CURRICULUM VITAE
Yan Guo, PhD
Office Address
549 Preston Research Building
VICC Cancer Biostatistics Center
Vanderbilt University School of Medicine
Nashville, TN 37232-6848
Phone:
E-mail:
Fax:
(615) 936-0816
yan.guo@vanderbilt.edu
(615) 936-2602
CURRENT POSITIONS
Assistant Professor
Department of Cancer Biology, Vanderbilt University.
Technical Director for Bioinformatics
Vanderbilt Technologies for Advanced Genomics Analysis and
Research Design (VANGARD), Vanderbilt Center for Quantitative
Sciences.
EDUCATION
2009 Doctor of Philosophy in Computer Science (focused on Bioinformatics)
Department of Computer Science, University of South Carolina.
2006 Master of Engineering in Computer Science
Department of Computer Science, University of South Carolina
2003 Bachelor of Science in Computer Science
Department of Computer Science, University of Minnesota
2001 Minor in Japanese
University of Minnesota
WORK EXPERIENCE
12/2012 – present
Technical Director for Bioinformatics, Vanderbilt Technologies for
Advanced Genomics Analysis and Research Design (VANGARD)
11/2011 – present
Assistant Professor (Non Tenure Track), Department of Cancer
Biology, Vanderbilt University
12/2009 – 10/2011 Bioinformatics System Engineer II, Vanderbilt Ingram Cancer
Center
11/2007 – 11/2009
Bioinformatics System Engineer I, Functional Genomic Shared
Resource, Vanderbilt University
05/2005 – 05/2007 Research Assistant, Bioinformatics Group at Department of
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01/2001 – 08/2001
Computer Science and Engineering, University of South Carolina
Software Engineer (Internship), National Instrument, Austin TX
PROFESSIONAL ACTIVITIES
Intramural
Committees
Hiring manager of bioinformatics search committee at Vanderbilt Center for
Quantitative Sciences (2012-present)
Mentees
Jiang Li, MS, Bioinformatics System Engineer II (2011 – 2013)
Mingsheng (Mike) Guo, PhD, Bioinformatics System Engineer II (2011 –
present)
Hui Wu, PhD, Bioinformatics System Engineer I (2013 – present)
Extramural
Professional Organization Member of TCGA Head and Neck Cancer work group (2011 – present)
Conferences
Member of program committee and session chair of International
Conference on Intelligent Biology and Medicine, Nashville, TN 2013.
Editorial
Cancer Biology and Research (2013 - present)
Journal of Next Generation: Sequencing & Applications (2013 - present)
Special Issue on Advances in Computational Genomics, BioMed Research
International (2014)
Referee
Cancer Epidemiology.
PLoS ONE
Bioinformatics
International Journal of Data Mining and Bioinformatics
Genomics
BMC Genomics
BMC Systems Biology
International Journal of Computational Biology and Drug Design
Genetic Epidemiology
G3, Genes, Genomes, Genetics
Biological Procedures Online
Advances in Genomics and Genetics
TEACHING EXPERIENCE
Courses
1. Undergraduate course: CSCI1113 (C++), Taught as teaching assistant at University of Minnesota,
2001.
2. Graduate course: CANB 347 Cancer Systems Biology Bioinformatics section (2012- present),
Vanderbilt University.
Invited Talks
1. AACR 2014, Methods Workshops: Next Generation Sequencing: From Bench to Bedside, “Lost
Treasures in Sequence Data”, April 5, 2014 San Diego, CA
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2. International Conference on Intelligent Biology and Medicine, “Read count RNAseq data analysis
comparison”, 2013 August 11-13, Nashville TN
3. Next Generation Sequencing Congress, “The Effect of Strand Bias in Illumina Sequencing Data”.
Boston, April 26-27, 2011,
Seminars
1. “Sequencing data analysis and data mining”, Department of Cardiology, Vanderbilt University,
October 2013
2. “Finding the lost treasures in NGS data”, Vanderbilt Ingram Cancer Center, April 2013
3. “Next Generation Sequencing Data Processing and Analysis”, Shanghai Center for
Bioinformatics Technology, January 2012
CONFERENCES AND WORKSHOPS:
1. Recomb-Seq WorkShop, Beijing, China April 11-12, 2013 (Poster Presentation)
2. TCGA Head and neck Cancer Data Analysis Workshop, Chapel Hill, NC Sept, 19-20, 2012
3. 1000 Genomes Project Community Meeting, Michigan, July 12-13, 2012 (Poster Presentation)
4. First Annual TCGA symposium, National Harbor, Maryland, November 2012 (Poster
Presentation)
5. Meharry Medical College/Vanderbilt Ingram Cancer Center U54 Cancer Partnership 10th annual
retreat, Nashville (Poster Presentation)
6. Vanderbilt Ingram Cancer Center Retreat, May, 2012 (Poster Presentation)
7. The 8th International R User Conference, Nashville TN, June 12th-15th, 2012
8. International Conference on Intelligent Biology and Medicine, 2012 April 22-24, Nashville TN
9. 5th Hands-on Workshop Interrogating Cancer Resistance to Targeted Therapeutics with Systems
Biology August 22-24, 2011, Nashville
10. Illumina Nashville User Group Meeting, Nashville, September 15th, 2011, Nashville
11. Genetic Analysis of Complex Human Diseases, University of Miami, Miller school of Medicine,
Hussman Institute for Human Genomics, May 23-26, 2011
12. Improving tree search in phylogenetic reconstruction from genome rearrangement data. 6th
Workshop on Experimental Algorithms (Abstract), June 2007 - Rome, Italy.
GRANTS/FUNDING
Primary Investigator
1. Vanderbilt Starbrite Funding: Verify Notch3 regulated genes in NSCLC cell line HCC2429
using Tagman PCR (2010)
2. Vanderbilt Starbrite Funding: Verification of heteroplasmy in Mitochondria (2010)
3. Vanderbilt Victor Grant: Comparing FFPE and Frozen Tumor RNAseq data quality (2011)
4. Vanderbilt Victor Grant: Mitochondria Mutation in Breast Cancer (2013)
Research Support
NCI R01 CA148667 (Zheng)
Consortium Study to Identify Breast Cancer Susceptibility Loci
02/01/11-01/31/16
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The major goal of this project is to improve our understanding of cancer genetics, biology, and etiology.
NCI P50 CA09510 (Coffey)
05/01/07-04/30/17
SPORE in GI cancer
The major goal of this project is to investigate the molecular features of gastrointestinal tumors.
NCI P30 CA068485 (Pietenpol)
09/10/10-08/31/15
Cancer Center Support Grant
The major goal of this project is to coordinate cancer-related activities of Vanderbilt University.
Doris Duke Charitable Foundation 2011048 (Kim)
02/01/11-01/31/16
MicroRNAs in Myelodysplastic Syndrome
The major goal of this project is to identify the effects of the knockdown and overexpression of miRNAs
in well-established cell models of maturation, in particular myeloid maturation, as well as in xenograft
models.
NIAID HHSN 272201300023I (Edwards)
09/13/13-09/12/23
Vaccine and Treatment Evaluation Unit (VTEU)
The major goal of this project is to continue developing and evaluating new and improved vaccines and
therapies against infectious diseases.
CONTINUED EDUCATION
1. Genetic Analysis of Complex Human Diseases, University of Miami, Miller school of Medicine,
Hussman Institute for Human Genomics, May 23-26, 2011
2. 3rd NIGMS-funded Short Course on Statistical Genetics & Genomics, University of Alabama,
July 8-12 2013,
3. Computational Genomics Workshop, The Center for Cell Circuits at Broad Institute, July 29-30,
2013 Boston (Travel Grant Awarded)
4. Mothur Workshop, Software for Describing and Comparing Microbial Communities, Detroit,
December 18-20, 2013
BOOK CHAPTER
1. Big Data Analytics in Bioinformatics and Healthcare, Chapter Name: Data Mining of High
Throughput Sequencing, to be published in Spring 2014 by IGI-Global.
PEER-REVIEWED PUBLICATIONS (* corresponding author; † equal contribution)
1. Guo Y*, Li C, Ye F, Shyr Y, “Evaluation of Read Count Based RNAseq Analysis Methods”, BMC
Genomics. Accepted.
2. Guo Y, Bosompem A, Zhong, X, Clark T, Shyr Y, Kim A, “A comparison of MicroRNA
Sequencing Reproducibility and Noise Reduction Using mirVana and TRIzol Isolation Methods”,
Int J Comput Biol Drug Des. Accepted.
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3. Weeke P, Mosley JD, Hanna D, Shaffer C, Delaney JT, Wells QS, Van Driest S, Karnes JH, Ingram
C, Guo Y, Shyr Y, Norris K, Kannankeril P, Ramirez AH, Smith J, Mardis ER, Nickerson D,
George AL Jr., Roden DM, “A greater burden of rare variants in important potassium channel genes
and their modulators increase the risk of drug induced long QT syndrome: an exome sequencing
study”. Journal of the American College of Cardiology, Accepted
4. Guo Y*, Sheng Q, Li J, Lehmann B, Bauer J, Pietenpol J, Shyr Y, “Comparative Study of Exome
Copy Number Variation Estimation Tools Using Array Comparative Genomic Hybridization as
Control”, Biomed Res Int 2013; 2013:915636.
5. Guo Y*, Li C, Cai Q, Shyr Y, “Very Low level Heteroplasmy mtDNA Variations Are Inherited in
Humans”, Journal of Genetics and Genomics. Accepted.
6. Mosley JD, Van Driest SL, Larkin EK, Weeke PE, Witte JS, Wells QS, Karnes JH, Guo Y,
Bastarache L, Olson LM, McCarty CA, Pacheco JA, Jarvik GP, Larson EB, Crosslin DR, Kullo IJ,
Tromp G, Kuivaniemi H, Carey DJ, Ritchie MD, Denny JC, Roden DM, “Mechanistic Phenotypes:
An Aggregative Phenotyping Strategy to Identify Disease Mechanisms Using GWAS Data”, PlOS
ONE, 2013. In press.
7. Guo Y*, Cai Q, Li C, Li J, Courtney R, Li CI, Zheng W, Long J, “An evaluation of allele frequency
estimation accuracy using pooled sequencing data”, Int J Comput Biol Drug Des, 2013;6(4):279-93.
8. Samuels D, Han L, Li J, Sheng Q, Clark T, Yu Shyr, Guo Y*, “Finding the Lost Treasures in exome
sequencing data”, Trends in Genetics, 2013 Oct;29(10):593-9.
9. Guo Y*, Sheng Q, Ye F, Clark T, Samuels DC, “Three-Stage Quality Control Strategies for DNA
Sequencing Data”, Brief Bioinform, 2013 Sep 24.
10. Guo Y*, Sheng Q, Li J, Ye F, Samuels DC, Shyr Y, “Large scale comparison of gene expression
levels by microarrays and RNAseq using TCGA data”, PloS ONE 2013 Aug 20;8(8):e71462.
11. Guo Y, Li J, Li CI, Shyr Y, “Evaluation of allele frequency estimation using pooled sequencing data
simulation”, ScientificWorldJournal 2013, 2013:895496.
12. Guo Y*, Li J, Li CI, Shyr Y, Samuels DC, “MitoSeek: extracting mitochondria information and
performing high throughput mitochondria sequencing analysis”, Bioinformatics, 2013 May
1;29(9):1210-1.
13. Liu Q†, Guo Y†, Jiang L, Long J, Zhang B, Shyr Y, “Steps to ensure accuracy in genotype and SNP
calling from Illumina sequencing data”, BMC Genomics, 2012;13 Suppl 8:S8.
14. Li CI, Su P, Guo, Y, Shyr Y, Sample size calculation for differential expression analysis of RNA-seq
data under Poisson distribution, Int J Comput Biol Drug Des, 2013 6(4), 358-375
15. Lu X, An H, Jin R, Zou M, Guo Y, Su P-F, Liu D, Shyr Y, Yarbrough WG, “PPM1A is a RelA
phosphatase with tumor suppressor-like activity”, OncoGene, 2013 Jul 1.
16. Yan L, Womack B, Wotton D, Guo Y, Shyr Y, Dave U, Li C, Hiebert S, Brandt S, and Hamid R,
“Tgif1 regulates the quiescence and self-renewal of hematopoietic stem cells”, Mol Cell Biol, 2013
Dec;33(24):4824-33.
17. Ivannov S, Panaccione A, Nonaka D, Prasad M, Boyd K, Brown B, Guo Y, Sewell A, Yarbrough W,
“Diagnostic SOX10 Gene Signatures in Salivary Adenoid Cystic and Breast Basal-like Carcinomas”,
Br J Cancer, 2013 Jul 23; 109(2): 444–451.
18. Guo Y, Li J, Li CI, Long J, Samuels DC, Shyr Y, “The effect of strand bias in illumina short-read
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sequencing data”, BMC Genomics, 2012 Nov 24;13:666.
Guo Y, Long J, Cai Q, He J, Zheng W, Li C, “Exome sequencing generates high quality data in
non-target regions”, BMC Genomics, 2012 May 20;13:194.
Guo Y, Cai Q, Samuels DC, Ye F, Long J, Li CI, Winther JF, Tawn EJ, Stovall M, Lähteenmäki
P, Malila N,Levy S, Shaffer C, Shyr Y, Shu XO, Boice JD Jr., “The use of next generation
sequencing technology to study the effect of radiation therapy on mitochondrial DNA mutation”,
Mutation Research, 2012 May 15;744(2):154-60.
Ivanov SV, Panaccione A, Brown B, Guo Y, Moskaluk CA, Wick MJ, Brown JL, Ivanova
AV, Issaeva N, El-Naggar AK, Yarbrough WG, “TrkC signaling is activated in adenoid cystic
carcinoma and requires NT-3 to stimulate invasive behavior”, Oncogene, 2013 Aug
8;32(32):3698-710.
Savani M, Guo Y, Carbone DP, Csiki I, “Sonic hedgehog pathway expression in non-small cell lung
cancer”, Ther Adv Med Oncol, 2012 Sep; 4(5): 225-33.
Zhuang G, Song W, Amato K, Hwang Y, Lee K, Boothby M, Ye F, Guo Y, Shyr Y, Lin L, Carbone D,
Brantley-Sieders D, Chen J, “Effects of Cancer-Associated EPHA3 Mutations on Lung Cancer”,
JNCI, 2012 Aug 8;104(15):1182-97.
24. Powell AE, Wang Y, Li Y, Poulin EJ, Means AL, Washington MK, Higginbotham JN, Juchheim
A, Prasad N,Levy SE, Guo Y, Shyr Y, Aronow BJ, Haigis KM, Franklin JL, Coffey RJ., “The
pan-ErbB negative regulator Lrig1 is an intestinal stem cell marker that functions as a tumor
suppressor”, Cell, 2012 Mar 30;149(1):146-58.
25. Yu DS, Zhao R, Hsu EL, Cayer J, Ye F, Guo Y, Shyr Y, Cortez D, “Cyclin-dependent kinase 9-cyclin
K functions in the replication stress response”, EMBO Rep, 2010 Nov;11(11):876-82.
26. Hatakeyama H, Cheng H, Wirth P, Counsell A, Marcrom S, Wood C, Pohlmann P, Gilbert J, Murphy
B, Yarbrough W, Wheeler D, Harari P, Guo Y, Shyr Y, Slebos R, Chung CH, “Regulation of
heparin-binding EGF-like growth factor by miR-212 and acquired cetuximab-resistance in head and
neck squamous cell carcinoma. PLoS ONE, 2010 Sep 13;5(9):e12702.
27. Guo Y, Ye F, Tang J, "Phylogenetic reconstruction with disk-covering and Bayesian approaches,"
BioInformatics and BioEngineering, BIBE 2008.
28. Ye F, Guo Y, Lawson A, and Tang J, "Improving tree search in phylogenetic reconstruction from
genome rearrangement data". JEA 4525/2007:352-364.
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