MCCMB 2019: Proceedings

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Eldar Abdullaev , Peter Arndt

Modelling Segmental Duplications in the Human Genome


Anahita Amiri , Gianfilippo Coppola , Soraya Scuderi , Feinan Wu , Tanmoy Roychowdhury , Flora Vaccarino , Alexej Abyzov

Transcriptome and epigenome landscape of human cortical development modeled in organoids


Darya Afenteva , Mikhail Orlov , Maria Poptsova

Joint mechanical, thermodynamic and electrostatic machine-learning model for prediction of nucleosome positions


Dmitry Afonnikov , Mikhail Genaev , Nikolay Shmakov , Zakhar Mustafin , Alexey Mukhin , Dmitrii Konstantinov , Alexey Doroshkov , Sergey Lashin

Analysis of out of reference transcripts from RNA-seq libraries in crops.


Sergey Aganezov , Fritz Sedlazeck , Sara Goodwin , Gayatri Arun , Isac Lee , Sam Kovaka , Michael Kirsche , Rachel Sherman , Robert Wappel , Melissa Kramer , Karen Kostroff , David Spector , Winston Timp , Michael Schatz , Richard McCombie

Reconstructing haplotype-specific cancer genome karyotypes with multiple sequencing technologies


Dana Aisina , Anatoliy Ivashchenko

Prediction of clusters of miRNA binding sites in mRNA candidate genes of luminal A and B subtypes breast cancer


Aigul Akimniyazova , Alexandra Kim

The interaction of miRNAs with mRNAs of genes in esophageal squamous cell carcinoma


Nikita Alexeev , Alexey Zabelkin

Estimating the true number of genome rearrangements between species


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

Variety of proline-specific peptidases in higher fungi


Alexander Andrianov , Grigory Nikolaev , Yuri Kornoushenko , Anna Karpenko , Alexander Tuzikov

Identification of Novel Potential HIV-1 Entry Inhibitors Targeting CD4-Binding Site of the Envelope gp120: Click Chemistry In Silico, Structure-based Docking and Molecular Dynamics Studies


Alexander Andrianov , Grigory Nikolaev , Yuri Kornoushenko , Jinghe Huang , Shibo Jiang , Alexander Tuzikov

In Silico Discovery of Novel HIV-1 Entry Inhibitor Scaffolds Based on Broad and Potent Neutralizing Antibody N6


Alexander Andrianov , Grigory Nikolaev , Yuri Kornoushenko , Sergey Usanov

Development of Novel 1,2,4-Triazole-Based Compounds as Potential Aromatase Inhibitors: a Computational Study


Dmitry Antipov , Mikhail Raiko , Alla Lapidus , Pavel Pevzner

metaplasmidSPAdes: Plasmid Detection and Assembly in Genomic and Metagenomic Datasets


Maria Starchevskaya , Yuri Vyatkin , Denis Antonets

Metagenomic analysis of Leptinotarsa decemlineata virome


Ivan Antonov , Maria Zamkova

Comparative genomics analysis of translational frameshifting in aerobic cobalt chelatase genes


Ksenia Anufrieva , Victoria Shender , Georgij Arapidi

Combining data from TCGA and GEO databases to predict the level of alternative spliced isoforms in cancer cells


N.V. Zakharevich , M.S. Nikitin , A.S. Kovtun , V.N. Danilenko , Irena I. Artamonova

Diversity of CRISPR/Cas systems in human microbiomes in health and disease


Aleksandr Arzamasov

Genomic encyclopedia of bifidobacterial carbohydrates utilization


Ekaterina Tulaeva , Vladimir Arzhanik

CH-π stacking interaction is not essential in antibody-carbohydrate binding


German Ashniev

Genomics-based inference of metabolic capabilities for biosynthesis and degradation of amino acids in the human gut microbiome.


Aleksandr Zenin , Yakov Tsepilov , Sodbo Sharapov , Evgeny Getmantsev , Leonid I. Menshikov , Peter O. Fedichev , Yurii Aulchenko

Genetic landscape of human healthspan





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Vladimir Babenko , N. Kudryavtseva

Medium spiny neurons genes pathways form four distinct clusters in stress affected murine model


Roman Babenko

FTO gene affects obesity specifically in Europeans


Yasin Bakis , Bahadir Altintas

Proposal of a new alignment free resampling method for phylogeny construction


Pavel Baranov

Translation initiation in mammals: Why so many starts?


Galina Glazko , Boris Zubaylov , Frank Emmert-Streib , Ancha Baranova , Yasir Rahmatallah

Analysis of proteome-transcriptome correlations with self-contained GSA enhances consensus colon cancer classification


Darya Mikhailova , Valeria Popova , Eugene Baulin , Mikhail Roytberg

Accounting for RNA secondary structure allows improved classification and prediction of RNA base triples


Jan Baumbach

Systems Medicine - or - What I learned about Arnold Schwarzenegger while studying breast cancer survival


Ayaz Belkozhayev , Raygul Niyazova

Characteristics of miRNA interaction with CDS mRNA genes associated with CAG trinucleotide repeat disorders development


Mélanie Mazurier , Cécile Ben

Genome-wide association study of quantitative disease resistance against Verticillium wilt in the model legume Medicago truncatula


Cécile Ben

-Omics approaches to unravel molecular responses to root microbes in legumes


Sven Bergmann

Robust and interpretable assessment of network module identification methods


Tatiana Bessonova , Sofya Garushyants , Eugenia Belousova , Inna Suvorova , Fyodor Kondrashov , Maria Tutukina , Olga Ozoline

Interplay of the Escherichia coli transcription factors involved in control of pathogenicity and translated as multiple protein forms


Aleksandra Bezmenova , Elena Zvyagina , Anna Fedotova , Maria Logacheva , Georgii Bazykin , Aleksey Kondrashov

The dependence of homologous recombination rate on the level of heterozygosity in hypervariable fungus Schizophyllum commune


Dmitry Biba , Galya Klink , Georgii Bazykin

Searching for compensatory frameshifting indels and determining their role in protein evolution


Kristina Perevoshchikova , Olga Bochkareva

Evolution of multi-chromosomal bacteria Vibrio spp


Semyon Bodrov , Olga Bondareva , Natalia Abramson

Mitochondrial phylogeny of Alticola Blanford, 1881 with dN/dS estimation


Valentina Boeva

Deciphering the role of DNA promoter hypermethylation in adrenocortical carcinoma


Alexander Bolbat , Natalia Sorokovikova , Irina Kaygorodova

On the use of 12S rRNA marker fragment for resolving phylogenetic relationships


Olga Bondareva , Semyon Bodrov , Natalia Abramson

Signatures of natural selection in mitochondrial genome of underground rodents.


Danila Bredikhin , Ricard Argelaguet , Damien Arnol , Oliver Stegle

Factor decomposition of structured single-cell omics data


Valentina Burskaia , Nadezhda A. Potapova , Ilya Artyushin , Georgii Bazykin

The search for bird mitochondrial genome adaptations to high altitude, migration, diving, wintering and flight


Andrey Buyan , Sergey Dmitriev , Ivan Kulakovskiy

Identification of the human ribosomal RNA contacts with mRNA-binding proteins using eCLIP data from ENCODE





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Leonardo Isaias Lopez Flores , Ernesto Borrayo Carbajal

Phylogenetic-based phenotype-related genetic marker selection method in Sechium edule


Alexander Cherkasov , Alina Ryabova , Elena Shagimardanova , Sabina Kondratyeva , Nariman Battulin , Oleg Gusev

Desiccation mediates stabilization of 3D chromatin structure in the cells of Polypedilum vanderplanki.


Samantha Chill , Anna Baranova

A Review of Current Bioinformatic Tools to Assess Mitochondrial Heteroplasmy





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Anastasia Danchurova , Nataliya Logvina , Timofei Zatsepin , Dmitri Pervouchine

Novel cross-regulatory events via AS-NMD among RNA-binding proteins


Ludmila Danilova

Differentially Methylated Super-Enhancers Regulate Target Gene Expression in Human Cancer


Ostroverkhova Daria , Moldogazieva Nurbubu , Porozov Yuri

Affinity of estrogen- and antiestrogen-binding to human alpha-fetoprotein: in silico study


Stepan Denisov , Aleksei Mironov , Dmitri Pervouchine

Tandem alternative splice sites may represent noise of splicing machinery


Marko Djordjevic , Jelena Repac , Bojan Bozic , Ognjen Milicevic

Analysis of CRISPR/Cas non-canonical functions


Hanna Dudko , Alexander Davidovskii , Valery Veresov

Structural modeling of MOAP-1-guided proapoptotic mitochondrial recruitment of tBid





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Artyom Egorov

svist4get: a simple visualization tool for genomic tracks from RNA-Seq, Ribo-Seq and other high-throughput sequencing data


Birgit Eisenhaber , Frank Eisenhaber

The 160k Natural Organism Library at the Bioinformatics Institute Singapore: A Treasure Trove for Mining Using Biological, Chemical, Genomic and in silico High-Throughput Screenings.


Frank Eisenhaber

Quantifying the progress in life sciences: Decline in gene and protein function discovery rate despite big omics data


Yakov A. Tsepilov , Maxim B. Freidin , Sodbo Zh. Sharapov , Aleksandra S. Shadrina , Elizaveta E. Elgaeva , Melody Palmer , Lennart C. Karssen , Pradeep Suri , Frances M. K. Williams , Yurii S. Aulchenko

Genome-wide association study of genetic principal components of four chronic musculoskeletal human pain types


Anna Elizarova , Yulia Medvedeva

miRNA-directed activation of genes in macrophages during Mycobacterium tuberculosis infection


Evgenia Elizarova , Arthur Zalevsky , Elena Lukyanova , Anna Kudryavtseva , Andrey Golovin

Effect of mutations associated with the development of paraganglioma on the structure of succinate dehydrogenase


Anton Eremeev , Alexander Spirov

Modeling SELEX for Promoters Using a Combination of Royal Road and Royal Staircase Fitness Functions


Ivan Rusinov , Marina Khachaturyan , Anna Ershova

Horizontal gene transfer of defense systems in microbial communities


Marina Khachaturyan , Ivan Rusinov , Anna Ershova

Diversity of Restriction-Modification Systems in Surface and Deep Layers of World Ocean





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Bahman Afsari , Emily Davis-Marcisak , Leslie Cope , Daria A. Gaykalova , Donald Geman , Sidharth Puram , Loyal A. Goff , Alexander V Favorov , Elana J Fertig

Uncovering hidden sources of transcriptional dysregulation arising from inter- and intra-tumor heterogeneity


Gennady Fedonin , Konstantin Chukreev , Konstantin Kuleshov , Anfisa Popova , Alexey Neverov

Gene coevolutionary network for drug resistance of M. tuberculosis


Jennifer Curry , Dahlia Besmer , Timothy Erick , Nury Steurtwald , Lopamudra Roy , Priyanka Grover , Shanti Rao , Sritama Nath , Jacob Ferrier , Robert Reid , Pinku Mukherjee

Indomethacin enhances anti-tumor efficacy of a MUC1 peptide vaccine against breast cancer in MUC1 transgenic mice





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Anastasiia Gainullina , Alexey Sergushichev , Maxim Artyomov

ImmGen Open Source Mononuclear Phagocyte Profiling Analysis


Martha Evteeva , Marina Galchenkova

New approaches for in silico artificial riboswitches design


Rozalina Galimullina , Ruslan Deviatiiarov , Elena Shagimardanova , Oleg Gusev

Functional annotation based on proteins alignment and paralogous expression in Polypedilum vanderplanki


Oxana Galzitskaya

M.A. Roytberg and the first library of disordered patterns in 3D protein structure


Jun Gao , Gen Li

Trinucleotide Base Pair Stacking Free Energy for Understanding TF-DNA Recognition and the Functions of SNPs


Michael Garton

Computational method generate highly stable D-amino acid peptides and proteins using a mirror image of the entire PDB


Sofya Garushyants , Maria Selifanova , Anna Kaznadzey , Georgii Bazykin

Mutational patterns in E.coli evolution


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

Promoter-level expression atlas of skeletal muscle in hibernating edible dormouse


Laurent Gentzbittel

WhoGEM, a genomic admixture-based prediction machine, that accurately predicts quantitative functional traits in plants.


Vadim Gladyshev

Systems Biology of Aging and Lifespan Control


Veronika Gordeeva , K. A. Babalyan , G.P.Arapidi , E.V. Generozov , V.M. Govorun

Construction of ensemble model for CNV calling using WES data


Ivo Grosse

Entropic Hourglass Patterns and the Emergence of Biodiversity


Rim Gubaev , Svetlana Goryunova , Denis Goryunov , Pavel Mazin , Stepan Boldyrev , Alina Chernova , Asiya Ayupova , Martynova Elena , Zhanna Mukhina , Yakov Demurin , Philipp Khaitovich

Mapping of genetic associations for agronomically important traits in Russian collection of rapeseeds (Brassica napus)


Valeria N. Timonina , Viktor N. Shamanskiy , Konstantin Yu. Popadin , Konstantin V. Gunbin

Seeking for mtDNA structural determinants of organisms longevity


Kristina E. Ushakova , Anastasia D. Sokol , Konstantin Yu. Popadin , Konstantin V. Gunbin

Mistranslation optimization of mitochondrial genes drives mammalians longevity. A hypothesis.


Tatiana Gurbich , Olesia Klimchuk , Ivan Stetsenko , Nikolay Plotnikov , Alexandr Rakitko , Anna Krasnenko , Valery Ilinsky

Predicting the percentage of duplicate reads in exome sequencing





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Laleh Haghverdi , John C. Marioni , Wolfgang Huber

A Soft Alignment of Multiple Omic t-SNEs


Yusuke Hiki , Takahiro Yamada , Olga Colzova , Richard Cornette , Gusev Oleg , Takahiro Kikawada , Akira Funahashi

Inference of transcriptional regulatory network driven by desiccation and rehydration in Polypedilum vanderplanki





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Elena Ignatieva

Reconstruction and analysis of the of protein-protein interaction network involved in the human body weight regulation


Anna Igolkina

Bayesian SEM model describes the latent mechanism linking genotypes and complex phenotypes


Irina Ilina , Julia Bubis , Elizaveta Solovyeva , Ksenia Kuznetsova

Comparison of Cysteine alkylating strategies in proteomics


Dmitry Ivankov

Algorithm for finding all combinatorially complete datasets in random mutagenesis data


Timofei Ivanov , D.D. Pervouchine

Mutually exclusive exons evolution


Anatoliy Ivashchenko , Aizhan Rakhmetullina

Prediction of osa-miRNA binding sites in human mRNA genes





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Olga Kalinina

Resistance to novel antibiotics studied with a combination of protein structure modelling and phylogenetic approach


Dmitry Karasev , Alexey Lagunin , Dmitry Filimonov , Boris Sobolev

Detection of the protein targets for small molecular ligands with use of the local sequence similarity estimation


Vadim Karnaukhov , Ekaterina Komech , Alena Novikova , Artem Mikelov , Mikhail Shugay , Anton Chugunov , Ivan Zvyagin

Computational approach for prediction of autoimmune disease-associated T-cell receptor epitopes


Lusine Khachatryan , Yang Xiang , Carine Poussin , James Battey , Adrian Stan , Stéphanie Boué , Nicolas Sierro , Julia Hoeng , Nikolai V. Ivanov

Are metagenomic data sufficiently informative to robustly predict inflammatory bowel disease status?


Ekaterina Khrameeva , Ilia Kurochkin , Philipp Khaitovich

Transcriptome map of the human, chimpanzee, bonobo, and macaque brains at the single-cell resolution


Galya Klink , Georgii Bazykin

Inference of changes of fitness landscape from sequence data with single-position resolution


Yuriy Kondrakhin , Semyon Kolmykov , Ivan Yevshin , Ruslan Sharipov , Anna Ryabova , Mikhail Kulyashov , Fedor Kolpakov

Combining GTRD ChIP-Seq datasets with FANTOM5’s transcription start sites for prediction of gene expression levels


Semyon Kolmykov , Yuriy Kondrakhin , Ivan Yevshin , Ruslan Sharipov , Mikhail Kulyashov , Fedor Kolpakov

Human cistrome - genome-wide map of human transcription factor binding sites derived from GTRD database


Dmitry Konovalov , Maria Poptsova

Role of guanine quadruplexes CpG methylation in epigenetic regulation


Vladislav V. Khrustalev , Tatyana A. Khrustaleva , Victor V. Poboinev , Alexander M. Arutyunyan , Aleksander L. Ksenofontov , Larisa V. Kordyukova

WI14 peptide corresponding to the inner domain of H1N1 Influenza hemagglutinin changes its secondary structure in acidic medium


Dmitry Korkin

Ancient genomic regions of extreme conservation: Insights into evolution, structural organization, and function


Ilia Korvigo , Ivan Reveguk , Mikhail Skoblov

Mutagenesis data in the modern age


Olga Kozlova , Guzel Gazizova , Elena Shagimardanova , Oleg Gusev

The whole-genome analysis of heat shock proteins system in extremophile nonbiting midges


Pavel Kravchenko , Dmitry Knorre

Evolution of mitochondrial DNA inheritance patterns


Pushpendra Kumar , Anil Sirohi

Analysis of plant-specific SBP-box transcription factors during flower and fruit development in plants of diverse families.


Anna Kurilovich , Maria Poptsova

The relationship between DNA secondary structures, epigenetic markers, transcription factors and structural somatic mutations in cancer genomes


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

Molecular components of nematode intestinal pacemaker


Elena Kyrova

Comparative analysis of genome sequences of polyphage Xanthomonas arboricola str. 3004





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Olga Lazareva , Hoan Van Do , Stefan Canzar , Jan Baumbach , Tim Kacprowski , Markus List

BiGAnts: network-constrained biclustering of patients and multi-omics data


Uroshlev Leonid , Ilicheva Irina , Nechipurenko Yury

Research of pattern for DNA fragmentation in plants


Victor Levitsky , Victoria Mironova , Elena Zemlyanskaya , Dmitry Oshchepkov , Tatyana Merkulova

The comprehensive analysis of motifs co-occurrence in ChIP-seq data with MCOT package


Anna Litvin , Zoe Chervontseva

Features of DNA sequences learned by neural networks





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Chitaranjan Mahapatra

Mathematical modeling of Vas Deferens Smooth Muscle Electrophysiology: Role of Ion Channels in Generating Electrical Activity


Andrei Lando , Ilya Vorontsov , Boytsov Alexander , Sergey Abramov , Natalia Klimenko , Ivan Kulakovskiy , Vsevolod Makeev

Change point identification in long Poisson series: application to DNase I and ChIP-seq data


Dmitry Malko , Dmitrii Romaniuk

A novel approach for prediction of immunopeptidomes.


Atamanova Maria

A Rapid Exact Solution for the Guided Genome Aliquoting Problem


Maria Duca , Rodica Martea

Interaction network between genes involved in defensive response to broomrape


Lev Mazaev , Stepan Denisov , Dmitri Pervouchine

Possible role of upstream open reading frames in NMD-dependent degradation of human mRNAs


Pavel Mazin

Toward genetic selection of dairy cows in Russia


Elena Matveishina , Yulia Medvedeva

Predicting DNA:RNA triplexes based on RNA secondary structure


Asia Mendelevich , Svetlana Vinogradova , Saumya Gupta , Andrey Mironov , Alexander Gimelbrant

Eliminating transcriptome-wide batch effects results in higher precision in allele-specific expression measurements


Alina A. Mikhailova , Kristina Ushakova , Alina G. Mikhaylova , Valeria Lobanova , Ilya Mazunin , Pavel Kravchenko , Dmitry Knorre , Alexandre Reymond , Konstantin Gunbin , Konstantin Popadin

Tandem repeats are selfish elements which mark the level of hidden recombination in animal mitochondrial genomes


Alina Mikhaylova , Alina Mikhaylova , Kristina Ushakova , Evgeniy Tretyakov , Konstantin Popadin , Alexander Reymond , Konstantin Gunbin , Dmitrii Knorre , Ilya Mazunin , Konstantin Khrapko , Sergey Nikolaev

Mitochondrial mutational spectrum in vertebrates is shaped by temperature and generation time.


Elizaveta Minina , Andrei Alexeevski , Eugene Sheval

Evolution of proteins of the nucleoplasmin family


Elena Minkina , Natalia Akberova , Elena Shagimardanova , Igor Adameyko , Oleg Gusev

The highly-variable enhancers in the intra-specific morphological diversity


Andrey Mironov , Alexey Gavrilov , Anastasya Zharikova , Alexandra Galitsyna , Sergey Razin

Red-C – a new method for RNA-chromatin interactome discover


Aleksei Mironov , Stepan Denisov , Olga Kalinina , Dmitri Pervouchine

Structural annotation of protein indels associated with splicing aberrations


Aleksandra Mitina , Yun-Mei Wang , Pavel Mazin , Anna Vanyushkina , Waltraud Mair , Olga Efimova , Philipp Khaitovich

Role of breast milk lipid composition in postnatal brain development


Mikhail Moldovan , Zoya Chervontseva , Mikhail Gelfand

mRNA editing: a genome-scale pre-adaptation in soft-bodied cephalopods


Denis Moshensky , Andrey Alexeevski

Essential and advantageous genes detection in bacterial genomes


Sabina Mukba , Petr Vlasov , Elena Alkalaeva

Molecular modelling of T7 RNA polymerase available to work with dna templates carrying artificial nucleotides


Vera Mukhina , Theresa Guo , Fernando Zamuner , Catriona Mitchell , Ludmila Danilova , Daria Gaykalova , Alexander Favorov

Characterization of epigenetic landscape of integrated HPV in oropharyngeal cancer


Stepan Pachganov , Khalimat Murtazalieva , Alexey Zarubin , Tatiana Taran , Duane Chartier , Tatiana Tatarinova

TransPrise – a deep learning approach for prediction of eukaryotic transcription start sites


Ekaterina Myasnikova , Spirov Alexander

Modeling of spatial and temporal expression patterns of the gene ensemble active both in early Drosophila segmentation and neurogenesis





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Elena Nabieva , Sofya K. Garushyants , Maria Logacheva , Tatyana Neretina , Viktoria Moskalenko , Natalia Libman , Denis Pyankov , Evgeniia Glazyrina , Georgii Bazykin , Anna Fedotova

Accurate fetal DNA variant calling in the presence of maternal cell contamination


Muhammad Naseem

Systems based deconvolution of Immune-defense Transcriptional Signatures in the Arabidopsis Shoot Apical Meristem


Sergey Naumenko

RNA sequencing as a diagnostic tool for exome- or gene panel-negative cases of neuromuscular Mendelian diseases


Tatiana Nepomnyashchikh , Denis Antonets , Tatiana Tregubchak , Alexander Shvalov , Elena Gavrilova , Sergei Shchelkunov , Rinat Maksyutov

Phylogenetic analysis of Chordopoxvirinae genomes with alignment-free approach


Daria Nikolaeva , Sofya Garushyants

Is habitat diversity associated with bacterial pangenome structure?


Ekaterina Noskova , Vladimir Ulyantsev , Pavel Dobrynin

Demographic Inference from the Allele Frequency Spectrum


Arina Nostaeva , Maria Poptsova

Patterns of associations of G-quadruplexes and histone modifications in human stem cells and brain tissue


Ivan Chudinov , Valeriia Novikova , Marija Zaičenoka , Veronika Abrasheva , Tatyana Ivanova , Konstantin Kozhemiakov , Victoria Scobeyeva , Ilya Artyushin , Egor Shchelkanov , Tatiana Moskvina , Mikhail Shchelkanov

The genome of new Echinophthiridae Enderlein species Antarctophthirus nevelskoy





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Vera Odintsova , Natalia Klimenko , Alexander Tyakht

Comparison of probability distributions for metagenomic sequence data


Konstantin Okonechnikov , Jens-Martin Hübner , Jesse Dixon , Stefan Pfister , Marcel Kool , Lukas Chavez

Chromosome conformation analysis of ependymoma tumors identifies putative target genes activated by distal oncogenic enhancers


Maria Osetrova , Ekaterina Khrameeva , Anna Tkachev , Aleksandra Mitina , Philipp Khaitovich

Comparative analysis of the lipid organization of various human brain regions


Evgeniya Oshchepkova , Yana Sizentsova , Daniil Wiebe , Viktoria Mironova

Search for cis-elements associated with response to dioxin in human


Alexander Osypov

Selection on physical properties of promoters and TFBS DNA affects protein content


Glenn Oyong , Maria Carmen Tan , Francisco Franco Jr. , Yves Ira Reyes , Chien-Chang Shen , Consolacion Ragasa

In Silico Docking of Labdane Diterpenoids Reveals Cytoprotective Activity against Cobra Venom and Novel In Vitro Antiophidian Neutralizing Activity





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Alexander Panchin , Yuri Panchin , Aleoshin Vladimir

A hypothesis on the evolution of Myxosporea - parasites that lack major apoptotic pathways


Umesh Panwar , Sanjeev Kumar Singh

Developing new inhibitor to diminish Integrase and LEDGF/p75 relation using an in silico approach


Wolfram Volkwein , Ralph Krafczyk , Zhenghuan Guo , Maximilian Josef Ludwig Johannes Fürst , Miriam Pfab , Kirsten Jung , Jürgen Lassak , Pravin Kumar Ankush Jagtap , Janosch Hennig Hennig , Marina Parr , Elena Mankina , Dmitrij Frishman , Jakub Macošek

Switching the Post-Translational Modification of Elongation Factor P


Dmitri Pervouchine , Yaroslav Popov , Andy Berry , Beatrice Borsari , Adam Frankish , Roderic Guigo

Integrative transcriptomic analysis suggests novel autoregulatory splicing events coupled with nonsense-mediated mRNA decay


Olga Vasyutkina , Dmitri Pervouchine

The role of RNA secondary structure in expression of non-collinear transcripts


Svetlana Kalmykova , Marina Kalinina , Dmitry Skvortsov , Dmitry Pervouchine

Impact of somatic mutations disrupting RNA structure on alternative splicing


Sergey Petrov , Artem Kasianov , Leonid Uroshlev , Vsevolod Makeev

Annotation of genome graphs


Olga Plotnikova , Mikhail Skoblov

Analysis of experimentally derived landscape of microRNA-mRNA human interactome


Aleksandra Polenova , Irina Gushchina , Vitas Švedas , Dmitry Nilov

Identification of new sulfonated inhibitors of human lactate dehydrogenase A through virtual screening and structural filtration


Anfisa Popova , Ksenia Safina , Vasily Ptushenko , Anastasia Stolyarova , Alexander Favorov , Alexey Neverov , Georgii Bazykin

Allele-specific non-stationarity in evolution of Influenza A surface proteins


Nadezhda Potapova , Anastasia Stolyarova , Shamil Sunyaev , Alexey Kondrashov

Reason of attraction between selectively neutral loci and its dependence on Ne


Nadezhda Potapova , Alexey Kondrashov

Microinversions on the evolutionary path connecting human and primates


Andrey Prjibelski , Dmitrii Meleshko , Hagen Tingler

De novo transcriptome assembly with spISO-seq data





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Michael Raevskiy , Yulia Medvedeva

Selection of key reprogramming and differentiation factors in the hemopoiesis by machine learning methods


Alexandr Rakitko , Iaroslav Popov , Igor Nizamutdinov , Valery Ilinsky

Genetic risk scores in multifactorial diseases.


Maria Molchanova , Vladimir Kutsenko , Olga Kalinina , Vasily Ramensky

Prediction of functional effect of short in-frame indels


Dmitry Ravcheev , Lubin Moussu , Ines Thiele

Comparative genomics analysis revealed novel types of bacterial microcompartments in the human gut microbiome


Mireille Regnier

Fun with clumps and automata


Ekaterina Romanova , Yulia Medvedeva

DNA methylation changes in regulatory regions in AML patients with mutations in transcription factors


Alina Ryabova , Alexander Cherkasov , Richard Cornette , Elena Shagimardanova , Takahiro Kikawada , Oleg Gusev

Metabolic shifts during desiccation-rehydration cycle in the anhydrobiotic insect P. vanderplanki


Aleksey Vanurin , Semen Doronin , Evgenia Tsybul’ko , Elena Pasyukova , Olga Rybina

A computational approach to identify transcription regulation patterns of functionally related genes in Drosophila melanogaster





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Ksenia Safina , Alexey Neverov , Georgii Bazykin

Epistatic interactions in protein sites that contribute to H5N1 virulence in mammals


Yuliya Sarana , Pavel Shelyakin

Comparative analysis of aphids microbiomes


Victoria Savinova , Anton Savostianov , Olga Tsoy , Sergey Ulyanov , Sergey Razin , Mikhail Gelfand , Ekaterina Khrameeva , Galitsyna Aleksandra

Prediction of Dictyostelium discoideum chromatin loops from genomic sequence


Vladimir Seplyarskiy

Clustered mutations in human germline


Roman Sergeev , Uladzislau Sataneuski , Alexandr Tuzikov

Algorithm for searching multi-SNP combinations associated with variation in binary phenotype


Svetlana Shabalina

Complexity and evolution of the mammalian transcriptome: the architecture of alternative transcription and splicing


Viktor Shamanskiy , Anastasia Sokol , Valeria Timonina , Konstantin Gunbin , Konstantin Popadin

A genetic handicap approach: how to estimate the genome-wide burden of slightly-deleterious variants in a model population


Sodbo Sharapov , Yakov Tsepilov , Lucija Klaric , Massimo Mangino , Gaurav Thareja , Alexandra Shadrina , Mirna Simurina , Concetta Dagostino , Julia Dmitrieva , Marija Vilaj , Frano Vuckovic , Tamara Pavic , Jerko Stambuk , Irena Trbojevic-Akmacic , Jasminka Kristic , Jelena Simunovic , Ana Momcilovic , Harry Campbell , Margaret Doherty , Malcolm Dunlop , Susan Farrington , Maja Pucic-Bakovic , Christian Gieger , Massimo Allegri , Edouard Louis , Michel Georges , Karsten Suhre , Tim Spector , Frances Williams , Gordan Lauc , Yurii Aulchenko

Genome-wide association study finds new loci affecting N-glycosylation of human blood plasma proteins


Yana Sharapova , Dmitry Suplatov , Vytas Svedas

Neuraminidase A from Streptococcus pneumoniae: Three Different Ways to Modulate Enzyme Activity


Abusaid Shaymardanov , Dmitry Svetlichnyy

Identification of species-specific DNA-regulatory elements in brain


Grigoriy Armeev , Galina Komarova , Alexey Shaytan

Integrating molecular modeling of nucleosomes with experimental data from EM, FRET and footprinting experiments


Dmitrii Shcherbinin , Mikhail Shugay

Construction of TCR’s CDR3 loops conformations using in silico step-by-step single amino acid mutation approach.


Vladimir Shchur , Thorfinn Sand Korneliussen , Rasmus Nielsen

ngsPSMC: genotype likelihood-based PSMC for analysis of low coverage NGS data


Maksim Shegay , Vytas Svedas , Vladimir Voevodin , Dmitry Suplatov , Nina Popova

Parallel computing in structural bioinformatics: efficient 3D-alignment of protein superfamilies on a supercomputer


Aleksei Shevkoplias , Zoe Chervontseva

Identification, evolution, and function of tryptophan leader peptides TrpL in alpha-proteobacteria


Olga Sigalova , Mattia Forneris , Katharina Bender , Judith Zaugg , Eileen Furlong

Identifying mechanisms regulating gene expression variation during embryonic development


Sergei Slavskii , Tatiana Shashkova , Georgii Bazykin , Fyodor Kondrashov , Yurii Aulchenko

Analysis of human height in the UK Biobank


Mikhail Slizen , Dovidchenko Nikita , Glyakina Anna , Galzitskaya Oksana

Genome comparison of a group of bacteria by KEGG-modules and pathways


Elina Smolkina , Dmitry Nilov

Searching for inhibitors against the open conformation of human lactate dehydrogenase A


Anastasia Sokol , Valeria Timonina , Ilya Mazunin , Konstantin Gunbin , Dmitry Knorre , Konstantin Popadin

Heat shock proteins buffer environmental and genetic perturbations: from short-term to long-term effects


Antonio del Sol

Single-cell Systems Biology Approaches to Stem Cell Research and Regenerative Medicine


Ruslan Soldatov

Transcriptional Dynamics of Single Cells


Evgeniia Sotnikova , Denis Goryunov , Anna Sheremet , Svetlana Goryunova

SAPPHIRE: automatic pipeline for data analysis of high throughput amplicon sequencing and phylogeny reconstruction


Alexander Spirov , Ekaterina Myasnikova

Transfer of Evolutionary Computation Techniques to in vitro Evolution: Tests in Silico


Anastasia Stolyarenko , Toomas Leinsoo , Yuri Abramov , Artem Ilyin , Pavel Mazin , Mikhail Klenov

The interplay of Piwi and heterochromatin proteins in transposable element silencing in the germline of Drosophila melanogaster


Anastasia Stolyarova , Aleksandra Bezmenova , Alexey Kondrashov , Georgii Bazykin

Prevalent epistatic interactions between amino acid sites in Schizophyllum commune


Vladimir Sukhov

Rare-event probability estimation in the functional gene set enrichment analysis


Rinat Sultanov , Arapidi Georgij , Konstantin Babalyan , Elena Sharova , Edward Generozov , Maria Lagarkova , Vadim Govorun

TP63 and TRIM29 axes regulate landscape of EMT associated active enhancers in the basal epithelium of the prostate


Shamil Sunyaev

Predicting polygenic phenotype from genotype


Dmitry Suplatov , Daria Timonina , Yana Sharapova , Vytas Svedas

Yosshi: the bioinformatic approach to protein disulfide engineering


Dmitry Suplatov , Yana Sharapova , Daria Timonina , Elena Schmalhausen , Kateryna Fesko , Nina Popova , Vladimir Muronets , Vladimir Voevodin , Vytas Svedas

Open-access Mustguseal platform to explore protein superfamilies


Valentine Suslov

Homology and Vavilov's law of homologous series I;Homology and Vavilov's law of homologous series II;Urbanization, domestication and destabilization


Inna Suvorova

Comparative study of the IclR family of transcription factors and their DNA binding motifs: structure and co-evolution


Abusaid Shaymardanov , Dmitry Svetlichnyy

Evolutionary analysis of cis-regulatory elements in the central nervous system of primates





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Alexander Mikheyev , Alexei Zarubin , Tatiana Tatarinova

Using museomics to solve historic puzzles


Shashkova Tatiana , Gorev Denis , Pakhomov Evgeny , Torgasheva Anna , Tsepilov Yakov , Joshi Peter , Aulchenko Yurii

Mining a database of billions of genetic associations to understand biology of complex human traits


Denis Goryunov , Evgenia Sotnikova , Maria Logacheva , Aleksey Troitsky

The mitochondrial genome of the moss Polytrichum commune (Polytrichopsida)


Yakov Tsepilov , Maxim Freidin , Melody Palmer , Lennart Karssen , Pradeep Suri , Yurii Aulchenko , Frances Williams

Insight into the genetic architecture of back pain and its risk factors from a large genome-wide association study


Vasily Tsvetkov , Vlad Belousov , Mikhail Shugay

Improving the prediction of T-cell epitopes by introducing self/non-self discrimination


Tamir Tuller

Computational modelling of novel gene expression rules and their applications


Maria N. Tutukina , Nataliya Yu. Markelova , Olga V. Alikina , Uliana S. Shvyreva , Mikhail S. Gelfand , Olga N. Ozoline

Sense and nonsense in studying the antisense transcription in prokaryotes


Alexander Tyshkovskiy , Vadim N. Gladyshev

Identification and application of gene expression signatures associated with lifespan extension





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Viktor Urban

Atomic-level modeling of the complexes of small-molecular inhibitors of PD-1/PD-L1 with PD-L1 dimers





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Olga A. Vakhrusheva , Elena A. Mnatsakanova , Yan Galimov , Tatiana V. Neretina , Evgeny S. Gerasimov , Svetlana G. Ozerova , Arthur O. Zalevsky , Irina A. Yushenova , Irina R. Arkhipova , Aleksey A. Penin , Maria D. Logacheva , Georgii A. Bazykin , Alexey S. Kondrashov

Signatures of genetic exchange in a natural population of the bdelloid rotifer Adineta vaga inferred from whole-genome data


Oleg Vishnevsky , Andrey Bocharnikov , Vadim Efimov , Elena Ignatieva

Context analysis of the core promoter region of mouse genes differently expressed in hypothalamic energy-sensing neurons in response to weight-loss


Petr Vlasov

The Intelligent Man's Burden: modern biology and biomedicine as an effective driving force on the boundary of science and education





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Donate Weghorn

Probabilistic approaches to positive and negative selection inference on coding regions in cancer





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Hiroshi Yoshida

A model of regenerating patterns using a random-walk model





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Konstantin Popadin , Elizaveta Zezyulya , Dmitriy Iliushchenko

Distribution of Runs Of Homozygosity (ROHs) along the human genome is shaped by recombination and purifying selection


Nikita Zhiganov , Alexander Martynov , Valeriya Tereshenkova , Elena Elpidina

Serine peptidases from the S1 family in Tenebrionidae beetles.


Svetlana Zhukova , Victoria Scobeyeva , Evgeny Konorov

CYP450 9e2 expression in black garden ant Lasius niger


Andrei Zinovyev

Inferring complex pseudo-time trajectories in single cell data using elastic principal graphs and STREAM pipeline


Andrei Zinovyev

Inferring complex pseudo-time trajectories in single cell data using elastic principal graphs and STREAM pipeline


Olga Zolotareva , Sahand Khakabimamaghani , Olga Isaeva , Martin Ester

Identification of Differentially Expressed Gene Modules in Heterogeneous Diseases


Dmitry Zubkov , Anna Tkachev , Alina Egorova , Elena Stekolschikova , Anna Vanyushkina , Philipp Khaitovich

Alterations of plasma lipid profile in schizophrenia


Oleg Zverkov , Kirill Mikhailov , Sergey Isaev , Leonid Rusin , Maria Logacheva , Alexey Penin , Leonid Moroz , Yuri Panchin , Vassily Lyubetsky , Vladimir Aleoshin

Dicyemida and Orthonectida: Two stories of body plan simplification