Download CURRICULUM VITAE Yan Guo, PhD Office Address 494 Preston

CURRICULUM VITAE
Yan Guo, PhD
494 Preston Research Building
Vanderbilt University School of Medicine
Nashville, TN 37232-6848
Office Address
Phone:
E-mail:
Fax:
(615) 936-0816
[email protected]
(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)
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 of Bioinformatics, Vanderbilt Technologies for
Advanced Genomics Analysis and Research Design (VANGARD)
11/2011 – present
Assistant Professor, 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
Computer Science and Engineering, University of South Carolina
01/2001 – 08/2001 Software Engineer (Internship), National Instrument, Austin TX
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PROFESSIONAL ACTIVITIES
Intramural
Committees
Hiring manager of bioinformatics search committee at Vanderbilt Center for
Quantitative Sciences (2012-present)
Oversight Committee member of Vanderbilt Genetics Institute (2016present)
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 – 2014)
Nikola Jovanovich (summer intern, 2014)
Quanhu Sheng, Post Doc (2012-2015)
Shilin Zhao, Post Doc (2012-present)
Pan Zhang, Post Doc, (2014-present)
Yulin Dai, Post Doc, (2016-present)
Jie Ping, Post Doc, (2016-present)
Extramural
Professional Organization Member of TCGA Head and Neck Cancer work group (2011 – 2014)
Conferences
Program committee member and session chair of International Conference
on Intelligent Biology and Medicine, 2013-2016.
Workshop/Tutorial Committee co-chair, International Conference on
Intelligent Biology and Medicine, 2016
Editorial
Cancer Biology and Research (2013 - present)
Managing Editor of International Journal of Computational Biology and
Drug Design (2014)
Guest Editor for Special Issue on Advances in Computational Genomics,
BioMed Research International (2014)
Lead Editor for Special Issue on Advances in Computational Biology and
Genomic, International Journal of Computational Biology and Drug Design
(2014)
Lead Editor for Special Issue Recent Advances in High Throughput
Sequencing Analysis, International Journal of Genomics, 2016
Referee
Journal (number of reviews)
Advances in Genomics and Genetics 1
Applied Microbiology and Biotechnology 1
Archives of Medical Science 1
Bioinformatics 5
Biological Procedures Online 1
Biomarker Insights 1
Biomedical Research International 1
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BMC Genomics 2
BMC Systems Biology 1
Briefings In Bioinformatics 5
Cancer Epidemiology 1
Current Drug Targets 1
EBioMedicine 1
Evolutionary Bioinformatics 1
Frontiers in Genetics 1
G3, Genes, Genomes, Genetics 1
Gene 1
Genetica 1
Genetic Epidemiology 3
Genome Biology 1
Genomics 1
Human Mutation 2
IEEE Transactions on Biomedical Engineering 1
International Journal of Cancer 1
International Journal of Computational Biology and Drug Design 1
International Journal of Data Mining and Bioinformatics 1
International Journal of Genomics 1
International Journal of Molecular Sciences 1
Journal of Genetics and Genome Research 1
Methods 1
Nature Protocols 1
Nucleic Acid Research 3
Peer J 1
PLOS ONE 2
Scientific Reports 2
TEACHING EXPERIENCE
Courses
1. EPID 8332: Advanced Methods for Epidemiology, (8 hours) spring 2016, Vanderbilt University
2. Center for Quantitative Sciences Summer Institute 2014-2016 (three years), Bioinformatics Course
Director (6 hours per year), Vanderbilt University
3. Advanced Biostatistics Workshop (3 hours), April 8th, 2015, National Institute of Biological
Sciences, Beijing China.
4. Advanced Biostatistics (2 hours), December 2014, National Chengkung University Taiwan.
5. BMIF 310: Foundation of Bioinformatics, (1hour per year) 2014-2015, Vanderbilt University.
6. MAGEC Molecular and Genetic Epidemiology Course: 1 lecture Title: RNA and mitochondrial
DNA sequencing, April, 2014, Vanderbilt University.
7. Graduate course: CANB 347 Cancer Systems Biology Bioinformatics section (2012- present),
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Vanderbilt University (5-6 hours per year).
8. Undergraduate course: CSCI1113 (C++), Taught as teaching assistant at University of Minnesota,
2001.
Invited Talks at Conferences
1. ICIBM 2016, title “The Discrepancy among Single Nucleotide Variants Detected by DNA and
RNA High Throughput Sequencing Data”, December, 2016
2. DNA Day 2016, title “Assessing Disease Risk Using Whole Genome Instead of Individual SNP”,
May 2016
3. Center for Quantitative Sciences, 2015 Retreat, title :mtDNA heteroplasmy and copy number
detection, October, 2015
4. International Conference on the Frontiers of Genomic Research, title: Finding the lost treasure of
genomic data with robust quality control”, National Cheng Kung University, Taiwan, December,
2014
5. 7th Annual World Cancer Congress, Title: High-throughput Sequencing in Mitochondrial DNA
Cancer Research, Nanjin, China, May 17, 2014
6. AACR 2014, Methods Workshops: Next Generation Sequencing: From Bench to Bedside, Title:
“Lost Treasures in Sequence Data”, April 5, 2014 San Diego, CA
7. International Conference on Intelligent Biology and Medicine, Title: “Read count RNAseq data
analysis comparison”, 2013 August 11-13, Nashville TN
8. Next Generation Sequencing Congress, Title: “The Effect of Strand Bias in Illumina Sequencing
Data”. Boston, April 26-27, 2011,
Invited Seminar/workshop
1. Title: “How Bioinformatics Helps Solve Biological Problems”, Northwest University of China,
China, March 28th, 2017
2. Title: “Bioinformatics: Perspectives and Future”, University of New Mexico, Comprehensive
Cancer Center, March 8th, 2017
3. Title: “Bioinformatics Overview and Future”, Roche Sequencing, Belmont, CA, Feb, 2017
4. Title: “Bioinformatics Overview and Future”, Abmart, Shanghai, Dec 26th, 2016
5. Title: “High Throughput Data Analysis, DNA, RNA, Microbiome Sequencing and Genotyping”,
Huston Texas, Dec 8th 2016, ICIBM 2016
6. Title: “Genotyping Data and Innovative Analyses”, National Chengkung University Taiwan, Oct
13th 2016
7. Title: “Using a Global Heterozygosity Measure for Phenotype Association Studies”, Department
of Biostatistics, Vanderbilt University, Nashville, Nov 18th, 2015
8. Title: “The advanced data mining and quality control of high throughput sequencing data”, ICIBM
2015, University of Indiana, Nov 13th, 2015
9. Title: “High quality data mining of the human genome”, Shanghai Jiaotong University, May 25th,
2015.
10. Title: “Genomic data mining and quality control”, Center For Quantitative Sciences Bioinformatics
Retreat, November 2014
11. Title: “Advanced genomic data quality control and data mining”, University of Kentucky,
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November, 2014.
Title: “Advanced genomic data analysis”, Center For Quantitative Sciences Bioinformatics Retreat,
October 2013
Title: “Sequencing data analysis and data mining”, Department of Cardiology, Vanderbilt
University, October 2013
Title: “Finding the lost treasures in NGS data”, Vanderbilt Ingram Cancer Center, April 2013
Title: “Bioinformatics Research”, Center For Quantitative Sciences Bioinformatics Retreat, August
2012
Title: “Next Generation Sequencing Data Processing and Analysis”, Shanghai Center for
Bioinformatics Technology, January 2012
CONFERENCES
Abstract/Poster Presented
1. Title: “a genome-wide association study of 58 patients with fibrosing mediastinitis”
2. AUA 2017, title: “The Relationship Between The Urinary Microbiome And Central Sensitization
In Women With Overactive Bladder”, May 2017
3. ARVO 2017, title: “Identification Of Hypoxia-Regulated Genes And Pathways In Mouse Retinal
Müller Cells By Rnaseq Analysis, May, 2017
4. Digestive Disease Week 2017, title “Loss Of TFF1 Activates BRD2 Through Down Regulation Of
Mir-143-3p In Gastric Cancer”
5. AACR 2017, title: “Organ-specific epigenetic reprogramming of leukemia cells: Clues to
chemoresistance.
6. ICIBM 2016, title: “Estimating Relative Mitochondria Copy Number Using Sequencing Data”,
December, 2016
7. AACR, 2016, title: “Robust Targeted Sequencing Strategy Identifies Highly Penetrant Mutations
in Hereditary Colorectal Cancer Cases from Colon Cancer Family Registry”
8. American College of Rheumatology Meeting 2016: title: “Small Rnaseq Reveals Different Plasma
Mirna Signature In Patients With RA And SLE: A Pilot Study”, November 2016
9. ISMB 2016, title: “Nucleotide Sequence Difference Between DNA-RNA And Blood-Tissue
Samples”.
10. Clinical Congress 2016, title: “Growth Differentiation Factor 15 (GDF15) Is A Novel Regulator Of
The Stem Cell-Like Phenotype In Neuroblastoma”, October, 2016,
11. Digestive Disease Week 2016, title: “Transcriptome Sequencing Identifies Potentially Functional
Gene Fusions In Esophageal Adenocarcinomas”.
12. Digestive Disease Week 2016, title: “Integrated Expression Analysis of Mouse and Human Gastric
Neoplasm Identifies Early Molecular Changes in Gastric Carcinogenesis”.
13. Digestive Disease Week 2016, title: “Characterization of miRNA networks in mouse and human
gastric cancer”.
14. 2016 Conference on Retroviruses and Opportunistic Infection, title: “Mitochondrial DNA Copy
Number and Neurocognitive Impairment in HIV-Infected Persons”
15. Digestive Disease Week 2015, Blum A, Varadan V, Guo Y, Kieber-Emmons AM, Ravi L, Chandar
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AK, Canto MI, Wang JS, Shaheen NJ, Barnholtz-Sloan J, Willis J, Markowitz S, Shyr Y, Chak A,
Guda K, Title: “Discovery of Novel Gene-Fusions in Esophageal Adenocarcinoma Using Next-Gen
RNA Sequencing”
16. Digestive Disease Week 2015, Varadan V, Blum A, Guo Y, Kieber-Emmons AM, Ravi L,
Kresak A, Chandar AK, Canto MI Wang JS, Shaheen NJ, Barnholtz-Sloan J, Willis J, Markowitz
S, Shyr Y, Chak A, Guda K, title: “Large-Scale Transcriptome Sequencing Identifies Two
Signaling Sub-Networks As Critical Mediators of Barrett's Carcinogenesis”
17. ICIBM 2015, title: “Precursor mRNA Abundance Estimation from total RNA sequencing”.
November, 2015
18. ICIBM 2015, title: “Mitochondria Single Nucleotide Variant among Six Blood Cell Types”.
November, 2015
19. 2016 Gastrointestinal cancers Syposium, title: “Frequent BRAF mutations in Colonic High-Grade
Neuroendocrine Carcinoma”, January 21-23, 2016
20. 14th Annual UT-KBRIN Bioinformatics Summit 2015, title: “Population structure analysis across
26 ancestries using dense genetic data”, March 20-22, 2015
21. 14th Annual UT-KBRIN Bioinformatics Summit 2015, title: “Practicality of Identifying
Mitochondria Variants from Exome and RNAseq data”, March 20-22, 2015
22. Digestive Disease Week 2015, title: “Large-scale Transcriptome Sequencing Identifies Two
Signaling Sub-Networks as Critical Mediators of Barrett’s Carcinogenesis”, May 17-19, 2015,
Washington DC
23. The American Society of Hemotology, title: “miRNA Predictors of Response to DNA
Methyltransferase Inhibitors”, December, 2014
24. ISMB 2014, title: RNA Somatic Mutation Caller (RSMC): accurately identifying somatic mutation
using RNAseq data, July, 2014
25. UT-KBRIN Bioinformatics Summit 2014, title: “Exon Deletion Detection”, April 11-13, Lake
Barkley, KY, 2014
26. Meharry Medical College/Vanderbilt Ingram Cancer Center U54 Cancer Partnership 13th annual
retreat, title: “Exon deletion detection in Notch1 of breast cancer”, Nashville, 2014
27. Recomb-Seq WorkShop, Beijing, title: “mitochondria detection using MitoSeek”, China April 1112, 2013
28. First Annual TCGA symposium, title: “evaluation of sequencing processing steps”, National
Harbor, Maryland, November 2012
29. Meharry Medical College/Vanderbilt Ingram Cancer Center U54 Cancer Partnership 10th annual
retreat, title: “The effect of radiation therapy on female child cancer patients and their offspring’s
mitochondria mutation”, Nashville, 2011
30. Vanderbilt Ingram Cancer Center Retreat, title: “mitochondria mutation in child cancer patients”,
May, 2012
31. 6th Workshop on Experimental Algorithms (Abstract), title: “Improving tree search in
phylogenetic reconstruction from genome rearrangement data”, June 2007 - Rome, Italy.
Conferences Attended:
1. International Conference on Intelligent biology and Medicine, 2016, December 2016, Huston TX
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DNA Day 2016, Dalian China, May, 2016
AACR 2016, New Orleans April, 2016
14th Annual UT-KBRIN Bioinformatics Summit 2015, March 20-22, 2015
International Conference on the Frontiers of Genomic Research, National Cheng Kung University,
Taiwan, December, 2014
7th Annual World Cancer Congress, Nanjin, China, May 17, 2014
UT-KBRIN Bioinformatics Summit 2014, April 11-13, Lake Barkley, KY, 2014
AACR 2014, April 5, 2014 San Diego, CA
Meharry Medical College/Vanderbilt Ingram Cancer Center U54 Cancer Partnership 13th annual
retreat, Nashville, 2014
International Conference on Intelligent Biology and Medicine, 2013 August 11-13, Nashville
Recomb-Seq WorkShop, Beijing, China April 11-12, 2013
First Annual TCGA symposium, National Harbor, Maryland, November 2012
1000 Genomes Project Community Meeting, Michigan, July 12-13, 2012
The 8th International R User Conference, Nashville TN, June 12th-15th, 2012
TCGA Head and neck Cancer Data Analysis Workshop, Chapel Hill, NC Sept, 19-20, 2012
International Conference on Intelligent Biology and Medicine, 2012 April 22-24, Nashville TN
Illumina Nashville User Group Meeting, Nashville, September 15th, 2011, Nashville
Next Generation Sequencing Congress, Boston, April 26-27, 2011,
Meharry Medical College/Vanderbilt Ingram Cancer Center U54 Cancer Partnership 10th annual
retreat, Nashville, 2011
5th Hands-on Workshop Interrogating Cancer Resistance to Targeted Therapeutics with Systems
Biology August 22-24, 2011, Nashville
GRANTS/FUNDING
Primary Investigator
1. American Cancer Society-Institutional Research Grant: Identification of lncRNA eQTLs predictive
of drug response in breast cancer (2015). Amount: $30,000
2. Vanderbilt Institute for Clinical and Translational Research Grant: lincRNA biomarkers for Breast
cancer drug response predictability (2014). Amount: $1877
3. Center for Quantitative Sciences Pilot Project: Mitochondria Mutation in Breast Cancer (2014),
amount: $10,000
4. Vanderbilt Institute for Clinical and Translational Research Grant: Verify Notch3 regulated genes
in NSCLC cell line HCC2429 using Tagman PCR (2010), Amount: $2000
5. Vanderbilt Institute for Clinical and Translational Research Grant: Verification of heteroplasmy in
Mitochondria (2010), Amount: $2000
6. Vanderbilt Institute for Clinical and Translational Research Grant: Comparing FFPE and Frozen
Tumor RNAseq data quality (2011), Amount: $2000
7. Vanderbilt Institute for Clinical and Translational Research Grant: Mitochondria Mutation in
Breast Cancer (2013), Amount: $2000
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Co-Investigator
NCI P50 CA098131 (Arteaga)
09/11/08-08/31/19
SPORE in breast cancer
The overall goal of this project is to conduct multidisciplinary, mechanism-based, translational research
of the highest possible impact that will contribute meaningfully to measurable progress in breast cancer.
Role: Bioinformatician
NCI P50 CA095103 (Coffey)
05/01/0704/30/17
SPORE in GI cancer
These four projects continue to focus on transforming how we diagnose and treat individuals with
colorectal cancer and deepening our understanding of the pathobiology of colorectal neoplasia.
Role: Bioinformatician
NCI RO1 CA206563 (El-Rifai)
11/01/15-11/30/16
Molecular Functions of APE1 in Barrett’s Esophagus
This study aims to characterize the molecular functions of APE1, a frequently overexpressed gene in
esophageal adenocarcinoma (EAC), in order to identify its biological, diagnostic, prognostic, and
possibly therapeutic significance.
Role: Bioinformatician
NCI R01 CA131225 (El-Rifai)
05/01/09-08/31/19
The Role of Aurora Kinase A in Upper Gastrointestinal Adenocarcinomas
The goal of this project is to characterize the molecular function(s) of AURKA, a frequently
overexpressed gene, in order to identify its biological, diagnostic, prognostic, and possibly therapeutic
significance.
Role: Bioinformatician
NCI R01 CA177372 (El-Rifai)
08/01/13-07/31/16
The Role of MiRNA Network in Gastric Cancer
The goal of this project is to gain further understanding of the role of H. Pylori in shaping the miRNA
signature and promoting the multi-step gastric tumorigenesis in order to identify diagnostic, prognostic
and possibly therapeutic miRNA targets in gastric cancer.
Role: Bioinformatician
NIDDKD R24 DK103067 (Harris)
09/18/14-06/30/19
Novel Integrated Analyses of Human Diabetic Nephropathy
This study will utilize novel methods to study the biochemical changes to the kidney in response to
diabetic nephropathy and will investigate the underlying mechanisms responsible for these changes.
Role: Bioinformatician
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NHLBI P01 HL116263 (Linton)
06/01/14-04/30/19
HDL Function in Human Disease
The major goal of this project is to define the mechanisms for HDL dysfunction in three distinct diseases
associated with increased risk for atherosclerotic cardiovascular disease.
Role: Bioinformatician
NCI R01 HL127173 (Linton)
01/01/16-12/31/19
Macrophage SR-BI Regulates Autophagy, Angiogenin and tRNA-derived Small RNAs
The major goal of this project is to leverage the novel roles of SR-BI in regulating autophagy,
angiogenin and tRNA-derived small RNAs to identify potential drug targets for nucleic acid-based
therapies to treat and prevent atherosclerosis.
Role: Co-Investigator
NCI U54 CA163072 (Moses)
09/23/11-08/31/16
MMC, VICC &TSU: Partners in eliminating cancer disparities
This project aims to improve the effectiveness of the VICC by creating a collaborative relationship
between MMC, VICC & TSU in the areas of cancer research; training and development; education and
outreach.
Role: Bioinformatician
NCI R21 CA201856 (Oates)
12/01/15-11/30/17
Prevention of Genomic Instability by a Scavenger of Bifunctional Electrophiles
The major goal of this project is to identify the endogenous carcinogens that are responsible for the
mutations of the genome that determine the malignant nature of these cancers.
Role: Co-Investigator
NHGRI U01 HG007674 (Phillips)
07/01/14-03/31/18
Vanderbilt Center for Undiagnosed Diseases (VCUD)
The Vanderbilt Center for Undiagnosed Disease will function in the NIH funded Network of
Undiagnosed Diseases to evaluate persons afflicted with undiagnosed illnesses and to ensure an
accurate and timely diagnosis can be made, that counseling and advice be given to the patient and care
givers, and to assist in diagnosing and treating similar patients in the whole human population.
Role: Bioinformatician
Completed Research Support
American Heart Association (Vickers)
07/01/1406/30/16
Novel small RNA intercellular communication networks mediated by HDL
The major goal of this project is to quantify inflammatory cell tDR export to HDL in
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hypercholesterolemia and to quantify the impact of inflammatory cell-originating HDL-tDRs in
recipient cells.
Role: Bioinformatician
NHGRI R03 HG008055 (Multi-PI: Ye, Samuels)
04/01/14-03/31/16
Elastic Net Analysis of Phenotype Relationships in Association Studies
The major goal of this project is to increase our understanding of the complex patterns in medical
conditions as documented in electronic medical records in order to discover how rare genetic variants
in genes for mitochondrial proteins affect health.
Role: Bioinformatician
NCI R01 CA137013 (Long)
07/01/09-05/31/13
Genome-wide copy number variation and breast cancer risk
The major goal of this project is to survey the entire human genome for copy number variations
associated with breast cancer.
Role: Bioinformatician
NCI R01 CA064277 (Zheng)
08/01/10-05/31/13
Shanghai Breast Cancer Study
The major goal of this project is to provide valuable information regarding the roles of gene-gene and
gene-environment interaction in the etiology of breast cancer.
Role: Bioinformatician
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
SKILLS
Omics Data Analysis: Exome sequencing, whole genome sequencing, targeted panel sequencing, RNAseq,
total RNAseq, small RNAseq, Chip-Seq, Microbiome Sequencing, gene expression microarray, genotyping
array, methylation array, pathway network analysis, cluster heatmap analysis, genome wide association
analysis, PheWAS, Mendelian Randomization, proteomic, Gene Set Enrichment Analysis.
Programming: C, C++, Java, Microsoft .net, Perl, Shell script, R.
PUBLICATIONS
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Book Chapter
1. AACR 2014 Education Book, chapter name: Lost Treasures in Sequence Data, 2014 AACR.
Editorial
2. Han L, Zheng S, Lu ZX, Su, Z, Guo Y, Advances in Computational Genomics, Biomed Research
International, 2014
3. Guo Y, Sheng Q, Advances in Computational Biology and Genomics, International Journal of
Computational Biology and Drug Design, 2015
4. Guo Y, Leng H, Sheng Q, Recent Advances in High Throughput Sequencing Analysis, International
Journal of Genomics, 2017
Peer-reviewed publications as first/co-first/last/corresponding authors († equal contribution)
5. Wang J, Samuels DC, Shyr Y, Guo Y, Thorough Evaluation of Illumina Genotyping Array Design
and Strand Correction, Bioinformatics, 2017
6. Guo Y, Zhao S, Sheng Q, Samuels DC, Shyr Y, The Discrepancy among Single Nucleotide Variants
Detected by DNA and RNA High Throughput Sequencing Data, BMC Genomics (accepted)
7. Zhao S, Jing W, Samuels DC, Sheng Q, Shyr Y, Guo Y, Strategies for Processing and Quality
Control of Illumina Genotyping Arrays, Briefings in Bioinformatics, 2017
8. Guo Y, Dai Y, Yu H, Zhao S, Samuels DC, Shyr Y, Improvements and Impacts of GRCh38 Human
Reference on High Throughput Sequencing Data Analysis, Genomics, 2017
9. Guo Y, Strickland SA, Li S, Mohan S, Bosompem A, Zhao S, Sheng Q, Kim AS, MicroRNAs and
tRNA-derived fragments predict the transformation of myelodysplastic syndromes to acute
myeloid leukemia, Leukemia and Lymphoma, 2017
10. Guo Y, Vickers K, Xiong Y, Zhao S, Sheng Q, Zhang P, Zhou W, Flynn CR, Comprehensive
Evaluation of Extracellular Small RNA Isolation Methods from Serum in High Throughput
Sequencing, BMC Genomic, 2017
11. Zhang P, Lehmann BD, Shyr Y, Guo Y, The Utilization of Formalin Fixed-Paraffin-Embedded
Specimens in High Throughput Genomic Studies, International Journal of Genomics, 2017
12. Guo Y, Warren Andersen S, Shu XO, Michailidou K, Bolla MK, Wang Q, Garcia-Closas M, Milne
RL, Schmidt MK, Chang-Claude J, Dunning A, Bojesen SE,Ahsan H, Aittomäki K, Andrulis
IL, Anton-Culver H, Arndt V, Beckmann MW, Beeghly-Fadiel A, Benitez J, Bogdanova
NV, Bonanni B, Børresen-Dale AL, Brand J, Brauch H, Brenner H, Brüning T, Burwinkel
B, Casey G, Chenevix-Trench G, Couch FJ, Cox A, Cross SS, Czene K, Devilee P, Dörk
T, Dumont M, Fasching PA, Figueroa J, Flesch-Janys D, Fletcher O, Flyger H, Fostira F, Gammon
M, Giles GG, Guénel P, Haiman CA, Hamann U, Hooning MJ, Hopper JL,Jakubowska A, Jasmine
F, Jenkins M, John EM, Johnson N, Jones ME, Kabisch M, Kibriya M, Knight JA, Koppert
LB, Kosma VM, Kristensen V, Le Marchand L, Lee E, Li J, Lindblom A, Luben R, Lubinski
J, Malone KE, Mannermaa A, Margolin S, Marme F, McLean C, Meijers-Heijboer H, Meindl
A, Neuhausen SL,Nevanlinna H, Neven P, Olson JE, Perez JI, Perkins B, Peterlongo P, Phillips
KA, Pylkäs K, Rudolph A, Santella R, Sawyer EJ, Schmutzler RK, Seynaeve C,Shah
M, Shrubsole MJ, Southey MC, Swerdlow AJ, Toland AE, Tomlinson I, Torres D, Truong T, Ursin
G, Van Der Luijt RB, Verhoef S, Whittemore AS,Winqvist R, Zhao H, Zhao S, Hall P, Simard
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J, Kraft P, Pharoah P, Hunter D, Easton DF, Zheng W, Body Mass Index Genetic Scores and Breast
Cancer Risk: Mendelian Randomization Analyses of Data from 145,000 women of European
Descent, PLOS Medicine, 2016, PMID: 27551723
Guo Y, Jing, H, Zhao S, Wu H, Sheng Q, Zhong X, Samuels DC, Shyr Y, Long J, Illumina
human exome genotyping array clustering and quality control. Nature Protocols, 2014, PMID:
25321409
Guo Y, Zhang P, Sheng Q, Zhao S, Hackett TA, lncRNA expression in the auditory forebrain
during postnatal development, Gene, 2016, PMID 27544636
Samuels DC, Wang J, Ye F, He J, Levinson RT, Sheng Q, Zhao S, Capro JA, Shyr Y, Zheng W,
Guo Y, Heterozygosity Ratio, a Robust Global Genomic Measure of Autozygosity and Its
Association with Height and Disease Risk, Genetics, 2016
Guo Y, Xiong Y, Sheng Q, Zhao S, Flynn CR, A microRNA expression-signature for human
NAFLD progression, Journal of Gastroenterology, 2016, PMID: 26874844, PMCID:
PMC4983265
Sheng Q, Vickers K, Zhao S, Wang J, Samuels DC, Koues O, Shyr Y, Guo Y, Multi-Perspective
Quality Control of Illumina RNA Sequencing Data Analysis, Briefings in Functional Genomics,
2016
Zhang P, Samuels DC, Wang J, Zhao S, Shyr Y, Guo Y, Mitochondria Single Nucleotide Variation
across Six Blood Cell Types, Mitochondrion, 2016
Zhang P, Samuels DC, Zhao S, Wang J, Shyr Y, Guo Y, Practicability of Mitochondrial
Heteroplasmy Detection through an Illumina Genotyping Array, Mitochondrion, 2016
Sheng Q, Zhao S, Li C, Shyr Y, Guo Y, Practicability of Detecting Somatic Point Mutation from
RNA High Throughput Sequencing Data, Genomics, 2016
Guo Y, Wu J, Zhao S, Ye F, Su Y, Clark T, Sheng Q, Lehmann B, Shu X, Cai Q, RNA sequencing
of Formalin-Fixed, Paraffin-Embedded Specimens for Gene Expression Quantification and Data
Mining, International Journal of Genomics, 2016
Peng D†, Guo Y†, Chen H, Zhao S, El-Rifai W, Integrated Analysis Reveals Complex Associations
between Genomics and Epigenomics in Esophageal Adenocarcinoma, Scientific Reports, 2017
Zhang P, Samuels DC, Lehmann B, Sricker T, Pietenpol J, Shyr Y, Guo Y, Mitochondria Sequence
Mapping Strategies and Practicability of Mitochondria Variant Detection from Exome and RNA
sequencing Data, Briefings in Bioinformatics, 2015
Vickers KC, Roteta, LA, Dilks H, Han L, Guo Y, Mining diverse small RNA species in the deep
transcriptome, Trends in Biochemical Sciences, 2015, PMID: 25435401, PMCID: PMC4362530
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 PMID: 23972387, PMCID: PMC3926691
26. Han L, Vickers KC, Samuels DC, Guo Y, Alternative Applications for Distinct RNA Sequencing
Strategies, Briefings in Bioinformatics, 2014, PMID:25246237
27. Guo Y, Sheng Q, Ye F, Clark T, Samuels DC, “Three-Stage Quality Control Strategies for DNA
Sequencing Data”, Briefing in Bioinformatics, 2013 Sep 24. PMID: 24067931
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28. Wang J, Raskin L, Samuels DC, Shyr Y, Guo Y, Genome Measures used for Quality Control are
Dependent on Gene Function and Ancestry, Bioinformatics, 2014, PMID: 25297068, PMCID:
PMC4308666
29. Guo Y, Li J, Li CI, Shyr Y, Samuels DC, “MitoSeek: extracting mitochondria information and
performing high throughput mitochondria sequencing analysis”, Bioinformatics, 2013, PMID:
23471301, PMCID: PMC4492415
30. Guo Y, Bosompem A, Sheng Q, Mohan S, Erdogan B, Ye F, Vickers KC, Sheng Q, Zhao S, Li CI,
Su PF, Jagasia M, Strickland SA, Griffith E, Kim A, Transfer RNA Detection by Small RNA Deep
Sequencing and Disease Association with Myelodysplastic Syndromes, BMC Genomics, 2015,
PMID:26400237, PMCID:PMC4581457
31. Guo Y, Zhao S, Sheng Q, Ye F, Li J, Lehmann, B, Pietenpol J, Samuels DC, Shyr Yu, MultiPerspective Quality Control of Illumina Exome Sequencing Data Using QC3, Genomics, 2014,
PMID 24703969
32. Guo Y, Li C, Ye F, Shyr Y, “Evaluation of Read Count Based RNAseq Analysis Methods”, BMC
Genomics. 2013, PMID: 24564449, PMCID: PMC4092879
33. Ye. F, Samuels, DC, Clark T, Guo, Y, High-Throughput Sequencing in Mitochondrial DNA
Research Mitochondrion. Mitochondrion, 2014, PMID: 24859348, PMCID: 4149223
34. 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, PMID: 23977046,
PMCID: 3748065
35. Guo Y, Li J, Li CI, Long J, Samuels DC, Shyr Y, “The effect of strand bias in Illumina short-read
sequencing data”, BMC Genomics, 2012 Nov 24;13:666. PMID: 23176052, PMCID:
PMC3532123 (2015 IF:4.0)
36. 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. PMID: 22607156, PMCID:
PMC3416685
37. 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. PMID: 22387842, PMCID: PMC3354959
38. Guo Y, Miyagi M, Zeng R, Sheng, Q, O18Quant: A Semi-automatic Strategy for Quantitative
Analysis of High-Resolution 16O/18O Labeled Data, Biomed Research International, 2014, PMID
24901003, PMID: 24901003, PMCID: PMC4037588
39. Guo Y, Zhao S, Lehmann B, Pietenpol J, Shyr Yu, Detection of internal exon deletion with exon
Del, BMC Bioinformatics, 2014, PMID: 25322818, PMCID: PMC4288651
40. 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. 2014. PMID 24878723
41. Guo Y, Zhao S, Bjoring M, Han L, Big Data Analytics in Bioinformatics and Healthcare, Chapter
Name: Data Mining of High Throughput Sequencing, IGI-Global. 2014
42. Guo Y, Su P, Li C, Zhao S, Ye F, Flynn CR, Shyr Yu, Statistical Strategies for microRNAseq Batch
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Effect Reduction, Transl Cancer Res 2014;3(3):260-265. doi: 10.3978/ j.issn.2218676X.2014.06.05, PMID: 25258704, PMCID: PMC4171948
Guo Y, Zhao S, Sheng Q, Shyr Y. MultiRankSeq: Multiperspective Approach for RNAseq
Differential Expression Analysis and Quality Control, Biomedical Research International, 2014,
PMID: 24977143, PMCID: PMC4058234
Guo Y, Li C, Cai Q, Shyr Y, “Very Low level Heteroplasmy mtDNA Variations Are Inherited in
Humans”, Journal of Genetics and Genomics. 2014. PMID: 24377867
Guo Y, Zhao S, Sheng Q, Guo M, Stricker T, Lehmann B, Pietenpol J, Samuels DC, Shyr Yu,
RNAseq by Total RNA Library Identifies Additional RNAs Compared to Poly(A) RNA library,
Biomed Research International, 2015
Ye F, Samuels DC, Guo Y, Detection of Mitochondrial Mutations in Cancer by Next Generation
Sequencing, Next Generation Sequencing & Applications, 2014
Guo Y, Zhao S, Li C, Sheng Q, Shyr Y, RNAseqPS: A Web Tool for Estimating Sample Size
and Power for RNAseq experiment, Cancer Informatics, 2014
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. PMID: 24303503, PMCID: PMC3835197
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):27993. PMID: 24088264, PMCID PMC4108916
Guo Y, Li J, Li CI, Shyr Y, “Evaluation of allele frequency estimation using pooled sequencing
data simulation”, ScientificWorldJournal 2013, 2013:895496. PMID: 23476151, PMCID:
PMC3582166
Guo Y, Ye F, Tang J, "Phylogenetic reconstruction with disk-covering and Bayesian approaches,"
BioInformatics and BioEngineering, BIBE 2008.
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, PMID: 23281772, PMCID:
PMC3535703
Zhao S†, Guo Y†, Sheng Q, Shyr Y, Advanced Heat Map and Clustering Analysis Using
Heatmap3, Biomed Research International, 2014, PMID: 4124803
PEER-REVIEWED PUBLICATIONS AS CO-AUTHOR
54. Panaccione A, Guo Y, Yarbrough W, Ivanov S, Expression Profiling Of Clinical Specimens
Supports The Existence Of Neural Progenitor-Like Stem Cells In Basal Breast Cancers, Clinical
Breast Cancer, 2017
55. Jovanovic B, Sheng Q, Seitz RS, Lawrence KD, Morris SW, Thomas LR, Hout DR, Schweitzer
BL, Guo Y, Pietenpol JA, Lehmann BD, Comparison of triple-negative breast cancer molecular
subtyping using RNA from matched fresh-frozen versus formalin-fixed paraffin-embedded tissue,
BMC Cancer, 2017
56. Oelsner KT, Guo Y, To SB, Non AL, Barkin S, Maternal BMI as a predictor of methylation of
obesity-related genes in saliva samples from preschool-age Hispanic children at-risk for obesity,
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BMC Genomics, 2017
Su P, Mau YL, Guo Y, Li CI, Liu Q, Boice J, Shyr Y, Bivariate Poisson models with varying offsets:
An application to the paired mitochondrial DNA dataset, Statistical Applications in Genetics and
Molecular Biology, 2017
Blum A, Venkitachalam S, Guo Y, Kieber-Emmons AM, Ravi L, Chandar AK, Iyer PG, Canto MI,
Wang JS, Shaheen NJ, Barnholtz-Sloan JS, Markowitz SD, Willis JE, Shyr Y, Chak A, Varadan V,
Guda K, RNA Sequencing Identifies Transcriptionally-Viable Gene Fusions in Esophageal
Adenocarcinomas, Cancer Research, 2016
Loganathan, S, Tang N, Fleming J, Ma Y, Guo Y, Borinstein S, Chiang C, Wang J, BET
bromodomain inhibitors suppress EWS-FLI1-dependent transcription and the IGF1 autocrine
mechanism in Ewing sarcoma, Oncotarget 2016
Eilertson B, Maruri F, Balckman A, Guo Y, Herrera M, van der Heijden Y, Shyr Y, Sterling T, A
Novel Resistance Mutation in eccC5 of the ESX-5 Secretion System Confers Ofloxacin Resistance
in Mycobacterium Tuberculosis, Journal of Antimicrobial Chemotherapy, 2016
Rabacal W, Pabbisetty SK, Hoek K, Cendron D, Guo Y, Maseda D, Sebzda E, Transcription factor
KLF2 regulates homeostatic NK cell proliferation and survival, PNAS, 2016
Ma Y, Wang L, Neitzel L, Loganathan S, Tang N, Emily C, Guo Y, Knapp S, Beauchamp R, Lee
E, Wang J, The MAPK Pathway Regulates Intrinsic Resistance to BET Inhibitors in Colorectal
Cancer. Clinical Cancer Research, 2016
Panaccione A, Zhang Yi, Mi Y, Mitani Y, Guo Y, Prasad M, McDonald H, El-Naggar AK,
Yarbrough W, Ivanov S, Chromosomal Abnormalities and Molecular Landscape of Metastasizing
Mucinous Salivary Adenocarcinoma, Oral Oncology
Strugill, E, Norris, S, Guo Y, Ohi R, Kinesin-5 inhibitor resistance is driven by kinesin-12, Journal
of Cell Biology, 2016, PMID: 27091450
NOTCH1 and SOX10 are Essential for Proliferation and Radiation Resistance of Cancer Stem-like
Cells in Adenoid Cystic Carcinoma, Panaccione A, Chang MT, Carbone BE, Guo Y, Moskaluk CA,
Virk RK, Chirboga L, Prasad ML, Judson B, Mehra S, Yarbrough WG, Ivanov SV, Clinical Cancer
Research, 2016, PMID: 27084744
McCann TS, Guo Y, McDonald H, Tansey W, Antagonistic roles for Asr1 and Ubp3 in
subtelomeric gene silencing PNAS, 2016
Herington J, Guo Y, Reese J, Paria B, Gene profiling the window of implantation: microarray
analyses from human and rodent models, Journal of Reproductive Health and Medicine, 2016
Flynn CR, Albaugh VL, Cai S, Cheung-Flynn J, Williams PE, Brucker RM, Bordenstein SR, Guo
Y, Wasserman DH, Abumrad NN, Bile Diversion to the Distal Small Intestine has comparable
metabolic benefits to bariatric surgery, Nature Communications, 2015, PMID:26197299, PMCID:
PMC4518285
Pickup M, Hover L, Guo Y, Gorska A, Chytil A, Novitskiy S, Moses H, Owens P, Deletion of
the BMP receptor BMPR1a impairs mammary tumor formation and metastasis, Oncotarget 2015
PMID: 26274893
15
70. Kavanaugh G, Zhao R, Guo Y, Mohni KN, Glick G, Lacy ME, Hutson MS, Ascano M, Cortez D,
Enhancer of Rudimentary Homolog affects the replication stress response through regulation of
RNA processing, Molecular Cell Biology, PMID: 26100022
71. Carroll C, Hunley T, Guo Y, Cortez D, A Novel Splice Site Mutation in SMARCAL1 Results in
Aberrant Exon Definition in a Child with Schimke Immunoosseous Dysplasia, American Journal
of Medical Genetics, 2015. PMID: 25943327
72. Spurlock CF, Tossberg, JT, Guo Y, Sriram S, Crooke SP, Aune TM, Expression and functions of
long noncoding RNAs during human T helper cell differentiation, Nature Communications.
PMID: 25621826, PMCID: PMC4333215
73. Spurlock CF, Tossberg, JT, Guo, Y, Sriram S, Crooke PS, Aune TM, Defective structural RNA
processing in relapsing-remitting multiple sclerosis, Genome Biology, PMID: 25885816,
PMC4403723
74. TCGA HNSCC work group, Comprehensive genomic characterization of head and neck
squamous cell carcinomas, Nature, 2015, PMID: 25631445
75. Goodings C, Smith E, Mathia E, Elliott, N, Cleveland S, Tripathi R, Layer J, Chen X, Guo Y,
Shyr Yu, Hamid R, Du Y, Dave, UP, Hhex is required at multiple stages of adult hematopoietic
stem and progenitor cell differentiation, Stem Cells, 2015, PMID: 25968920
76. Hoek K, Samir P, Niu X, Howard LM, Prasad N, Galassie A, Liu Q, Allos TM, Guo Y, Shyr Y,
Levy SE, Joyce S, Edwards KM, Link AJ, A Cell-based Systems Biology Assessment of Human
Blood to Monitor Immune Responses Following Influenza Vaccination, PLOS ONE, 2015, PMID
26706537
77. Di Salvo TG, Guo Y, Su YR, Clark T, Brittain E, Absi T, Maltais S, Hemnes A, Right ventricular
long noncoding RNA expression in human heart failure, Pulm Circ - 2015 Mar;5(1):135-61
78. Hackett TA, Guo Y, Clause A, Hackett NJ, Garbett K, Zhang P, Poley Daniel, Mirnics K,
Transcriptional maturation of the mouse auditory forebrain, BMC Genomics, 2015, PMID:
26271746
79. Zhang B, Jia WH, Matsuda K, Kweon SS, Matsuo K, Xiang YB, Shin A, Jee SH, Kim DH, Cai
Q, Long J, Shi J, Wen W, Yang G, Zhang Y, Li C, Li B, Guo Y, Ren Z, Ji BT, Pan ZZ,
Takahashi A, Shin MH, Matsuda F, Gao YT, Oh JH, Kim S, Ahn YO, Chan A, Chang-Claude J,
Slattery M, Gruber S, Schumacher F, Stenzel S, Casey G, Kim HR, Jeong JY, Park JW, Li HL,
Hosono S, Cho SH, Kubo M, Shu XO, Zeng YX, Zheng W, Genome-wide association study in
East Asians identifies six novel risk loci for colorectal cancer, Nature Genetics, 2014, PMCID:
PMC3679924
80. Parfenov M, Pedamallu CS, Gehlenborg N, Freeman SS, Danilova L, Bristow CA, Lee S,
Hadjipanayis AG, Ivanova EV, Wilkerson MD, Protopopov A, Yang L, Seth S, Song X, Tang J,
Ren X, Zhang J, Pantazi A, Santoso N, Xu AW, Mahadeshwar H, Wheeler DA, Haddad RI, Jung
J, Ojesina AI, Issaeva N, Yarbrough WG, Hayes DN, Grandis JR, El-Naggar, Meyerson M, Park
PJ, Chin Lynda, Seidman JG, Hammerman PS, Kucherlapati R, the Cancer Genome Atlas
Network, Characterization of HPV and host genome interactions in primary head and neck
cancers. Proc Natl Acad Sci U S A 2014, 111(43):15544-15549. PMID:25313082, PMCID:
PMC4217452
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81. 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. PMID: 22829656, PMCID: PMC3611812
82. 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 panErbB negative regulator Lrig1 is an intestinal stem cell marker that functions as a tumor suppressor”,
Cell, 2012 Mar 30;149(1):146-58. PMID: 22464327, PMCID: PMC3563328
83. Saraswati S, Guo Y, Atkinson J, Young P, Prolonged hypoxia induces MCT4 expression in
MSCs resulting in a secretome that is deleterious to cardiovascular repair, Stem Cells, 2014
84. Goodings C, Tripathi R, Cleveland SM, Elliott N, Guo Y, Shyr Y, Dave, UP, Enforced
expression of E47 has differential effects on Lmo2-induced T-cell leukemias, Leukemia
Research, 2014, PMID 25499232
85. Sheng Q, Li R, Dai J, Li Q, Su Z, Guo Y, Li C, Shyr Y, Zeng R, Removing isobaric-related ions
significantly improves the peptide/protein identification sensitivity of high resolution tandem
mass spectrometry data, Molecular & Cellular Proteomics, 2014, PMID: 25435543
86. 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, Exome Sequencing Implicates an Increased Burden of
Rare Potassium Channel Variants in the Risk of Drug-Induced Long QT Interval Syndrome,
Journal of the American College of Cardiology, 2014, PMID: 24561134
87. Cleveland SM, Goodings C, Tripathi RM, Elliott N, Thompson MA, Guo Y, Shyr Y, Dave, UP,
LMO2 induces T-cell leukemia with epigenetic deregulation of CD4, Experimental Hematology,
2014, PMID: 24792354
88. 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. PMID: 24349080, PMCID: PMC3861317
89. 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):3698710. PMID: 23027130
90. Li CI, Su P, Guo, Y, Shyr Y, Sample size calculation for differential expression analysis of RNAseq data under Poisson distribution, Int J Comput Biol Drug Des, 2013 6(4), 358-375, PMID:
24088268, PMCID: PMC3874726
91. 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. PMID: 23812431,
PMCID: PMC3897569
92. 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. PMID: 24100014, PMCID: PMC3889555
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93. Ivanov 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. PMID: 23799842, PMCID:
PMC3721393
94. 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. PMID: 22942905, PMCID:
PMC3424496
95. Yu DS, Zhao R, Hsu EL, Cayer J, Ye F, Guo Y, Shyr Y, Cortez D, “Cyclin-dependent kinase 9cyclin K functions in the replication stress response”, EMBO Rep, 2010 Nov;11(11):876-82. PMID:
20930849, PMCID: PMC2966956
96. 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. PMID: 20856931,
PMCID: PMC2938338
97. Ye F, Guo Y, Lawson A, and Tang J, "Improving tree search in phylogenetic reconstruction from
genome rearrangement data". JEA 4525/2007:352-364, 2007
18