2016 LAB NEWS
2015 LAB NEWS
- The lab hosted the visit of Prof. Yanchun Liang from
Jilin University, China from during Summer 2015.
a powerful tool at the junction of plant biology and computer
- The lab organized a reception on May 6, 2015 in honor of
Dr. Trupti Joshi to celebrate her new position and recognize her
tremendous contributions to the lab.
- Dr. Trupti Joshi transitioned to Director, Translational
Bioinformatics position with MU School of Medicine under Dean's
Office and Assistant Research Professor in Department of
Molecular Microbiology and Immunology effective May 1, 2015.
While she will establish her independent lab, Trupti will
continue to collaborate on research projects and jointly advise
students in the lab.
2014 LAB NEWS
- The group had a fall picnic at at Battlecreek Paintball.
- Zhiquan He successfully defended his Ph.D. dissertation
and joined MathWorks.
and iPlant streamline complex bioinformatics analysis
- A SoyKB Workshop was given at Soy2014 (Molecular and
Cellular Biology of the Soybean 15th Biennial Conference)
- P3DB had a workshop at the IPG Symposium on Plant
Protein Phosphorylation, Columbia, Missouri, May 28-30, 2014.
- Trupti Joshi was promoted to Assistant Research
Professor in Department of Computer Science, a core faculty
member at Informatics Institute, and Associate Director at
Digital Biology Lab.
- The lab received a new grant "Prediction and Control of
the Performance of Anaerobic Digestion of Animal Manure through
Metagenomics for Renewable Energy" from USDA (PI Guolu Zheng;
Co-PIs Dong Xu and Zhiqiang Hu).
2013 LAB NEWS
2012 LAB NEWS
- Chao Zhang successfully defended his Ph.D. dissertation
and joined Connell University as a postdoc fellow.
- Allison Tegge successfully defended her Ph.D.
dissertation and joined Virginia Tech as a postdoc fellow.
- Franklin D. Levi got his B.S. degree and joined
Mizzou won first place in Emergency Management Functionality at
the Joplin, Mo Hackathon. Lab member Michael Fitzpatrick was on
Franklin was a top winner at the MegaMiner Aritificial
- Dong Xu (PI), Ioan Kosztin, Yi Shang, and Jingfen Zhang
received a 5-year NIH RO1 grant "Development of MUFOLD for
Building High-Accuracy Protein Structure Models" with
- Dong Xu gave a keynote talk "Protein Structure
Prediction and Clustering Using MUFOLD" at the 8th International
Symposium on Bioinformatics Research and Applications
(ISBRA'12), Dallas, Texas, May 21, 2012.
- Kapil S. Patil, Meshari S. Alazmi and Curtis Bollinger
graduated with their M.S. Degrees.
- The lab had a Spring Picnic to Ha Ha Tonka State Park in
- Trupti Joshi presented her paper "Soybean Knowledge Base
(SoyKB): a web resource for soybean translational genomics" at
the Tenth Asia Pacific Bioinformatics Conference (APBC 2012) in
Melbourne, Australia, 17-19 January 2012.
2011 LAB NEWS
- The lab hosted the visit of Prof. Luonan Chen from
Chinese Academy of Sciences in the summer.
- Yang Xu obtained an M.S. degree and started a job at
- Jianjiong Gao successfully defended his Ph.D.
dissertation and joined Memorial Sloan-Kettering Cancer Center.
- The United Soybean Board project led by Henry Nguyen
(PI) and Gary Stacy, and Dong Xu, "Construction of Proteome and
Metabolome Maps of Soybean to Improve Yield and Value-Added
Traits" has been extended for three more years.
- The research grant "Development of Virtual Patient
Examination System" (Dong Xu, PI; Ye Duan, Co-PI) from Cerner,
Inc has been extended for another year.
- The lab had a group picnic at Lake of Ozarks.
- The lab hosted the visit of Prof. Yanchun Liang from
Jilin University, China from during January 2010- April 2011.
2010 LAB NEWS
- Trupti Joshi and Chao Zhang gave presentations at the
2010 IEEE International Conference on Bioinformatics &
Biomedicine (BIBM 10).
- Dong Xu delivered a keynote talk "MUFOLD for Protein 3D
Structure Prediction: A New Solution to an Old Challenge" at the
2010 IEEE International Conference on Bioinformatics &
Biomedicine (BIBM 10).
- Dong Xu delivered a keynote talk "Machine-Learning Based
Data Processing (Characterizing posttranslational modifications
by decoding protein sequences)" at International Conference on
Audio, Language and Image Processing (ICALIP 2010).
- Guan N. Lin (Nick) successfully defended his Ph.D.
dissertation and joined University of California –San
- Jianjiong Gao presented a talk “Musite: Global
Prediction of General and Kinase-Specific Phosphorylation
Sites” at ISMB 2010.
- The lab received 3 new grants:
Systems View of Root Hair Response to Abiotic Stress
developmental and environmental responses, Gary Stacy, PI; David
Koppenaal, Co-PI; Ljiljana Pasa-Tolic, Co-PI; Jianlin Cheng,
Co-PI; Dong Xu, Co-PI, DOE, $1M, 9/1/10 to 8/30/13.
- (2). GEPR: Soybean root hairs, a model for single-cell
plant biology developmental and environmental responses, Gary
Stacy, PI; Jianlin Cheng, Co-PI; Dong Xu, Co-PI, NSF, $1.5M,
8/1/10 to 7/31/14.
- (3) Development of Virtual Patient Examination System,
Dong Xu, PI; Ye Duan, Co-PI, Cerner, Inc, $225,000, 4/1/10 to
- The lab had a summer picnic at Meramec on Aug 28 2010.(Pictures)
Xu became Editor-in-Chief of International Journal of
Functional Informatics and Personalised Medicine (IJFIPM).
- Gyan Srivastava got his Ph.D. degree and joined Harvard
Medical School with joint appointments in Brigham and Women
Hospital and Broad Institute.
Biology Laboratory participated in the soybean genome project
with a paper in Nature.
- Trupti Joshi presented her paper "Prediction of novel
miRNAs and associated target genes in Glycine max" at the Eighth
Asia Pacific Bioinformatics Conference (APBC 2010) in Bangalore,
India, 18-21 January 2010.
2009 LAB NEWS
- Robin Kramer joined the National Center for Genome
Resources (NCGR) in Santa Fe.
- Guan Ning Lin presented his paper "Sequence-based
prediction of protein folding rates using contacts, secondary
structures and support vector machines" at the IEEE
International Conference on Bioinformatics and Biomedicine (BIBM
2009), at Washington DC, Nov 2009.
- The lab had a group outing at Lake of Ozark on September
- Dong Xu gave a keynote talk "New Frontiers in
Translational Research with Next-Generation Sequencing and
Proteomics Analyses" at International Joint Conference on
Bioinformatics, Systems Biology and Intelligent Computing
(IJCBS), Shanghai, China, August 3-5, 2009.
- Zhao Song got his Ph.D. And joined Microsoft.
- Guan Ning Lin received Outstanding Graduate Student
Award of MU Informatics Institute in March 2009.
Xu is a Program Co-Chair for the 2009 IEEE International
Conference on Bioinformatics & Biomedicine (BIBM 09).
- Guan Ning Lin presented his paper "ComPhy: Prokaryotic
Composite Distance Phylogenies Inferred from Whole-Genome Gene
Sets" at the Seventh Asia Pacific Bioinformatics Conference
(APBC 2009) in Beijing, China, 13-16 January 2009.
2008 LAB NEWS
team of three labs (Dong Xu, Yi Shang, and Ioan Kosztin)
achieved good performance in CASP8, and Dong Xu gave an invited
talk at the CASP8 conference.
- Dong Xu (PI), Yi Shang, and Ioan Kosztin successfully
renewed their NIH grant on "New Scoring, Assembly and Evaluation
Techniques for Protein Structure Prediction" for three more
Dong Xu, James Keller, Mihail Popescu, and Rajkumar Bondugula
published a new book entitled "Applications of Fuzzy Logic in
- Gyan P. Srivastava presented his paper "Functional
Annotation from Meta-Analysis of Microarray Datasets" at the
IEEE International Conference on Bioinformatics and Biomedicine
(BIBM 2008), Philadelphia, Pennsylvania.
- Christopher Bottoms presented his paper "Wanted: Unique
Names for Unique Atom Positions. PDB-Wide Analysis of
Diastereotopic Atom Names of Small Molecules Containing
Diphosphate" at the Fifth Annual MCBIOS Conference. Systems
Biology: Bridging the Omics.
- Jingfeng Zhang
delivered a baby girl.
- Kun Zhang (UCSD), Huidong Shi, and Dong Xu obtained a
new NIH grant on "Genome-scale analysis of DNA methylation in
CpG islands with bisulfite sequencing".
- The lab hosted the visit of Shunfu Xu Nanjing Medical
University, China from during January 2008 - April 2008.
- The lab received 4 new grants:
(1) Dong Xu,
jointly with Himadri Pakrasi (PI) et al., Discovery and
Utilization of Enzymes for Renewable Biofuels Production,
Missouri Life Science Trust Fund, January 2008 - December 2009.
(2) Dong Xu, jointly with Henry Nguyen (PI) and Gary
Stacy, Construction of Proteome and Metabolome Maps of Soybean
to Improve Yield and Value-Added Traits, United Soybean Board,
January 2008 - December 2010.
(3) Dong Xu (PI), jointly
with Jianlin Chen, Henry Nguyen, and Gary Stacy, Developing a
Web Server for Soybean Translational Genomics, Missouri Soybean
Merchandising Council (MSMC), April 2008 - April 2010.
Dong Xu, jointly with Ye Duan et al. (PI), 3D Facial Phenotype
Exploration for Autism, July 2008 - July 2009.
2007 LAB NEWS
- MUPRED SSP
developed at the lab is featured in the IEEE Computational
Intelligence society's magazine.
- Chao Zhang, Trupti Joshi and Nick Lin won the "Best
Poster" award for "GENEFAS: A Tool to Predict Protein Function
Using Multiple Sources of Data" at the IEEE 7th International
Conference on Bioinformatics and Bioengineering (BIBE 2007)
conference in October 2007.
- The lab had a summer picnic at Mark Twain State Park on
- The lab hosted the visit of Professor Prof.
Guohuo Lin from University of Alberta during August 1 -
- Dong Xu is promoted to full professor starting from
September 1, 2007.
- Huidong Shi and Dong Xu received a research grant
"High-Throughput Bisulfite Sequencing Method for Exploring the
Breast Cancer Epigenome" from US Army.
- Rajkumar Bondugula obtained his Ph.D. degree in Computer
Science and started as a researcher at Biotechnology HPC
Software Applications Institute, Fort Detrick, Maryland.
- Dong Xu is appointed to be a member of NIH Biodata
Management and Analysis Panel for the period of July 1,
2007-June 30, 2011.
- Dong Xu received Senior Faculty Research Award, College
of Engineering, University of Missouri-Columbia, 2007.
- Gyan Prakash Srivastava is a winner in the category of
Biological Sciences at the 2007 MU Research and Creative
- Dong Xu is appointed as the Chair of Computer Science
Department starting from January 1, 2007.
2006 LAB NEWS
- Dr. Patrick Zhao from the Samuel Roberts Noble
Foundation visited the lab.
- Dr. A. Keith Dunker from Informatics Indiana University
Schools of Medicine & Informatics visited the lab.
- Dr. Arcady Mushegian from Stowers Institute visited the
- Dr. Ying Xu from University of Georgia visited the lab.
- Rajkumar Bondugula won the First Place for the poster
"MUPRED: Protein Secondary Prediction System" in the 1st Student
Poster Competition sponsored by the IEEE-CIS Mizzou Chapter and
the College of Engineering at the University of
- The lab had a summer trip to Lake of Ozark on July 8.(Pictures)
- Mihail Popescu accepted a tenure-track position at the
Health Management and Informatics Department, University of
Missouri-Columbia, starting from July.
- Dong Xu (PI), Yi Shang, and Ioan Kosztin received an NIH
grant on "New Scoring, Assembly and Evaluation Techniques for
Protein Structure Prediction".
- Sarah Yu from Vanderbilt University, Nashville and Erik
Taylor from University of Texas, Austin are doing summer
internships at the lab.
- Peter Dempsey won the prestigious Benton Scholarship
given by Curtis Benton and Barbara Kortright Benton in March.
- Rajkumar Bondugula received GSA Superior Graduate
Achievement Award in March.
2005 LAB NEWS
- The lab had a fall group picnic at the Katy Trail.
- The lab moved to the Life Sciences Center
on September 26th.
- The lab hosted the visit of Professor Luonan Chen from
the Department of Electrical Engineering and Electronics, Osaka
Sangyo University during July 27 - August 20. He gave a
talk titled "Designing and analyzing gene regulatory
networks" on August 15th.
- Dr. Xiufeng Wan started as an Assistant Professor at the
Department of Microbiology, Miami University after a two-year
postdoctoral at the lab.
- Zach Nichols from the University of South Carolina,
Jacob Traas from the University of Michigan, Ann Arbor, and
Ricardo J. Restrepo at the University of Missouri, Columbia, are
doing summer internships at the lab.
- The lab had a spring group picnic at the Katy Trail on
May 22, 2005. (Pictures)
- Peter Dempsey won the Chancellor's Award for Excellence
in Undergraduate Research for the development in BioAnalyzer in
- Ashwin Ganapathy obtained an M.S. degree from MU
Computer Science Department and will start as a Bioinformatics
Specialist at Expergen, Inc, Madison, WI in January 2005.
2004 LAB NEWS
- Dong Xu (PI), jointly with Gary Stacey Dave Emerich and
Xinhua Zhuang received a grant "Computational Analyses of
Protein Mass Spectroscopy Data" from Monsanto Research Funds for
Oct. 2004 - Sept. 2006.
- Dr. Nengbing Tao and Dr. Maolong Lu from Monsanto
visited the lab on November 17, 2004.
- Trupti Joshi is appointed as Lab Manager, starting from
October 25, 2004.
- The lab had a group picnic at Lake Dixie on October 16,
- Prof.Luonan Chen from Osaka Sangyo University, Japan
visited the lab and gave a seminar on campus on October 8, 2004.
- Dr. Dong Xu's son Benjamin
Wenlong Xu was born with 7 pounds and 14 ounces on September
- Ognen Duzlevski won the first place in the state level
Karate tournament in September 2004.
- Dr. Dong Xu is teaching Computational
Methods in Bioinformatics during Fall 2004 semester.
- Yu Chen obtained Ph.D. degree from University of
Tennessee and joined Novartis, Inc. in August.
Guohuo Lin from University of Alberta visited the lab during
July 15 to August 6.
- Yu Chen was awarded "Science Alliance Awards for
Outstanding Scholarly Achievement" by the Division of
Biology, University of Tennessee, Knoxville in the amount of
- Ashwin Ganapathy is selected as one of the Region
Finalist for the EMBS-Whitaker Student Paper Competition, IEEE
EBMS Conference to be held in San Francisco, CA on September
- Lei Wang from University of Texas, Dallas, joined the
Digital Biology Laboratory as an Intern from June till August.
- Prof.Jie Liang from University of Illinois at Chicago
visited the lab on April 13, 2004.
- Rajkumar Bondugula awarded “Outstanding Computer
Science Graduate Student in the College of Engineering”
during Missouri Honor awards ceremony held on March12th, 2004.
- February 2004. Dr. Dong Xu is appointed as a part-time
faculty, U.S. Department of Energy Higher Education Research
Experience at the Oak Ridge National Laboratory for
Distinguished Visiting Scientists and Faculty.
- Dr. Dong Xu taught cs303- Design and
Analysis of Algorithms-I during Winter 2004 semester.
- Dr. Dong Xu became a core faculty member in Biomedical
and Health Informatics Research Training Program.
2003 LAB NEWS
- Digital Biology Laboratory Website was launched on
- Dr. Nickolai Alexandrov, Manager for Bioinformatics,
Ceres Inc. visited Digital Biology Lab on 10/16/2003.(Seminar)
- Dr. Dong Xu taught cecs301- Computational Bioinformatics
during Fall 2003 semester.
- Digital Biology Laboratory was successfully set up on