MCCMB 2017: Proceedings

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Polina Avdyunina , Peter Vlasov

Human SNP associations with genetically determined disorders


Olga Bezsudnova , Ekaterina Guseva , Ivan Rusinov , Anna Ershova , Andrei Alexeevski

Lateral transfer of restriction-modification systems and their components


Dana Aisina , Oksana Yurikova , Anatoliy Ivashchenko

Features of mIR-1322 binding sites in the coding area of mRNA orthologic genes


Mariia Andrianova , Georgii Bazykin , Daniel Bredikhin , Vladimir Seplyarskiy

Changes in mutational processes and patterns of mutations during cancer development


Nikita Alkin , Yakov Dunaevsky , Mikhail Belozersky , Galina Belyakova , Valeriia Tereshchenkova , Irina Filippova , Elena Elpidina

Spectrum of proline-specific peptidases in dikarya fungi


Artem Artemov , Vladimir Seplyarskiy

Dormant origins initiate short-scale replication forks: an evidence from cancer genomes and Okazaki fragments sequencing


German Ashniev , Dmitry Rodionov

Inference of phenotypes for amino acid metabolism in human gut microbiome using subsystems approach


Arghavan Alisoltani , Anousheh Alisoltani , Esmaeil Ebrahimie , Hossein Fallahi , Naser Aliye Feto

NGS-SSR based Biomarkers for Diagnosis of Human Diseases


Ksenia Anufrieva , Victoria Shender , Georgij Arapidi

The interplay between Spliceosomal Components and Cellular Stress mediated by chemo- and radiotherapy


Taejeong Bae , Livia Tomasini , Jessica Mariani , Bo Zhou , Alexander Urban , Alexej Abyzov , Flora Vaccarino

Frequency and properties of mosaic somatic mutations in a normal developing brain


Denis Antonets , Nikolay Russkikh

Using machine learning approach to improve base calling in next generation sequencing data


Anastasia Anashkina , Yuri Kravatsky , Eugene Kuznetsov , Alexei Adzhubei

Approach to interactions modeling utilizing multiple docking servers


Alexander Andrianov , Grigorij Nikolaev , Ivan Kashyn , Alexander Tuzikov

De novo design of potential HIV-1 entry inhibitors based on the click chemistry concept: a computational study


Grigoriy Armeev , Anna Gribkova , Alexey Shaytan

Integrative modelling methods for understanding nucleosome dynamics.


Lidia Smirenina , Andrei Alexeevski

Comparative analysis of non-local events in strain evolution within prokaryotic species


Ivan Antonov , Andrey Marakhonov , Maria Zamkova , Mikhail Skoblov , Yulia Medvedeva

Fast identification of statistically significant lncRNA-RNA interactions in a transcriptome-wide search


Ivan Kashyn , Alexander Tuzikov , Viktor Andrianov , Alexander Andrianov

In silico discovery of novel fusion inhibitor scaffolds targeting a membrane proximal external region of HIV-1 gp41


Kirill S Antonets , Polina B Drozdova , Anton A Nizhnikov

Optimums of the environmental conditions affect amyloidogenic properties of prokaryotic proteomes


Alexander Abramov , Marsel Kabilov , Olga Koulakova , Alexey Tupikin , Pavel Mazin , Vera Mukhina , Olga Favorova , Alexander Favorov , Ludmila Danilova

Gene expression profiling in peripheral blood mononuclear cells reveals dependency on multiple sclerosis activity


Alexander Andrianov , Yuri Kornoushenko , Mikhail Kisel , Alexander Tuzikov

Computational design and biological evaluation of novel HIV-1 entry inhibitors based on glycosphingolipids


Irina Abnizova , Rene te Boekhorst , Arthur Dergilev , Fyodor M. Naumenko , Yuriy L. Orlov

DNA sequence complexity measures and analysis of short sequencing reads


Dmitriy Arkhipov , Sergey Lomin , Yulia Myakushina , Dmitriy Osolodkin , Georgy Romanov

Molecular modelling and BiFC studies of protein-protein interactions in cytokinin signaling


Konstantin Gunbin , Denis Antonets , Tatyana Nepomnyashchikh

Poxviral chemokine-binding proteins: theoretical study of structure and function evolution


Alina Astakhova , Vladislav Gorbatenko , Marina Sergeeva

ARE-mediated regulatory system in glioma





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Louis Bengyella , Naser Feto

Proteomics analysis and mining of effector weaponries of Cochliobolus lunatus reveals CL[xxx]LHM-motif during colonization of potato leaf


Olga Bondareva , Raisa Chetverikova , Mike Rayko , Natalja Abramson

Molecular adaptations of subterranean rodents to underground lifestyle


Valentina Burskaia , Sergey Naumenko , Georgii Bazykin

Evidence of Balansing Selection in Parallel Evolution of Closely Related Gammarus Species Genomes


Caroline Louis-Brennetot , Agathe Peltier , Simon Durand , Cécile Pierre-Eugène , Virginie Raynal , Heather C. Etchevers , Sophie Thomas , Alban Lermine , Estelle Daudigeos-Dubus , Birgit Geoerger , Martin F. Orth , Thomas G. P. Grünewald , Elise Diaz , Bertrand Ducos , Didier Surdez , Angel M. Carcaboso , Irina Medvedeva , Thomas Deller , Valérie Combaret , Eve Lapouble , Gaelle Pierron , Sandrine Grossetête-Lalami , Sylvain Baulande , Gudrun Schleiermacher , Emmanuel Barillot , Hermann Rohrer , Olivier Delattre , Isabelle Janoueix-Lerosey , Valentina Boeva

Analysis of neuroblastoma super-enhancer landscape identifies two distinct malignant cell types


Danila Bredikhin , Dmitri Pervouchine , Andrey Mironov

Associations between alternative polyadenylation and RNA secondary structure


Vladimir Babenko , Anatoly Bragin , Irina Medvedeva , Irina Chadaeva , Yuri Orlov

Analysis of alternative splicing events by RNA-seq data in glioblastoma: model cases


Anton Petrov , Boris Burkov , Alex Bateman

RNAcentral: Progress in the Development of the Non-coding RNA Sequence Database


Pavel Baranov

Protein synthesis: From the whole translatome to individual codons and back.


Polina Tikhonova , Eugene Baulin , Mikhail Roytberg

Short stems in RNA secondary structure


Aleksei Dolgov , Alexander Ksenofontov , Elena Bogacheva , Aleksandr Shishkov

Detailing the Quaternary Structure of the Helical Virus using Tritium Planigraphy


Tatiana Bessonova , Uliana Shvyreva , Diana Gagarinskaya , Sergey Antipov , Maria Tutukina , Olga Ozoline

The Dps bacterial nucleoid protein is associated with sugar metabolism


Ilya Bizin , Anna Sokolenko , Ekaterina Kuligina

Validation of novel hereditary cancer genes identified upon exome sequencing: a focus on primer design


Victor Tkachev , Anton Burzin , Nicolas Borisov

FLOating Window Projective Separator (FloWPS): a method of data transfer for expression-based features from cell lines to cancer patients during SVM-based prediction of drug efficiency in personalized medicine


Olga Bochkareva , Elena Moroz , Iakov Davydov

Evolution of Burkholderia spp


Anastasia Medvedeva , Eugene Baulin , Mikhail Roytberg

RNA triplexes within the known RNA 3D structures


Aleksandra Bezmenova , Alexey Penin , Elena Zvyagina , Artem Kasianov , Tatiana Neretina , Georgii Bazykin , Alexey Kondrashov

Accumulation of mutations in experimental evolution of basidiomycete fungus Schizophyllum commune





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Alexander Cherkasov , Kirill Arshavsky , Vladimir Sychev , Margarita Levinskikh , Oleg Gusev

Long-term space flight mediated changes in promoter landscape in Zebrafish (Danio rerio) tissues.





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Arthur Dergilev , Juriy Orlov , Vladimir Babenko

Analysis of distal gene regulation based on ChIP-seq and ChIA-PET data and biophysical models of chromosome contacts


Andjela Rodic , Bojana Blagojevic , Konstantin Severinov , Magdalena Djordjevic , Marko Djordjevic

Understanding key features of CRISPR/Cas system induction through modeling


Alexey Doroshkov , Dmitry Konstantinov , Dmitry Afonnikov , Konstantin Gunbin

Molecular evolution analysis of genetic network related to plant trichome development


Thangadurai Devarajan , Rakesh Tawadare , Rayappa Bharamappa Khandagave , Manjunath Chouraddi , Sangeetha Jeyabalan , Rachappa Sutagundi , Abhishek Mundaragi

Phylogenetic Analyses of Sugarcane Cultivars for Sugar Content and Early Maturation using Simple Sequence Repeat Markers


Aleksei Dolgov , Elena Bogacheva , Alexander Ksenofontov , Aleksandr Shishkov

Detailing the Quaternary structure of the virus using tritium planigraphy


Ruslan Deviatiiarov , Oleg Gusev

CAGE application for avian embryogenesis


Victor Urban , Anna Dudko , Valery Veresov

Structural insights into TOM-mediated proapoptotic activation of Bax


Stepan Denisov , Svetlana Iarovenko , Mikhail Gelfand

Appearance of new splice sites on human lineage is associated with positive selection and splicing changes





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

Avoidance of restriction-modification systems sites in the metagenome of Antarctic Deep Lake shows interaction of species in the metagenomic community


Aleksey Eliseev , Dmitry Chudakov , Mikhail Shugay

Comparative analysis of V-D-J rearrangement junction sequences that encode T-cell receptors recognizing similar and distinct antigens





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Gleb Fisunov , Irina Garanina , Daria Evsyutina , Tatiana Semashko , Vadim Govorun

Reconstruction of transcription control networks in Mollicutes by high-throughput identification of promoters


Alexei Finkelstein , Sergiy Garbuzynskiy

There and back again: A stereoscopic view on the protein folding puzzle


Platon Bykadorov , Marina Fridman , Nina Oparina , Vsevolod Makeev

IGNG1-IGNG3 locus, its possible role in the multiple sclerosis, and biases SNP allele frequencies for europeoid and non-europeoid populations





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Nataly Gubanova , Yuriy Orlov , Anatoly Bragin

Transcriptome profiling of primary glioma cell cultures


Lubov Gapa , Vladimir Gorshkov , Rim Gubaev , Nataliya Gogoleva , Elena Vetchinkina , Yuri Gogolev

De novo transcriptome analysis of two early developmental stages of shiitake mushroom


Konstantin Gunbin , Mikhail Ponomarenko , Valentin Suslov , Fedor Gusev , Gennady Fedonin , Evgeny Rogaev

Evolution of brain active gene promoters in human lineage towards the increased plasticity of gene regulation


Elena Bogacheva , Anastasia Golovko , Aleksandr Bogachev , Aleksei Dolgov , Victor Radjuhin

Influenza Virus Nuclear Export Protein (NEP) 3D Structure Reconstruction Probed as an Example for Improvement of Approach to the Protein 3D Structures Prediction


Irina Garanina , Daria Evsutina , Gleb Fisunov

Identification of bacteria transcription factor targets by machine learning


A Kulandaisamy , S Binny Priya , R Sakthivel , Svetlana Tarnovskaya , Ilya Bizin , Peter Hönigschmid , Dmitrij Frishman , M. Michael Gromiha

MutHTP: Mutations in Human Transmembrane Proteins


Aleksandra Galitsyna , Sergey Starikov , Ekaterina Khrameeva , Sergey Ulianov , Yuri Shevelyov , Mikhail Gelfand , Sergey Razin

3D chromatin organization of lamin-depleted cells in Drosophila


Rim Gubaev , Vladimir Gorshkov , Olga Petrova , Amina Daminova , Natalia Gogoleva , Olga Parfirova , Yuri Gogolev

Transcriptome analysis of pectobacteria-infected tobacco plants


Aleksandra Galitsyna , Anastasia Zharikova , Alexey Gavrilov , Maria Logacheva , Sergey Razin , Andrey Mironov

RNA-DNA interactions in chromatin


Tapash Ghosh

A view of protein evolution from the perspective of yeast protein-complexes


Victor Golyshev , Alexander Lomzov , Dmitry Pyshnyi

Comparison small nucleic acids derivatives hybridization parameters obtained by molecular dynamics and experimentally


Ekaterina Grafskaia , Vladislav Babenko , Nikolay Anikanov , Nadezhda Polina , Daria Kharlampieva , Pavel Bobrovsky , Vassili Lazarev

Discovery of Novel Cell-Penetrating Antimicrobial Peptides by Transcriptome Deep Analysis


Oxana Galzitskaya , Michail Lobanov

Non-random distribution of homo-repeats in eukaryotic and bacterial proteomes and their impact on biological functions


Guzel Gazizova , Oksana Tyapkina , Olga Kozlova , Elena Shagimardanova , Oleg Gusev

Tissue-specific transcriptional profile in the edible dormice is strongly affected by hibernation





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

Gene Ontology terms in scoring of docked protein models


Siarhei Hladyshau , Denis Tsygankov

A multi-scale model of cellular morphodynamics





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Elena Kyrova , Julia Panycheva , Aleksandr Ignatov

Diversity of the HrpF/NolX/PopF protein in plant pathogenic bacteria


Dmitry Ivankov

Self-consistency test reveals systematic bias in programs for prediction destabilization upon mutation


Nikolai Ivanov

Nicotiana genomes: beyond tobacco


Dmitry Ivankov

Exact correspondence between walks in nucleotide and protein sequence spaces


Svetlana Iarovenko , Stepan Denisov

Context-dependent selection of upstream start codons in Homo sapiens lineage


Laura Aviñó Esteban , Natalya Bogatyreva , Fyodor Kondrashov , Dmitry Ivankov

Finding multi-dimensional epistasis in high-throughput experimental data at the level of individual genotypes


Elena Ignatieva , Alexander Igoshin , Nikolay Yudin

Reconstruction and analysis of the human protein-protein interaction network involved in response to tick-borne encephalitis virus infection


Anna Igolkina , Georgii Bazykin , Evgeny Andronov

The Evolutionary Moulding in plant-microbial symbiosis: coevolution of signal transduction systems


Saher Islam , Amna Arshad Bajwa , Yasir Zahoor , Muhammad Abdullah , Wasim Shehzad

Genomic Selection of Superior Nili Ravi Buffalo Bull for Increasing Milk Production in Pakistan


Elena Ignatieva

Reconstruction and analysis of the protein-protein interaction network involving GWAS genes associated with elevated body mass index





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Sergei Kliver , Gaik Tamazian , Vladimir Brukhin , Stephen O’Brien , Aleksey Kommisarov

KrATER: K-mer Analysis Tool Easy to Run


Evgenia Khodzhaeva , Zoe Chervontseva

Ribosome drop-off rate in E. coli depends on mRNA properties


Bogdan Kirillov

Distinguishing highly and lowly active CRISPR/Cas9 sgRNA via Inception-based Deep Convolutional Neural Network


Olga Kiseleva , Ekaterina Poverennaya

Proteoforms scouting in HepG2 cell line


Lada Koneva , Yanxiao Zhang , Shama Virani , Pelle Hall , Jonathan McHugh , Douglas Chepeha , Gregory Wolf , Thomas Carey , Laura Rozek , Maureen Sartor

Identification and characterization of HPV-host fusion transcripts in HNSCCs


Anastasiia Kotova , Leonid Adonin

Aurelia japonica: molecular and chromosomal evidence


Sofya Kasatskaya , Elena Matveyshina

Distinct features of the T cell receptor repertoire in human regulatory T-cells


Peter Kharchenko

Analysis of clone-specific molecular and phenotypic characteristics


Olga Kozlova , Shuji Shigenobu , Oleg Gusev

New version of sleeping chironomid’s genome assembly using Illumina and PacBio data


Larisa Kiseleva , David Simpson , Michael Cohen , Igor Goryanin

Shotgun sequencing based detection of microbial community shifts during multi-step electrogenic bacteria selection


Alexander Gress , Vasily Ramensky , Olga V. Kalinina

Spatial distribution of coding diseases-associated single-nucleotide variants in complexes of the corresponding protein with other molecules


Svetlana Kuznecova , D. Suzuki , M. Logacheva , Olga Kozlova , T. Kikawada , Rushan Sabirov , Oleg Gusev

Using de novo transcriptome for identification genes involved in cryotolerance in the turtle leech Ozobranchus jantseanus.


Ekaterina Khrameeva , Daniel Bredikhin , Sergey Ulyanov , Mikhail Gelfand , Sergey Razin

Dictyostelium discoideum chromosomes are partitioned into unstable globular domains


Ekaterina Khrameeva , Aleksandra Galitsyna , Sergey Ulyanov , Sergey Razin , Yuri Shevelyov , Mikhail Gelfand

Histone acetylation level regulates formation of topologically associating domains in Drosophila


Andi Dhroso , Nathan Johnson , Saptaparni Bandyopadhyay , Dmitry Korkin

Evidence of ancient extreme conservation of genomic regions in animal genomes


Anton Karazeev , Maxim Holmatov , Anatolii Zaikovskii , Ilia Korvigo , Mikhail Skoblov

Advanced Parser for Biomedical Texts


Dmitry Karasev , Polina Savosina , Alexander Veselovsky , Dmitry Filimonov , Boris Sobolev

Identification of amino acid residues affecting on the specificity of interaction of protein kinases and small molecular inhibitors


Md. Shafiqul Islam Sikdar , Jung-Sup Kim

Characterization of genes encoding target enzymes related in amino acid biosynthesis and herbicide resistance


Aman Chandra Kaushik , Deeksha Gautam , Shakti Sahi

Cure for Primary Dopaminergic Midbrain Neurons by GPR139 Agonists using Structure based Virtual Screening and Molecular Dynamics Simulation


Youri Kravatsky , Vladimir Chechetkin , Nikolai Tchurikov

NGS application for mutational stability monitoring of viral drug targets


Kamil Khafizov , Anna Speranskaya , Anastasia Krinitsina , Evgeniya Samokhina , Maria Logacheva , German Shipulin

Using DNA Metabarcoding to Identify the Composition of Herbal Teas: Comparative Analysis of Illumina and Ion Semiconductor High-throughput Sequencing Platforms


Fyodor Kondrashov

Large scale fitness landscape of a protein-coding gene


A.O. Kosolapova , M.V. Belousov , K.S. Antonets , S.A. Bondarev , G.A. Zhouravleva , A.A. Nizhnikov

Identification of amyloid-forming proteins in the Escherichia coli proteome





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Yaw-Ling Lin , Wen-Pei Chen , Jia-Ying Lin , Ming-Li Liou

Machine Learning Approaches in Metagenomic Sequencing Analysis Related to Human Oral Microbiota Composition Associated with Periodontitis


Rudolph Layko , Vadim Nazarov , Mikhail Shugay

Convolutional architecture for prediction of peptide-MHC binding affinities


Semen Leyn , Oleg Kursanov , Xiaoqung Li , Lourdes Mujak , Fernando Garcia-Alcalde , Martin Ebeling , Andrei Osterman

Evolutionary genomics of antibiotic resistance


Alexander Lomzov , Dmitrii Pyshnyi

Influence of nucleotide sequence on conformational flexibility of the RNA dangling ends in the complexes with DNA: molecular dynamics studies


Abdullah M. Khamis , Anna V. Lioznova , Artem V. Artemov , Vasily Ramensky , Vladimir B. Bajic , Yulia A. Medvedeva

CpG traffic lights are markers of regulatory regions in humans





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Sofia Mariasina , Olga Petrova , Chi-Fon Chang , Tai Huang , Ilia Osterman , Alexey Mantsyzov , Petr Sergiev , Vladimir Polshakov

Cofactor-binding studies of the Williams Syndrome related methyltransferase WBSCR27 in solution


Alexey Morgunov , Alexander Gunnarsson , Norbert Fehér , Madan Babu

Investigating residue coevolution in proteins from a structural perspective


Valentina Maslova , Andrey Golovin

Rational design of catalytic antibody A.17


Nataliya Markelova , Maria Tutukina , Irina Masulis , Fyodor Kondrashov , Olga Ozoline

Antisense transcription may contribute to a fine-tuned expression of sugar regulators in Escherichia coli


Alexey Makunin

Isolated chromosome sequencing for evolutionary genomics


Ekaterina Myasnikova , Andrey Makashov , Alexander Spirov

Robustness of Hunchback gene pattern formation due to dynamic equilibrium in gap gene system in an early Drosophila embryo


Pavel Mazin , Margarida Cardoso-Moreira , Philipp Khaitovich1 , Henrik Kaessmann

Widespread conservation of developmental regulation of alternative splicing in mammals


Elena Minkina , Ruslan Deviatiarov , Takahiro Kikawada , Oleg Gusev

Genome under extreme desiccation: shifting transcription initiation regions in anhydrobiotic cell line


Arthur Murtazin , Semen Leyn , Dmitry Rodionov

Genomic reconstruction of metabolic pathways for the utilization of carbohydrates in the human intestinal microbiota


Kyoko Miura

Tumour resistance in induced pluripotent stem cells derived from naked mole-rats


Dmitry Malko , Nadia Bykova

In silico prediction of new minor histocompatibility antigens.





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Karol Nienałtowski , Katarzyna Andryka , Karolina Zakrzewska , Tomasz Jetka , Michał Komorowski

Detecting origins of interferons signalling sensitivity


Alexander Nesmelov , Ruslan Deviatiiarov , Elena Shagimardanova , Richard Cornette , Takahiro Kikawada , Oleg Gusev

Modeling of components of desiccation stress in anhydrobiotic cells


Sergey Naumenko

Interpreting genomes and transcriptomes of patients with rare genetic diseases


Elena Nabieva , Georgii Bazykin

SELVa: Simulator of Evolution with Landscape Variation


Gökhan Gün , Güniz Özer , Muhammad Naseem

Assessing and integrating the various levels of complexity in plant-microbe interactions





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Marina Orlova , Alexandr Shershebnev , Dmitry Borisevich , Ivan Stetsenko , Daria Plakhina , Anna Krasnenko , Dmitry Korostin

Workflow for replicable Sanger sequencing of NGS-derived mutations in clinical application


Maria Osetrova , Georgij Arapidi , Ol'ga Ivanova , Ivan Butenko , Vadim Govorun

De novo identification and taxonomic analysis of human blood peptides, not being a product of known human genes


Alexander Osypov

Differential expression meta-analysis may help to reveal the basis of energy metabolic deficiency common to neurodegenerative diseases


Tatiana Subkhankulova , Irina Abnizova , Yuriy Orlov

Novel ChIP-Seq simulation software (isChIP) for data analysis optimization


Anatoly Bragin , Vladimir Babenko , Yuriy Orlov , Arthur Dergilev , Irina Chadaeva , Arcady Markel

Differential alternative splicing by RNA-seq data in brain areas of laboratory rats with aggressive behavior


Alexander Osypov , Eugenia Krutinina , Gleb Krutinin , Svetlana Kamzolova

Role of electrostatics in transcription regulation in prokaryotes


Alexander Osypov

Codons and amino acids biases around transcription factors binding sites are due to their electrostatics


Anna Obraztsova , Mikhail Shugay , Dmitriy Chudakov

Bioinformatic analysis of the antibody repertoire induced in young and old donors in response to yellow fever vaccination


Konstantin Okonechnikov , Aki Imai-Matsushim , Lukas Paul , Alexander Seitz , Thomas F. Meyer , Fernando Garcia-Alcalde

InFusion: advancing discovery of fusions genes and chimeric transcripts from RNA-sequencing data


Alexander Osypov , Peter Kolosov , Nikolay Aseyev , Ekaterina Chesnokova , Mikhail Roshchin , Natalia Bal , Pavel Balaban

Near single-cell transcriptomics analysis of differential expression in Helix lucorum statocysts under microgravity


Alexander Osypov

DEPPDB v.3 and its use to study electrostatic and other physical properties of genome DNA and its elements, relevant to their biologycal functions





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Olga Plotnikova , Mikhail Skoblov

Expression analysis of human miRNA - mRNA interactome


Irina Poverennaya , Denis Gorev , Victor Yacovlev , Mikhail Roytberg

Exon-Intron Structure Database: a tool for intron analysis


Inna Povolotskaya , Aitor Serres-Armero , Tomas Marques-Bonet

Contribution of copy number variants to phenotypic diversity of domestic dog breeds.


Sergey Pesyak , Ekaterina Snigir

Descriptive analysis of Arabidopsis thaliana L. protein-protein interaction network: revealing of key members.


Kirill Prosvirov , Andrey Mironov , Ruslan Soldatov

The analysis of upstream open reading frame using comparative genetics.


Alexander Predeus , Tyler Ulland , Ivan Arbuzov , Yaming Wang , Wilbur Song , Vasiliki Lampropoulou , Monika Bambouskova , Fadi Towfic , Susan Gilfillan , Ekaterina Loginicheva , Brian Edelson , Benjamin Zeskind , Marco Colonna , Maxim Artyomov

Global transcriptional network reveals that tocopherols rescue TREM2-driven microglial dysfunction in vivo


Dmitry Svetlichnyy , Dmitry Pervouchine

Approaches to building spatio-temporal models of splicing regulation that include RNA structure


Alexander Panchin , Yuri Panchin , Alexander Tuzhikov

Regression analysis for automated detection of horizontal gene transfer


Marina Parr , Dmitrii Frishman

Sequence and structure features of GroE substrates orthologs in Mycoplasma


Maya Polishchuk , Inbal Paz , Yael Mandel-Gutfreund

SMARTIV: a novel method for RNA sequence and structure motif discovery from in-vivo binding data


Alexandra Pogorelskaya , Andrey Mironov , Ruslan Soldatov

Detection of signal beyond secondary structure from SHAPE experiment


Yuri Panchin , Victor Kuznetsov , Georgy Slivko-Koltchik , Dmitry Voronov

Ion channels in defecation motor program in nematode Heterorhabditis megidis


Kseniya Petrova , Ivan Antonov

Dual coding regions prediction


Nadezhda Potapova , Georgii Bazykin , Alexey Kondrashov

Negative selection in Drosophila melanogaster missense alleles





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Alina Ryabova , Alexander Cherkasov , Nariman Battulin , Veniamin Fishman , Varvara Lukyanchikova , Oleg Gusev

Determining the spatial chromatin organization upon desiccation process in the insect cells using Hi-C technology.


Dmitry Ravcheev , Ines Thiele

Comparative genomics analysis of human gut microbiome demonstrated broad distribution of metabolic pathways for mucin glycans foraging


Kirill Romanenkov , Andrey Alexeevski

A new method of evaluating genome assemblies based on kmers frequencies


Alexander Arzamasov , Matvei Khoroshkin , Semen Leyn , Dmitry Rodionov

Metabolic exchange by essential vitamins in the human intestinal microbiota


Cristian Riccio , Mélanie Tanguy , Lise Frézal

reaBuilding a pipeline for analysis of short-d RNA-seq data and natural transcriptomic variation in Caenorhabditis elegans


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

Avoidance of recognition sites of restriction-modification systems as bacteriophage anti-restriction strategy


Ivan Reveguk , Ivan Sosin , Ilia Korvigo , Mikhail Skoblov

Applying deep-learning techniques to identification of pathogenic amino acid substitutions





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Marat Sabirov , Alexander Spirov , Ekaterina Myasnikova

Scaling of the active transport systems in oocyte: 3D agent-based simulations


Alexandra Simonova , Andrei Alexeevski

Brucella and Bartonella nucleotide pangenome comparative analysis


Rinat Sultanov , Georgij Arapidi , Konstantine Babalyan , Veronika Gordeeva , Edward Generozov , Vadim Govorun

Construction of regulatory networks by integrating gene expression, promoter methylation and copy number alteration data for prostate cancer


Polina Shichkova , Ekaterina Khrameeva , Philipp Khaitovich

The effect of SNPs on gene regulation and metabolic processes in autism


Vladimir Seplyarskiy , Yegor Bazykin , Shamil Sunyaev

Error-prone bypass of pre-existing damages during the replication of the lagging strand is substantial source of mutations in cancers and germline


Prakash Saudagar , Santanu Sasidharan , Shweta Raj Raj

Identification of novel inhibitor of MAPKs from Leishmania donovani: Comparative in-silico analysis


Alexander Stepanov , Tatiana Karelina , Nikolay Markevich , Timothy Nicholas

Model of multisite tau protein phosphorylation for prediction of sensitivity to therapeutic interventions.


Elena Stavrovskaya , Alexander Favorov , Andrey Mironov

Epigenome marks interaction defines chromatin compartments


Meenu Saraf , Stuti Patel

Comparative analysis of PR gene expression in tomato inoculated with rhizobacterial Lipopolysaccharides against Fusarium oxysporum f. sp. lycopersici


Sergey Starikov , Alexandra Galitsyna , Ekaterina Khrameeva , Mikhail Gelfand

Alteration of the chromatin structure in response to lamin depletion


Nataliia Sukharicheva , Maria Tutukina , Irina Masulis , Olga Ozoline

H-NS nuceloid protein binds to the oppA-oppB intergenic region of the E. coli oppABCDF operon and controls oppB expression.


Yana Sharapova , Dmitry Suplatov , Vytas Švedas

Molecular Modeling of Catalytic and Lectin Domains in Neuraminidase A from Streptococcus pneumoniae


Dmitry Suplatov , Kirill Kopylov , Yana Sharapova , Vytas Švedas

Allosteric inhibitor Doramapimod can bind to human p38α MAP Kinase even when the activation loop is in the DFG-in state


Margarita Samborskaya , Ekaterina Khrameeva , Andrey Mironov , Mikhail Gelfand

Interplay between chromatin contact frequency and expression levels in Drosophila melanogaster, Mus musculus and Homo sapiens genomes


Anastasia Stolyarova , Elena Nabieva , Vasiliy Ptushenko , Georgii Bazykin

Сauses of single position fitness landscape changes


Natalia V. Sernova , Lidia P. Kurochkina , Pavel I. Semenyuk , Vadim V. Mesyanzhinov , Costa Georgopoulos , Ricardo A. Bernal

Pseudomonas aeruginosa phage EL chaperonin and a proposed model of its folding cycle.


Ruslan Soldatov

Single cell transcriptomics reveals sequential fate selection points and mechanism of cell fate commitment of the neural crest


Xianbin Su , Yi Shi , Xin Zou , Zhao-Ning Lu , Ze-Guang Han

Developmental trajectory of liver stem/progenitor cells at single-cell resolution


Christian Solis-Calero , Hernandes H Carvalho

Structural dynamics of Interaction between human telomeric DNA G-quadruplex 21-mer and naphthalene diimide compound MM4


Boris Sobolev , Dmitry Karasev , Darya Veselova , Alexander Veselovsky , Alexander Archakov

3D features of proteins and their structural changes related to phosphorylation


Ekaterina Savitskaya , Sofia Medvedeva , Olga Musharova , Konstantin Kuznedelov , Ekaterina Semenova , Konstantin Severinov

Determinants of spacer choice during naïve and primed CRISPR adaptation by type I-E CRISPR-Cas system of Escherichia coli


Dmitry Suplatov , Elena Schmalhausen , Vladimir Muronets , Vytas Švedas

Bioinformatic analysis of subfamily-specific positions reveals a previously unknown regulatory site in Glyceraldehyde 3-phosphate dehydrogenase family of proteins





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Svetlana Tarnovskaya , Artem Kiselev , Anna Kostareva , Dmitrij Frishman

Analysis of mutations associated with idiopathic restrictive cardiomyopathy


Maria Tutukina , Sergey Antipov , Uliana Shvyreva , Tatiana Bessonova , Elena Preobrazhenskaya , Yuri Purtov , Fyodor Kondrashov , Olga Ozoline

The Dps nucleoid protein from E. coli: is DNA protection accompanied by transcriptional regulation?


Nadezhda Terekhanova , Nikolai Mugue

Parallel adaptation to the freshwater in a number of independent White Sea populations of threespine sticklebacks


Sophya Tolstoukhova , Evgenii Ofitserov , Mark Izraelson , Vadim Nazarov

Deep learning model for prediction of probability for thymic selection for T-cell receptor sequences


Alexander Kel , Tatiana Tatarinova

TRANSFAC-ing the rice genome





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Anna Dudko , Valery Veresov

Cryo-electron microscopy-based integrative atomic-resolution modeling of the TOM GIP complex


Olga A. Vakhrusheva , Elena A. Mnatsakanova , Yan Galimov , Tatiana V. Neretina , Aleksey A. Penin , Maria D. Logacheva , Georgii A. Bazykin , Alexey S. Kondrashov

The signatures of recombination and gene conversion in the bdelloid rotifer Adineta vaga


Aleksandra Vasileva , Ilya Bizin , Oleg Talalov , Andrei Kozlov , Alexey Masharsky , Dmitrij Frishman

Accurate HIV-1 population diversity analysis using deep sequencing with Primer ID approach


Nadezda Volkova , Bettina Meier , Ye Hong , Victor Gonzalez Huici , Susanna Cooke , Sam Behjati , Peter Campbell , Anton Gartner , Moritz Gerstung

Mutational signatures of DNA repair deficiencies and cytotoxin exposures in C. elegans


Ivan Yevshin , Ruslan Sharipov , Oxana Volkova

Assessment of translation efficiency from ribosome profiling and mRNA-seq data


Yuri Kondrakhin , Ruslan Sharipov , Oxana Volkova

Prediction of start codons and mRNA translation efficiency using RiboSeq-based weight matrices


Svetlana Vinogradova , Saumya Gupta , Sébastien Vigneau , Alexander Gimelbrant

Genes with clonal monoallelic expression contribute disproportionally to expression variation in humans


Peter Vlasov , Oriol Pich i Rosello , Anna Vlasova , Polina Shichkova , Fyodor Kondrashov

The impact of human genetic variability on ligand-protein interactions and individual drug response





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Chen-Hsiang Yeang

A quantitative framework of integrating multi-modal cancer genomic data





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Vassily Lyubetsky , Roman Gershgorin , Lev Rubanov , Alexandr Seliverstov , Oleg Zverkov

Evolution and Systematics of Plastids of Rhodophytic Branch


Vasily Zubov

Dissecting epigenetic effects of Polycomb-group proteins in epidermal self-renewal and differentiation


Olga Zolotareva , Elena Bragina , Irirna Goncharova , Maxim Freidin , Ralf Hofestädt

Identification of new potential targets for treatment of coinciding asthma and hypertension


Laura Cantini , Laurence Calzone , Emmanuel Barillot , Loredana Martignetti , Andrei Zinovyev

InfoSigMap: Google Maps of informative gene signatures visualizes their compositional and functional redundancies in transcriptomic studies


Anatoliy Zubritskiy , Yulia A. Medvedeva

Role of DNA sequence in establishing histone modifications in humans