Curriculum Vitae

Curriculum Vitae, March, 2015
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Shuangchun “Jeremy” Yan, Ph.D.
Postdoctoral Research Fellow
Massachusetts General Hospital / Harvard Medical School
Mailing address: 27 Jefferson St Apt 3, Cambridge, MA 02141
Phone: 1-540-200-8848
E-mail: [email protected]
EDUCATION
P HD
BS
PLANT PATHOLOGY, PHYSIOLOGY AND WEED SCIENCE, 12/2010, Virginia Tech, VA, USA
BIOLOGY, 07/2005, Sichuan University, Chengdu, China
RESEARCH EXPERIENCE
POSTDOCTORAL RESEARCH FELLOW - 2/2012 TO CURRENT
Massachusetts General Hospital; Harvard Medical School; Shriners Hospital for Children Boston, Massachusetts, USA
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Mechanisms behind hyper-susceptibility to infection after trauma using mouse and Drosophila trauma and
Pseudomonas aeruginosa infection models.
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Biomarker discovery for susceptibility to infection based on transcriptome, proteome, and clinical characteristics.
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Characterizing a novel ALDH gene involved in hyper-susceptibility to infection.
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Preclinical investigation of novel antioxidant therapies to prevent and reduce incidents of mortality and
morbidities caused by trauma & infections.
POSTDOCTORAL FELLOW - 1/2011 TO 1/2012
Monterey Bay Aquarium Research Institute, California, USA
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Systems biology approach to study the physiology and responses to environmental stress of Micromonas, a
photosynthetic marine picoeukaryote.
GRADUATE RESEARCH ASSISTANT - PHD RESEARCH - 1/2006 TO 12/2010
Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Virginia, USA
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Characterized the effects and mode of action of HopM1, a Type III secreted effector using Pseudomonas syringae
strains and tomato/Arabidopsis infection models. Micro-evolution of hopM1.
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Applied comparative genomics, genetics and molecular biology to study the mechanisms for host and non-host
interactions, host-range evolution of closely related P. syringae strains.
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Contributed to the design and construction of PAMDB.org, an MLST database of plant-associated microbes.
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Illumina and 454 pyrosequencing of a dozen of P. syringae strains and the genome assembly and analysis.
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Applied MLST, maximum-likelihood, Baysian inference and other methods to investigate population genetics and
molecular evolution among a group of closely related P. syringae strains.
RESEARCH ASSISTANT - ROTATION STUDENT - 8/2005-12/2005
Molecular Plant Sciences Program, Virginia Tech, Virginia, USA
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Studied myo-inositol synthesis and its physiological significance in Arabidopsis.
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Cloning of root specialized Arabidopsis terpene synthase genes.
UNDERGRADUATE RESEARCH ASSISTANT - 9/2003 - 6/2005
College of Life Sciences, Sichuan University, Chengdu, China
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Tissue culture and transient transformation of Jatropha curcas.
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Brassicaceae pollen in vitro culture and maturation, undergraduate degree thesis.
Curriculum Vitae, March, 2015
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BIBLIOGRAPHY
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Yan S, Liu H, Vinatzer BA. BACTERIAL TYPE III EFFECTOR HOPM1 CAUSE AMBIVALENT CELL DEATH AND CONFERS
NON-PATHOGENIC PSEUDOMONAS FLUORESCENS PATHOGEN-LIKE VIRULENCE. Manuscript pending submission, 2015.
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Tsurumi A, Que Y, Yan S, Tompkins RG, Rahme LG, Ryan CM. DO STANDARD BURN MORTALITY FORMULAE WORK
ON A POPULATION OF SEVERELY BURNED CHILDREN AND ADULTS? In revision to Burns, December 2014.
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Yan S, Tsurumi A, Que Y-A, Ryan CM, Bandyopadhaya A, Morgan AA, Flaherty PJ, Tompkins RG, Rahme LG.
PREDICTION OF MULTIPLE INFECTIONS AFTER SEVERE BURN TRAUMA: A PROSPECTIVE COHORT STUDY. Annals of surgery
261, no. 4 (2015).
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McRose D, Guo J, Monier A, Sudek S, Wilken S, Yan S, Mock T, Archibald J, Begley T, Adrian Reyes-Prieto A,
Worden A. ALTERNATIVES TO VITAMIN B1 UPTAKE REVEALED WITH DISCOVERY OF RIBOSWITCHES IN MULTIPLE MARINE
UNICELLULAR EUKARYOTES. ISME J (2014) 8, 2517–2529.
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Sarris PF, Trantas EA, Baltrus DA, Bull CT, Wechter WP, Yan S, et al. COMPARATIVE GENOMICS OF MULTIPLE
STRAINS OF PSEUDOMONAS CANNABINA PV. ALISALENSIS, A POTENTIAL MODEL PATHOGEN OF BOTH MONOCOTS AND
DICOTS. PLoS ONE. 2013;8(3):e59366.
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Cai R, Yan S, Liu H, Leman S, Vinatzer BA. RECONSTRUCTING HOST RANGE EVOLUTION OF BACTERIAL PLANT
PATHOGENS USING PSEUDOMONAS SYRINGAE PV. TOMATO AND ITS CLOSE RELATIVES AS A MODEL. Infection, Genetics
and Evolution, Volume 11, Issue 7, October 2011, Pages 1738-1751
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Cai R*, Lewis J*, Yan S, et al. THE PLANT PATHOGEN PSEUDOMONAS SYRINGAE PV. TOMATO IS GENETICALLY
MONOMORPHIC AND UNDER STRONG SELECTION TO EVADE TOMATO IMMUNITY. *Co-First Author. PLoS Pathog 7(8):
e1002130. doi:10.1371/journal.ppat.1002130.
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Almeida N, Yan S, et al. PAMDB, A MULTILOCUS SEQUENCE TYPING AND ANALYSIS DATABASE AND WEBSITE FOR
PLANT-ASSOCIATED MICROBES. Phytopathology (2010) vol. 100 (3) pp. 208-15.
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Almeida N*, Yan S*, Lindeberg M*, et al. (2009) A DRAFT GENOME SEQUENCE OF PSEUDOMONAS SYRINGAE PV.
TOMATO T1 REVEALS A TYPE III EFFECTOR REPERTOIRE SIGNIFICANTLY DIVERGENT FROM THAT OF PSEUDOMONAS
SYRINGAE PV. TOMATO DC3000. Mol Plant Microbe Interact 22: 52-62. *These authors contributed equally to this
work. One of the five most-read papers in MPMI online in January 2009.
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Yan S, et al. THE ROLE OF RECOMBINATION IN THE EVOLUTION OF THE MODEL PLANT PATHOGEN PSEUDOMONAS
SYRINGAE PV. TOMATO DC3000, A VERY ATYPICAL TOMATO STRAIN. Appl Environ Microbiol 74: 3171-3181.
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Mohr TJ, Liu H, Yan S, Morris CE, Castillo JA, Jelenska J, & Vinatzer BA. NATURALLY OCCURRING NONPATHOGENIC ISOLATES OF THE PLANT PATHOGEN SPECIES PSEUDOMONAS SYRINGAE LACK A TYPE III SECRETION
SYSTEM AND EFFECTOR GENE ORTHOLOGUES. J Bacteriol 190: 2858-2870.
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Morris CE, Sands DC, Vinatzer BA, Glaux C, Guilbaud C, Buffiere A, Yan S, Dominguez H, & Thompson BM. THE
LIFE HISTORY OF THE PLANT PATHOGEN PSEUDOMONAS SYRINGAE IS LINKED TO THE WATER CYCLE. ISME J (2008) 2,
321-334.
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Vinatzer BA & Yan S. MINING THE GENOMES OF PLANT PATHOGENIC BACTERIA: HOW NOT TO DROWN IN GIGABASES OF
SEQUENCE. Molecular Plant Pathology (2008) 9, 105-118.
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Deng J, Yan S, et al. EFFECTS OF DIFFERENT ANTIBIOTICS AT VARIOUS CONCENTRATIONS ON CULTURE OF JATROPHA
CURCAS. Chin J Appl Environ Biol (2005) 11(2): 156~159.
AWARDS
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2012, MGH Postdoc Association Travel Award
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2010, Kriton Hatzios Scholarship
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2010, John L. Johnson Memorial Scholarship,
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2009, GSA Travel Fund, Virginia Tech
Curriculum Vitae, March, 2015
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2008, GSA Graduate Research and Development Project Grant, Virginia Tech
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2005, Honor Graduate Award, Sichuan University
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SELECTED POSTER AND ORAL PRESENTATIONS
ORAL PRESENTATIONS
• Boston-area Antimicrobial Research Network Symposium, 2015. Yan S, et al. EARLY PREDICTION OF SEVERE
INFECTIONS IN PATIENTS. 03/2015 Broad Institute, Boston.
POSTER PRESENTATIONS
• Clinical Research Day Poster Presentation 10/2014, Massachusetts General Hospital, Boston, MA, USA
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Military Health System Research Symposium 7/2014, Fort Lauderdale, Florida, USA
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XIV International Congress on Molecular Plant-Microbe Interactions 7/2008, Quebec City, Canada
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19th International Conference on Arabidopsis Research 7/2008 Montreal, Canada
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XIII International Congress on Molecular Plant-Microbe Interactions 7/2007, Sorrento, Italy
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8th Conference of the European Foundation for Plant Pathology 8/2006 Copenhagen, Denmark
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Conference for Genomes, Evolution, and Bioinformatics 5/2006 Tempe, Arizona, USA
KEY LAB & COMPUTATIONAL EXPERIENCE AND SKILLS
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PCR and qPCR; western; ELISA; cloning and other basic molecular biology techniques; fluorescent microscopy;
confocal microscopy; fruit fly culture and infection model; fruit fly genetics; basic plant histology; plan tissue
culture; mammalian cell culture; flow cytometry; and more.
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R programming; Microarray/transcriptome analysis; Python and Perl programming for bioinformatics; Gene &
pathway enrichment analysis; Clinical data analysis; Molecular evolution; Advanced user of OS X, Linux and
Windows; Web design and HTML/CSS.
TEACHING EXPERIENCE
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2006 to 2010, Advised undergraduate research assistants working on research projects.
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Spring 2008, Teaching assistant for an undergraduate course, Plant Physiology lab.
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Spring 2006, Teaching assistant for an undergraduate course, General and Principle Biology Lab,
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2004, repared educational/scientific illustrations of cellular processes for a biology textbook in China.
SERVICES
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2009-2010, Secretary and treasurer, PPWS Graduate Student Organization.
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2009, Designer, Molecular Plant Sciences program logo.
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2008-2009, Cabinet member and delegate, Virginia Tech GSA.
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2008-2009, Board member, Virginia Tech Registered Student Organization Budget Board.
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2008-2009, Panelist, Graduate Honor System at Virginia Tech.
MEMBERSHIP
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2007-2012, The American Society For Microbiology (ASM)
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2006-2010, International Society of Plant-Microbe Interaction (IS-MPMI)
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Phi Sigma Biological Honor Society
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Gamma Sigma Delta, The Honor Society of Agriculture