Publications

Data Science

Avali VR, Cooper GF, Gopalakrishnan V. Application of Bayesian logistic regression to mining biomedical data. AMIA Annu Symp Proc. 2014;2014266-73. PubMed PMID: 25954328; PMCID: PMC4419893.
Jiang X, Cai B, Xue D, Lu X, Cooper GF, Neapolitan RE. A comparative analysis of methods for predicting clinical outcomes using high-dimensional genomic datasets. J Am Med Inform Assoc. 2014 Oct;21(e2):e312-9. doi: 10.1136/amiajnl-2013-002358. PubMed PMID: 24737607; PMCID: PMC4173174.
Bakan A, Dutta A, Mao W, Liu Y, Chennubhotla C, Lezon TR, Bahar I. Evol and ProDy for bridging protein sequence evolution and structural dynamics. Bioinformatics. 2014 Sep 15;30(18):2681-3. doi: 10.1093/bioinformatics/btu336. PubMed PMID: 24849577; PMCID: PMC4155247.
Korotchenko VN, Saydmohammed M, Vollmer LL, Bakan A, Sheetz K, Debiec KT, Greene KA, Agliori CS, Bahar I, Day BW, Vogt A, Tsang M. In vivo structure-activity relationship studies support allosteric targeting of a dual specificity phosphatase. Chembiochem. 2014 Jul 7;15(10):1436-45. doi: 10.1002/cbic.201402000. PubMed PMID: 24909879; PMCID: PMC4118675.
Katz TA, Vasilatos SN, Harrington E, Oesterreich S, Davidson NE, Huang Y. Inhibition of histone demethylase, LSD2 (KDM1B), attenuates DNA methylation and increases sensitivity to DNMT inhibitor-induced apoptosis in breast cancer cells. Breast Cancer Res Treat. 2014 Jul;146(1):99-108. doi: 10.1007/s10549-014-3012-9. PubMed PMID: 24924415.
Zhu J, Zhang Y, Ghosh A, Cuevas RA, Forero A, Dhar J, Ibsen MS, Schmid-Burgk JL, Schmidt T, Ganapathiraju MK, Fujita T, Hartmann R, Barik S, Hornung V, Coyne CB, Sarkar SN. Antiviral activity of human OASL protein is mediated by enhancing signaling of the RIG-I RNA sensor. Immunity. 2014 Jun 19;40(6):936-48. doi: 10.1016/j.immuni.2014.05.007. PubMed PMID: 24931123; PMCID: PMC4101812.
Erwin GD, Oksenberg N, Truty RM, Kostka D, Murphy KK, Ahituv N, Pollard KS, Capra JA. Integrating diverse datasets improves developmental enhancer prediction. PLoS Comput Biol. 2014 Jun;10(6):e1003677. doi: 10.1371/journal.pcbi.1003677. PubMed PMID: 24967590; PMCID: PMC4072507.
Gough AH, Chen N, Shun TY, Lezon TR, Boltz RC, Reese CE, Wagner J, Vernetti LA, Grandis JR, Lee AV, Stern AM, Schurdak ME, Taylor DL. Identifying and quantifying heterogeneity in high content analysis: application of heterogeneity indices to drug discovery. PLoS One. 2014;9(7):e102678. doi: 10.1371/journal.pone.0102678. PubMed PMID: 25036749; PMCID: PMC4103836.
Koes DR, Camacho CJ. Shape-based virtual screening with volumetric aligned molecular shapes. J Comput Chem. 2014 Sep 30;35(25):1824-34. doi: 10.1002/jcc.23690. PubMed PMID: 25049193; PMCID: PMC4140985.
Harlow L, Gochuico BR, Rosas IO, Doyle TJ, Osorio JC, Travers TS, Camacho CC, Oddis CV, Ascherman DP. Anti-citrullinated heat shock protein 90 antibodies identified in bronchoalveolar lavage fluid are a marker of lung-specific immune responses. Clin Immunol. 2014 Nov;155(1):60-70. doi: 10.1016/j.clim.2014.08.004. PubMed PMID: 25150019; PMCID: PMC4629481.
Liu B, Bhatt D, Oltvai ZN, Greenberger JS, Bahar I. Significance of p53 dynamics in regulating apoptosis in response to ionizing radiation, and polypharmacological strategies. Sci Rep. 2014 Sep 1;46245. doi: 10.1038/srep06245. PubMed PMID: 25175563; PMCID: PMC4150106.
Strickler AG, Vasquez JG, Yates N, Ho J. Potential diagnostic significance of HSP90, ACS/TMS1, and L-plastin in the identification of melanoma. Melanoma Res. 2014 Dec;24(6):535-44. doi: 10.1097/CMR.0000000000000115. PubMed PMID: 25191796.
Suryawanshi S, Huang X, Elishaev E, Budiu RA, Zhang L, Kim S, Donnellan N, Mantia-Smaldone G, Ma T, Tseng G, Lee T, Mansuria S, Edwards RP, Vlad AM. Complement pathway is frequently altered in endometriosis and endometriosis-associated ovarian cancer. Clin Cancer Res. 2014 Dec 1;20(23):6163-74. doi: 10.1158/1078-0432.CCR-14-1338. PubMed PMID: 25294912; PMCID: PMC4252715.
Cheng MH, Bahar I. Complete mapping of substrate translocation highlights the role of LeuT N-terminal segment in regulating transport cycle. PLoS Comput Biol. 2014 Oct;10(10):e1003879. doi: 10.1371/journal.pcbi.1003879. PubMed PMID: 25299050; PMCID: PMC4191883.
Cai C, Chen L, Jiang X, Lu X. Modeling signal transduction from protein phosphorylation to gene expression. Cancer Inform. 2014;13(Suppl 1):59-67. doi: 10.4137/CIN.S13883. PubMed PMID: 25392684; PMCID: PMC4216050.
Fang Q, Inanc B, Schamus S, Wang XH, Wei L, Brown AR, Svilar D, Sugrue KF, Goellner EM, Zeng X, Yates NA, Lan L, Vens C, Sobol RW. HSP90 regulates DNA repair via the interaction between XRCC1 and DNA polymerase β. Nat Commun. 2014 Nov 26;55513. doi: 10.1038/ncomms6513. PubMed PMID: 25423885; PMCID: PMC4246423.
Tang S, Ding Y, Sibille E, Mogil J, Lariviere WR, Tseng GC. Imputation of Truncated p-Values For Meta-Analysis Methods and Its Genomic Application. Ann Appl Stat. 2014 Dec;8(4):2150-2174. doi: 10.1214/14-AOAS747. PubMed PMID: 25541588; PMCID: PMC4274812.
King AJ, Cooper GF, Hochheiser H, Clermont G, Visweswaran S. Development and Preliminary Evaluation of a Prototype of a Learning Electronic Medical Record System. AMIA Annu Symp Proc. 2015;20151967-75. PubMed PMID: 26958296; PMCID: PMC4765593.
Eyal E, Lum G, Bahar I. The anisotropic network model web server at 2015 (ANM 2.0). Bioinformatics. 2015 May 1;31(9):1487-9. doi: 10.1093/bioinformatics/btu847. PubMed PMID: 25568280; PMCID: PMC4410662.
Kwun HJ, Shuda M, Camacho CJ, Gamper AM, Thant M, Chang Y, Moore PS. Restricted protein phosphatase 2A targeting by Merkel cell polyomavirus small T antigen. J Virol. 2015 Apr;89(8):4191-200. doi: 10.1128/JVI.00157-15. PubMed PMID: 25631078; PMCID: PMC4442354.
Nasu M, Emi M, Pastorino S, Tanji M, Powers A, Luk H, Baumann F, Zhang YA, Gazdar A, Kanodia S, Tiirikainen M, Flores E, Gaudino G, Becich MJ, Pass HI, Yang H, Carbone M. High Incidence of Somatic BAP1 alterations in sporadic malignant mesothelioma. J Thorac Oncol. 2015 Apr;10(4):565-76. doi: 10.1097/JTO.0000000000000471. PubMed PMID: 25658628; PMCID: PMC4408084.
Mao W, Kaya C, Dutta A, Horovitz A, Bahar I. Comparative study of the effectiveness and limitations of current methods for detecting sequence coevolution. Bioinformatics. 2015 Jun 15;31(12):1929-37. doi: 10.1093/bioinformatics/btv103. PubMed PMID: 25697822; PMCID: PMC4481699.
Leone JP, Lee AV, Brufsky AM. Prognostic factors and survival of patients with brain metastasis from breast cancer who underwent craniotomy. Cancer Med. 2015 Jul;4(7):989-94. doi: 10.1002/cam4.439. PubMed PMID: 25756607; PMCID: PMC4529337.
Manohar R, Li Y, Fohrer H, Guzik L, Stolz DB, Chandran UR, LaFramboise WA, Lagasse E. Identification of a candidate stem cell in human gallbladder. Stem Cell Res. 2015 May;14(3):258-69. doi: 10.1016/j.scr.2014.12.003. PubMed PMID: 25765520; PMCID: PMC4439375.
Lee AV, Oesterreich S, Davidson NE. MCF-7 cells--changing the course of breast cancer research and care for 45 years. J Natl Cancer Inst. 2015 Jul;107(7): doi: 10.1093/jnci/djv073. PubMed PMID: 25828948.
Gau DM, Lesnock JL, Hood BL, Bhargava R, Sun M, Darcy K, Luthra S, Chandran U, Conrads TP, Edwards RP, Kelley JL, Krivak TC, Roy P. BRCA1 deficiency in ovarian cancer is associated with alteration in expression of several key regulators of cell motility - A proteomics study. Cell Cycle. 2015;14(12):1884-92. doi: 10.1080/15384101.2015.1036203. PubMed PMID: 25927284; PMCID: PMC4614952.
Naeini MP, Cooper GF, Hauskrecht M. Obtaining Well Calibrated Probabilities Using Bayesian Binning. Proc Conf AAAI Artif Intell. 2015 Jan;20152901-2907. PubMed PMID: 25927013; PMCID: PMC4410090.
Zuo ZH, Yu YP, Ding Y, Liu S, Martin A, Tseng G, Luo JH. Oncogenic Activity of miR-650 in Prostate Cancer Is Mediated by Suppression of CSR1 Expression. Am J Pathol. 2015 Jul;185(7):1991-9. doi: 10.1016/j.ajpath.2015.03.015. PubMed PMID: 25956032; PMCID: PMC4484220.
Farabaugh SM, Boone DN, Lee AV. Role of IGF1R in Breast Cancer Subtypes, Stemness, and Lineage Differentiation. Front Endocrinol (Lausanne). 2015;659. doi: 10.3389/fendo.2015.00059. PubMed PMID: 25964777; PMCID: PMC4408912.
Luo JH, Liu S, Zuo ZH, Chen R, Tseng GC, Yu YP. Discovery and Classification of Fusion Transcripts in Prostate Cancer and Normal Prostate Tissue. Am J Pathol. 2015 Jul;185(7):1834-45. doi: 10.1016/j.ajpath.2015.03.008. PubMed PMID: 25963990; PMCID: PMC4483459.
Mony JT, Zhang L, Ma T, Grabosch S, Tirodkar TS, Brozick J, Tseng G, Elishaev E, Edwards RP, Huang X, Vlad AM. Anti-PD-L1 prolongs survival and triggers T cell but not humoral anti-tumor immune responses in a human MUC1-expressing preclinical ovarian cancer model. Cancer Immunol Immunother. 2015 Sep;64(9):1095-108. doi: 10.1007/s00262-015-1712-6. PubMed PMID: 25998800; PMCID: PMC4545381.
Chen L, Cai C, Chen V, Lu X. Trans-species learning of cellular signaling systems with bimodal deep belief networks. Bioinformatics. 2015 Sep 15;31(18):3008-15. doi: 10.1093/bioinformatics/btv315. PubMed PMID: 25995230; PMCID: PMC4668779.
Rahaman MM, Reinders FG, Koes D, Nguyen AT, Mutchler SM, Sparacino-Watkins C, Alvarez RA, Miller MP, Cheng D, Chen BB, Jackson EK, Camacho CJ, Straub AC. Structure Guided Chemical Modifications of Propylthiouracil Reveal Novel Small Molecule Inhibitors of Cytochrome b5 Reductase 3 That Increase Nitric Oxide Bioavailability. J Biol Chem. 2015 Jul 3;290(27):16861-72. doi: 10.1074/jbc.M114.629964. PubMed PMID: 26001785; PMCID: PMC4505432.
Travers T, Shao H, Joughin BA, Lauffenburger DA, Wells A, Camacho CJ. Tandem phosphorylation within an intrinsically disordered region regulates ACTN4 function. Sci Signal. 2015 May 26;8(378):ra51. doi: 10.1126/scisignal.aaa1977. PubMed PMID: 26012634; PMCID: PMC4522051.
Logan GJ, Dabbs DJ, Lucas PC, Jankowitz RC, Brown DD, Clark BZ, Oesterreich S, McAuliffe PF. Molecular drivers of lobular carcinoma in situ. Breast Cancer Res. 2015 Jun 4;1776. doi: 10.1186/s13058-015-0580-5. PubMed PMID: 26041550; PMCID: PMC4453073.
Bakan A, Kapralov AA, Bayir H, Hu F, Kagan VE, Bahar I. Inhibition of Peroxidase Activity of Cytochrome c: De Novo Compound Discovery and Validation. Mol Pharmacol. 2015 Sep;88(3):421-7. doi: 10.1124/mol.115.097816. PubMed PMID: 26078313; PMCID: PMC4551054.
Koes DR, Camacho CJ. Indexing Volumetric Shapes with Matching and Packing. Knowl Inf Syst. 2015 Apr 1;43(1):157-180. doi: 10.1007/s10115-014-0729-z. PubMed PMID: 26085707; PMCID: PMC4465823.
Jiang S, Katz TA, Garee JP, DeMayo FJ, Lee AV, Oesterreich S. Scaffold attachment factor B2 (SAFB2)-null mice reveal non-redundant functions of SAFB2 compared with its paralog, SAFB1. Dis Model Mech. 2015 Sep;8(9):1121-7. doi: 10.1242/dmm.019885. PubMed PMID: 26092125; PMCID: PMC4582101.
Louis DN, Feldman M, Carter AB, Dighe AS, Pfeifer JD, Bry L, Almeida JS, Saltz J, Braun J, Tomaszewski JE, Gilbertson JR, Sinard JH, Gerber GK, Galli SJ, Golden JA, Becich MJ. Computational Pathology: A Path Ahead. Arch Pathol Lab Med. 2016 Jan;140(1):41-50. doi: 10.5858/arpa.2015-0093-SA. PubMed PMID: 26098131; PMCID: PMC4996078.
Visweswaran S, Ferreira A, Ribeiro GA, Oliveira AC, Cooper GF. Personalized Modeling for Prediction with Decision-Path Models. PLoS One. 2015;10(6):e0131022. doi: 10.1371/journal.pone.0131022. PubMed PMID: 26098570; PMCID: PMC4476684.
Geskin A, Legowski E, Chakka A, Chandran UR, Barmada MM, LaFramboise WA, Berg J, Jacobson RS. Needs Assessment for Research Use of High-Throughput Sequencing at a Large Academic Medical Center. PLoS One. 2015;10(6):e0131166. doi: 10.1371/journal.pone.0131166. PubMed PMID: 26115441; PMCID: PMC4483235.
Nayak SR, Harrington E, Boone D, Hartmaier R, Chen J, Pathiraja TN, Cooper KL, Fine JL, Sanfilippo J, Davidson NE, Lee AV, Dabbs D, Oesterreich S. A Role for Histone H2B Variants in Endocrine-Resistant Breast Cancer. Horm Cancer. 2015 Dec;6(5-6):214-24. doi: 10.1007/s12672-015-0230-5. PubMed PMID: 26113056; PMCID: PMC4807402.
Cooper GF, Bahar I, Becich MJ, Benos PV, Berg J, Espino JU, Glymour C, Jacobson RC, Kienholz M, Lee AV, Lu X, Scheines R, Center for Causal Discovery team.. The center for causal discovery of biomedical knowledge from big data. J Am Med Inform Assoc. 2015 Nov;22(6):1132-6. doi: 10.1093/jamia/ocv059. PubMed PMID: 26138794; PMCID: PMC5009908.
Bahar I, Cheng MH, Lee JY, Kaya C, Zhang S. Structure-Encoded Global Motions and Their Role in Mediating Protein-Substrate Interactions. Biophys J. 2015 Sep 15;109(6):1101-9. doi: 10.1016/j.bpj.2015.06.004. PubMed PMID: 26143655; PMCID: PMC4576147.
Leone JP, Bhargava R, Theisen BK, Hamilton RL, Lee AV, Brufsky AM. Expression of high affinity folate receptor in breast cancer brain metastasis. Oncotarget. 2015 Oct 6;6(30):30327-33. doi: 10.18632/oncotarget.4639. PubMed PMID: 26160847; PMCID: PMC4745802.
Edwards RP, Huang X, Vlad AM. Chronic inflammation in endometriosis and endometriosis-associated ovarian cancer: New roles for the "old" complement pathway. Oncoimmunology. 2015 May;4(5):e1002732. doi: 10.1080/2162402X.2014.1002732. PubMed PMID: 26155393; PMCID: PMC4485759.
Ogoe HA, Visweswaran S, Lu X, Gopalakrishnan V. Knowledge transfer via classification rules using functional mapping for integrative modeling of gene expression data. BMC Bioinformatics. 2015 Jul 23;16226. doi: 10.1186/s12859-015-0643-8. PubMed PMID: 26202217; PMCID: PMC4512094.
Baumgartner MP, Camacho CJ. Choosing the Optimal Rigid Receptor for Docking and Scoring in the CSAR 2013/2014 Experiment. J Chem Inf Model. 2016 Jun 27;56(6):1004-12. doi: 10.1021/acs.jcim.5b00338. PubMed PMID: 26222931; PMCID: PMC4744803.
Grover P, Shi H, Baumgartner M, Camacho CJ, Smithgall TE. Fluorescence Polarization Screening Assays for Small Molecule Allosteric Modulators of ABL Kinase Function. PLoS One. 2015;10(7):e0133590. doi: 10.1371/journal.pone.0133590. PubMed PMID: 26222440; PMCID: PMC4519180.
Edmunds LR, Sharma L, Wang H, Kang A, d'Souza S, Lu J, McLaughlin M, Dolezal JM, Gao X, Weintraub ST, Ding Y, Zeng X, Yates N, Prochownik EV. c-Myc and AMPK Control Cellular Energy Levels by Cooperatively Regulating Mitochondrial Structure and Function. PLoS One. 2015;10(7):e0134049. doi: 10.1371/journal.pone.0134049. PubMed PMID: 26230505; PMCID: PMC4521957.
Liao S, Hartmaier RJ, McGuire KP, Puhalla SL, Luthra S, Chandran UR, Ma T, Bhargava R, Modugno F, Davidson NE, Benz S, Lee AV, Tseng GC, Oesterreich S. The molecular landscape of premenopausal breast cancer. Breast Cancer Res. 2015 Aug 7;17104. doi: 10.1186/s13058-015-0618-8. PubMed PMID: 26251034; PMCID: PMC4531812.
Chandran UR, Luthra S, Santana-Santos L, Mao P, Kim SH, Minata M, Li J, Benos PV, DeWang M, Hu B, Cheng SY, Nakano I, Sobol RW. Gene expression profiling distinguishes proneural glioma stem cells from mesenchymal glioma stem cells. Genom Data. 2015 Sep 1;5333-336. doi: 10.1016/j.gdata.2015.07.007. PubMed PMID: 26251826; PMCID: PMC4523279.
Haliloglu T, Bahar I. Adaptability of protein structures to enable functional interactions and evolutionary implications. Curr Opin Struct Biol. 2015 Dec;3517-23. doi: 10.1016/j.sbi.2015.07.007. PubMed PMID: 26254902; PMCID: PMC4688206.
Koes DR, Pabon NA, Deng X, Phillips MA, Camacho CJ. A Teach-Discover-Treat Application of ZincPharmer: An Online Interactive Pharmacophore Modeling and Virtual Screening Tool. PLoS One. 2015;10(8):e0134697. doi: 10.1371/journal.pone.0134697. PubMed PMID: 26258606; PMCID: PMC4530941.
Casa AJ, Hochbaum D, Sreekumar S, Oesterreich S, Lee AV. The estrogen receptor alpha nuclear localization sequence is critical for fulvestrant-induced degradation of the receptor. Mol Cell Endocrinol. 2015 Nov 5;41576-86. doi: 10.1016/j.mce.2015.08.007. PubMed PMID: 26272024.
Boisen MM, Andersen CL, Sreekumar S, Stern AM, Oesterreich S. Treating gynecologic malignancies with selective estrogen receptor downregulators (SERDs): promise and challenges. Mol Cell Endocrinol. 2015 Dec 15;418 Pt 3322-33. doi: 10.1016/j.mce.2015.04.035. PubMed PMID: 26276546.
Brown DD, Dabbs DJ, Lee AV, McGuire KP, Ahrendt GM, Bhargava R, Davidson NE, Brufsky AM, Johnson RR, Oesterreich S, McAuliffe PF. Developing in vitro models of human ductal carcinoma in situ from primary tissue explants. Breast Cancer Res Treat. 2015 Sep;153(2):311-21. doi: 10.1007/s10549-015-3551-8. PubMed PMID: 26283301.
Katz TA, Liao SG, Palmieri VJ, Dearth RK, Pathiraja TN, Huo Z, Shaw P, Small S, Davidson NE, Peters DG, Tseng GC, Oesterreich S, Lee AV. Targeted DNA Methylation Screen in the Mouse Mammary Genome Reveals a Parity-Induced Hypermethylation of Igf1r That Persists Long after Parturition. Cancer Prev Res (Phila). 2015 Oct;8(10):1000-9. doi: 10.1158/1940-6207.CAPR-15-0178. PubMed PMID: 26290394; PMCID: PMC4677681.
Abdelraheem EM, Camacho CJ, Dömling A. Focusing on shared subpockets - new developments in fragment-based drug discovery. Expert Opin Drug Discov. 2015;10(11):1179-87. doi: 10.1517/17460441.2015.1080684. PubMed PMID: 26296101; PMCID: PMC4933841.
Yu YP, Liu S, Huo Z, Martin A, Nelson JB, Tseng GC, Luo JH. Genomic Copy Number Variations in the Genomes of Leukocytes Predict Prostate Cancer Clinical Outcomes. PLoS One. 2015;10(8):e0135982. doi: 10.1371/journal.pone.0135982. PubMed PMID: 26295840; PMCID: PMC4546524.
Lu S, Lu KN, Cheng SY, Hu B, Ma X, Nystrom N, Lu X. Identifying Driver Genomic Alterations in Cancers by Searching Minimum-Weight, Mutually Exclusive Sets. PLoS Comput Biol. 2015 Aug;11(8):e1004257. doi: 10.1371/journal.pcbi.1004257. PubMed PMID: 26317392; PMCID: PMC4552843.
Keskin O, Dyson HJ, Bahar I. Biomolecular Systems Interactions, Dynamics, and Allostery: Reflections and New Directions. Biophys J. 2015 Sep 15;109(6):E01-2. doi: 10.1016/j.bpj.2015.08.005. PubMed PMID: 26377787; PMCID: PMC4576319.
Kroon E, Schulze JO, Süß E, Camacho CJ, Biondi RM, Dömling A. Discovery of a Potent Allosteric Kinase Modulator by Combining Computational and Synthetic Methods. Angew Chem Int Ed Engl. 2015 Nov 16;54(47):13933-6. doi: 10.1002/anie.201506310. PubMed PMID: 26385475; PMCID: PMC4721676.
Hu D, Gur M, Zhou Z, Gamper A, Hung MC, Fujita N, Lan L, Bahar I, Wan Y. Interplay between arginine methylation and ubiquitylation regulates KLF4-mediated genome stability and carcinogenesis. Nat Commun. 2015 Sep 30;68419. doi: 10.1038/ncomms9419. PubMed PMID: 26420673; PMCID: PMC4598737.
Xing J, Lee RE. Putting it all on pigmentation: Heuristics of a bold and stochastic cell fate decision. Sci Signal. 2015 Oct 6;8(397):fs17. doi: 10.1126/scisignal.aad2816. PubMed PMID: 26443702.
Ciriello G, Gatza ML, Beck AH, Wilkerson MD, Rhie SK, Pastore A, Zhang H, McLellan M, Yau C, Kandoth C, Bowlby R, Shen H, Hayat S, Fieldhouse R, Lester SC, Tse GM, Factor RE, Collins LC, Allison KH, Chen YY, Jensen K, Johnson NB, Oesterreich S, Mills GB, Cherniack AD, Robertson G, Benz C, Sander C, Laird PW, Hoadley KA, King TA, TCGA Research Network., Perou CM. Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer. Cell. 2015 Oct 8;163(2):506-19. doi: 10.1016/j.cell.2015.09.033. PubMed PMID: 26451490; PMCID: PMC4603750.
Santa-Maria CA, Blackford A, Nguyen AT, Skaar TC, Philips S, Oesterreich S, Rae JM, Desta Z, Robarge J, Henry NL, Storniolo AM, Hayes DF, Blumenthal RS, Ouyang P, Post WS, Flockhart DA, Stearns V, Consortium on Breast Cancer Pharmacogenomics (COBRA).. Association of Variants in Candidate Genes with Lipid Profiles in Women with Early Breast Cancer on Adjuvant Aromatase Inhibitor Therapy. Clin Cancer Res. 2016 Mar 15;22(6):1395-402. doi: 10.1158/1078-0432.CCR-15-1213. PubMed PMID: 26463708; PMCID: PMC4794377.
Wang P, Bahreini A, Gyanchandani R, Lucas PC, Hartmaier RJ, Watters RJ, Jonnalagadda AR, Trejo Bittar HE, Berg A, Hamilton RL, Kurland BF, Weiss KR, Mathew A, Leone JP, Davidson NE, Nikiforova MN, Brufsky AM, Ambros TF, Stern AM, Puhalla SL, Lee AV, Oesterreich S. Sensitive Detection of Mono- and Polyclonal ESR1 Mutations in Primary Tumors, Metastatic Lesions, and Cell-Free DNA of Breast Cancer Patients. Clin Cancer Res. 2016 Mar 1;22(5):1130-7. doi: 10.1158/1078-0432.CCR-15-1534. PubMed PMID: 26500237; PMCID: PMC4775406.
Oesterreich S, Henry NL, Kidwell KM, Van Poznak CH, Skaar TC, Dantzer J, Li L, Hangartner TN, Peacock M, Nguyen AT, Rae JM, Desta Z, Philips S, Storniolo AM, Stearns V, Hayes DF, Flockhart DA. Associations between genetic variants and the effect of letrozole and exemestane on bone mass and bone turnover. Breast Cancer Res Treat. 2015 Nov;154(2):263-73. doi: 10.1007/s10549-015-3608-8. PubMed PMID: 26536870; PMCID: PMC4807610.
Kim S, Herazo-Maya JD, Kang DD, Juan-Guardela BM, Tedrow J, Martinez FJ, Sciurba FC, Tseng GC, Kaminski N. Integrative phenotyping framework (iPF): integrative clustering of multiple omics data identifies novel lung disease subphenotypes. BMC Genomics. 2015 Nov 11;16924. doi: 10.1186/s12864-015-2170-4. PubMed PMID: 26560100; PMCID: PMC4642618.
Li H, Chang YY, Yang LW, Bahar I. iGNM 2.0: the Gaussian network model database for biomolecular structural dynamics. Nucleic Acids Res. 2016 Jan 4;44(D1):D415-22. doi: 10.1093/nar/gkv1236. PubMed PMID: 26582920; PMCID: PMC4702874.
Liu S, Tsai WH, Ding Y, Chen R, Fang Z, Huo Z, Kim S, Ma T, Chang TY, Priedigkeit NM, Lee AV, Luo J, Wang HW, Chung IF, Tseng GC. Comprehensive evaluation of fusion transcript detection algorithms and a meta-caller to combine top performing methods in paired-end RNA-seq data. Nucleic Acids Res. 2016 Mar 18;44(5):e47. doi: 10.1093/nar/gkv1234. PubMed PMID: 26582927; PMCID: PMC4797269.
Naeini MP, Cooper GF, Hauskrecht M. Binary Classifier Calibration Using a Bayesian Non-Parametric Approach. Proc SIAM Int Conf Data Min. 2015;2015208-216. doi: 10.1137/1.9781611974010.24. PubMed PMID: 26613068; PMCID: PMC4657569.
Yang G, Kramer MG, Fernandez-Ruiz V, Kawa MP, Huang X, Liu Z, Prieto J, Qian C. Development of Endothelial-Specific Single Inducible Lentiviral Vectors for Genetic Engineering of Endothelial Progenitor Cells. Sci Rep. 2015 Nov 27;517166. doi: 10.1038/srep17166. PubMed PMID: 26612671; PMCID: PMC4661691.
Needham S, Yates N, Barrientos R, Steel M, Lee M. Clinical and Pharmaceutical Solutions through Analysis (CPSA BRASIL 2015): on the way to innovation - pharmaceutical/analytical technology, regulation and knowledge management. Bioanalysis. 2015 Dec;7(23):2977-9. doi: 10.4155/bio.15.216. PubMed PMID: 26617112.
Jacobson RS, Becich MJ, Bollag RJ, Chavan G, Corrigan J, Dhir R, Feldman MD, Gaudioso C, Legowski E, Maihle NJ, Mitchell K, Murphy M, Sakthivel M, Tseytlin E, Weaver J. A Federated Network for Translational Cancer Research Using Clinical Data and Biospecimens. Cancer Res. 2015 Dec 15;75(24):5194-201. doi: 10.1158/0008-5472.CAN-15-1973. PubMed PMID: 26670560; PMCID: PMC4683415.
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