Program in Bioinformatics & Proteomics/Genomics

Alexei Fedorov, Ph.D.

Associate Professor of Medicine
Director of Bioinformatics Lab
The University of Toledo
3000 Arlington Avenue
Toledo, OH 43614-5809
Phone: (419) 383-5270
FAX: (419) 383-3102

E-mail Address:

BPG Course Director:
BIPG6100/7100 Intro to Bioinformatic Computation, Spring Semester
BIGP6400/8400 Applications of BPG, Spring Semester
BIPG5400/7400 Intro to Modern Biomedical Databases, Summer Semester




- Origin and evolution of introns.
- Computer mining of novel genes.
- Prediction of constitutive and alternative splicing.
- Information content of genes beyond the coding meaning – codon bias
  and context-dependent codon bias. How are these biases created and maintained?
- Principles of genome organization.

Alternative Splicing Mutation Database (ASMD)

Genomic Mid-Range Inhomogeneity (GMRI) Program



Full version of Curriculum Vita (in PDF format)

REPRESENTATIVE PUBLICATIONS (pdf available by clicking on link):

1.  Fedorov A., Fedorova L.  Where is the difference in the genomes of humans and annelids?  Genome Biology 2006, Vol. 7, No. 1, Article 203, pp 1-2.

2.  Fedorova L., Fedorov A.  Puzzles of the human genome:  why do we need our introns?  Current Genomics 2005, Vol. 6, No 8, 589-595.

3.  Shepelev V., Fedorov A. Advances in the Exon-Intron Database (EID).  Briefings in Bioinformatics 2006, 7:  178-185.

4.  Shao X., Shepelev V., Fedorov A. Bioinformatic analysis of exon repetition, exon scrambling and transplicing in humans.  2005.  Bioinformatics.  (ahead of print; see on-line PubMed:  16308355).

5.  Fedorov A, Stombaugh J., Harr M.W., Yu S., Nasalean L., Shepelev V. Computer identification of snoRNA genes using a Mammalian Orthologous Intron Database.  Nucl. Acids Res.  2005. 33, 4578-4583.

6.  Fedorov A., Fedorova L.  Introns:  mighty elements from RNA world.  J. Molec Evol.   2004, 59, 718-721.

7.  Fedorov A. and Hartman H.  What does microsporidian E.cuniculi tell us about the origin of eukaryotic cell? J. Molec Evol.  2004, 59, 695-702.

8.  Fedorov A., Roy S., Fedorova L., Gilbert W. Mystery of intron gain.  Genome Research 2003, 13, 2236-2241.

9.  Fedorov A., Federova L. Exonic splicing enhancers.  2003 in Encyclopedia of the Human Genome, Nature Publishing Group, London, v 2, 386-391.

10.  Fedorova L., Fedorov A.  Introns in gene evolution.  Genetica 2003, 118:123-131.

11.  Roy S*., Fedorov A*.,  Gilbert W. Large-scale comparison of intron positions in mammalian genes shows intron loss but no gain.  PNAS, 2003, 100: 7158-7162.  (*equal contribution)

12.  Fedorov A., Roy S., Cao X., Gilbert W. Phylogenetically older introns strongly correlate with module boundaries in ancient proteins.  Genome Research 2003, 13:  1155-1157.

13.  Fedorov A., Merican A.F., Gilbert W. Large-scale comparison of intron positions between plant, animal and fungal genes.  PNAS, 2002, 99, 16128-16133.

14.  Hartman H. & Fedorov A. The origin of the eukaryotic cell - a genomic investigation.  PNAS 2002, 99, 1420-1425.

15.  Fedorov A., Saxonov S., Gilbert W. Regularities of context-dependent codon bias in eukaryotic genes.  Nucl. Acids Res. 2002, 30 (5), 1192-1197.

16.  Fedorov A., Cao, X., Saxonov S., DeSouza S., Roy S.W., Gilbert W. Intron distribution difference for 276 ancient and 131 modern genes suggests the existence of ancient introns.  PNAS 2001, 98, 13177-13182.

17.  Fedorov A., Saxonov S., Federova L., Daizadeh I. Comparison of intron-containing and intron-lacking genes elucidates putative exonic splicing enhancers.  Nucl. Acids Res. 2001, v. 1464-1469.

Last Updated: 3/22/15