MCCMB 2021: Proceedings

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Eldar Abdullaev

Modelling Segmental Duplications in the Human Genome


Alexej Abyzov

Early developmental asymmetries in cell lineage trees in living individuals


Ivan Agafonov , Maria Poptsova

Transformer-based model for recognition of quadruplexes using information on physical and chemical DNA properties


Andrey Y. Ageev , Eric Bishop­von Wettbergb , Sergey V. Nuzhdina , Maria Samsonovaa , Konstantin Kozlov

Numerical study of the flowering time model of wild chickpeas


Evgeniia Alekseeva , K. Safina , E. Nabieva , S. Garushyants , G. Klink , G. Bazykin

SARS-CoV-2 escapes cytotoxic T cell immune response during long-term infection of immunocompromised patient with non-Hodgkin’s lymphoma


Maria A. Andrianova , Georgii A. Bazykin , Vladimir B. Seplyarskiy

Variation of mutation rate between individual cells


Nikolay E. Russkikh , G.M. Ryazantsev , Denis V. Antonets , Y.V. Vyatkin , A.V. Makarov , E.V. Shaburova

Functional domain annotation of protein sequences with deep metric learning


Nikolay Russkikh , Denis V. Antonets , Dmitry Shtokalo , Alexander Makarov , Yuri Vyatkin , Alexey Zakharov , Evgeny Terentyev

Style transfer with variational autoencoders is a promising approach to RNA-Seq data harmonization and analysis


Ivan Antonov

Two Cobalt Chelatase Subunits Can Be Generated from a Single chlD Gene via Programed Frameshifting


German Ashniev , Natalia Sernova , Alexey Shevkoplias , Ivan Rodionov , Irina Rodionova , Alexey Vitreschak , Mikhail Gelfand , Dmitry A Rodionov

Evolution of Transcriptional Regulation of Histidine Metabolism in Gram-positive Bacteria


Yurii Aulchenko

Quantitative genetics of human protein N-glycosylation


Nadezhda Azbukina , Z.N. Seferbekova , A.A. Zharikova , V.E. Ramensky , A. Gress , S. Keller , O.V. Kalinina

Intragenic compensatory variants: does the distance matter?




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Roman Babenko , Vladimir Babenko

Population specific enhancer affecting optic disc development timespan underlies Glaucoma predisposition.


Vladimir N. Babenko , Roman O. Babenko , Igor B. Rogozin

Assessing proteome diversity raised by alternative splicing in Brain RNA-Seq data


Sagnik Banerjee , Priyanka Bhandary , Margaret Woodhouse , Taner Sen , Roger Wise , Carson Andorf

Enhancing eukaryotic gene structures by implementing statistical changepoint analysis of expression data using FINDER - a completely automated gene annotator


Pavel V. Baranov

Translational landscape of human 3’ UTRs


Antonio Barbadilla , Sònia Casillas , Jesús Murga

Population genomics and population multi-omics of adaptation


Yury A. Barbitoff , Dmitry A. Alexeev , Alexander V. Predeus

Investigation of the genetic architecture of human traits on the phenome scale


Geoff Barton

Bringing Human Population Genetics to Protein Structure


Ilya S. Belalov , Timofei M. Ivanov , Marina Kalinina , Dmitri D. Pervouchine

Origin and splicing of mutually excluding exons and pre-mRNA secondary structure in human genes of voltage-gated calcium channels


Yekaterina S. Pavlova , David Paez-Espino , Andrew Yu. Morozov , Ilya S. Belalov

The power law of CRISPR-Cas systems


Evgenia A. Belousova , Anastasia V. Stolyarova , Alexey S. Kondrashov , Georgii A. Bazykin

Dynamics of dN/dS at short evolutionary distances


Julia Belyaeva , Alexander Zlobin , Andrey Golovin

Multiscale investigation into the active site composition of AmiN kinase


Aleksandra V. Bezmenova , Elena Zvyagina , Tatiana Neretina , Anna Fedotova , Georgii Bazykin , Alexey Kondrashov

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


Kristina Y. Perevoshchikova , Vera Emelianenko , Mikhail S. Gelfand , Fyodor Kondrashov , Olga O. Bochkareva

Evolutionary benefits of bacterial genomes with chromids


Elizaveta Bogdanova , Shaitan K.V. , Novoseletsky V.N.

The expansion of the range of microbial rhodopsins by their artificial sequences


Dmitrii Bondaruk , E.V. Golubkova , L.A. Mamon

Application of the intron sequence of the NXF1 gene in mammalian phylogeny


Nicolas M. Borisov , Anton Buzdin

Multi-platform cross-harmonization of gene expression profiles obtained using mRNA next-generation sequencing and microarray hybridization


A.M. Andrianov , Yu.V. Kornoushenko , A.D. Karpenko , Ivan P. Bosko , A.M. Yushkevich , K.V. Furs , A.V. Tuzikov

Structure-Based Identification of Small Molecule Inhibitors for Selective Targeting of SARS-CoV-2 Main Protease: An Integrative Computational Approach


Danila Bredikhin , Oliver Stegle

Multimodal by default: designing the next generation of methods and tools for single-cell multi-omics


Valentina Burskaia , Ilja Artyushin , Nadezhda Potapova , Kirill Konovalov , Georgii A. Bazykin

Convergent adaptation in mitochondria of phylogenetically distant birds: does it exist?


Michelle F. Buyanova , Arthur O. Zalevsky , Andrey V. Golovin

Calcium coordination in enzymes: the intertwining of structural and functional features


Nikolai S. Bykov , Aleksandra A. Galitsyna

HiChew: a tool update for TAD boundaries clustering in development




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Alexander V. Cherkasov , Alina Ryabova , Olga Kozlova , Alexander Finoshin , Oksana Kravchuk , Ekaterina Khrameeva

The Spatial Organization of the genome of sea sponge Halisarca dujardini


Maria Chernigovskaya , Victor Greiff

Modular assembly of immune-event-labeled synthetic AIRR-datasets for the development and benchmarking of AIRR-based machine learning


Alexander Chervov , Andrei Zinovyev

Trajectory inference methods applied to clinical and bulk transcriptomomic data




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Fawaz Dabbaghie , Tobias Marschall , Olga Kalinina

MSAtoGFA: a Graph Representation of Multiple Sequence Alignments


Ludmila Danilova , John Wrangle , James G. Herman , Leslie Cope

DNA-Methylation for the Detection and Distinction of 19 Human Malignancies


Christophe Dessimoz

Laying foundations for very large-scale comparative genomics


Andrei A. Deviatkin , Galina Karganova , Yulia Vakulenko , Ivan Kholodilov , Alexander Lukashev

Tick-borne encephalitis virus phylodynamics


Supantha Dey

Gene expression pattern in Edward syndrome: A bioinformatic analysis on what creates significant low life expectancy


Igor D. Diankin , A. V. Golovin

A neural network approach to the QM / MM metadynamics' quantum mechanical description level


Olga Dolgova , Oscar Lao

Artificial intelligence applied to population genomics and paleogenomics


Mikhail G. Dozmorov , Spiro C. Stilianoudakis

preciseTAD: a machine-learning framework for predicting boundaries of 3D genomic elements


Natalia O. Dranenko , Maria Tutukina , Olga Bochkareva

The Classification of ipaH Genes in Shigella and Enteroinvasive Escherichia


Alexey I. Drozhdev , A.A. Galitsyna , M.S. Gelfand

The analysis of Drosophila melanogaster Hi-C maps with autocorrelation function and Fourier transform


Maria Duk , A.Kanapin , A.Samsonova , A.Sokolkova , T.Rozhmina , M.Samsonova

Genomic blueprints of flax diversification and improvement




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Bogdan E. Efimenko , Alexandr Voronka , Sergey Oreshkov , Konstantin Popadin , Konstantin V Gunbin

Secondary structure of the SARS-CoV-2 genome affects molecular evolution


Artyom A. Egorov , Andrey I. Buyan , Vadim N. Gladyshev , Ivan V. Kulakovskiy , Sergey E. Dmitriev

Protein-coding potential of the human repetitive elements


Elizaveta E. Elgaeva , Maxim B. Freidin , Frances M. K. Williams , Pradeep Suri , Yurii S. Aulchenko , Yakov A. Tsepilov

Insights into the genetic components of chronic back pain


Evgenia Elizarova , A.S. Zlobin , A.V. Golovin , A.Y. Mulkidjanian

Catalytic mechanism of MnmE GTPase as a member of ion-dependent GTPases class


Vera Emelianenko , Anna Kaznadzey , Maria Tutukina , Olga Bochkareva

Two sequence variants of yjjM gene in the Escherichia coli genomes




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Alexander Favorov , Vasiliy Ramensky , Andrey Mironov

Telling the story of best friends: marker rank statistics


Alla Fedorova , Stephen Kiniry , Pavel Baranov

Discovery of non-AUG PANTs: Proteoforms with Alternative N Termini


Alexandra Yu. Filatova , Andrey Marakhonov , Mariia Piatkova , Viktoria Demakova , Daria Bessonova , Olga Kuziakova , Aleksandr Romanishin , Tatyana Vasilyeva , Kristina Karandasheva , Viktoria Serzhanova , Mikhail Skoblov

Disruption of uORFs translation is an underestimated cause of Mendelian disorders


A. Lapin , M. Sindeeva , E. Malkin , M. Avetisian , A. Taskina , T. Shashkova , O. Kardymon , Veniamin Fishman

Learning the cell states using deep neural networks for cell type-specific interpretation of disease variants


Karla Paniagua , Yufang Jin , Mario A. Flores

Predicted Spike-ORF8 Genomic RNA-RNA Interaction Unique to SARS-CoV-2 May Allosterically Impact the Rate of Nucleocapsid Sub-genomic RNA Synthesis


Marina Fridman , P. Bykadorov

Allele specific transcription factor binding sites mark positive selection loci in the human genome




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Alima Galieva , Alina A. Mikhailova , Alina G. Mikhailova , Victor Shamanskiy , Valeria Lobanova , Kristina Ushakova , Konstantin Gunbin , Konstantin Popadin

Asymmetrical mutagenesis drives aminoacid composition of the human mitochondrial genome


Evgeniy Galimov , A. Yakimovich

Tandem segmentation-classification approach for localization of morphological predictors of C. elegans lifespan and movement


Aleksandra A. Galitsyna , Mikhail D. Magnitov , Aleksey A. Gavrilov , Andrey A. Mironov

RedC-nf: an automatized pipeline to map RNA-DNA interactions


Oxana V. Galzitskaya , S.R. Kurpe , S.Y. Grishin , A.V. Glyakina , M.V. Slizen , A.V. Panfilov , A.P. Kochetov , E.I. Deruysheva , A.V. Machulin , A.K. Surin

Creation of new antibacterial peptides


Azat Garaev , M.D. Magnitov , S.V. Ulianov , S.V. Razin

Pentads: a novel pile-up analysis tool for assessing the alterations of chromatin compartments using Hi-C data


Sergiy O. Garbuzynskiy , A.V. Finkelstein

Calculation of Sublimation Entropy and Dissociation Constants from a Simple Evaluation of Movement Range of Molecules in Crystals


Sergey S. Pintus , Ilya R. Akberdin , Ivan Yevshin , Fedor A. Kolpakov , Oksana Tyapkina , Leniz Nurullin , Islam Nigmetzyanov , Ruslan Devyatiyarov , Elena Shagimardanova , Pavel Makhnovskii , Daniil Popov , Oleg Gusev , Guzel R. Gazizova

Whole-genome atlas of transcribed regulatory elements expression during time-course disuse and recovery in skeletal muscles of rats


Vadim N. Gladyshev

Quantifying and Manipulating the Aging Process


Anton Goloborodko

Unraveling the structure of paired homologs and sister chromatids with Hi-C and polymer modeling


Ekaterina Nikolaevna Grafskaia , Maja Malakhova , Victoria Lavrenova , Ivan Latsis , Vladislav Babenko , Vassili Lazarev

Machine-learning model for prediction of new antimicrobial peptides: Hirudo medicinalis metagenome case study


Lisa Grigorashvili , Mikhail Gelfand , Zoe Chervontseva

Feature extraction by neural network trained to predict RNA structure


Elizaveta Grigoreva , Alexander Tkachenko , Aleksandar Beatovic , Serafima Arkhimandritova , Dmitry Karzhaev , Vladimir Volkov , Cecile Ben , Laurent Gentzbittel , Elena Potokina

Dissection of Loci Underlying Flowering Time of Guar (Cyamopsis tetragonoloba (L.) Taub.) via Integrated Transcriptome-Metabolome Analysis


Rim Gubaev , S.Boldyrev , E. Martynova , A. Chernova , T. Kovalenko , S. Goryunova , D. Goryunov , T. Peretyagina , Y. Demurin , P. Khaitovich

QTL mapping of oleic acid content and tocopherol composition in sunflower from VNIIMK collection


Konstantin V. Gunbin , Konstantin Popadin

Automatic reconstruction of species-specific mitochondrial mutational spectra based on DNA polymorphisms


Yury Gusarov , Alina G. Mikhailova , Sergey Oreshkov , Alina A. Mikhailova , Dmitry Knorre , Leonard V. Polishchuk , Alexander Kuptsov , Konstantin V. Gunbin , Valentina Burskaya , Konstantin Popadin

Mitochondrial mutational spectrum in birds: evidence of increased oxidative damage in species with high level of metabolism




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Stanislav Iablokov , Dmitry A Rodionov

Binary metabolic phenotypes and phenotype diversity metrics for functional characterization of microbial communities


Anna Igolkina , Nina Noujdina , Travis Longcore , Eric von Wettberg , Maria Samsonova , Sergey Nuzhdin

Models for crop species diversification within and between centers of domestication


Dmitrii Iliushchenko , Konstantin Popadin , Konstantin V Gunbin

mtDNA mammalian evolution: mice evolve by many little steps while elephants with a few big ones


Ivan Ilnitskiy , A.A. Mironov , A.A. Zharikova

Evolutionary repertoire of eukaryotic chromatin-associated proteins


Aleksandr Poslavsky , Dmitry N. Ivankov

New algorithms for finding combinatorially complete datasets in high-throughput mutagenesis experimental data


Aleksandra Galitsyna , Alexey Ivanov , Mikhail Gelfand

Current advances and future perspectives on single-cell Hi-C bioinformatics


Tim Ivanov , Dmitri Pervouchine

Tandem exon duplications expanding splicing repertoire




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Stanislav A. Bondarev , Theo Falgarone , Jeremy Leclercq , Galina A. Zhouravleva , Andrey V. Kajava

Co-aggregation of amyloids: from structural principles to in silico prediction


Marina Kalinina , Olga Babadei , Dmitry Skvortsov , Svetlana Kalmykova , Olga Dontsova , Dmitri Pervouchine

Long-range RNA-RNA pairings in human pre-mRNAs and their implications in alternative splicing


Ekaterina Kamanova , M.E. Starchevskaya , T.S. Nepomnyashchikh , Denis V. Antonets

Viral metagenomic analysis of publicly available genomic and transcriptomic samples from Simuliidae and Ceratopogonidae insects


Asia Kamyshnikova , Anastasia V. Stolyarova , Georgii A. Bazykin , Alexey S. Kondrashov

Inversions and translocations in a highly polymorphic fungus Schizophyllum commune


Mikhail Karasikov , Harun Mustafa , Daniel Danciu , Gunnar Rätsch , André Kahles

Indexing Sequencing Data at Petabase Scale


Anastasia Karlsen , O.V. Kuzmin , F.A. Asadi Mobarhan , O.V. Isaeva , S.S. Sleptsova , Victor A. Manuylov , Andrei A. Pochtovyi , Vladimir A. Gushchin , K.K. Kyuregyan , M.I. Mikhailov

Evolution of different genotypes of hepatitis B and hepatitis delta viruses in endemic region


Vadim Karnaukhov , Wayne Paes , Thomas Partridge , Simon Brackenridge , Persephone Borrow , Isaac B. Woodhouse , Hashem Koohy , Annalisa Nicastri , Nicola Ternette , Dmitrii Scherbinin , Ivan V. Zvyagin , Dmitry M. Chudakov , Mikhail Shugay

HLA binding preferences of self-peptides are biased towards proteins with specific molecular functions


Alexander Andrianov , Yury V. Karnaushanka , Anna D. Karpenka , Ivan P. Bosko , Zhanna Ignatovich , Elena Koroleva , Julia Siniutsich

Design and Bioinformatics Analysis of Novel 2-Arylaminopyrimidine-Based Compounds as Potential Bcr-Abl Tyrosine Kinase Inhibitors


Nataliia Kashko , Dmitry Knorre

Search for the genetic determinants of yeast mtDNA suppressivity


Lusine Khachatryan , Carine Poussin , Yang Xiang , Adrian Stan , James Battey , Giuseppe Lo Sasso , Stephanie Boue , Nicolas Sierro , Nikolai V. Ivanov , Manuel C Peitsch , Julia Hoeng

The sbvIMPROVER Metagenomics Diagnostics for Inflammatory Bowel Disease Challenge: Results and Lessons Learned


Eldar Khaibulin , Alina G. Mikhailova , Victor Shamanskiy , Konstantin Popadin

mtDNA codon usage of Chordata is primarily shaped by mutational spectra


Darya Khaleneva , O.V. Bondareva , S.Yu. Bodrov , T.V. Petrova , E.A. Genelt-Yanovskiy , N.I. Abramson

In search of molecular traces of adaptations to life in high mountains in mammals


Evgenia Khodzhaeva , Zoe Chervontseva , Mikhail Gelfand

Composition of metabolic loci in bacterial genomes


Maksim Kholmatov , Judith B. Zaugg

Multiomic view of gene regulation in Plasmacytoid Dendritic Cells


Bogdan Kirillov , Maxim Panov

Deterministic DNA embeddings with no predefined k-­mer length


Ilya Kirov , Pavel Merkulov , Sofya Gvaramiya , Murad Omarov , Maxim Dudnikov , Elizaveta Kolganova , Roman Komakhin , Mikhail Divashuk , Gennady Karlov , Alexander Soloviev

Sensitive mapping of transposon insertions using Cas9-Targeted Nanopore sequencing and a novel pipeline


Pavel Kravchenko , Dmitry Knorre

Evolution of mitochondrial DNA inheritance patterns


Galina Koltsova , S. Namsrayn , A. Koltsov

A comparative genomic study of attenuated and virulent strains of the African swine fever virus genotype I and serogroup 2


Fedor Kondrashov

Heterogeneity of the GFP fitness landscape and data-driven protein design


Nikita Konstantinovsky , Nikita Kazakov , Maria Poptsova

Generative-Adversarial Neural Networks for Quadruplex and Z-DNA prediction


Eugene Koonin

The world of viruses, its global organization and evolution


Yuliya Kordonskaya , Vladimir Timofeev , Yulya Dyakova , Margarita Marchenkova , Yuriy Pisarevskiy , Michael Kovalchuk

Precipitant ions influence on lysozyme mono- and oligomers stability investigated by molecular dynamics simulation


Aleksei Korzhenkov

A comparison of computational tools for average nucleotide identity estimation


Pavel I. Kos , Aleksandra A. Galitsyna , Sergey V. Ulianov , Mikhail S. Gelfand , Sergey V. Razin , Alexander V. Chertovich

Bi-directional study chromatin organization into the eukaryotic nuclei cell


Sergey Abramov , Alexandr Boytsov , Dariia Bykova , Marina V. Fridman , Alexander V. Favorov , Ilya E. Vorontsov , Dmitry D. Penzar , Vsevolod J. Makeev , Ivan Yevshin , Semyon K. Kolmykov , Fedor Kolpakov , Ivan V. Kulakovskiy

Peeking inside the clockworks of regulatory single-nucleotide variants with ADASTRA and ANANASTRA


Georgy F. Kurakin , Anna Samoukina , Nadezhda Potapova

Evolutionary insights into microbial oxylipin signalling


Ivan A. Kuznetsov , Yakov A. Tsepilov , Yurii S. Aulchenko

Genotype-by-environmental interactions for chronic back pain




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Pavel Latyshev , Maria Poptsova

Transfer learning for whole-genome G-quadruplex annotation


Alexander V. Lebedinsky , Ilya Kublanov , Evgenii Frolov , Elizaveta Bonch-Osmolovskaya , Nikolay Chernyh

Dating gene cluster acquisition: The case of Form III RubisCO-mediated transaldolase variant of the Calvin cycle


Anna Valeryevna Litvin , Maria S. Shoshinova , Alexander S. Yakushev , Anna S. Lapashina , Boris A. Feniouk

Bioinformatic analysis of prokaryotic rotary ATPases: revealing the correlations between coupling ion type and microorganism physiology


Valeria Lobanova , Alina A. Mikhailova , Alina G. Mikhailova , Victor Shamanskiy , Kristina Ushakova , Alima Galieva , Konstantin Popadin

A billion-year trend of amino acid substitutions in the mitochondrial genome: comparative analysis of different taxa


A. Kanapin , A. Samsonova , A. Logachev , M. Bankin , T. Rozhmina , M. Samsonova

Comparative genomics of flax pathogen Fusarium oxysporum f.sp. lini


G.A. Shilovsky , O.A. Zverkov , L.I. Rubanov , A.V. Seliverstov , Vassily A. Lyubetsky

Complex evolution of Fbxl21 gene in mammals




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Gaik Tamazian , Alexander Kanapin , Anastasia Samsonova , Sergey V. Malov

On Selective Imputation Using Beagle v.5.


Viktor Mamontov , Yaroslav Ispolatov , Ekaterina Semenova , Konstantin Severinov

The stochastic nature of the interaction between CRISPR interference and replication events provides the coexistence of virus and bacteria populations


Sergey Margasyuk , Z. Chervontseva , A. Danchurova , Dmitri Pervouchine

Sequence determinants of cross-regulatory feedback loops in RNA-binding protein interaction network


Sofia Mariasina , A. Izzi , E. Denisova , O. Dontsova , P. Sergiev

High-Throughput Splicing Efficiency Analysis System


Marko Djordjevic , Magdalena Djordjevic , Andjela Rodic , Igor Salom , Ognjen Milicevic , Bojana Ilic , Dusan Zigic , Stefan Stojku

A systems biology approach to understanding SARS-CoV-2 transmissibility in population


Georgy A. Meshcheryakov , Maria G. Samsonova , Anna Igolkina

mtmlSEM with random effects uncovers genotype-phenotype associations through pleitropic SNPs


Alina G. Mikhailova , Alima Galieva , Kristina Ushakova , Valeria Lobanova , Alina A. Mikhailova , Victor Shamanskiy , Leonard Polishchuk , Dmitry Knorre , Konstantin Khrapko , Konstantin Gunbin , Ilya Mazunin , Valerian Yurov , Konstantin Popadin

A billion-year trend of amino acid substitutions in the mitochondrial genome


Mariia Minaeva , Khalimat Murtazalieva , Yulia Medvedeva

Using protein-protein interaction and gene networks to improve Connectivity Map


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

The atlas of expression of cis-regulatory elements of human craniofacial embryonic tissues


Aleksei Mironov , Stepan Denisov , Alexander Gress , Olga V. Kalinina , Dmitri D. Pervouchine

An extended catalogue of tandem alternative splice sites in human tissue transcriptomes


Ksenia G. Kuznetsova , A.A. Kliuchnikova , A.O. Goncharov , M.A. Pyatnitskiy , L.I. Levitsky , M.V. Ivanov , M.V. Gorshkov , Sergei A. Moshkovskii

Proteome recoding by A-to-I mRNA editing


Evgeniy A. Mozheiko , Maria Gridina , Emil Valeev , Veniamin Fishman , Ludmila P. Nazarenko , Maria E. Lopatkina , Igor N. Lebdev , Maria I. Yablonskaya , Viktoria Yu Voinova , Zhanna G. Markova , Nadezhda V. Shilova

Efficient detection of structural variations using capture-Hi-C data


Ekaterina Myasnikova , Alexander Spirov

Optimization of the directed evolution experimental design by the genetic algorithm theory


Dmitry E. Mylarshchikov , Andrey Mironov

A sensitive method for search for orthologs of de novo annotated lncRNAs




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Sergey Naumenko

Bcbio – a set of best practices NGS data processing pipelines for bioinformatics cores and diagnostic labs


Tatyana S. Nepomnyashchikh , D.V. Antonets , M.E. Starchevskaya , T.V. Tregubchak , A.N. Shvalov , E.V. Gavrilova , S.N. Shchelkunov , Rinat A. Maksyutov

Analysis of Poxviridae and Coronaviridae genomes using k-mer frequency profiles and comparison with alignment-based approach


Maksim A. Nesterenko , V.V. Starunov , S.V. Shchenkov , S.A. Denisova

The digenean complex life cycle: phylostratigraphy analysis of molecular signatures


M.S. Nikitin , N.V. Zakharevich , I.I. Artamonova

Evolution scheme of the CRISPR-Cas locus in Xanthomonas citri can be reconstructed based on its spacers content, but the result disagrees with the strain phylogeny for the species


Mikhail A. Nikitin , Simha I. Borman , Daria Yu. Romanova , Maria D. Logacheva , Leonid L. Moroz

Comparative genomics of placozoans: fast evolution of neuronal genes in nerveless animals


Alexander Andrianov , Grigory I. Nikolaev , Nikita Shuldov , Ivan P Bosko , Alexander Tuzikov

A Deep Learning-Based Approach for Prediction of Potential HIV-1 Entry Inhibitors Targeting CD4-Binding Site of GP120


Daria Nikolaeva , Sofya K. Garushyants

Is bacterial species pangenome structure associated with habitat diversity?


Dmitry K. Nilov , I.V. Gushchina , D.A. Suplatov , V.K. Švedas

vsFilt: a new tool for structural filtration and virtual screening


Ekaterina Noskova , Vladimir Ulyantsev

New features in GADMA for efficient and flexible inference of demographic history


Arina Nostaeva , Tatiana Shashkova , Lennart Karssen , Yurii Aulchenko

A potential of polygenic risk scores as a tool to inform population screening for breast cancer




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David R. Ghasemi , Konstantin Okonechnikov , Jan-Philipp Mallm , Kati Ernst , Katharina Bauer , Michelle S. Liberio , Laura Giese , Kendra K. Maass , Marcel Kool , David T.W. Jones , Andreas von Deimling , Stefan M. Pfister , Andrey Korshunov , Kristian W. Pajtler

Single nucleus RNA-sequencing data reveals intra-tumoral heterogeneity in medulloblastoma brain tumors with extensive nodularity


Nina Oparina , Malin Erlandsson , Karin M.E. Adersson , Venkatagavan Chandrasekaran , Anastasios Damdimopoulos , Sofia T. Silfverswärd , Maria I. Bkarewa

Chromatin association of BIRC5/survivin protein genome binding in human CD4+ T cells


Maria Osetrova , Ekaterina Khrameeva , Anna Tkachev , Elena Stekolschikova , Aleksandra Mitina , Olga Efimova , Philipp Khaitovich

Lipidome composition of the healthy adult human brain


Aleksandra Ozerova , Mikhail Gelfand

Pupae recapitulate the embryonic expression program in insects undergoing radical metamorphosis




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Marina A. Pak , Dmitry N. Ivankov

Study of influence of homology modeling on the prediction of protein stability change upon mutation


Alexander Y. Panchin

What can substitution biases tell us about the origin of SARS-CoV-2


Vera Panova , Eugene Baulin , Anna Karyagina , Andrey Alexeevski , Sergey A Spirin

Classification of families of DNA-recognizing protein domains based on structural features of DNA-protein complexes


Marina Parr , Dmitrij Frishman , Tamir Tuller

Genomic determinants of viral host diversity


Karina Pats , Ferdinand Molnar

Structural descriptors-based clustering for the evaluation of the patterns in 3D-structure of vitamin D receptor


Svetlana Kalmykova , Marina Kalinina , Alexey Mironov , Stepan Denisov , Dmitry Skvortsov , Dmitri Pervouchine

Conserved long-range base pairings are associated with pre-mRNA processing of human genes


Evangelia Petsalaki

Identification of phenotype-specific networks from paired gene expression-cell shape imaging data


Soumita Podder

In-silico identification of key regulators instigating the pre-meiotic phase during respiration in Saccharomyces cerevisiae


Konstantin Popadin

A>G is a hallmark of oxidative damage in mitochondrial and bacterial genomes


Artem Y. Pronozin , D. Afonnikov

Identification and structural analysis of long noncoding RNAs




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Ovidiu Radulescu , Charbel Choufani , Thierry Lorca , Anna Castro

Which wiring of the cell cycle opens the path to mitotic and meiotic division?


Vasily Ramensky , Anastasia Zharikova , Anna Kiseleva , Yuri Vyatkin , Maria Zaichenoka , Evgenia Sotnikova , Olga Kurilova , Olga Skirko , Svetlana Shalnova , Alexandra Ershova , Alexey Meshkov , Oksana Drapkina

Targeted sequencing of 242 clinically important genes in a sample of Russian population from Ivanovo region


Marat Kazanov , Semen Leyn , Dmitry A. Rodionov

Computational inference of metabolic phenotypes for new bacterial isolate and metagenome-assembled genomes


Elena Rukhlova , Anastasia Bakulina , Dmitry Shcherbakov , Iuliia Merkuleva

Structure-based design of monoclonal antibodies against SARS-CoV-2


I. Rusinov , A. Ershova , A. Alexeevski , A. Karyagina , S. Spirin

Restriction-modification systems in microbiome of Antarctic Deep Lake


Grigory Ryabykh , Anastasiya Zharikova , Andrey Sigorskikh , Yuriy Korostelev , Andrey Mironov

A new database for genome-wide RNA-chromatin interactome




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Marat Sabirov , Ekaterina Khrameeva

Supposed properties of enhancers associated with human-specific brain genes


Ksenia Safina , Georgii Bazykin , Yulia Sidorina , Natalya Efendieva , Elena Belonosova , Dmitry Kireev

Molecular epidemiology of HIV in Oryol district, Russia


Aleksandr Sarachakov , Viktor Svekolkin , Zoya Antysheva , Jessica Brown , Alexander Bagaev , Nathan Fowler , Mikhail Gelfand

MutAnt: Mutation annotation machine learning algorithm for pathogenicity evaluation of single nonsynonymous nucleotide substitutions in cancer cells


Viktoria Scobeyeva , Svetlana Zhukova , N. Yu. Oparina , I. Artyushin

Xenobiotic associated CYP450 9e2 family in Formicinae: protein family evolution and population study of black garden ant Lasius niger CYP9E2 genes expression


Maria Selifanova , Galina Klink , Anastasia Stolyarova , Georgy Bazykin

Genome-wide search for positive selection in Schizophyllum commune


Ariadna Semenova , Olga O. Bochkareva

Evolution of Insertions Sequences in the Evolution of Intracellular Pathogens B. mallei


Ilya Senatorov , Olga V. Kalinina

How to improve real-life applicability of drug-target interaction prediction?


Vladimir Seplyarskiy

Precise mutation rate estimation on an individual site level


Maria Y. Serebrennikova , Ekaterina Grafskaia , Vassili Lazarev

Development of a searching algorithm for new cell-penetrating peptides using machine learning methods


Gennady Korotkevich , Vladimir Sukhov , Nikolay Budin , Boris Shpak , Maxim N. Artyomov , Alexey A. Sergushichev

Fast gene set enrichment analysis with multi-level Monte-Carlo approach


Nurislam Maratovich Shaikhutdinov , Galina Klink , Sofya Garushyants , Olga Kozlova , Elena Shagimardanova , Guzel Gazizova , Natalia Gogoleva , Andrey Przhiboro , Oleg Gusev , Georgii Bazykin

Genomic adaptations of chironomids to extreme environments


Victor Shamanskiy , Alina Mikhailova , Kristina Ushakova , Alina Mikhaylova , Sergei Oreshkov , Dmitry Knorre , Evgenii Tretiakov , Ilia Mazunin , Konstantin V Gunbin , Konstantin Khrapko , Konstantin Popadin

Somatic deletions in the human mitochondrial genome: the global secondary structure, G-quadruplexes and direct nucleotide repeats explain majority of breakpoints


Varvara Lukyanchikova , Miroslav Nuriddinov , Polina Belokopytova , Alena Taskina , Jiangtao Liang , Maarten J.M.F. Reijnders , Livio Ruzzante , Robert M. Waterhouse , Zhijian Tu , Igor V. Sharakhov , Veniamin Fishman

Anopheles mosquitoes revealed new principles of 3D genome organization in insects


Sodbo Sharapov , Yakov A. Tsepilov , Elizaveta E. Elgaeva , Evgeny S. Tiys , Arina Nostaeva , Frano Vuckovic , Irena Trbojević-Akmačič , Michel Georges , Karsten Suhre , Nishi Chaturvedi , Harry Campbell , Malcolm Dunlop , Frances Williams , Matthias B. Schulze , Tim Spector , Gordan Lauc , Yurii S. Aulchenko

Mapping genes involved in control of N-glycosylation of blood glycoproteins through a large genome-wide association study


Vladimir Shchur , Evgeniy Khomutov , Kenenbek Arzymatov , Viktoriya Vasileva

Deep learning for demographic inference from whole-genome sequences


Sergei V. Shekhovtsov , Alexandra A. Shipova , Tatiana V. Poluboyarova , Sergei E. Peltek

Using transcriptomic data for reconstruction of earthworm phylogeny on the example of the Eisenia nordenskioldi complex


Mason Liang , Mikhail Shishkin , Vladimir Shchur , Rasmus Nielsen

Estimating the timing of multiple admixture events using 3-locus Linkage Disequilibrium


Vladimir A. Shitov , B. Eisenhaber , S. Sinha , C. K. Jadalanki , Q. W. Tan , F. L. Sirota , F. Eisenhaber

Sequence analysis of human TMTC proteins reveals their enzymatic activity and ligand binding sites


Alexey Shkolikov , Aleksandra Galitsyna , Mikhail Gelfand

Deep learning model for Hi-C maps prediction


Kseniia Sholokhova , Konstantin Gunbin , Victor Shamanskiy , Louis-Alexandre Ongaro , Konstantin Popadin

A search of embryonic selection traces: transmission disequilibrium of slightly-deleterious variants from parents to the offspring with Down syndrome


Oleg Shpynov , Roman Chernyatchik , Petr Tsurinov , Maxim Artyomov

SPAN and JBR - tools for semi-supervised peak calling


Artemy Shumskiy , Dmitrii Smirnov , Ekaterina Khrameeva , Deborah Toiber

Regulation of splicing in Sirt6-KO mouse brain


Andrey Sigorskikh , Grigory Ryabykh , Yuri Korostelev , Anastasiya Zharikova , Andrey Mironov

New RNAs revealed by RNA-chromatin interactions


Mikhail Y. Skoblov , Mikhail Gatupov , Ivan Reveguk , Andrey Marakhonov , Igor Bychkov , Alexandra Filatova

Genome-wide search for pathogenic splice variants manifested in different genetic backgrounds


Dmitrii Smirnov , Ekaterina Khrameeva

optimalTAD: a novel algorithm for Topologically Associating Domain optimal set prediction


Andrey Sobolev , V. Ivanova , S. Ulianov , A. Tyakht , Mikhail Solovyev , Tatiana Slepova , A. Merkel

Chromosome conformation of the hyperthermophilic archaeon Thermofilum adornatus


Anastasia D. Sokol , Alina Mikhailova , Konstantin Gunbin , Konstantin Popadin

The species-specific burden of slightly deleterious mutations in mammals


Ruslan Soldatov , P. Kharchenko

Joint model of RNA velocity on transcriptional manifold


Ignat V. Sonets , Valeriia Ivanova , Petr Vasiliev , Sergey Ulianov , Alexander Tyakht

Investigating microbial diversity of spontaneous fermentation beer and cider using Hi-C metagenomics


Maxim I. Sorokin , Alexander Simonov , Victor Tkachev , Anton Buzdin

New database and software for topology-based pathway analysis of human gene expression data: overview and application example


Aleksei Efremov , Sergey A. Spirin

Predicting quality of phylogenetic inference by machine learning


Alexei Efremov , Andrey Sigorskikh , Dmitry Penzar , Anna Karyagina , Sergey A. Spirin

PhyloBench, a benchmark for evaluation of phylogenetic programs


Vladimir Shchur , Vadim Spirin , Victor Pokrovskii , Evgeni Burovski , Russell Corbett­Detig

Fast simulation of viral genealogies in global pandemic


Alexander V. Spirov , Ekaterina M. Myasnikova

Reverse transfer of ideas from genetic algorithms to synthetic biology


Alexander V. Spirov , Ekaterina M. Myasnikova , Marat A. Sabirov

Modeling of active transport of bicoid mRNA in early Drosophila embryo development


Maria Starchevskaya , Denis V Antonets , Yuri Vyatkin , Tatyana Tregubchak , Tatyana Bauer , Ekaterina Kamanova , Tatyana Nepomnyaschih , Ulyana Rotskaya , Elena Kosman

The rich inner world of Colorado potato beetles – a metagenomic survey of viral diversity in public data


Anastasia V. Stolyarova , T.V. Neretina , A.S. Kondrashov , G.A. Bazykin

Within-gene epistatic selection in genetically diverse populations


Sergei V. Strelkov , Anastasia V. Lilina , Giel Stalmans , Pieter-Jan Vermeire , Jan Fiala , Petr Novak

Integrative approach to intermediate filament structure


Vladimir Sukhov , Maxim Artyomov , Alexey Sergushichev

Gene Set Co-regulation Analysis


Daria Timonina , Yana Sharapova , Vytas Švedas , Dmitry Suplatov

Zebra3D: a tool for bioinformatic analysis of 3D-determinants of functional diversity in protein superfamilies using machine learning


Dmitry Suplatov , Yana Sharapova , Vytas Švedas

Functional significance of structural plasticity of the loop 422-437 in the active site of Neuraminidase A from Streptococcus pneumoniae


Svetlana Surkova , Maria Samsonova , Konstantin Kozlov

Image processing methods for analysis of cellular structure of epithelial tissue




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Liu Cao , Mustafa Guler , Azat Tagirdzhanov , Yiyuan Lee , Alexey Gurevich , Hosein Mohimani

MolDiscovery: Learning Mass Spectrometry Fragmentation of Small Molecules


Gaik Tamazian , Alexander Kanapin , Anastasia Samsonova , Sergey V. Malov

On Selective Imputation Using Beagle v.5.


Julia Terentjeva , Maria Poptsova

Identification of conservative patterns of G-quadruplexes and transcription binding sites


Stanislav Tikhonov , Alexander Tyshkovskiy

Utilizing machine learning methods and cellular gene expression patterns of longevity for identification of new lifespan-extending interventions


Daria Timonina , Yana Sharapova , Vytas Švedas , Dmitry Suplatov

Bioinformatic analysis of local 3D-structure patterns in protein superfamilies


Valeria N. Timonina , Anastasia Sokol , Evgenii Tretiakov , Konstantin V Gunbin , Konstantin Popadin

Heat shock protein 90 as a long-term buffer of a species-specific mutational burden


Anna Timoshchuk , Nadezhda A. Potapova , Gordan Lauc , Tim Spector , Sodbo Sharapov , Yurii S. Aulchenko

Data-driven approach for traits definition for multivariate genetic analysis of N-glycome composition


Evgeny Tiys , Gulnara R. Svishcheva , Sofia G. Feoktistova , Elizaveta E. Elgaeva , Sodbo Z. Sharapov , Yakov A. Tsepilov

Shared heredity: a method to model genetic basis of correlated traits


Andrey Tomarovsky , Azamat A. Totikov , Violetta R. Beklemisheva , Polina L. Perelman , Natalia A. Serdyokova , Tatiana Bulyonkova , Ksenia A. Koniaeva , Alexei V. Abramov , Alexander S. Graphodatsky , Klaus-Peter Koepfli , Roger A. Powell , Sergei F. Kliver

Assembly and annotation of the sable (Martes zibellina) and pine marten (Martes martes) genomes


Azamat Totikov , Andrey A. Tomarovsky , Polina Perelman , Natalia Serdyokova , Violetta R. Beklemisheva , Tatiana M. Bulyonkova , Karol Zub , Viktor V. Panov , Anna S. Mukhacheva , Alexei V. Abramov , Klaus-Peter Koepfli , Alexander S. Graphodatsky , Jose Melo-Ferreira , Sergei F. Kliver

Reconstruction of the demographic history for three populations of the least weasel Mustela nivalis


Petr Tsurinov , Oleg Shpynov , Maxim Artyomov , Nina Lukashina , Daria Likholetova

FARM – new Association Rule Mining method using Fishbone diagrams


Maria N. Tutukina , Tatiana A. Bessonova , Anna A. Rybina , Anna D. Kaznadzey , Uliana S. Shvyreva , Fyodor A. Kondrashov , Mikhail S. Gelfand , Olga N. Ozoline

Black holes in the regulation of biofilm formation in Escherichia coli




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Leonid Uroshlev , A.P. Beletskiy

Prediction of inton-exon gene structure for reads by a convolution neural network


Kristina Ushakova , Alina A. Mikhailova , Alina G. Mikhailova , Victor Shamanskiy , Alima Galieva , Valeria Lobanova , Valeria Timonina , Valerian Yurov , Maria Olyanich , Dmitrii Iliushchenko , Aleksandr Smirnov , Ilya Mazunin , Leonard Polishchuk , Dmitry Knorre , Konstantin Khrapko , Konstantin Gunbin , Jacques Fellay , Konstantin Popadin

Mutational spectrum of the human mitochondrial genome: somatic and germline signatures differ




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Sergey Vakulenko , John Reinitz , Ovidiu Radulescu , Dmitry Grigoriev

Fitness landscape learning, canalization and fast evolution


Anna Valyaeva , Maria A. Tikhomirova , Anastasia A. Zharikova , Anna V. Fedotova , Andrey A. Mironov , Eugene V. Sheval

Semi-extractability of coding and non-coding RNAs


Anastasiia Velikanova , Aleksandra Mitina , Elena Stekolschikova , Olga Efimova , Ekaterina Tyulkova , Elena Rybnikova , Pavel Mazin , Philipp Khaitovich

Systematic analysis of age-dependent lipidome alterations in rat tissues


Maria Vlasenok , Dmitri Pervouchine

De novo identification of alternative polyadenylation from RNA-seq data


Alexandr Voronka , Bogdan Efimenko , Sergei Oreshkov , Konstantin Gunbin , Konstantin Popadin

Analysis of the mutation spectrum and selective constraints of SARS-CoV-2




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Yulia Yakovleva , Sivarajan Karunanithi , Marcello Pirritano , Franziska Drews , Martin Simon , Alexey Potekhin

Small RNAs in Paramecium response to Preeria caryophila infection


Daria Yanovskaya , M.A. Skutel , O.S. Musharova , A. B. Isaev

Modelling of the evolutionary pathway from anti-restriction to anti-CRISPR function


Yuki Yoshida , Olga Kozlova , Nurislam Shaikhutdinov , Oleg Gusev , Takahiro Kikawada

A single chromosome driving rapid extremotolerant adaptation in an insect


Andrey A. Yurchenko , Tirzah B. P. Lajus , Hiva Fassihi , Chikako Nishigori , Konstantin Gunbin , Fatemeh Rajabi , Ismael Padioleau , Carlos F. M. Menck , Alain Sarasin , Patricia Kannouche , Sergey Nikolaev

Genomic analysis of skin cancers from Xeroderma Pigmentosum subgroups revealed mechanisms behind UV mutational signatures formation


Valerian A. Yurov , Konstantin Popadin

Let's go analytic! Two exact models of the mtDNA mutagenesis and their ramifications




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Alexey Zabelkin , Yulia Yakovleva , Olga Bochkareva , Nikita Alexeev

Method for detection of parallel adaptation with genome rearrangements in bacterial populations


Konstantin Zaitsev , Maria Firulyova , Maxim N. Artyomov

Single Cell Navigator allows cross-matching of public scRNA-seq data: study case of tumor immune microenvironments


Olga O. Zaitseva , Sodbo Sharapov , Gordan Lauc , Lucija Klaric , Yakov Tsepilov

Causal relationships between human IgG N-glycosylation traits and twelve associated diseases


Arthur O. Zalevsky , Alexander Zlobin , Andrey Golovin

pmx.qmmm: automated protein structure and topology generation for QM/MM calculations


Anton A. Zamyatin , Pavel Avdeyev , Jiangtao Liang , Atashi Sharma , Chujia Chen , Varvara Lukyanchikova , Nikita Alexeev , Zhijian Tu , Max A Alekseyev , Igor V. Sharakhov

Assembling genomes on chromosome-level leading by the example of two malaria vector genomes


Nikita Zernov , L.S. Hunanyan

In silico design of inhibitors of cathepsin G based on β-ketophosphonate


Anastasia A. Zharikova , Andrey I. Sigorskikh , Yuriy D. Korostelev , Andrey A. Mironov

RNA-DNA integractome analysis


Irina Zhegalova , A. Galitsyna , A. Luzhin , S. Ulianov , E. Khrameeva

Features of chromatin structure & gene expression during D. discoideum development


Alina A. Zhukova , G.A. Zakharov , M.M. Kulak , A.F. Saifitdinova

Primary sequence of the Japanese quail's nucleolar organizer region


Dinara Ziganshina , Khalimat Murtazalieva , Yulia Medvedeva

Development of method for predicting synergistic combinations of small molecules based on RNA-seq data


Andrei Zinovyev

Unraveling transcriptional intratumoral heterogeneity at single cell level


Alexander S. Zlobin , Anatoliy Kirichenko , Tatyana Shashkova , Natalya Volkova , Pavel Borodin , Lennart Karssen , Yakov Tsepilov , Yurii Aulchenko

A platform for storage and analysis of results of genome-wide association studies of sheep


Olga Zolotareva , Olga I. Isaeva , Zoe Chervontseva , Alexey Savchik , Evgenia Zotova , Olga Lazareva , David B. Blumenthal , Nina K. Wenke , Martin Ester , Jan Baumbach

DESMOND 2.0: Identification of differentially expressed biclusters and investigation of their network properties