Profile: This research group works on problems from the fields of Bioinformatics, Biotechnology, Data Mining, and Information Retrieval. The group's research projects includes Comparative Genomics of Bacterial genomes, Genomic databases, Pattern Discovery in sequences and structures, micro-array data analysis, prediction of regulatory elements, primer design, probe design, phylogenetic analysis, medical image processing, image analysis, data integration, data mining, information retrieval, knowledge discovery in electronic medical records, and more.

Publications, Posters, & Software(Click here)

Faculty Members	Prof. Giri Narasimhan (Bioinformatics) girics.fiu.edu	Prof. Tao Li (Data Mining) taolics.fiu.edu	Prof. Vagelis Hristidis (Information Retrieval) vageliscs.fiu.edu
PhD Students	Xing Yang xyang006cs.fiu.edu General Bioinformatics
Undergraduate Students	Ruskin Miller rmill002cs.fiu.edu Comparative Genomics	Gisela Gonzalez ggonz031fiu.edu Metagenomics
Recent Graduates	Chengyong Yang (PhD, 2006) Email Data Mining & Microarray Analysis Now at: Applied BioSystems, Inc.	Gaolin Zheng (PhD, 2006) Email Microarray Analysis Now at: North Carolina Central University	Patricia Buendia (PhD, 2006) Email Phylogenetics Now at: University of Miami
Recent Graduates	Roxana Ordonez (B.S., 2008) rordo001fiu.edu Comparative Genomics Now PhD student at: UC - San Francisco	Camilo Valdes (B.S., 2008) cvalde03cs.fiu.edu Comparative Genomics Now at CCS, U Miami	Tom Milledge (MS, 2008) tmille01cs.fiu.edu Structure Pattern Discovery Now at: Duke University
Recent Graduates	Erliang Zeng (PhD, 2008) ezeng001cs.fiu.edu Protein-Protein Interactions; Data Mining Now at: Notre Dame University	Michael Robinson (M.S., 2009) Bioinformatics Databases, High-Performance Computing mrobi002cs.fiu.edu	Andres Parra (Ph. D., 2009) nparr003fiu.edu Medical Image Registration

Recent Awards and Honors

• G. Narasimhan
  School of Computer Science Best Research Award, 2007.
  FIU Faculty Senate Award for Excellence in Research, 2004.
  School of Computer Science Best Research Award, 2004.
• Vagelis Hristidis
  School of Computer Science Best Research Award, 2006.
• Tao Li
  School of Computer Science Best Research Award, 2005.
• A. Nestor Parra
  MARC-ABR Summer Research Award, 2006.
• E. Zeng
  Excellence Award, School of Computer Science, 2007-08.
  Presidential Fellowship, FIU, 2003-05.
  Summer Internship, Centocor Inc., 2006.
  Travel Award, GAA, 2004-05.
  Travel Award, College of Arts and Science, 2005.
  Travel Award, SCIS, FIU, 2007.
• M. Robinson
  CyberBridges CIARA Fellowship 2007.
  
• R. Ordonez
  MBRS-RISE Graduate Research Fellowship 2002-06.
• T. Milledge
  CyberBridges CIARA Fellowship 2006.
  IBM Co-op program, Summer and Fall 2006.
  MARC-ABR Summer Research Award, 2005.
• P. Buendia
  MBRS-RISE Graduate Research Fellowship 2002-06.
• C. Yang
  Summer Internship, Affymetrix Inc., 2005.
  Excellence Award, School of Computer Science, 2005-06.
  Best Presentation, 3rd Prize, Graduate Forum, 2004-05.
  Best Presentation, 1st Prize, Graduate Forum, 2003-04.
• G. Zheng
  IBM Co-op program, Summer and Fall 2006. MARC-ABR Summer Research Award, 2005.
  Dissertation Year Fellowship, Graduate School, FIU, 2005-06.
  Excellence Award, School of Computer Science, 2005-06.
  Summer Internship, Centocor Inc., 2004.
  DOE Travel Award, 2004.
  Summer Internship, GNF Research Institute, 2003.

Current Funding Sources

• NIH MBRS-SCORE (Title: Integrated Genomic Databases and Microarray Analysis) [PI: Narasimhan]
• NIH MBRS-SCORE (Title: Role of P. aeruginosa beta-lactamase genes)
• NSF CREST: Center for Research Excellence in Science and Technology (Subproject Title: Multi-dimensional and Multi-modal Data Modeling and Query Research )

Recently Completed Funded Projects

• NIH Pre-NPEBC: Bioinformatics Center for Excellence Planning Grant (Title: Bioinformatics for Mouse Phenotype Analysis)
• NIH MARC-U*STAR Institutes (Title: Quantifying Biology in the Classroom (The Q.BIC Plan))
• FIU ABR: Access to Biomedical Research (Title Software for Designing Degenerate Primers to Amplify Resistance Gene Homologues from T. Cacao) [PI: Narasimhan]
• FIU ABR: Access to Biomedical Research (Title Integrated Genomic Databases and Microarray Analysis ) [PI: Narasimhan]

Current Research Collaborators

• Prof. Segun George, Professor of Statistics, Mathematical Sciences Department, The University of Memphis, TN.
• Prof. Martin Handfield, Center for Molecular Microbiology and Department of Oral Biology, University of Florida, Gainesville.
• Prof. Sawsan Khuri, The Dr. John T. Macdonald Foundation Center for Medical Genetics, University of Miami School of Medicine, Miami, FL.
• Prof. David Kuhn, Department of Biological Sciences, Florida International University, Miami, FL.
• Prof. Stephen Lory, Professor, Harvard Medical School, Boston, MA.
• Prof. Kalai Mathee, Associate Professor, Department of Biological Sciences, Florida International University, Miami, FL.
• V. Renugopalakrishnan, BioFold Inc.
• Prof. Sanjeev Samant, Radiation Oncology, St. Jude Cancer Research Hospital.

Graduated Students

• Gaolin Zheng, PhD (Computer Science, 2006), M.S. (Bioinformatics, 2001). First Employment: Assistant Professor, North Carolina Central University, Durham, NC. E-mail: gzhengnccu.edu, PhD (Computer Science, 2006).
• Patricia Buendia, PhD (Computer Science, 2006). First Employment: Center for Computational Science & Dept of Biology, University of Miami, Miami, FL. E-mail: PBuendiamiami.edu, PhD (Computer Science, 2006).
• Chengyong Yang, PhD (Computer Science, 2006), First Employment: Algorithm Developer, Senior Engineer, Molecular and Cell Biology-RnD, Applied Biosystems Inc., Foster City, CA. E-mail: chengyong.yanglifetech.com, PhD (Computer Science, 2006).
• Yuan Gao, PhD (Computer Science, 2001), M.S. (Computer Science, 1998). Previous Employments: Bioinformatics and Pattern Discovery Group, IBM T.J.Watson Research Center, NY; and Postdoctoral Fellow, Harvard Medical School; Current Employment: Assistant Professor, Computer Science, Virginia Commonwealth University. Current E-mail: ygaovcu.edu.
• Minchi Hu, M.S. (Computer Science, 2004).
• Yong Wang, M.S. (Computer Science, 2003).
• Xintao Wei, M.S. (Computer Science, 2003).
• Dr. Xiao-rui He, M.D., Ph.D. (Physiology), M.S. (Bioinformatics, 2001).
• Junmin Liu, M.S. (Bioinformatics, 2001).
• Ning Xu, BD ClonTech Inc., San Jose, CA; E-mail: ningning_memyahoo.com, M.S. (Bioinformatics, 2000).
• Qichang Li, M.S. (Biomedical Engineering, 2000).
• Changsong Bu, Idax Inc., VA; E-mail: changsongbuyahoo.com, M.S. (Bioinformatics, 1999).
• Peter Dimitrov, First Employment: Genomics Institute of the Novartis Research Foundation, CA. E-mail: dimitrovgnf.org
• Hari Tammana, Human Transcriptome Project, Affymetrix, CA. E-mail: hari_tammanaaffymetrix.com, M.S. (Computer Science, 1998).
• Xuning Wang, Parke Davis Pharmaceutical Research, MI., M.S. (Computer Science, 1998).
• Dr. Zhou Ji, St. Jude Research Hospital, TN., M.S. (Computer Science, 2000).
• Dr. Meera Krishnan, Teacher for AP Biology, Ridgeway High School, M.S. Bioinformatics 2002.

Past Research Collaborators

• Dr. Tom Sutter, Professor and Feinstone Chair of Excellence, Molecular Microbiology and Cell Sciences, The University of Memphis, TN.
• Yuan Gao, Bioinformatics and Pattern Discovery Group, IBM T.J.Watson Research Center, NY. E-mail: yuan888_98hotmail.com.
• Dr. Isidore Rigoutsos, Manager, Bioinformatics and Pattern Discovery Group, IBM T.J.Watson Research Center, NY.
• Dr. Soren Molin, Professor, Molecular Microbial Ecology Group, Danish Technical University, Copenhagen, Denmark.

Important Bioinformatics Conferences

• CSB, RECOMB, ISMB, PSB, CAMDA, ICBA, WABI, IWBRA, AGBT, Biology of Genomes, CSHL, HUGO-HGM, ISPA, and more...