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Curriculum Vitae

Andrey A. Shabalin, Ph.D.

Assistant Professor
Center for Biomarker Research and Precision Medicine
Virginia Commonwealth University

1112 East Clay Street
McGuire Hall, Room 219
Richmond, VA 23298

E-mail: ashabalin@vcu.edu
Phone: (919) 923-8325
Website: shabal.in
GitHub: github.com/andreyshabalin
Google Scholar: scholar.google.com/citations?hl=en&user=wXj_PpsAAAAJ
NCBI Bibliography: ncbi.nlm.nih.gov/sites/myncbi/1lO_9pCfUhMkh/bibliography/51285584/public

Education:

2005 – 2010, Ph.D. in Statistics, Department of Statistics and Operations Research,
University of North Carolina at Chapel Hill. Professor Andrew B. Nobel, adviser
2002 – 2004, M.A. in Economics, New Economic School, Moscow, Russia
1997 – 2002, M.S. in Mathematics (with honors), Moscow State University, Moscow, Russia.

Positions:

2014 – now, Assistant Professor, VCU
2012 – 2014, Postdoctoral Research Associate, VCU, Professor Edwin van den Oord
2010 – 2012, Postdoctoral Research Associate, UNC, Professor Fred A. Wright
2004 – 2005, Economist, Centre for Economic and Financial Research, Moscow, Russia
2004 – 2005, Research Assistant, New Economic School, Moscow, Russia

Publications:

High density methylation QTL analysis in human blood via next-generation sequencing of the methylated genomic DNA fraction (2015)
J.L. McClay*, A.A. Shabalin*(co-first authors), ..., K.A. Aberg, and E.J.C.G. van den Oord
Genome biology, 16:291
DOI: 10.1186/s13059-015-0842-7, PMID: 26699738, PMCID: PMC4699364
http://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0842-7

Candidate gene methylation studies are at high risk of erroneous conclusions (2015)
A.A. Shabalin, K.A. Aberg, and E.J.C.G. van den Oord
Epigenomics, 7(1), 13-5
DOI: 10.2217/epi.14.70, PMID: 25687462
http://www.futuremedicine.com/doi/abs/10.2217/epi.14.70

An integrated map of structural variation in 2,504 human genomes (2015)
P.H. Sudmant, ..., A.A. Shabalin (co-author 62 of 83)
Nature, 526, 75–81
DOI: 10.1038/nature15394, PMID: 26432246, PMCID: PMC4617611
http://www.nature.com/nature/journal/v526/n7571/abs/nature15394.html

The Genotype-Tissue Expression (GTEx) pilot analysis: multi-tissue gene regulation in humans (2015)
K.G. Ardlie, ..., A.A. Shabalin (co-author 22 or 139)
Science 348 (6235), 648-660
DOI: 10.1126/science.1262110, PMID: 25954001, PMCID: PMC4547484
http://www.ncbi.nlm.nih.gov/pubmed/25954001

A Whole Methylome CpG-SNP Association Study of Psychosis in Blood and Brain Tissue (2015)
E.J.C.G. van den Oord, S.L. Clark, L.Y. Xie, A.A. Shabalin, M.G. Dozmorov, G. Kumar, Swedish Schizophrenia Consortium, V.I. Vladimirov, P.K.E. Magnusson, and K.A. Aberg
Schizophrenia bulletin, 182
DOI: 10.1093/schbul/sbv182, PMID: 26656881, PMCID: PMC4903046
http://schizophreniabulletin.oxfordjournals.org/content/early/2016/02/05/schbul.sbv182

Deep Sequencing of Three Loci Implicated in Large-Scale Genome-Wide Association Study Smoking Meta-Analyses (2015)
S.L. Clark, J.L. McClay, D.E. Adkins, K.A. Aberg, G. Kumar, S. Nerella, L. Xie, A.L. Collins, J.J. Crowley, C.R. Quakenbush, C.E. Hillard, G. Gao, A.A. Shabalin, R.E. Peterson, W.E. Copeland, J.L. Silberg, H. Maes, P.F. Sullivan, E.J. Costello, and E.J.C.G. van den Oord
Nicotine & Tobacco Research, 166
DOI: 10.1093/ntr/ntv166
http://ntr.oxfordjournals.org/content/early/2015/08/16/ntr.ntv166

Combined whole methylome and genomewide association study implicates CNTN4 in alcohol use (2015)
S.L. Clark, K.A. Aberg, S. Nerella, G. Kumar, J.L. McClay, W. Chen, L.Y. Xie, A. Harada, A.A. Shabalin, G. Gao, S.E. Bergen, C.M. Hultman, P.K.E. Magnusson, P.F. Sullivan, and E.J.C.G. van den Oord
Alcoholism: Clinical and Experimental Research, 39 (8), 1396-1405
DOI: 10.1111/acer.12790, PMID: 26146898, PMCID: PMC4515164
http://onlinelibrary.wiley.com/doi/10.1111/acer.12790/full

Refinement of schizophrenia GWAS loci using methylome-wide association data (2015)
G. Kumar, S.L. Clark, J.L. McClay, A.A. Shabalin, D.E. Adkins, L. Xie, R. Chan, S. Nerella, Y. Kim, P.F. Sullivan, C.M. Hultman, P.K.E. Magnusson, K.A. Aberg, and E.J.C.G. van den Oord
Human Genetics, 134 (1), 77-87
DOI: 10.1007/s00439-014-1494-5, PMID: 25284466, PMCID: PMC4282961
http://link.springer.com/article/10.1007%2Fs00439-014-1494-5

Quantitative trait locus mapping methods for diversity outbred mice (2014)
D.M. Gatti, K.L. Svenson, A.A. Shabalin, L.Y. Wu, W. Valdar, P. Simecek, N. Goodwin, R. Cheng, D. Pomp, A. Palmer, E.J. Chesler, K.W. Broman, G.A. Churchill
G3: Genes Genomes Genetics, 2014 vol. 4 no. 9, 1623-1633
DOI: 10.1534/g3.114.013748, PMID: 25237114, PMCID: PMC4169154
http://www.g3journal.org/content/4/9/1623

The Genotype-Tissue Expression (GTEx) project (2013)
J. Lonsdale, J. Thomas, ..., A.A. Shabalin (co-author 98 of 127)
Nature Genetics, 45 (6), 580-585
DOI: 10.1038/ng.2653, PMID: 23715323, PMCID: PMC4010069
http://www.nature.com/ng/journal/v45/n6/abs/ng.2653.html

Heritability and genomics of gene expression in peripheral blood (2014)
F.A. Wright, ..., A.A. Shabalin (co-author 25 of 39)
Nature Genetics, 46 (5), 430-437
DOI: 10.1038/ng.2951, PMID: 24728292, PMCID: PMC4012342
http://www.nature.com/ng/journal/v46/n5/full/ng.2951.html

Resolving the polymorphism-in-probe problem is critical for correct interpretation of expression QTL studies (2013)
A. Ramasamy, D. Trabzuni, J.R. Gibbs, A. Dillman, D.G. Hernandez, S. Arepalli, R. Walker, C. Smith, G.P. Ilori, A.A. Shabalin, Y. Li, A.B. Singleton, M.R. Cookson, J. Hardy, M. Ryten, M.E. Weale
Nucleic acids research, 41 (7), e88-e88
DOI: 10.1093/nar/gkt069, PMID: 23435227, PMCID: PMC3627570
http://nar.oxfordjournals.org/content/41/7/e88

Reconstruction of a low-rank matrix in the presence of Gaussian noise (2013)
A.A. Shabalin and A.B. Nobel
Journal of Multivariate Analysis, 118, 67-76
DOI: 10.1016/j.jmva.2013.03.005
http://www.sciencedirect.com/science/article/pii/S0047259X13000328

Matrix eQTL: Ultra fast eQTL analysis via large matrix operations (2012)
A.A. Shabalin
Bioinformatics, 28 (10): 1353-1358
DOI: 10.1093/bioinformatics/bts163, PMID: 22492648, PMCID: PMC3348564
http://bioinformatics.oxfordjournals.org/content/28/10/1353

seeQTL: A searchable database for human eQTLs (2012)
K. Xia, A.A. Shabalin, ..., and F.A. Wright
Bioinformatics, 28 (3): 451-452
DOI: 10.1093/bioinformatics/btr678, PMID: 22171328, PMCID: PMC3268245
http://bioinformatics.oxfordjournals.org/content/28/3/451

Computational tools for discovery and interpretation of Expression Quantitative Trait Loci (eQTL) (2012)
F.A. Wright, A.A. Shabalin, and I. Rusyn
Pharmacogenomics, 13 (3), 343-352
DOI: 10.2217/pgs.11.185, PMID: 22048815, PMCID: PMC3295835
http://www.futuremedicine.com/doi/abs/10.2217/pgs.11.185

Basal-like Breast Cancer DNA copy number losses identify genes involved in genomic instability, response to therapy, and patient survival (2012)
V.J. Weigman, H.H. Chao, A.A. Shabalin, ..., and C.M. Perou
Breast Cancer Research and Treatment, 133 (3), 865-880
DOI: 10.1007/s10549-011-1846-y, PMCID: PMC3387500
http://link.springer.com/article/10.1007/s10549-011-1846-y

Sex-specific Gene Expression in BXD Mouse Liver (2010)
D. Gatti, N. Zhao, E. Chesler, B. Bradford, A.A. Shabalin, R. Yordanova, L. Lu, and I. Rusyn
Physiological Genomics, 42 (3), 456-468
DOI: 10.1152/physiolgenomics.00110.2009, PMID: 20551147, PMCID: PMC2929887
http://physiolgenomics.physiology.org/content/42/3/456

Finding large average submatrices in high dimensional data (2009)
A.A. Shabalin, V.J.Weigman, C.M. Perou, and A.B. Nobel
Annals of Applied Statistics, 3(3), 985-1012, 2009
DOI: 10.1214/09-AOAS239
http://projecteuclid.org/euclid.aoas/1254773275
http://www.jstor.org/stable/30242874

FastMap: Fast eQTL mapping in homozygous populations (2009)
D.M. Gatti*, A.A. Shabalin*(co-first authors), T.C. Lam, F.A. Wright, I. Rusyn, and A.B. Nobel
Bioinformatics, 25(4):482, 2009
DOI: 10.1093/bioinformatics/btn648, PMCID: PMC2642639
http://bioinformatics.oxfordjournals.org/content/25/4/482

The Set2/Rpd3S pathway suppresses cryptic transcription without regard to gene length or transcription frequency (2009)
C. Lickwar, B. Rao, A.A. Shabalin, A.B. Nobel, B.D. Strahl, and J.D. Lieb
PLoS ONE, 4(3), e4886, 2009
DOI: 10.1371/journal.pone.0004886, PMID: 19295910, PMCID: PMC2654109
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0004886

Merging two gene-expression studies via cross-platform normalization (2008)
A.A. Shabalin, H. Tjelmeland, C. Fan, C.M. Perou, and A.B. Nobel
Bioinformatics, 24(9):1154, 2008
DOI: 10.1093/bioinformatics/btn083
http://bioinformatics.oxfordjournals.org/content/24/9/1154

Detection of Low Rank Signals in Noise and Fast Correlation Mining with Applications to Large Biological Data (2010)
A.A. Shabalin
Ph.D. Dissertation. UNC-CH, Department of Statistics and Operations Research
https://cdr.lib.unc.edu/record/uuid:6a46e597-9e72-44f1-bd73-f643501bc0db

Submitted and working papers:

Estimation of Interpretable eQTL Effect Sizes Using a Log of Linear Model
J. Palowitch, A.A. Shabalin, Y. Zhou, A.B. Nobel, and F.A. Wright
https://arxiv.org/abs/1605.08799

Local genetic effects on gene expression across 44 human tissues
F. Aguet, ..., A.A. Shabalin (co-author 24 of 50)
http://biorxiv.org/content/early/2016/09/09/074450

A non-parametric statistical framework for integrating heterogeneous prior information in large-scale multiple testing
A.A. Shabalin, J. Bukzar, J.L. McClay, K.A. Aberg, and E.J.C.G. van den Oord

An empirical bayes approach for Multiple Tissue eQTL Analysis
G. Li, A.A. Shabalin, I. Rusyn, F.A. Wright, and A.B. Nobel
http://arxiv.org/abs/1311.2948

FastMap 2.0: Fast Association Mapping in Heterozygous Populations
D.M. Gatti, A.A. Shabalin, M. Sypa, T.C. Lam, F.A. Wright, A.B. Nobel, and I. Rusyn
http://comptox.unc.edu/fastmap.php

Programming languages:

R (creating packages for CRAN and Bioconductor, vectorization, see Matrix eQTL, RaMWAS)
Matlab (multithreaded and GPU programming, vectorization, see LAS, XPN)
Java, C# (multithreaded programming, complex data structures, see LAS, FastMap)
Gauss, SPSS, Stata

Software developed:

Matrix eQTL. Ultra fast eQTL analysis via large matrix operations
 R at CRAN, http://www.bios.unc.edu/research/genomic_software/Matrix_eQTL/

RaMWAS. Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms
 R (with C/C++) at Bioconductor, https://github.com/andreyshabalin/ramwas

Filematrix. File-Backed Matrix Class with Convenient Read and Write Access
 R at CRAN, https://github.com/andreyshabalin/filematrix

fastCircularPermutations. Very fast circular permutation analysis on binary outcomes
 R (with C/C++) at GitHub, https://github.com/andreyshabalin/fastCircularPermutations

ACMEeqtl. Estimation of Interpretable eQTL Effect Sizes Using a Log of Linear Model
 R (with C/C++) at GitHub, https://github.com/andreyshabalin/ACMEeqtl

DOQTL. Genotyping and QTL Mapping in Diversity Outbred Mice
 R at Bioconductor, https://bioconductor.org/packages/release/bioc/html/DOQTL.html

LAS Biclustering. Finding large average submatrices in high-dimensional data.
 C# (with GUI) and Matlab, https://genome.unc.edu/las/

FastMap. Fast gene expression quantitative trait loci mapping tool.
 Java (with GUI), http://comptox.unc.edu/fastmap.php

XPN. Cross-platform normalization method for combining gene expression data
 Matlab, https://genome.unc.edu/xpn/

SWITCHdna. SupWald identification of DNA copy changes
 R, https://genome.unc.edu/pubsup/SWITCHdna/

Teaching Experience:

Introduction to Statistics, Instructor, UNC-CH, Spring – Fall 2009
Responsibilities: conduct lectures, design homework and exams, grade exams.

Econometrics and Time-series analysis, Instructor,
State University of Humanities, Moscow, Russia, Fall 2003 – Spring 2004
Responsibilities: complete charge of the course – choose textbook, conduct lectures, etc.

Applied Time Series Econometrics, Econometrics IV, and Continuous Time Finance,
Instructor Assistant, New Economic School, Moscow, Russia, Fall 2004 – Spring 2005.
Responsibilities: conduct sessions, grade homework and exams.

Elements of Statistics, Instructor Assistant,
International College of Economics and Finance, Moscow, Russia, Fall 2003 – Spring 2004
Responsibilities: conduct sessions, grade homework and exams.

Reviewed for:

Annals of Applied Statistics
Bioinformatics
BMC Bioinformatics
BMC Genomics
Human Molecular Genetics
IEEE/ACM Transactions on Computational Biology and Bioinformatics
IEEE Transactions on Information Theory
Journal of Computational and Graphical Statistics
Journal of Multivariate Analysis
Nucleic Acids Research
Pattern Recognition
PLOS Genetics
Quantile (Moscow, Russia)
Statistics and Computing
Transactions on Computational Biology and Bioinformatics


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