MCCMB 2015: Proceedings

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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 tumor­specific 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



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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



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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 5’ untranslated regions’ structure in Bacilli and Clostridia genomes



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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



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Anna Ershova, Ivan Rusinov, Anna Karyagina, Sergei Spirin, Andrei Alexeevski

GATC avoidance in bacteria with DpnI/DpnII complementary R-M systems



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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



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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 “pangenome” based approach


Konstantin Gunbin, Valentin Suslov, Mikhail Ponomarenko, Fedor Gusev, Eugeny Rogaev

Evolution of core promoters in hominids towards the increased “norm of reaction” 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 Švedas

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



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Anna Hadarovich, Ivan Anishchenko, Petras Kundrotas, Ilya Vakser, Alexander Tuzikov

Quantitative comparison of functional properties in protein-protein complexes


Peter A.C.‘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



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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 Cuscó, 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



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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


Pınar Kavak, Bekir Ergüner, Bayram Yüksel, Duran Üstek, Mahmut Şamil Sağıroğlu, Tunga Güngör, 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 Kiełbasa, 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



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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



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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 Tödt, 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



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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-2′-dGTP behavior in active site of human DNA polymerase β: structural investigation in silico



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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?



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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



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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



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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 α,ω-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 ζ 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 Švedas

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



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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.



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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



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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



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Tural Yarahmadov, Jia-­ying Zhu, Alexander Martynov, Elena Elpidina

Effect of Cry3Aa toxin on gut peptidases expression levels in Tenebrio molitor larvae.



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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