MCCMB 2015: Proceedings
BACK		A B C D E F G H I J K L M N O P Q R S T U V W X Y Z A up Irina Abnizova, Natalia Safronova, Rene Te Boekhorst, Vladimir Babenko, Irina Medvedeva, Yuriy Orlov Context analysis of SNP containing sites in mammalian genomes Evgeniy Aksianov, Andrey Alexeevski Sequence alignment of non-superposable beta-sheets Max Alekseyev, Sergey Aganezov Scaffold assembly based on genome rearrangement analysis Anton Alexandrov, Maxim Artyomov Computational prediction of MHC class I tumorÒ-specific antigens Andrei Alexeevski, Boris Nagaev, Maxim Nikolaev NPGe, a new tool for closely related genomes alignment and analysis Alexander Andrianov, Ivan Kashyn, Alexander Tuzikov Molecular Dynamics Simulations to Identify the Binding Hot Spots of the HIV-1 Coat Protein GP41 and Broadly Neutralizing Antibody 10E8 Alexander Andrianov, Ivan Kashyn, Alexander Tuzikov Computer-Aided Identification of Small-Molecule HIV-1 Entry Inhibitors Mimicking Cellular Receptor CD4 Alexander Andrianov, Ivan Kashyn, Alexander Tuzikov Virtual Screening of Novel Anti-HIV-1 Agents Based on a Broadly Neutralizing Antibody VRC01 and Evaluation of Their Potential Inhibitory Activity by Molecular Docking and Dynamics Simulations Ivan Antonov, Mikhail Skoblov Antisense interactions of long noncoding RNAs in human cells Maxim Artyomov, Abhishek Jha, Stanley Ching-cheng Huang, Alexey Sergushichev, Vicky Lampropoulou, Yulia Ivanova, Ekaterina Loginicheva, Karina Chmielewski, Kelly Stewart, Juliet Ashall, Bart Everts, Edward Pearce, Edward Driggers Network integration of parallel metabolomic-transcriptional data reveals novel metabolic modules regulating divergent macrophage polarization B up Vladimir Babenko, Vladimir Matvienko Tale on the transposons on chromatin landscape Haihua Bai, Qizhu Wu, Huiguang Wu, Gegentana Gegentana, Wenyan Huo, Suyalatu Suyalatu, Nuomin Wu, Ming Chen Identification of the susceptibility gene loci associated with ischemic stroke in a Mongolian population in China Pavel Baranov Assessing protein synthesis with ribosome profiling Maria Baranova, Maria Logacheva, Aleksey Penin, Vladimir Seplyarskiy, Yana Safonova, Sergey Naumenko, Anna Klepikova, Evgeniy Gerasimov, Georgii Bazykin, Timothy James, Alexey Kondrashov Extremely high polymorphism level in fungi S. commune: the cause and the importance for population genomics Ancha Baranova, Wang Lei, Tiange Cui, Boris Veytsman, Alexey Moskalev Distance-based profiling aids in evaluation of ageing-related phenomena Eugene Baulin, Alice Korinevskaya, Mikhail Roytberg Long-range stem-based RNA tertiary motifs Georgii Bazykin Change of single-position fitness landscapes and its causes Maxim S. Belenikin, Anastasya A. Krinitsina, Marya D. Logacheva, Sergey V. Kuptsov, Anna S. Speranskaya Adiantum hispidulum chloroplast genome high-throughput sequencing and comparative analysis of cpDNA inverted repeat regions of Adiantum species Maxim Belenikin, Ekaterina Lukyanova, Sergei Ayvazyan Finding of compound heterozygous mutations in the ALDH7A1 gene. Clinical case. Maxim Belenikin Studying of epileptic encephalopathies using NimbleGen-based target panels Ilya V Bizin, Anna P Sokolenko, Ekatherina Sh Kuligina, Evgeny N Imyanitov, Dmitrij Frishman A bioinformatics pipeline for analysing germline mutations in human breast cancer by exome sequencing Olga Bochkareva, Marat Kazanov Evolutionary history of rearrangements in Burkholderia spp. Valentina Boeva, Emmanuel Barillot, Jean-francois Laes Detection of short size mutations and copy number alterations in ultra-deep targeted sequencing data Olga Bondareva, Michail Gelfand Study of lactobacteria's genomes evolution Alexander Bykov, Konstantin Shavkunov, Olga Ozoline Changing the transcriptional activity of genome regulatory loci by PCR-mutagenesis C up Alexander Cherkasov, Elena Shagimardanova, Olga Kozlova, Maria Logacheva, Takahiro Kikawada, Oleg Gusev Whole genome analysis of variety and expression of heat-shock protein encoding genes during desiccation stress in an anhydrobiotic midge Polypedium vanderplanki Zoe Chervontseva, Anna Obraztsova, Elena Stavrovskaya, Andrey Mironov The evolution of 5ò?? untranslated regionsò?? structure in Bacilli and Clostridia genomes D up German Demidov, Vitaly Gursky Stochastic modeling of enhancer molecular configurations German Demidov, Julia Vnuchkova, Anton Bragin A Novel Statistical Algorithm to Detection of Large-scale Deletions in PCR-enriched Target Sequencing Data Arthur Dergilev, Anatoly Svichkarev, Yuriy Orlov Computer analysis of genome co-localization of transcription factor binding sites based on ChIP-seq data Veronika Dubinkina, Alexander Tyakht, Dmitry Alexeev Assessment of k-mer spectrum applicability for metagenomic dissimilarity analysis of human gut microbiota Arina Dymova, Konstantin Kozlov, Maria Samsonova, Vitaly Gursky Combined sequenced-based model of the Drosophila gap gene network E up Anna Ershova, Ivan Rusinov, Anna Karyagina, Sergei Spirin, Andrei Alexeevski GATC avoidance in bacteria with DpnI/DpnII complementary R-M systems F up Alexander Favorov, Vasily Ramensky, Daniil Bredikhin, Andrey Mironov Genes that are best friends: rank-backwards-rank analysis of correlation matrix Gennady Fedonin, Alexey Neverov Characterization of highly diverse viral populations by fast reference selection and accurate read mapping Pavel Flegontov, Evgeny Gerasimov, Vojtech David A read mapper for investigation of U-insertion/deletion RNA editing Alistair Forrest Mammalian Systems biology: FANTOM5 promoters, enhancers and cell type specific regulation G up Aleksandra Galitsyna, Ekaterina Khrameeva, Sergey Ulyanov Spatial configuration of the alpha-globin gene domain in three cell types of G.gallus Oxana Galzitskaya, Nikita Dovidchenko, Olga Selivanova, Maria Suvorina, Alexey Surin, Alexey Finkelstein Determination of the size of folding nuclei of protofibrils from the concentration dependence of the rate and lag-time of their formation Irina Garanina, Pavel Mazin Splicing sites evolution in primates prefrontal cortex Sofya Garushyants, Larisa Kiseleva, Hongwu Ma, David J.w. Simpson, Viatcheslav Fedorovich, Michael F. Cohen, Igor Goryanin Comparative metagenomic profiling of two pilot-scale microbial fuel cells treating industrial wastewaters Guzel Gazizova, Oksana Tyapkina, Maria Logacheva, Leniz Nurullin, Ivan Vikhlyantsev, Akihiko Ishihara, Noriaki Ishioka, Oleg Gusev How to escape from muscle atrophy: whole-genome analysis of gene expression in edible dormouse (Glis glis) during immobilization Evgeny Gersimov, Pavel Flegontov Human-guided genome assembly finishing software Olga Golosova, Yuriy Vaskin NGS Data Analysis with Unipro UGENE Alexander Gorbalenya, Chris Lauber, Siamaque Kazem, Alexander A. Kravchenko, Els van der Meijden, Sander Kooijman, Mariet Feltkamp Fast evolution of a conserved residue of polyomaviruses defines a new mechanism of adaptation that operates by accelerated codon-constrained Val-Ala (COCO-VA) toggling within an intrinsically disordered protein region Mikhail Gorshkov, Lev Levitsky, Mark Ivanov, Irina Tarasova, Anna Lobas, Marina Pridatchenko, Julia Bubis, Elizaveta Solovyeva A family of open-source tools for deep data mining in large-scale mass spectrometry-based proteome analyses Denis Goryunov, Boris Nagaev, Michail Ignatov, Andrei Alexeevski, Alexey Troitsky Moss phylogeny reconstructed from 24 full mitogenome sequences using new ò??pangenomeò?? based approach Konstantin Gunbin, Valentin Suslov, Mikhail Ponomarenko, Fedor Gusev, Eugeny Rogaev Evolution of core promoters in hominids towards the increased ò??norm of reactionò?? of gene regulation in the lineages of Homo sapiens Konstantin Gunbin, Valentin Suslov, Yuri Orlov Rare amino acid changes fixation drives divergence in Metazoa evolution Oleg Gusev, Alexander Nesmelov, Ruslan Deviatiarov, Elena Shagimardanova, Jun Okada, Richard Cornette, Maria Logacheva, Alexei Penin, Al Forrest, Takahiro Kikawada Single cell molecular toolkit for inducible resistance to complete desiccation Irina Gushchina, Dmitry Nilov, Alexandra Zakharenko, Olga Lavrik, Vytas Õšvedas Molecular model of tyrosyl-DNA phosphodiesterase 1 for a structure-based screening for its inhibitors Dmytro Guzenko, Sergei Strelkov Constrained Modelling of an Intermediate Filament Dimer H up Anna Hadarovich, Ivan Anishchenko, Petras Kundrotas, Ilya Vakser, Alexander Tuzikov Quantitative comparison of functional properties in protein-protein complexes Peter A.C.ò??t Hoen, Eleonora de Klerk, Seyed Yahya Anvar, Ivo F.A.C. Fokkema, Martijn Vermaat, Klaske A.M.H. Thiadens, Marieke von Lindern, Stephen W. Turner, Johan T den Dunnen Novel insights in the regulation of mRNA transcription, processing and translation through integration of mRNA sequencing data I up Elena V. Ignatieva Functional characterization of genes controlling mature mammalian adipocyte network. Anna Igolkina, Maria Samsonova Method to predict the percentage of cell types in human blood Dmitry Ivankov, Marc Corrales, Pol CuscÓÃ, Dinara Usmanova, Heng-chang Chen, Natalya Bogatyreva, Guillaume Filion Testing applicability of machine learning for protein folding rate prediction Dmitry Ivankov, Natalya Bogatyreva Methods for protein folding rate prediction Anatoliy Ivashchenko, Raigul Niyazova, Olga Berillo, Shara Atambayeva, Anna Pyrkova Features of miR-574-5p and miR-574-3p binding sites in mRNA of target genes Anatoliy Ivashchenko, Aigul Alybaeva, Raigul Niyazova Binding sites of miRNAs with transcription factors' genes of Camelus ferus and Homo sapiens Anna Ivshina, Vladimir Kuznetsov, Zhiqun Tang, Motakis Efthimios, Ghim Siong Ow Genome wide survival prediction and network analysis stratifies breast cancers into three reproducible subclasses determined by novel genetic grading signatures J up K up Olga Kalinina, Saskia Metzler, Silvia Caprari Sequence and structural analysis of related proteins in distant viral species Anastasia Kalinina, Alexandra Suvorikova, Vladimir Spokoiny, Mikhail Gelfand The method for homologous recombination detection within bacterial species PÔÁnar Kavak, Bekir ErgÓÌner, Bayram YÓÌksel, Duran Ó?stek, Mahmut Õ?amil SaÔ?ÔÁroÔ?lu, Tunga GÓÌngÓÆr, Can Alkan Improving genome assemblies using multi-platform sequence data Sergey Kazakov, Vladimir Ulyantsev, Veronika Dubinkina, Alexander Tyakht, Dmitry Alexeev MetaFast: fast reference-free graph-based comparison of shotgun metagenomic data Kamil Khafizov, Rene Staritzbichler, Maxim Ivanov, Marcus Stamm, Lucy Forrest Anchoring patterns and point mutations in pairwise alignments using AlignMe Peter Kharchenko Classifying transcriptional and genetic heterogeneity in single-cell measurements Matvei Khoroshkin, Semen Leyn, Dmitry Rodionov Transcriptional Regulation of the Carbohydrate Metabolism in the Bifidobacterium Genus Ekaterina Khrameeva, Sergey Ulyanov, Alexey Gavrilov, Yuri Shevelyov, Sergey Razin Active chromatin regions are sufficient to define borders of topologically associated domains in D. melanogaster interphase chromosomes Szymon KieÕ?basa, Jelle Goeman, Hein Putter, Dorret Boomsma, Eline Slagboom, Kai Ye Alignment-free telomere length estimation from whole genome NGS data Olesya Klimchuk, Daria Dibrova, Armen Mulkidjanian OLESA: Operon Loci Examination and Sorting Application Galya V Klink, Georgii A Bazykin Analysis of prevalence of epistasis on the basis of huge phylogenies Valeria Kogan, Peter Fedichev, Dmitry Podolsky, Ivan Molodtcov, Alexander Zenin, Andrey Tarkhov, Leonid I. Menshikov, Robert J. Shmookler Reis Critical dynamics of gene networks is behind ageing and Gompertz law Fyodor Kondrashov Chartering the local fitness landscape of the green fluorescent protein Maria Kondratova, Emmanuel Barillot, Andrei Zinovyev, Inna Kuperstein Atlas of Cancer Signaling Network: from intracellular networks to tumoral microenviroment Ilia Korvigo, Elizabeth Pershina, Anna Igolkina, Alexander Dolnik, Gaik Tamazyan, Yury Porozov, Evgeny Andronov The Evolutionary Space of bacterial 16S rRNA gene Boris Kovarsky, Alexander Tyakht, Dmitry Alexeev Recent genomic changes in the human gut microbiome Olga Kozlova, Yoshitaka Suetsugu, Takahiro Kikawada, Maria Logacheva, Alexey Kondrashov, Oleg Gusev Molecular basics of different mechanisms of desiccation tolerance in Chironomidae midges Galina Kravatskaya, Vladimir Chechetkin, Nikolay Tchurikov, Yuri Kravatsky Genome Track Analyzer : New tool for genome-wide study of correlations between distributed genome features Ekaterina Kulakova, Guoliang Li, Yijun Ruan, Yuriy Orlov Computer analysis of chromosome contacts obtained by ChIA-PET and Hi-C technologies Ivan Kulakovskiy, Ilya Vorontsov, Grigory Khimulya, Darya Nikolaeva, Vsevolod Makeev Selection pressure on breast cancer somatic mutations revealed by bioinformatics sequence analysis Nickolay Kulemin, Vladimir Naumov, Sveltana Danilenko, Eduard Generozov A utility for whole-genome prediction of complex medical traits Vladimir Kuznetsov, Piroon Jenjaroenpun, Thidathip Wongsurawat, Surya Pavan Yenamandra Quantitative Structural Model for Prediction and Analysis of R-loop Forming Sequences in the Genomes Svetlana Kuznetsova, D. Suzuki, Maria Logacheva, T. Kikawada, Rushan Sabirov, Oleg Gusev Transcriptomic of the leech Ozobranchus jantseanus L up Viktoriya Lavrekha, Nadezda Omelyanchuk, Victoria Mironova Mathematical modeling of morphogenetic regulation of the meristem zone formation in the plant root Semen Leyn, Yukari Maezato, Margie Romine, Dmitry Rodionov Carbohydrate utilization capacity of unicyanobacterial consortia derived from hypersaline lake microbial mats Jia Li, Marie-anne Poursat, Stefan Michiels, Daniel Gautheret A model for scoring damaging mutations in the non-coding tumoral genome based on germline and tumor data Alexander Lifanov, Vsevolod Makeev, Natalia Esipova Conserved Regions of DNA Forming Nucleosomes in Transcriptional Regulatory Modules Are Close in Space Alexander Lomzov, Viktor Golyshev, Vitaly Gorelov, Dmitry Pyshnyi Hybridization energy of native and modified DNA duplexes calculated using molecular dynamics Elena Lopatina, M.D. Kazanov Evolution of Burkholderia spp. Qiang Lyu, Haiou Li, Lu Sun, Sheng Luo, Xiaoyan Xia, Peide Qian Modeling Protein Loop Structure by Cyclic Coordinate Descent-based Approach Vassily Lyubetsky, Lev Rubanov, Oleg Zverkov, Leonid Rusin, Alexandr Seliverstov, Andrey Zaraisky A method of detecting local gene synteny rearrangement M up Vladimir Makarenkov, Dunarel Badescu Assessing the impact of horizontal gene transfer on the evolution of prokaryotes Maria Matveeva, Maria Logacheva, Oleg Gusev Comparative plastid genomics of non-photosynthetic Orchidaceae and Ericaceae plants Grigoriy Mavropulo-Stoliarenko Atom subtypes present in protein structures: introducing dynamic atom similarity measure. Oleg Mayboroda, Aswin Verhoeven, Magnus Palmblad Mobilis in MoBiLe: Students in a Dynamic Research Field Pavel Mazin Expression regulation of desiccation-resistance genes in Polypedilum vanderplanki Yulia Medvedeva, Andreas Lennartsson, Finn Drablos Epifactors: a comprehensive database of human epigenetic factors and complexes Margarita Meer, Inna Povolotskaya, Peter Vlasov, Viktoria Shcherbakova, Fyodor Kondrashov Evolution of TAG codon in Methanosarcina Vladislava Milchevskaya, Grischa TÓÆdt, Khristina Havas, Kiran Patil, Toby J. Gibson Improved gene annotations for microarray based identifications of reporter metabolites in recurrent breast cancer Yury Milchevskiy, Sergey Lukshin, Alexey Nikitin, Vladimir Tymanyan Local protein structure prediction based on physicochemical properties of amino acids Aleksandra Minochkina, Peter Vlasov Rational drug design of ligands for MD2/TLR4/CD14 signalling cascade as perspective adjuvants of anti-bacterial vaccines Victoria Mironova, Nadya Omelyanchuk, Victor Levitsky Search for simple and composite auxin responsive elements in Arabidopsis thaliana genome Vladislav Misko The construction of gene networks for Mycobacterium Tuberculosis by analyzing next-generation sequencing data Chanchal K Mitra, Kalyani Korla Modelling the Metabolic Pathways Nurbubu Moldogazieva, Dmitry Argun, Anastasia Gearsim, Ruslan Khanmuradov, Innokenty Mokhosoev, Oleg Komarov, Alexander Terentiev, Konstantin Shaitan Sequence analysis in short functionally important peptides by combination of bioinformatics, molecular dynamics and testing of biological activity Mikhail Moldovan, Svetlana Petrova Comparative genomics analysis of thiamine-pyrophosphate riboswitches in fungal genomes Sergei Moshkovskii, Ksenia Kuznetsova, Dmitry Karpov, Mark Ivanov, Irina Ilina, Maria Karpova, Lev Levitsky, Mikhail Gorshkov Exome-based proteogenomics of human cancer cell lines Armen Mulkidjanian, Daria Dibrova, Michael Galperin, Eugene Koonin Emergence of Membrane Bioenergetics from Ancient Systems of Na+/K+ Homeostasis Ekaterina Myasnikova, Alexander Spirov A method for model comparison based on the parameter sensitivity measures N up Boris Nagaev NPG-explorer: a new tool for nucleotide pangenome construction and analysis of closely related prokaryotic genomes Sergey Naumenko, Ksenia Lezhnina Building the set of orthologous genes for 66 Gammaridae transcriptomes Alexander Nesmelov, Elena Shagimardanova, Maria Logacheva, Richard Cornette, Takahiro Kikawada, Oleg Gusev Antioxidant system of desiccation-tolerant insect Polypedilum vanderplanki Ekaterina Nevedomskaya, Hector Keun O2PLS as an integrative tool in systems oncology Raigul Niyazova, Olga Berillo, Shara Atambayeva, Anna Pyrkova, Anatoliy Ivashchenko Interactions between miRNAs and mRNAs of apoptosis genes in lung cancer Raigul Niyazova, Olga Berillo, Shara Atambayeva, Anatoliy Ivashchenko The interaction of miRNAs with mRNAs of the cell cycle genes in lung cancer German Novalovsky, Daria Dibrova, Armen Mulkidjanian Phylogenomic analysis of the type I NADH:quinone-oxidoreductase Konstantin Novikov, Alexei Romanyukha, Yannis Kalaidzidis, Akhila Chandrashaker, Marino Zerial A new method for identification of molecular motor role in endocytosis Alex Nyporko The 8-oxo-7,8-dihydro-2ò?Â-dGTP behavior in active site of human DNA polymerase ÞÂ: structural investigation in silico O up Yuriy Orlov, Haihua Bai, Haiping Liu, Suyalatu Suyalatu, Ming Chen, Qizhu Wu, Vladimir Babenko, Olga Posukh, Ludmila Osipova GWAS studies of SNPs related to type 2 diabetes in a Mongolian population sample in China Yuriy Orlov, Anatoly Bragin, Nataly Kudryavtseva, Arcady Markel, Ekaterina Kulakova, Anastasia Spitsina Differential gene expression by RNA-seq data in brain structures of laboratory animals with aggressive and tolerant behavior Dmitrii Ostromyshenskii, Olga Podgornaya The genome wide analysis of the large tandem repeats in the closely related species Alexander Osypov Why are genome regulatory regions AT-enriched? P up Alexander Panchin, Alexander Tuzhikov, Yuri Panchin Detection of genomic contaminations and horizontal gene transfer with in silico metagenomic experiments Artem Petrov, Vladimir Arzhanik, Oleg Koliasnikov A novel Arg H52 and Tyr H33 conservative binding motif in antibodies: a correlation between sequence of immunoglobulins and their binding properties Anfisa Popova, Lyudmila Karan, Sergey Gavrilov, Alexey Neverov BCVISS: a web application for analyzing mixed 16S rRNA gene chromatograms Tatiana Popova, Elodie Manie, Marc-henri Stern Genomic structural instability and homologous recombination deficiency in breast and ovarian cancers Nadezhda Potapova, Maria Baranova, Georgii Bazykin, Alexey Kondrashov Accumulation of mutations in nonsense alleles of Drosophila melanogaster Irina Poverennaia, Tatiana Astakhova, Mikhail Roytberg Investigation of exon-intron structure multiple alignments Kirill Prosvirov, Ruslan Soldatov At least 6% of conserved miRNAs` sites are misaligned. Irina Pulyakhina, V.A.Takhaveev, M.Vermaat, M.S. Gelfand, J.F.J. Laros, P.A.C.'t Hoen, BIOS consortium The impact of biological ageing on RNA processing Mikhail Pyatnitskiy, Dmitriy Karpov, Ekaterina Poverennaya, Andrey Lisitsa, Sergei Moshkovskii Searching For Essential Cancer Proteins: Analysis Of Hypomutated Genes In Skin Melanoma Q up R up Dmitry Ravcheev, Ines Thiele Genomic analysis of the respiration the microbiota of human intestine Olga Rogacheva, Vasily Stefanov, Boris Shchegolev, Elena Vershinina cAMP-induced conformational changes of Protein Kinase A Ia A-domain Alexander Rosenthal Network of the Country Tuberculosis Portals Maga Rowicka, Norbert Dojer, Abhishek Mitra, Ji Li, Yea-lih Lin, Anna Kubicka, Magdalena Skrzypczak, Krzysztof Ginalski, Philippe Pasero Inferring direction of replication fork and mechanism of DNA damage using sequencing data Ivan Rusinov, Anna Ershova, Anna Karyagina, Sergey Spirin, Andrey Alexeevski Estimation of selection pressure on degenerate sequences in genomes: choice of method S up Ekaterina Savitskaya, Ekaterina Semenova, Daria Vorontsova, Sofia Medvedeva, Maria Logacheva, Konstantin Severinov Autoimmune primed CRISPR adaptation in I-E and I-F systems: comparative analysis of new spacer selection mechanisms Kirill Scherbakov, Mikhail Dubinin, Viktor Samartsev Docking method reveals binding patterns of ÞÁ,ß?-dioc acids by albumin Vladimir Seplyarskiy, Ruslan Soldatov, Konstantin Popadin, Styliano Antonarakis, Sergey Nikolaev APOBEC induced mutations are strongly enriched on the lagging strand during replication in human cancers Roman Sergeev, Ivan Kavaliou, Andrei Gabrielian, Alex Rosenthal, Alexander Tuzikov Mutation analysis of M. tuberculosis nucleotide sequences from patients in Belarus Elena Shagimardanova, Takahiro Kikawada, Oleg Gusev Comparative metabolomic profiling of desiccation tolerant midge Daria Shalaeva, Dmitry Cherepanov, Armen Mulkidjanian Modeling the role of positively charged moieties in hydrolysis of nucleoside triphosphates Igor Sharakhov, Ashley Peery, Anastasia Naumenko, Xiaofang Jiang, Brantley Hall, Maria Sharakhova, Zhijian Tu, Gleb Artemov, Vladimir Stegniy Genome mapping revealed scaffold misassemblies and elevated gene shuffling on the X chromosome in malaria mosquitoes Konstantin S. Shavkunov, Olga A. Glazunova, Klaus Neuhaus, Olga N. Ozoline Bacteria revived from an ancient bison gut Anatoliy Shlikht, Natalia Kramorenko Automated workplace of bioinformatics Boris Sobolev, Dmitry Karasev, Alexander Veselovsky, Dmitry Filimonov, Vladimir Poroikov, Nina Oparina Detecting the features of functional specificity in protein families based on the local sequence similarity Ruslan Soldatov, Vladimir Seplyarskiy, Georgii Bazykin Differential activity of polymerase ÞÆ associated with replication timing and gene bodies in humans: evidence from mutational signatures Gleb Speshilov Comprehensive comparison of RNA-seq based methods for differential splicing analysis Alexander Spirov, Ekaterina Myasnikova, David Holloway Dynamic modeling of genes for spatial patterning in embryo development on the example of the Drosophila segmentation gene hunchback Anastasia Spitsina, Natalya Podkolodnaya, Vadim Efimov, Vladimir Babenko, Yuriy Orlov Computer tool for gene expression data processing and correlation analysis Elena Stavrovskaya, Alexander Favorov, Sarah Wheelan, Andrey Mironov StereoGene: a tool for fast correlation assessment and its application to the analysis of bivalent histone methylation Dmitry Suplatov, Nikolay Panin, Tatyana Shcherbakova, Ilyas Khaliullin, Vytas Õšvedas Bioinformatic analysis of diverse protein superfamilies to design improved enzymes Inna Suvorova, Dmitry Rodionov Reconstruction of GABA and taurine metabolic regulons, controlled by MocR-subfamily transcription factors T up Evgeny Taranov, Alexander Lebedinsky DegenPrimer: a software for in silico simulation of multiplex PCR with degenerate primers Oleg Tarasov, Polina Drozdova, Elina Radchenko, Dmitry Polev, Pavel Dobrynin, Sergey Inge-vechtomov Sequencing genomes of Saccharomyces cerevisiae strains belonging to the Peterhof Genetic Collection helps elucidate the origin of several widely used laboratory strains Svetlana Tarnovskaya, Artem Kiselev, Anna Kostareva, Dmitrij Frishman Structural analisys of mutations assosiated with idiopatic restrictive cardiomyopathy in cytoskeletal and sarcomeric proteins Michael Tartakovsky Building a Sustainable Bioinformatics Program Through Integrated Support Tatiana Tatarinova, Nickolai Alexandrov Analysis of variation in 3000 rice genomes project Nadezhda Terekhanova, Georgii Bazykin, Ruslan Soldatov, Vladimir Seplyarskiy Local variation of the mutation rate across the primate phylogeny Anastasiya Terskikh, Alexander Kanapin, Anastasiya Samsonova Analysis of mutational landscape of patients with chronic lymphocytic leukemia Anastasia Teterina The evolution of cod protein coding genes: intra- and interspecies levels Olga Tsoy, Larisa Kiseleva, Igor Goryanin Microbial composition and metabolic potential development in microbial fuel cells during wastewater treatment Maria Tutukina, Inna Suvorova, Valery Panyukov, Jeffrey Cole, Olga Ozoline Revealing and comparing regulons of homologues transcription factors UxuR and ExuR in Escherichia coli. U up Leonid Uroshlev, Vsevolod Makeev Prediction of cation binding sites using structural water Dinara Usmanova, Fyodor Kondrashov A model of protein evolution within local fitness landscape changing with time V up Aleksandra Vasileva, Michael Kiening, Dmitrij Frishman Secondary structures in the coding regions of mRNAs: literature survey and comparison of prediction methods Valery Veresov, Anna Dudko TOM-complex structure modeling Dmitry Vinogradov, Natalia Lazarevich, Maria Logacheva, Ekaterina Kotelnikova Alternative splicing in hepatocellular carcinoma Svetlana Vinogradova, Ruslan Soldatov, Andrey Mironov Probing-directed structured elements detection in RNA sequences Oxana Volkova, Yriy Kondrakhin, Ruslan Sharipov Estimation of translational importance of mammalian mrna nucleotide sequence characteristics based on ribosomal profiling data W up X up Y up Tural Yarahmadov, Jia-Ò-ying Zhu, Alexander Martynov, Elena Elpidina Effect of Cry3Aa toxin on gut peptidases expression levels in Tenebrio molitor larvae. Z up Arthur Zalevsky, Artem Dyuba, Andrey Golovin Unraveling CD spectra of G-quadruplexes Ilya Zharov, Yuriy Korostelev Correlations of substitutions predict specific protein-DNA contacts in the MerR family of transcriptional factors Igor Zhulin, Ogun Adebali, Alexander Reznik Evolutionary analysis of NPC1 improves prediction of disease causing missense mutations Igor Zhulin A universal signaling mechanism in bacterial chemoreceptors Ekaterina Zhuravleva, Yulia Medvedeva, Elena Stavrovskaya, Leslie Cope, Andrey Mironov, Vsevolod Makeev, Sarah Wheelan, Alexander Favorov Evaluation of the positional correlations between whole genome annotations: novel statistical approaches development, advancement of the GenometriCorr methodologies Andrei Zinovyev, Anne Biton, Francois Radvanyi Revealing mechanisms of cancer progression by pan-cancer deconvolution of tumoral transcriptomes Olga Zolotareva, Fedor Gusev, Schahram Akbarian, Evgeny Rogaev Bioinformatics Analysis of Active Chromatin Allelic imbalance Across Genome: Testing Cerebral Neurons in Schizophrenia and Autism