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CURRICULUM VITAE
Fei Ye, PhD
CONTACT INFORMATION
Office Address:
Division of Cancer Biostatistics
Department of Biostatistics
Vanderbilt University School of Medicine
Vanderbilt Center for Quantitative Sciences
495 Preston Research Building
Nashville, TN 37232-6848
Phone Number:
(615) 936-5169
E-mail:
[email protected]
EDUCATION
2004– 2007
Doctor of Philosophy in Biostatistics
School of Public Health, University of South Carolina.
Dissertation: Statistical Approaches for High-Dimensional Bioinformatics
Data.
2002 – 2004
Master of Science in Public Health in Biostatistics
School of Public Health, University of South Carolina
Master’s thesis: Two-Stage Balanced Design for Phase II Oncology
Clinical Trials.
1997 – 2001
Bachelor of Science in Computer Science
Southwest University for Nationalities, China.
PROFESSIONAL EXPERIENCE
2009– present
Assistant Professor of Biostatistics, Division of Cancer
Biostatistics, Department of Biostatistics, Vanderbilt University School
of Medicine.
Vanderbilt Center for Quantitative Sciences.
2007– 2009
Instructor in Biostatistics, Division of Cancer Biostatistics,
Department of Biostatistics, Vanderbilt University School of Medicine.
Cancer Biostatistics Center, Vanderbilt University.
2006 – 2007
Biostatistician II, Division of Cancer Biostatistics, Department of
Biostatistics, Vanderbilt University School of Medicine.
Cancer Biostatistics Center, Vanderbilt University.
2005 – 2006
Research Assistant, Bioinformatics Group at Department of
Computer Science and Engineering, University of South Carolina
2004 – 2005
Teaching Assistant, Department of Epidemiology & Biostatistics,
1
University of South Carolina
Course assisted: Intermediate Biometrics & Survival Analysis.
2004
Biostatistician (Research Intern), Biostatistics Shared Resource,
Vanderbilt Ingram Cancer Center, Vanderbilt University.
2003
Research Assistant, South Carolina Cancer Center, University of
South Carolina.
2003
Research Intern, Biostatistics Shared Resource, Vanderbilt Ingram
Cancer Center, Vanderbilt University.
2002 – 2003
Research Assistant, Department of Epidemiology & Biostatistics,
University of South Carolina.
2002
Graduate Assistant, Department of Basic Pharmaceutical Science,
University of South Carolina.
2001
Software Engineer, Saye Computer Science & Technology Co., Ltd.
Hang Zhou, China.
2001
Computer Analyst (Intern), Shanghai Cancer Institute. Shanghai,
China.
TEACHING EXPERIENCE
Spring 2012
Department of Cancer Biology Methodology Course, Vanderbilt University.

Invited lecture: “t, ANOVA, and things beyond ANOVA”.
Fall 2010
MPH Program Clinical Trials, Vanderbilt University,
Fall 2011
EPID 332, Advanced Methods Modules in Epidemiology, Vanderbilt University

Spring 2012

Statistical methods for repeated measures

Analysis of repeated cross-sectional studies
EPID 332, Advanced Methods Modules in Epidemiology, Vanderbilt University

Fall 2012
Statistical methods for repeated measures
MPH Program Biostatistics I, Vanderbilt University

Fall 2012
Invited lecture: “Basic statistics”.
Stata sessions
EPID 332, Advanced Methods Modules in Epidemiology, Vanderbilt University

Statistical methods for repeated measures; mixed models
Fall 2013
EPID 332, Advanced Methods Modules in Epidemiology, Vanderbilt University
Fall 2013
MPH Program Biostatistics I, Vanderbilt University,


Spring 2014
Statistical methods in biomarker data analysis
Introduction to Clinical and Translational Research

Fall 2014
Invited lecture: “Correlation and linear regression” and Stata sessions
EPID 332, Advanced Methods Modules in Epidemiology, Vanderbilt University

Spring 2014
Statistical methods in clinical trials
Invited lecture: “Introduction to clinical trial design and analysis”
MPH Program Biostatistics I, Vanderbilt University,

Invited lectures: “Correlation and linear regression” and “Logistic
2
regression and diagnosis”

2012-2014
Stata sessions
Ph.D. Dissertation Committee for Kara Ann Michels (Member; Chair: Digna
Velez Edwards and Katherine E. Hartman)
2014-present
Ph.D. Dissertation Committee for Michelle Lynne Baglia (Member; Chair:
Xiao-ou Shu)
Summer 2014
Vanderbilt Center for Quantitative Sciences Summer Institute

Invited lecture: “Statistical considerations in high-throughput RNAi
screens
for
identifying
genes
mediating
sensitivity
to
chemotherapeutic drugs”.
Dec 2014
Advanced Biostatistics, National Cheng Kung University, Taiwan

Invited lectures: “Build prediction models with biomarkers”.

R simulation: Bayesian and MCMC, Metropolis-Hastings and Gibbs
sampler, random walk, basic limit theorems.
2014- present
M.S. Thesis Committee Chair for Run Fan
2015-present
Ph.D. Dissertation Committee for Zhiguo Zhao (Member; Chair: Wei Zheng)
May 2015
Shanghai CDC

Invited lecture: “Development and validation of breast cancer
prognosis models”
RESEARCH SUPERVISION
Department of Biostatistics, Vanderbilt University School of Medicine.
Zhiguo Zhao, MS, Biostatistician III
Pengcheng Lu, MS, Biostatistician III
Kang-Hsien Fan, MS, Biostatistician III
Vanderbilt Center for Quantitative Sciences:
Mingsheng Guo, PhD, Bioinformatician II
Liping Du, MS, Bioinformatician II
Sheau-Chiann Chen, PhD
OTHER PROFESSIONAL ACTIVITIES
2013-
Faculty member, Vanderbilt Technologies for Advanced Genomics Analysis and Research
Design (VANGARD)
2012-Present
Member, Vanderbilt Ingram Cancer Center (VICC) Data & Safety Monitoring
Committee (DSMC)
2010-Present
Biostatistics Review, Vanderbilt Ingram Cancer Center (VICC) Scientific Review Committee
(SRC)
2010-Present
Biostatistics core faculty, Meharry-Vanderbilt-TSU U54 Cancer Partnership
2009-Present
Statistics Review, Vanderbilt Institute for Clinical and Translational Research (VICTR) Grant
Review Studio
3
GRANTS
1R03CA178680-01A1 (PI: Fei Ye)
04/10/2014 – 03/31/2016
$156,875
NIH/NCI
Development and Evaluation of Prediction Models for Breast Cancer Prognosis
1R03HG008055-01 (PIs: David Samuels, Fei Ye)
08/15/2014 – 07/31/2016
$157,000
NIH/NHGRI
Elastic Net Analysis of Phenotype Relationships in Association Studies
AWARDS AND HONORS
2010
Vanderbilt's Recognition and Reward
CERTIFICATES
Certificate for Completion: Genetic Analysis of Complex Human Diseases, University of Miami, Miller school of
Medicine, Hussmann Institute for Human Genomics, May 23-26, 2011
MANUSCRIPT REVIEW FOR
Statistics in Medicine, PLOS Computational Biology, Physiological Genomics, The Journal of Nuclear Medicine,
Translational Cancer Research, Journal of Statistical Computation and Simulation.
Co-reviewed: Clinical Trials, Clinical Cancer Research, Carcinogensis, Journal of Clinical Oncology, PLoS, Cancer,
Cancer Epidemiology Biomarkers and Prevention
PUBLICATIONS
Research Papers
1. Osusky KL, Hallahan DE, Fu A, Ye F, Shyr Y, Geng L “The receptor tyrosine kinase inhibitor SU11248 impedes
endothelial cell migration, tubule formation, and blood vessel formation in vivo, but has little effect on existing
tumor vessels”. Angiogenesis. 2004; 7: 225-33.
2. Ye F and Shyr Y, “Balanced two-stage design for phase II clinical trials”, Clin Trials. 2007; 4(5):514-24.
3. Guo Y*, Ye F* (equal contribution), and Tang J, "Phylogenetic Reconstruction with Disk-Covering and Bayesian
Approaches," In Proceedings of BIBE. IEEE 2008, 1-6.
4. Frangoul H, AI-Jadiry MF, Shyr Y, Ye F, Shakhtour B, and Al-Hadad SA, “Chemotherapy shortage in Iraq and
outcome of childhood acute lymphocytic leukemia”. N Engl J Med. 2008 Jul 24:359 (4):435-437.
5. Mutter R, Lu B, Carbone DP, Csiki I, Johnson DH, Morrow JD, Sandler AB, Shyr Y, Ye F, Hak Choy “A phase II
study of celecoxib in combination with paclitaxel, carboplatin, and radiotherapy for patients with inoperable
stage IIIA/B NSCLC”, Clin Cancer Res. 2009; Mar 15;15(6):2158-65.
4
6. Geng L, Rachakonda G, Morré DJ,
Morre DM,
Crooks PA, Sonar VN, Roti Roti JL, Rogers B Greco S, Ye F,
Salleng K, Freeman ML, and Sekhar KR, “Indolyl-quinuclidinols inhibit ENOX activity and endothelial cell
morphogenesis while enhancing radiation-mediated control of tumor vasculature”, FASEB J. 2009 Sep;
23(9):2986-95.
7. Davies SS, Traustadóttir T, Stock AA, Ye F, Shyr Y, Harman SM, and Roberts II LJ, “Ischemia/reperfusion
unveils impaired capacity of older adults to restrain oxidative insult”,
Free Radic Biol Med., 2009 Oct
1;47(7):1014-8.
8. Lovejoy CA, Xu X, Bansbach CE, Glick GG, Zhao R, Ye F, Sirbu BM, Titus LC, Shyr Y, Cortez D, “Functional
genomic screens identify CINP as a genome maintenance protein”, Proc Natl Acad Sci USA. 2009 Nov
17;106(46):19304-9.
9. Kobayashi H, Huang J, Ye F, Shyr Y, Blackwell TS, Lin PC, “Interleukin-32beta propagates vascular
inflammation azd exacerbates sepsis in a mouse model”, PLoS One. 2010 Mar 5;5(3):e9458.
10. Bauer JA, Ye F, Marshall CB, Lehmann BD, Pendleton CS, Shyr Y, Arteaga CL, Pietenpol JA, “RNA interference
(RNAi) screening approach identifies agents that enhance paclitaxel activity in breast cancer cells”, Breast
Cancer Res. 2010 Jun 24;12(3):R41.
11. 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.
12. Fohn LE, Rodriguez A, Kelley MC, Ye F, Shyr Y, Stricklin G, Robbins JB, “D2-40 lymphatic marker for detecting
lymphatic invasion in thin to intermediate thickness melanomas: association with sentinel lymph node status
and prognostic value-a retrospective case study”, J Am Acad Dermatol. 2011 Feb;64(2):336-45.
13. Reiner J, Ye F, Kashikar ND, Datta PK, “STRAP regulates c-Jun ubiquitin-mediated proteolysis and cellular
proliferation”, BBRC 2011 Apr:407(2):372-77.
14. Villegas R, Xiang YB, Elasy T, Li HL, Yang G, Cai H, Ye F, Gao YT, Shyr Y, Zheng W, Shu XO. “Fish, shellfish,
and long-chain n-3 fatty acid consumption and risk of incident type 2 diabetes in middle-aged Chinese men and
women”, Am J Clin Nutr 2011 Aug; 94(2):543-51.
15. Deeley MA, Chen A, Datteri R, Noble JH, Cmelak AJ, Donnelly EF, Malcolm AW, Moretti L, Jaboin J, Niermann
K, Yang ES, Yu DS, Ye F, Koyama T, Ding GX, Dawant BM, “Comparison of manual and automatic
segmentation methods for brain structures in the presence of space-occupying lesions: a multi-expert study”,
Phys. Med. Biol. 2011 56 4557.
16. Dexheimer JW, Talbot TR, Ye F, Shyr Y, Jones I, Gregg WM, Aronsky D, A Computerized Pneumococcal
Vaccination Reminder System In The Adult Emergency Department, Vaccine, 2011 Sep 16;29(40):7035-41.
5
17. Fox EM, Miller TW, Balko JM, Kuba MG, Sánchez V, Smith RA, Liu S, González-Angulo AM, Mills GB, Ye F,
Shyr Y, Manning HC, Buck E, Arteaga CL. “A kinome-wide screen identifies the Insulin/IGF-I receptor pathway
as a mechanism of escape from hormone dependence in breast cancer”. Cancer Res. 2011 Nov 1;71(21):677384.
18. Sosman JA, Kim KB, Schuchter L, Gonzalez R, Pavlick AC, Weber JS, McArthur GA, Hutson TE, Moschos SJ,
Flaherty KT, Hersey P, Kefford R, Lawrence D, Puzanov I, Lewis KD, Amaravadi RK, Chmielowski B, Lawrence
HJ, Shyr Y, Ye F, Li J, Nolop KB, Lee RJ, Joe AK, Ribas A. “Survival in BRAF V600-mutant advanced melanoma
treated with vemurafenib”. N Engl J Med. 2012 Feb 23;366(8):707-14.
19. Guo Y, Cai Q, Samuels DC, Ye F, Long J, Li CI, Winther JF, Tawn EJ, Stovall M, Lähteenmäki P, Malia 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.” Mutat Res. 2012 May 15;744(2):154-60.
20. Xu BJ, An QA, Srinivasa Gowda S, Yan W, Pierce LA, Abel TW, Rush SZ, Cooper MK, Ye F, Shyr Y, Weaver
KD,Thompson RC, “Identification of blood protein biomarkers that aid in the clinical assessment of patients with
malignant glioma.” Int J Oncol. 2012 Jun;40(6):1995-2003.
21. Samanta D, Gonzalez AL, Nagathihalli N, Ye F, Carbone DP, Datta PK. “Smoking attenuates transforming
growth factor-β-mediated tumor suppression function through downregulation of Smad3 in lung cancer.” Cancer
Prev Res (Phila). 2012 Mar;5(3):453-63.
22. Zhuang G, Song W, Amato K, Hwang Y, Lee K, Boothby M, Ye F, Guo Y, Shyr Y, Lin L, Carbone D, BrantleySieders D, Chen J, ”Cancer-associated EphA3 mutation3 attenuate tumor-suppressive effects of normal EphA3
in lung cancer” JNCI, 2012 Aug 8;104(15):1183-98.
23. Giuse NB, Koonce TY, Storrow AB, Kusnoor SV, Ye F. “Using health literacy and learning style preferences to
optimize the delivery of health information.” J Health Commun. 2012;17 Suppl 3:122-40.
24. Talati M, Seeley E, Ihida-Stansbury K, Delisser H, McDonald H, Ye F, Zhang X, Shyr Y, Caprioli R, Meyrick B.
“Altered expression of nuclear and cytoplasmic histone H1 in pulmonary artery and pulmonary artery smooth
muscle cells in patients with IPAH.” Pulm Circ. 2012 Jul;2(3):340-51.
25. Ye F, Bauer JA, Pientenpol JA, Shyr Y, “Statistical practice in high-throughput siRNA/shRNA screens identifying
genes mediating sensitivity to chemotherapeutic drugs”. BMC Genomics. 2012 Dec 13(Suppl 8):S3.
26. Ye F, Shyr Y, “Adaptive clinical trial design: from simple dose-finding trials to large-scale personalized medicine
trials”, PMO. 2012 Sep;1(4):35-47.
27. 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.
6
28. Guo Y, Li C, Ye F, Shyr Y, “Evaluation of Read Count Based RNAseq Analysis Methods”, BMC Genomics. 2013,
14 (Suppl 8):S2.
29. Guo Y, Zhao S, Ye F, Sheng Q, Shyr Y, “MultiRankSeq: Multi-Perspective Approach for RNAseq Differential
Expression Analysis and Quality Control", Biomed Res Int. vol. 2014. doi:10.1155/2014/248090.
30. Ye F, Samuels DC, Guo Y, “High-Throughput Sequencing in Mitochondrial DNA Research Mitochondrion”,
Mitochondrion. 2014 May 20. pii: S1567-7249(14)00078-6.
31. Guo Y, Zhao S, Sheng Q, Ye F, Li J, Lehmann B, Pietenpol DC, Shyr Y, “Multi-Perspective Quality Control of
Illumina Exome Sequencing Data Using QC3”, Genomics. 2014 May - June;103(5-6):323-328. doi:
10.1016/j.ygeno.2014.03.006. Epub 2014 Apr 3.
32. Dulek DE, Newcomb DC, Goleniewska K, Cephus J, Zhou W, Reiss S, Toki S, Ye F, Zaynagetdinov R, Sherrill
TP, Blackwell
TS, Moore
ML, Boyd
KL, Kolls
JK, Peebles
RS
Jr.,
“Allergic airway inflammation decreases lung bacterial burden following acuteKlebsiella pneumoniae infection
in a neutrophil and CCL8-dependent manner”, Infect Immun. 2014 Jun 23. pii: IAI.00035-14.
33. Amato KR, Wang S, Hastings AK, Youngblood VM, Santapuram PR, Chen H, Cates JM, Colvin DC, Ye F,
Brantley-Sieders DM, Cook RS, Tan L, Gray NS, Chen J, “Genetic and pharmacologic inhibition of EPHA2
promotes apoptosis in NSCLC”. J. Clin. Invest. 2014;124:2037–2049.
34. Ye F, David C, Samuels, Guo Y, “Detection of Mitochondrial Mutations in Cancer by Next Generation
Sequencing”. Next Generat Sequenc & Applic 2014 1:1.
35. Guo Y, Zhao S, Su PF, Li CI, Ye F, Flynn CR, Shyr Y, "Statistical strategies for microRNAseq batch effect
reduction”. Transl Cancer Res 2014 Jun;3(3):260-265
36. Dexheimer JW, Abramo TJ, Arnold DH, Johnson KB, Shyr Y, Ye F, Fan K, Patel N, Aronsky D. “Implementation
and Evaluation of a Computerized Asthma Management System in a Pediatric Emergency Department: A
Randomized Clinical Trial”. Int J Med Inform. 2014 Nov;83(11):805-13. doi: 10.1016/j.ijmedinf.2014.07.008.
Epub 2014 Aug 8.
37. Baglia ML, Cai Q, Zheng Y, Wu J, Su Y, Ye F, Bao PP, Cai H, Zhao Z, Balko J, Zheng W, Lu W, Shu XO, “Dual
specificity phosphatase 4 gene expression in association with triple-negative breast cancer outcome”, Breast
Cancer Res Treat. 2014 Nov;148(1):211-20.
38. Novitskiy SV , Forrester E, Pickup MW, Gorska AE, Chytil A, Aakre M, Polosukhina D, Owens P, Yusupova DR,
Zhao Z, Ye F, Shyr Y, and Moses HL, “Attenuated transforming growth factor beta signaling promotes
metastasis in a model of HER2 mammary carcinogenesis”, Breast Cancer Research. 2014, 16:425
7
39. Bhola NE, Jansen VM, Bafna S, Giltnane JM, Balko JM, Estrada MV, Meszoely I, Mayer I, Abramson V, Ye F,
Sanders M, Dugger TC, Allen EV, Arteaga CL, “Kinome-wide Functional Screen Identifies Role of PLK1 in
Hormone-Independent, ER-Positive Breast Cancer”, Cancer Res 2015 Jan 15;75(2):405-14.
40. Joghnston DB, Friedman DL, Morgans AK, Decker I, Berry E, Ye F, Zhao S, Puzanov I, Sosman JA, Lovly CM,
“Survivorship in immune therapy: assessing chronic immune toxicities, health outcomes, and functional status
among long-term ipilimumab survivors at a single referral center”, Cancer Immunol Res, 2015 Feb 3.
41. Reddy OL, Cates JM, Gellert LL, Crist HS, Yang Z, Yamashita H, Taylor JA 3rd, Smith JA Jr, Chang SS, Cookson
MS, You C, Barocas DA, Grabowska MM, Ye F, Wu XR, Yi Y, Matusik RJ, Kaestner KH, Clark PE, DeGraff DJ,
“Loss of FOXA1 drives sexually dimorphic changes in urothelial differentiation and is an independent predictor
of poor prognosis in bladder cancer”, Am J Pathol. 2015 May;185(5):1385-95.
42. Johnson DB, Peng C, Abramson RG, Ye F, Zhao S, Wolchok JD, Sosman JA, Carvajal RD, Ariyan CE.
“Clinical Activity of Ipilimumab in Acral Melanoma: A Retrospective Review", The oncologist, accepted.
Book Reviews
1.
Ye F, Shyr Y, “Review of book: Optimal High-Throughput Screening: Practical Experimental Design and Data
Analysis for Genome-Scale RNAi Research”. 2014. Book Reviews, JASA, 109:505, 453.
Book Chapters
1.
Ye F, Guo Y, Lawson A, and Tang J, "Improving Tree Search In Phylogenetic Reconstruction from Genome
Rearrangement Data". Experimental Algorithms: Springer Berlin Heidelberg; 2007. p. 352-64. ISBN: 978-3540-72844-3.
2.
Idrees K, Ye F, Shyr Y, Merchant N, “Statistical Issues in Data Monitoring - Data Safety Monitoring Boards",
Success in Academic Surgery: Clinical Trials. Springer. ISBN: 978-1-4471-4678-0 (Print) 978-1-4471-4679-7
(Online)
3.
Ye F, Shyr Y, “Statistical Consideration in Predictive and Prognostic Markers”, Biomarkers in Cancer Screening
and Early Detection. Wiley. In press.
PRESENTATIONS, SEMINARS AND WORKSHOPS
1.
Ye F, “Balanced two-stage design for oncology phase II clinical trials”. Clinical Trials, Vol 1, Supplement 1,
2004; 25th Annual Meeting of the Society for Clinical Trials, May 2004. New Orleans, Louisiana.
2.
Ye F, “Particle Filtration Approach of Phylogenetic Reconstruction from Genome Rearrangement Data”. August
2007. Vanderbilt University. Nashville, TN.
8
3.
Ye F, “Two-Stage Clinical Trial Designs for Multiple Endpoints with Correlated Observations”.
International
Biometrics Society, Eastern North American Region, March 2008. Arlington, VA.
4.
Ye F, “Design and Analysis of Phase III Clinical Trials”, 2008 Cancer Biostatistics Workshop, Vanderbilt
University. June 2008. Nashville, TN.
5.
Ye F, “Randomization in Clinical Trials”, CRC Research Skills Workshop Series. Vanderbilt Clinical Research
Center. July 2009. Nashville, TN.
6.
Ye F, “Oncology Clinical Trial Design – Phase I, Phase II, and Phase III Trials”, August 2009. – Vanderbilt
University School of Medicine, Division of Continuing Medical Education. Nashville, TN.
7.
Ye F, “When p>>n: Case Studies in High-Dimensional Data Analysis”, September 2009. Cornell Medical
College, New York.
8.
Ye F, “Statistical Practice in High-Throughput siRNA Screens Identifying Genes Mediating Sensitivity to
Chemotherapeutic Drugs”. 2009 Cancer Biostatistics Workshop, Vanderbilt University. November 2009.
Nashville, TN.
9.
Ye F, Zhao Z, “What You See May Not be What You Get – A Brief Introduction to Overfitting”, 2010 Cancer
Biostatistics Workshop, Vanderbilt University. April 2010. Nashville, TN
10. Ye F, “Statistical Practice in High-Throughput RNAi Screens Identifying Genes Mediating Sensitivity to
Chemotherapeutic Drugs”. – Joint Statistical Meetings 2010. Vancouver, Canada.
11. Ye F, “Randomization”, CRC Research Skills Workshop Series. Vanderbilt Clinical Research Center. August
2010. Nashville, TN.
12. Ye F, “Development and validation of a prediction model with survival outcomes for lung cancer patients”,
Invited Lecture, 2010. Tangkang University, Taiwan.
13. Ye F, “Clinical Trial Design”, CRC Research Skills Workshop Series, Vanderbilt University. October 2011.
Nashville, TN.
14. Guo Y, Ye F, “Preprocessing and Analysis of Next Generation Sequencing Data”, January 2012. Shanghai
Center for Bioinformation Technology, China.
15. Ye F, “Analysis of High-Throughput RNAi Screening Data in Identifying Genes Mediating Sensitivity to
Chemotherapeutic Drugs: Statistical Approaches and Perspectives”, April 2012. The International Conference
on Intelligent Biology and Medicine (ICIBM) 2012. Nashville, TN.
9
16. Ye F, “Application of High-Dimensional Data Analysis in Medical Research”, May 2012. Workshop for Chronic
Disease Epidemiology and Prevention. Shanghai, China.
17. Ye F, “Statistical Issues in High-Throughput RNAi Screening Studies”, August 2014. Vanderbilt Center for
Quantitative Statistics Summer Institute.
CONFERENCE ABSTRACTS AND POSTERS
1.
Ewing G, Giglia J, Vusirikala M, Ye F, Shyr Y, Chinratanalab W, Ruffner K, Kassim A, Jagasia M, Engelhardt
B, Brandt S, Morgan D, Stein R, Greer J, Schuening F, and Goodman S, “CD34 dose and chronic graft versus
host disease (cGVHD) affect survival in allogeneic Peripheral Blood Stem Cell Transplantation (alloPBSCT)
following Non-Myeloablative (NM) conditioning: the Vanderbilt University/Nashville VA SCT program
experience”. BMT Tandem Meeting of the American Society of Bone Marrow Transplantation, Feb 2007 Keystone, Colorado.
2.
Ye F, Guo Y, and Tang J, “Improving tree search in phylogenetic reconstruction from genome rearrangement
data”.
3.
6th Workshop on Experimental Algorithms, June 2007 - Rome, Italy.
Mutter RW, Csiki I, Ye F, Johnson D, Dang T, Carbone D, Morrow J, Sandler A, Lu B, and Hak Choy “A phase
II study of celecoxib in combination with paclitaxel, carboplatin, and radiotherapy for patients with inoperable
stage IIIA/B Non-Small Cell Lung Cancer”, International Journal of Radiation Oncology Biology Physics, Vol69,
Issue 3, S524, 2007.
4.
Fohn LE, Stricklin G, Robbins J, Shyr Y, Rodriguez A, Ye F, “D2-40 detected lymphatic invasion and sentinel
node status in melanoma”, Journal of Cutaneous Pathology 2008; December 36(1):108; The 45th Annual
American Society of Dermatopathology, October 2008 – San Francisco, CA.
5.
Dexheimer JW, Talbot TR, Ye F, Shyr Y, Jones I, Gregg WM, Aronsky D, “Implementing a computerized
pneumococcal vaccination reminder system in an emergency Department: A prospective study”, AMIA Annual
Symposium Proceedings. 2008 Nov 6:867.
6.
Geng L, Rachakonda G, Morré DJ,
Morre DM,
Crooks PA, Sonar VN, Roti Roti JL, Rogers B Greco S, Ye
F, Salleng K, Freeman ML, and Sekhar KR, “Indolyl-quinuclidinols inhibit ENOX activity and endothelial cell
morphogenesis while enhancing radiation-mediated control of tumor vasculature”, RRS 55th Annual Meeting
of the Radiation Research Society, October 2009 – Savannah GA.
7.
Ye F, “Statistical Practice in High-Throughput siRNA/shRNA Screens Identifying Genes Mediating Drug
Sensitivity”, 2009 Cancer Epidemiology, Biostatistics, and Bioinformatics Retreat, Vanderbilt Ingram Cancer
Center, December 2009 – Nashville TN.
8.
Ye F and Yu Shyr, “Identify Genes Mediating Chemotherapeutic Drug Sensitivity by Analyzing High-Throughput
siRNA/shRNA Screens”, 9th Annual U54 Cancer Partnership Retreat, Meharry Medical College, January 2010
10
– Nashville TN.
9.
Fox EM, Miller TW, Ye F, Shyr Y, Arteaga CL, “RNAi screening identifies the insulin/insulin-like growth factor-I
receptor pathway as a mechanism of escape from hormone dependence in estrogen receptor-positive breast
cancer”, 2010 San Antonio Breast Cacncer Symposium – San Antonio, TX.
10. Miller TW, Fox EM, Balko JM, Jiang A, Smith RA, Manning HC, Ye F, Shyr Y, Arteaga CL, “Hormone-dependent, E2F-directed transcriptional program”, 2010 San
Antonio Breast Cacncer Symposium – San Antonio, TX.
11. Guo Y, Ye F, et al., “A Study of Radiation Effect on Mitochondria Mutation Using High-throughput Sequencing
Technology”, 10th Annual U54 Cancer Partnership Retreat, Meharry Medical College, January 2011 – Nashville
TN.
12. Guo Y, Ye F, Bjoing M, “Lost Treasures in Sequencing Data”, AACR 2014, Methods Workshop – San Diego,
CA.
13. Baglia ML, Cai Q, Zheng Y, Wu J, Su Y, Ye F, Bao PP, Cai H, Zhao Z, Zheng W, Lu W, Shu XO, “Dual specificity
phosphatase 4 gene expression in triple negative breast cancer”, AACR 2014, Poster Session – San Diego,
CA.
14. Ichihara E, Bauer JA, Lu P, Ye F, Cross D, Pao W, Lovly CM, “A kinome-wide siRNA screen identifies
modifiers of sensitivity to the EGFR T790M-targeted tyrosine kinase inhibitor (TKI), AZD9291, in EGFR
mutant lung adenocarcinoma”, AACR 2015, Poster Session – Philadelphia, PA
15. Liu Y, Cai Q, Ye F, Zheng Y, Wu J, Su Y, Cai H, Bao PP, Zheng W, Lu W, Shu XO, “Abstract LB-296: Tumor
tissue microRNA expression in association with triple negative breast cancer recurrence and mortality”, Cancer
Res, October 1, 2014 74; LB-296.
16. Amato K, Wang S, Hastings A, Chen H, Colvin D, Ye F, Chen J, “Abstract A01: The role of EphA2 in KRAS
mutant non-small cell lung cancer”, Mol Cancer Res, December 201412; A01.
17. Johnson DB, Menzies AM, Zimmer L, Eroglu Z, Ye F, Zhao S, Rizos H, Sucher A, Scolyer RA, Gutzmer R,
Gogas H, Kefford RF, Thompson JF, Becker JC, Berking C, Egberts F, Loquai C, Goldinger S, Pupo GM, Hugo
W, Kong X, Garraway LA, Sosman JA, Ribas A, Lo RS, Long GV, Schadendorf D, “BRAF inhibitor acquired
resistance: A multicenter meta-analysis of the spectrum and clinical implications of resistance mechanisms”,
ASCO 2015.
11