Publications

Systems Biology

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.
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.
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.
Barroso-González J, Thomas G. Endosome traffic machinery meets the p53-p21 axis. Mol Cell Oncol. 2015;2(2):e975075. doi: 10.4161/23723556.2014.975075. PubMed PMID: 25815376; PMCID: PMC4372196.
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.
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.
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.
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.
Dombernowsky SL, Samsøe-Petersen J, Petersen CH, Instrell R, Hedegaard AM, Thomas L, Atkins KM, Auclair S, Albrechtsen R, Mygind KJ, Fröhlich C, Howell M, Parker P, Thomas G, Kveiborg M. The sorting protein PACS-2 promotes ErbB signalling by regulating recycling of the metalloproteinase ADAM17. Nat Commun. 2015 Jun 25;67518. doi: 10.1038/ncomms8518. PubMed PMID: 26108729; PMCID: PMC4481878.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Concha-Benavente F, Srivastava RM, Trivedi S, Lei Y, Chandran U, Seethala RR, Freeman GJ, Ferris RL. Identification of the Cell-Intrinsic and -Extrinsic Pathways Downstream of EGFR and IFNγ That Induce PD-L1 Expression in Head and Neck Cancer. Cancer Res. 2016 Mar 1;76(5):1031-43. doi: 10.1158/0008-5472.CAN-15-2001. PubMed PMID: 26676749; PMCID: PMC4775348.
Kostka D, Friedrich T, Holloway AK, Pollard KS. motifDiverge: a model for assessing the statistical significance of gene regulatory motif divergence between two DNA sequences. Stat Interface. 2015;8(4):463-476. doi: 10.4310/SII.2015.v8.n4.a6. PubMed PMID: 26709360; PMCID: PMC4689439.
Begum F, Sharker MH, Sherman SL, Tseng GC, Feingold E. Regionally Smoothed Meta-Analysis Methods for GWAS Datasets. Genet Epidemiol. 2016 Feb;40(2):154-60. doi: 10.1002/gepi.21949. PubMed PMID: 26707090; PMCID: PMC4724289.
McDade KK, Chandran U, Day RS. Improving Cancer Gene Expression Data Quality through a TCGA Data-Driven Evaluation of Identifier Filtering. Cancer Inform. 2015;14149-61. doi: 10.4137/CIN.S33076. PubMed PMID: 26715829; PMCID: PMC4686346.
Batal I, Cooper G, Fradkin D, Harrison J, Moerchen F, Hauskrecht M. An Efficient Pattern Mining Approach for Event Detection in Multivariate Temporal Data. Knowl Inf Syst. 2016 Jan;46(1):115-150. doi: 10.1007/s10115-015-0819-6. PubMed PMID: 26752800; PMCID: PMC4704806.
Chang LC, Li B, Fang Z, Vrieze S, McGue M, Iacono WG, Tseng GC, Chen W. A computational method for genotype calling in family-based sequencing data. BMC Bioinformatics. 2016 Jan 16;1737. doi: 10.1186/s12859-016-0880-5. PubMed PMID: 26772743; PMCID: PMC4715317.
Li X, Cai H, Zheng W, Tong M, Li H, Ao L, Li J, Hong G, Li M, Guan Q, Yang S, Yang D, Lin X, Guo Z. An individualized prognostic signature for gastric cancer patients treated with 5-Fluorouracil-based chemotherapy and distinct multi-omics characteristics of prognostic groups. Oncotarget. 2016 Feb 23;7(8):8743-55. doi: 10.18632/oncotarget.7087. PubMed PMID: 26840027; PMCID: PMC4891001.
Gurda GT, Ambros T, Nikiforova MN, Nikiforov YE, Lucas PC, Dabbs DJ, Lee AV, Brufsky AM, Puhalla SL, Bhargava R. Characterizing Molecular Variants and Clinical Utilization of Next-generation Sequencing in Advanced Breast Cancer. Appl Immunohistochem Mol Morphol. 2017 Jul;25(6):392-398. doi: 10.1097/PAI.0000000000000322. PubMed PMID: 26862949.
Tejero J, Kapralov AA, Baumgartner MP, Sparacino-Watkins CE, Anthonymutu TS, Vlasova II, Camacho CJ, Gladwin MT, Bayir H, Kagan VE. Peroxidase activation of cytoglobin by anionic phospholipids: Mechanisms and consequences. Biochim Biophys Acta. 2016 May;1861(5):391-401. doi: 10.1016/j.bbalip.2016.02.022. PubMed PMID: 26928591; PMCID: PMC4821708.
Delgado E, Boisen MM, Laskey R, Chen R, Song C, Sallit J, Yochum ZA, Andersen CL, Sikora MJ, Wagner J, Safe S, Elishaev E, Lee A, Edwards RP, Haluska P, Tseng G, Schurdak M, Oesterreich S. High expression of orphan nuclear receptor NR4A1 in a subset of ovarian tumors with worse outcome. Gynecol Oncol. 2016 May;141(2):348-356. doi: 10.1016/j.ygyno.2016.02.030. PubMed PMID: 26946093; PMCID: PMC5154956.
Uppal R, Mandava G, Romagnoli KM, King AJ, Draper AJ, Handen AL, Fisher AM, Becich MJ, Dutta-Moscato J. How can we improve Science, Technology, Engineering, and Math education to encourage careers in Biomedical and Pathology Informatics? J Pathol Inform. 2016;72. doi: 10.4103/2153-3539.175375. PubMed PMID: 26955500; PMCID: PMC4763503.
Becker MA, Ibrahim YH, Oh AS, Fagan DH, Byron SA, Sarver AL, Lee AV, Shaw LM, Fan C, Perou CM, Yee D. Insulin Receptor Substrate Adaptor Proteins Mediate Prognostic Gene Expression Profiles in Breast Cancer. PLoS One. 2016;11(3):e0150564. doi: 10.1371/journal.pone.0150564. PubMed PMID: 26991655; PMCID: PMC4798554.
Zhang M, Liu G, Xue F, Edwards R, Sood AK, Zhang W, Yang D. Copy number deletion of RAD50 as predictive marker of BRCAness and PARP inhibitor response in BRCA wild type ovarian cancer. Gynecol Oncol. 2016 Apr;141(1):57-64. doi: 10.1016/j.ygyno.2016.01.004. PubMed PMID: 27016230; PMCID: PMC4967351.
Wu SY, Rupaimoole R, Shen F, Pradeep S, Pecot CV, Ivan C, Nagaraja AS, Gharpure KM, Pham E, Hatakeyama H, McGuire MH, Haemmerle M, Vidal-Anaya V, Olsen C, Rodriguez-Aguayo C, Filant J, Ehsanipour EA, Herbrich SM, Maiti SN, Huang L, Kim JH, Zhang X, Han HD, Armaiz-Pena GN, Seviour EG, Tucker S, Zhang M, Yang D, Cooper LJ, Ali-Fehmi R, Bar-Eli M, Lee JS, Ram PT, Baggerly KA, Lopez-Berestein G, Hung MC, Sood AK. A miR-192-EGR1-HOXB9 regulatory network controls the angiogenic switch in cancer. Nat Commun. 2016 Apr 4;711169. doi: 10.1038/ncomms11169. PubMed PMID: 27041221; PMCID: PMC4822037.
Sverchkov Y, Cooper GF. A Bayesian Approach for Identifying Multivariate Differences Between Groups. Adv Intell Data Anal. 2015 Oct;9385275-285. doi: 10.1007/978-3-319-24465-5_24. PubMed PMID: 27069983; PMCID: PMC4825814.
Hain E, Camacho CJ, Koes DR. Fragment oriented molecular shapes. J Mol Graph Model. 2016 May;66143-54. doi: 10.1016/j.jmgm.2016.03.017. PubMed PMID: 27085751; PMCID: PMC4862882.
Edmunds LR, Otero PA, Sharma L, D'Souza S, Dolezal JM, David S, Lu J, Lamm L, Basantani M, Zhang P, Sipula IJ, Li L, Zeng X, Ding Y, Ding F, Beck ME, Vockley J, Monga SP, Kershaw EE, O'Doherty RM, Kratz LE, Yates NA, Goetzman EP, Scott D, Duncan AW, Prochownik EV. Abnormal lipid processing but normal long-term repopulation potential of myc-/- hepatocytes. Oncotarget. 2016 May 24;7(21):30379-95. doi: 10.18632/oncotarget.8856. PubMed PMID: 27105497; PMCID: PMC5058687.
Kim SH, Kaschula CH, Priedigkeit N, Lee AV, Singh SV. Forkhead Box Q1 Is a Novel Target of Breast Cancer Stem Cell Inhibition by Diallyl Trisulfide. J Biol Chem. 2016 Jun 24;291(26):13495-508. doi: 10.1074/jbc.M116.715219. PubMed PMID: 27129776; PMCID: PMC4919436.
Kim S, Lin CW, Tseng GC. MetaKTSP: a meta-analytic top scoring pair method for robust cross-study validation of omics prediction analysis. Bioinformatics. 2016 Jul 1;32(13):1966-73. doi: 10.1093/bioinformatics/btw115. PubMed PMID: 27153719; PMCID: PMC6280887.
Gau D, Veon W, Zeng X, Yates N, Shroff SG, Koes DR, Roy P. Threonine 89 Is an Important Residue of Profilin-1 That Is Phosphorylatable by Protein Kinase A. PLoS One. 2016;11(5):e0156313. doi: 10.1371/journal.pone.0156313. PubMed PMID: 27228149; PMCID: PMC4882052.
Banerjee Mustafi S, Chakraborty PK, Naz S, Dwivedi SK, Street M, Basak R, Yang D, Ding K, Mukherjee P, Bhattacharya R. MDR1 mediated chemoresistance: BMI1 and TIP60 in action. Biochim Biophys Acta. 2016 Aug;1859(8):983-93. doi: 10.1016/j.bbagrm.2016.06.002. PubMed PMID: 27295567; PMCID: PMC4958591.
Huo Z, Ding Y, Liu S, Oesterreich S, Tseng G. Meta-analytic framework for sparse K-means to identify disease subtypes in multiple transcriptomic studies. J Am Stat Assoc. 2016;111(513):27-42. doi: 10.1080/01621459.2015.1086354. PubMed PMID: 27330233; PMCID: PMC4908837.
Erdem C, Nagle AM, Casa AJ, Litzenburger BC, Wang YF, Taylor DL, Lee AV, Lezon TR. Proteomic Screening and Lasso Regression Reveal Differential Signaling in Insulin and Insulin-like Growth Factor I (IGF1) Pathways. Mol Cell Proteomics. 2016 Sep;15(9):3045-57. doi: 10.1074/mcp.M115.057729. PubMed PMID: 27364358; PMCID: PMC5013316.
Sikora MJ, Johnson MD, Lee AV, Oesterreich S. Endocrine Response Phenotypes Are Altered by Charcoal-Stripped Serum Variability. Endocrinology. 2016 Oct;157(10):3760-3766. doi: 10.1210/en.2016-1297. PubMed PMID: 27459541; PMCID: PMC5045515.
Richardson S, Tseng GC, Sun W. Statistical Methods in Integrative Genomics. Annu Rev Stat Appl. 2016 Jun;3181-209. doi: 10.1146/annurev-statistics-041715-033506. PubMed PMID: 27482531; PMCID: PMC4963036.
Gyanchandani R, Kota KJ, Jonnalagadda AR, Minteer T, Knapick BA, Oesterreich S, Brufsky AM, Lee AV, Puhalla SL. Detection of ESR1 mutations in circulating cell-free DNA from patients with metastatic breast cancer treated with palbociclib and letrozole. Oncotarget. 2017 Sep 15;8(40):66901-66911. doi: 10.18632/oncotarget.11383. PubMed PMID: 28978004; PMCID: PMC5620144.
Kim S, Oesterreich S, Kim S, Park Y, Tseng GC. Integrative clustering of multi-level omics data for disease subtype discovery using sequential double regularization. Biostatistics. 2017 Jan;18(1):165-179. doi: 10.1093/biostatistics/kxw039. PubMed PMID: 27549122; PMCID: PMC5255053.
Sikora MJ, Jacobsen BM, Levine K, Chen J, Davidson NE, Lee AV, Alexander CM, Oesterreich S. WNT4 mediates estrogen receptor signaling and endocrine resistance in invasive lobular carcinoma cell lines. Breast Cancer Res. 2016 Sep 20;18(1):92. doi: 10.1186/s13058-016-0748-7. PubMed PMID: 27650553; PMCID: PMC5028957.
Hauskrecht M, Batal I, Hong C, Nguyen Q, Cooper GF, Visweswaran S, Clermont G. Outlier-based detection of unusual patient-management actions: An ICU study. J Biomed Inform. 2016 Dec;64211-221. doi: 10.1016/j.jbi.2016.10.002. PubMed PMID: 27720983; PMCID: PMC5207478.
Lu S, Cai C, Yan G, Zhou Z, Wan Y, Chen V, Chen L, Cooper GF, Obeid LM, Hannun YA, Lee AV, Lu X. Signal-Oriented Pathway Analyses Reveal a Signaling Complex as a Synthetic Lethal Target for p53 Mutations. Cancer Res. 2016 Dec 1;76(23):6785-6794. doi: 10.1158/0008-5472.CAN-16-1740. PubMed PMID: 27758891; PMCID: PMC5165695.
Farabaugh SM, Chan BT, Cui X, Dearth RK, Lee AV. Lack of interaction between ErbB2 and insulin receptor substrate signaling in breast cancer. Cell Commun Signal. 2016 Oct 21;14(1):25. doi: 10.1186/s12964-016-0148-8. PubMed PMID: 27765041; PMCID: PMC5073819.
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