Tsoi cv umms_8_6_15

Lam C. Tsoi (Alex), M.S., Ph.D. 1

Lam C. Tsoi (Alex), M.S., Ph.D.
Research Assistant Professor
University of Michigan
Department of Dermatology
Department of Computational Medicine and Bioinformatics
7421 Medical Sciences I
1301 E. Catherine St.
Ann Arbor, Michigan, USA 48109-5609
Cell: 843-817-2132
Office: 734-764-7069
alextsoi@umich.edu
tsoi.teen@gmail.com
Education and Training
Education
08/2001-06/2002 transferred (Major: Biology), Chinese University of Hong Kong, Hong
Kong
08/2002-12/2002 transferred (Major: Biology), Trident Technical College, Charleston,
SC, USA
01/2003-05/2005 B.S. (Major: Biology, Minor: Mathematics), College of Charleston,
Charleston, SC, USA
08/2005-10/2008 M.S. in Biomedical Science (Bioinformatics)
Thesis: “Evaluation of genome-wide association study results through
development”, Medical University of South Carolina, Charleston, SC,
USA
11/2008-10/2010 Ph.D., with Distinction in Biomedical Science (Bioinformatics)
Dissertation: “Using Ontology Fingerprint to Enhance Analysis of High
Throughput Experimental Results”, Medical University of South
Carolina, Charleston, SC, USA
Post-doctoral training
11/2010-08/2015 Postdoctoral Fellow, Center for Statistical Genetics, Department of
Biostatistics, School of Public Health, University of Michigan, Ann
Arbor, MI, USA
Academic Appointments
08/2015-present Research Assistant Professor, Department of Dermatology, University of
Michigan Medical School, Ann Arbor, MI, USA
08/2015-present Research Assistant Professor, Department of Computational Medicine
and Bioinformatics, University of Michigan Medical School, Ann Arbor,
MI, USA


Research Interests
My primary research interest is to use genomics data to provide biological inferences for human
cutaneous diseases. I am particularly interested in the development of analysis pipelines,
computational approaches, and bioinformatics tools to data-mine information from biological
experiments. I have strong interest in investigating the pathology and genetic architecture of
complex disorders, in particular autoimmune diseases such as psoriasis. I have taken the systems
biology approach in designing and developing data integration and bioinformatics methods to
analyze high dimensional data to make biological inferences regarding networks or interactions
that play significant roles in the disease mechanism.
Research Support
Current
Funding Agency: NIH/NIAMS
Grant/Contract No.: R01-AR065183
Title of Project: Functional Genomics of Psoriasis
Principal Investigator: James T. Elder
Role in Grant: Research Fellow
Inclusive dates: 04/2014-06/2015
Funding amount: $350,000 annually
Past
Funding Agency: NIH/NLM
Grant/Contract No.: T15 LM07438-02
Title of Project: Training of Toolmakers for Bio-Medical Informatics
Principal Investigator: Xinghua Lu
Role in Grant: Graduate research assistant
Funding amount: $1,727,872
Funding Agency: NIH/NCRR
Grant/Contract No.: 5P20RR017677
Title of Project: COBRE in lipidomics and pathobiology
Principal Investigator: Lina M. Obeid
Role in Grant: Graduate research assistant
Funding amount: $2,146,200
Title of Project: Combined Analysis of Gene Expression and Genetic Variation in Psoriasis


Title of Project: Identification of Psoriatic Arthritis Genes
Title of Project: Linkage Analysis of Familial Psoriasis
Honors and Awards
2004 Fellowship for population dynamics by NOAA
2004 College of Charleston Academic Year Research Award (AYRA)
2004 Academic Achievement Merit Scholarship
2004 College of Charleston Research Presentation Grant (RPG) award
2005 College of Charleston School of Sciences and Mathematics (SSM) annual award
2007 Travel award from the 8th
International Conference of System Biology
2008 Medical University of South Carolina Student Research Day 1st
place in
Bioinformatics presentation
2009 International Conference of Biomedical Ontology (ICBO) stipend award
2009 Hollings Cancer Center Symposium Outstanding Scientific Poster 2nd
place
2009 Among the best performers in Dialogue for Reverse Engineering Assessment and
Method (DREAM) 4 Challenge 3: Predictive Signaling Network Modeling
2011 Semifinalist for Trainee Research Award, American Society of Human Genetics
for abstract submission to the 12th International Congress of Human Genetics
Memberships in Professional Societies
2008-present American Society of Human Genetics


Editorial Positions, Boards, and Peer-Review Service
Study Sections
2014 External grant reviewer for Italian Telethon Foundation
Journal Reviewer
Acta Dermato-Venereologica
American Medical Informatics Association 2014 Annual Symposium
Archives of Dermatological Research
Clinical Epidemiology
Human Molecular Genetics
International Society for Computational Biology (ISCB)-Asia Conference on Computational
Genomics, (SCCG) 2012
Journal of Investigative Dermatology
PLOS Computational Biology
PLOS ONE
Teaching
2006 Teaching Assistant, Introduction to Bioinformatics (graduate level), MUSC
2007 Teaching Assistant, Introduction to Bioinformatics (graduate level), MUSC
2012-2013 Principal Advisor for Michael Joseph Kirsch II (College of Literature, Science
and Arts) in the Undergraduate Research Opportunity Program (UROP) in the
University of Michigan. Project: Integration of Gene Models in Multiple
Biological Databases
Visiting Professorships, Seminars, and Presentations
5/2010 “Using Ontology Fingerprint to enhance analysis of high throughput
experimental results.” Center for Statistical Genetics, University of
Michigan (Ann Arbor, MI).
11/2012 “Fifteen novel psoriasis susceptibility loci: Disease-specific signals
highlight the role of innate immunity.” American Society of Human
Genetics annual meeting (San Francisco, CA).
2/2015 “Systems Biology approaches to provide inferences and discoveries for
high-throughput experiments.” Bioinformatics program, Department of
Biology, University of Memphis (Memphis, TN).
2/2015 “Systems Biology approaches to provide inferences and discoveries for
high-throughput experiments.” School of Biomedical Informatics,
University of Texas Health Science Center at Houston (Houston, TX).


Bibliography
1. Tsoi LC, Zheng WJ. A method of microarray data storage using array data type.
Computational Biology and Chemistry 31(2):143-7, 2007.
2. Bradshaw S, Zheng WJ, Tsoi LC, Gilkeson GS, Zhang XK: A role for Fli-1 in B cell
proliferation: implications for SLE pathogenesis. Clinical Immunology 129(1):19-30,
2008.
3. Bryan TP, Tsoi LC, and de Buron I. Development of the philometrids Philometra
overstreeti and Philometroid paralichthydis in the experimentally infected copepod
Oithona colcarva. Folia Parasitologica 55:313-315, 2008.
4. Tsoi LC, Patel R, Zhao W, Zheng WJ. Text Mining Approach to Evaluate Terms for
Ontology Development. J. Biomedical Informatics 42(5): 824-830, 2009.
5. Tsoi LC, Boehnke M, Klein R, Zheng WJ. Evaluation of Genome-wide Association
Study Results through Development of Ontology Fingerprint. Bioinformatics 25(10):1314-
20, 2009.
6. de Buron I, France SC, Roumillat B, Connors V, Tsoi LC: Philometrids of the southern
flounder Paralichthys lethostigma: a multidimensional approach to determine their
diversity. Journal of Parasitology 97(3):466-75, 2011.
7. Tsoi LC, Qin T, Slate EH, Zheng WJ: Consistently differential expression pattern
(CDEP) on microarray data to identify genes related to metastatic behavior. BMC
Bioinformatics 12:438, 2011.
8. Ellinghaus E, Stuart PE, Ellinghaus D, Nair RP, Debrus S, Raelson JV, Belouchi M,
Tejasvi T, Li Y, Tsoi LC, Onken AT, Esko T, Metspalu A, Rahman P, Gladman DD,
Bowcock AM, Helms C, Krueger GG, Koks S, Kingo K, Gieger C, Wichmann HE,
Mrowietz U, Weidinger S, Schreiber S, Abecasis GR, Elder JT, Weichenthal M, Franke
A. Genome-Wide Meta-Analysis of Psoriatic Arthritis Identifies Susceptibility Locus at
REL. J Invest Dermatol. 132(4):1133-40, 2011.
9. Tsoi LC*, Spain SL*, Knight J*, Ellinghaus E*, et al: Fifteen novel psoriasis
susceptibility loci: disease-specific signals highlight the role of innate immunity. Nat
Genet. 44(12): 1341-8, 2012 (cited over 200 times as of May 2015).
10. Qin T, Tsoi LC, Sims KL, Lu X, Zheng WJ: Signaling network prediction by the
Ontology Fingerprint enhanced Bayesian network. BMC Systems Biology. 6 Suppl S:S3,
2012.
11. Gesty-Palmer D, Maudsley S, Yuan L, Martin B, Wood WH III, Lee MH, Janech MG,
Tsoi LC, Zheng WJ, and Luttrel LM, β-Arrestin Selective G Protein-Coupled Receptor
Agonists Engender Unique Biological Efficacy In Vivo. Molecular Endocrinology. ;
27(2):296-314, 2013.
12. Ellinghaus D, Baurecht H, Esparza-Gordillo J, Rodríguez E, Matanovic A, Marenholz I,
Hübner N, Schaarschmidt H, Novak N, Michel S, Maintz L, Werfel T, Meyer-Hoffert U,
Hotze M, Prokisch H, Heim K, Herder C, Hirota T, Tamari M, Kubo M, Takahashi A,
Nakamura Y, Tsoi LC, Stuart P, Elder JT, et al: High-density genotyping study identifies


four new susceptibility loci for atopic dermatitis. Nature Genetics 45(7):808-12, 2013.
13. Li B*, Tsoi LC*, Nair RP, Ding J, Gudjonsson JE, Stuart PE, Tejasvi T, Voorhees JJ,
Kang HM, Abecasis GR, Elder JT: Large-scale transcriptome analysis using RNA-seq
reveals new insights into psoriasis biology. Journal of Investigative Dermatology 134(7):
1828-38, 2014.
14. Qin T, Matmati N, Tsoi LC, Mohanty BK, Gao N, Tang J, Lawson AB, Hannun YA,
Zheng WJ. Finding pathway-modulating genes from a novel Ontology Fingerprint-
derived gene network. Nucleic Acid Research 42(18), 2014.
15. Okada Y, Han B, Tsoi LC, Start PE, Ellinghaus E, Tejasvi T, Chandran V, et al. Fine-
mapping major histocompatibility complex associations in psoriasis and its clinical
subtypes. American Journal of Human Genetics 95(2): 162-72, 2014.
16. Baurecht H, Hotze M, Brand S, Büning C, Cormican P, Corvin A, Ellinghaus D,
Ellinghaus E, Esparza-Gordillo J, Fölster-Holst R, Franke A, Gieger C, Hubner N, Illig T,
Irvine AD, Kabesch M, Lee YAE, Lieb W, Marenholz I, McLean WHI, Morris DW,
Mrowietz U, Nair R, Nöthen MM, Novak N, O’Regan GM, the PAGE consortium,
Schreiber S, Smith C, Strauch K, Stuart PE, Trembath R, Tsoi LC, Weichenthal M,
Barker J, Elder JT, Weidinger S, Cordell HJ, Brown SJ. Genome-wide comparative
analysis of atopic dermatitis and psoriasis gives insight into opposing genetic mechanisms.
American Journal of Human Genetics 96(1):104-20, 2015.
17. Tsoi LC, Iyer MK, Stuart PE, Tejasvi T, Li B, Ding J, Gudjonsson JE, Kang HM, Nair
RP, Chinnaiyan A, Abecasis GR, Elder JT. Analysis of long non-coding RNAs highlights
tissue-specific expression patterns and epigenetic profiles in normal and psoriatic skin.
Genome Biology 16:24, 2015. (designated as highly accessed paper)
18. Tsoi LC#
, Elder JT, Abecasis GR#
. Graphical algorithm for integration of genetic and
biological data. Bioinformatics 31(8):1243-9, 2015.
19. Koch M, Baurecht H, Ried JS, Rodriguez E, Schlesinger S, Volks N, Gieger C, Rückert I,
Heinrich L, Willenborg C, Smith C, Peters A, Thorand B, Koenig W, Lamina C, Jansen
H, Kronenberg F, Seissler J, Thiery J, Rathmann W, Schunkert H, Erdmann J, Barker J,
Nair R, Tsoi LC, Elder JT, Mrowietz U, et al. Psoriasis and cardiometabolic traits:
modest association and distinct genetic architectures. Journal of Investigative
Dermatology 135(5):1283-93, 2015.
20. Tsoi LC, Spain, SL, Ellinghaus E, Stuart PE, et al. Enhanced meta-analysis and
replication studies identify five new psoriasis susceptibility loci. Nature
Communications 6:7001, 2015.
21. Das S, Stuart PE, Ding J, Tejasvi T, Li Y, Tsoi LC, Chandran V, Fischer J, Helms C,
Duffin KC, Voorhees JJ, Bowcock AM, Krueger GG, Lathrop GM, Nair RP, Rahman P,
Abecasis GR, Gladman D, Elder JT. Fine-mapping of eight psoriasis susceptibility loci.
European Journal of Human Genetics. 23(6):844-53, 2015.
22. Ding J, Sidore C, Butler TJ, Wing MK, Qian Y, Meirelles O, Busonero F, Tsoi LC,
Maschio A, Angius A, Kang HM, Nagaraja R, Cucca F, Abecasis GR, Schlessinger D.
Assessing Mitochondrial DNA Variation and Copy Number in Lymphocytes of ~2,000
Sardinians using Tailored Sequencing Analysis Tools. PLoS Genet. 14;11(7), 2015.
#
Corresponding author


Conference Abstracts
1. Tsoi, LC, Sancho G (2004) Behavioral analyses of Thermarces cerberus in hydrothermal
vents. South Carolina Academy of Sciences, Charleston, SC
2. Tsoi, LC, de Buron I (2004) Survivorship and the possible intermediate host of
philometrid nematode Margolisianum bulbosum. Undergraduate Research Symposium,
College of Charleston, Charleston, SC.
3. Tsoi, LC, de Buron I (2004) Survivorship and development of philometrid nematode
Margolisianum bulbosum. College of Charleston Convocation for SUR awardees,
College of Charleston, Charleston, SC.
4. Tsoi, LC, Connors V, de Buron I (2005) Lifespan and infectivity of the philometrid
nematode Maragolisianum bulbosum larvae. Southeastern Society of Parasitologists,
Charleston, SC.
5. Tsoi LC, Zheng WJ (2006) Using array data type to store microarray data in an object-
relational database--PostgreSQL. Medical University of South Carolina Student Research
Day, Charleston, SC.
6. Tsoi LC, Zheng WJ (2007) Using array data type to store microarray data in object-
relational database--PostgreSQL. 3rd SC-INBRE Bioinformatics Research Symposium at
Clemson University, SC.
7. Tsoi LC, Zheng WJ (2007) A method of microarray data storage using array data type.
National Library of Medicine Informatics Training conference. Stanford University,
Stanford, CA.
8. de buron I, Bryan TP, Tsoi, LC (2007) Development and Pathogenicity of Philometra
overstreeti and Philometroides paralichthydis in the cyclopoid copepod Oithona
colcarva. 7th International Symposium on fish parasites, Viterbo, Italy.
9. Tsoi LC, Watson, D, Zheng WJ (2007) Identification of genes with common differential
expression pattern across different metastatic microarray data. 8th International
Conference of Systems Biology, Long Beach, CA.
expression pattern across different metastatic microarray data. 7th Medical University of
South Carolina Hollings Cancer center Annual Scientific Research Retreat, Charleston,
SC.
expression pattern across different metastatic microarray data. National Library of
Medicine Informatics Training Conference. NIH Campus, Bethesda, MD.
12. Tsoi LC, Boehnke M, Klein, RL, Zheng WJ (2008) Ontology fingerprints to
quantitatively characterize genes and diseases for genome wide association study. 56th
American Society of Human Genetics Annual Meeting, Philadelphia, PA.
13. Tsoi LC, Alberg AJ, Boehnke M, Zheng WJ (2009) Assessment of genome-wide
association study results of Lung Cancer by combining ontological data with biomedical
literature. Medical University of South Carolina Hollings Cancer Center Spring


Symposium, Charleston, SC.
14. Tsoi LC, Boehnke M, Klein, RL, Zheng WJ (2009) Ontology finger prints to
quantitatively characterize genes and diseases for genome wide association study.
National Library of Medicine Informatics Training conference. Oregon Health & Science
University, Portland, OR.
15. Zheng WJ, Tsoi LC, Boehnke M, Klein, RL (2009) Using Ontology Fingerprints to
evaluate genome-wide association study results. International Conference of Biomedical
Ontology, University at Buffalo, Buffalo, NY.
16. Qin T, Tsoi LC, Lawson, A, Zheng WJ (2009) A bayesian hierarchical model to derive
novel gene networks from gene ontology fingerprints. International Conference of
Biomedical Ontology, University at Buffalo, Buffalo, NY.
17. Spain SL, Li Y, Knight J, Tsoi LC, Stuart PH, Ellinghaus E, Kang HM, Chen W, Tejasvi
T, Barker J, Abecasis GR, Nair RP, Elder JT, Franke A, and Trembath R (2011) A meta-
analysis of Genome-Wide Association studies in psoriasis identifies additional
susceptibility loci. The Genomics of Common Diseases Meeting 2011 in HInxton,
Cambridge, UK.
18. Tsoi LC, Nair R, Li B, Ding J, Gudjonsson J, Stuart PE, Tejasvi T, Kang HM Abecasis
G, Elder JT (2011) Large-scale transcriptome analysis using RNA-seq reveals new
insights into psoriasis biology. 61st Annual Meeting of the American Society of Human
Genetics in Montreal, Canada.
19. Nair RP, Ellinghaus E, Tsoi LC, Esko, T, Stuart PH, Tejasvi T, Li B, Chandran V, Pellett
F, Peddle L, Weichenthal M, Weidinger S, Mrowietz U, Balschun T, Voorhees J,
Abecasis GR, Rahman P, Gladman DD, Franke A, Elder J (2011) Replication of eighteen
psoriasis genetic associations in Caucasians. Psoriasis: from Gene to Clinic 2011,
London, UK.
20. Tsoi LC, West S, Knight J, Ellinghaus E, et al (2012) Fifteen novel psoriasis
susceptibility loci: Disease-specific signals highlight the role of innate immunity. 62nd
Annual Meeting of the American Society of Human Genetics in San Francisco, USA.
21. Lambert S, Swindell WR, Tsoi LC, Drumright BL, Stoll SW, Nair RP, Elder JT (2013)
Gene expression signature of TRAF3IP2-silenced keratinocytes reveals unexpected
effects on KC differentiation and cytokine responses. 2013 Annual Meeting of
International Investigative Dermatology in Edinburgh, Scotland.
22. Tejasvi T, Tsoi LC, Stuart PE, Nair RP, Voorhees JJ, Elder JT (2013) Transcriptome
analysis reveals that severity of psoriasis is correlated with expression of genes involved
in epidermal differentiation and proliferation. 2013 Annual Meeting of International
Investigative Dermatology in Edinburgh, Scotland.
23. Nair RP, Tsoi LC, Stuart PE, Chandran V, Tejasvi T, Ellinghaus E, Voorhees JJ,
Weichenthal M, Franke A, Abecasis GR, Rahman P, Gladman D, Elder JT (2013) Meta-
analysis of psoriasis and psoriatic arthitis identifies three new susceptibility loci. 2013
Annual Meeting of International Investigative Dermatology in Edinburgh, Scotland.
24. Tsoi LC, Iyer MK, Stuart PE, Tejasvi T, Li B, Ding J, Gudjonsson JE, Kang HM, Nair
RP, Chinnaiyan A, Abecasis GR, Elder JT (2013) Transcriptional profiling of lncRNAs
reveals important biological roles in psoriasis. 63rd Annual Meeting of the American


Society of Human Genetics in Boston, USA.
25. Nair RP, Tsoi LC, Ghosh M, Kaba M, Tejasvi T, Stuart PE, Voorhees JJ, Abecasis GR,
Sharma VK, Elder JT (2014) Genome wide association study of psoriasis in India.
Annual meeting of the Society of Investigative Dermatology in Albuquerque, New
Mexico.
26. Rittie L, Tejasvi T, Tsoi LC, Swindell WR, Nair RP, Elder JT (2014) Microanatomy of
psoriasis: Sebaceous gland atrophy contributes to downregulation of lipid metabolism
genes. Annual meeting of the Society of Investigative Dermatology in Albuquerque, New
Mexico.
27. Tsoi LC, Elder JT, Abecasis GR. (2014) Graphical algorithm for integration of genetic
and biological data: Proof of principle using psoriasis as a mode. 64th Annual Meeting
of the American Society of Human Genetics in San Diego, USA.
28. Elder JT, Tsoi LC, Iyer MK, Start PE, et al (2015) Analysis of long non-coding RNAs
highlights tissue-specific expression patterns and epigenetic profiles in normal and
psoriatic skin. Society for Investigative Dermatology annual meeting in Atlanta, USA.
29. Niehues H, Tsoi LC, Rodijk-Olthuis D, van Vlijmen-Willems IMJJ, van den Bogaard
EH, Zeeuwen PLJM Elder JT, Schalkwijk J (2015) LCE3B/C deletion – more than just a
loss of two proteins. Gordon Research Conference: Barrier Function of Mammalian Skin
in New Hampshire, USA.

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