Xin (James) Li
Curriculum Vitae
Department of Biostatistics, Bioinformatics, and
Biomathematics
Lombardi Comprehensive Cancer Center
Georgetown University Medical Center
4000 Reservoir Rd, NW
Building D, Suite 180
Washington, DC 20057
Education
Email: xl35@georgetown.edu
Work: +1 202-687-8533
Fax: +1 202-687-2581
2011
Ph.D., Information Systems
Mentor: Aryya Gangopadhyay, Ph.D.
Dissertation Title: Privacy Preserving Principal Component Analysis on Distributed
Bioinformatics Datasets
University of Maryland, Baltimore County
2003
Master of Science, Information Systems
University of Maryland, Baltimore County
2001
Master of Management, Management Science
Beijing University of Aeronautics and Astronautics
1998
Bachelor of Engineering, Management Information Systems
Beijing University of Aeronautics and Astronautics
 Privacy Preserving Data Mining for Biomedical Informatics Applications
o Allows Multiple Parties (Data Providers) to Collaborate Together
o Obtains Data Mining Results from the Global View of Multiple Datasets
o Without Sharing/Merging Original Data to Protect the Privacy
 Computational Methods and Algorithms for High Dimensional “Omics” Data
o High Through-put (Parallel / ”Next-generation”) Sequencing Data Analysis
o Gene Expression / CNV / CGH Microarray Data Analysis
o MicroRNA Profiling Data Analysis
 Transfer Learning Applications on Biomedical Informatics and Bioinformatics
 Business Intelligence Applications on Healthcare Industry
 Web-based Online Workflow (Pipeline) / Database System for Biomedical Research
 Ontology-driven Data Integration for Biomedical Informatics and Bioinformatics
Research
Interests
Research
Experience
March 10th, 2015
2011-
2006-2011
Assistant Professor of Bioinformatics
Department of Biostatistics, Bioinformatics, and Biomathematics
Lombardi Comprehensive Cancer Center, Medical Center
Georgetown University
 Conduct Machine Learning & Data Mining Research
 Provide Statistical and Informatics Collaboration to Biomedical Researchers
 Lead of In-house Bioinformatics tools and systems development
 Teach Bioinformatics and Statistical Programming Courses
Research Associate, Bioinformatician
Department of Biostatistics, Bioinformatics, and Biomathematics
Lombardi Comprehensive Cancer Center, Medical Center
Georgetown University
 Design, Development, and Maintain In-house Bioinformatics Tools/Databases
 Statistical and Informatics Consulting Service to Biomedical Researchers
o Microarray gene expression data (Affymetrix, Agilent, Illumina)
o MicroRNA data (ABI, NanoString)
Page 1 of 6
Xin (James) Li
Curriculum Vitae
o
High-throughput sequencing data (Illumina, Roche 454)
2003-2005
Associate Faculty (Online master program)
Department of Information Systems
University of Maryland, Baltimore County
2001-2003,
2006
Graduate Assistant
Department of Information Systems
University of Maryland, Baltimore County
1998-2001
Research Assistant
Department of Management Information Systems, School of Management
Beijing University of Aeronautics and Astronautics
Technical Skills
Teaching
Activities
March 10th, 2015
R/Bioconductor, Matlab, SPSS
Linux, Windows Server Series
Hadoop
Oracle, NoSQL, MS SQL Server, MySQL, PostgreSQL
Apache, Tomcat
C, Java/JSP/JWS, VB/VBA, Perl, PHP, PL-SQL
BOWTIE, Tophat, Galaxy, BRB-ArrayTools
Partek Genomics Suite, GeneSpring, Ingenuity, Pathway Studio, StatMiner
Fall 2012
Fall 2013
Course Name: Bioinformatics for “Omics” Data
Program: Georgetown University Biostatistics Master Program
Role: Course Creator, Designer, & Instructor
Fall 2011
Fall 2012
Fall 2013
Course Name: Introduction to Statistical Software (R Programming)
Program: Georgetown University Biostatistics Master Program
Role: Course Designer & Instructor
Summer 2004,
2005
Course Name: Database Systems
Program: UMBC Online Information Systems Master Program
Role: Associate Faculty
Fall 2003, 2004
Course Name: Healthcare Informatics
Program: UMBC Online Information Systems Master Program
Role: Associate Faculty
Spring 2004,
2005
Course Name: Information Systems Analysis and Design
Program: UMBC Online Information Systems Master Program
Role: Associate Faculty
Spring 2002
Course Name: Electronic Commerce
Program: UMBC Online Information Systems Master Program
Role: Teaching Assistant
Fall 2003
Spring 2003
Course Name: Excel VBA for Decision Support Systems
Program: UMBC Information Systems Undergraduate
Role: Teaching Assistant
Course Name: Scripting Languages
Page 2 of 6
Xin (James) Li
Curriculum Vitae
March 10th, 2015
Program: UMBC Information Systems Undergraduate
Role: Teaching Assistant
Mentoring
Activities
2012-
2011-2012
Yitao Wang, Master Student, Georgetown Biostatistics
Practicum Project: Cross-experimental Gene Expression Analysis of Obesity on Pooled Public
Microarray Data
2011-2012
Siwen He, Master Student, Georgetown Biostatistics
Practicum Project: Weighted Principal Component Analysis Application on Gene Set
Enrichment Analysis
2011-2012
Benjamin Scheich, Master Student, Georgetown Biostatistics
Practicum Project: Predicting Tumor Stages of Lung Cancer Adenocarcinoma Tumors from
Pooled Microarray Data Using Machine Learning Methods
2011-
Publications
Yi-Ying Chen, Master Student, Georgetown Biostatistics
Processing And Analysis of RNA-seq Data and its Comparison to Corresponding Gene
Expression Microarray Data
Xuefei Jia, Master Student, Georgetown Biostatistics
Academic Advisee
Book Chapters
1.
Li X and Gangopadhyay A. "Applications of Web Services in Bioinformatics." Peer-to-peer
Computing: The Evolution of A Disruptive Technology. Ed. Goodman B and Subramanian
R. Idea Group Publishing, 2005: 265-277.
Referred
Journal Papers
1.
Li X*, Scheich B. "Predicting Tumor Stages of Lung Cancer Adenocarcinoma Tumors from
Pooled Microarray Data using Machine Learning Methods." International Journal of
Computational Biology and Drug Design (2015).
Artym VV, Swatkoski S, Matsumoto K, Campbell CB, Petrie RJ, Dimitriadis EK, Li X,
Mueller S, Bugge TH, Gucek M, Yamada KM. "Dense fibrillar collagen is a potent inducer
of invadopodia via a specific signaling network." Journal of Cell Biology 208.3 (2015):
331-350.
Li H, Li X, Smerin S.E., Zhang L, Jia M, Xing G, Su Y.A., Wen J, Benedek D, Ursano R.
"Mitochondrial gene expression profiles and metabolic pathways in the amygdala
associated with exaggerated fear in an animal model of PTSD." Frontiers in Neurology
(2014).
Shah N, Wang J, Selich-Anderson J, Graham G, Siddiqui H, Li X, Khan J, Toretsky J. "PBX1
Is a Favorable Prognostic Biomarker as It Modulates 13-cis Retinoic Acid-Mediated
Differentiation in Neuroblastoma." Clinical Cancer Research 20.16 (2014): 4400-12.
Srivastava A, Goldberger H, Dimtchev A, Marian C, Soldin O, Li X, Collins SP, Suy S, Kumar
D. "Circulatory miR-628-5p is downregulated in prostate cancer patients." Tumor Biology
(2014).
Pollock CB, McDonough S, Wang VS, Lee H, Ringer L, Li X, Prandi C, Lee RJ, Feldman AS,
Koltai H, Kapulnik Y, Rodriguez OC, Schlegel R, Albanese C, Yarden RI "Strigolactone
analogues induce apoptosis through activation of p38 and the stress response pathway
in cancer cell lines and in conditionally reprogramed primary prostate cancer cells."
Oncotarget. 5(6):1683-98. (2014)
Srivastava A, Goldberger H, Dimtchev A, Ramalinga M, Chijioke J, Marian C, Oermann E,
Uhm S, Kim J S, Chen L N, Li X, Berry D L, Kallakury B V S, Chauhan S C, Collins S P, Suy S,
Kumar D. "MicroRNA Profiling in Prostate Cancer - The Diagnostic Potential of Urinary
miR-205 and miR-214." PLoS One 8.10 (2013): e76994.
2.
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5.
6.
7.
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Xin (James) Li
Curriculum Vitae
8.
9.
10.
11.
12.
13.
14.
15.
16.
17.
Referred
Articles on
Conference
Proceedings
1.
2.
3.
4.
5.
6.
Invited Talk
March 10th, 2015
Sun N, Li D, Fonzi W, Li X, Zhang L, Calderone R. "Multidrug Resistant Transporter Mdr1p
Mediated Uptake of a Novel Antifungal Compound." Antimicrobial Agents and
Chemotherapy (2013). [Forthcoming]
Karve TM, Preet A, Sneed R, Salamanca C, Li X, Xu J, Kumar D, Rosen EM, Saha T. “BRCA1
regulates follistatin function in ovarian cancer and human ovarian surface epithelial
cells.” PLoS One. 2012;7(6):e37697.
Karve TM, Li X, and Saha T. "BRCA1-mediated signaling pathways in ovarian
carcinogenesis." Functional Integrative Genomics 12.1 (2012): 63-79.
Li X. "Privacy Preserving Principal Component Analysis Clustering for Distributed
Heterogeneous Gene Expression Datasets." International Journal of Computational
Models and Algorithms in Medicine 2.4 (2011).
Upadhyay G, Yin Y, Yuan H, Li X, Derynck R, Glazer RI. "Stem cell antigen-1 enhances
tumorigenicity by disruption of growth differentiation factor-10 (GDF10)–dependent
TGF-β signaling." PNAS 108.19 (2011): 7820-7825.
Pollock CB, Yin Y, Yuan H, Zeng X, King S, Li X, Kopelovich L, Albanese C, and Glazer R.
"PPARδ Activation Acts Cooperatively with 3-Phosphoinositide-Dependent Protein
Kinase-1 to Enhance Mammary Tumorigenesis." PLoS ONE 6.1 (2011).
Pollock CB, Rodriguez O, Martin PL, Albanese C, Li X, Kopelovich L, and Glazer RI.
"Induction of Metastatic Gastric Cancer by Peroxisome Proliferator-Activated Receptor
δ Activation." PPAR Research 2010 (2010).
Li X. "Privacy Preserving Clustering for Distributed Homogeneous Gene Expression
Datasets." International Journal of Computational Models and Algorithms in Medicine
1.3 (2010): 31-54.
Liu H, Bebu, I, and Li X. "Microarray Probes and Probe Sets." Frontier of Biological
Science (Elite Ed) 1.2 (2010): 325-38.
Li X, Chen A. "Modeling and Analysis of Production – Distribution System in supply Chain
Management." Journal of Beijing University of Aeronautics and Astronautics (Social
Sciences Edition) 14.3 (2001): 27-29.
Li X. "A Novel Privacy Preserving Clustering Method." 2009. New Orleans, LA: The 40th
Annual Meeting of the Decision Sciences Institute.
Liu H, Li X, Yoon V and Clarke R. "Annotating breast cancer microarray samples using
ontologies." 2008. Washington, DC: The American Medical Informatics Association
(AMIA) 2008 Annual Symposium.
Li X. "Knowledge Based, Data Driven and Object-Relational Workflow Management for
Microarray Processing Pipeline." 2007. Orlando, FL: the 2007 International Conference
on Cybernetics and Information Technologies, Systems, and Applications.
Li X. "A Flexible Database Integration Approach Using Object-relational Model." 2006.
San Antonio: The 37th Annual Meeting of the Decision Sciences Institute, San Antonio.
Li X and Zhang D. "A prototype of business process management using Web Services."
2005. San Diego: Information Resources Management Association annual conference.
Li X and Chiang W. "A Simulation Study on Double-Direction Information Sharing In
Supply Chain Management." 2004. Las Vegas: Second Western Business and
Management Annual Conference.
Nov. 20th, 2014
“Advances in methods on enriched and integrated analysis for high-throughput ‘-omics’
data”, Department of Mathematical Sciences, New Jersey Institute of Technology, Newark,
NJ
Nov. 4th, 2014
“RNA-Seq Gene Expression Data Analysis Pipeline: Methods, Tools and Issues”
RNA-Seq, From Lab Bentch to Laptop, NIH Bio-TRAC Workshop.
Bethesda, MD
Page 4 of 6
Xin (James) Li
Curriculum Vitae
Leadership
University
Service
Sept. 27th, 2013
“MicroRNA Data Analysis in GESR”
Exiqon workshop 2013: Expression and function of non-coding RNA.
Washington, DC
June 14th, 2013
“Cancer Epigenomics: Data Generation and Software Solutions”
The First Annual Meeting of Mid-Atlantic Directors and Staff of Scientific Cores.
Frederick, MD
May 15th, 2012
“Issues and Applications on Microarray Data Analysis Pipeline, GSEA, and Data Mining”
Advanced Microarray Analysis and Pathway Integration, NIH Bio-TRAC Workshop.
Bethesda, MD
March 2nd, 2012
“Privacy Preserving Principal Component Analysis Clustering for Distributed Bioinformatics
Datasets”
Department of Biostatistics, Bioinformatics, and Biomathematics, Georgetown University
Washington, DC
2005-2006
Graduate student representative, the Faculty Promotion and Tenure Committee, Department
of Information Systems, University of Maryland, Baltimore County
2004-2005
Senator, Graduate Student Association, University of Maryland, Baltimore County
2001-2002
Vice President, Chinese Student and Scholar Association, University of Maryland, Baltimore
County
2006-
2006-2011
Departmental
Service
March 10th, 2015
2011-
Service to scientific community
Bioinformatician, Genomics and Epigenomics Shared Resource, Lombardi Comprehensive
Cancer Center, Georgetown University Medical Center
Bioinformatician, Proteomics and Metabolomics Shared Resource, Lombardi Comprehensive
Cancer Center, Georgetown University Medical Center
Coordinator, Workshops in Bioinformatics and Statistics, Department of Biostatistics,
Bioinformatics, and Biomathematics, Georgetown University
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Editorial Board Member of Data Mining and Bioinformatics
Editorial Board Member of Computational Models and Algorithms in Medicine
Reviewer of Bioinformatics
Reviewer of Biomedical Informatics
Reviewer of BMC Bioinformatics
Reviewer of Briefings of Bioinformatics
Reviewer of Expert Systems with Applications
Reviewer of EURASIP Journal on Bioinformatics and Systems Biology
Reviewer of G3: Genes, Genomes, Genetics
Reviewer of Annual Symposiums of American Medical Informatics Association (AMIA)
Reviewer of AMIA Clinical Research Informatics Summit
Reviewer of International Conference on Information Systems, Technology and
Management
Reviewer of International Conference of Information Systems
Reviewer of International Conference on Intelligent Biology and Medicine
Reviewer of Annual Meetings of Decision Support Institute
Page 5 of 6
Xin (James) Li
Curriculum Vitae
Professional Membership
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Reviewer of Workshop on E-Business
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Institute of Electrical and Electronics Engineers
Association for Computing Machinery
International Society for Computational Biology
Association for Information Systems
March 10th, 2015
References upon Request
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