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Research Articles

IDG Consortium Total: 82 publications

█ Tech Dev 1: Gary Johnson (UNC)1U01 MH104999 + 3

Stuhlmiller, T.J., Miller, S.M., Zawistowski, Kazuhiro Nakamura, K., Beltran, A.,  Duncan, J.S., Collins, K.L.A., Granger, D.A., Rachel A. Reuther, R.A., Graves, L.M., Gomez, S.M., Kuan, P-F., Joel S. Parker, J.S., Chen, X., Sciaky, N., Carey, L.A., Shelton Earp, H.S., Jin, J., Johnson, G.L. (2015) Inhibition of Lapatinib-induced Kinome Reprogramming in ERBB2-positive Breast Cancer by Targeting BET Family Bromodomains, Cell Reports

Tsai YS, Dominguez D, Gomez SM, Wang Z. Transcriptome-wide identification and study of cancer-specific splicing events across multiple tumors. Oncotarget.Mol Pharmacol. 2015 Mar 30;6(9):6825-39. PMID: 25749525

Butler KV, Bohn K, Hrycyna CA, Jin J. Non-Substrate Based, Small Molecule Inhibitors of the Human Isoprenylcysteine Carboxyl Methyltransferase. Medchemcomm. 2016 May 1;7(5):1016-1021. Epub 2016 Apr 14. PMID: 27547295 PMCID: PMC4990076

█ Tech Dev 2: Bryan Roth and Brian Shoichet (UNC/UCSF) 1U01 MH104974 + 7

Kroeze WK, Sassano MF, Huang XP, Lansu K, McCorvy JD, Giguère PM, Sciaky N, Roth BL. PRESTO-Tango as an open-source resource for interrogation of the druggable human GPCRome. Nat Struct Mol Biol. 2015 Apr 20. doi: 10.1038/nsmb.3014. [Epub ahead of print] 

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. The TLQP-21 peptide activates the G-protein-coupled receptor C3aR1 via a folding-upon-binding mechanism. Structure. 2014 Dec 2;22(12):1744-53. doi: 10.1016/j.str.2014.10.001. Epub 2014 Nov 13.

Huang XP, Karpiak J, Kroeze WK, Zhu H, Chen X, Moy SS, Saddoris KA, Nikolova VD, Farrell MS, Wang S, Mangano TJ, Deshpande DA, Jiang A, Penn RB, Jin J, Koller BH, Kenakin T, Shoichet BKRoth BL. Allosteric ligands for the pharmacologically dark receptors GPR68 and GPR65. Nature. 2015 Nov 26;527(7579):477-83. doi: 10.1038/nature15699. Epub 2015 Nov 9. PMID: 26550826

Roth BLKroeze WK. Integrated Approaches for Genome-wide Interrogation of the Druggable Non-olfactory G Protein-coupled Receptor Superfamily.  J Biol Chem. 2015 Aug 7;290(32):19471-7. doi: 10.1074/jbc.R115.654764. Epub 2015 Jun 22. Review. PMID: 2610062​

Zhu H, Aryal DK, Olsen RH, Urban DJ, Swearingen A, Forbes S, Roth BL, Hochgeschwender U., Cre-dependent DREADD (Designer Receptors Exclusively Activated by Designer Drugs) mice., Genesis. 2016 Aug;54(8):439-46. doi: 10.1002/dvg.22949. Epub 2016 Jun 3 PMID: 27194399

Sato S, Huang XP, Kroeze WK, Roth BL., Discovery and Characterization of Novel GPR39 Agonists Allosterically Modulated by Zinc. Mol Pharmacol. 2016 Dec;90(6):726-737. PMID: 27754899

Vardy E, Sassano MF, Rennekamp AJ, Kroeze WK, Mosier PD, Westkaemper RB, Stevens CW, Katritch V, Stevens RC, Peterson RT, Roth BL., Single Amino Acid Variation Underlies Species-Specific Sensitivity to Amphibian Skin-Derived Opioid-like Peptides. Chem Biol. 2015 Jun 18;22(6):764-75. doi: 10.1016/j.chembiol.2015.05.012. PMID: 26091169 PMCID: PMC4507497

█  Tech Dev 3: Joanna Yeh and David Kokel  (MGH/UCSF) 1U01 MH105027 + 2

Giancarlo Bruni, Andrew J. Rennekamp, Andrea Velenich, Matthew McCarroll, Leo Gendelev, Ethan Fertsch, Jack Taylor, Parth Lakhani, Dennis Lensen, Tama Evron, Paul J. Lorello, Xi-Ping Huang, Sabine Kolczewski, Galen Carey, Barbara J. Caldarone, Eric Prinssen, Bryan L. Roth, Michael J. Keiser, Randall T. Peterson, David Kokel. Zebrafish behavioral profiling identifies multi-target antipsychotic-like compounds. Nat Chem Biol. 2016 Jul;12(7):559-66. doi: 10.1038/nchembio.2097. Epub 2016 May 30. PMID: 27239787

Andrew J. Rennekamp, Xi-Ping Huang, You Wang, Samir Patel, Paul J. Lorello, Lindsay Cade,  Andrew P. W. Gonzales, Jing-Ruey Joanna Yeh, Barbara J. Caldarone, Bryan L. Roth, David Kokel and Randall T. Peterson. Sigma-1 receptor ligands control a switch between passive and active threat responses. Nat Chem Biol. 2016 Jul;12(7):552-8. doi: 10.1038/nchembio.2089. Epub 2016 May 30. PMID: 27239788

█ Tech Dev 4: Michael McManus  (UCSF) 1U01 MH105028 + 1

Boettcher M, McManus MT. Choosing the Right Tool for the Job: RNAi, TALEN, or CRISPR. Mol Cell. 2015 May 21;58(4):575-85. doi: 10.1016/j.molcel.2015.04.028. PMCID: PMC4441801

█ Tech Dev 5: Susumu Tomita  (Yale) 1U01 MH104984 + 1

Yamasaki T, Hoyos-Ramirez E, Martenson JS, Morimoto-Tomita M, Tomita S. GARLH Family Proteins Stabilize GABAA Receptors at Synapses. Neuron. 2017 Mar 8;93(5):1138-1152.e6. doi: 10.1016/j.neuron.2017.02.023. PMID: 28279354

█ Tech Dev 6: Steve Finkbeiner  (Gladstone) 1U01 MH105035 + 6

Finkbeiner S., Frumkin M., Kassner PD, Cell-Based Screening: Extracting Meaning from Complex Data, Neuron 2015 Apr 8;86(1):160-174.  doi:10.1016/j.neuron.2015.02.023.

Barmada SJ, Serio A, Arjun A, Bilican B, Daub A, Ando DM, Tsvetkov A, Pleiss M, Li X, Peisach D, Shaw C, Chandran S, Finkbeiner S. Autophagy induction enhances TDP43 turnover and survival in neuronal ALS models. Nat Chem Biol. 2014 Aug;10(8):677-85. PubMed PMID: 24974230; PubMed Central PMCID: PMC4106236.

Finkbeiner S, Frumkin M, Kassner PD. Cell-based screening: extracting meaning from complex data. Neuron. 2015 Apr 8;86(1):160-74. PubMed PMID: 25856492; PubMed Central PMCID: PMC4457442.

Shaby BA, Skibinski G, Ando M, LaDow ES, Finkbeiner S. A three-groups model for high-throughput survival screens. Biometrics. 2016 Jan 28; PubMed PMID: 26821783; NIHMSID: 757531.

Skibinski G, Hwang V, Ando DM, Daub A, Lee AK, Ravisankar A, Modan S, Finucane MM, Shaby BA, Finkbeiner S., Nrf2 mitigates LRRK2- and α-synuclein-induced neurodegeneration by modulating proteostasis. Proc Natl Acad Sci U S A. 2017 Jan 31;114(5):1165-1170. doi: 10.1073/pnas.1522872114., PMID: 28028237

Haston KM, Finkbeiner S., Clinical Trials in a Dish: The Potential of Pluripotent Stem Cells to Develop Therapies for Neurodegenerative Diseases., Annu Rev Pharmacol Toxicol. 2016;56:489-510. doi: 10.1146/annurev-pharmtox-010715-103548. Review. PMID: 26514199, PMCID: PMC4868344

█ Tech Dev 7: Jun Qin  (Baylor) 1U01 MH105026 + 1

Shi W, Li K, Song L, Liu M, Wang Y, Liu W, Xia X, Qin Z, Zhen B, Wang Y, He F, Qin J, Ding C. Transcription Factor Response Elements on Tip: A Sensitive Approach for Large-Scale Endogenous Transcription Factor Quantitative Identification. Ana Chem.2016 Dec 20;88(24):11990-11994. doi: 10.1021/acs.analchem.6b03150. Epub 2016 Nov 30. PMID: 28193032

█ ISMMS KMC site: Avi Ma’ayan and Joel Dudley 1U54 CA189201 + 44

Ma’ayan A, Rouillard AD, Clark NR, Wang Z, Duan Q, Kou Y. Lean Big Data Integration in Systems Biology and Systems Pharmacology. Trends in Pharmacological Sciences. 35(9):450-60 (2014) PMID: 25109570

Shameer K, Readhead B, Dudley JT. Computational and experimental advances in drug repositioning for accelerated therapeutic stratification. Current Topics in Medicinal Chemistry. 2015;15(1):5-20. PMID: 25579574

Wang Z, Clark NR, Ma’ayan A. Dynamics of the discovery process of protein-protein interactions from low content studies. BMC Syst Biol. 2015; 9: 26

Gundersen GW, Jones MR, Rouillard AD, Kou Y, Monteiro CD, Feldmann AS, Hu KS, Ma'ayan A. GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions. Bioinformatics. 2015 May 13. pii: btv297. [Epub ahead of print]  

Kidd BA, Readhead BP, Eden C, Parekh S, Dudley JT. Integrative network modeling approaches to personalized cancer medicine. Per Med. 2015 Jun 1;12(3):245-257., PMID: 27019658

Rouillard AD, Wang Z, Ma’ayan A. Abstraction for Data Integration: Fusing Mammalian Molecular, Cellular and Phenotype Big Datasets for Better Knowledge Extraction.Computational Biology and Chemistry pii: S1476-9271(15)00083-3 (2015) PMID: 26297300,

Khan JA, Mendelson A, Kunisaki Y, Birbrair A, Kou Y, Arnal-Estapé A, Pinho S, Ciero P, Nakahara F, Ma'ayan A, Bergman A, Merad M, Frenette PS., Fetal liver hematopoietic stem cell niches associate with portal vessels., Science. 2016 Jan 8;351(6269):176-80. doi: 10.1126/science.aad0084. Epub 2015 Dec 3.

Zichen Wang, Neil R. Clark, and Avi Ma'ayan. Drug Induced Adverse Events Prediction with the LINCS L1000 Data. Bioinformatics. 2016 Aug 1;32(15):2338-45. doi: 10.1093/bioinformatics/btw168. Epub 2016 Apr 1., PMID: 27153606

Kong DS, Kim J, Lee IH, Kim ST, Seol HJ, Lee JI, Park WY, Ryu G, Wang Z, Ma'ayan A, Nam DH. Integrative radiogenomic analysis for multicentric radiophenotype in glioblastoma. Oncotarget. 2016 Feb 1. doi: 10.18632/oncotarget.7115. [Epub ahead of print]

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. Evaluation of direct-to-consumer low-volume lab tests in healthy adults. J Clin Invest. 2016 Mar 28. pii: 86318. doi: 10.1172/JCI86318. [Epub ahead of print]

Shameer K, Badgeley MA, Miotto R, Glicksberg BS, Morgan JW, Dudley JT. Translational bioinformatics in the era of real-time biomedical, health care and wellness data streams. Brief Bioinform. 2016 Feb 14. pii: bbv118. [Epub ahead of print]

Kidd, Brian A; Wroblewska, Aleksandra; Boland, Mary R; Agudo, Judith; Merad, Miriam; Tatonetti, Nicholas P; Brown, Brian D; Dudley, Joel T, Mapping the effects of drugs on the immune system., Nat Biotechnol 2016 Jan;34(1):47-54. doi: 10.1038/nbt.3367. Epub 2015 Nov 30., PMID: 26619012

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, An Integrated Transcriptome Atlas of Embryonic Hair Follicle Progenitors, Their Niche, and the Developing Skin., Dev Cell. 2015 Sep 14;34(5):577-91. doi: 10.1016/j.devcel.2015.06.023. Epub 2015 Aug 6., PMID: 26256211

Li, Li; Cheng, Wei-Yi; Glicksberg, Benjamin S; Gottesman, Omri; Tamler, Ronald; Chen, Rong; Bottinger, Erwin P; Dudley, Joel T, Identification of type 2 diabetes subgroups through topological analysis of patient similarity., Sci Transl Med 2015 Oct 28;7(311):311ra174. doi: 10.1126/scitranslmed.aaa9364., PMID: 26511511

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, Morphine Regulated Synaptic Networks Revealed by Integrated Proteomics and Network Analysis., Mol Cell Proteomics 2015 Oct;14(10):2564-76. doi: 10.1074/mcp.M115.047977. Epub 2015 Jul 6., PMID: 26149443.

Xu, Ke; Schadt, Eric E; Pollard, Katherine S; Roussos, Panos; Dudley, Joel T, Genomic and network patterns of schizophrenia genetic variation in human evolutionary accelerated regions., Mol Biol Evol 32 (5): 1148-60 (2015).

Björkegren, Johan L M; Kovacic, Jason C; Dudley, Joel T; Schadt, Eric E, Genome-wide significant loci: how important are they? Systems genetics to understand heritability of coronary artery disease and other common complex disorders., J Am Coll Cardiol 65 (8): 830-45 (2015).

Baida, Gleb; Bhalla, Pankaj; Kirsanov, Kirill; Lesovaya, Ekaterina; Yakubovskaya, Marianna; Yuen, Kit; Guo, Shuchi; Lavker, Robert M; Readhead, Ben; Dudley, Joel T; Budunova, Irina, REDD1 functions at the crossroads between the therapeutic and adverse effects of topical glucocorticoids., EMBO Mol Med 7 (1): 42-58 (2015).

Duan, Qiaonan; Wang, Zichen; Fernandez, Nicolas F; Rouillard, Andrew D; Tan, Christopher M; Benes, Cyril H; Ma'ayan, Avi, Drug/Cell-line Browser: interactive canvas visualization of cancer drug/cell-line viability assay datasets., Bioinformatics 30 (22): 3289-90 (2014).

Wang, Zichen; Clark, Neil R; Ma'ayan, Avi, Dynamics of the discovery process of protein-protein interactions from low content studies., BMC Syst Biol 9: 26 (2015), PubMed Abstract: pubmed/26048415 

Rouillard AD, Gundersen GW, Fernandez NF, Wang Z, Monteiro CD, McDermott MG, Ma'ayan A, The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. Database (Oxford). 2016 Jul 3;2016. pii: baw100. doi: 10.1093/database/baw100. Print 2016. PMID: 27374120, PMCID: PMC4930834

Wang Z, Monteiro CD, Jagodnik KM, Fernandez NF, Gundersen GW, Rouillard AD, Jenkins SL, Feldmann AS, Hu KS, McDermott MG, Duan Q, Clark NR, Jones MR1, Kou Y, Goff T1, Woodland H, Amaral FM, Szeto GL, Fuchs O, Schüssler-Fiorenza Rose SM, Sharma S, Schwartz U, Bausela XB, Szymkiewicz M, Maroulis V, Salykin A, Barra CM, Kruth CD, Bongio NJ, Mathur V20, Todoric RD, Rubin UE, Malatras A, Fulp CT, Galindo JA, Motiejunaite R, Jüschke C, Dishuck PC, Lahl K, Jafari M, Aibar S, Zaravinos A, Steenhuizen LH, Allison LR, Gamallo P, de Andres Segura F, Dae Devlin T, Pérez-García V, Ma'ayan A., Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd., Nat Commun. 2016 Sep 26;7:12846. doi: 10.1038/ncomms12846.

Qiaonan Duan, St Patrick Reid, Neil R Clark, Zichen Wang, Nicolas F Fernandez, Andrew D Rouillard, Ben Readhead, Sarah R Tritsch, Rachel Hodos, Marc Hafner, Mario Niepel, Peter K Sorger, Joel T Dudley, Sina Bavari, Rekha G Panchal & Avi Ma’ayan, L1000CDS2: LINCS L1000 characteristic direction signatures search engine. npj Systems Biology and Applications 2, Article number: 16015 (2016) doi:10.1038/npjsba.2016.15

Mallipattu SK, Guo Y, Revelo MP, Roa-Peña L, Miller T, Ling J, Shankland SJ, Bialkowska AB, Ly V, Estrada C, Jain MK, Lu Y, Ma'ayan A, Mehrotra A, Yacoub R, Nord EP, Woroniecki RP, Yang VW, He JC., Krüppel-Like Factor 15 Mediates Glucocorticoid-Induced Restoration of Podocyte Differentiation Markers., J Am Soc Nephrol. 2016 Jun 10. pii: ASN.2015060672. [Epub ahead of print], PMID: 27288011

Morgan DJ, Poolman TM, Williamson AJ, Wang Z, Clark NR, Ma'ayan A, Whetton AD, Brass A, Matthews LC, Ray DW., Glucocorticoid receptor isoforms direct distinct mitochondrial programs to regulate ATP production., Sci Rep. 2016 May 26;6:26419. doi: 10.1038/srep26419., PMID: 27226058

Kuleshov MV, Jones MR, Rouillard AD, Fernandez NF, Duan Q, Wang Z, Koplev S, Jenkins SL, Jagodnik KM, Lachmann A, McDermott MG, Monteiro CD, Gundersen GW, Ma'ayan A., Enrichr: a comprehensive gene set enrichment analysis web server 2016 update., Nucleic Acids Res. 2016 Jul 8;44(W1):W90-7. doi: 10.1093/nar/gkw377. Epub 2016 May 3., PMID: 27141961

Hodos RA, Kidd BA, Shameer K, Readhead BP, Dudley JT., In silico methods for drug repurposing and pharmacology., Wiley I Interdiscip Rev Syst Biol Med. 2016 May;8(3):186-210. doi: 10.1002/wsbm.1337. Epub 2016 Apr 15. Review., PMID: 27080087

Rezza A, Wang Z, Sennett R, Qiao W, Wang D, Heitman N, Mok KW, Clavel C, Yi R, Zandstra P, Ma'ayan A, Rendl M., Signaling Networks among Stem Cell Precursors, Transit-Amplifying Progenitors, and their Niche in Developing Hair Follicles., Cell Rep. 2016 Mar 29;14(12):3001-18. doi: 10.1016/j.celrep.2016.02.078. Epub 2016 Mar 19., PMID: 27009580

Ruderfer DM, Charney AW, Readhead B, Kidd BA, Kähler AK, Kenny PJ, Keiser MJ, Moran JL, Hultman CM, Scott SA, Sullivan PF, Purcell SM, Dudley JT, Sklar P., Polygenic overlap between schizophrenia risk and antipsychotic response: a genomic medicine approach., Lancet Psychiatry. 2016 Apr;3(4):350-7. doi: 10.1016/S2215-0366(15)00553-2. Epub 2016 Feb 23., PMID: 26915512

Clark NR, Szymkiewicz M, Wang Z, Monteiro CD, Jones MR, Ma'ayan A., Principal Angle Enrichment Analysis (PAEA): Dimensionally Reduced Multivariate Gene Set Enrichment Analysis Tool., Proceedings (IEEE Int Conf Bioinformatics Biomed). 2015 Nov;2015:256-262., PMID: 26848405

Readhead B, Haure-Mirande JV, Zhang B, Haroutunian V, Gandy S, Schadt EE, Dudley JT, Ehrlich ME., Molecular systems evaluation of oligomerogenic APP(E693Q) and fibrillogenic APP(KM670/671NL)/PSEN1(Δexon9) mouse models identifies shared features with human Alzheimer's brain molecular pathology., Mol Psychiatry. 2016 Aug;21(8):1099-111. doi: 10.1038/mp.2015.167. Epub 2015 Nov 10., PMID: 26552589

Gundersen GW, Jagodnik KM, Woodland H, Fernandez NF, Sani K, Dohlman AB, Ung PM, Monteiro CD, Schlessinger A, Ma'ayan A. , GEN3VA, Aggregation and analysis of gene expression signatures from related studies.BMC Bioinformatics. 2016;17(1):461. PMID: 27846806

Wang Z, Ma'ayan A., An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study.,F1000Research. 2016;5:1574: PMID: 27583132

Asada N, Kunisaki Y, Pierce H, Wang Z, Fernandez NF, Birbrair A, Ma'ayan A, Frenette PS. Differential cytokine contributions of perivascular haematopoietic stem cell niches. Nat Cell Biol. 2017 Feb 20. doi: 10.1038/ncb3475. PMID: 28218906

Shameer K, Glicksberg BS, Hodos R, Johnson KW, Badgeley MA, Readhead B, Tomlinson MS, O'Connor T, Miotto R, Kidd BA, Chen R, Ma'ayan A, Dudley JT. Systematic analyses of drugs and disease indications in RepurposeDB reveal pharmacological, biological and epidemiological factors influencing drug repositioning.  Brief Bioinform. 2017 Feb 15. doi: 10.1093/bib/bbw136. PMID: 28200013

Li L, Greene I, Readhead B, Menon MC, Kidd BA, Uzilov AV, Wei C, Philippe N, Schroppel B, He JC, Chen R, Dudley JT, Murphy B.,  Novel Therapeutics Identification for Fibrosis in Renal Allograft Using Integrative Informatics Approach. Sci Rep. 2017 Jan 4;7:39487. doi: 10.1038/srep39487. PMID: 28051114, PMCID: PMC5209709.

Cohain A, Divaraniya AA, Zhu K, Scarpa JR, Kasarskis A, Zhu J, Chang R, Dudley JT, Schadt EE.,
Exploring The Reproducibility of Probabilistic Causal Molecular Network Models.  Pac Symp Biocomput. 2016;22:120-131. PMID: 27896968, PMCID: PMC5161348

Li L, Boland MR, Miotto R, Tatonetti NP, Dudley JT., Replicating Cardiovascular Condition-Birth Month Associations. Sci Rep. 2016 Sep 14;6:33166. doi: 10.1038/srep33166. PMID: 27624541, PMCID: PMC5021975

von Schimmelmann M, Feinberg PA, Sullivan JM, Ku SM, Badimon A, Duff MK, Wang Z, Lachmann A, Dewell S, Ma'ayan A, Han MH, Tarakhovsky A, Schaefer A., Polycomb repressive complex 2 (PRC2) silences genes responsible for neurodegeneration. Nat Neurosci. 2016 Oct;19(10):1321-30. doi: 10.1038/nn.4360. PMID: 27526204, PMCID: PMC5088783

Glicksberg BS, Li L, Badgeley MA, Shameer K, Kosoy R, Beckmann ND, Pho N, Hakenberg J, Ma M, Ayers KL, Hoffman GE, Dan Li S, Schadt EE, Patel CJ, Chen R, Dudley JT., Comparative analyses of population-scale phenomic data in electronic medical records reveal race-specific disease networks., Bioinformatics. 2016 Jun 15;32(12):i101-i110. doi: 10.1093/bioinformatics/btw282., PMID: 27307606, PMCID: PMC4908366

Sengupta PP, Huang YM, Bansal M, Ashrafi A, Fisher M, Shameer K, Gall W, Dudley JT., Cognitive Machine-Learning Algorithm for Cardiac Imaging: A Pilot Study for Differentiating Constrictive Pericarditis From Restrictive Cardiomyopathy., Circ Cardiovasc Imaging. 2016 Jun;9(6). pii: e004330. doi: 10.1161/CIRCIMAGING.115.004330., PMID: 27266599

Miotto R, Li L, Kidd BA, Dudley JT., Deep Patient: An Unsupervised Representation to Predict the Future of Patients from the Electronic Health Records.,  Sci Rep. 2016 May 17;6:26094. doi: 10.1038/srep26094.
PMID: 27185194, PMCID: PMC4869115

Duarte LF, Young AR, Wang Z, Wu HA, Panda T, Kou Y, Kapoor A, Hasson D, Mills NR, Ma'ayan A, Narita M, Bernstein E., Histone H3.3 and its proteolytically processed form drive a cellular senescence programme.,  Nat Commun. 2014 Nov 14;5:5210. doi: 10.1038/ncomms6210., PMID: 25394905, PMCID: PMC4235654.

Ma'ayan A, Duan Q., A blueprint of cell identity., Nat Biotechnol. 2014 Oct;32(10):1007-8. doi: 10.1038/nbt.3035. PMID: 25299921, PMCID: PMC4274604

█ UNM KMC site: Tudor Oprea U54 CA189205 + 10

Subramani Mani, Daniel Cannon, Robin Ohls, Tudor Oprea, Stephen Mathias, Karri Ballard, Oleg Ursu, Cristian Bologa. Protein biomarker druggability profiling, Journal of Biomedical Informatics, 66, 241-247, March 2017.

Yu Lin, Saurabh Mehta, Hande Kucuk McGinty, John Paul Turner, Dusica Vidovic, Michele Forlin, Amar Koleti, Dac-Trung Nguyen, Lars Juhl Jensen, Rajarshi Guha, Stephen L Mathias, Oleg Ursu, Vasileios Stathias, Jianbin Duan, Nooshin Nabizadeh, Caty Chung, Christopher Mader, Ubbo Visser, Jeremy J Yang, Cristian G Bologa, T Oprea, Stephan C Schurer. Drug Target Ontology to Classify and Integrate Drug Discovery Data, bioRxiv, 117564, January 2017.

Tudor I. Oprea and John P. Overington, Computational and Practical Aspects of Drug Repositioning, Drug Repurposing, Rescue and Repositioning, March 2015: 28-35.

Benet, L.Z., Hosey, C.M., Ursu, O., Oprea, T.I. BDDCS, the Rule of 5 and drugability. Adv. Drug Deliv. Rev. 101: 89-98 (2016) S0169409X16301491

Yang, J.J., Ursu, O., Lipinski, C.A., Sklar, L.A., Oprea, T.I., Bologa, C.G. Badapple: promiscuity patterns from noisy evidence. J. Cheminf. 8:1-14 (2016) S0169409X16301491

George-Thompson AM, Ursu O, Babkin P, Iancu CV, Whang A, Oprea TI, Choe JY. Discovery of a specific inhibitor of human GLUT5 by virtual screening and in vitro transport evaluation. Scientific Reports, Epub 2016 Apr 14.

Santos, R., Ursu, O., Gaulton, A., Bento, A.P., Donadi, R.S., Bologa, C., Karlsson, A., Al-Lazikani, B., Hersey, A., Oprea, T.I., & Overington, J.P. A Comprehensive Map of Molecular Drug Targets. Nature Rev. Drug Discov. doi:10.1038/nrd.2016.230 (2016)

Ursu, O., Holmes, J., Knockel, J., Bologa, C.G., Yang, J.J., Mathias, S.L., Nelson, S.J., & Oprea, T.I. DrugCentral: online drug compendium. Nucl Acids Res., Database issue, doi:10.1093/nar/gkw993 (2017)

Oprea, T.I, & Hasselgren, C. Predicting Target and Chemical Druggability. In Comprehensive Medicinal Chemistry 3e Vol. 3, “In Silico Drug Discovery Tools”, edited by Davis, A.M. & Edge, C. (2017).

Liu, T., Oprea, T., Ursu, O., Hasselgren, C. and Altman, R.B., 2016. Estimation of Maximum Recommended Therapeutic Dose Using Predicted Promiscuity and Potency. Clinical and Translational Science. 2016 Oct 13. doi: 10.1111/cts.12422. [Epub ahead of print]

NCATS KMC sub-site: Rajarshi Guha + 1

D-T Nguyen, S. Mathias, C. Bologa, S. Brunak, N. Fernandez, A. Gaulton, A. Hersey, J. Holmes, L. J. Jensen, A. Karlsson, G. Liu, A. Ma’ayan, G. Mandava, S. Mani, S. Mehta, J. Overington, J. Patel, A. D. Rouillard, S. Schurer, T. Sheils, A. Simeonov, L. A. Sklar, N. Southall, O. Ursu, D. Vidovic, A. Waller, J. Yang, A. Jadhav, T. Oprea, R. Guha, “Pharos: Collating Protein Information to Shed Light on the Druggable Genome”, Nucleic Acids Research (2017) - accepted

NNFCPR KMC sub-site: Lars Juhl Jensen + 2

A. Santos, K. Tsafou, C. Stolte, S. Pletscher-Frankild, S.I. O’Donoghue and L.J. Jensen. Comprehensive comparison of large-scale tissue expression datasets. PeerJ,3, e1054, 2015.

S. Pyysalo, J. Campos, J.M. Cejuela, F. Ginter, K. Hakala, C. Li, P. Stenetorp and L.J. Jensen. Sharing annotations better: RESTful Open Annotation. To appear in Proceedings of the 53rd Annual Meeting of the Association for Computational Linguistics, 2015.

U of Miami KMC sub-site: Stephan Schurer + 4

Maykel Cruz-Monteagudo, Stephan Schürer, Eduardo Tejera, Yunierkis Pérez-Castillo, José L. Medina-Franco, Aminael Sánchez-Rodríguez, Fernanda Borges. Systemic QSAR and phenotypic virtual screening: chasing butterflies in drug discovery. Science Direct, March, 2017.

Yu Lin, Saurabh Mehta, Hande Kucuk McGinty, John Paul Turner, Dusica Vidovic, Michele Forlin, Amar Koleti, Dac-Trung Nguyen, Lars Juhl Jensen, Rajarshi Guha, Stephen L. Mathias, Oleg Ursu, Vasileios Stathias, Jianbin Duan, Nooshin Nabizadeh, Caty Chung, Christopher Mader, Ubbo Visser, Jeremy J. Yang, Cristian G. Bologa, Tudor Oprea, Stephan C. Schurer. Drug Target Ontology to Classify and Integrate Drug Discovery Data. Biorxiv, March 16, 2017. 1doi: cross listed under KMC UNM)

Sharma R, Schürer SC and Muskal SM. High quality, small molecule-activity datasets for kinase research [version 2; referees: 2 approved]. F1000Research 2016, 5(Chem Inf Sci):1366 doi: 10 .12688/f1000research.8950.2

Maillet, E.L.; Milon, N.; Heghinian, M.D.; Fishback, J.; Schürer, S.C.; Garamszegi, N.; Mash, D.C. “Noribogaine is a G-protein biased κ-opioid receptor agonist” Neuropharmacology 2015, 99, 675-688, doi:10.1016/j.neuropharm.2015.08.032; 815300770


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