Computer Science: Extensive experience in Java, Perl, C++, SQL (Oracle

LONGLONG YANG

*** ******** ****, ****, ** *****

acac2q@r.postjobfree.com

919-****-***(home), 919-***-****(cell)

EDUCATION

M.S. Master of Computer Science, North Carolina State University, Raleigh,

May 2001

Ph.D. Molecular Evolution, North Carolina State University, Raleigh,

December 2000

B.S. Plant Protection, Shanxi Agricultural University, Taigu, Shanxi,

China, June 1983

SPECIAL SKILLS

Computer Science: Extensive experience in Java, Perl, C++, SQL (Oracle,

MySQL and MS-SQL), and HTML(5); additional experiences in R, JavaScript,

CSS, XML, JAXB, JSON, Ant, Axis, JSP and servlet, JSF, AJAX, Spring,

Hibernate, Apache Tomcat; IIS, web services (SOAP, RESTful); NetBeans,

Eclips, Visual Studio (Express); Subversion and jCVS.

Operating system: Linux, Unix, Windows and Macintosh environments.

Bioinformatics: Managing, archiving and analyzing large-scale data from

microarray gene expression, Next Generation Sequencing (NGS), cDNA screen

and proteomics using commercial, open-source or self-developed software

tools and packages.

Database development and administration (Oracle, MySQL, MS-SQL), public or

commercial database resources with local implementation (NCB Entrez Gene,

Gene Ontology, and network/pathway databases like IntAct, Bind, KEGG,

GeneGO minibase, etc.) and new databases for genomic biology and toxicology

research.

Molecular Biology: laboratory techniques in genomic DNA and RNA extraction,

purification, cDNA library construction, cloning, EST (Expression Sequence

Tag), PCR, RT-PCR, sequencing, electrophoresis.

Text analytics, machine learning and data mining, web crawling.

EXPERIENCE

Technical Advisor, 9/2010-present, Pangene InfoAnalytics Technologies LLC.

Algorithm designation, implementation and software development for text

analytics, including web crawling, information extraction, sentiment

analysis, document summarization, categorization, concept mining, etc..

WIAS - Web Information Analysis System, a Java application to apply Natural

Language Processing (NLP) techniques to automatically analyze large

corpora. Including but not limited to entity extraction, document

summarization and categorization.

Senior Bioinformatics Research Associate, 12/2003-present, Institute for

Chemical Safety Sciences, Center for Genomic Biology and Bioinformatics,

The Hamner Institutes for Health Sciences (Previously, CIIT Centers for

Health Research).

SOFTWARE DEVELOPMENT:

SPRinGS - Signaling Pathway Reconstruction in Genome Screens, a Java

application as a plugin of the Cytoscape for analyzing high throughput cDNA

screen data in Oracle database and building interaction networks with

implementation of the shortest path algorithm.

NetAtlas - a Cytoscape plugin in java to examine signaling networks based

on tissue gene expression data stored in MySQL database (published).

PINATA (Protein Interaction Network Analysis Tools and Archive) - a Java

application as a LIMS and data analysis and visualization tools for

proteomics study with MySQL database; Including interfaces for

experimental designation, sample registration, data loader from Mass Spec

analysis results, image loader for gel images into databases, annotation of

gel images and samples, blast search, protein-protein interactions and

network/pathway construction.

BMDExpress - a software in Java for the benchmark dose analysis of toxic

genomics data with back-end MySQL databases for array annotation and Gene

Ontology enrichment analysis; fitting dose-response or time-course

microarray gene expression data to continuous models of BMDS (EPA),

originally in C and Fortran, called via JNI with re-compiled dynamically

shared libraries for Windows (.dll) or Linux/Unix (.os), or directly use

executables (.exe, Windows only); multi-threaded programming for improved

performance (published).

PowerRMA - a Java application to perform Affymetrix microarray data

normalization from large set of CEL files, with interfaces to interact with

NCBI-GEO data series and perform RMA normalization given a species and

platform, calculating fold changes and perform other statistical analysis

based on sample information in XML format from NCBI-GEO.

Hockey Stick threshold model implemented as a Java GUI for does and

response data with system calls to functions of the model originally

written in R, for users unfamiliar with R.

WEB APPLICATIONS:

LIMS - web-based implementation for the Functional Genomics Core facilities

supporting Affymetrix platforms (GCOS and TitanArray) with MIAME compliant

databases (MySQL and MS-SQL), including sample registration, experiment

setup, array annotation, data analysis and archiving, as well as web tools

for automatically creating SOFT files for NCBI GEO submission; Perl CGI and

JavaServer Faces (JSF), Ajax; Apache Tomcat and IIS.

Electronic Laboratory Notebook - IIS, ASP.NET, AJAX.NET, Razor and C#.

Web services (XML) - pathway database (Oracle) for modeling and simulation

with web services deployed on Tomcat for database insertion and retrieval;

Microarray gene annotation, Entrez Gene and Gene Ontology (GO) web

services with MySQL databases.

DATABASE DEVELOPMENT AND MANAGEMENT:

Implemented GeneNet as a back-end database (Oracle) for GeneSpring, a

commercial software for microarray data analysis.

Entrez Gene, Gene Ontology (GO) and other publicly available interaction

network/ pathway databases (BIND, Intact) with MySQL, local implementation

with Perl scripts for automatic updating.

Other MySQL databases including development and management of cDNA and

siRNA screen data, siRNA designation, Affymetrix chip annotations

databases.

DATA ANALYSIS:

Micorarray gene expression, NGS (Next Genereation Sequence), ToxCast

simulation data and high-throughput sDNA screen data using commercial, open-

source, and self-developed software and tools such as GeneSpring, Partek,

PathwayAssist, Ingenuity Pathways Analysis (IPA), Bio-conductor R packages,

BMDExpress, etc..

Research Associate, 5/2002-12/2003, Virginia Bioinformatics Institute,

Virginia Polytechnic Institute and State University.

Phylogenomics/Comparative genomics of approximately 70 pathogen and

bacteria species/strains. Developed 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. Using Perl scripts

and Java to integrate software on an automatic pipeline for analysis of

bacteria genomes including Blast search, database search (hmmpfam and

Wise2), alignment of homologue sequence groups and protein domains,

phylogenetic tree construction and relational database development (MySQL).

Applyied Web Service, XML and SOAP with Java applications to access

databases, developed phylogenetic web service and client side GUI.

Data Analyst/Scientific Curator, 10/2001-5/2002, Computational Biology

Resource and Mouse Genome Informatics, The Jackson Laboratory. DNA sequence

data 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 (MGD).

Web Master, 6-9/2001, technical support for the development of Chinese

Career Key web page at NC State. HTML, CSS, JavaScript, and Perl CGI.

Research Assistant, 6/1996-5/2000. North Carolina State University.

Molecular evolution, oligonucleotide primer design, DNA extraction, gene

amplification with PCR and RT-PCR, DNA purification and dye terminator

cycle sequencing of multiple genes from multiple species for referring

their phylogenetic relationships.

Data analysis: sequence assembly, editing and alignment (GDE, ClustalW),

sequence analysis (GCG, BLAST, FASTA), and phylogenetic tree construction

(PAUP*, MacClade, Philip).

Research Associate, 1/1987-6/96. Institute of Zoology, Chinese Academy of

Sciences, Beijing. Insect biodiversity and conservation biology, ecology,

and systematics.

Species diversity and conservation biology of animals; Evolutionary

ecology, foraging behavior and pollination biology of bees.

Biology and systematics of families Agromyzidae, Tachinidae (Diptera), and

Apoidea (Hymenoptera).

ACADEMIC HONOURS and AWARDS

The outstanding published paper in 2007, "Advancing the Science of Risk

Assessment. A Method to Integrate Benchmark Dose Estimates with Genomic

Data to Assess the Functional Effects of Chemical Exposure" Toxicological

Sciences. 98(1):240-248. Presented by The Risk Assessment Specialty Section

at the Annual Meeting of the Society of Toxicology, Seattle, Washington,

March, 2008

Scholarship from Chinese Academy of Sciences, 9/1983-7/86.

Research Assistantship from North Carolina State University, 7/1996-6/2000.

SELECTED PUBLICATIONS

Thomas 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 Jan 25.

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):47-52

Yang, L., Bruce C Allen and Russell S Thomas. 2007. BMDExpress: a software

tool for the benchmark dose analyses of genomic data. BMC Genomics 2007,

8:387

Halsey, 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 controlsGenome Biol. 8(6):R104.

Thomas, R.S., B.C. Allen, A Nong, 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: 1505-1519

Okazaki, 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: 173-211

Yang, 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

Huang, C., and L. Yang. 1998. Influences of habitat changes in the tropical

rainforest on the fauna and species diversity of Acridoidea in

Xishuangbanna. Chinese Biodiversity 6(2): 122-131.

Yang, L., Y. Wu, and W. Zhou. 1997. Comparative study on the niche of Osmia

excavata Alfken and O. jacoti Cockerell in apple orchards. Acta

Entomologica Sinica 40(3): 265-270.

Yang, L., H. Xu, and Y. Wu. 1997. Comparative studies of nesting, foraging

behavior and pollination ecology of Osmia excavata Alfken and Osmia jacoti

Cockerell in apple orchards (Hymenoptera: Megachilidae). Acta Ecologica

Sinica 17(1): 1-6

Yang, L. 1995. Agromyzidae (Diptera). In Xue Wan-qi (Ed.), Chinese Flies

(Diptera). Liaoning Science and Technology Publishing House. pp.464-507.

Yang, L., and Y. Wu. 1990. Preliminary study of kiwifruit pollinating bees

in China. Chinese Apiculture 1: 2-4.

REFERENCES Provided up request.

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