MCCMB 2013: Proceedings





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 β-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



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



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



Natalia Demidenko, Maria Logacheva, Aleksey Penin

Comparison of abiotic stress response systems between Arabidopsis thaliana and Fagopyrum esculentum



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



Elisabete Fernandes, António Pacheco, Carlos Penha-Gonçalves

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



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 ТАТА-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)





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 Hönigschmid, 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 Paša-Tolić, Matthias Birschenk, Iris Antes, Richard Smith, Michael Galperin, Pavel Pevzner, Dmitrij Frishman

Proteogenomic analysis of bacterial signal peptides



Guoli Ji, Yong Zeng, Xiaohui Wu, Meishuang Tang

PLS-based Characteristic Selection and Identification of Gene Expression Profiles



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 Karacaören

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



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



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

Béla Albert Marosi, Oleksandr Zinenko, Ioan Ghira, Jelka Jelka Crnobrnja-Isailović, Petros Lymberakis, Tibor Sós, 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



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



Konstantin Okonechnikov, Thomas Meyer, Fernando García-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



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





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



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 Göbels

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 Švedas

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



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



Leonid Uroshlev, Julie Bernauer, Vsevolod Makeev

Determination of sort and position of ions in RNA-ions interaction with using empirical potential method



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





Yu Xue, Zexian Liu, Han Cheng

Computational analysis of protein phosphorylation networks from the phosphoproteomic data



Andrei Yakovlev, Vladimir Shuvalov

A semi-classical modeling of reversible charge separation in reaction centers of photosynthesis



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