2024

51. Crossley ER, Fedorova L, Mulyar OA, Freeman R, Khuder S, Fedorov A. Computational identification of ultra-conserved elements in the human genome: a hypothesis on homologous DNA pairing NAR Genom Bioinform. 2024 Jul 2;6(3):lqae074. doi: 10.1093/nargab/lqae074. eCollection 2024 PMID: 38962254

2023

50. Fedorova L,Crossley ER, Mulyar OA, Qiu S, Freeman R, Fedorov A. Profound Non-Randomness in Dinucleotide Arrangements within Ultra-Conserved Non-Coding Elements and the Human Genome Biology (Basel).2023 Aug 12;12(8):1125. doi: 10.3390/biology12081125. PMID: 37627009

2022

49. Fedorova L, Mulyar OA, Lim J, Fedorov A. Nucleotide Composition of Ultra-Conserved Elements Shows Excess of GpC and Depletion of GG and CC Dinucleotides Genes (Basel). 2022 Nov 7;13(11):2053. doi: 10.3390/genes13112053; PMID: 36360290

48. Fedorova L, Khrunin A, Khvorykh G, Lim J, Thornton N, Mulyar OA, Limborska S, and Fedorov A. Analysis of common SNPs across continents reveals major genomic differeneces between human populations GENES (Basel) 2022, 13, 1472 : e0232167. https://doi.org/10.3390/genes.13081472.

2020

47. Khvorykh GV, Mulyar OA, Fedorova L, Khrunin AV, Limborska SA, and Fedorov A. Global Picture of Genetic Relatedness and the Evolution of Humankinds Biology (Basel) 2020; 9(11):392. doi: 10.3390/biology9110392

46. Paudel R, Fedorova L, and Fedorov A. Adapting Biased Gene Conversion theory to account for intensive GC-content deterioration in the human genome by novel mutations PLoS ONE 2020, 15(4): e0232167. https://doi.org/10.1371/journal.pone.0232167.

2019

45. Khrunin AV, Khvorykh GV, Fedorov A, and Limborska SA. Genomic landscape of signals of positive natural selection in populations of North Eurasia: a view from Northern Russia PLoS ONE 2020, 15(2):e0228778. doi: 10.1371/journal.pone.0228778.

2018

44. Yeo J, Morales DA, Chen T, Crawford EL, Zhang X, Blomquist TM, Levin AM, Massion PP, Arenberg DA, Midthun DE, Mazzone PJ, Nathan SD, Wainz RJ, Nana-Sinkam P, Willey PFS, Arend TJ, Padda K, Qiu S, Fedorov A, Hernandez DR, Hammersley JR, Yoon Y, Safi F, Khuder SA, Willey JC. RNAseq analysis of bronchial epithelial cells to identify COPD-associated genes and SNPsBMC Pulm Med. 2018;18(1):42. doi: 10.1186/s12890-018-0603-y. PMID: 29506519

43. Dutta R, Saha-Mandal A, Cheng X, Qiu S, Serpen J, Fedorova L, and Fedorov A. Human Genomes carry widespread signatures of GC biased gene conversionBMC Genomics. 2018;19(1):256. doi: 10.1186/s12864-018-4593-1. PMID: 29661137

2017

42. Dutta R, Mainsah J, Yatskiv Y, Chakrabortty S, Brennan P, Khuder B, Qiu S, Fedorova L, and Fedorov A. Intricacies in arrangement of human common haplotypes suggest “Great Admixture” that created modern people BMC Genomics, 2017 Jun 5;18(1):433, PMID: 28583085

2016

41. Fedorova L, Qiu S, Dutta R, and Fedorov A. Atlas of cryptic genetic relatedness among 1000 human genomes Genome Biol Evol 8:777-790, 2016.

2015

40. Qiu S and Fedorov A. “Maruyama’s allelic age revised by whole-genome GEMA simulations” Genomics 105:282-287, 2015.

39. Al-Khudhair A, Qiu S, Wyse M, Chowdhury S, Cheng X, Bekolsynov D, Fedorova L, Fedorov A. An exhaustive computation of the differences between 1092 sequenced human genomes. “Inference Of Distant Genetic Relations In Humans Using “1000 Genomes” Genome Biol Evol 7:481-492, 2015.

2014

38. Gorlova O, Fedorov A, Logothetis C, Amos C, and Gorlov I. Genes with a large intronic burden show greater evolutionary conservation at the protein level. BMC Evolutionary Biology. 2014,14(1):50.

37. Qiu S, Mcsweeny A, Choulet S, Saha-Mandal A, Fedorova L, and Fedorov A. Genome Evolution by Matrix Algorithms (GEMA): Cellular Automata Approach to Population Genetics. Genome Biol Evol. 2014, 6(4):988–999.

36. Akkuratov E, Walters L, Saha-Mandal A, Khandekar S, Crawford E, Zirbel CL, Leisner S, Prakash A, Fedorova L, Fedorov A. “Bioinformatics analysis of plant orthologous introns: identification of an intronic tRNA-like sequence”. GENE, 2014, 548:81-90.

2013

35. Nabiyouni M., Prakash A., Fedorov A. "Vertebrate codon bias suggest a highly GC-rich ancestral genome." Gene, 2013;519(1):113-119.

2012

34. Shepard S., McSweeny A., Serpen G., Fedorov A. "Binary-absrtacted Markov models and their application to sequence classification." Nucleic Acids Research, 2012, 40(11):4765-4773.

2011

33. Yu B, Fey P, Kestin-Pilcher KE, Fedorov A, Prakash A, Chisholm RL, Wu JY. Spliceosomal genes in the D. discoideum genome: a comparison with those in H. sapiens, D. melanogaster, A. thaliana and S. cerevisiae. Protein Cell. 2011, May;2(5):395-409.

32. Prakash A., Bechtel J., Fedorov A. “Genomic MRI – a public resource for studying sequence patterns within genomic DNA”. J Vis Exp. 2011; 9;(51). pii: 2663..

31. Rearick D., Prakash A., McSweeny A., Shepard S.S., Fedorova L., and Fedorov A. “Critical association of ncRNA with introns” Nucleic Acids Research, 2011;39(6):2357-66.

30. Fedorova L. and Fedorov A. “Mid-range Inhomogeneity of Eukaryotic Genomes” TheScientificWorld Journal: Genes & Genomics. 2011, 11:842-854.

29. Fedorov A., Fedorova L. “An Intricate Mosaic of Genomic Patterns at Mid-range Scale” Chapter for a book “Advances in Genome Sequence Analysis and Pattern Discovery”. Science, Engineering, and Biology Informatics, Vol. 7; Eds: L. Elnitski, H. Piontkivska, and L.R.Welch. World Scientific Publishing Co. Pte. Ltd. Singapore, 2011.

2009

28. Shepard S., McCreary M., Fedorov A. “The peculiarities of large intron splicing in animals”, PLoS ONE, 2009, 4(11):e7853.

27. Prakash A., Shepard S., Mileyeva-Biebesheimer O., He J., Hart B., Chen M., Amarachiniha S., Bechtel J., Fedorov A. “Molecular forces shaping human genomic sequence at mid-range scales”, BMC Genomics 2009, 10:513.

2008

26. Bechtel J.M., Wittenschlaeger T., Dwyer T., Song J., Arunachalam S., Ramakrishnan S.K., Shepard S., Fedorov A. Genomic mid-range inhomogeneity correlates with an abundance of RNA secondary structures. BMC Genomics 2008, 9:284.

25. Bechtel J. M., Rajesh P., Ilikchyan I., Deng Y., Mishra P.K., Wang G., Wu X., Afonin K., Grose W., Wang Y., Khuder S., and Fedorov A. Calculation of Splicing Potential from the Alternative Splicing Mutation Database Research Notes 2008, 1:4.

24. Bechtel J. M., Rajesh P., Ilikchyan I., Deng Y., Mishra P.K., Wang G., Wu X., Afonin K., Grose W., Wang Y., Khuder S., and Fedorov A. The Alternative Splicing Mutation Database: a hub for investigations of alternative splicing using mutational evidence. Research Notes 2008, 1:3.

23. Bazeley P.S., Shepelev V., Talebizadeh Z., Butler M.G., Fedorova L., Filatov V., Fedorov A. noTARGET shows that human orphan snoRNA targets locate close to alternative splice junctions. Gene 2008, 408:172-179.

2007

22. Havlioglu N., Wang J., Fushimi K., Vibranovski M.D., Kan Z., Gish W., Fedorov A., Long M., Wu J.Y. An intronic signal for alternative splicing in the human genome. PloS ONE 2007, 11:e1246.

2006

21. 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.

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

19. Shao X., Shepelev V., Fedorov A. Bioinformatc analysis of exon repetition, exon scrambling and trans-splicing in humans. Bioinformatics 2006, 22:692-698.

2005

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

17. 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.

2004

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

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

2003

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

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

12. 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)

10. 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.

2002

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

8. Roy S., Fedorov A., Gilbert W. The signal of ancient introns is obscured by intron density and homolog number. PNAS 2002, 99, 15513-15517.

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

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

5. Endo T., Fedorov A., DeSouza S., Gilbert W. Do introns favor or avoid regions of amino acid conservation? Mol.Biol.Evol. 2002, 19, 521-525.

2001

4. Roy S., Lewis B., Fedorov A., Gilbert W. Footprints of primordial introns on the eukaryotic genome TIG 2001, 17, 496-499.

3. 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.

2. Fedorova L., Daizadeh I., Fedorov A., Ryskov A.P. In silico analysis of the restriction fragment length distribution of the human genome. Genetika (Russian) 2001, 37, 456-466.

1. Fedorov A., Saxonov S., Fedorova L., Daizadeh I. Comparison of intron-containing and intron-lacking genes elucidates putative exonic splicing enhancers. Nucl. Acids Res. 2001, v. 29, 1464-1469.