Публикации

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 SNPs. BMC Pulm Med. 2018;18(1):42. doi: 10.1186/s12890-018-0603-y. PMID: 29506519;

Dutta R, Saha-Mandal A, Cheng X, Qiu S, Serpen J, Fedorova L, Fedorov A. 1000 Human Genomes carry widespread signatures of GC biased gene conversion. BMC Genomics. 2018;19(1):256. doi: 10.1186/s12864-018-4593-1. PMID: 29661137

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.

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.

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

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.

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. PMID:24629165

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; PubMed PMID:24723728.

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.

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

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.

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.

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.

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):2357-2366.

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

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.

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

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, 10:2054

Sbv IMPROVER project team (in alphabetical order), Boue S, Fields B, Hoeng J, Park J, Peitsch MC, Schlage WK, Talikka M; Challenge Best Performers (inalphabetical order), Binenbaum I, Bondarenko V, Bulgakov OV, Cherkasova V, Diaz-Diaz N, Fedorova L, Guryanova S, Guzova J, Koroleva G, Kozhemyakina E, Kumar R, Lavid N, Lu Q, Menon S, Ouliel Y, Peterson SC, Prokhorov A, Sanders E, Schrier S, Schwaitzer Neta G, Shvydchenko I, Tallam A, Villa-Fombuena G, Wu J, Yudkevich I, Zelikman M. Enhancement of COPD biological networks using a web-based collaboration interface. F1000Res. 2015 Jan 29;4:32.

Liu J, Ramakrishan SK, Khuder SS, Eaw MK. Muturi HT, Lester SG, Lee SC, Lee SJ, Fedorova LV, Kim AJ, Mohamed IE, Gatto-Weis C, Eisenmann KM, Conrad PB, Najjar SM. High calorie diet exacerbates prostate neoplasia in mice with haploinsufficiency of PTEN tumor suppression gene. Mol Metab, 4(3), 186-98, 2014

Hinds TD Jr., Sodhi K, Meadow C, Fedorova L, Kim DH, Puri N, Peterson FJ, Shapiro JI, Abraham NG, Kappas A. Increased HO-1 levels ameliorate the development of fatty liver via reduction of heme and recruitment of FGF21. Obesity 2013 Jul 9. doi: 10.1002/oby.2055

Monu S, Pesce P, Sodhi K, Boldrin M, Fedorova L, Saserdoti D, Peterson S, Abraham NG, Kappas A. HO-1 induction improves type-1 cardio-renal syndrome in mice with impaired AngII-induced lymphocyte activation. Hypertension 2013 Aug;62(2):310-6

Fedorova LV*, Tamirisa A, Kennedy DJ, Haller ST, Budnyy G, Shapiro JI, Malhotra D. Mitochondrial impairment in the five-six nephrectomy model of chronic renal failure: proteomic approach. 2013, BMC Nephrology, 4;14(1):209. *Corresponding author.

Fedorova LV*, Sodhi K, Gatto-Weis C, Puri N, Hinds T Jr, Shapiro JI, Malhotra D, Peroxisome proliferator-activated receptor δ agonist, HPP593, prevents kidney cell death under ischemic hypoxia. 2013, PLoS ONE 8(5): e64436. doi:10.1371/journal.pone.0064436 *Corresponding author.

Fedorova L,* Gatto-Weis C, Smaili S, Khurshid N, Shapiro JI, Malhotra D and Horrigan T. Down-regulation of the transcription factor snail in the placentas of patients with preeclampsia and in a rat model of preeclampsia Reproductive Biology and Endocrinology, 2012, doi: 10.1186/1477-7827-10-15 *Corresponding author

Fedorova L.V., Raju V., El-Okdi N., Shidyak A., Kennedy D.J., Vetteth S., Giovannucci D.R., Bagrov A.Y., Fedorova O.V., Shapiro J.I., Malhotra D. The Cardiotonic Steroid Hormon Marinobufagenin Induces Renal Fibrosis. Implication of Epithelial to Mesenchymal Transition. Am J Physiol Renal Physiol. 2009, 296: F922-932

Elkareh J., Periyasamy S.M., Shidyak A., Vetteth S., Schroeder J., Raju V., Hariri I.M., El-Okdi N., Gupta S., Fedorova L., Liu J., Fedorova O.V., Kahaleh B.M., Xie Z., Malhotra D., Watson D.K., Bagrov A.Y., Shapiro J.I. Marinobufagenin Induces Increases in Procollagen Expression in a Process Involving Protein Kinase C and Fli-1: Implications for Uremic Cardiomyopathy. Am J Physiol Renal Physiol, 2009, 296(5):F1219-26

El-Okdi, N., Smaili, S., Raju, V., Shidyak, A., Gupta, S., Fedorova, L., Elkareh, J., Periyasamy, S., Shapiro, A., Kahaleh, M., Malhotra, D., Xie, Z., Chin, K-V., Shapiro, J. The Effects of Cardiotonic Steroids on Dermal Collagen Synthesis and Wound Healing. J Appl. Physiol. 2008, Jul;105(1):30-6

Lee, S.J., Heinrich, G., Fedorova, L., Al-Share, Q.Y., Ledford, K.J., Fernstrom, M.A., McInerney, M.F., Gatto-Weis, C., and Najjar, S.M. The Insulin Resistant L-SACC1 Mouse: A Novel Model of Non-Alcoholic Steatohepatitis. Gastroenterology 2008 Dec;135(6):2084-95.