Alumni

Tony Chen (2020-2022)

Academic advisor: Briana Stephenson
Tony is a second year PhD student in the Biostatistics PhD program. His primary research interest is high-dimensional methodology related to genomics and EHR data.

Lauren Hsu (2020-2022)

Academic advisor: John Quackenbush
Lauren is a second year PhD student in the Biostatistics PhD program. Her primary research interest is computational biology and bioinformatics, and in particular, in methods and tool development for integrative analysis of heterogeneous biological datasets, especially singlecell and/or multi-modal data.

Jenna Landy (2020-2022)

Academic advisor: Paige Williams
Jenna is a second year PhD student in the Biostatistics PhD program. Her primary research interests are genomic data science, particularly for applications to cancer research.

Jordan Rossen (2020-2022)

Academic advisors, Alkes Price and Liming Liang
Jordan is a second year student in the Population Heath Sciences (Epidemiology) PhD program. His primary research interests are methods for polygenic risk prediction in non-European populations.

Arpan Sarkar (2020-2022)

Academic advisor, Curtis Huttenhower
Arpan is a second year PhD student in the Biostatistics PhD program. His primary research interests are Homology search, sequence alignment, and deep learning with respect to natural language processing.

 

 

In 2017 NIGMS announced they would no longer accept T32 applications for the NIH parent announcement under which the previous grant, T32GM074897 was funded.  As a result, the renewal of the Statistical Genetics/Genomics and Computational Biology training grant was submitted as a new grant application to the NIGMS specific FOA.  The successful application, T32GM135117, was funded starting in July 2019 and has the same goal to train the next generation of quantitative genomic scientists to have a strong understanding of, and commitment to, cutting-edge methodological and collaborative research in statistical genetics/genomics and bioinformatics/computational biology with applications in genetic epidemiology, molecular biology and genomic medicine.

Listed below are some of the alumni of the previous grant:

Catherine Xue (2018-)

Luli Zou (2018-)

Derek Shyr (2018-)

Daniel Li (2018-)

Noah Connally (2017-)

Sarah Kalia (2017-)

Harrison Reeder (2017-)

Jane Liang (2017-)

Yuri Ahuja (2017-)

Shayna Stein (2016-)

Andy Shi (2016-)

Kamrine Poels (2016-)

Luke O’Connor (2016-2019)

Michele S. Zemplenyi (2015-2020)

Matthew S. Ploenzke (2015-2020)

Daphne M. Tsoucas (2014-2018)

Zack McCaw (2014-2019)

  • Successful F31 Grant: “Innovations in Genome Wide Association Testing Inspired by Obstructive Sleep Apnea Phenotypes” Grant Number: F31HL140822

Shirley X. Liao (2014-2019)

Emily M. Slade (2013-2018)

Matthew O. Goodman (2013-2018)

Stephanie F. Chan (2013-2018)

Richard T. Barfield (2012-2017)

Current Position: Postdoctoral Researcher, Fred Hutchinson Cancer Research Center

Publications while in training include:

  • Goldlust IS, Hermetz KE, Catalano LM, Barfield RT, Cozad R, Wynn G, Ozdemir AC, Conneely KN, Mulle JG, Dharamrup S, Hegde MR, Kim KH, Angle B, Colley A, Webb AE, Thorland EC, Ellison JW, Rosenfeld JA, Ballif BC, Shaffer LG, Demmer LA; Unique Rare Chromosome Disorder Support Group, Rudd MK. Mouse model implicates GNB3 duplication in a childhood obesity syndrome Proc Natl Acad Sci U S A. 2013 Sep 10;110(37):14990-4. doi: 10.1073/pnas.1305999110 PMCID:PMC3773733
  • Barfield RT, Almli LM, Kilaru V, Smith AK, Mercer KB, Duncan R, Klengel T, Mehta D, Binder EB, Epstein MP, Ressler KJ, Conneely KN. Accounting for population stratification in DNA methylation studies. Genet Epidemiol. 2014 Apr;38(3):231-41. doi: 10.1002/gepi.21789. [PubMed – in process]

Godwin Yung (2011-2016)

Current Position: Senior Statistician, Takeda Pharmaceuticals, Cambridge, MA.

Publications while in training include:

  • Chan LW, Lin X, Yung G, Lui T, Chiu YM, Wang F, Tsui NB, Cho WC, Yip SP, Siu PM, Wong SC, Yung BY. Novel structural co-expression analysis linking the NPM1-associated ribosomal biogenesis network to chronic myelogenous leukemia. Scientific reports. 2015;5:10973. Epub 2015/07/25. doi: 10.1038/srep10973. PubMed PMID: 26205693; PMCID: PMC4513283.
  • Yung G, Lin X. Validity of using ad hoc methods to analyze secondary traits in case-control association studies. Genetic epidemiology. 2016;40(8):732-43. Epub 2016/09/28. doi: 10.1002/gepi.21994. PubMed PMID: 27670932; PMCID: PMC5170877.

Emma Schwager Holdrich (2011-2017)

Current Position: statistical consultant for VL45, Inc.

Publications while in training include:

  • Schwager, E., Ventz, S., Mallick, H., and Huttenhower, C. (2017). A Bayesian Method for Detecting Pairwise Associations in Compositional Data. PLoS Computational Biology, 13:e1005852. PMID: 29140991
  • Sinha, R., Abu-Ali, G., Vogtmann, E. V., Fodor, A. A., Ren, B., Amir, A., Schwager, E., The Microbiome Quality Control Project Consortium, Abnet, C. C., Knight, R., White, O., and Huttenhower, C. (2017). Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium. Nature Biotechnology, 35:1077–1086. PMID: 28967885
  • Yasuda, K., Hsu, T., Gallini, C., McIver, L., Schwager, E., Shi, A., DuLong, C., Schwager, R., AbuAli, G., Franzosa, E. A., Garrett, W. S., Huttenhower, C., and Morgan, X. C. (2017). Fluoride Depletes Acidogenic Taxa in Oral but Not Gut Microbial Communities in Mice. mSystems, 4:e00047–17. PMID: 28808691

Shelley Liu (2011-2016) 

Current Position: Assistant Professor at Icahn School of Medicine at Mount Sinai, New York, NY.

Publications while in training include:

  • Liu SH, Erion G, Novitsky V, De Gruttola V. Viral Genetic Linkage Analysis in the Presence of Missing Data. PloS one. 2015;10(8):e0135469. Epub 2015/08/25. doi: 10.1371/journal.pone.0135469. PubMed PMID: 26301919; PMCID: PMC4547719.

Tristan Hayeck (2010-2015)

Current Position: Postdoctoral Research Scientist, Columbia University Medical Center, Institute for Genomic Medicine, New York, NY.

Publications while in training include:

  • Hayeck TJ, Zaitlen NA, Loh PR, Vilhjalmsson B, Pollack S, Gusev A, Yang J, Chen GB, Goddard ME, Visscher PM, Patterson N, Price AL. Mixed model with correction for case-control ascertainment increases association power. American journal of human genetics. 2015;96(5):720-30. Epub 2015/04/22. doi: 10.1016/j.ajhg.2015.03.004. PubMed PMID: 25892111; PMCID: PMC4570278.
  • Vilhjalmsson BJ, Yang J, Finucane HK, Gusev A, Lindstrom S, Ripke S, Genovese G, Loh PR, Bhatia G, Do R, Hayeck T, Won HH, Kathiresan S, Pato M, Pato C, Tamimi R, Stahl E, Zaitlen N, Pasaniuc B, Belbin G, Kenny EE, Schierup MH, De Jager P, Patsopoulos NA, McCarroll S, Daly M, Purcell S, Chasman D, Neale B, Goddard M, Visscher PM, Kraft P, Patterson N, Price AL. Modeling Linkage Disequilibrium Increases Accuracy of Polygenic Risk Scores. American journal of human genetics. 2015;97(4):576-92. Epub 2015/10/03. doi: 10.1016/j.ajhg.2015.09.001. PubMed PMID: 26430803; PMCID: PMC4596916.
  • Hayeck TJ, Loh PR, Pollack S, Gusev A, Patterson N, Zaitlen NA, Price AL. Mixed Model Association with Family-Biased Case-Control Ascertainment. American journal of human genetics. 2017;100(1):31-9. Epub 2016/12/27. doi: 10.1016/j.ajhg.2016.11.015. PubMed PMID: 28017371; PMCID: PMC5223022.

Ian Barnett (2010-2014)

Current Position: Assistant Professor, Department of Biostatistics and Epidemiology University of Pennsylvania

Publications while in training include:

  • Barnett IJ, Lee S, Lin X. Detecting rare variant effects using extreme phenotype sampling in sequencing association studies. Genetic epidemiology. 2013;37(2):142-51. Epub 2012/11/28. doi: 10.1002/gepi.21699. PubMed PMID: 23184518; PMCID: PMC3601902.
  • Barnett IJ, Lin X. Analytic P-value calculation for the higher criticism test in finite d problems. Biometrika. 2014;101(4):964-70. Epub 2014/01/01. doi: 10.1093/biomet/asu033. PubMed PMID: 25750439; PMCID: PMC4350786.
  • Fan T, Fang SC, Cavallari JM, Barnett IJ, Wang Z, Su L, Byun HM, Lin X, Baccarelli AA, Christiani DC. Heart rate variability and DNA methylation levels are altered after short-term metal fume exposure among occupational welders: a repeated-measures panel study. BMC public health. 2014;14:1279. Epub 2014/12/17. doi: 10.1186/1471-2458-14-1279. PubMed PMID: 25512264; PMCID: PMC4302115.
  • Barnett I, Khanna T, Onnela JP. Social and Spatial Clustering of People at Humanity’s Largest Gathering. PloS one. 2016;11(6):e0156794. Epub 2016/06/04. doi: 10.1371/journal.pone.0156794. PubMed PMID: 27258037; PMCID: PMC4892527.
  • Barnett I, Onnela JP. Change Point Detection in Correlation Networks. Scientific reports. 2016;6:18893. Epub 2016/01/08. doi: 10.1038/srep18893. PubMed PMID: 26739105; PMCID: PMC4703970.

Mitchell Machiela (2008-2012)

Current Position: Tenure Track Investigator, Laboratory of Genetic Susceptibility (LGS) National Cancer Institute

Publications while in training include:

  • Beebe-Dimmer JL, Levin AM, Ray AM, Zuhlke KA, Machiela MJ, Halstead-Nussloch BA, Johnson GR, Cooney KA, Douglas JA. Chromosome 8q24 markers: risk of early-onset and familial prostate cancer. Int J Cancer. 2008 Jun 15;122(12):2876-9. doi: 10.1002/ijc.23471. PMCID: PMC2695763.
  • Levin AM, Machiela MJ, Zuhlke KA, Ray AM, Cooney KA, Douglas JA. Chromosome 17q12 variants contribute to risk of early-onset prostate cancer. Cancer Res.2008 Aug 15;68(16):6492-5. doi: 10.1158/0008-5472.CAN-08-0348. PMCID: PMC2562290.
  • Machiela MJ, Lindström S, Allen NE, Haiman CA, Albanes D, Barricarte A, BerndtSI, Bueno-de-Mesquita HB, Chanock S, Gaziano JM, Gapstur SM, Giovannucci E, Henderson BE, Jacobs EJ, Kolonel LN, Krogh V, Ma J, Stampfer MJ, Stevens VL,Stram DO, Tjønneland A, Travis R, Willett WC, Hunter DJ, Le Marchand L, Kraft P. Association of type 2 diabetes susceptibility variants with advanced prostate cancer risk in the Breast and Prostate Cancer Cohort Consortium. Am J Epidemiol. 2012 Dec 15;176(12):1121-9. doi: 10.1093/aje/kws191. Epub 2012 Nov 28. PMCID: PMC3571230.
  • Machiela MJ, Chen C, Liang L, Diver WR, Stevens VL, Tsilidis KK, Haiman CA, Chanock SJ, Hunter DJ, Kraft P; National Cancer Institute Breast and Prostate Cancer Cohort Consortium. One thousand genomes imputation in the National Cancer Institute Breast and Prostate Cancer Cohort Consortium aggressive prostate cancer genome-wide association study. Prostate. 2013 May;73(7):677-89. doi:10.1002/pros.22608. Epub 2012 Dec 19. PMCID: PMC 3962143.
  • Faye LL, Machiela MJ, Kraft P, Bull SB, Sun L. Re-ranking sequencing variants in the post-GWAS era for accurate causal variant identification. PLoS Genet. 2013;9(8):e1003609. doi: 10.1371/journal.pgen.1003609. Epub 2013 Aug 8. PMCID: PMC3738448.
  • Machiela MJ, Chanock SJ. Detectable clonal mosaicism in the human genome. Semin Hematol. 2013 Oct;50(4):348-59. doi: 10.1053/j.seminhematol.2013.09.001. PMCID: PMC3855860.
  • Machiela MJ, Chanock SJ. GWAS is going to the dogs. Genome Biology 2014, 15:105. doi:10.1186/gb4166. PMCID: PMC4014671.

Jennifer Sinnott (2008-2012)

Current Position: Assistant Professor in the Department of Statistics at Ohio State University, Columbus, OH

Publications while in training include:

  • Stark JR, Wiklund F, Grönberg H, Schumacher F, Sinnott JA, Stampfer MJ, Mucci LA, Kraft P. Toll-like receptor signaling pathway variants and prostate cancer mortality. Cancer Epidemiol Biomarkers Prev. 2009 Jun;18(6):1859-63. PMCID:PMC2833418.
  • Stark JR, Perner S, Stampfer MJ, Sinnott JA, Finn S, Eisenstein AS, Ma J, Fiorentino M, Kurth T, Loda M, Giovannucci EL, Rubin MA, Mucci LA. Gleason score and lethal prostate cancer: does 3 + 4 = 4 + 3? J Clin Oncol. 2009 Jul 20;27(21):3459-64. PMCID: PMC2717753.
  • Penney KL, Pyne S, Schumacher FR, Sinnott JA, Mucci LA, Kraft PL, Ma J, Oh WK, Kurth T, Kantoff PW, Giovannucci EL, Stampfer MJ, Hunter DJ, Freedman ML. Genome-wide association study of prostate cancer mortality. Cancer Epidemiol Biomarkers Prev. 2010 Nov;19(11):2869-76. PMCID: PMC3197738.
  • Fiorentino M, Judson G, Penney K, Flavin R, Stark J, Fiore C, Fall K, Martin N, Ma J, Sinnott J, Giovannucci E, Stampfer M, Sesso HD, Kantoff PW, Finn S, Loda M, Mucci L. Immunohistochemical expression of BRCA1 and lethal prostate cancer. Cancer research 2010; 70(8): 3136-3139. PMCID: PMC3049266.
  • Penney KL*, Sinnott JA*, Fall K, Pawitan Y, Hoshida Y, Kraft P, Stark JR, Fiorentino M, Perner S, Finn S, Calza S, Flavin R, Freedman ML, Setlur S, Sesso HD, Andersson SO, Martin N, Kantoff PW, Johansson JE, Adami HO, Rubin MA, Loda M, Golub TR, Andrén O, Stampfer MJ, Mucci LA. mRNA expression signature of Gleason grade predicts lethal prostate cancer. J Clin Oncol. 2011 Jun 10;29(17):2391-6. PMCID: PMC3107753. (* co-first-authors)
  • Wang S, Wu J, Suburu J, Gu Z, Cai J, Axanova LS, Cramer SD, Thomas MJ, Perry DL, Edwards IJ, Mucci LA, Sinnott JA, Loda MF, Sui G, Berquin IM, Chen YQ. Effect of dietary polyunsaturated fatty acids on castration-resistant Pten-null prostate cancer. Carcinogenesis. 2012 Feb;33(2):404-12.PMCID: PMC3271270.
  • Sinnott JA, Kraft P. Artifact due to differential error when cases and controls are imputed from different platforms. Hum Genet. 2012 Jan;131(1):111-9. PMCID: PMC3217156.
  • Sinnott JA, Cai T. Omnibus risk assessment via accelerated failure time kernel machine modeling. Biometrics. 2013 Dec;69(4):861-73. PMCID: PMC3869038.
  • Zu K, Martin NE, Fiorentino M, Flavin R, Lis RT, Sinnott JA, Finn S, Penney KL, Ma J, Fazli L, Gleave ME, Bismar TA, Stampfer MJ, Pollak MN, Loda M, Mucci LA, Giovannucci E. Protein expression of PTEN, insulin-like growth factor I receptor (IGF-IR), and lethal prostate cancer: a prospective study. Cancer Epidemiol Biomarkers Prev. 2013 Nov;22(11):1984-93. PMCID: PMC3818474.
  • Penney KL, Stampfer MJ, Jahn JL, Sinnott JA, Flavin R, Rider JR, Finn S, Giovannucci E, Sesso HD, Loda M, Mucci LA, Fiorentino M. Gleason grade progression is uncommon. Cancer Res. 2013 Aug 15;73(16):5163-8. PMCID: PMC3775342.
  • Flavin RJ, Pettersson A, Hendrickson WK, Fiorentino M, Finn SP, Kunz L, Judson G, Lis RT, Bailey D, Fiore C, Nuttall EJ, Martin NE, Stack EC, Penney KL, Rider JR, Sinnott JA, Sweeney CS, Sesso HD, Fall K, Giovannucci EL, Kantoff PW, Stampfer MJ, Loda M, Mucci LA. SPINK1 Protein Expression and Prostate Cancer Progression. Clin Cancer Res. 2014 Sep 15;20(18):4904-11. doi: 10.1158/1078-0432.CCR-13-1341. Epub 2014 Mar 31. PMCID: PMC4167171.
  • Book Chapter: Sinnott, JA, and Cai T. “High-Dimensional Regression Models.” Handbook of Survival Analysis (2013): 93.

Sihai Dave Zhao (2007-2012)

Current Position: Assistant Professor at the University of Illinois at Urbana-Champaign, Department of Statistics, Champaign, IL

Publications while in training include:

  • Li Y, Dicker L, Zhao SD. The Dantzig Selector for Censored Linear Regression Models. Stat Sin. 2014 Jan 1;24(1):251-2568. PMCID: PMC3903419.
  • Zhao SD, and Li Y. Principled sure independence screening for Cox models with ultra-high-dimensional covariates. J Multivar Anal. 2012 Feb 1;105(1):397-411. (PMCID: PMC3293491 [Available on 2013/2/1]).
  • Goguen LA, Chapuy CI, Li Y., Zhao SD, Annino DJ. Neck dissection after chemoradiation – timing and complications. Arch Otolaryngol Head Neck Surg. 2010;136(11):1071-1077. (http://archotol.ama-assn.org/cgi/content/full/136/11/1071).
  • Stryjewski, T. P., Benadretti, D. B., Zhao, S. D., Rowe, S., and Mitnick, C. D., “Preliminary clinical outcomes from the Peruvian National Cataract Elimination Plan”. Rev Panam Salud Publica. 2010 Oct;28(4):282-8. (PMID: 21152716).
  • Zhao, S. D. and Li, Y. A note on optimal weights and variable selections for multivariate survival data. Science in China Series A, 2009; 52, 1131–1133.
  • Janket, SJ, Bollu, P, Zhao, SD. “Questionable performance of a questionnaire” Journal of Dental Research, 2008; 87(10): E1-E1.

Jessica Larson (2007-2012)

Current Position: Senior Scientist II, Asuragen, Inc., Austin, TX

Publications while in training include:

  • Larson JL, Yuan GC Epigenetic domains found in mouse embryonic stem cells via a hidden Markov model. BMC Bioinformatics. 2010 Nov 12;11:557. doi: 10.1186/1471-2105-11-557. PMCID:PMC2992069
  • Larson JL, Yuan GC.Chromatin states accurately classify cell differentiation stages. PLoS One. 2012;7(2):e31414. doi: 10.1371/journal.pone.0031414. Epub 2012 Feb 20. PMCID: PMC3282719
  • Larson JL, Huttenhower C, Quackenbush J, Yuan GC. A tiered hidden Markov model characterizes multi-scale chromatin states. Genomics. 2013 Jul;102(1):1-7. doi: 10.1016/j.ygeno.2013.03.009. Epub 2013 Apr 6. PMCID: PMC3676702
  • Pozniak CD, Sengupta Ghosh A, Gogineni A, Hanson JE, Lee SH, Larson JL, Solanoy H, Bustos D, Li H, Ngu H, Jubb AM, Ayalon G, Wu J, Scearce-Levie K, Zhou Q, Weimer RM, Kirkpatrick DS, Lewcock JW. Dual leucine zipper kinase is required for excitotoxicity-induced neuronal degeneration. J Exp Med. 2013 Nov 18;210(12):2553-67. doi: 10.1084/jem.20122832. Epub 2013 Oct 28. PMCID: PMC3832926
  • Pozniak CD, Sengupta Ghosh A, Gogineni A, Hanson JE, Lee SH, Larson JL, Solanoy H, Bustos D, Li H, Ngu H, Jubb AM, Ayalon G, Wu J, Scearce-Levie K, Zhou Q, Weimer RM, Kirkpatrick DS, Lewcock JW. Dual leucine zipper kinase is required for excitotoxicity-induced neuronal degeneration. J Exp Med. 2013 Nov 18;210(12):2553-67. doi: 10.1084/jem.20122832. PMCID: PMC3832926.

Layla Parast (2007-2012)

Current Position: Associate Statistician with Rand Corporation, Santa Monica, CA

Publications while in training include:

  • Parast L, Cheng S, Cai T. Landmark Prediction of Long Term Survival Incorporating Short Term Event Time Information. J Am Stat Assoc. 2012;107(500):1492-1501. Epub 2012 Aug 21. PMCID: PMC3535339.
  • Parast L, Cai T. Landmark risk prediction of residual life for breast cancer survival. Stat Med. 2013 Sep 10;32(20):3459-71. doi: 10.1002/sim.5776. Epub 2013 Mar 14. PMCID: PMC3744612.
  • Lu MT, Demehri S, Cai T, Parast L, Hunsaker AR, Goldhaber SZ, Rybicki FJ. Axial and reformatted 4-chamber RV/LV diameter ratios on CT pulmonary angiography as predictors of death after acute pulmonary embolism. AJR Am J Roentgenol. 2012 Jun;198(6):1353-60. (PMID: 22623548).
  • Parast L, Cheng SC, Cai T. Incorporating short-term outcome information to predict long-term survival with discrete markers. Biom J. 2011 Mar;53(2):294-307. doi: 10.1002/bimj.201000150. Epub 2011 Feb 21. PMCID: PMC3472667.
  • Qi L, Parast L, Powers C, Cai T, Hu FB, Doria A. Genetic Susceptibility to Coronary Heart Disease in Type 2 Diabetes: Three Independent Studies. J Am Coll Cardiol. 2011 Dec 13;58(25):2675-82. [Received the American Diabetes Association Michaele Modan Memorial Award, June 2010.] PMCID: PMC3240896.

Jessie Hsu (2006-2012)

Current Position: Statistical Scientist at Genentech, Inc., South San Francisco, CA

Publications while in training include:

  • Snuderl M, Kolman OK, Chen YB, Hsu JJ, Ackerman AM, Dal Cin P, Ferry JA, Harris NL, Hasserjian RP, Zukerberg LR, Abramson JS, Hochberg EP, Lee H, Lee AI, Toomey CE, Sohani AR. “B-cell lymphomas with concurrent IGH-BCL2 and MYC rearrangements are aggressive neoplasms with clinical and pathologic features distinct from Burkitt lymphoma and diffuse large B-cell lymphoma.” American Journal of Surgical Pathology, 2010 Mar; 34(3):327-40. (PMCID: PMC3152212).
  • Atkins MB, Hsu J, Lee S, Cohen GI, Flaherty LE, Sosman JA, Sondak VK, Kirkwood JM. “Phase III Trial Comparing Concurrent Biochemotherapy With Cisplatin, Vinblastine, Dacarbazine, Interleukin-2, and Interferon Alfa-2b With Cisplatin, Vinblastine, and Dacarbazine Alone in Patients With Metastatic Malignant Melanoma (E3695): A Trial Coordinated by the Eastern Cooperative Oncology Group”. Journal of Clinical Oncology 2008 26(35) 5748-5754. (PMCID: PMC2645104).

Keith Betts (2005-2010)

Current Position: Vice President at Analysis Group Inc., Los Angeles, CA

Publications while in training include:

  • Alm El-Din MA, Hughes KS, Finkelstein DM, Betts KA, Yock TI, Tarbell NJ, Aisenberg AC, Taghian AG. “Breast Cancer After Treatment of Hodgkin’s Lymphoma: Risk Factors that Really Matter.” Int J Radiat Oncol Biol Phys, 2008; 69(3):S27.
  • Signorovitch JE, Wu EQ, Betts KA, Parikh K, Kantor E, Guo A, Bollu VK, Williams D, Wei LJ, DeAngelo DJ.Curr Med Res Opin. Comparative efficacy of nilotinib and dasatinib in newly diagnosed chronic myeloid leukemia: a matching-adjusted indirect comparison of randomized trials. 2011 Jun;27(6):1263-71. doi: 10.1185/03007995.2011.576238. Epub 2011 Apr 28. (not federally funded)
  • Sikirica V, Pliszka SR, Betts KA, Hodgkins P, Samuelson T, Xie J, Erder H, Dammerman R, Robertson B, Wu EQ. Comparative treatment patterns, resource utilization, and costs in stimulant-treated children with ADHD who require subsequent pharmacotherapy with atypical antipsychotics versus non-antipsychotics. J Manag Care Pharm. 2012 Nov-Dec;18(9):676-89. (not federally funded)
  • Signorovitch JE, Sikirica V, Erder MH, Xie J, Lu M, Hodgkins PS, Betts KA, Wu EQ. Matching-adjusted indirect comparisons: a new tool for timely comparative effectiveness research.Value Health. 2012 Sep-Oct;15(6):940-7. doi: 10.1016/j.jval.2012.05.004. (not federally funded)
  • Erder MH, Signorovitch JE, Setyawan J, Yang H, Parikh K, Betts KA, Xie J, Hodgkins P, Wu EQ. Identifying patient subgroups who benefit most from a treatment: using administrative claims data to uncover treatment heterogeneity. J Med Econ. 2012;15(6):1078-87. doi: 10.3111/13696998.2012.689270. Epub 2012 Jun 14. (Not federally funded)

Michael Wu (2004-2009)

Current Position: Assistant Member in the Biostatistics and Biomathematics Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center

Publications while in training include:

  • Wu MC, Zhang L, Wang Z, Christiani DC and Lin X. Sparse linear discriminant analysis for simultaneous testing for the significance of a gene set/pathway and gene selection. Bioinformatics, 2009; 25(9): 1145-51. (PMCID: PMC2732305.)
  • Huang YT, Heist RS, Chirieac LR, Lin X, Skaug V, Zienolddiny S, Haugen A, Wu MC, Wang Z, Su L, Asomaning K and Christiani DC. Genome-Wide Analysis of Survival in Early-Stage Non-Small-Cell Lung Cancer. J Clin Oncol, 2009. (PMCID: PMC2690391.)
  • Engbring, J.A., Hossain, R., VanOsdol, S.J., Kaplan-Singer, B., Wu, M, Hibino, S., Koblinski, JE. “The laminin alpha-1 chain derived peptide, AG73, increases fibronectin levels in breast and melanoma cancer cells”. Clinical and Experimental Metastasis, 2008; 25(3):241-52. Epub 2008 Jan 10. (PMID: 18185912).
  • Wu, M, Cai, T, Lin, X. “A parametric permutation test for regression coefficients in LASSO regularized regression.” Submitted to Journal of the American Statistical Association.
  • Harezlak J, Wu MC, Wang M, Schwartzman A, Christiani DC and Lin X. Biomarker discovery for arsenic exposure using functional data. Analysis and feature learning of mass spectrometry proteomic data. J Proteome Res, 2008; 7(1): 217-24. (PMID: 18173220).
  • Ji H, Ramsey MR, Hayes DN, Fan C, McNamara K, Kozlowski P, Torrice C, Wu MC, Shimamura T, Perera SA, Liang MC, Cai D, Naumov GN, Bao L, Contreras CM, Li D, Chen L, Krishnamurthy J, Koivunen J, Chirieac LR, Padera RF, Bronson RT, Lindeman NI, Christiani DC, Lin X, Shapiro GI, Janne PA, Johnson BE, Meyerson M, Kwiatkowski DJ, Castrillon DH, Bardeesy N, Sharpless NE and Wong KK. LKB1 modulates lung cancer differentiation and metastasis. Nature, 2007; 448(7155): 807-10. (PMID: 17676035).

Patrick Loerch (2003-2008)

Current Position: Senior Director of Medical Informatics, IKU Celgene Corporation, San Francisco, CA

Publications while in training include:

  • Loerch P, Lu T, Dakin KA, Vann JM, Isaacs A, et al. “Evolution of the Aging Brain Transcriptome and Synaptic Regulation.” PLoS ONE, 2008; Oct 2;3(10):e3329 (PMID: PMC2553198).
  • Yankner B, Lu T, and Loerch P. “The Aging Brain.”Annual Review of Pathology: Mechanisms of Disease, 2008; 3:41-66. (PMID: 18039130).
  • Oberdoerffer P, Michan S, McVay M, Mostoslavsky R, Vann J, Park SK, Hartlerode A, Stegmuller J, Hafner A, Loerch P, Wright SM, Mills KD, Bonni A, Yankner BA, Scully R, Prolla TA, Alt FW and Sinclair DA. SIRT1 redistribution on chromatin promotes genomic stability but alters gene expression during aging. Cell, 2008; 135(5): 907-18. (PMCID: PMC2853975).

James Signorovitch (2002-2007)

Current Position: Managing Principal Analysis Group, Inc, Research-Intensive

Publications while in training include:

  • Sadow, CA; Silverman, SG; O’Leary, MP, Signorovitch JE. “Bladder cancer detection with CT urography in an academic medical center” Radiology, 2008; 249(1): 195-202. (PMID: 18796677).
  • Moukarbel, GV; Signorovitch, JE; Pfeffer, MA, et al. “Risk factors for gastrointestinal bleeding in post-myocardial infarction patients: Results from the VALIANT trial”, Journal of the American College of Cardiology, 2008; 51(10) A248-A248.
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