Digital Biology Laboratory

Zhiquan He successfully defended his Ph.D. dissertation and joined MathWorks.

The group had a fall picnic at Shryocks Callaway Farms. (pics)

Michael Ryan Fitzpatrick got his B.S. degree and joined Stanford for graduate study.

Prof. Jing Zhang from Yale University visited the lab for two months.

Dong Xu serves as Associate Editor-in-Chief, IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB).

Dong Xu co-organized a Cold Spring Harbor Asia conference, "Frontiers in Bioinformatics and Computational Biology", on September 23-27, 2013.

Yang Liu and Hongxin Zhang won the champion in a badminton competition at the university.

DigBio Lab 10th Anniversary Retreat at The Lodge of Four Season on May 20-21.(pics)

Trupti Joshi successfully defended her Ph.D. dissertation.

Trupti Joshi received the best poster award at 2013 MCBIOS Conference.

Michael Ryan Fitzpatrick received Outstanding Senior Award and Shiyuan Chen received Outstanding M.S. Award at the Missouri Honor Awards ceremony. (pics)

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 Microsoft.

Team Mizzou won first place in Emergency Management Functionality at the Joplin, Mo Hackathon. Lab member Michael Fitzpatrick was on the team.

Danny Franklin was a top winner at the MegaMiner Aritificial Intelligence competition.

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 $1,394,443.

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 April. Pictures

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.

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 MasterCard.

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.

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 Diego.

Jianjiong Gao presented a talk “Musite: Global Prediction of General and Kinase-Specific Phosphorylation Sites” at ISMB 2010.

The lab received 3 new grants:
(1)  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 12/31/10

The lab had a summer picnic at Meramec on Aug 28 2010.(Pictures)

Dong 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.

Digital 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.

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 27 (Pictures)

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.

Dong 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.

The 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 years.

Dong Xu, James Keller, Mihail Popescu, and Rajkumar Bondugula published a new book entitled "Applications of Fuzzy Logic in Bioinformatics."

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.
(4) Dong Xu, jointly with Ye Duan et al. (PI), 3D Facial Phenotype Exploration for Autism, July 2008 - July 2009.

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 Aug 25.(Pictures)

The lab hosted the visit of Professor Prof. Guohuo Lin from University of Alberta during August 1 - September 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 Activities Forum.

Dong Xu is appointed as the Chair of Computer Science Department starting from January 1, 2007.

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 lab.

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 Missouri-Columbia.

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.

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 April.

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.

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, 2004. (Picture)

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 15, 2004.

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.

Prof. 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 $3,000.

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 2004.

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.


Digital Biology Laboratory Website was launched on December 2003.

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 September 2003.

 

Department of Computer Science College of Engineering University of Missouri-Columbia

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