IDG Publications 

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The Target Watch series in Nature Reviews Drug Discovery:
  1.  "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.)
  2.  "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.)
  3.  "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)
  4.  "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
  5.  "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)
  6.  "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)
  7.  "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)
  8.  "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)
  9.  "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)
  10.  "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)
  11.  "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)
  12.  "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)
  13.  "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)
  14.  "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)
  15.  "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)
  16.  "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)
  17.  "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  )
  18.  “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
  19.  "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 
  20.  "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 
  21.  "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
  22.  "Novel drug targets in 2023" by Sorin Avram, Liliana Halip, Ramona Curpan & Tudor I. Oprea (Nature Reviews Drug Discovery, 23, 330 (2024)) https://doi.org/10.1038/d41573-024-00057-9
 
 
Publication Title Authors Journal Publication Date Page No PubMedID
PIP4K2C inhibition reverses autophagic flux impairment induced by SARS-CoV-2. Karim M, Mishra M, Lo CW, Saul S, Cagirici HB, Tran DHN, Agrawal A, Ghita L, Ojha A, East MP, Gammeltoft KA, Sahoo MK, Johnson GL, Das S, Jochmans D, Cohen CA, Gottwein J, Dye J, Neff N, Pinsky BA, Laitinen T, Pantsar T, Poso A, Zanini F, Jonghe S, Asquith CRM, Einav S. bioRxiv. 2024 Apr 17;   38659941
MRGPRX4 mediates phospho-drug-associated pruritus in a humanized mouse model. Chien D CC, Limjunyawong N, Cao C, Meixiong J, Peng Q, Ho C, Fay JF, Roth BL, Dong X. Sci Transl Med. 2024 May 8;   38718132
Rummagene: massive mining of gene sets from supporting materials of biomedical research publications. Clarke DJB, Marino GB, Deng EZ, Xie Z, Evangelista JE, Ma'ayan A. Commun Biol. 2024 Apr 20;   38643247
Discovery and optimization of narrow spectrum inhibitors of Tousled like kinase 2 (TLK2) using quantitative structure activity relationships. Asquith CRM, East MP, Laitinen T, Alamillo-Ferrer C, Hartikainen E, Wells CI, Axtman AD, Drewry DH, Tizzard GJ, Poso A, Willson TM, Johnson GL. Eur J Med Chem. 2024 Apr 2;   38636130
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
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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
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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
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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
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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
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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
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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
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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
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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
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