| | | 20,000+ Fresh Resumes Monthly | |
|
|
| |
Click here or scroll down to respond to this candidateCandidate's Name
PHONE NUMBER AVAILABLEEMAIL AVAILABLEhttps://LINKEDIN LINK AVAILABLESPECIAL SKILLSExtensive experiences in Java, C++, Perl, PHP, Python, R and Shiny; JavaScript, TypeScript, Node.js Angular, Vue.js, HTML(5), jQuery, CSS, AJAX, XML, JAXB, JSON, Ant, Axis, JSP and servlet, JSF, Spring Core, Spring Boot, SQL, Hibernate, myBatis, JDBC, ODBC; Apache Tomcat, IIS, JBoss, IBM WebSphere, Docker; AWS, Azure; Web services (SOAP), microservices (REST); NetBeans, Eclipse, RStudio, Anaconda3; GIT, bitbucket, Subversion; JIRA, Jenkins, Knime; CI/CD, TDD and BDD; 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 from microarray gene expression, Next Generation Sequencing (NGS), cDNA screens and proteomics using commercial, open-source or self-developed software tools and packages.Text analytics: NLP, sentiment analysis, machine learning, data mining, web crawling, 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, 2/2021-7/2024.ASRC Federal Data Solutions Civilian & Health Operating Group, Research Data Management and Reporting (RDMR) Contract, National Institute of Environmental Health Sciences (NIEHS).Create new R scripts for parametric and nonparametric stats of data from different sources and studies in excel files, integrated as components in KNIME pipeline.Refactor Java applications for statistical analysis of data from genotoxicity studies with bug fixes and significant improvement in flexibility and performance.Refactor, modularize and re-use existing R and python scripts with TDD (Test-Driven Development) for statistical analysis, graphic visualization and reporting of various types of data from CEBS data warehouse, DataMart and data files. Design new tables in Oracle database with improved performance and flexibility.Develop TGx-HDACi and TGx-DDI Biomarkers for Classification of Toxicants web application (UI) in PHP, Laravel and R scripts to analyze gene expression data for class predictions of chemicals using biomarkers derived by the nearest shrunken centroid (NSC) method (a linear machine learning algorithm), with TDD and BDD.Implement continuous integration (CI) and continuous deployment (CD) pipelines with Jenkins for data manipulation and stats analysis.Manage projects and tasks with JIRA.Java Technology Lead, 11/2018-2/2021.Conduent Business Services LLC., InfoSys LimitedSupport Conduent healthcare applications, UI, Web Services and Oracle databases with Spring Core and Spring Boot, Hibernate, Struts, JSP, JavaScript, jQuery.Develop, improve, enhance, debug, deploy and test web applications on DEV and UAT environments and Azure productions.Fix vulnerabilities after OWASP web application security testing, such as Cross Site Scripting (XSS) and SQL Injection, etc..Develop microservices for Power BI applications in Java.Senior Programmer/Analyst, 2/2014-11/2018.National Toxicology Program (NTP), National Institute of Environmental Health Sciences (NIEHS), contacted at DS Technologies, Inc.develop applications in Java, Python, R, R Shiny and Spotfire for integration, management, analysis and visualization of microarray gene expression, high throughput transcriptome resequencing, histopathology and hematology data in CEBS (Chemical Effects in Biological Systems), a public Oracle database repository.Work in team to implement web based LIMS with Oracle database for the NTP lab at NIEHS to perform data collection, management, manipulation, statistic analysis and visualization.Create the Python library cebsPy with statistical tests/methods used for analysis of CEBS data, implement microservices and RESTful APIs using Python and Django with TDD.Develop the first JSF web application for dose response models and histopathology studies.Develop the first PHP web application for biomarker classification based on gene expression data of test chemicals.Work in team to develop command line application for generation PDF reports with more than 60 report types using Java, Hibernate, myBatis and iText.Senior Bioinformatics Research Associate, 12/2003-2/2014.Center for Genomic Biology and Bioinformatics, the Hamner Institutes for Health Sciences.Software Development: Java Swing applications include BMDExpress (published) for the benchmark dose analysis of dose-response or time-course microarray gene expression data with ANOVA, GO and pathway enrichment tests; NetAtlas (published) as a Cytoscape plugin for examining signaling networks based on tissue gene expression data stored in MySQL database; SPRinGS for signaling pathway reconstruction in genome screens; GEAX for gene expression analysis cross (X) species; PowerRMA for very large sets (several thousands) of Affymetrix microarray data normalization from CEL files and basic statistics computation; Hockey Stick threshold model (original model in R) for does and response data.Implement the LIMS for labs performing high through screening, microarray gene expression, NGS, live cell imaging and real-time cytometry studies, including experimental design, instruments setup, data collection, analysis, etc..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) and other publicly available interaction network/ pathway databases (BIND, Intact) with local MySQL, using Perl scripts for automatic updating; new MySQL databases for cDNA and siRNA screen data, siRNA designation, Affymetrix chip annotation and back-end databases of the LIMS.Data Analysis: Microarray gene expression, NGS (Next Generation Sequencing), ToxCast assays and simulation, high-throughput cDNA/siRNA screens, proteomics, cell imaging and cytometry data from toxicogenomics and caner biology research; commercial, open-source, and developed software and tools such as GeneSpring, PathwayAssist, BMDExpress, Partek, Ingenuity Pathways 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 State University.Perform Phylogenomics/Comparative genomics analysis of approximately 70 pathogen and bacteria species/strains.Develop phylogenetic web service and client side GUI in Java, SOAP, XML and MySQL databases.Develop a phylogenetic component to the informatics system of pathogens - Pathogen Portal or "PathPort", for rapid detection, identification, and forensic attribution of high-priority pathogens, whether causing diseases (impacting on human or agriculture productivity) or potentially used as biological weapons.Develop Perl scripts and Java application to integrate a pipeline for automatic analysis of bacteria genomes including Blast search, database search (hmmpfam and Wise2), alignment of homologous sequence groups, and construction of phylogenetic tree.Data Analyst/Scientific Curator, 10/2001-5/2002.Computational Biology Resource and Mouse Genome Informatics, the Jackson Laboratory.Nucleotide sequence and microarray gene expression data analysis, bioinformatics software evaluation. Accessing Celera Discovery System, Sequencher, gene prediction, cluster analysis for RIKEN clones (mouse) and gene annotation of Mouse Genome Database.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, Fostel J. 2017. The TGx-28.65 biomarker online application for analysis of transcriptomics data to identify DNA damage-inducing chemicals in human cell cultures. Environ Mol Mutagen. 58(7):529-535. (https://pubmed.ncbi.nlm.nih.gov/28766826/)Thomas RS, et.al. 2013. Temporal Concordance Between Apical and Transcriptional 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, Cote I, Yang L, Healy E, Black MB, Clewell HJ 3rd, Allen BC, Andersen ME. 2013. Temporal concordance between apical and transcriptional points of departure for 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 chemical risk 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-mediated adaptive response and related stress responses to hypochlorous acid in mouse 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 tissue gene expression. In Silico Biol. 8(1):47-52Yang, L., Bruce C Allen and Russell S Thomas. 2007. BMDExpress: a software tool 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. A functional map of NFB signaling identifies novel modulators and multiple system 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 Estimates with 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 genomic biomarkers to predict increased lung tumor incidence in 2-year rodent cancer 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 Technologies for 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 and R. S. Thomas. 2006. Genome-wide analysis of human HSF1 signaling reveals a transcriptional program linked to cellular adaptation and survival. Mol. BioSyst. (2), 627-639.Baldarelli, R. M., et al. 2003. Connecting Sequence and Biology in the Laboratory Mouse. Genome Research 13: 1505-1519Okazaki, Y. et al. 2002. Analysis of the mouse transcriptome based on functional 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. Phylogenetic revision of Agapophytinae subf.n. (Diptera: Therevidae) based on molecular and morphological evidence. Systematic Entomology 26: 173-211Yang, L. 2000. Molecular Phylogenetics of the Therevidae and their position among 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-level phylogeny of the Therevidae (Diptera: Insecta) based on 28S ribosomal and elongation factor 1 alpha gene sequences. Molecular Phylogenetics and Evolution 15(3): 440-451 |
