Publications
ORCID ID: 0000-0003-1575-5732
Antipsychotic behavioral phenotypes in the mouse Collaborative Cross recombinant inbred inter-crosses.
Giusti-Rodriguez, P, Xenakis, J, Crowley, JJ, Nonneman, RJ, DeCristo, DM, Ryan, A., Quackenbush, CR, Miller, DR, Shaw, GD, Zhabotynsky, V. and Sullivan, P (2019)
(under review Genetics) (2019) doi: 10.1101/761353
A statistical method for joint estimation of cis-eQTLs and parent-of-origin effects using RNA-seq human data under family trio design.
Zhabotynsky V, Sun W, Inoue K, Magnuson T, Calabrese M (2019)
Biometrics PMID: 30666629
The Association between Copy Number Aberration, DNA Methylation, and Gene Expression
Sun W, Bunn P, Jin C, Little P, Zhabotynsky V, Perou CM, Hayes DN, Chen M, Lin DY (2018)
Nucleic Acids Research doi: 10.1093/nar/gky131 PMID: 29529299
IsoDOT Detects Differential RNA-Isoform Expression/Usage With Respect to a Categorical or Continuous Covariate With High Sensitivity and Specificity
Wei Sun, Yufeng Liu, James J Crowley, Ting-Huei Chen, Hua Zhou, Haitao Chu, Shunping Huang, Pei-Fen Kuan, Yuan Li, Darla Miller, Ginger Shaw, Yichao Wu, Vasyl Zhabotynsky, Leonard McMillan, Fei Zou, Patrick F Sullivan, Fernando Pardo-Manuel de Villena (2015)
Journal of the American Statistical Association 2015 November, vol 110, no 511: 975-986; doi: 10.1080/01621459.2015.1040880
Analyses of Allele-Specific Gene Expression in Highly Divergent Mouse Crosses Identifies Pervasive Allelic Imbalance
James J Crowley, Vasyl Zhabotynsky, Wei Sun, Shunping Huang, Isa Kemal Pakatci, Yunjung Kim, Jeremy R Wang, Andrew P Morgan, John D Calaway, David L Aylor, Zaining Yun, Timothy A Bell, Ryan J Buus, Mark E Calaway, John P Didion, Terry J Gooch, Stephanie D Hansen, Nashiya N Robinson, Ginger D Shaw, Jason S Spence, Corey R Quackenbush, Cordelia J Barrick, Randal J. Nonneman, Kyungsu Kim, James Xenakis, Yuying Xie, William Valdar, Alan B Lenarcic, Wei Wang, Catherine E Welsh, Chen-Ping Fu, Zhaojun Zhang, James Holt, Zhishan Guo, David W Threadgill, Lisa M Tarantino, Darla R Miller, Fei Zou, Leonard McMillan, Patrick F Sullivan, Fernando Pardo-Manuel de Villena (2015)
Nat Genet. 2015 April, vol 47, no 4: 353-360; doi: 10.1038/ng.3222; PMCID: PMC4380817, NIHMSID: NIHMS658905
A Novel Statistical Approach for Jointly Analyzing RNA-Seq Data from F1 Reciprocal Crosses and Inbred Lines
Fei Zou, Wei Sun, James J Crowley, Vasyl Zhabotynsky, Patrick F Sullivan, Fernando Pardo-Manuel de Villena (2014)
Genetics 2014 May, vol 197, no 1; 389-399; doi: 10.1534/genetics.113.160119; PMID: 24561482, PMCID: PMC4012495
The genome architecture of the Collaborative Cross mouse genetic reference population
Collaborative Cross Consortium (2012)
Genetics 2012 February, vol 190, no 2: 389-401; doi: 10.1534/genetics.111.132639; PMID: 22345608, PMCID: PMC3276630
Transcriptome atlases of mouse brain reveals differential expression across brain regions and genetic backgrounds
Wei Sun, Seunggeun Lee, Vasyl Zhabotynsky, Fei Zou, Fred A Wright, James J Crowley, Zaining Yun, Ryan J Buus, Darla R Miller, Jeremy Wang, Leonard McMillan, Fernando Pardo-Manuel de Villena, Patrick F Sullivan (2012)
G3: Genes| Genomes| Genetics 2012 February, vol 2, no 2: 203-211; doi: 10.1534/g3.111.001602; PMID: 22384399, PMCID: PMC3284328
Dissertation
Presentations and Posters
Xenakis J, Kim KS, Zhabotynsky V, Mi X, Crowley JJ, Sullivan P, Pardo-Manuel De Villena F A Statistical Model of Methylation Sequencing Data Identifies Novel Differentially Methylated CpG's and Provides Insights into the Role of Methylation in X-chromosome Inactivation and the Silencing of Transposable Elements (2019) The 33th International Mammalian Genome Conference
Giusti Rodriguez P, Xenakis JG, Crowley JJ, Nonneman RJ, DeCristo DM, Ryan A, Quackenbush CR,Miller DR, Shaw GD, Zhabotynsky V, Sullivan PF, Fernando Pardo Manuel de Villena, Zou F Antipsychotic behavioral phenotypes of Collaborative Cross recombinant inbred intercrosses (RIX) (2018) The 32th International Mammalian Genome Conference
RNA-seq analysis protocol and method comparison
Zhabotynsky V, Hu YJ, Zou F, Sun W
eQTL Analysis Using Human RNA-seq Data with TReCASE and RASQUAL (2018)
ENAR 2018 Spring Meeting with IMS and sections of ASA
Parent of origin effects under Trio Design
Zhabotynsky V, Sun W, Inoue K, Magnuson T, Calabrese M
Unbiased Estimation of Parent-of-Origin Effects Using RNA-seq Data from Human (2017)
ENAR 2017 Spring Meeting with IMS and sections of ASA
Peng XL, Zhabotynsky V, East MP, Voltzke KJ, Sprague D, Herrera Loeza SJ, Moffitt RA, Rashid NU, Graves LM, Johnson GJ, Yeh JJ Kinome profiling in pancreatic cancer reveals subtype-specific drug (2017) 2017 UNC Lineberger Comprehensive Cancer Center Scientific Retreat
Alleviating noise due to cell composition
Sun W, Bunn P, Jin C, Little P, Zhabotynsky V, Perou CM, Hayes DN, Chen M, Lin D
Tissue Purity and cell composition challenges in estimation of association between somatic copy number aberration, DNA methylation and gene expression (2016)
2016 UNC Lineberger Annual Scientific Retreat
Xenakis JG, Zhabotynsky V, Zou A score statistic for testing variance components in the shared random effects setting with applications to a complex mouse study (2016) 2016 Joint Statistical Meetings
TReCASE
Zou F, Sun W, Crowley JJ, Zhabotynsky V, Sullivan PF, Pardo-Manuel de Villena F, Xenakis J , Giuisti P
TReCASE: a powerful method to detect differential gene expression using total and allele specific RNA-seq data (2014)
The 12th Annual Centers of Excellence in Genomic Science Grantee Meeting
Crowley JJ, Zhabotynsky V, Sun W, Huang S, Pakatci I, Kim Y, Wang J, Morgan A, Calaway J, Aylor D, Yun Z, Bell T, Buus R, Calaway M, Didion J, Gooch T, Hansen S, Robinson N, Shaw G, Spence J, Quackenbush C, Barrick C, Xie Y, Valdar W, Lenarcic A, Wang W, Welsh C, Fu CP, Zhang Z, Holt J, Guo Z, Threadgill D, Tarantino L, Miller D, Zou F, McMillan L, Sullivan P, Pardo-Manuel de Villena F Pervasive Allelic Imbalance Revealed By Allele-Specific Gene Expression In Highly Divergent Mouse Crosses (2013) The 12th Annual Centers of Excellence in Genomic Science Grantee Meeting
Holt JM, Wang J, Zhabotynsky V, Kim Y, Crowley JJ, Zou F, Sullivan P, Pardo-Manuel de Villena F, McMillan L A Visualization Tool For Exploring the Gene Expression Landscape in a Full Three-Founder Diallele (2013) The 27th International Mammalian Genome Conference
Software
rxSeq
rxSeq at CRAN repository
(vignette)
local copy of rxSeq_0.99.3
(Reciprocal Cross in RNA-seq. Zhabotynsky V, Sun W, Zou F)
asSeq
asSeq_0.99.2
(asSeq: A set of tools for the study of allele-specific RNA-seq data. Sun W, Zhabotynsky )
Sun W (2012). A Statistical Framework for eQTL Mapping Using RNA-seq Data. Biometrics, 68(1), 1-11
Sun W, Hu Y (2013). eQTL mapping using RNA-seq data. Statistics in biosciences, 5(1), 198-219.
isoform
isoform_0.99.1
(
isoform: A set of tools for RNA isoform study using RNA-seq data. Sun W
)
Sun W, Yufeng Liu, Crowley JJ, Chen TH, Zhou H, Ha C, Huang S, Kuan PF, Li Y, Miller D, Shaw G, Wu Y, Zhabotynsky V, McMillan L, Zou F, Sullivan PF, Pardo-Manuel de Villena F IsoDOT Detects Differential RNA-Isoform Expression/Usage With Respect to a Categorical or Continuous Covariate With High Sensitivity and Specificity. (2015) JASA, 110(511), 975-986
DRPathway GUI
DRPathway v1.0
(
Dose-response pathway analysis for gene expression: Graphical User Interface. Li Z, Barry W, Sypa M, Zhabotynsky V, Idowu S, Rusyn I, Wright F
)