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Click here or scroll down to respond to this candidate Candidate's Name
PHONE NUMBER AVAILABLE EMAIL AVAILABLE https://LINKEDIN LINK AVAILABLESPECIAL SKILLSExtensive experiences in Java, C++, Perl, PHP, Python, R, R Markdown, RShiny, JavaScript, SQL, HTML(5), CSS, AJAX, XML, JAXB, JSON, Ant, Axis, JSPand servlet, JSF, Spring Core, Spring Boot, Hibernate, myBatis, JDBC, ODBC;Apache Tomcat, IIS, JBoss, IBM WebSphere, Docker; AWS, Azure; Web services(SOAP, RESTful); NetBeans, Eclipse, RStudio, Anaconda3; GIT, bitbucket,Subversion; JIRA, Jenkins, Knime; Linux, Unix and Windows.Database development and administration, Oracle, MySQL, MS-SQL, PostgreSQL,data warehouse, DataMart, Data Lake.Bioinformatics: Managing, archiving, and analyzing large-scale data frommicroarray gene expression, Next Generation Sequencing (NGS), cDNA screensand proteomics using commercial, open-source or self-developed softwaretools and packages.Text analytics: NLP, sentiment analysis, machine learning, data mining, webcrawling, entity extraction, document summarization and categorization.EDUCATIONM.S. Master of Computer Science, North Carolina State University, Raleigh,May 2001Ph.D. Molecular Evolution, North Carolina State University, Raleigh,December 2000B.S. Plant Protection, Shanxi Agricultural University, Taigu, Shanxi,China, June 1983EXPERIENCESenior App. Development Engineer, 2/2021-present.ASRC Federal Data Solutions - Civilian & Health Operating Group, ResearchData Management and Reporting (RDMR) Contract, National Institute ofEnvironmental Health Sciences (NIEHS).. Create new R scripts for parametric or nonparametric stats calculationswith data from different sources and studies in excel files.. Refactor Java application for statistical analysis of genotoxicitystudies with bug fixes and significant improvement in flexibility andperformance.. Refactor, modularize and re-use existing or create new R scripts, pythonscripts for statistical analysis, graphic visualization and reporting ofvarious types of data from CEBS data warehouse, DataMart and data files.Design new tables in Oracle database and implement analysis pipelines withimproved performance and flexibility.. Developed "TGx-HDACi and TGx-DDI Biomarkers for Classification ofToxicants" as PHP web application (UI) with back-end R scripts for classpredictions of chemicals at a dose level based on trained gene signaturesand machine learning (ML), deployed on AWS.. Manage projects and tasks with JIRA; setup projects and run applicationsin Jenkins.Java Technology Lead, 11/2018-2/2021.Conduent Business Services LLC., InfoSys Limited. Supporting Conduent healthcare applications, UI, Web Services and Oracledatabases. Struts, Spring Core and Spring Boot, JSP, JavaScript, Hibernate.. Develop, improve, enhance, debug, deploy and test, web applications onDEV and UAT environments with productions with Azure.. Fix vulnerabilities after OWASP web application security testing, such asCross Site Scripting (XSS) and SQL Injection, etc... Develop microservices for Power BI applications.Senior Programmer/Analyst, 2/2014-11/2018.National Toxicology Program (NTP), National Institute of EnvironmentalHealth Sciences (NIEHS), contacted at DS Technologies, Inc.. Integration, management, analysis and visualization of microarray geneexpression, high throughput transcriptome resequencing data, histopathologyand hematology data for CEBS (Chemical Effects in Biological Systems), apublic Oracle database repository.. Data analysis pipeline with Perl, Java, Python and R; Softwareapplications and UI development with Java (JSF), PHP and Spotfire.. Implement multiple statistical tests/methods and RESTful APIs usingPython.. Developed the first JSF web application for benchmark dose responsemodels and histopathology studies.. Developed the first PHP web application for biomarker classificationbased on gene expression data of test chemicals.. Worked in team to develop command line application for generation PDFreports with more than 60 report types using Java, Hibernate, myBatis andiText;Senior Bioinformatics Research Associate, 12/2003-2/2014.Center for Genomic Biology and Bioinformatics, the Hamner Institutes forHealth Sciences (Previously, CIIT Centers for Health Research).. Software Development: Java Swing applications include BMDExpress(published) for the benchmark dose analysis of dose-response or time-coursemicroarray gene expression data with ANOVA, GO and pathway enrichmenttests; NetAtlas (published) as a Cytoscape plugin for examining signalingnetworks based on tissue gene expression data stored in MySQL database;SPRinGS for signaling pathway reconstruction in genome screens; GEAX forgene expression analysis cross (X) species; PowerRMA for very large sets(several thousands) of Affymetrix microarray data normalization from CELfiles and basic statistics computation; Hockey Stick threshold model(original model in R) for does and response data.. Web services (XML) for network/pathway modeling and simulation database(Oracle), Entrez Gene, Gene Ontology (GO), and Microarray gene annotation(MySQL).. Database Implementation, Development and Management: GeneNet as a back-end database (Oracle) for GeneSpring; Entrez Gene, Gene Ontology (GO) andother publicly available interaction network/ pathway databases (BIND,Intact) with local MySQL, using Perl scripts for automatic updating; newMySQL databases for cDNA and siRNA screen data, siRNA designation,Affymetrix chip annotation and LIMS back-end databases.. Data Analysis: Microarray gene expression, NGS (Next GenerationSequencing), ToxCast assays and simulation, high-throughput cDNA/siRNAscreens, proteomics, cell imaging and cytometry data from toxicogenomicsand caner biology research; commercial, open-source, and developed softwareand tools such as GeneSpring, PathwayAssist, BMDExpress, Partek, IngenuityPathways Analysis (IPA), Cytoscape, Bio-conductor R packages, SamTools,Bowtie, JMP (SAS), Perl scripts, etc..Research Associate, 5/2002-12/2003.Virginia Bioinformatics Institute, Virginia Polytechnic Institute and StateUniversity.. Phylo-genomics/Comparative genomics of approximately 70 pathogen andbacteria species/strains. Developed a phylogenetic component to theinformatics system of pathogens - Pathogen Portal or "PathPort", for rapiddetection, identification, and forensic attribution of high-prioritypathogens, whether causing diseases (impacting on human or agricultureproductivity) or potentially used as biological weapons. Using Perl scriptsand Java to integrate software on an automatic pipeline for analysis ofbacteria genomes including Blast search, database search (hmmpfam andWise2), alignment of homologue sequence groups and protein domains,phylogenetic tree construction and relational database development (MySQL);phylogenetic web service (XML and SOAP) and client side GUI using Java anddatabases; PBS (cluster).Data Analyst/Scientific Curator, 10/2001-5/2002.Computational Biology Resource and Mouse Genome Informatics, the JacksonLaboratory.. Nucleotide sequence and microarray gene expression data analysis,bioinformatics software evaluation. Accessing Celera Discovery System,Sequencher, gene prediction, cluster analysis for RIKEN clones (mouse) andgene annotation of Mouse Genome Database (MGD).SELECTED PUBLICATIONSPhillips JR, et. al. 2019. BMDExpress 2: enhanced transcriptomic dose-response analysis workflow. Bioinformatics. 35(10): 1780-1782.Jackson MA, Yang L, Lea I, Rashid A, Kuo B, Williams A, Lyn Yauk C, FostelJ. 2017. The TGx-28.65 biomarker online application for analysis oftranscriptomics data to identify DNA damage-inducing chemicals in humancell cultures. Environ Mol Mutagen. 58(7):529-535.(https://pubmed.ncbi.nlm.nih.gov/28766826/)Thomas RS, et.al. 2013. Temporal Concordance Between Apical andTranscriptional Points of Departure for Chemical Risk Assessment. Toxicol.Sci, 134(1): 180-194.Tappenden, D.M., H. J. Hwang, L. Yang, R. S. Thomas, and J. J. LaPres,2013. The Aryl-hydrocarbon Receptor Protein Interaction Network (AHR-PIN)as Identified by Tandem Affinity Purification (TAP) and Mass Spectrometry.Journal of Toxicology. (Access)Thomas RS, Wesselkamper SC, Wang NC, Zhao QJ, Petersen DD, Lambert JC, CoteI, Yang L, Healy E, Black MB, Clewell HJ 3rd, Allen BC, Andersen ME. 2013.Temporal concordance between apical and transcriptional points of departurefor chemical risk assessment. Toxicol. Sci. 2013 Jul; 134(1):180-94Thomas RS, Clewell HJ 3rd, Allen BC, Yang L, Healy E, Andersen ME. 2012.Integrating pathway-based transcriptomic data into quantitative chemicalrisk assessment: A five chemical case study. Mutat Res. 2012 Aug 15;746(2):135-43.Woods CG, Fu J, Xue P, Hou Y, Pluta LJ, Yang L, Zhang Q, Thomas RS,Andersen ME, Pi J. 2009. Dose-dependent transitions in Nrf2-mediatedadaptive response and related stress responses to hypochlorous acid inmouse macrophages. Toxicol Appl Pharmacol. 238(1): 27-36.Yang, L., John R. Walker, John B. Hogenesch and Russell S. Thomas1. 2008.NetAtlas: A Cytoscape plugin to examine signaling networks based on tissuegene expression. In Silico Biol. 8(1):47-52Yang, L., Bruce C Allen and Russell S Thomas. 2007. BMDExpress: a softwaretool for the benchmark dose analyses of genomic data. BMC Genomics 2007,8:387Halsey, T.A., L. Yang, J. R Walker, J. B Hogenesch and R. S Thomas. 2007. Afunctional map of NFB signaling identifies novel modulators and multiplesystem controls. Genome Biol. 8(6):R104.Thomas, R.S., B.C. Allen, ANong, L. Yang, E. Bermbudez, H.J.Clewell III,and M.E. Andersen. 2007. A Method to Integrate Benchmark Dose Estimateswith Genomic Data to Access the Functional Effects of Chemical Exposure.Toxicol. Sci. 98(1): 240-248.Thomas RS, Pluta L, Yang L, Halsey TA. 2007. Application of genomicbiomarkers to predict increased lung tumor incidence in 2-year rodentcancer bioassays. Toxicol Sci. 97(1): 55-64.Thomas, R S., T. M. O'Connell, L Pluta*, R. D. Wolfinger, L. Yang* and T.J. Page. 2007. A Comparison of Transcriptomic and Metabonomic Technologiesfor Identifying Biomarkers Predictive of Two-Year Rodent Cancer Bioassays.Toxicol. Sci. 96(1): 40-46.Page, T. J. D. Sikder, L. Yang, L. Pluta, R. D. Wolfinger, T. Kodadek andR. S. Thomas. 2006. Genome-wide analysis of human HSF1 signaling reveals atranscriptional program linked to cellular adaptation and survival. Mol.BioSyst. (2), 627-639.Baldarelli, R. M., et al. 2003. Connecting Sequence and Biology in theLaboratory Mouse. Genome Research 13: 1505-1519Okazaki, Y. et al. 2002. Analysis of the mouse transcriptome based onfunctional annotation of 60,770 full-length cDNAs. Nature 420: 563-573(among 136 co-authors, annotated ~3,500 clones)Winterton, S., L. Yang, B.M. Wiegmann, and D.K. Yeates. 2001. Phylogeneticrevision of Agapophytinae subf.n. (Diptera: Therevidae) based on molecularand morphological evidence. Systematic Entomology 26: 173-211Yang, L. 2000. Molecular Phylogenetics of the Therevidae and their positionamong the families of the Asiloidea (Insecta: Diptera). Ph.D. dissertation.North Carolina State University. pp. ix + 106. figures, tables.Yang, L., B. M. Wiegmann, D. K. Yeates, and M. E. Irwin. 2000. Higher-levelphylogeny of the Therevidae (Diptera: Insecta) based on 28S ribosomal andelongation factor - 1 alpha gene sequences. Molecular Phylogenetics andEvolution 15(3): 440-451Huang, C., and L. Yang. 1998. Influences of habitat changes in the tropicalrainforest on the fauna and species diversity of Acridoidea inXishuangbanna. Chinese Biodiversity 6(2): 122-131. |
