Roman Sutormin. Home Page


About me

CV

Publications

Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, Dehal P, Ware D, Perez F, Canon S, Sneddon MW, Henderson ML, Riehl WJ, Murphy-Olson D, Chan SY, Kamimura RT, Kumari S, Drake MM, Brettin TS, Glass EM, Chivian D, Gunter D, Weston DJ, Allen BH, Baumohl J, Best AA, Bowen B, Brenner SE, Bun CC, Chandonia JM, Chia JM, Colasanti R, Conrad N, Davis JJ, Davison BH, DeJongh M, Devoid S, Dietrich E, Dubchak I, Edirisinghe JN, Fang G, Faria JP, Frybarger PM, Gerlach W, Gerstein M, Greiner A, Gurtowski J, Haun HL, He F, Jain R, Joachimiak MP, Keegan KP, Kondo S, Kumar V, Land ML, Meyer F, Mills M, Novichkov PS, Oh T, Olsen GJ, Olson R, Parrello B, Pasternak S, Pearson E, Poon SS, Price GA, Ramakrishnan S, Ranjan P, Ronald PC, Schatz MC, Seaver SMD, Shukla M, Sutormin RA, Syed MH, Thomason J, Tintle NL, Wang D, Xia F, Yoo H, Yoo S, Yu D.
KBase: The United States Department of Energy Systems Biology Knowledgebase. Nat Biotechnol. 2018 Jul 6;36(7):566-569.
PubMed

Mazin PV, Shagimardanova E, Kozlova O, Cherkasov A, Sutormin R, Stepanova VV, Stupnikov A, Logacheva M, Penin A, Sogame Y, Cornette R, Tokumoto S, Miyata Y, Kikawada T, Gelfand MS, Gusev O.
Cooption of heat shock regulatory system for anhydrobiosis in the sleeping chironomid Polypedilum vanderplanki. Proc Natl Acad Sci U S A. 2018 Mar 6;115(10):E2477-E2486.
PubMed

Vinogradova SV, Sutormin RA, Mironov AA, Soldatov RA.
Probing-directed identification of novel structured RNAs. RNA Biol. 2016;13(2):232-42.
PubMed

Leushkin EV, Logacheva MD, Penin AA, Sutormin RA, Gerasimov ES, Kochkina GA, Ivanushkina NE, Vasilenko OV, Kondrashov AS, Ozerskaya SM.
Comparative genome analysis of Pseudogymnoascus spp. reveals primarily clonal evolution with small genome fragments exchanged between lineages. BMC Genomics. 2015 May 21;16:400.
PubMed

Denisov SV, Bazykin GA, Sutormin R, Favorov AV, Mironov AA, Gelfand MS, Kondrashov AS.
Weak negative and positive selection and the drift load at splice sites. Genome Biol Evol. 2014 May; 6(6):1437-47.
PubMed   Pdf

Novichkov PS, Kazakov AE, Ravcheev DA, Leyn SA, Kovaleva GY, Sutormin RA, Kazanov MD, Riehl W, Arkin AP, Dubchak I, Rodionov DA.
RegPrecise 3.0 -- A resource for genome-scale exploration of transcriptional regulation in bacteria. BMC Genomics. 2013 Nov; 14(1):745.
PubMed   Pdf

Leushkin EV, Sutormin RA, Nabieva ER, Penin AA, Kondrashov AS, Logacheva MD.
The miniature genome of a carnivorous plant Genlisea aurea contains a low number of genes and short non-coding sequences. BMC Genomics. 2013 Jul; 14(1):476.
PubMed   Pdf

Kurmangaliyev YZ, Sutormin RA, Naumenko SA, Bazykin GA, Gelfand MS.
Functional implications of splicing polymorphisms in the human genome. Hum Mol Genet. 2013 Sep; 22(17):3449-59. Epub 2013 May 2.
PubMed   Pdf

Nikulova AA, Favorov AV, Sutormin RA, Makeev VJ, Mironov AA.
CORECLUST: identification of the conserved CRM grammar together with prediction of gene regulation. Nucleic Acids Res. 2012 Jul; 40(12):e93. Epub 2012 Mar 15.
PubMed   Pdf

Sadovskaya NS, Sutormin RA, Gelfand MS.
Recognition of transmembrane segments in proteins: review and consistency-based benchmarking of internet servers. J Bioinform Comput Biol. 2006 Oct;4(5):1033-1056.
PubMed   Pdf

Sutormin RA, Mironov AA.
Membrane probability profile construction based on amino acids sequences multiple alignment. Mol Biol (Mosk). 2006 May-Jun;40(3):541-545.
PubMed   Pdf (english), (russian)

Kalinina OV, Makeev VJ, Sutormin RA, Gelfand MS, Rakhmaninova AB.
The channel in transporters is formed by residues that are rare in transmembrane helices. In Silico Biol. 2003;3(1-2):197-204.
PubMed   Pdf

Sutormin RA, Rakhmaninova AB, Gelfand MS.
BATMAS30: amino acid substitution matrix for alignment of bacterial transporters. Proteins. 2003 Apr 1;51(1):85-95.
PubMed   Pdf

Only in russian: Information Systems, 2002.
Pdf


Constructed data

BATMAS series of substitution matrices


PhD Thesis (dissertation work)

Main text (in russian)   Abstract (synopsis)


Some helpful classes

NibParser.java
TwoBitParser.java