Amit Bahl
Thesis title and defense date: Design and Application of Multi-functional Microarrays for Toxoplasma gondii, January 2008
Irina Bochkis
Post-doctoral Fellow, Regev Lab, Broad Institute
Thesis title and defense date: Hepatic Metabolic Regulatory Networks of Foxa2, November 20, 2008.
Recent publications:
Irina M Bochkis, Nir E Rubins, Peter White, Emma E Furth, Joshua R Friedman & Klaus H Kaestner. Hepatocyte-specific ablation of Foxa2 alters bile acid homeostasis and results in endoplasmic reticulum stress. Nature Medicine. Published online: 27 July 2008 | doi:10.1038/nm.1853.
Behr R, Sackett SD, Bochkis IM, Le PP, Kaestner KH. Impaired male fertility and atrophy of seminiferous tubules caused by haploinsufficiency for Foxa3. Dev Biol. 2007 Jun 15; 306(2):636-45. Epub 2007 Apr 5.
Phuc Le P, Friedman JR, Schug J, Brestelli JE, Parker JB, Bochkis IM, Kaestner KH. Glucocorticoid receptor-dependent gene regulatory networks. PLoS Genet. 2005 Aug;1(2):e16. Epub 2005 Aug 5.
ZhongQiang (John) Chen
Post-doctoral Fellow, Roos Lab, University of Pennsylvania
Thesis title and defense date: Identification of proteins associated with specialized (secretory) organelles in apicomplexan parasites, December 10, 2009.
Ryan Coleman
Post-doctoral fellow, Shoichet Lab, University of California-San Francisco
Thesis title and defense date: Shortest Geometric Paths Analysis in Structural Biology, August 28, 2009.
Recent publications:
Carlsson, J.*, Coleman, R.G.*, Setola, V.*, Irwin, J.J., Fan, H., Schlessinger, A., Sali, A., Roth, B.L., Shoichet, B.K. Comparing Structure-based Ligand Dis-covery from a Homology Model and the Crystal Structure of the Dopamine D3 Receptor. Nature Chemical Biology Accepted.
Coleman, R.G., Sharp, K.A. Protein Pockets: Inventory, Shape, and Comparison. Journal of Chemical Information and Modeling. 50(4), 589-603, 2010. http://dx.doi.org/10.1021/ci900397t.
Coleman, R.G., Sharp, K.A. Shape and Evolution of Thermostable Protein Structure. Proteins: Structure, Function, and Bioinformatics. 78(2), 420-433, 2010. http://dx.doi.org/10.1002/prot.22558
Coleman, R.G., Sharp, K.A. Finding and characterizing tunnels in macromolecules with application to ion channels and pores. Biophysical Journal. 96(2), 632-645, 2009. http://dx.doi.org/10.1529/biophysj.108.135970
Cheng, A.C., Coleman, R.G., Smyth, K.T., Cao, Q., Soulard, P., Caffrey, D.R., Salzberg, A.C., Huang, E.S. Structure-based maximal affinity model predicts small-molecule druggability. Nature Biotechnology. 25(1), 71-75, 2007. http://dx.doi.org/10.1038/nbt1273
Coleman, Ryan G., Kim A. Sharp (2006). Travel Depth, a new shape descriptor for macromolecules: Application to ligand binding. Journal of Molecular Biology 362(3), pp. 441-458, 22 September 2006.
Zelent, B., Vanderkooi, J.M., Coleman, R.G., Gryczynski, I., and Gryczynski Z. Protonation of excited state pyrene-1-carboxylate by phosphate and organic acids in aqueous solution studied by fluorescence spectroscopy. Biophysical Journal 91, pp. 3864-3871, November 2006.
Sharon Diskin
Post-doctoral Fellow, Maris Lab, University of Pennsylvania
Thesis title and defense date: The Role of Germline and Tumor DNA Copy Number in Neuroblastoma Tumorgenesis, April 22, 2008.
Recent publications:
Cole KA, Attiyeh EF, Mosse YP, Laquaglia MJ, Diskin SJ, Brodeur GM, Maris JM. A functional screen identifies miR-34a as a candidate neuroblastoma tumor suppressor gene. Mol Cancer Res. 2008 May;6(5):735-42. PMID: 18505919 [PubMed - in process]
Maris JM, Mosse YP, Bradfield JP, Hou C, Monni S, Scott RH, Asgharzadeh S, Attiyeh EF, Diskin SJ, Laudenslager M, Winter C, Cole KA, Glessner JT, Kim C, Frackelton EC, Casalunovo T, Eckert AW, Capasso M, Rappaport EF, McConville C, London WB, Seeger RC, Rahman N, Devoto M, Grant SF, Li H, Hakonarson H. Chromosome 6p22 locus associated with clinically aggressive neuroblastoma. N Engl J Med. 2008 Jun 12;358(24):2585-93. Epub 2008 May 7. PMID: 18463370 [PubMed - indexed for MEDLINE]
Guttman M, Mies C, Dudycz-Sulicz K, Diskin SJ, Baldwin DA, Stoeckert CJ Jr, Grant GR. Assessing the significance of conserved genomic aberrations using high resolution genomic microarrays. PLoS Genet. 2007 Aug;3(8):e143. PMID: 17722985 [PubMed - indexed for MEDLINE]
Mosse YP, Diskin SJ, Wasserman N, Rinaldi K, Attiyeh EF, Cole K, Jagannathan J, Bhambhani K, Winter C, Maris JM. Neuroblastomas have distinct genomic DNA profiles that predict clinical phenotype and regional gene expression. Genes Chromosomes Cancer. 2007 Oct;46(10):936-49. PMID: 17647283 [PubMed - indexed for MEDLINE]
Diskin SJ, Eck T, Greshock J, Mosse YP, Naylor T, Stoeckert CJ Jr, Weber BL, Maris JM, Grant GR. STAC: A method for testing the significance of DNA copy number aberrations across multiple array-CGH experiments. Genome Res. 2006 Sep;16(9):1149-58. Epub 2006 Aug 9. PMID: 16899652 [PubMed - indexed for MEDLINE]
Wang Q, Diskin S, Rappaport E, Attiyeh E, Mosse Y, Shue D, Seiser E, Jagannathan J, Shusterman S, Bansal M, Khazi D, Winter C, Okawa E, Grant G, Cnaan A, Zhao H, Cheung NK, Gerald W, London W, Matthay KK, Brodeur GM, Maris JM. Integrative genomics identifies distinct molecular classes of neuroblastoma and shows that multiple genes are targeted by regional alterations in DNA copy number. Cancer Res. 2006 Jun 15;66(12):6050-62. PMID: 16778177 [PubMed - indexed for MEDLINE]
Diskin S, Kumar J, Cao Z, Schuman JS, Gilmartin T, Head SR, Panjwani N. Detection of differentially expressed glycogenes in trabecular meshwork of eyes with primary open-angle glaucoma. Invest Ophthalmol Vis Sci. 2006 Apr;47(4):1491-9. PMID: 16565384 [PubMed - indexed for MEDLINE]
Chintala SK, Wang N, Diskin S, Mattox C, Kagemann L, Fini ME, Schuman JS. Matrix metalloproteinase gelatinase B (MMP-9) is associated with leaking glaucoma filtering blebs. Exp Eye Res. 2005 Oct;81(4):429-36. PMID: 16185954 [PubMed - indexed for MEDLINE]
Greshock J, Naylor TL, Margolin A, Diskin S, Cleaver SH, Futreal PA, deJong PJ, Zhao S, Liebman M, Weber BL. 1-Mb resolution array-based comparative genomic hybridization using a BAC clone set optimized for cancer gene analysis. Genome Res. 2004 Jan;14(1):179-87. Epub 2003 Dec 12. PMID: 14672980 [PubMed - indexed for MEDLINE]
Kissinger JC, Brunk BP, Crabtree J, Fraunholz MJ, Gajria B, Milgram AJ, Pearson DS, Schug J, Bahl A, Diskin SJ, Ginsburg H, Grant GR, Gupta D, Labo P, Li L, Mailman MD, McWeeney SK, Whetzel P, Stoeckert CJ, Roos DS. The Plasmodium genome database. Nature. 2002 Oct 3;419(6906):490-2. No abstract available. PMID: 12368860 [PubMed - indexed for MEDLINE]
Schug J, Diskin S, Mazzarelli J, Brunk BP, Stoeckert CJ Jr. Predicting gene ontology functions from ProDom and CDD protein domains. Genome Res. 2002 Apr;12(4):648-55. PMID: 11932249 [PubMed - indexed for MEDLINE]
Bahl A, Brunk B, Coppel RL, Crabtree J, Diskin SJ, Fraunholz MJ, Grant GR, Gupta D, Huestis RL, Kissinger JC, Labo P, Li L, McWeeney SK, Milgram AJ, Roos DS, Schug J, Stoeckert CJ Jr. PlasmoDB: the Plasmodium genome resource. An integrated database providing tools for accessing, analyzing and mapping expression and sequence data (both finished and unfinished). Nucleic Acids Res. 2002 Jan 1;30(1):87-90. PMID: 11752262 [PubMed - indexed for MEDLINE]
Perry Evans
Thesis title and defense date: Modeling virus-host networks, July 29, 2010.
Logan Everett
Thesis title and defense date: Genomic Methods for Studying the Post-Translational Regulation of Transcription Factors, July 16, 2010.
Recent publications:
Everett L, Vo A, Hannenhalli S. PTM-Switchboard--a database of posttranslational modifications of transcription factors, the mediating enzymes and target genes. Nucleic Acids Res. 2009 Jan;37(Database issue):D66-71. Epub 2008 Oct 15.
Everett L, Wang LS, Hannenhalli S. Dense subgraph computation via stochastic search: application to detect transcriptional modules. Bioinformatics. 2006 Jul 15;22(14):e117-23.
Adam Ewing
Thesis title and defense date: The Role of L1 Retrotransposition in Human Genomic Variability, September 14, 2010.
Recent publications:
Hancks D.C., Ewing A.D., Chen J.E., Tokunaga K., Kazazian H.H. Jr. Exon-trapping mediated by the human retrotransposon SVA. Genome Res. 2009 Nov;19(11):1983-91.
Ewing A.D., Kazazian H.H. Jr. High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes. Genome Res. 2010 Jun 8. [Epub ahead of print]
Sheng Guo
Thesis title and defense date: Computational Analysis and Application of Genotype and Phenotype on Drosophilia Odorant Receptors and RNA, September 26. 2008.
Dexter Hadley
Thesis title and defense date: Genome-scale annotation of genetic factors underluying neurotransmission and neuropsychiatric disease, October 2007
Recent publications:
Wang K, Li M, Hadley D, Liu R, Glessner J, Grant SF, Hakonarson H, Bucan M. PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res. 2007 Nov; 17(11):1665-74. Epub 2007 Oct 5.
Hadley D, Murphy T, Valladares O, Hannehalli S, Ungar L, Kim J, Bucan M. Patterns of Sequence Conservation in Presynaptic Neural Genes. Genome Biol. 2006; 7(11):R105.
Marcin Imielinski
Postdoctoral Fellow, Meyerson Lab, Broad Institute of MIT and Harvard
Clinical Fellow, Pathology, Massachusetts General Hospital
Thesis title and defense date: In silico analysis of microbial biosynthetic capabilities at the genome scale, December 2005
Recent publications:
Halász A, Kumar V, Imieliński M, Belta C, Sokolsky O, Pathak S, Rubin H. Analysis of lactose metabolism in E. Coli using reachability analysis of hybrid systems. IET Syst Biol. 2007 March; 1(2):130-48.
Imielinski M, Belta C, Rubin H, Halasz A. Systematic analysis of conservation relations in E. coli genome-scale metabolic network reveals novel growth media. Biophys J. 2006 Apr 15; 90(8):2659-72
Imielinski M., Belta C., Halasz A., and Rubin H. Characterizing elementary combinations of producible species in metabolic networks, Proceedings of Foundations of Systems Biology and Engineering (FOSBE). 2005 August, 298-302.
Imielinski, M., Belta, C., Halasz, A., Rubin, H. Investigating metabolite essentiality through genome-scale analysis of Escherichia coli production capabilities. Bioinformatics. 2005 May 1; 21(9):2008-16.
D'Cruz CM, Moody SE, Master SR, Hartman JL, Keiper EA, Imielinski MB, Cox JD, Wang JY, Ha SI, Keister BA, Chodosh LA. Persistent parity-induced changes in growth factors, TGF-beta3, and differentiation in the rodent mammary gland. Molecular Endocrinology. 2002 Sep; 16(9):2034-51.
Miler Lee
Post-doctoral Associate, Department of Genetics, Yale School of Medicine
Thesis title and defense date: Modular Organization and Composability of RNA, October 9, 2009.
Recent publications:
Buckley PT*, Lee MT*, Sul JY, Miyashiro KY, Bell TJ, Fisher SA, Kim J, Eberwine J. 2011. Cytoplasmic intron retention provides multiple mechanisms for localizing dendritic mRNAs. Neuron 69(5). (*joint first authors) Bell TJ, Miyashiro KY, Sul JY, Buckley PT, Lee MT, McCullough R, Jochems J, Kim J, Cantor CR, Parsons TD, Eberwine JH. 2010. Intron retention facilitates splice variant diversity in calcium-activated big potassium channel populations. Proc Natl Acad Sci U S A, doi: 10.1073/pnas.1015264107.
Sul JY, Wu CW, Zeng F, Jochems J, Lee MT, Kim TK, Peritz T, Buckley P, Cappelleri DJ, Maronski M, Kim M, Kumar V, Meaney D, Kim J, Eberwine J. 2009. Transcriptome transfer produces a predictable cellular phenotype. Proc Natl Acad Sci U S A 106(18).
May E, Lee MT, Dolan P, Crozier P, Brozik S, Manginell M. 2008. Computational sensing and in vitro classification of GMOs and biomolecular events. Proc. of the 26th Army Science Conference.
Lee MT and Kim J. 2008. Self containment, a property of modular RNA structures, distinguishes microRNAs. PLoS Comput. Biol. 4(8).
Zhandong Liu
Assistant Professor, Department of Pediatrics, Baylor College of Medicine
Thesis title and defense date: The Quantative Prediction of Signal Pathway Activity through Genome-wide Gene Expression Data, April 15, 2010.
Molly Megraw
Uwe Ohler Lab, Duke University
Thesis title and defense date: Regulation of MicroRNA Transcription, June 2007
Recent publications:
Brady SM, Zhang L, Megraw M, Martinez NJ, Jiang E, Yi CS, Liu W, Zeng A, Taylor-Teeples M, Kim D, Ahnert S, Ohler U, Ware D, Walhout AJM, Benfey P (2011). A Stele-Enriched Gene Regulatory Network in the Arabidopsis Root. Molecular Systems Biology, 7:459.
Iizasa H, Wulff BE, Alla NR, Maragkakis M, Megraw M, Hatzigeorgiou A, Iwakiri D, Takada K, Wiedmer A, Showe L, Lieberman P, Nishikura K (2010). Editing of Epstein-Barr virus-encoded BART6 microRNAs controls their dicer targeting and consequently affects viral latency. J Biol Chem, 285:33358-70.
Megraw M, Sethupathy P, Gumireddy K, Jensen ST, Huang Q, Hatzigeorgiou AG. (2009). Isoform specific gene auto-regulation via miRNAs: a case study on miR-128b and ARPP-21. Theoretical Chemistry Accounts, Advance Online Publication, DOI:10.1007/s00214-009-0647-4.
Megraw M, Pereira F, Jensen ST, Ohler U, Hatzigeorgiou AG. (2009). A transcription factor affinity based code for mammalian transcription initiation. Genome Research, 19:644-56.
M. Megraw, P. Sethupathy, B. Corda, and A.G. Hatzigeorgiou (2007). miRGen: A database for the study of animal microRNA genomic organization and function. Nucleic Acids Research, 35:D149-D155.
P. Sethupathy, M. Megraw, and A.G. Hatzigeorgiou (2006). A guide through current computational approaches for the identification of mammalian microRNA targets. Nature Methods, 3:881-6.
M. Megraw, V. Baev, V. Rusinov, S.T. Jensen, K. Kalantidis, and A.G. Hatzigeorgiou (2006). MicroRNA promoter element discovery in Arabidopsis. RNA, 12:1612-9.
L. Zhang, J. Huang, N. Yang, J. Greshock, M. Megraw, A. Giannakakis, S. Liang, T.L. Naylor, A. Barchetti, M.R. Ward, G. Yao, A. Medina, A. O'brien-Jenkins, D. Katsaros, A. Hatzigeorgiou, P.A. Gimotty, B.L. Weber, G. Coukos. (2006). microRNAs exhibit high frequency genomic alterations in human cancer. PNAS, 103:9136-41.
K. Szafranski, M. Megraw, M. Reczko, and A. G. Hatzigeorgiou (2006). Support Vector Machines for Predicting microRNA Hairpins. Proceedings of the 2006 International Conference on Bioinformatics and Computational Biology, 270-276.
Rithun Mukherjee
Thesis title and defense date: Viral Diversity by Deep Sequencing: Approaches to Analyzing Effects of anti-HIV Treatments, September 30, 2011.
Thomas Petty
Thesis title and defense date: The Structure of a Multidomain P53 Oligomer Bound to DNA;
Applications of Probabilistic Protein Design, January 4, 2010.
Jeremy Purvis
Post-doctoral Fellow, Galit Lahav Laboratory, Department of Systems Biology, Harvard University
Thesis title and defense date: A Systems Approach to Cellular Signal Transduction, June 2009
Recent publications:
Shah PP, Wang T, Kaletsky RL, Myers MC, Purvis JE, Jing H, Huryn DM, Greenbaum DC, Smith III AB, Bates P, Diamond SL. A small molecule oxocarbazate inhibitor of human cathepsin L blocks SARS and Ebola pseudotype virus infection into HEK 293T cells. (2010) Mol Pharmacol. 78(2):319-24.
Chatterjee MS, Purvis JE, Brass LF, Diamond SL. Pairwise Agonist Scanning of human platelets reveals the high-dimensional calcium response to combinatorial mediators of thrombosis. (2010) Nat Biotechnol. 28(7):727-32.
Purvis JE, Radhakrishnan R, Diamond SL. Steady-state kinetic modeling constrains cellular resting states and dynamic behavior. (2009) PLoS Comput Biol. 5(3):e1000298.
Purvis JE, Chatterjee MS, Brass LF, Diamond SL. A molecular signaling model of platelet phosphoinositide and calcium regulation during homeostasis and P2Y1 activation. (2008) Blood 112(10):4069-79.
Purvis J, Ilango V, Radhakrishnan R. Role of Network Branching in Eliciting Differential Short-Term Signaling Responses in the Hyper-Sensitive Epidermal Growth Factor Receptor Mutants Implicated in Lung Cancer. (2008) Biotechnol Prog. 24(3):540-53.
Shah PP, Myers MC, Beavers MP, Purvis JE, Jing H, Grieser HJ, Sharlow ER, Napper AD, Huryn DM, Cooperman BS, Smith AB, Diamond SL. Kinetic Characterization and Molecular Docking of a Novel, Potent, and Selective Slow-binding Inhibitor of Human Cathepsin L. (2008) Mol Pharmacol. 74(1):34-41.
Purvis J, Liu Y, Ilango V, Radhakrishnan R. Efficacy of tyrosine kinase inhibitors in the mutants of the epidermal growth factor receptor through a multiscale molecular/systems model for phosphorylation and inhibition. Proceedings of Foundations of Systems Biology in Engineering. 2007.
Liu, Y.*, J. Purvis*, A. Shih, J. Weinstein, N. Agrawal, and R. Radhikrishnan (2007). A Multiscale Computational Approach to Dissect Early Events in the Erb Family Receptor Mediated Activation, Differential Signaling, and Relevance to Oncogenic Transformations. Annals of Biomedical Engineering, Vol. 35, No. 6, pp. 1012–1025, June 2007. (* equal contribution)
Purvis, Jeremy, Vibitha Ilango, and Ravi Radhakrishnan. Role of Network Branching in Eliciting Differential Short-Term Signaling Responses in the Hypersensitive Epidermal Growth Factor Receptor Mutants Implicated in Lung Cancer. Biotechnology Progress. Web Release Date: 16-Apr-2008
Shah, Parag P., Michael C. Myers, Mary Pat Beavers, Jeremy E. Purvis, Huiyan Jing, Heather J. Grieser, Elizabeth R. Sharlow, Andrew D. Napper, Donna M. Huryn, Barry S. Cooperman, Amos B. Smith, and Scott L. Diamond. Kinetic Characterization and Molecular Docking of a Novel, Potent, and Selective Slow-binding Inhibitor of Human Cathepsin L. Molecular Pharmacology. Published on Web. April 10, 2008.
Praveen Sethupathy
Post-doctoral Research Fellow,Dr. Francis S. Collins Labratory at the National Human Genome Research Institute (NHGRI) within the National Institutes of Health (NIH)
Thesis title and defense date: Analysis on the Role of Gene Regulatory Elements in Human Health and Evolution, March 2008
Recent publications:
P. Sethupathy and S. Hannenhalli (2008). A tutorial of the Poisson Random Field model in population genetics. Technical Report No. MS-CIS-08-01, University of Pennsylvania Department of Computer and Information Science.
P. Sethupathy, H. Giang, J.B. Plotkin, and S. Hannenhalli. (2008). Genome-wide analysis of natural selection on human cis-elements. Submitted.
P. Sethupathy*, C. Borel*, M. Gagnebin, G.R. Grant, S. Deutsch, T.S. Elton, A.G. Hatzigeorgiou, and S.E. Antonarakis (2007). Human miR-155 on chromosome 21 differentially interacts with its polymorphic target in the AGTR1 3’UTR – a mechanism for functional SNPs related to phenotypes. American Journal of Human Genetics, 81:405-413. (* equal contribution)
Y. Kawahara*, B. Zinshteyn*, P. Sethupathy, H. Iizasa, A.G. Hatzigeorgiou, and K. Nishikura (2007). Redirection of silencing targets by adenosine-to-inosine editing of microRNAs. Science, 315:1137-1140. (* equal contribution)
M. Megraw, P. Sethupathy, B. Corda, and A.G. Hatzigeorgiou (2006). miRGen: a database for the study of microRNA genomic organization and function. Nucleic Acids Research, 35:D149-D155.
P. Sethupathy, M. Megraw and A.G. Hatzigeorgiou (2006). A guide through current computational approaches for the identification of mammalian microRNA targets. Nature Methods, 3:881-886.
P. Sethupathy, B. Corda and A.G. Hatzigeorgiou (2006). TarBase: A comprehensive database of experimentally supported animal microRNA targets. RNA, 12:192-197.
P. Sethupathy*, M. Megraw*, M.I. Barrasa, and A.G. Hatzigeorgiou (2005). Computational Identification of Regulatory Factors Involved in MicroRNA Transcription. Lecture Notes in Computer Science, 3746:457-468. (* equal contribution)
Daniel Simola
Post-doctoral Fellow, Berger Lab, University of Pennsylvania
Thesis title and defense date: Evolution of Genome-Wide Gene Regulation in the Budding Yeast Cell- Division Cycle, September 3, 2009.
Recent publications:
Anchal Vishnoi, Praveen Sethupathy, Daniel F. Simola, Joshua B. Plotkin, and Sridhar Hannenhalli (2011) Genome-wide survey of natural selection on functional, structural, and network properties of polymorphic sites in Saccharomyces paradoxus. Molecular Biology and Evolution. doi: 10.1093/molbev/msr085.
Daniel F. Simola, Chantal Francis, Paul Sniegowski, and Junhyong Kim (2010) Heterochronic Evolution Reveals Modular Timing Changes in Budding Yeast Transcriptomes. Genome Biology 11:R105.
Kathleen Sprouffske
Post-doctoral Fellow, Sniegowski Lab, University of Pennsylvania
Thesis title and defense date: Modeling the evolutionary and differentiation dynamics of neoplastic progression, January 21, 2011
Geetu Tuteja
Post-doctoral Fellow, Kaestner Lab, University of Pennsylvania
Thesis title and defense date: Illuminating Transcriptional Regulation with Genome-wide Binding Data, December 15, 2008.
Recent publications:
Tuteja G, Jensen ST, White P, Kaestner KH. Cis-regulatory modules in the mammalian liver: composition depends on strength of Foxa2 consensus site. Nucleic Acids Res. 2008 Jul;36(12):4149-57. Epub 2008 Jun 13.
Tuteja G, Kaestner KH. Forkhead transcription factors II. Cell. 2007 Oct 5;131(1):192.
Tuteja G, Kaestner KH. SnapShot: forkhead transcription factors I. Cell. 2007 Sep 21;130(6):1160.
Zhi Wei
Assistant Professor, Computer Science Department, New Jersey Institute of Technology
Thesis title and defense date: Statistics Methods for Network-Based Analysis on Genomic Data, March 2008
Recent publications:
Wei, Z. and Li, H. A Hidden Spatial-temporal Markov Random Field Model for Network-based Analysis of Time Course Gene Expression Data. Annals of Applied Statistics, 2008 2: 408-429
Wei, Z. and Li, M. Genome-wide Association Analysis of Rheumatoid Arthritis in a Canadian Population, BMC Proceedings, 2007, 1(Suppl 1):S19
Wei, Z. and Li, H. A Markov Random Field Model for Network-based Analysis of Genomic Data, Bioinformatics, 2007 23:1537-1544
Wei, Z. and Li, H. Nonparametric Pathway-Based Regression Models for Analysis of Genomic Data. Biostatistics, 2007 8: 265-284
Wei, Z. and Jensen, S.T. GAME: detecting cis-regulatory elements using a genetic algorithm. Bioinformatics, 2006 22:1577-1584