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International Moscow Conference on Computational Molecular Biology MCCMB'2015 MCCMB'2015 International Moscow Conference on Computational Molecular Biology MCCMB'2015 PROGRAM Moscow, Russia July 16-19, 2015 1 MCCMB'2015 Short Program Thursday, 16 July 2015 9.00 Registration and morning coffee 10.00 (MSU, Biological Faculty) 10.00 Opening 10.10 (MSU, Biological Faculty, auditorium M1) Session: Bacterial genomics (M1) 10.10 Emergence of Membrane Bioenergetics from 10.50 Ancient Systems of Na+/K+ Homeostasis Armen Mulkidjanian 10.50 A universal signaling mechanism in bacterial 11.10 chemoreceptors Igor Zhulin 11.10 Genomic analysis of the respiration the microbiota 11.30 of human intestine Dmitry Ravcheev 11.30-12.00 Coffee break Session: Transcriptomics (M1) 12.00 Classifying transcriptional and genetic heterogeneity 12.40 in single-cell measurements Peter Kharchenko 12.40 Network integration of parallel metabolomic- 13.00 transcriptional data reveals novel metabolic modules regulating divergent macrophage polarization Maxim Artyomov 3 MCCMB'2015 13.00 Differential gene expression by RNA-seq data in 13.20 brain structures of laboratory animals with aggressive and tolerant behavior Yuriy Orlov 13.20-15.00 Lunch break Session: Replication and chromatin (M1) 15.00 Inferring direction of replication fork and mechanism 15.40 of DNA damage using sequencing data Maga Rowicka 15.40 APOBEC-induced mutations are strongly enriched on 16.00 the lagging strand during replication in human cancers Vladimir Seplyarsky 16.00 Diversity and Domestication in Oenological Yeasts 16.40 David Sherman 16.40-18.40 Coffee break and Poster session 18.40 Buses depart for the Conference dinner 19.00 19.00 Dinner 4 MCCMB'2015 Friday, 17 July 2015 09.00-10.00 Morning coffee 10.00 OMICS -2015 (Skolkovo satellite) 12.40 (MSU, Biological Faculty, auditorium M1 ) 10.10 Introduction Yuri Nikolsky 10.15 Introduction Pakhomov or Meyer 10.20 Introduction of Jury 10.30 Presentation of projects 12.10 Projects 1-10 12.10-12.40 Coffee break 12.40 OMICS -2015 (Skolkovo satellite) cont'd 15.00 (MSU, Biological Faculty, auditorium M1 ) 12.40 Presentation of projects 12.10 Projects 11-20 14.20 Jury Counting 14.40 14.40 Announcement of winners, presentation of awards, 15.00 conclusion 10.00 MoBiLe 10Y symposium (Leiden satellite) 13.00 (MSU, Faculty of Bioengineering and Bioinformatics, auditorium 221) 10.00 Welcome 10.10 A.E.Gorbalenya, A.Alexeevski 5 MCCMB'2015 10.10 Fast evolution of a conserved residue of 10.40 polyomaviruses defines a new mechanism of adaptation that operates by accelerated codon- constrained Val-Ala (COCO-VA) toggling within an intrinsically disordered protein region A.E.Gorbalenya 10.40 The impact of biological ageing on RNA processing 11.00 I.Pulyakhina, V.A.Takhaveev, M. Vermaat, M.S. Gelfand, J.F.J. Laros, P.A.C. 't Hoen, BIOS consortium 11.00 Probing-directed structured elements detection in 11.20 RNA sequences Svetlana Vinogradova 11.20 Mobilis in MoBiLe: Students in a Dynamic Research 11.50 Field O.A. Mayboroda 11.50-12.10 Coffee break 12.10 Novel insights in the regulation of mRNA 12.40 transcription, processing and translationthrough integration of mRNA sequencing data P.A.C. 't Hoen 12.40 Active chromatin regions are sufficient to define 13.00 borders of topologically associated domains in D. melanogaster interphase chromosomes E.Khrameeva, S.Ulyanov, A.Gavrilov, Yu.Shevelyov, M.Gelfand, and S.Razin 13.00-14.00 Lunch break 14.40 MoBiLe 10Y symposium (Leiden satellite) cont'd 15.50 (Faculty of Bioengineering and Bioinformatics, auditorium 221) 14.00 Alignment-free telomere length estimation from 14.30 whole genome NGS data S.M.Kielbasa 6 MCCMB'2015 14.30 A comparison of two methods for detection of 14.50 exceptional words in genomic sequences of prokaryotes Ivan Rusinov 14.50 Peptide search engine approach for detection of 15.10 translated mutations P.Sinitcyn, S.Tyanova, M.Mann and J.Cox 15.10 NPG-explorer: a new tool for nucleotide pangenome 15.30 construction and analysis of closely related prokaryotic genomes Boris Nagaev 15.30 O2PLS as an integrative tool in systems oncology 15.50 E.Nevedomskaya and H.Keun Session: Medical bioinformatics (MSU, Biological Faculty, auditorium M1) 15.20 Building a Sustainable Bioinformatics Program 15.50 Through Integrated Support Michael Tartakovsky 15.50 Network of the Country Tuberculosis Portals 16.20 Alexander Rosenthal Session: Cancer-1 (M1) 16.20 Deciphering gene interaction to explain tumor 17.00 progression Emmanuel Barillot 17.00-17.30 Coffee break Session: Cancer-2 (M1) 17.30 A model for scoring damaging mutations in the non- 17.50 coding tumoral genome based on germline and tumor data Jia Li 7 MCCMB'2015 17.50 Selection pressure on breast cancer somatic 18.10 mutations revealed by bioinformatics sequence analysis Ivan Kulakovskiy 18.10 Searching For Essential Cancer Proteins: Analysis Of 18.30 Hypomutated Genes In Skin Melanoma Mikhail Pyatnitskiy 18.30 Revealing mechanisms of cancer progression by 19.10 pan-cancer deconvolution of tumoral transcriptomes Andrei Zinovyev 8 MCCMB'2015 Saturday, 18 July 2015 09.00-10.00 Morning coffee Session: Methods and algorithms (M1) 10.00 Analysis of variation in 3000 rice genomes project 10.20 Tatiana Tatarinova 10.20 Distance-based profiling aids in evaluation of 10.40 ageing-related phenomena Ancha Baranova 10.40 Scaffold assembly based on genome rearrangement 11.00 analysis Max Alekseyev 11.00 A method for model comparison based on the 11.20 parameter sensitivity measures Ekaterina Myasnikova 11.20 Method to predict the percentage of cell types in 11.40 human blood Anna Igolkina 11.40-12.10 Coffee break Session: Systems biology: Mammals and beyond (M1) 12.10 Mammalian Systems biology 12.50 Alistar Forrest 12.50 Genomics of Lifespan Control 13.30 Vadim Gladyshev 13.30-15.00 Lunch break Session: Genomics of regulation (M1) 15.00 Computer analysis of genome co-localization of 15.20 transcription factor binding sites based on ChIP-seq data Arthur Dergilev 9 MCCMB'2015 15.20 Search for simple and composite auxin responsive 15.40 elements in Arabidopsis thaliana genome Victoria Mironova 15.40 Antisense interactions of long noncoding RNAs in 16.00 human cells Ivan Antonov Session: Viruses – 1 (M1) 16.00 Challenges in virus genomics 16.40 Manja Marz 16.40-17.10 Coffee break Session: Viruses – 2 (M1) 17.10 Sequence and structural analysis of related proteins 17.30 in distant viral species Olga Kalinina Session: Proteins (M1) 17.30 Bioinformatic analysis of diverse protein 17.50 superfamilies to design improved enzymes Dmitry Suplatov 17.50 Detecting the features of functional specificity in 18.10 protein families based on the local sequence similarity Boris Sobolev 18.10 Determination of the size of folding nuclei of 18.30 protofibrils from the concentration dependence of the rate and lag-time of their formation Oxana Galzitskaya 18.30 Assessing protein synthesis with ribosome profiling 19.10 Pavel Baranov 10 MCCMB'2015 Sunday, 19 July 2015 09.00-10.00 Morning coffee Session: Genomics of anhydrobiosis (M1) 10.00 Anhydrobiosis in the sleeping chironomids: where 10.40 are we now Takahiro Kikawada 10.40 Expression regulation of desiccation-resistance 11.00 genes in Polypedilum vanderplanki Pavel Mazin 11.00 Molecular basics of different mechanisms of 11.20 desiccation tolerance in Chironomidae midges Olga Kozlova 11.20 Adapting to extremes: linking metabolome and 11.40 genome of an anhydrobiotic insects Elena Shagimardanova 11.40-12.10 Coffee break Session: Toolkits for anhydrobiosis research (M1) 12.10 Single cell molecular toolkit for inducible resistance 12.50 to complete desiccation Oleg Gusev 12.50 Genetic toolkit for investigation of anhydrobiosis: 13.30 promoters and RNAi Richard Cornette 13.30-15.00 Lunch break Session: Genome structure (M1) 15.00 Genome mapping revealed scaffold misassemblies 15.20 and elevated gene shuffling on the X chromosome in malaria mosquitoes Igor Sharakhov 11 MCCMB'2015 15.20 Detection of short size mutations and copy number 15.40 alterations in ultra-deep targeted sequencing data Valentina Boeva 15.40 Genomic structural instability and homologous 16.00 recombination deficiency in breast and ovarian cancers Tatiana Popova 16.00 Genome Track Analyzer : New tool for genome-wide 16.20 study of correlations between distributed genome features Galina Kravatskaya 16.20 Tale on the transposons on chromatin landscape 16.40 Vladimir Babenko 16.40-17.10 Coffee break Session: Evolution (M1) 17.10 Assessing the impact of horizontal gene transfer on 17.30 the evolution of prokaryotes Vladimir Makarenkov 17.30 Rare amino acid changes fixation drives divergence 17.50 in Metazoa evolution Konstantin Gunbin 17.50 Evolution of TAG codon in Methanosarcina 18.10 Margarita Meer 18.10 A model of protein evolution within local fitness 18.30 landscape changing with time Dinara Usmanova 18.30 Chartering the local fitness landscape of the green 19.10 fluorescent protein Fedor Kondrashov 19-10-19.20 Closing 19.30 Farewell party 12 MCCMB'2015 Extended Program Thursday, 16 July 2015 9.00 Registration and morning coffee 10.00 (MSU, Biological Faculty) 10.00 Opening 10.10 (MSU, Biological Faculty, auditorium M1) Session: Bacterial genomics (M1) 10.10 Emergence of Membrane Bioenergetics from 10.50 Ancient Systems of Na+/K+ Homeostasis Armen Mulkidjanian It is well known that the cytoplasm of living cells, generally, contains more potassium ions than sodium ions. The prevalence of K+ ions is crucial for the activity of numerous (nearly) universal, key enzymes, including those components of the translation system that even preceded the Last Universal Cellular Ancestor (LUCA). In modern prokaryotic cells, the [K+]/[Na+] ratio > 1.0 is maintained by ion-tight cellular membranes and an arsenal of ion pumps. It is unlikely that modern-type ion-tight membranes made of two- tail lipids, not to mention a plethora of ion- pumping machines, were present in the very first cells.
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