Data Software
Resume:
Jiancong Xu
Kirkland, WA *****
Phone: 865-***-****
Email: abngwv@r.postjobfree.com
VISA STATUS: Permanent Resident
SUMMARY: research specialist with successful track record, wide-ranged and thorough knowledge
spanning from molecular biology, biochemistry to computational modeling; able to communicate
across multiple disciplines and provide scientific expertise in biotechnology industry.
PROFESSIONAL SKILLS
7 years research experience in developing and applying computational models and algorithms to study
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complex biological systems/processes, including structure-based protein modeling, multiscale
modeling, binding free energy calculations, quantum mechanics/molecular mechanics studies,
homology modeling, ab initio protein structure prediction, virtual screening and QSAR.
Solid background in molecular and cellular biology, genetics and hands-on experience with
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experimental techniques; familiar with chip/sequencing-based high-throughput methodologies.
Experienced in Fortran, C++, PERL, TcL, and shell script programming; 4 million CPU hours
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experience with world-top supercomputers; 10+ year experience in the use of Linux, Windows, and
cluster batch system.
Experienced with statistical analyses of high-throughput genome data; familiar with many
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bioinformatics tools such as sequence alignment programs (BLAST or related, HMMER, HHpred,
ClustalW2 etc.) and genome-scale functional analysis methods; experience with NCBI and GenBank
databases.
Proven ability to establish and manage collaborations, to understand research objectives, and to apply
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and guide development of advanced computational approaches toward scientific discovery.
Strong presentation and communication skills; excellent scientific writing skills, especially in writing
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peer reviewed papers and developing proposals submitted to NIH, NSF, DOE and supercomputing
facilities.
Quick learner, highly organized, open-minded person with proactive approach to learn and
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practice new technologies
EXPERIENCE
Senior Research Fellow/Guest Lecturer, Center for Molecular Biophysics, Oak Ridge National Lab,
2007-2009
• Built a sequence-based classifier by incorporating protein structure features to identify and
disseminate protein domains from genome database. Used homology modeling and docking
programs to build structural models.
• Performed multi-scale simulations of microbe-enzymes-biomass interface; wrote software
programs in PERL and C++ for analyzing large amounts of data sets. Work highlighted in DOE
News.
• Built a close liaison with other institutions and DOE project managers to plan, schedule, and
coordinate detailed phases of projects. Supervised 5 undergraduate and 2 graduate students.
• Taught graduate course Introduction to Molecular Biophysics; prepared all the teaching materials;
organized and led Journal club Genome Science & Technology.
Research Assistant, Center for Biophysical Modeling and Simulation, University of Utah, 2002 -2007
• Developed theoretical and computational methods and co-implemented the DL-EVB software
package for membrane protein simulations; successfully modeled the proton translocation process
in cytochrome c oxidase and influenza M2 channel (Teragrid Science Highlight: Fighting the
Flu).
Discovered a novel proton pumping mechanism in cytochrome c oxidase, published as feature
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article in Proceedings of National Academy of Science and Journal of the American Chemical
Society,
Conducted computational modeling of enzymatic reaction and ion transport in the membrane
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protein cytochrome c oxidase using free energy perturbation and statistical mechanics
methods.
Scholarship Researcher, Interdisciplinary Center for Scientific Computing, University of
Heidelberg/German Cancer Research Center, Germany, 2000-2002.
• Research and experiment on computational genome annotation; utilized data mining algorithms
and various data sources to conduct large-scale statistical analysis of the functions of full-length
cDNA. Evaluated the accuracy of gene prediction softwares.
• Applied continuum electrostatic modeling methods to calculate the protonation probability of
bacteriorhodopsin during photocycle.
Bioinformatics Analyst, United Gene Holding LTD. Shanghai, China, 1998-2000.
• Developed computational algorithms, software and databases for the collection, interpretation and
dissemination of the large-scale post-genome data generated by human genome research.
EDUCATION
2007 Ph.D in Computational Chemistry, University of Utah
2002 M.S. in Molecular and Cellular Biology, University of Heidelberg, Germany
1998 B.S. in Genetics and Genetic Engineering, Fudan University, Shanghai, China
AWARDS AND HONORS
2006 Protons & Membrane Reactions Gordon Research Conference Award
2002 Dow Chemical First-Year Scholarship from University of Utah
2000-2002 Molecular and Cellular Biology Program Scholarship sponsored by C.H.S. Stiftungs-
GmbH, Heidelberg and the German Academic Exchange Service
1995-1998 Renmin Scholarship from Fudan University (top 5% in a class of 150)
1994 Outstanding Freshman Scholarship from Fudan University (top 2% of all freshmen)
SELECTED PUBLICATIONS (OUT OF 12)
J. Xu, M. Crowley and J. C. Smith, Building a Foundation for Structure-Based Cellulosome Design for
Cellulosic Ethanol: Insight into Cohesin-Dockerin Complexation from Computer Simulation. Protein
Science, 2009, 18 (5):949-959, DOE highlight.
J. Xu, M. A. Sharpe, Lin, Q, S. Ferguson-Miller and G. A. Voth, Storage of an Excess Proton in the
Hydrogen-bonded Network of the D-pathway of Cytochrome c Oxidase: Identification of a Protonated
Water Cluster. Journal of the American Chemical Society, 2007, 129: 2910-2913.
J. Xu and G. A. Voth, Free Energy Profiles for H+ Conduction in the D-pathway of Cytochrome c
Oxidase: A Study of the Wild Type and N98D Mutant. Biochimica et Biophysica Acta (BBA) –
Bioenergetics, 2006, 1757: 852-859
J. Xu and G. A. Voth, Computer Simulation of Explicit Proton Translocation in Cytochrome c Oxidase:
The D-pathway. Proceedings of National Academy of Sciences of the United States of America, 2005,
102(19): 6795-6800, feature article.
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