Alexei Fedorov
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Associate Professor
Vice Director of Bioinformatics and Proteomics/Genomics Program, Medicine , College of Medicine and Life Sciences
Contact Info
Publications
selected publications
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Article (Faculty180)
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2017
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2017Strategies To Identify Common Low Effect COPD Risk Variants. American Journal of Respiratory and Critical Care Medicine. 195:1.
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2015Inference of distant genetic relations in humans using "1000 genomes". Genome Biol Evol. 7:481-92.
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2015Maruyama's allelic age revised by whole-genome GEMA simulations. Genomics. 105:282-7.
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2014
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2014Genome evolution by matrix algorithms: cellular automata approach to population genetics. Genome Biol Evol. 6:988-99.
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2013Vertebrate codon bias indicates a highly GC-rich ancestral genome. Gene. 519:113-9.
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2012Exploiting mid-range DNA patterns for sequence classification: binary abstraction Markov models. Nucleic Acids Res. 40:4765-73.
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2011Critical association of ncRNA with introns. Nucleic Acids Res. 39:2357-66.
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2011Mid-range inhomogeneity of eukaryotic genomes. ScientificWorldJournal. 11:842-54.
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2009Evolution of genomic sequence inhomogeneity at mid-range scales. BMC Genomics. 10:513.
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2009The peculiarities of large intron splicing in animals. PLoS One. 4:e7853.
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2008Calculation of splicing potential from the Alternative Splicing Mutation Database. BMC Res Notes. 1:4.
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2008Genomic mid-range inhomogeneity correlates with an abundance of RNA secondary structures. BMC Genomics. 9:284.
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2007An intronic signal for alternative splicing in the human genome. PLoS One. 2:e1246.
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2006Advances in the Exon-Intron Database (EID). Brief Bioinform. 7:178-85.
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2006Where is the difference between the genomes of humans and annelids?. Genome Biol. 7:203.
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2005Computer identification of snoRNA genes using a Mammalian Orthologous Intron Database. Nucleic Acids Res. 33:4578-83.
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2005Puzzles of the human genome: Why do we need our introns?. Current Genomics. 6:589-595.
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2004What does the microsporidian E. cuniculi tell us about the origin of the eukaryotic cell?. J Mol Evol. 59:695-702.
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2003Introns in gene evolution. Genetica. 118:123-31.
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2003Mystery of intron gain. Genome Res. 13:2236-41.
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2003Phylogenetically older introns strongly correlate with module boundaries in ancient proteins. Genome Res. 13:1155-7.
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2002Do introns favor or avoid regions of amino acid conservation?. Mol Biol Evol. 19:521-252.
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2002Large-scale comparison of intron positions among animal, plant, and fungal genes. Proc Natl Acad Sci U S A. 99:16128-33.
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2002Regularities of context-dependent codon bias in eukaryotic genes. Nucleic Acids Res. 30:1192-7.
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2002The origin of the eukaryotic cell: a genomic investigation. Proc Natl Acad Sci U S A. 99:1420-5.
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2001Comparison of intron-containing and intron-lacking human genes elucidates putative exonic splicing enhancers. Nucleic Acids Res. 29:1464-9.
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2001Footprints of primordial introns on the eukaryotic genome. Trends Genet. 17:496-501.
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2001Intron distribution difference for 276 ancient and 131 modern genes suggests the existence of ancient introns. Proc Natl Acad Sci U S A. 98:13177-82.
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2001
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2000EID: the Exon-Intron Database-an exhaustive database of protein-coding intron-containing genes. Nucleic Acids Res. 28:185-90.
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1998DNA Taxoprints of some Lacertidae lizards: taxonomic and phylogenetic implications. Molecular Biology. 32:151-160.
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1998Influence of exon duplication on intron and exon phase distribution. J Mol Evol. 46:263-71.
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1997
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1997
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1997Restriction endonuclease analysis of highly repeated DNA sequences sheds light on genetic relatedness of lower taxa of animals. Molecular Biology. 31:202-209.
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1997Restriction endonuclease analysis of highly repetitive DNA as a phylogenetic tool. J Mol Evol. 45:332-6.
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1995Comparison of DNA repeats elements of mammals fam. Erinacea using restriction analysis. Genetika (Russian). 31:1498-1506.
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1994
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1993DNA Taxoprint Analysis of Family Lacertidae Species. Molecular Biology. 27:883-890.
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1993[Study of the minimum frequency of phase 2 introns]. Mol Biol (Mosk). 27:519-30.
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1992Taxonomic analysis of DNA repeated sequences. Molecular biology. 26:361-365.
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1982Thermo-emf anomaly in lithium-magnesium alloys. Soviet Journal of Experimental and Theoretical Physics Letters. 35:462.
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Article (Web of Science)
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2020Global Picture of Genetic Relatedness and the Evolution of Humankind. BIOLOGY-BASEL. 9.Full Text via DOI: 10.3390/biology9110392 PMID: 33182715
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2020Adapting Biased Gene Conversion theory to account for intensive GC-content deterioration in the human genome by novel mutations. PLOS ONE. 15.Full Text via DOI: 10.1371/journal.pone.0232167 PMID: 32353016
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2020Genomic landscape of the signals of positive natural selection in populations of Northern Eurasia: A view from Northern Russia. PLOS ONE. 15.Full Text via DOI: 10.1371/journal.pone.0228778 PMID: 32023328
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20181000 human genomes carry widespread signatures of GC biased gene conversion. BMC GENOMICS. 19.Full Text via DOI: 10.1186/s12864-018-4593-1
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2017Intricacies in arrangement of SNP haplotypes suggest "Great Admixture" that created modern humans. BMC GENOMICS. 18.Full Text via DOI: 10.1186/s12864-017-3776-5
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2015Maruyama's allelic age revised by whole-genome GEMA simulations. GENOMICS. 105:282-287.Full Text via DOI: 10.1016/j.ygeno.2015.02.005
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2015Inference of Distant Genetic Relations in Humans Using "1000 Genomes". GENOME BIOLOGY AND EVOLUTION. 7:481-492.Full Text via DOI: 10.1093/gbe/evv003
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2014Bioinformatics analysis of plant orthologous introns: identification of an intronic tRNA-like sequence. GENE. 548:81-90.Full Text via DOI: 10.1016/j.gene.2014.07.012
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2014Genome Evolution by Matrix Algorithms: Cellular Automata Approach to Population Genetics. GENOME BIOLOGY AND EVOLUTION. 6:988-999.Full Text via DOI: 10.1093/gbe/evu075
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2013Vertebrate codon bias indicates a highly GC-rich ancestral genome. GENE. 519:113-119.Full Text via DOI: 10.1016/j.gene.2013.01.033
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2012Exploiting mid-range DNA patterns for sequence classification: binary abstraction Markov models. NUCLEIC ACIDS RESEARCH. 40:4765-4773.Full Text via DOI: 10.1093/nar/gks154
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2011Genomic MRI - a Public Resource for Studying Sequence Patterns within Genomic DNA. JOVE-JOURNAL OF VISUALIZED EXPERIMENTS.Full Text via DOI: 10.3791/2663
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2011Spliceosomal genes in the D. discoideum genome: a comparison with those in H. sapiens, D. melanogaster, A. thaliana and S. cerevisiae. PROTEIN & CELL. 2:395-409.Full Text via DOI: 10.1007/s13238-011-1052-z
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2011Critical association of ncRNA with introns. NUCLEIC ACIDS RESEARCH. 39:2357-2366.Full Text via DOI: 10.1093/nar/gkq1080
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2009The Peculiarities of Large Intron Splicing in Animals. PLOS ONE. 4.Full Text via DOI: 10.1371/journal.pone.0007853
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2009Evolution of genomic sequence inhomogeneity at mid-range scales. BMC GENOMICS. 10.Full Text via DOI: 10.1186/1471-2164-10-513
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2008Genomic mid-range inhomogeneity correlates with an abundance of RNA secondary structures. BMC GENOMICS. 9.Full Text via DOI: 10.1186/1471-2164-9-284
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2008snoTARGET shows that human orphan snoRNA targets locate close to alternative splice junctions. GENE. 408:172-179.Full Text via DOI: 10.1016/j.gene.2007.10.037
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Chapter (Faculty180)
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2011An Intricate Mosaic of Genomic Patterns at Mid-range Scale. Science, Engineering, and Biology Informatics. World Scientfiic Publishing Company.
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1991The investigation of mutant genes and human normal polymorphism. Metabolism and enzymology of nucleic acids including gene and protein engineering. Slovak Academy of Sciences. 7.
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1988Detection of beta-globin intron mutation in a beta-thalassemic patient from Azerbaijan. Metabolism and enzymology of nucleic acids including gene manipulations. Plenum Press. 6.
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Proceedings Paper (Web of Science)
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2009Computation of putative targets for human and mouse snoRNAs, responsible for Prader-Willi Syndrome.. 2009 OHIO COLLABORATIVE CONFERENCE ON BIOINFORMATICS, PROCEEDINGS. 58-58.Full Text via DOI: 10.1109/OCCBIO.2009.36
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Review Article (Web of Science)
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2011Mid-Range Inhomogeneity of Eukaryotic Genomes. THESCIENTIFICWORLDJOURNAL. 842-854.Full Text via DOI: 10.1100/tsw.2011.82
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Contact
full name
- Alexei Fedorov
visualizations
Cumulative publications in Scholars@UToledo