College of Medicine
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University of Nebraska Medical Center
Home — College of Medicine — Department of Genetics, Cell Biology and Anatomy — Research — Guda Lab — Education

Education

I have been teaching bioinformatics courses for the past 15 years and I have a strong record in developing bioinformatics curriculum and new certification or graduate programs in bioinformatics. I have developed and taught a number of graduate-level courses in bioinformatics at SUNY-Albany and UNMC. I also developed the core curriculum for a ‘Bioinformatics Certification Program’ in 2001 at University of California San Diego extension (UCSD Ext.) and received the ‘Instructor of the year award’ in 2003 from this program.

Recently, I played a key role in the development of newly approved Biomedical Informatics (BMI) graduate program, which is a joint program between UNMC and UNO (University of Nebraska at Omaha) campuses. Currently, I serve as a member of the Joint BMI Graduate Program Coordination Committee, and also as the Director of the Bioinformatics Track in the BMI program at UNMC. Currently, I supervise six PhD students in my laboratory.

Teaching

Courses taught at UNMC
  • GCBA 815: Tools and Algorithms in Bioinformatics
    2013-current
  • PHAR 820:Current Methods in Neurosciences
    2012-current
  • GCBA 815: Introductory Workshop on Bioinformatics
    2011-2012
  • GCBA 915: Advanced Workshop on Bioinformatics
    2012-2013
Courses taught at SUNY-Albany
  • Principles of Bioinformatics (BIO540)
    2005-2009
  • Advanced Topics in Bioinformatics (STA670/BIO603/CSI660)
    2006-2010
  • Introductory Workshop on Bioinformatics
    2008-2010
Teaching Experience at University of California, San Diego

"Instructor of the year 2002"award from the Department of Biosciences, UCSD Extension

  • Tools and Algorithms in Bioinformatics
    2001-2004
  • Advanced Tools and Algorithms in Bioinformatics
    2002-2004
  • Protein Data Analysis and Modeling in Bioinformatics
    2000-2002
Workshops & Tutorials
  • Bioinformatics On-site Training at Pfizer, La Jolla, CA
    2004
  • Introduction to Bioinformatics at Intelligent Enterprise Solutions, Inc., San Jose, CA
    2003
  • Bioinformatics Tutorial at International Conference on Computers and its Applications, San Diego, CA
    2003
  • Speaker, Workshop on Computer-Aided Drug Design, UCSD Extension La Jolla, CA
    2001 

Useful Links

Major Data Submission Centers
  • NCBI (National Center for Biotechnology Information)
  • EBI (European Bioinformatics Institute)
  • RCBI/PDB (Research Collaboratory for Structural Bioinformatics)
Archival or Primary Databases
  • GenBank at NCBI
  • UNIPROT at EBI (previously SWISS-PROT and TrEMBL)
  • PDB (Protein Data Bank) at RCSB -Structural Database
Sequence Databases
  • PROSITE (A database of protein profiles and patterns)
  • PRODOM (ThePROteinDOMain Database-built from UNIPROT)
  • PFAM (Protein families database of alignments and HMMs)
  • BLOCKS (Blocks WWW Server obtained from PROSITE)
  • INTERPRO (Integrated Resource of Protein Domains and Functional Sites)
  • Integr8 (Integrated browser to access complete genomes and proteomes at EBI)
Structure Databases
  • CATH (Class Architecture, Topology & Homologous super family)
  • SCOP (Structural Classification of Proteins)
  • FSSP (Fold classification based on Structure-Structure alignment of Proteins)
  • HSSP (A database of Homology-derived Secondary Structure of Proteins)
  • HOMSTRAD (Homologous Structure Alignment Database)
  • DSSP (Database of Secondary Structure Assignments)
  • VAST (Vector Alignment Search Tool)
Specialized Databases/Web Resources
  • UCSC Genome Browser
  • Ensembl Genome Browser
  • GO (The Gene Ontology)
  • KEGG (Kyoto Encyclopedia of Genes and Genomes)
  • OMIM (Online Mendelian Inheritance in Man)
  • ENZYME (Enzyme Nomenclature Database)
  • BRENDA (Comprehensive Enzyme Database)
  • PMD (Protein Mutant Database)
  • COG (Clusters of Orthologous Groups of proteins)
  • DIP (Database of Interacting proteins)
Useful Tools
  • BLAST (Pair-wise sequence alignment tools)
  • CLUSTALW (Multiple sequence alignment tool)
  • CD-HIT (Protein sequence clustering tool)
  • PROFILEMAKE (Builds profiles for sequence families)
  • HMMER (Software suite for sequence analysis using HMMs)
  • PHYLIP (Software suite for phylogenetic analysis)
  • PIPMAKER (Software suite for sequence comparison)
  • MVIEW (Multiple sequence alignment viewer)
  • JALVIEW (Multiple sequence alignment viewer and editor)
Data Formats
Interesting Bioinformatics Resources
Suggested Reading