MCCMB 2013: Proceedings
		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 Azat Abdullatypov, Anatoly Tsygankov Mapping the molecular tunnels in three nickel-iron hydrogenases Irina Abnizova Detection of some new statistical biases in next generation sequencing, Illumina platform Dmitry Afonnikov, Kirill Medvedev, Konstantin Gunbin, Yurii Vorobjev Influence of high temperature and high pressure on the Nip7 proteins from the hyperthermophilic archaea P. abyssi and P. furiosus: molecular dynamics simulation analysis Rosa Aghdam, Changiz Eslahchi, Mojtaba Ganjali A New algorithm for Inferring Gene Regulatory Networks Based On Combination of Bayesian Approach and MIT Score. Ilya Akberdin, T.m. Khlebodarova, V.v. Kogai, S.i. Fadeev, V.a. Likhoshvai Modeling of nitrite utilization in the E.coli cell: flux analysis Evgeniy Aksianov, Andrei Alexeevski Protein 3D architectures and structural motifs: automated annotation Jaroslav Albert, Marianne Rooman Fast and accurate solutions to the chemical master equation for multimeric systems Max Alekseyev, Shuai Jiang Simultaneous Solution to Synteny Blocks Construction and Genome Rearrangements Problems Ilya Altukhov, Dmitry Ischenko, Sergey Kovalchuk, Dmitry Alexeev Label-free quantitative proteomics and a systematic analysis of Helicobacter pylori Alexander M. Andrianov, Yuri V. Kornoushenko, Ivan V. Anishchenko, Vladimir F. Eremin, Alexander V. Tuzikov Structural Analysis of the Envelope GP120 V3 Loop for Some HIV-1 Variants Circulating in the Countries of Eastern Europe Alexander M. Andrianov, Ivan A. Kashyn, Alexander V. Tuzikov Computer-Aided Search for Novel HIV-1 Entry Inhibitors Based on a Broadly Neutralizing Antibody Against the Envelope gp120 V3 Loop Alexander M. Andrianov, Yuri V. Kornoushenko, Ivan A. Kashyn, Alexander V. Tuzikov Computer Modeling of Novel Anti-HIV-1 Agents Presenting Water-Soluble Analogs of Glycosphingolipid ?-Galactosylceramide Denis Antonets, Dmitry Grudin Using novel Generic String kernel to predict peptide-MHC binding affinity Ivan Antonov, Pavel Baranov, Mark Borodovsky Detection of frameshifts and improving genome annotation Irena I. Artamonova, Anna A. Gogleva CRISPR systems in microbiomes Artem Artemov, Mikhail Gelfand, Alexander Favorov, Andrey Mironov Exploring protein occupancy patterns defining the specificity of interactions between DNA fragments Tatiana Astakhova, Ivan Tsitovich, Victor Yacovlev, Mikhail Roytberg Dependence between lengths and phases of introns B up Pavel Baranov, Audrey Michel, Patrick O'connor, K Roy Choudhury, Andrew Firth, Gene-Wei Li, Nicholas Ingolia, Jonathan Weissman, John Atkins Elucidating mechanisms of translation with computational analysis of ribo-seq data. Nikolay Bardukov, Taras Sipko, Anton Pheophilov, Valery Glazko Polyloci genotyping by means of DNA fragments flanked by short inverted repeats in musk oxen genomes Serafim Batzoglou Genome Evolution During Progression to Breast Cancer Eugene Fedorovich Baulin, Mikhail Abramovich Roytberg The database of RNA secondary structure elements Georgii A. Bazykin, Adam D. Hayward, Virpi Lummaa Accumulation of deleterious mutations and fitness in a pre-industrial human population Maxim Belenikin, Natalya Melnikova, Anna Speranskaya, Anastasya Krinitsina, Nadejda Bolsheva, Valentina Lakunina, Olga Rachinskaya, Alexey Dmitriev, Marya Darii, Anna Kudryavtseva, Alexander Zelenin, Olga Muravenko Identification and characterization of microRNA in Linum usitatissimum Maxim Belenikin, Natalya Melnikova, Anna Speranskaya, Anastasya Krinitsina, Nadejda Bolsheva, Valentina Lakunina, Olga Rachinskaya, Alexey Dmitriev, Marya Darii, Anna Kudryavtseva, Alexander Zelenin, Olga Muravenko Identification of aluminum-responsive sRNA in flax (Linum usitatissimum) by high-throughput sequencing Maxim Belenikin, Natalya Melnikova, Anna Speranskaya, Anastasya Krinitsina, Nadejda Bolsheva, Valentina Lakunina, Olga Rachinskaya, Alexey Dmitriev, Marya Darii, Anna Kudryavtseva, Alexander Zelenin, Olga Muravenko Sequencing, de novo transcriptome assembly and differential expression analysis of flax genotrophs Maxim Belenikin, Anastasya Krinitsina, Asya Sadritdinova, Anastasya Snezhkina, Alexey Dmitriev, Nina Oparina, Anna Kudryavtseva, Natalya Melnikova, Anna Speranskaya Investigation of Pin-II family genes variability in Solanum species by long amplicons sequencing on GS Junior (454) Sasha Belostotsky RNA polymerase II may interact with different transcription factors during elongation according to out-of-peak ChIP-seq signal analysis Sasha Belostotsky Integration of protein-protein and protein-DNA interaction. Approach for protein complexes-on-DNA database Sasha Belostotsky Protein-protein and protein-DNA interaction are not obviously positively correlated Sasha Belostotsky Integration of protein-protein and protein-DNA interaction. Approach for protein complexes-on-DNA database Sasha Belostotsky Hypothesis of biological networks as a system of linked oscillators. Very briefly Olga Berillo, Anatoliy Ivashchenko MicroRNAs bind with mRNAs of genes involving in mitochondrial apoptosis pathway Olga Bochkareva, Marat Kazanov, Evgeny Gordienko Evolutionary history of recombination events in E.coli, Shigella and Salmonella genomes Valentina Boeva, Tatiana Popova, Kevin Bleakley, Andrei Zinovyev, Jean-Philippe Vert, Isabelle Janoueix-Lerosey, Olivier Delattre, Emmanuel Barillot Predicting copy number alterations and allelic status in cancer genomes with Control-FREEC using whole genome or exome sequencing data Elena Bogacheva, Alexandr Ksenofontov, Alexandr Shishkov Assessment of applicability of the program Rosetta for the determination of membrane associated proteins structure. M1 influenza virus protein Alexandr Burenin, Alexey Betin, Natalia Massarskaya, Maksim Nikitin Determination of protein-ligand affinity by spectral correlation interferometry C up Charles Cantor Detection of RNA sequences in living cells by RNA mediated protein complementation Jelena Chuklina, Nikolay Lyubimov, Elena Evguenieva-Hackenberg, Mikhail Gelfand Analysis of Transcriptional Regulation of Bradyrhizobium japonicum Based on dRNA-seq Data Andrey Chursov, Dmitrij Frishman, Alexander Shneider Computational Analysis of Influenza RNA Structures: New Hypotheses for Old Problems D up Natalia Demidenko, Maria Logacheva, Aleksey Penin Comparison of abiotic stress response systems between Arabidopsis thaliana and Fagopyrum esculentum E up Boris Efeykin, Sergei Spiridonov, Kirill Mikhailov, Vladimir Aleoshin, Yuri Panchin Genome survey of nematomorph worm Gordionus alpestris using NGS Mariya Elkina, Valery Glazko LTR-retrotransposons of the family Pseudoviridae in the genomes of monocotyledonous and dicotyledonous plants. Timur Erkenov, Valery Glazko Choosing markers for genome scanning of local and trotter horse breeds Anna Ershova, Alexandr Lyaschuk, Vladidmir Lunin, Anna Karyagina, Sergey Spirin, Andrey Alexeevski Prediction and analysis of separated restriction-modification systems in prokaryotic genomes Anna Ershova, Ivan Rusinov, Anna Karyagina, Sergey Spirin, Andrey Alexeevski Occurrence of Restriction-Modification systems? recognition sites in genomes of bacteria, archaea and their viruses Micaela Polay Espinoza, Lise Gratadou, Camille Fong Chih Kai, Sophie Germann, Etienne Dardenne, Cyril F. Bourgeois, Didier Auboeuf DDX5/DDX17 RNA helicases : Two master genes controlling skeletal myogenesis F up Elisabete Fernandes, Ant?nio Pacheco, Carlos Penha-Gon?alves Skew-Normal Composite Interval Mapping Zoya Fetisova, Vladilen Duzhenko, Tatiana Cherenkova Baseplate BChl a Subantenna as a Universal Interface between BChl c/d/e Subantenna and Plasma Membrane BChl a Subantenna in Photosynthetic Green Bacteria Alexandra Filatova, Andrey Marakhonov, Ancha Baranova, Mikhail Skoblov Phylogenetic analysis of ASCL gene family Dmitri Fomenko, Vadim Gladyshev, Grant Pierre Systems Biology of Hydrogen Peroxide Mediated Signaling Marina Fridman, Nina Oparina, Ivan Kulakovskiy, Vsevolod Makeev Origine and expansion of microsatellites is associated with conversion more than with replication Marina Fridman, Dmitrijs Lvovs, Nina Oparina, Vsevolod Makeev Insertion-deletion polymorphisms as indication of mechanisms of tandem repeats evolution in human genome G up Oxana Galzitskaya, Michail Lobanov Occurrence of disordered patterns and homorepeats in eukaryotic and bacterial proteomes Sergiy Garbuzynskiy, Natalia Marchenko, Maria Kondratova Protein Folding Nuclei Database Anna Gladkikh, Oleg Kotsar, Olga Belykh Metagenomic approach in studying of bacterial communities in Lake Baikal Vadim Gladyshev Understanding aging and control of lifespan through genome analyses Oleg Glotov, Irina Tarkovskaia, Ekaterina Ditkina, Elena Vashukova, Andrey Glotov, Tatyana Ivashchenko The association analysis of lipid metabolism gene polymorphisms with BMI, waist circumference and blood lipidogramm parameters in women Ivan Gorlov, Alexei Fedorov, Christopher Logothetis, Olga Gorlova, Christopher Amos Genes with a large intronic burden show a higher evolutionary conservation on protein level Denis Goryunov, Maria Logacheva, Michail Ignatov, Alexey Troitsky The mitochondrial genome of moss Brachythecium rivulare B.S.G. (Hypnales, Brachytheciaceae) Alexandre Goultiaev, Rene Olsthoorn Computational search for functional structures in viral RNA genomes Anton Grigorev Fast and Accurate Full Genome Alignment Procedure Anton Grigorev, Alexey Manturov Stochastic Logical Model of DNA Replication Dynamics Andrey Grigoriev, Sulbha Choudhari, Ruchi Lohia How to sequence a glacier: a computational biologist?s rough guide Konstantin Gunbin, Sergey Lashin The gene flow between ancient and modern humans: how often the hybridization occurred and what are population consequences? Konstantin Gunbin, Mikhail Ponomarenko, Dmitry Afonnikov Human brain origin and the evolution of ÒÀÒÀ-boxes of protein-coding genes expressed in brain Konstantin Gunbin, Dmitry Afonnikov Metazoa evolution: the relation between molecular evolution of orthologous protein groups and aromorphoses Vitaly Gursky, Anna Igolkina Probing different thermodynamic models of transcriptional gene regulation in case study of even-skipped gene regulatory region in Drosophila Oleg Gusev, Elena Sahgimardanova, Yoshitaka Suetsugu, Noriaki Satoh, Maria Logacheva, Alexei Penin, Dmitry Alexeev, Vadim Govorun, Georgy Bazykin, Alexey Kondrashov, Takahiro Kikawada Drying without dying: multi-omics analysis of mechanisms of anhydrobiosis in the sleeping chironomid Polypedilum vanderplanki (Diptera) H up I up Elena Ignatieva LM-KnB - the knowledge base on molecular genetics mechanisms controlling human lipid metabolism. Maksim Imakev, Geoffrey Fudenberg, Leonid Mirny Chromosomal Architecture Changes Upon Cell Differentiation Dmitry Ischenko, Vasiliy Popkov, Dmitry Alexeev The development of the method for the analysis of proteomics data Dmitry Ivankov, Natalya Bogatyreva, Peter H?nigschmid, Bastian Dislich, Sebastian Hogl, Peer-Hendrik Kuhn, Dmitrij Frishman, Stefan Lichtenthaler Quantitative proteomic analysis of regulated intramembrane proteolysis with QARIP web-server Dmitry Ivankov, Samuel Payne, Stefano Bonissone, Si Wu, Roslyn Brown, Ljiljana Pa?a-Toli?, Matthias Birschenk, Iris Antes, Richard Smith, Michael Galperin, Pavel Pevzner, Dmitrij Frishman Proteogenomic analysis of bacterial signal peptides J up Guoli Ji, Yong Zeng, Xiaohui Wu, Meishuang Tang PLS-based Characteristic Selection and Identification of Gene Expression Profiles K up Aleksandra Kanygina, Aleksander Manolov Automatic identification of horizontal gene transfer events in bacterial genomes Nermin Pinar Karabulut, Murodzhon Akhmedov, Murat Cokol A drug-gene network for understanding drug mechanism of action Burak Karaca?ren Assessment of Population Structure with a Bayesian Genomic Model in F2 Mice Dataset Pavel Karpov, Oleg Demchuyk, Vasyl Britsun, Dmytro Volochnyk, Yaroslav Blume Discovery of new anti-TB compounds that target Mycobacterial FtsZ: high-throughput screening and molecular docking Artem Kasianov, Maria Logacheva, Vsevolod Makeev, Aleksey Penin De novo sequencing, assembly and characterization of genome in tetraploid plant Capsella bursa-pastoris Anna Kaznadzey, Pavel Shelyakin Structure, classification, evolution and phylogenetics of carbohydrate metabolism gene loci in bacteria Philipp Khaitovich Insights into human evolution from metabolome studies Peter Kharchenko, Artyom Alekseyenko, Andrey Gorchakov, Mitzi Kuroda Bayesian Analysis of Mass Spec Enrichment in integrative studies of chromatin-associated complexes Ekaterina Khrameeva, Mikhail Gelfand, Philipp Khaitovich Association between changes in lipid catabolism and increased gene flow from Neanderthals to Europeans Vladislav Khrustalev, Sergey Lelevich, Eugene Barkovsky Deep insights into the history of hexokinases evolution based on mutational pressure theory Tatyana Khrustaleva, Vladislav Khrustalev, Eugene Barkovsky Structural context around amino acid residues binding Mn+2 ions in bacterial proteins Tatsiana Kirys, Alexander Tuzikov Protein docking algorithm based on structural homology with protein-protein interfaces Larisa Kiseleva, Igor Goryanin Integration of bioinformatics tools for metagenomic analyses Anna Klepikova, Natalia Demidenko, Maria Logacheva, Aleksey Penin The method of gene expression analysis in complex morphological systems Galya Klink, Georgii Bazykin Analysis of prevalence of epistasis on the basis of huge phylogenies Natalie Kobets, Dmitrii Goncharov, Alexandr Seliverstov, Oleg Zverkov, Vassily Lyubetsky Comparative analysis of apicoplast-targeted proteins in Toxoplasma gondii and other Apicomplexa species Alexey Kolodkin, Andrew Ignatenko, Evangelos Simeonidis, Vineet Vineet Sangar, Charley Choe, Bernhard Peters, Hans V. Westerhoff, Nilgun Yilmaz, Nathan D. Price, Rudi Balling, Nathan Brady ROS systems biology: In silico reconstruction of the emergence of cellular ROS-managing system Aleksey Komissarov Recovery and annotation of satellite DNA sequences from assembled and unassembled reads Alexey Kondrashov Accumulation of deleterious alleles in modern human populations Larisa Kordyukova, Ramil Mintaev, Andrei Alexeevski Co-evolution analysis to predict protein-protein interactions within the Influenza virus envelope Anton Korobeynikov, Alla Lapidus, Pavel Pevzner SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing Yuriy Korostelev, Han Dingding, Ekaterina Khrameeva, Mikhail Gelfand, Philipp Khaitovich Expression analysis of medium-length RNA in the human, chimpanzee, macaque and mouse brains Maxim Koroteev, Jonathan Miller, No Third Author No Third Author Exact dynamics of duplications and mutations in whole genome sequences Alina Korovkina, Anna Klepikova, Maria Logacheva, Aleksey Penin Role of CHB3 protein in DNA-binding specificity of SWI/SNF chromatin remodeling complex Sergei Koshman, Alexei Zinchenko, Alexei Nekrasov Research of residue contacts within the polypeptide chains depending on the density of information in the sequence Boris Kovarsky, Pavel Mazin, Dmitry Alexeev Analysis of genetic variety of human gut metagenome Galina Kravatskaya, Vladimir Chechetkin, Yury Kravatsky, Vladimir Tumanyan Analysis of nucleotide sequences in promoter regions of supercoiling-sensitive genes: How to relate microarray expression data with genomic sequences Andrzej Kudlicki Maximum Parsimony Interpretation of Chromatin Capture Experiments Anna Kudryavtseva, Anastasiya Snezhkina, Alexey Dmitriev, George Krasnov, Asiya Sadritdinova, Nataliya Melnikova, Oleg Stepanov, Valentina Lakunina, Maria Darii, Leunid Uroshlev, Nina Oparina Differential expression of glycolysis pathway genes in renal, lung and breast cancer Ivan Kulakovskiy, Victor Levitsky, Dmitry Oshchepkov, Ilya Vorontsov, Vsevolod Makeev From ChIP-Seq data to improved transcription factor binding sites models Inna Kuperstein, David Cohen, Laurence Calzone, Maia Chanrion, Daniel Louvard, Sylvie Robine, Andrei Zinovyev, Emmanuel Barillot Modelling signalling networks for explaining synthetic gene interactions leading to invasive phenotype in colon cancer mouse model L up Semen Leyn, Dmitry Rodionov Comparative genomics reconstruction of transcriptional regulons for metal homeostasis and autotrophic pathways in Archaea Ksenia V. Lezhnina, Alexey D. Neverov, Alexey S. Kondrashov, Georgii A. Bazykin Intrasubtype reassortments cause adaptive amino acid replacements in H3N2 influenza genes Hong-Ye Li, Wei-Dong Yang, Jian-Wei Zheng Systems-level analysis of metabolic responses of the diatom Phaeodactylum tricornutum to phosphorus stress Alexander Lifanov, Vsevolod Makeev, Natalia Esipova Positioning of Nucleosomes at DNA Containing Short Periodic Sequences Vassily Lyubetsky, Semen Korolev, Alexandr Seliverstov, Oleg Zverkov Rho-dependent attenuation of sulfur metabolism in mycobacteria M up Natalia Malygina, Natalia Voynova Distinctive properties of Staphylococcus aureus mevalonate kinase 3D structure: modeling of substrate binding sites Andrey Marakhonov, Nataliya Sadovskaya, Egor Borzov, Ancha Baranova, Mikhail Skoblov New insights from Affymetrix expression microarray data analysis B?la Albert Marosi, Oleksandr Zinenko, Ioan Ghira, Jelka Jelka Crnobrnja-Isailovi?, Petros Lymberakis, Tibor S?s, Octavian Popescu Molecular data confirm recent fluctuations of northern border of dice snake (Natrix tessellata) range in Eastern Europe Alexander Martynov, Brenda Oppert, Elena Elpidina Diversity of cysteine cathepsins in two coleopterans, Tenebrio molitor and Tribolium castaneum Pavel Mazin, Philipp Khaitovich Conserved age-related splicing regulation in primate brains Alice Mchardy Computational methods for studying the phenotypic evolution of human influenza A viruses Kirill Medvedev, Konstantin Gunbin, Yury Vorobjev, Dmitry Afonnikov Influence of high temperature and high pressure on the Nip7 proteins from the hyperthermophilic archaea P. abyssi and P. furiosus: molecular dynamics simulation analysis Yulia Medvedeva, Abdullah Khamis, Ivan Kulakovskiy, Vladimir Bajic Effects of cytosine methylation on transcription factor binding sites Alexey Mekler, Irina Knyazeva, Vladimir Dmitrenko, Alexey Iershov, Vadim Kavsan Gene expression profiling for subtyping of glial tumors Alexey Moskalev, Valeria Kogan, Mikhail Shaposhnikov, Ekaterina Plyusnina, Sergei Plyusnin, Anastasia Snezhkina, Peter Fedichev, Anna Kudryavtseva Analysis of RNASeq data of fruit flies affected by low dose gamma-irradiation, dioxin, toluene and formaldehyde Ekaterina Myasnikova Identifiability analysis and predictive power of the gene circuit model N up Elena Nabieva, Maria Logacheva, Ekaterina Kotelnikova, Mikhail Pyatnitskiy, Dmitry Vinogradov, Nikolai Mugue, Alexey Kondrashov, Natalia Lazarevich Whole-exome sequencing in hepatocellular carcinoma Sergey Naumenko, Nina Popova Inferring phylogeny of Baikal gammarids using transcriptome sequencing Daniil Naumoff Evolution and Classification of GH101 Family Glycoside Hydrolases: Four Years Later Leonid Nazarov, Alexey Gavrilov, Alexander Chertovich, Michael Tamm Anomalous diffusion in crumpled (fractal) globules and the dynamics of diffusion-limited reactions in the chromatin. Lidia Nefedova, Anna Smel'kova, Anton Lavrenov, Felix Urusov, Natalia Romanova, Alexander Kim Integration specificity of the mobile element Tirant in the Drosophila melanogaster genome Zahra Noormohammadi, Masoud Sheidai, Zahra Mahdavipour, Kazem Mahdigholi STRUCTURE and reticulation analysis of genetic diversity in Prunus scoparia populations Konstantin Novikov, Alexei Gratchev, Julia Kzhyshkowska, Olesya Melnichenko, Alexei Romanyukha Mathematical model of self-organizing and adaptable intracellular transport network O up Konstantin Okonechnikov, Thomas Meyer, Fernando Garc?a-Alcalde Advancing fusion gene detection from RNA-seq data Nina Oparina, Aleona Rybina, Vladlen Skvortsov Human multigene disorders: functional analysis of known associated genes. Nina Oparina, Belenky Mikhail, Sergey Lysenkov, Peter Chang, Viktoria Scobeyeva The Draft Genome of Black Garden Ant Lasius niger: preadaptation to urbanization? Nina Oparina, Platon Bykadorov, Marina Fridman Trinucleotide repeats in the human genome: structural characteristics and role in health and disease Yuriy Orlov, Dmitri Afonnikov, Nariman Battulin, Oleg Serov, Nikolay Kolchanov, Guoliang Li, Yijun Ruan 3D organization of chromosomes mediated by RNAPII complex contacts in human genome Alexander Osypov The role of electrostatics in the transcription regulation in prokaryotes. DNA phenotype Vladimir Ovchinnikov, Dmitry Afonnikov, Gennady Vasilyev, Alexey Katokhin, Elena Kashina, Vyatcheslav Mordvinov Computational and experimental analysis of mirna genes of opisthorchiidae family liver flukes Olga Ozoline, Konstantin Shavkunov, Olga Glazunova, Eugeny Fesenko, Maria Tutukina, Sergey Kiselev, Sergey Antipov, Victoria Pokusaeva, Valeriy Panyukov Promoter islands as instruments of bacterial evolution P up Alexander Panchin, Sergey Spirin, Sofya Medvedeva, Andrey Alexeevski, Yuri Panchin Strong negative selection on CpG dinucleotides in the human genome: a comparison of de novo and inherited mutation rates Alexander Panchin, Alexander Tuzhikov, Qunfeng Dong, David Nelson, Terrence O'brien, Valery Shestopalov Taxonomic Unit Identification Tool: a bioinformatical approach for the improvement of human cornea microbiome classification using 16S rRNA gene sequencing Dmitri Papatsenko, Henia Darr, Ivan Kulakovskiy, Vsevolod Makeev, Ihor Lemischka Buffering meta-stable pluripotent states in embryonic stem cells Dmitri Pervouchine, Sarah Djebali, Alessandra Breschi, Julien Lagarde, Thomas Gingeras, Roderic Guigo Deep sequencing survey of alternative splicing in human and mouse Robert Pesch, Ralf Zimmer CroCo: The Cross-Species Network Conservation Framework Anton Pheophilov, Nikolay Bardukov, Tatiana Glazko, Valery Glazko Sites homologous to helitron family and their polymorphism in mammal genomes Valery Polyanovsky, Vladimir Tumanyan Application of evolutionary model in the evaluation of the quality of pair wise alignment of amino acid sequences Sergei Pustovoit Statistical analysis of nucleotide sequences of a cytochrome c oxidase subunit 1 (CO1) mtDNA arctic (Liopsetta glacialis) and striped (Liopsetta pinnifasciata) flounder (Pleuronectidae) of the Sea of Okhotsk Q up R up Alexey Raevsky, Pavel Kapov, Yaroslav Blume Structure modeling, molecular screening and docking of mammalian AMPK and its plant homolog KIN10 for new ATP-competitive inhibitors Thomas Rattei Comparative genomics and metagenomics of viruses Georgy Romanov, Sergey Lomin, Dmitry Arkhipov Molecular evolution of cytokinin receptors: a phylogenetic analysis Georgy Romanov, Victor Sukhoverov Dynamic model for proliferative growth in cell structures of plant type Georgy Romanov, Mikhail Steklov, Sergey Lomin, Dmitry Osolodkin Computational prediction of amino acid residues essential for ligand-binding selectivity of cytokinin receptors Georgy Romanov, Mikhail Steklov, Sergey Lomin New structural motifs in the ligand-binding module of cytokinin receptors Maga Rowicka Landscape of double-stranded DNA breaks in human genome and its correlation with sequence motifs and DNA bendability S up Asiya Sadritdinova, Maxim Belenikin De-novo transcriptome assembly of starfish, Asterias rubens Dariya Samofalova, Pavel Karpov, Yaroslav Blume Search of effective protein phosphatases inhibitors using nanochemical approaches and evaluation of their biological activity in silico Ekaterina Savitskaya, Ekaterina Semenova, Kirill Datsenko, Konstantin Severinov, A Strotskaya High-throughput analysis of type I-E CRISPR adaptation in E. coli Pavel Semenyuk, Valentin Makarov, Dmitry Abashkin, Eugeny Dobrov Structural Properties of Barley Stripe Mosaic Virus Virions Vladimir Seplyarskiy, Alex Kondrashov, Timothy James High-resolution study of recombination in a highly polymorphic fungus Schizophyllum commune Roman Sergeev, Alexander Tuzikov Approach to mutation analysis of genetic sequences and building mutational database in context of HIV/AIDS and Tuberculosis treatment Igor Sharakhov, Nick Kinney, Alexey Onufriev The effect of chromosome-nuclear envelope attachments on 3D genome organization Igor Sharakhov, Phillip George, Chantal Vaury, Silke Jensen Organization and evolution of piRNA clusters in mosquitoes Maria Sharakhova, Vladimir Timoshevskiy, Becky Debruyn, Devid Severson, Igor Sharakhov Genomic features of individual chromosomes in yellow fever mosquito Pavel Shelyakin Identification and classification of Clostridium difficile promoters Mikhail Shugay, Javier Novo Computational Analysis of Oncogenic Gene Fusions Boris Sobolev, Alexandr Veselovsky, Vladimir Poroikov Prediction of protein posttranslational modifications: comparative analysis of known approaches Vladimir Sokolov, Vitali Likhoshvai, Yuri Matushkin Computational study of translation elongation features in Mycoplasma Ruslan Soldatov, Svetlana Vinogradova, Andrey Mironov RNASurface: fast and accurate identification of motifs with high structural potential Anatoly Sorokin, Evgenia Temlyakova, Timur Dzhelyadin, Svetlana Kamzolova Can proteins read letters? Evgeniya Sotnikova, Gleb Kosovsky, Olga Levitskaya, Valeriy Glazko Bovine leukemia virus sequences and rate of nucleotide exchange Sergei Spirin, Yury Pekov, Kirill Romanenkov, Alexey Salnikov Nhunt: solving the low complexity problem for nucleic acid homology search Sergei Spirin, Mikhail Krivozubov, Florian G?bels Estimation of relative effectiveness of phylogenetic programs by machine learning Alexander Spirov Dynamical systems analysis of the gene regulatory network: on example of Drosophila early segmentation Elena Stavrovskaya, Alexander Favorov, Andrey Mironov Fast assessment of the correlation between different coverage-like genomic features and their combinations Vasily Stefanov, Olga Rogacheva, Boris Shchegolev, Elena Vershinina, Elena Savvateeva-Popova, Gennadii Mikhailov Understanding of the cAMP-induced conformational transition of Protein Kinase A I? A-domain. Role of the invariant R209 Vasily Stefanov, Olga Ksenofontova Insulin Drugs Development: Influence of Mutations on Ligand-Receptor Interactions Mikhail Steklov, Sergey Lomin, Georgy Romanov, Dmitry Osolodkin Revelation of the amino acid residues essential for ligand-binding selectivity of cytokinin receptors from arabidopsis and maize by computational approach. Gary Stormo Improved methods for determining TF specificity Tatiana Subkhankulova Epigenetic profiling of cardiac stem cells from the adult mammalian heart Shamil Sunyaev Human germ line and somatic mutation rates: evolution, biology and statistical genetics Dmitry Suplatov, Evgeny Kirilin, Vakil Takhaveev, Vytas ?vedas Zebra: web-server for bioinformatic analysis of large protein superfamilies to identify variable amino acid residues responsible for functional diversity Valentin V. Suslov, Petr Ponomarenko, Mikhail Ponomarenko, Nikolay Kolchanov, Birgit Eisenhaber, Frank Eisenhaber Multiple DNA sites of binding to NFAT5 can contribute to gene expression as bookmarkers or A solution for an ill-posed inverse problem Yulia M. Suvorova, Eugene V. Korotkov The database of triplet periodicity change points Inna Suvorova GntR family of bacterial transcription factors and their binding motifs: structure and co-evolution Ryohei Suzuki, Daisuke Komura, Shumpei Ishikawa, Kazuki Yamamoto Restraint-based 3D Shape Manipulation Method using Hand Gestures for Interactive Molecular Dynamics Lada Sycheva, Mikhail Shneider, Petr Leiman Structure of the central spike complex from the Type VI Secretion System T up Tatiana Tatarinova, Eran Elhaik Geographic Population Structure (GPS) of worldwide human populations infers biogeographical origin down to home village Tatiana Tatarinova, Alona Chubatiuk, Michael Neely, Alan Schumitzky NonPEST: a nonparametric method for Transcription Start Site prediction Evgenia Temlyakova, Anatoly Sorokin Prediction of the bacterial promoter regions by DNA electrostatic properties Nadezhda Terekhanova, Georgii Bazykin, Alexey Kondrashov, Nikolai Mugue Patterns of genomic divergence during adaptation to fresh water in the threespine stickleback Gasterosteus aculeatus Olga Troyanskaya Tissue-specific understanding of human disease from functional genomic data Ekaterina Tsareva, Olga Kulakova, Dmitrijs Lvovs, Alexander Favorov, Alexey Boyko, Olga Favorova Discriminative selection of alternative disease-modifying treatment in multiple sclerosis patients Denis Tsygankov, Andrei Karginov, Timothy Elston, Klaus Hahn Dissecting kinase-mediated downstream pathways with temporal and spatial control of its activation Dmitrij Turaev, Michael Sommer, Thomas Rattei Evaluation framework for the taxonomic classification of metagenomic sequences Alexander Tyakht, Dmitry Alexeev, Elena Kostryukova, Sergei Roumiantsev Disbalance of gut microbiota during cancer treatment in pediatric patients detected using metagenomic sequencing U up Leonid Uroshlev, Julie Bernauer, Vsevolod Makeev Determination of sort and position of ions in RNA-ions interaction with using empirical potential method V up Olga Vakhrusheva, Alexey Kondrashov, Georgii Bazykin Epistasis in ultraconserved non-coding elements Sergei Vakulenko, Dmitry Grigoriev, John Reinitz, Andreas Weber Evolution as a hard combinatorial problem} Yuriy Vaskin, Mikhail Fursov UGENE toolkit: Bioinformatics "Swiss army knife" Paola Vera-Licona, Andrei Zinovyev, Eric Bonnet, Inna Kuperstein, Olga Kel-Margoulis, Alexander Kel, Thierry Dubois, Gordon Tucker, Emmanuel Barillot A Signaling Pathway Rationale for the Design of Combination Therapies for Cancer Valery Veresov, Alexander Davidovskii Antiapoptotic Action of Bcl-xL through Interaction with the VDAC2/tBid/Bax complex: in silico analysis Valery Veresov, Alexander Davidovskii Antiapoptotic Action of Mcl-1 and A-1(Bfl-1) via Interaction with the VDAC2/Bak complex Svetlana Vinogradova, Andey Mironov LncRNAs and their role in chromatin modifications W up X up Yu Xue, Zexian Liu, Han Cheng Computational analysis of protein phosphorylation networks from the phosphoproteomic data Y up Andrei Yakovlev, Vladimir Shuvalov A semi-classical modeling of reversible charge separation in reaction centers of photosynthesis Z up Alex Zelikovsky, Alexander Artyomenko, Nicholas Mancuso, Pavel Skums, Ion Mandoiu kGEM: An Expectation Maximization Algorithm for Amplicon-Based Error-Correction Ilya Zharov Substitution Correlation in sequences of Transcriptional Factors from MerR Family and their Binding Sites Anna Zhukova, David James Sherman Knowledge-based generalization of metabolic networks: An applicational study Andrei Zinovyev, Inna Kuperstein, Emmanuel Barillot, Wolf-Dietrich Heyer Mechanisms of genetic interactions and cancer treatment