, Natarajan; Jablons, David; Jura, Natalia | The Journal of biological chemistry. | 2019 09 13; | 31341017 | |
| Design, Synthesis, and Characterization of Ogerin-Based Positive Allosteric Modulators for G Protein-Coupled Receptor 68 (GPR68). | Yu, Xufen; Huang, Xi-Ping; Kenakin, Terry P; Slocum, Samuel T; Chen, Xin; Martini, Michael L; Liu, Jing; Jin, Jian | Journal of medicinal chemistry. | 2019 08 22; | 31298539 | |
| VEGAS as a Platform for Facile Directed Evolution in Mammalian Cells. | English, Justin G; Olsen, Reid H J; Lansu, Katherine; Patel, Michael; White, Karoline; Cockrell, Adam S; Singh, Darshan; Strachan, Ryan T; Wacker, Daniel; Roth, Bryan L | Cell. | 2019 Jul 25; | 31280962 | |
| OSCI: standardized stem cell ontology representation and use cases for stem cell investigation. | He, Yongqun; Duncan, William D; Cooper, Daniel J; Hansen, Jens; Iyengar, Ravi; Ong, Edison; Walker, Kendal; Tibi, Omar; Smith, Sam; Serra, Lucas M; Zheng, Jie; Sarntivijai, Sirarat; Schürer, Stephan; O'Shea, K Sue; Diehl, Alexander D | BMC bioinformatics. | 2019 Apr 25; | 31272389 | |
| Exploring the dark genome: implications for precision medicine. | Oprea, Tudor I | Mammalian genome : official journal of the International Mammalian Genome Society. | 2019 Aug; | 31270560 | |
| Molecular pharmacology of metabotropic receptors targeted by neuropsychiatric drugs. | Roth, Bryan L | Nature structural & molecular biology. | 2019 Jul; | 31270468 | |
| The human endogenous metabolome as a pharmacology baseline for drug discovery. | Bofill, Andreu; Jalencas, Xavier; Oprea, Tudor I; Mestres, Jordi | Drug discovery today. | 2019 09; | 31226432 | |
| CoCoScore: context-aware co-occurrence scoring for text mining applications using distant supervision. | Junge, Alexander; Jensen, Lars Juhl | Bioinformatics (Oxford, England). | 2020 Jan 01; | 31199464 | |
| ChEA3: transcription factor enrichment analysis by orthogonal omics integration. | Keenan, Alexandra B; Torre, Denis; Lachmann, Alexander; Leong, Ariel K; Wojciechowicz, Megan L; Utti, Vivian; Jagodnik, Kathleen M; Kropiwnicki, Eryk; Wang, Zichen; Ma'ayan, Avi | Nucleic acids research. | 2019 Jul 02; | 31114921 | |
| Geneshot: search engine for ranking genes from arbitrary text queries. | Lachmann, Alexander; Schilder, Brian M; Wojciechowicz, Megan L; Torre, Denis; Kuleshov, Maxim V; Keenan, Alexandra B; Ma'ayan, Avi | Nucleic acids research. | 2019 Jul 02; | 31114885 | |
| modEnrichr: a suite of gene set enrichment analysis tools for model organisms. | Kuleshov, Maxim V; Diaz, Jennifer E L; Flamholz, Zachary N; Keenan, Alexandra B; Lachmann, Alexander; Wojciechowicz, Megan L; Cagan, Ross L; Ma'ayan, Avi | Nucleic acids research. | 2019 Jul 02; | 31069376 | |
| Publisher Correction: Structural basis of ligand recognition at the human MT1 melatonin receptor. | Stauch, Benjamin; Johansson, Linda C; McCorvy, John D; Patel, Nilkanth; Han, Gye Won; Huang, Xi-Ping; Gati, Cornelius; Batyuk, Alexander; Slocum, Samuel T; Ishchenko, Andrii; Brehm, Wolfgang; White, Thomas A; Michaelian, Nairie; Madsen, Caleb; Zhu, Lan; Grant, Thomas D; Grandner, Jessica M; Shiriaeva, Anna; Olsen, Reid H J; Tribo, Alexandra R; Yous, Saïd; Stevens, Raymond C; Weierstall, Uwe; Katritch, Vsevolod; Roth, Bryan L; Liu, Wei; Cherezov, Vadim | Nature. | 2019 May; | 31048811 | |
| A Perspective on Extreme Open Science: Companies Sharing Compounds without Restriction. | Drewry, David H; Wells, Carrow I; Zuercher, William J; Willson, Timothy M | SLAS discovery : advancing life sciences R & D. | 2019 Jun; | 31034310 | |
| Structural basis of ligand recognition at the human MT1 melatonin receptor. | Stauch, Benjamin; Johansson, Linda C; McCorvy, John D; Patel, Nilkanth; Han, Gye Won; Huang, Xi-Ping; Gati, Cornelius; Batyuk, Alexander; Slocum, Samuel T; Ishchenko, Andrii; Brehm, Wolfgang; White, Thomas A; Michaelian, Nairie; Madsen, Caleb; Zhu, Lan; Grant, Thomas D; Grandner, Jessica M; Shiriaeva, Anna; Olsen, Reid H J; Tribo, Alexandra R; Yous, Saïd; Stevens, Raymond C; Weierstall, Uwe; Katritch, Vsevolod; Roth, Bryan L; Liu, Wei; Cherezov, Vadim | Nature. | 2019 May; | 31019306 | |
| XFEL structures of the human MT2 melatonin receptor reveal the basis of subtype selectivity. | Johansson, Linda C; Stauch, Benjamin; McCorvy, John D; Han, Gye Won; Patel, Nilkanth; Huang, Xi-Ping; Batyuk, Alexander; Gati, Cornelius; Slocum, Samuel T; Li, Chufeng; Grandner, Jessica M; Hao, Shuming; Olsen, Reid H J; Tribo, Alexandra R; Zaare, Sahba; Zhu, Lan; Zatsepin, Nadia A; Weierstall, Uwe; Yous, Saïd; Stevens, Raymond C; Liu, Wei; Roth, Bryan L; Katritch, Vsevolod; Cherezov, Vadim | Nature. | 2019 May; | 31019305 | |
| Improving the Utility of the Tox21 Dataset by Deep Metadata Annotations and Constructing Reusable Benchmarked Chemical Reference Signatures. | Cooper, Daniel J; Schürer, Stephan | Molecules (Basel, Switzerland). | 2019 Apr 23; | 31018579 | |
| GSK2801, A BAZ2/BRD9 Bromodomain Inhibitor, Synergizes with BET Inhibitors to Induce Apoptosis in Triple-Negative Breast Cancer. | Bevill, Samantha M; Olivares-Quintero, Jose F; Sciaky, Noah; Golitz, Brian T; Singh, Darshan; Beltran, Adriana S; Rashid, Naim U; Stuhlmiller, Timothy J; Hale, Andrew; Moorman, Nathaniel J; Santos, Charlene M; Angus, Steven P; Zawistowski, Jon S; Johnson, Gary L | Molecular cancer research : MCR. | 2019 Apr 18; | 31000582 | |
| Engineering a haematopoietic stem cell niche by revitalizing mesenchymal stromal cells. | Nakahara, Fumio; Borger, Daniel K; Wei, Qiaozhi; Pinho, Sandra; Maryanovich, Maria; Zahalka, Ali H; Suzuki, Masako; Cruz, Cristian D; Wang, Zichen; Xu, Chunliang; Boulais, Philip E; Ma'ayan, Avi; Greally, John M; Frenette, Paul S | Nature cell biology. | 2019 Apr 15; | 30988422 | |
| D2 Dopamine Receptor G Protein-Biased Partial Agonists Based on Cariprazine. | Shen, Yudao; McCorvy, John D; Martini, Michael L; Rodriguiz, Ramona M; Pogorelov, Vladimir M; Ward, Karen M; Wetsel, William C; Liu, Jing; Roth, Bryan L; Jin, Jian | Journal of medicinal chemistry. | 2019 May 09; | 30964661 | |
| Cheminformatics Tools for Analyzing and Designing Optimized Small-Molecule Collections and Libraries. | Moret, Nienke; Clark, Nicholas A; Hafner, Marc; Wang, Yuan; Lounkine, Eugen; Medvedovic, Mario; Wang, Jinhua; Gray, Nathanael; Jenkins, Jeremy; Sorger, Peter K | Cell chemical biology. | 2019 Mar 12; | 30956147 | |
| Discovery of Covalent CDK14 Inhibitors with Pan-TAIRE Family Specificity. | Ferguson, Fleur M; Doctor, Zainab M; Ficarro, Scott B; Browne, Christopher M; Marto, Jarrod A; Johnson, Jared L; Yaron, Tomer M; Cantley, Lewis C; Kim, Nam Doo; Sim, Taebo; Berberich, Matthew J; Kalocsay, Marian; Sorger, Peter K; Gray, Nathanael S | Cell chemical biology. | 2019 Mar 11; | 30930164 | |
| Defining Structure-Functional Selectivity Relationships (SFSR) for a Class of Non-Catechol Dopamine D1 Receptor Agonists. | Martini, Michael L; Liu, Jing; Ray, Caroline; Yu, Xufen; Huang, Xi-Ping; Urs, Aarti; Urs, Nikhil; McCorvy, John D; Caron, Marc G; Roth, Bryan L; Jin, Jian | Journal of medicinal chemistry. | 2019 Apr 11; | 30875219 | |
| DREADD Agonist 21 Is an Effective Agonist for Muscarinic-Based DREADDs in Vitro and in Vivo. | Thompson, Karen J; Khajehali, Elham; Bradley, Sophie J; Navarrete, Jovana S; Huang, Xi Ping; Slocum, Samuel; Jin, Jian; Liu, Jing; Xiong, Yan; Olsen, Reid H J; Diberto, Jeffrey F; Boyt, Kristen M; Pina, Melanie M; Pati, Dipanwita; Molloy, Colin; Bundgaard | ACS pharmacology & translational science. | 2018 Sep 14; | 30868140 | |
| How to Prepare a Compound Collection Prior to Virtual Screening. | Bologa, Cristian G; Ursu, Oleg; Oprea, Tudor I | Methods in molecular biology (Clifton, N.J.). | 2019; | 30848459 | |
| Leveraging Big Data to Transform Drug Discovery. | Glicksberg, Benjamin S; Li, Li; Chen, Rong; Dudley, Joel; Chen, Bin | Methods in molecular biology (Clifton, N.J.). | 2019; | 30848458 | |
| How to Develop a Drug Target Ontology: KNowledge Acquisition and Representation Methodology (KNARM). | Küçük McGinty, Hande; Visser, Ubbo; Schürer, Stephan | Methods in molecular biology (Clifton, N.J.). | 2019; | 30848456 | |
| How structure informs and transforms chemogenetics. | Roth, Bryan L | Current opinion in structural biology. | 2019 08; | 30818201 | |
| An African-specific haplotype in MRGPRX4 is associated with menthol cigarette smoking. | Kozlitina, Julia; Risso, Davide; Lansu, Katherine; Olsen, Reid Hans Johnson; Sainz, Eduardo; Luiselli, Donata; Barik, Arnab; Frigerio-Domingues, Carlos; Pagani, Luca; Wooding, Stephen; Kirchner, Thomas; Niaura, Ray; Roth, Bryan; Drayna, Dennis | PLoS genetics. | 2019 02; | 30768591 | |
| SGC-GAK-1: A Chemical Probe for Cyclin G Associated Kinase (GAK). | Asquith, Christopher R M; Berger, Benedict-Tilman; Wan, Jing; Bennett, James M; Capuzzi, Stephen J; Crona, Daniel J; Drewry, David H; East, Michael P; Elkins, Jonathan M; Fedorov, Oleg; Godoi, Paulo H; Hunter, Debra M; Knapp, Stefan; Müller, Susanne; Torrice, Chad D; Wells, Carrow I; Earp, H Shelton; Willson, Timothy M; Zuercher, William J | Journal of medicinal chemistry. | 2019 Mar 14; | 30768268 | |
| Predicting opioid dependence from electronic health records with machine learning. | Ellis, Randall J; Wang, Zichen; Genes, Nicholas; Ma'ayan, Avi | BioData mining. | 2019; | 30728857 | |
| Ultra-large library docking for discovering new chemotypes. | Lyu, Jiankun; Wang, Sheng; Balius, Trent E; Singh, Isha; Levit, Anat; Moroz, Yurii S; O'Meara, Matthew J; Che, Tao; Algaa, Enkhjargal; Tolmachova, Kateryna; Tolmachev, Andrey A; Shoichet, Brian K; Roth, Bryan L; Irwin, John J | Nature. | 2019 Feb; | 30728502 | |
| WNT Activates the AAK1 Kinase to Promote Clathrin-Mediated Endocytosis of LRP6 and Establish a Negative Feedback Loop. | Agajanian, Megan J; Walker, Matthew P; Axtman, Alison D; Ruela-de-Sousa, Roberta R; Serafin, D Stephen; Rabinowitz, Alex D; Graham, David M; Ryan, Meagan B; Tamir, Tigist; Nakamichi, Yuko; Gammons, Melissa V; Bennett, James M; Couñago, Rafael M; Drewry, David H; Elkins, Jonathan M; Gileadi, Carina; Gileadi, Opher; Godoi, Paulo H; Kapadia, Nirav; Müller, Susanne; Santiago, André S; Sorrell, Fiona J; Wells, Carrow I; Fedorov, Oleg; Willson, Timothy M; Zuercher, William J; Major, Michael B | Cell reports. | 2019 Jan 02; | 30605688 | |
| Dermal Condensate Niche Fate Specification Occurs Prior to Formation and Is Placode Progenitor Dependent. | Mok, Ka-Wai; Saxena, Nivedita; Heitman, Nicholas; Grisanti, Laura; Srivastava, Devika; Muraro, Mauro J; Jacob, Tina; Sennett, Rachel; Wang, Zichen; Su, Yutao; Yang, Lu M; Ma'ayan, Avi; Ornitz, David M; Kasper, Maria; Rendl, Michael | Developmental cell. | 2019 Jan 07; | 30595537 | |
| Mining data and metadata from the gene expression omnibus. | Wang, Zichen; Lachmann, Alexander; Ma'ayan, Avi | Biophysical reviews. | 2019 Feb; | 30594974 | |
| Drug and disease signature integration identifies synergistic combinations in glioblastoma. | Stathias, Vasileios; Jermakowicz, Anna M; Maloof, Marie E; Forlin, Michele; Walters, Winston; Suter, Robert K; Durante, Michael A; Williams, Sion L; Harbour, J William; Volmar, Claude-Henry; Lyons, Nicholas J; Wahlestedt, Claes; Graham, Regina M; Ivan, Michael E; Komotar, Ricardo J; Sarkaria, Jann N; Subramanian, Aravind; Golub, Todd R; Schürer, Stephan C; Ayad, Nagi G | Nature communications. | 2018 12 14; | 30552330 | |
| Far away from the lamppost. | Oprea, Tudor I; Jan, Lily; Johnson, Gary L; Roth, Bryan L; Ma'ayan, Avi; Schürer, Stephan; Shoichet, Brian K; Sklar, Larry A; McManus, Michael T | PLoS biology. | 2018 Dec; | 30532236 | |
| A Comparative Study of the Pharmacokinetics of Clozapine N-Oxide and Clozapine N-Oxide Hydrochloride Salt in Rhesus Macaques. | Allen, Daicia C; Carlson, Timothy L; Xiong, Yan; Jin, Jian; Grant, Kathleen A; Cuzon Carlson, Verginia C | The Journal of pharmacology and experimental therapeutics. | 2019 Feb; | 30523062 | |
| Temporal proteomic profiling of postnatal human cortical development. | Breen, Michael S; Ozcan, Sureyya; Ramsey, Jordan M; Wang, Zichen; Ma'ayan, Avi; Rustogi, Nitin; Gottschalk, Michael G; Webster, Maree J; Weickert, Cynthia Shannon; Buxbaum, Joseph D; Bahn, Sabine | Translational psychiatry. | 2018 Dec 05; | 30518843 | |
| BioJupies: Automated Generation of Interactive Notebooks for RNA-Seq Data Analysis in the Cloud. | Torre, Denis; Lachmann, Alexander; Ma'ayan, Avi | Cell systems. | 2018 Nov 08; | 30447998 | |
| Critical period plasticity-related transcriptional aberrations in schizophrenia and bipolar disorder. | Smith, Milo R; Readhead, Ben; Dudley, Joel T; Morishita, Hirofumi | Schizophrenia research. | 2019 05; | 30442475 | |
| Integrative bioinformatics identifies postnatal lead (Pb) exposure disrupts developmental cortical plasticity. | Smith, Milo R; Yevoo, Priscilla; Sadahiro, Masato; Austin, Christine; Amarasiriwardena, Chitra; Awawda, Mahmoud; Arora, Manish; Dudley, Joel T; Morishita, Hirofumi | Scientific reports. | 2018 11 06; | 30401819 | |
| DrugCentral 2018: an update. | Ursu, Oleg; Holmes, Jayme; Bologa, Cristian G; Yang, Jeremy J; Mathias, Stephen L; Stathias, Vasileios; Nguyen, Dac-Trung; Schürer, Stephan; Oprea, Tudor | Nucleic acids research. | 2018 Oct 29; | 30371892 | |
| Darkness in the Human Gene and Protein Function Space: Widely Modest or Absent Illumination by the Life Science Literature and the Trend for Fewer Protein Function Discoveries Since 2000. | Sinha, Swati; Eisenhaber, Birgit; Jensen, Lars Juhl; Kalbuaji, Bharata; Eisenhaber, Frank | Proteomics. | 2018 Nov; | 30265449 | |
| Covalent inhibitors of EGFR family protein kinases induce degradation of human Tribbles 2 (TRIB2) pseudokinase in cancer cells. | Foulkes, Daniel M; Byrne, Dominic P; Yeung, Wayland; Shrestha, Safal; Bailey, Fiona P; Ferries, Samantha; Eyers, Claire E; Keeshan, Karen; Wells, Carrow; Drewry, David H; Zuercher, William J; Kannan, Natarajan; Eyers, Patrick A | Science signaling. | 2018 Sep 25; | 30254057 | |
| Coral: Clear and Customizable Visualization of Human Kinome Data. | Metz, Kathleen S; Deoudes, Erika M; Berginski, Matthew E; Jimenez-Ruiz, Ivan; Aksoy, Bulent Arman; Hammerbacher, Jeff; Gomez, Shawn M; Phanstiel, Douglas H | Cell systems. | 2018 09 26; | 30172842 | |
| Drug Gene Budger (DGB): an application for ranking drugs to modulate a specific gene based on transcriptomic signatures. | Wang, Zichen; He, Edward; Sani, Kevin; Jagodnik, Kathleen M; Silverstein, Moshe C; Ma'ayan, Avi | Bioinformatics (Oxford, England). | 2019 Apr 01; | 30169739 | |
| Podocyte-Specific Induction of Krüppel-Like Factor 15 Restores Differentiation Markers and Attenuates Kidney Injury in Proteinuric Kidney Disease. | Guo, Yiqing; Pace, Jesse; Li, Zhengzhe; Ma'ayan, Avi; Wang, Zichen; Revelo, Monica P; Chen, Edward; Gu, Xiangchen; Attalah, Ahmed; Yang, Yaqi; Estrada, Chelsea; Yang, Vincent W; He, John C; Mallipattu, Sandeep K | Journal of the American Society of Nephrology : JASN. | 2018 Aug 24; | 30143559 | |
| Gut Microbial ?-Glucuronidase Inhibition via Catalytic Cycle Interception. | Pellock, Samuel J; Creekmore, Benjamin C; Walton, William G; Mehta, Naimee; Biernat, Kristen A; Cesmat, Andrew P; Ariyarathna, Yamuna; Dunn, Zachary D; Li, Bo; Jin, Jian; James, Lindsey I; Redinbo, Matthew R | ACS central science. | 2018 Jul 25; | 30062115 | |
| Artificial Intelligence in Cardiology. | Johnson, Kipp W; Torres Soto, Jessica; Glicksberg, Benjamin S; Shameer, Khader; Miotto, Riccardo; Ali, Mohsin; Ashley, Euan; Dudley, Joel T | Journal of the American College of Cardiology. | 2018 06 12; | 29880128 | |
| eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks. | Clarke, Daniel J B; Kuleshov, Maxim V; Schilder, Brian M; Torre, Denis; Duffy, Mary E; Keenan, Alexandra B; Lachmann, Alexander; Feldmann, Axel S; Gundersen, Gregory W; Silverstein, Moshe C; Wang, Zichen; Ma'ayan, Avi | Nucleic acids research. | 2018 Jul 02; | 29800326 | |
| Integration of protein phosphorylation, acetylation, and methylation data sets to outline lung cancer signaling networks. | Grimes, Mark; Hall, Benjamin; Foltz, Lauren; Levy, Tyler; Rikova, Klarisa; Gaiser, Jeremiah; Cook, William; Smirnova, Ekaterina; Wheeler, Travis; Clark, Neil R; Lachmann, Alexander; Zhang, Bin; Hornbeck, Peter; Ma'ayan, Avi; Comb, Michael | Science signaling. | 2018 05 22; | 29789295 | |
| Application of Integrated Drug Screening/Kinome Analysis to Identify Inhibitors of Gemcitabine-Resistant Pancreatic Cancer Cell Growth. | Krulikas, Linas J; McDonald, Ian M; Lee, Benjamin; Okumu, Denis O; East, Michael P; Gilbert, Thomas S K; Herring, Laura E; Golitz, Brian T; Wells, Carrow I; Axtman, Allison D; Zuercher, William J; Willson, Timothy M; Kireev, Dmitri; Yeh, Jen Jen; Johnson, Gary L; Baines, Antonio T; Graves, Lee M | SLAS discovery : advancing life sciences R & D. | 2018 09; | 29742358 | |
| A proteomics landscape of circadian clock in mouse liver. | Wang, Yunzhi; Song, Lei; Liu, Mingwei; Ge, Rui; Zhou, Quan; Liu, Wanlin; Li, Ruiyang; Qie, Jingbo; Zhen, Bei; Wang, Yi; He, Fuchu; Qin, Jun; Ding, Chen | Nature communications. | 2018 Apr 19; | 29674717 | |
| Proteomic analysis defines kinase taxonomies specific for subtypes of breast cancer. | Collins, Kyla A L; Stuhlmiller, Timothy J; Zawistowski, Jon S; East, Michael P; Pham, Trang T; Hall, Claire R; Goulet, Daniel R; Bevill, Samantha M; Angus, Steven P; Velarde, Sara H; Sciaky, Noah; Oprea, Tudor I; Graves, Lee M; Johnson, Gary L; Gomez, Shawn M | Oncotarget. | 2018 Mar 20; | 29643987 | |
| Massive mining of publicly available RNA-seq data from human and mouse. | Lachmann, Alexander; Torre, Denis; Keenan, Alexandra B; Jagodnik, Kathleen M; Lee, Hoyjin J; Wang, Lily; Silverstein, Moshe C; Ma'ayan, Avi | Nature communications. | ; | 29636450 | |
| Unexplored therapeutic opportunities in the human genome. | Oprea, Tudor I; Bologa, Cristian G; Brunak, Søren; Campbell, Allen; Gan, Gregory N; Gaulton, Anna; Gomez, Shawn M; Guha, Rajarshi; Hersey, Anne; Holmes, Jayme; Jadhav, Ajit; Jensen, Lars Juhl; Johnson, Gary L; Karlson, Anneli; Leach, Andrew R; Ma'ayan, Avi; Malovannaya, Anna; Mani, Subramani; Mathias, Steven L; McManus, Michael T; Meehan, Terrence F; von Mering, Christian; Muthas, Daniel; Nguyen, Dac-Trung; Overington, John P; Papadatos, George; Qin, Jun; Reich, Christian; Roth, Bryan L; Schürer, Stephan C; Simeonov, Anton; Sklar, Larry A; Southall, Noel; Tomita, Susumu; Tudose, Ilinca; Ursu, Oleg; Vidovic, Du?ica; Waller, Anna; Westergaard, David; Yang, Jeremy J; Zahoránszky-Köhalmi, Gergely | Nature reviews. Drug discovery. | 2018 May; | 29567993 | |
| A proteomic landscape of diffuse-type gastric cancer. | Ge, Sai; Xia, Xia; Ding, Chen; Zhen, Bei; Zhou, Quan; Feng, Jinwen; Yuan, Jiajia; Chen, Rui; Li, Yumei; Ge, Zhongqi; Ji, Jiafu; Zhang, Lianhai; Wang, Jiayuan; Li, Zhongwu; Lai, Yumei; Hu, Ying; Li, Yanyan; Li, Yilin; Gao, Jing; Chen, Lin; Xu, Jianming; Zh | Nature communications. | 2018 03 08; | 29520031 | |
| The Transcriptionally Permissive Chromatin State of Embryonic Stem Cells Is Acutely Tuned to Translational Output. | Bulut-Karslioglu, Aydan; Macrae, Trisha A; Oses-Prieto, Juan A; Covarrubias, Sergio; Percharde, Michelle; Ku, Gregory; Diaz, Aaron; McManus, Michael T; Burlingame, Alma L; Ramalho-Santos, Miguel | Cell stem cell. | 2018 03 01; | 29499153 | |
| Datasets2Tools, repository and search engine for bioinformatics datasets, tools and canned analyses. | Torre, Denis; Krawczuk, Patrycja; Jagodnik, Kathleen M; Lachmann, Alexander; Wang, Zichen; Wang, Lily; Kuleshov, Maxim V; Ma'ayan, Avi | Scientific data. | 2018 Feb 27; | 29485625 | |
| Unexplored therapeutic opportunities in the human genome. | Oprea, Tudor I; Bologa, Cristian G; Brunak, Søren; Campbell, Allen; Gan, Gregory N; Gaulton, Anna; Gomez, Shawn M; Guha, Rajarshi; Hersey, Anne; Holmes, Jayme; Jadhav, Ajit; Jensen, Lars Juhl; Johnson, Gary L; Karlson, Anneli; Leach, Andrew R; Ma'ayan, Avi; Malovannaya, Anna; Mani, Subramani; Mathias, Stephen L; McManus, Michael T; Meehan, Terrence F; von Mering, Christian; Muthas, Daniel; Nguyen, Dac-Trung; Overington, John P; Papadatos, George; Qin, Jun; Reich, Christian; Roth, Bryan L; Schürer, Stephan C; Simeonov, Anton; Sklar, Larry A; Southall, Noel; Tomita, Susumu; Tudose, Ilinca; Ursu, Oleg; Vidovic, Du?ica; Waller, Anna; Westergaard, David; Yang, Jeremy J; Zahoránszky-Köhalmi, Gergely | Nature reviews. Drug discovery. | 2018 May; | 29472638 | |
| Mass Spectrometry-Based Proteomics Reveals Potential Roles of NEK9 and MAP2K4 in Resistance to PI3K Inhibition in Triple-Negative Breast Cancers. | Mundt, Filip; Rajput, Sandeep; Li, Shunqiang; Ruggles, Kelly V; Mooradian, Arshag D; Mertins, Philipp; Gillette, Michael A; Krug, Karsten; Guo, Zhanfang; Hoog, Jeremy; Erdmann-Gilmore, Petra; Primeau, Tina; Huang, Shixia; Edwards, Dean P; Wang, Xiaowei; Wang, Xuya; Kawaler, Emily; Mani, D R; Clauser, Karl R; Gao, Feng; Luo, Jingqin; Davies, Sherri R; Johnson, Gary L; Huang, Kuan-Lin; Yoon, Christopher J; Ding, Li; Fenyö, David; Ellis, Matthew J; Townsend, R Reid; Held, Jason M; Carr, Steven A; Ma, Cynthia X | Cancer research. | 2018 05 15; | 29472518 | |
| L1000FWD: fireworks visualization of drug-induced transcriptomic signatures. | Wang, Zichen; Lachmann, Alexander; Keenan, Alexandra B; Ma'ayan, Avi | Bioinformatics (Oxford, England). | ; | 29420694 | |
| Machine learning in cardiovascular medicine: are we there yet? | Shameer, Khader; Johnson, Kipp W; Glicksberg, Benjamin S; Dudley, Joel T; Sengupta, Partho P | Heart (British Cardiac Society). | 2018 07; | 29352006 | |
| Dual gene activation and knockout screen reveals directional dependencies in genetic networks. | Boettcher, Michael; Tian, Ruilin; Blau, James A; Markegard, Evan; Wagner, Ryan T; Wu, David; Mo, Xiulei; Biton, Anne; Zaitlen, Noah; Fu, Haian; McCormick, Frank; Kampmann, Martin; McManus, Michael T | Nature biotechnology. | 2018 Feb; | 29334369 | |
| Integration of pan-cancer transcriptomics with RPPA proteomics reveals mechanisms of epithelial-mesenchymal transition. | Koplev, Simon; Lin, Katie; Dohlman, Anders B; Ma'ayan, Avi | PLoS computational biology. | 2018 01; | 29293502 | |
| Structure-inspired design of ?-arrestin-biased ligands for aminergic GPCRs. | McCorvy, John D; Butler, Kyle V; Kelly, Brendan; Rechsteiner, Katie; Karpiak, Joel; Betz, Robin M; Kormos, Bethany L; Shoichet, Brian K; Dror, Ron O; Jin, Jian; Roth, Bryan L | Nature chemical biology. | 2017 Dec 11; | 29227473 | |
| Cell-specific prediction and application of drug-induced gene expression profiles. | Hodos, Rachel; Zhang, Ping; Lee, Hao-Chih; Duan, Qiaonan; Wang, Zichen; Clark, Neil R; Ma'ayan, Avi; Wang, Fei; Kidd, Brian; Hu, Jianying; Sontag, David; Dudley, Joel | Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. | 2018; | 29218867 | |
| Quantitative, Wide-Spectrum Kinase Profiling in Live Cells for Assessing the Effect of Cellular ATP on Target Engagement. | Vasta, James D; Corona, Cesear R; Wilkinson, Jennifer; Zimprich, Chad A; Hartnett, James R; Ingold, Morgan R; Zimmerman, Kristopher; Machleidt, Thomas; Kirkland, Thomas A; Huwiler, Kristin G; Ohana, Rachel Friedman; Slater, Michael; Otto, Paul; Cong, Mei; | Cell chemical biology. | 2018 02 15; | 29174542 | |
| Drug target ontology to classify and integrate drug discovery data. | Lin, Yu; Mehta, Saurabh; Küçük-McGinty, Hande; Turner, John Paul; Vidovic, Dusica; Forlin, Michele; Koleti, Amar; Nguyen, Dac-Trung; Jensen, Lars Juhl; Guha, Rajarshi; Mathias, Stephen L; Ursu, Oleg; Stathias, Vasileios; Duan, Jianbin; Nabizadeh, Nooshin; | Journal of biomedical semantics. | 2017 Nov 09; | 29122012 | |
| Predicting age by mining electronic medical records with deep learning characterizes differences between chronological and physiological age. | Wang, Zichen; Li, Li; Glicksberg, Benjamin S; Israel, Ariel; Dudley, Joel T; Ma'ayan, Avi | Journal of biomedical informatics. | 2017 Dec; | 29113935 | |
| Common and cell-type specific responses to anti-cancer drugs revealed by high throughput transcript profiling. | Niepel, Mario; Hafner, Marc; Duan, Qiaonan; Wang, Zichen; Paull, Evan O; Chung, Mirra; Lu, Xiaodong; Stuart, Joshua M; Golub, Todd R; Subramanian, Aravind; Ma'ayan, Avi; Sorger, Peter K | Nature communications. | 2017 Oct 30; | 29084964 | |
| Identification and Optimization of 4-Anilinoquinolines as Inhibitors of Cyclin?G Associated Kinase. | Asquith, Christopher R M; Laitinen, Tuomo; Bennett, James M; Godoi, Paulo H; East, Michael P; Tizzard, Graham J; Graves, Lee M; Johnson, Gary L; Dornsife, Ronna E; Wells, Carrow I; Elkins, Jonathan M; Willson, Timothy M; Zuercher, William J | ChemMedChem. | 2018 Jan 08; | 29072804 | |
| D4dopamine receptor high-resolution structures enable the discovery of selective agonists. | Wang, Sheng; Wacker, Daniel; Levit, Anat; Che, Tao; Betz, Robin M; McCorvy, John D; Venkatakrishnan, A J; Huang, Xi-Ping; Dror, Ron O; Shoichet, Brian K; Roth, Bryan L | Science (New York, N.Y.). | 2017 10 20; | 29051383 | |
| Discovery of new GPCR ligands to illuminate new biology. | Roth, Bryan L; Irwin, John J; Shoichet, Brian K | Nature chemical biology. | 2017 Nov; | 29045379 | |
| Biased signaling of the proton-sensing receptor OGR1 by benzodiazepines. | Pera, Tonio; Deshpande, Deepak A; Ippolito, Michael; Wang, Bin; Gavrila, Adelina; Michael, James V; Nayak, Ajay P; Tompkins, Eric; Farrell, Eleni; Kroeze, Wesley K; Roth, Bryan L; Panettieri Jr, Reynold A; Benovic, Jeffrey L; An, Steven S; Dulin, Nickolai O; Penn, Raymond B | FASEB journal : official publication of the Federation of American Societies for Experimental Biology. | ; | 29042451 | |
| Report and Application of a Tool Compound Data Set. | Butler, Kyle V; MacDonald, Ian A; Hathaway, Nathaniel A; Jin, Jian | Journal of chemical information and modeling. | 2017 Nov 02; | 29035535 | |
| Formalizing drug indications on the road to therapeutic intent. | Nelson, Stuart J; Oprea, Tudor I; Ursu, Oleg; Bologa, Cristian G; Zaveri, Amrapali; Holmes, Jayme; Yang, Jeremy J; Mathias, Stephen L; Mani, Subramani; Tuttle, Mark S; Dumontier, Michel | Journal of the American Medical Informatics Association : JAMIA. | 2017 Nov 01; | 29016968 | |
| Clustergrammer, a web-based heatmap visualization and analysis tool for high-dimensional biological data. | Fernandez, Nicolas F; Gundersen, Gregory W; Rahman, Adeeb; Grimes, Mark L; Rikova, Klarisa; Hornbeck, Peter; Ma'ayan, Avi | Scientific data. | 2017 Oct 10; | 28994825 | |
| A Bioinformatic Algorithm for Analyzing Cell Signaling Using Temporal Proteomic Data. | Zhang, Chunchao; Chen, Yue; Mao, Xinfang; Huang, Yin; Jung, Sung Yun; Jain, Antrix; Qin, Jun; Wang, Yi | Proteomics. | 2017 Nov; | 28940701 | |
| Complex systems biology. | Ma'ayan, Avi | Journal of the Royal Society, Interface. | 2017 Sep; | 28931638 | |
| A high-conductance chemo-optogenetic system based on the vertebrate channel Trpa1b. | Lam, Pui-Ying; Mendu, Suresh K; Mills, Robert W; Zheng, Baohui; Padilla, Hugo; Milan, David J; Desai, Bimal N; Peterson, Randall T | Scientific reports. | 2017 Sep 19; | 28928472 | |
| Assembly rules for GABAA receptor complexes in the brain. | Martenson, James S;Yamasaki, Tokiwa;Chaudhury, Nashid H;Albrecht, David;Tomita, Susumu | eLife | 28816653 | ||
| Progress towards a public chemogenomic set for protein kinases and a call for contributions. | Drewry, David H; Wells, Carrow I; Andrews, David M; Angell, Richard; Al-Ali, Hassan; Axtman, Alison D; Capuzzi, Stephen J; Elkins, Jonathan M; Ettmayer, Peter; Frederiksen, Mathias; Gileadi, Opher; Gray, Nathanael; Hooper, Alice; Knapp, Stefan; Laufer, St | PloS one. | 2017; | 28767711 | |
| Intracoronary Imaging, Cholesterol Efflux, and Transcriptomics after Intensive Statin Treatment in Diabetes. | Chamaria, Surbhi; Johnson, Kipp W; Vengrenyuk, Yuliya; Baber, Usman; Shameer, Khader; Divaraniya, Aparna A; Glicksberg, Benjamin S; Li, Li; Bhatheja, Samit; Moreno, Pedro; Maehara, Akiko; Mehran, Roxana; Dudley, Joel T; Narula, Jagat; Sharma, Samin K; Kini, Annapoorna S | Scientific reports. | 2017 Aug 01; | 28765529 | |
| How Ligands Illuminate GPCR Molecular Pharmacology. | Wacker, Daniel; Stevens, Raymond C; Roth, Bryan L | Cell. | 2017 Jul 27; | 28753422 | |
| From flamingo dance to (desirable) drug discovery: a nature-inspired approach. | Sánchez-Rodríguez, Aminael; Pérez-Castillo, Yunierkis; Schürer, Stephan C; Nicolotti, Orazio; Mangiatordi, Giuseppe Felice; Borges, Fernanda; Cordeiro, M Natalia D S; Tejera, Eduardo; Medina-Franco, José L; Cruz-Monteagudo, Maykel | Drug discovery today. | 2017 Jun 15; | 28624633 | |
| Activation of tumor suppressor protein PP2A inhibits KRAS-driven tumor growth. | Sangodkar, Jaya; Perl, Abbey; Tohme, Rita; Kiselar, Janna; Kastrinsky, David B; Zaware, Nilesh; Izadmehr, Sudeh; Mazhar, Sahar; Wiredja, Danica D; O'Connor, Caitlin M; Hoon, Divya; Dhawan, Neil S; Schlatzer, Daniela; Yao, Shen; Leonard, Daniel; Borczuk, A | The Journal of clinical investigation. | 2017 Jun 01; | 28504649 | |
| Deep learning for healthcare: review, opportunities and challenges. | Miotto, Riccardo; Wang, Fei; Wang, Shuang; Jiang, Xiaoqian; Dudley, Joel T | Briefings in bioinformatics. | 2017 May 06; | 28481991 | |
| A mouse tissue transcription factor atlas. | Zhou, Quan; Liu, Mingwei; Xia, Xia; Gong, Tongqing; Feng, Jinwen; Liu, Wanlin; Liu, Yang; Zhen, Bei; Wang, Yi; Ding, Chen; Qin, Jun | Nature communications. | 2017 Apr 21; | 28429721 | |
| Reply: Deep Learning With Unsupervised Feature in Echocardiographic Imaging. | Narula, Sukrit; Shameer, Khader; Salem Omar, Alaa Mabrouk; Dudley, Joel T; Sengupta, Partho P | Journal of the American College of Cardiology. | 2017 04 25; | 28427589 | |
| L1000CDS(2): LINCS L1000 characteristic direction signatures search engine. | Duan, Qiaonan; Reid, St Patrick; Clark, Neil R; Wang, Zichen; Fernandez, Nicolas F; Rouillard, Andrew D; Readhead, Ben; Tritsch, Sarah R; Hodos, Rachel; Hafner, Marc; Niepel, Mario; Sorger, Peter K; Dudley, Joel T; Bavari, Sina; Panchal, Rekha G; Ma'ayan, Avi | NPJ systems biology and applications. | 2016; | 28413689 | |
| Dopaminergic control of anxiety in young and aged zebrafish. | Kacprzak, Victoria; Patel, Neil A; Riley, Elizabeth; Yu, Lili; Yeh, Jing-Ruey J; Zhdanova, Irina V | Pharmacology, biochemistry, and behavior. | 2017 06; | 28408289 | |
| TIN-X: target importance and novelty explorer. | Cannon, Daniel C; Yang, Jeremy J; Mathias, Stephen L; Ursu, Oleg; Mani, Subramani; Waller, Anna; Schürer, Stephan C; Jensen, Lars Juhl; Sklar, Larry A; Bologa, Cristian G; Oprea, Tudor I | Bioinformatics (Oxford, England). | 2017 Aug 15; | 28398460 | |
| In silico design of novel probes for the atypical opioid receptor MRGPRX2. | Lansu, Katherine; Karpiak, Joel; Liu, Jing; Huang, Xi-Ping; McCorvy, John D; Kroeze, Wesley K; Che, Tao; Nagase, Hiroshi; Carroll, Frank I; Jin, Jian; Shoichet, Brian K; Roth, Bryan L | Nature chemical biology. | 2017 May; | 28288109 | |
| GARLH Family Proteins Stabilize GABAA Receptors at Synapses. | Yamasaki, Tokiwa; Hoyos-Ramirez, Erika; Martenson, James S; Morimoto-Tomita, Megumi; Tomita, Susumu | Neuron. | 2017 Mar 08; | 28279354 | |
| Systemic QSAR and phenotypic virtual screening: chasing butterflies in drug discovery. | Cruz-Monteagudo, Maykel; Schürer, Stephan; Tejera, Eduardo; Pérez-Castillo, Yunierkis; Medina-Franco, José L; Sánchez-Rodríguez, Aminael; Borges, Fernanda | Drug discovery today. | 2017 Mar 06; | 28274840 | |
| A Whole-Genome RNA Interference Screen Reveals a Role for Spry2 in Insulin Transcription and the Unfolded Protein Response. | Pappalardo, Zachary; Gambhir Chopra, Deeksha; Hennings, Thomas G; Richards, Hunter; Choe, Justin; Yang, Katherine; Baeyens, Luc; Ang, Kenny; Chen, Steven; Arkin, Michelle; German, Michael S; McManus, Michael T; Ku, Gregory M | Diabetes. | 2017 Jun; | 28246293 | |
| Protamine is an antagonist of apelin receptor, and its activity is reversed by heparin. | Le Gonidec, Sophie; Chaves-Almagro, Carline; Bai, Yushi; Kang, Hye Jin; Smith, Allyson; Wanecq, Estelle; Huang, Xi-Ping; Prats, Hervé; Knibiehler, Bernard; Roth, Bryan L; Barak, Larry S; Caron, Marc G; Valet, Philippe; Audigier, Yves; Masri, Bernard | FASEB journal : official publication of the Federation of American Societies for Experimental Biology. | 2017 06; | 28242772 | |
| Differential cytokine contributions of perivascular haematopoietic stem cell niches. | Asada, Noboru; Kunisaki, Yuya; Pierce, Halley; Wang, Zichen; Fernandez, Nicolas F; Birbrair, Alexander; Ma'ayan, Avi; Frenette, Paul S | Nature cell biology. | 2017 Mar; | 28218906 | |
| Systematic analyses of drugs and disease indications in RepurposeDB reveal pharmacological, biological and epidemiological factors influencing drug repositioning. | Shameer, Khader; Glicksberg, Benjamin S; Hodos, Rachel; Johnson, Kipp W; Badgeley, Marcus A; Readhead, Ben; Tomlinson, Max S; O'Connor, Timothy; Miotto, Riccardo; Kidd, Brian A; Chen, Rong; Ma'ayan, Avi; Dudley, Joel T | Briefings in bioinformatics. | 2017 Feb 15; | 28200013 | |
| Transcription Factor Response Elements on Tip: A Sensitive Approach for Large-Scale Endogenous Transcription Factor Quantitative Identification. | Shi, Wenhao; Li, Kai; Song, Lei; Liu, Mingwei; Wang, Yunzhi; Liu, Wanlin; Xia, Xia; Qin, Zhaoyu; Zhen, Bei; Wang, Yi; He, Fuchu; Qin, Jun; Ding, Chen | Analytical chemistry. | 2016 12 20; | 28193032 | |
| Automated cell type discovery and classification through knowledge transfer. | Lee, Hao-Chih; Kosoy, Roman; Becker, Christine E; Dudley, Joel T; Kidd, Brian A | Bioinformatics (Oxford, England). | 2017 Jun 01; | 28158442 | |
| Protein biomarker druggability profiling. | Mani, Subramani; Cannon, Daniel; Ohls, Robin; Oprea, Tudor; Mathias, Stephen; Ballard, Karri; Ursu, Oleg; Bologa, Cristian | Journal of biomedical informatics. | 2017 Feb; | 28131723 | |
| Integrative Analysis of Disease Signatures Shows Inflammation Disrupts Juvenile Experience-Dependent Cortical Plasticity. | Smith, Milo R; Burman, Poromendro; Sadahiro, Masato; Kidd, Brian A; Dudley, Joel T; Morishita, Hirofumi | eNeuro. | 2016 Nov-Dec; | 28101530 | |
| Novel Therapeutics Identification for Fibrosis in Renal Allograft Using Integrative Informatics Approach. | Li, Li; Greene, Ilana; Readhead, Benjamin; Menon, Madhav C; Kidd, Brian A; Uzilov, Andrew V; Wei, Chengguo; Philippe, Nimrod; Schroppel, Bernd; He, John Cijiang; Chen, Rong; Dudley, Joel T; Murphy, Barbara | Scientific reports. | 2017 Jan 04; | 28051114 | |
| Nrf2 mitigates LRRK2- and α-synuclein-induced neurodegeneration by modulating proteostasis. | Gaia Skibinski, Vicky Hwang, Dale Michael Ando, Aaron Daub, Alicia K. Lee, Abinaya Ravisankar, Sara Modan, Mariel M. Finucane, Benjamin A. Shaby, and Steven Finkbeiner | Proceedings of the National Academy of Sciences of the United States of America. | 2017 Jan 31; | 1165–1170 | 28028237 |
| Genomic Analysis of Kidney Allograft Injury Identifies Hematopoietic Cell Kinase as a Key Driver of Renal Fibrosis. | Wei, Chengguo; Li, Li; Menon, Madhav C; Zhang, Weijia; Fu, Jia; Kidd, Brian; Keung, Karen L; Woytovich, Christopher; Greene, Ilana; Xiao, Wenzhen; Salem, Fadi; Yi, Zhengzi; He, John Cijiang; Dudley, Joel T; Murphy, Barbara | Journal of the American Society of Nephrology : JASN. | 2017 May; | 27927780 | |
| A comprehensive map of molecular drug targets. | Santos, Rita; Ursu, Oleg; Gaulton, Anna; Bento, A Patrícia; Donadi, Ramesh S; Bologa, Cristian G; Karlsson, Anneli; Al-Lazikani, Bissan; Hersey, Anne; Oprea, Tudor I; Overington, John P | Nature reviews. Drug discovery. | 2017 01; | 27910877 | |
| Pharos: Collating protein information to shed light on the druggable genome. | Nguyen, Dac-Trung; Mathias, Stephen; Bologa, Cristian; Brunak, Soren; Fernandez, Nicolas; Gaulton, Anna; Hersey, Anne; Holmes, Jayme; Jensen, Lars Juhl; Karlsson, Anneli; Liu, Guixia; Ma'ayan, Avi; Mandava, Geetha; Mani, Subramani; Mehta, Saurabh; Overington, John; Patel, Juhee; Rouillard, Andrew D; Schürer, Stephan; Sheils, Timothy; Simeonov, Anton; Sklar, Larry A; Southall, Noel; Ursu, Oleg; Vidovic, Dusica; Waller, Anna; Yang, Jeremy; Jadhav, Ajit; Oprea, Tudor I; Guha, Rajarshi | Nucleic acids research. | 2017 Jan 4; | 27903890 | |
| EXPLORING THE REPRODUCIBILITY OF PROBABILISTIC CAUSAL MOLECULAR NETWORK MODELS. | Cohain, Ariella; Divaraniya, Aparna A; Zhu, Kuixi; Scarpa, Joseph R; Kasarskis, Andrew; Zhu, Jun; Chang, Rui; Dudley, Joel T; Schadt, Eric E | Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. | 2016; | 27896968 | |
| EXPLORING BRAIN TRANSCRIPTOMIC PATTERNS: A TOPOLOGICAL ANALYSIS USING SPATIAL EXPRESSION NETWORKS. | Kuncheva, Zhana; Krishnan, Michelle L; Montana, Giovanni | Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. | 2016; | 27896963 | |
| GEN3VA: aggregation and analysis of gene expression signatures from related studies. | Gundersen, Gregory W; Jagodnik, Kathleen M; Woodland, Holly; Fernandez, Nicholas F; Sani, Kevin; Dohlman, Anders B; Ung, Peter Man-Un; Monteiro, Caroline D; Schlessinger, Avner; Ma'ayan, Avi | BMC bioinformatics. | 2016 Nov 15; | 27846806 | |
| DrugCentral: online drug compendium. | Ursu, Oleg; Holmes, Jayme; Knockel, Jeffrey; Bologa, Cristian G; Yang, Jeremy J; Mathias, Stephen L; Nelson, Stuart J; Oprea, Tudor I | Nucleic acids research. | 2017 Jan 4; | 27789690 | |
| Gold Nanoparticle Reprograms Pancreatic Tumor Microenvironment and Inhibits Tumor Growth. | Saha, Sounik; Xiong, Xunhao; Chakraborty, Prabir K; Shameer, Khader; Arvizo, Rochelle R; Kudgus, Rachel A; Dwivedi, Shailendra Kumar Dhar; Hossen, Md Nazir; Gillies, Elizabeth M; Robertson, J David; Dudley, Joel T; Urrutia, Raul A; Postier, Russell G; Bha | ACS nano. | 2016 12 27; | 27758098 | |
| Discovery and Characterization of Novel GPR39 Agonists Allosterically Modulated by Zinc. | Sato, Seiji; Huang, Xi-Ping; Kroeze, Wesley K; Roth, Bryan L | Molecular pharmacology. | 2016 Dec; | 27754899 | |
| Estimation of Maximum Recommended Therapeutic Dose Using Predicted Promiscuity and Potency. | Liu, T; Oprea, T; Ursu, O; Hasselgren, C; Altman, R B | Clinical and translational science. | 2016 12; | 27736015 | |
| Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd. | Wang, Zichen; Monteiro, Caroline D; Jagodnik, Kathleen M; Fernandez, Nicolas F; Gundersen, Gregory W; Rouillard, Andrew D; Jenkins, Sherry L; Feldmann, Axel S; Hu, Kevin S; McDermott, Michael G; Duan, Qiaonan; Clark, Neil R; Jones, Matthew R; Kou, Yan; Goff, Troy; Woodland, Holly; Amaral, Fabio M R; Szeto, Gregory L; Fuchs, Oliver; Schüssler-Fiorenza Rose, Sophia M; Sharma, Shvetank; Schwartz, Uwe; Bausela, Xabier Bengoetxea; Szymkiewicz, Maciej; Maroulis, Vasileios; Salykin, Anton; Barra, Carolina M; Kruth, Candice D; Bongio, Nicholas J; Mathur, Vaibhav; Todoric, Radmila D; Rubin, Udi E; Malatras, Apostolos; Fulp, Carl T; Galindo, John A; Motiejunaite, Ruta; Jüschke, Christoph; Dishuck, Philip C; Lahl, Katharina; Jafari, Mohieddin; Aibar, Sara; Zaravinos, Apostolos; Steenhuizen, Linda H; Allison, Lindsey R; Gamallo, Pablo; de Andres Segura, Fernando; Dae Devlin, Tyler; Pérez-García, Vicente; Ma'ayan, Avi | Nature communications. | 2016 Sep 26; | 27667448 | |
| Replicating Cardiovascular Condition-Birth Month Associations. | Li, Li; Boland, Mary Regina; Miotto, Riccardo; Tatonetti, Nicholas P; Dudley, Joel T | Scientific reports. | 2016 Sep 14; | 27624541 | |
| An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study. | Wang, Zichen; Ma'ayan, Avi | F1000Research. | 2016 Jul 5; | 27583132 | |
| Non-Substrate Based, Small Molecule Inhibitors of the Human Isoprenylcysteine Carboxyl Methyltransferase. | Butler, Kyle V; Bohn, Kelsey; Hrycyna, Christine A; Jin, Jian | MedChemComm. | 2016 May 1; | 27547295 | |
| Structure-based discovery of opioid analgesics with reduced side effects. | Manglik, Aashish; Lin, Henry; Aryal, Dipendra K; McCorvy, John D; Dengler, Daniela; Corder, Gregory; Levit, Anat; Kling, Ralf C; Bernat, Viachaslau; Hübner, Harald; Huang, Xi-Ping; Sassano, Maria F; Giguère, Patrick M; Löber, Stefan; Da Duan; Scherrer, Gr | Nature. | 2016 09 08; | 27533032 | |
| Polycomb repressive complex 2 (PRC2) silences genes responsible for neurodegeneration. | von Schimmelmann, Melanie; Feinberg, Philip A; Sullivan, Josefa M; Ku, Stacy M; Badimon, Ana; Duff, Mary Kaye; Wang, Zichen; Lachmann, Alexander; Dewell, Scott; Ma'ayan, Avi; Han, Ming-Hu; Tarakhovsky, Alexander; Schaefer, Anne | Nature neuroscience. | 2016 Oct; | 27526204 | |
| Identification of Novel Smoothened Ligands Using Structure-Based Docking. | Lacroix, Celine; Fish, Inbar; Torosyan, Hayarpi; Parathaman, Pranavan; Irwin, John J; Shoichet, Brian K; Angers, Stephane | PloS one. | 2016; | 27490099 | |
| The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. | Rouillard, Andrew D; Gundersen, Gregory W; Fernandez, Nicolas F; Wang, Zichen; Monteiro, Caroline D; McDermott, Michael G; Ma'ayan, Avi | Database : the journal of biological databases and curation. | 2016; | 27374120 | |
| Comparative analyses of population-scale phenomic data in electronic medical records reveal race-specific disease networks. | Glicksberg, Benjamin S; Li, Li; Badgeley, Marcus A; Shameer, Khader; Kosoy, Roman; Beckmann, Noam D; Pho, Nam; Hakenberg, Jörg; Ma, Meng; Ayers, Kristin L; Hoffman, Gabriel E; Dan Li, Shuyu; Schadt, Eric E; Patel, Chirag J; Chen, Rong; Dudley, Joel T | Bioinformatics (Oxford, England). | 2016 Jun 15; | 27307606 | |
| Krüppel-Like Factor 15 Mediates Glucocorticoid-Induced Restoration of Podocyte Differentiation Markers. | Mallipattu, Sandeep K; Guo, Yiqing; Revelo, Monica P; Roa-Peña, Lucia; Miller, Timothy; Ling, Jason; Shankland, Stuart J; Bialkowska, Agnieszka B; Ly, Victoria; Estrada, Chelsea; Jain, Mukesh K; Lu, Yuan; Ma'ayan, Avi; Mehrotra, Anita; Yacoub, Rabi; Nord, Edward P; Woroniecki, Robert P; Yang, Vincent W; He, John C | Journal of the American Society of Nephrology : JASN. | 2016 Jun 10; | 27288011 | |
| Cognitive Machine-Learning Algorithm for Cardiac Imaging: A Pilot Study for Differentiating Constrictive Pericarditis From Restrictive Cardiomyopathy. | Sengupta, Partho P; Huang, Yen-Min; Bansal, Manish; Ashrafi, Ali; Fisher, Matt; Shameer, Khader; Gall, Walt; Dudley, Joel T | Circulation. Cardiovascular imaging. | 2016 Jun; | 27266599 | |
| ?1 receptor ligands control a switch between passive and active threat responses. | Rennekamp, Andrew J; Huang, Xi-Ping; Wang, You; Patel, Samir; Lorello, Paul J; Cade, Lindsay; Gonzales, Andrew P W; Yeh, Jing-Ruey Joanna; Caldarone, Barbara J; Roth, Bryan L; Kokel, David; Peterson, Randall T | Nature chemical biology. | 2016 Jul; | 27239788 | |
| Zebrafish behavioral profiling identifies multitarget antipsychotic-like compounds. | Bruni, Giancarlo; Rennekamp, Andrew J; Velenich, Andrea; McCarroll, Matthew; Gendelev, Leo; Fertsch, Ethan; Taylor, Jack; Lakhani, Parth; Lensen, Dennis; Evron, Tama; Lorello, Paul J; Huang, Xi-Ping; Kolczewski, Sabine; Carey, Galen; Caldarone, Barbara J; Prinssen, Eric; Roth, Bryan L; Keiser, Michael J; Peterson, Randall T; Kokel, David | Nature chemical biology. | 2016 Jul; | 27239787 | |
| Badapple: promiscuity patterns from noisy evidence. | Yang, Jeremy J; Ursu, Oleg; Lipinski, Christopher A; Sklar, Larry A; Oprea, Tudor I; Bologa, Cristian G | Journal of cheminformatics. | 2016; | 27239230 | |
| Glucocorticoid receptor isoforms direct distinct mitochondrial programs to regulate ATP production. | Morgan, David J; Poolman, Toryn M; Williamson, Andrew J K; Wang, Zichen; Clark, Neil R; Ma'ayan, Avi; Whetton, Anthony D; Brass, Andrew; Matthews, Laura C; Ray, David W | Scientific reports. | 2016; | 27226058 | |
| Cre dependent DREADD (designer receptors exclusively activated by designer drugs) mice. | Zhu, Hu; Aryal, Dipendra K; Olsen, Reid H J; Urban, Daniel J; Swearingen, Amanda; Forbes, Stacy; Roth, Bryan L; Hochgeschwender, Ute | Genesis (New York, N.Y. : 2000). | 2016 May 19; | 27194399 | |
| Deep Patient: An Unsupervised Representation to Predict the Future of Patients from the Electronic Health Records. | Miotto, Riccardo; Li, Li; Kidd, Brian A; Dudley, Joel T | Scientific reports. | 2016 May 17; | 27185194 | |
| BDDCS, the Rule of 5 and drugability. | Benet, Leslie Z; Hosey, Chelsea M; Ursu, Oleg; Oprea, Tudor I | Advanced drug delivery reviews. | 2016 Jun 1; | 27182629 | |
| Systems Medicine Approaches to Improving Understanding, Treatment, and Clinical Management of Neuroendocrine Prostate Cancer. | Yadav, Kamlesh K; Shameer, Khader; Readhead, Ben; Yadav, Shalini S; Li, Li; Kasarskis, Andrew; Tewari, Ashutosh K; Dudley, Joel T | Current pharmaceutical design. | 2016; | 27174811 | |
| Drug-induced adverse events prediction with the LINCS L1000 data. | Wang, Zichen; Clark, Neil R; Ma'ayan, Avi | Bioinformatics (Oxford, England). | 2016 Aug 1; | 27153606 | |
| Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. | Kuleshov, Maxim V; Jones, Matthew R; Rouillard, Andrew D; Fernandez, Nicolas F; Duan, Qiaonan; Wang, Zichen; Koplev, Simon; Jenkins, Sherry L; Jagodnik, Kathleen M; Lachmann, Alexander; McDermott, Michael G; Monteiro, Caroline D; Gundersen, Gregory W; Ma'ayan, Avi | Nucleic acids research. | 2016 Jul 8; | 27141961 | |
| In silico methods for drug repurposing and pharmacology. | Hodos, Rachel A; Kidd, Brian A; Shameer, Khader; Readhead, Ben P; Dudley, Joel T | Wiley interdisciplinary reviews. Systems biology and medicine. | 2016 May; | 27080087 | |
| Discovery of a specific inhibitor of human GLUT5 by virtual screening and in vitro transport evaluation | George-Thompson AM, Ursu O, Babkin P, Iancu CV, Whang A, Oprea TI, Choe JY | Scientific Reports | Epub 2016 Apr 14. | 27074918 | |
| Integrative network modeling approaches to personalized cancer medicine | Kidd BA, Readhead BP, Eden C, Parekh S, Dudley JT | Personalized Medicine | 2015 Jun 1 | 12(3):245-257 | 27019658 |
| Integrative network modeling approaches to personalized cancer medicine. | Kidd BA, Readhead BP, Eden C, Parekh S, Dudley JT. | Personalized Medicine | 2015 Jun 1 | 12(3):245-257. | 27019658 |
| Evaluation of direct-to-consumer low-volume lab tests in healthy adults | Kidd BA, Hoffman G, Zimmerman N, Li L, Morgan JW, Glowe PK, Botwin GJ, Parekh S, Babic N, Doust MW, Stock GB, Schadt EE, Dudley JT | J Clin Invest | 2016 Mar 28 | pii: 86318. doi: 10.1172/JCI86318. [Epub ahead of print] | 27018593 |
| Signaling Networks among Stem Cell Precursors, Transit-Amplifying Progenitors, and their Niche in Developing Hair Follicles. | Rezza, Amélie; Wang, Zichen; Sennett, Rachel; Qiao, Wenlian; Wang, Dongmei; Heitman, Nicholas; Mok, Ka Wai; Clavel, Carlos; Yi, Rui; Zandstra, Peter; Ma'ayan, Avi; Rendl, Michael | Cell reports. | 2016 Mar 29; | 27009580 | |
| In Vitro and In Vivo Characterization of the Alkaloid Nuciferine. | Farrell, Martilias S; McCorvy, John D; Huang, Xi-Ping; Urban, Daniel J; White, Kate L; Giguere, Patrick M; Doak, Allison K; Bernstein, Alison I; Stout, Kristen A; Park, Su Mi; Rodriguiz, Ramona M; Gray, Bradley W; Hyatt, William S; Norwood, Andrew P; Webs | PloS one. | 2016; | 26963248 | |
| Polygenic overlap between schizophrenia risk and antipsychotic response: a genomic medicine approach. | Ruderfer, Douglas M; Charney, Alexander W; Readhead, Ben; Kidd, Brian A; Kähler, Anna K; Kenny, Paul J; Keiser, Michael J; Moran, Jennifer L; Hultman, Christina M; Scott, Stuart A; Sullivan, Patrick F; Purcell, Shaun M; Dudley, Joel T; Sklar, Pamela | The lancet. Psychiatry. | 2016 Apr; | 26915512 | |
| Docking Screens for Novel Ligands Conferring New Biology. | Irwin, John J; Shoichet, Brian K | Journal of medicinal chemistry. | 2016 05 12; | 26913380 | |
| Translational bioinformatics in the era of real-time biomedical, health care and wellness data streams | Shameer K, Badgeley MA, Miotto R, Glicksberg BS, Morgan JW, Dudley JT | Brief Bioinform | 2016 Feb 14 | pii: bbv118. [Epub ahead of print] | 26876889 |
| Integrative radiogenomic analysis for multicentric radiophenotype in glioblastoma | Kong DS, Kim J, Lee IH, Kim ST, Seol HJ, Lee JI, Park WY, Ryu G, Wang Z, Ma'ayan A, Nam DH | Oncotarget | 2016 Feb 1 | doi: 10.18632/oncotarget.7115. [Epub ahead of print] | 26863628 |
| Principal Angle Enrichment Analysis (PAEA): Dimensionally Reduced Multivariate Gene Set Enrichment Analysis Tool. | Clark, Neil R; Szymkiewicz, Maciej; Wang, Zichen; Monteiro, Caroline D; Jones, Matthew R; Ma'ayan, Avi | Proceedings. IEEE International Conference on Bioinformatics and Biomedicine. | 2015 Nov; | 256-262 | 26848405 |
| Leveraging Large-scale Behavioral Profiling in Zebrafish to Explore Neuroactive Polypharmacology. | McCarroll, Matthew N; Gendelev, Leo; Keiser, Michael J; Kokel, David | ACS chemical biology. | 2016 Apr 15; | 26845413 | |
| A three-groups model for high-throughput survival screens. | Shaby, Benjamin A; Skibinski, Gaia; Ando, Michael; LaDow, Eva S; Finkbeiner, Steven | Biometrics. | 2016 Jan 28; | 26821783 | |
| Fetal liver hematopoietic stem cell niches associate with portal vessels. | Khan, Jalal A; Mendelson, Avital; Kunisaki, Yuya; Birbrair, Alexander; Kou, Yan; Arnal-Estapé, Anna; Pinho, Sandra; Ciero, Paul; Nakahara, Fumio; Ma'ayan, Avi; Bergman, Aviv; Merad, Miriam; Frenette, Paul S | Science (New York, N.Y.). | 2016 Jan 8; | 176-80 | 26634440 |
| Mapping the effects of drugs on the immune system. | Kidd, Brian A; Wroblewska, Aleksandra; Boland, Mary R; Agudo, Judith; Merad, Miriam; Tatonetti, Nicholas P; Brown, Brian D; Dudley, Joel T | Nature biotechnology. | 2016 Jan; | 47-54 | 26619012 |
| Molecular systems evaluation of oligomerogenic APP(E693Q) and fibrillogenic APP(KM670/671NL)/PSEN1(?exon9) mouse models identifies shared features with human Alzheimer's brain molecular pathology. | Readhead, B; Haure-Mirande, J-V; Zhang, B; Haroutunian, V; Gandy, S; Schadt, E E; Dudley, J T; Ehrlich, M E | Molecular psychiatry. | 2015 Nov 10; | 26552589 | |
| Allosteric ligands for the pharmacologically dark receptors GPR68 and GPR65. | Huang, Xi-Ping; Karpiak, Joel; Kroeze, Wesley K; Zhu, Hu; Chen, Xin; Moy, Sheryl S; Saddoris, Kara A; Nikolova, Viktoriya D; Farrell, Martilias S; Wang, Sheng; Mangano, Thomas J; Deshpande, Deepak A; Jiang, Alice; Penn, Raymond B; Jin, Jian; Koller, Bever | Nature. | 2015 Nov 26; | 477-83 | 26550826 |
| Identification of type 2 diabetes subgroups through topological analysis of patient similarity. | Li, Li; Cheng, Wei-Yi; Glicksberg, Benjamin S; Gottesman, Omri; Tamler, Ronald; Chen, Rong; Bottinger, Erwin P; Dudley, Joel T | Science translational medicine. | 2015 Oct 28; | 311ra174 | 26511511 |
| Noribogaine is a G-protein biased ?-opioid receptor agonist. | Maillet, Emeline L; Milon, Nicolas; Heghinian, Mari D; Fishback, James; Schürer, Stephan C; Garamszegi, Nandor; Mash, Deborah C | Neuropharmacology. | 2015 Dec; | 675-88 | 26302653 |
| Reprint of ''Abstraction for data integration: Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction''. | Rouillard, Andrew D; Wang, Zichen; Ma'ayan, Avi | Computational biology and chemistry. | 2015 Dec; | 123-38 | 26297300 |
| An Integrated Transcriptome Atlas of Embryonic Hair Follicle Progenitors, Their Niche, and the Developing Skin. | Sennett, Rachel; Wang, Zichen; Rezza, Amélie; Grisanti, Laura; Roitershtein, Nataly; Sicchio, Cristina; Mok, Ka Wai; Heitman, Nicholas J; Clavel, Carlos; Ma'ayan, Avi; Rendl, Michael | Developmental cell. | 2015 Sep 14; | 577-91 | 26256211 |
| Computational and Practical Aspects of Drug Repositioning. | Oprea, Tudor I; Overington, John P | Assay and drug development technologies. | 2015 Jul-Aug; | 299-306 | 26241209 |
| Comprehensive comparison of large-scale tissue expression datasets | Santos A, Tsafou K, Stolte C, Pletscher-Frankild S, O'Donoghue SI, Jensen LJ. | Peer J | 2015 June 30 | 26157623 | |
| Morphine Regulated Synaptic Networks Revealed by Integrated Proteomics and Network Analysis. | Stockton Jr, Steven D; Gomes, Ivone; Liu, Tong; Moraje, Chandrakala; Hipólito, Lucia; Jones, Matthew R; Ma'ayan, Avi; Morón, Jose A; Li, Hong; Devi, Lakshmi A | Molecular & cellular proteomics : MCP. | 2015 Oct; | 2564-76 | 26149443 |
| Publisher?s Note:Abstraction for data integration:Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction. | Rouillard, Andrew D; Wang, Zichen; Ma'ayan, Avi | Computational biology and chemistry. | 2015 Oct; | 104-19 | 26101093 |
| Integrated Approaches for Genome-wide Interrogation of the Druggable Non-olfactory G Protein-coupled Receptor Superfamily. | Roth, Bryan L; Kroeze, Wesley K | The Journal of biological chemistry. | 2015 Aug 7; | 19471-7 | 26100629 |
| Dynamics of the discovery process of protein-protein interactions from low content studies. | Wang, Zichen; Clark, Neil R; Ma'ayan, Avi | BMC systems biology. | 2015; | 26 | 26048415 |
| Choosing the Right Tool for the Job: RNAi, TALEN, or CRISPR. | Boettcher, Michael; McManus, Michael T | Molecular cell. | 2015 May 21; | 575-85 | 26000843 |
| GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions. | Gundersen, Gregory W; Jones, Matthew R; Rouillard, Andrew D; Kou, Yan; Monteiro, Caroline D; Feldmann, Axel S; Hu, Kevin S; Ma'ayan, Avi | Bioinformatics (Oxford, England). | 2015 Sep 15; | 3060-2 | 25971742 |
| PRESTO-Tango as an open-source resource for interrogation of the druggable human GPCRome. | Kroeze, Wesley K; Sassano, Maria F; Huang, Xi-Ping; Lansu, Katherine; McCorvy, John D; Giguère, Patrick M; Sciaky, Noah; Roth, Bryan L | Nature structural & molecular biology. | 2015 May; | 362-9 | 25895059 |
| Inhibition of Lapatinib-Induced Kinome Reprogramming in ERBB2-Positive Breast Cancer by Targeting BET Family Bromodomains. | Stuhlmiller, Timothy J; Miller, Samantha M; Zawistowski, Jon S; Nakamura, Kazuhiro; Beltran, Adriana S; Duncan, James S; Angus, Steven P; Collins, Kyla A L; Granger, Deborah A; Reuther, Rachel A; Graves, Lee M; Gomez, Shawn M; Kuan, Pei-Fen; Parker, Joel | Cell reports. | 2015 Apr 21; | 390-404 | 25865888 |
| Cell-Based Screening: Extracting Meaning from Complex Data | Finkbeiner S., Frumkin M., Kassner PD | Neuron | 2015 Apr 8 | 86(1):160-174 | 25856492 |
| Genome-wide significant loci: how important are they? Systems genetics to understand heritability of coronary artery disease and other common complex disorders. | Björkegren, Johan L M; Kovacic, Jason C; Dudley, Joel T; Schadt, Eric E | Journal of the American College of Cardiology. | 2015 Mar 3; | 830-45 | 25720628 |
| Genomic and network patterns of schizophrenia genetic variation in human evolutionary accelerated regions. | Xu, Ke; Schadt, Eric E; Pollard, Katherine S; Roussos, Panos; Dudley, Joel T | Molecular biology and evolution. | 2015 May; | 1148-60 | 25681384 |
| Computational and experimental advances in drug repositioning for accelerated therapeutic stratification | Shameer K, Readhead B, Dudley JT. | Current Topics in Medicinal Chemistry | 2015 | 25579574 | |
| REDD1 functions at the crossroads between the therapeutic and adverse effects of topical glucocorticoids. | Baida, Gleb; Bhalla, Pankaj; Kirsanov, Kirill; Lesovaya, Ekaterina; Yakubovskaya, Marianna; Yuen, Kit; Guo, Shuchi; Lavker, Robert M; Readhead, Ben; Dudley, Joel T; Budunova, Irina | EMBO molecular medicine. | 2015 Jan; | 42-58 | 25504525 |
| The TLQP-21 peptide activates the G-protein-coupled receptor C3aR1 via a folding-upon-binding mechanism | Cero C, Vostrikov VV, Verardi R, Severini C, Gopinath T, Braun PD, Sassano MF, Gurney A, Roth BL, Vulchanova L, Possenti R, Veglia G, Bartolomucci A. | Structure | 2014 Dec 2 | 22(12):1744-53. | 25456411 |
| Lean Big Data integration in systems biology and systems pharmacology. | Ma'ayan, Avi; Rouillard, Andrew D; Clark, Neil R; Wang, Zichen; Duan, Qiaonan; Kou, Yan | Trends in pharmacological sciences | 2014 Sep | 450-460 | 25109570 |
| Drug/Cell-line Browser: interactive canvas visualization of cancer drug/cell-line viability assay datasets. | Duan, Qiaonan; Wang, Zichen; Fernandez, Nicolas F; Rouillard, Andrew D; Tan, Christopher M; Benes, Cyril H; Ma'ayan, Avi | Bioinformatics (Oxford, England). | 2014 Nov 15; | 3289-90 | 25100688 |
| Autophagy induction enhances TDP43 turnover and survival in neuronal ALS models. | Barmada, Sami J; Serio, Andrea; Arjun, Arpana; Bilican, Bilada; Daub, Aaron; Ando, D Michael; Tsvetkov, Andrey; Pleiss, Michael; Li, Xingli; Peisach, Daniel; Shaw, Christopher; Chandran, Siddharthan; Finkbeiner, Steven | Nature chemical biology. | 2014 Aug; | 24974230 | |
| LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures. | Duan, Qiaonan; Flynn, Corey; Niepel, Mario; Hafner, Marc; Muhlich, Jeremy L; Fernandez, Nicolas F; Rouillard, Andrew D; Tan, Christopher M; Chen, Edward Y; Golub, Todd R; Sorger, Peter K; Subramanian, Aravind; Ma'ayan, Avi | Nucleic acids research | 2014 Jul | W449-60 | 24906883 |