Research Topics
| Alexei FedorovSummaryAffiliation: Medical University of Ohio Country: USA Publications
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Detail Information
Publications
Computer identification of snoRNA genes using a Mammalian Orthologous Intron DatabaseAlexei Fedorov
Department of Medicine, Program in Bioinformatics and Proteomics Genomics, Medical University of Ohio, Toledo, OH 43614, USA
Nucleic Acids Res 33:4578-83. 2005..One case represented a novel snoRNA gene, and another three cases, putative snoRNAs. Our programs are publicly available and can be easily adapted and/or modified for searching any conserved motifs within mammalian introns...- Where is the difference between the genomes of humans and annelids?Alexei Fedorov
Department of Medicine, Medical University of Ohio, Toledo, OH 43614, USA
Genome Biol 7:203. 2006..For hundreds of millions of years vertebrates have preserved exon-intron structures descended from their last common ancestor with the annelids... - The peculiarities of large intron splicing in animalsSamuel Shepard
Department of Medicine, University of Toledo, Toledo, Ohio, USA
PLoS ONE 4:e7853. 2009.... - Advances in the Exon-Intron Database (EID)Valery Shepelev
Department of Medicine and Program in Bioinformatics and Proteomics/Genomics, Medical University of Ohio, Toledo OH 43614, USA
Brief Bioinform 7:178-85. 2006..This fact is due to a combination of biological reasons and also to errors in sequence annotations. The EID is freely available at www.meduohio.edu/bioinfo/eid/... - Bioinformatic analysis of exon repetition, exon scrambling and trans-splicing in humansXiang Shao
Department of Medicine and Program in Bioinformatics and Proteomics/Genomics, Medical University of Ohio, Toledo, 43614, USA
Bioinformatics 22:692-8. 2006..meduohio.edu/bioinfo/software.html. The Laboratory website is available at http://www.meduohio.edu/medicine/fedorov Supplementary information: Supplementary file is available at http://www.meduohio.edu/bioinfo/software.html... - Critical association of ncRNA with intronsDavid Rearick
University of Toledo Health Science Campus, University of Toledo Health Science Campus, University of Toledo Health Science Campus, Toledo, OH 43614, USA
Nucleic Acids Res 39:2357-66. 2011..We propose that such an association between human introns and ncRNAs has a pronounced synergistic effect with important implications for fine-tuning gene expression patterns across the entire genome... - Genomic mid-range inhomogeneity correlates with an abundance of RNA secondary structuresJason M Bechtel
Program in Bioinformatics and Proteomics Genomics, University of Toledo Health Science Campus, Toledo, OH 43614, USA
BMC Genomics 9:284. 2008..A separate genomic issue that has yet to be thoroughly elucidated is the role that RNA secondary structure (SS) plays in gene expression... - snoTARGET shows that human orphan snoRNA targets locate close to alternative splice junctionsPeter S Bazeley
Program in Bioinformatics and Proteomics Genomics, University of Toledo Health Science Campus, Toledo, OH 43614, USA
Gene 408:172-9. 2008..The snoTARGET resource is freely available at: (http://hsc.utoledo.edu/depts/bioinfo/snotarget.html)... - Mid-range inhomogeneity of eukaryotic genomesLarisa Fedorova
Department of Medicine, University of Toledo, Health Science Campus, Toledo, Ohio, USA
ScientificWorldJournal 11:842-54. 2011.... - What does the microsporidian E. cuniculi tell us about the origin of the eukaryotic cell?Alexei Fedorov
Department of Medicine, Medical College of Ohio, Toledo OH 43614, USA
J Mol Evol 59:695-702. 2004..cuniculi, a minimal eukaryotic cell that has removed all inessential proteins, still preserves most of the ESPs that make it a member of the Eukarya. The locations and functions of these ESPs point to the earliest history of eukaryotes... - Mystery of intron gainAlexei Fedorov
Department of Medicine, Medical College of Ohio, Toledo, Ohio 43614, USA
Genome Res 13:2236-41. 2003..elegans, or in 5 million years in Arabidopsis. Either new introns do not arise via transposition of other introns or intron transposition must have occurred so early in evolution that all traces of homology have been lost... - Evolution of genomic sequence inhomogeneity at mid-range scalesAshwin Prakash
Program in Cardiovascular and Metabolic Diseases Track, Biomedical Sciences, Toledo, OH 43614, USA
BMC Genomics 10:513. 2009..g. A+G and G+T) as well as for individual bases. Various types of MRI regions are 4-20 times enriched in mammalian genomes compared to their occurrences in random models... - Regularities of context-dependent codon bias in eukaryotic genesAlexei Fedorov
Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
Nucleic Acids Res 30:1192-7. 2002..Codons with the same nucleotides in the second and third positions and the same N1 context have a statistically significant correlation of their relative abundances... - Do introns favor or avoid regions of amino acid conservation?Toshinori Endo
The Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts 02138, USA
Mol Biol Evol 19:521-252. 2002.... - Large-scale comparison of intron positions among animal, plant, and fungal genesAlexei Fedorov
Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
Proc Natl Acad Sci U S A 99:16128-33. 2002.... - The origin of the eukaryotic cell: a genomic investigationHyman Hartman
Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Proc Natl Acad Sci U S A 99:1420-5. 2002..This formation of the nucleus would restore the three cellular domains as the Chronocyte was not a cell that belonged to the Archaea or to the Bacteria... - Phylogenetically older introns strongly correlate with module boundaries in ancient proteinsAlexei Fedorov
Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
Genome Res 13:1155-7. 2003.... - Large-scale comparison of intron positions in mammalian genes shows intron loss but no gainScott W Roy
Biological Laboratories, 16 Divinity Avenue, Cambridge, MA 02138, USA
Proc Natl Acad Sci U S A 100:7158-62. 2003.... - Introns in gene evolutionLarisa Fedorova
Vision Research Laboratories, New England Medical Center, Tufts University School of Medicine, Boston, MA 02111, USA
Genetica 118:123-31. 2003..Each has provided insight: the latter through elucidating the transposon capabilities of introns, and the former through understanding the importance of introns in genomic recombination leading to gene rearrangements and evolution... - Introns: mighty elements from the RNA worldAlexei Fedorov
J Mol Evol 59:718-21. 2004..We propose that ancient introns could act as markers of RNA subsets, directing them to different functions... - The signal of ancient introns is obscured by intron density and homolog numberScott William Roy
Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
Proc Natl Acad Sci U S A 99:15513-7. 2002..This finding matches the expectation of the mixed model of intron origin, in which a fraction of phase zero introns are left from the assembly of the first genes, while other introns have been added in the course of evolution... - An intronic signal for alternative splicing in the human genomeNecat Havlioglu
Department of Pathology, Saint Louis University, St Louis, Missouri, United States of America
PLoS ONE 2:e1246. 2007..Together, these results suggest that the In100-like elements represent a family of intronic signals for alternative splicing in the human genome...