Mikhail S. Gelfand

Publication Activity (10 Years)

Years Active: 1992-2023
Publications (10 Years): 19

Top Topics

Image Segmentation Methods

Recurrent Neural Networks

Selected Papers

Computational Biology

Top Venues

J. Bioinform. Comput. Biol.

Briefings Bioinform.

Publications

Victoria A Kobets, Sergey V. Ulianov, Aleksandra A. Galitsyna, Semen A. Doronin, Elena A. Mikhaleva, Mikhail S. Gelfand, Yuri Y. Shevelyov, Sergey V. Razin, Ekaterina E. Khrameeva
HiConfidence: a novel approach uncovering the biological signal in Hi-C data affected by technical biases. Briefings Bioinform. 24 (2) (2023)
Aleksandra A. Galitsyna, Mikhail S. Gelfand
Single-cell Hi-C data analysis: safety in numbers. Briefings Bioinform. 22 (6) (2021)
Pavel I. Kos, Aleksandra A. Galitsyna, Sergey V. Ulianov, Mikhail S. Gelfand, Sergey V. Razin, Alexander V. Chertovich
Perspectives for the reconstruction of 3D chromatin conformation using single cell Hi-C data. PLoS Comput. Biol. 17 (11) (2021)
Aleksey K. Fedorov, Mikhail S. Gelfand
Towards practical applications in quantum computational biology. Nat. Comput. Sci. 1 (2) (2021)
Nikolai S. Bykov, Olga M. Sigalova, Mikhail S. Gelfand, Aleksandra A. Galitsyna
HiChew: a Tool for TAD Clustering in Embryogenesis. ISBRA (2020)
Michal Rozenwald, Aleksandra A. Galitsyna, Grigory V. Sapunov, Ekaterina E. Khrameeva, Mikhail S. Gelfand
using epigenetic features. PeerJ Comput. Sci. 6 (2020)
Sergei Starikov, Ekaterina Khrameeva, Mikhail S. Gelfand
Prediction of chromatin spatial structure characteristics using machine learning methods. BIBM (2018)
Sergey V. Ulianov, Semen A. Doronin, Ekaterina E. Khrameeva, Pavel I. Kos, Sergey S. Starikov, Aleksandra A. Galitsyna, Artem Luzhin, Mikhail S. Gelfand, Alexander V. Chertovich, Sergey V. Razin, Yuri Y. Shevelyov
Nuclear lamina maintains global spatial organization of chromatin in Drosophila cultured cells. BIBM (2018)
Olga Pushkareva, Alexander Kurashenko, Uliana Moskvina, Anatoly R. Rubinov, Mikhail S. Gelfand
Clustering and Comparison of Hierarchies in the Spatial Organization of Chromatin. BIBM (2018)
Evgeny E. Akkuratov, Mikhail S. Gelfand, Ekaterina Khrameeva
Neanderthal and Denisovan ancestry in Papuans: A functional study. J. Bioinform. Comput. Biol. 16 (2) (2018)
Olga Tsoy, Aleksandra A. Galitsyna, Ekaterina Khrameeva, Sergey V. Ulianov, Mikhail S. Gelfand, Sergey V. Razin
The chromatin structure of Dictyostelium discoideum. BIBM (2018)
Mikhail S. Gelfand
Introduction to Papers Selected from MCCMB'17. J. Bioinform. Comput. Biol. 16 (2) (2018)
Pavel I. Kos, Aleksandra A. Galitsyna, Sergey V. Ulianov, Mikhail S. Gelfand, Sergey V. Razin, Alexander V. Chertovich
Reconstruction of the chromatin 3D conformation from single cell Hi-C data. BIBM (2018)
Michal Rozenwald, Ekaterina Khrameeva, Grigory V. Sapunov, Mikhail S. Gelfand
Prediction of 3D Chromatin Structure Using Recurrent Neural Networks. BIBM (2018)
Mikhail S. Gelfand
Introduction to selected papers from MCCMB 2015. J. Bioinform. Comput. Biol. 14 (2) (2016)
Anastasia S. Kalinina, Alexandra L. Suvorikova, Vladimir G. Spokoiny, Mikhail S. Gelfand
Detection of homologous recombination in closely related strains. J. Bioinform. Comput. Biol. 14 (2) (2016)
Ekaterina Khrameeva, Geoffrey Fudenberg, Mikhail S. Gelfand, Leonid A. Mirny
History of chromosome rearrangements reflects the spatial organization of yeast chromosomes. J. Bioinform. Comput. Biol. 14 (2) (2016)
Sergey Pirogov, Alexander Rybko, Anastasia S. Kalinina, Mikhail S. Gelfand
Recombination Processes and Nonlinear Markov Chains. J. Comput. Biol. 23 (9) (2016)
Andrey V. Zaika, Iakov I. Davydov, Mikhail S. Gelfand
Selectoscope: A Modern Web-App for Positive Selection Analysis of Genomic Data. ISBRA (2016)
Sylvia Rueda, Sana Fathima, Caroline L. Knight, Mohammad Yaqub, Aris Papageorghiou, Bahbibi Rahmatullah, Alessandro Foi, Matteo Maggioni, Antonietta Pepe, Jussi Tohka, Richard V. Stebbing, John McManigle, Anca Ciurte, Xavier Bresson, Meritxell Bach Cuadra, Changming Sun, Gennady V. Ponomarev, Mikhail S. Gelfand, Marat D. Kazanov, Ching-Wei Wang, Hsiang-Chou Chen, Chun-Wei Peng, Chu-Mei Hung, J. Alison Noble
Evaluation and Comparison of Current Fetal Ultrasound Image Segmentation Methods for Biometric Measurements: A Grand Challenge. IEEE Trans. Medical Imaging 33 (4) (2014)
Gennady V. Ponomarev, Vladimir L. Arlazarov, Mikhail S. Gelfand, Marat D. Kazanov
ANA HEp-2 cells image classification using number, size, shape and localization of targeted cell regions. Pattern Recognit. 47 (7) (2014)
Dmitri D. Pervouchine, Ekaterina Khrameeva, Marina Pichugina, Olexii Nikolaienko, Mikhail S. Gelfand, Petr Rubtsov, Andrey A. Mironov
Evidence for Widespread Association of Mammalian Splicing and Conserved Long-Range RNA Structures. RECOMB (2012)
Ekaterina Khrameeva, Mikhail S. Gelfand
Biases in read coverage demonstrated by interlaboratory and interplatform comparison of 117 mRNA and genome sequencing experiments. BMC Bioinform. 13 (S-6) (2012)
Pavel S. Novichkov, Dmitry A. Rodionov, Elena D. Stavrovskaya, Elena S. Novichkova, Alexei E. Kazakov, Mikhail S. Gelfand, Adam P. Arkin, Andrey A. Mironov, Inna Dubchak
RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach. Nucleic Acids Res. 38 (Web-Server-Issue) (2010)
Gennady G. Fedonin, Mikhail S. Gelfand
Machine Learning Study of DNA Binding by Transcription Factors from the LacI Family. PRIB (2010)
Konstantin Yu. Gorbunov, Olga N. Laikova, Dmitry A. Rodionov, Mikhail S. Gelfand, Vassily A. Lyubetsky
Evolution of Regulatory Motifs of Bacterial Transcription Factors. Silico Biol. 10 (3-4) (2010)
Pavel V. Mazin, Mikhail S. Gelfand, Andrey A. Mironov, Aleksandra B. Rakhmaninova, Anatoly R. Rubinov, Robert B. Russell, Olga V. Kalinina
An automated stochastic approach to the identification of the protein specificity determinants and functional subfamilies. Algorithms Mol. Biol. 5 (2010)
Pavel S. Novichkov, Olga N. Laikova, Elena S. Novichkova, Mikhail S. Gelfand, Adam P. Arkin, Inna Dubchak, Dmitry A. Rodionov
RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes. Nucleic Acids Res. 38 (Database-Issue) (2010)
Olga V. Kalinina, Mikhail S. Gelfand, Robert B. Russell
Combining specificity determining and conserved residues improves functional site prediction. BMC Bioinform. 10 (2009)
Mikhail S. Gelfand, Alexei E. Kazakov, Yuri D. Korostelev, Olga N. Laikova, Andrey A. Mironov, Aleksandra B. Rakhmaninova, Dmitry A. Ravcheev, Dmitry A. Rodionov, Alexei G. Vitreschak
Evolution of Regulatory Systems in Bacteria (Invited Keynote Talk). ISBRA (2009)
Natalia V. Sernova, Mikhail S. Gelfand
Identification of replication origins in prokaryotic genomes. Briefings Bioinform. 9 (5) (2008)
Ekaterina O. Ermakova, Ramil N. Nurtdinov, Mikhail S. Gelfand
Overlapping Alternative donor splice Sites in the Human genome. J. Bioinform. Comput. Biol. 5 (5) (2007)
Alexei E. Kazakov, Michael J. Cipriano, Pavel S. Novichkov, Simon Minovitsky, Dmitry V. Vinogradov, Adam P. Arkin, Andrey A. Mironov, Mikhail S. Gelfand, Inna Dubchak
RegTransBase - a database of regulatory sequences and interactions in a wide range of prokaryotic genomes. Nucleic Acids Res. 35 (Database-Issue) (2007)
Dmitry A. Rodionov, Mikhail S. Gelfand, Jonathan D. Todd, Andrew R. J. Curson, Andrew W. B. Johnston
Computational Reconstruction of Iron- and Manganese-Responsive Transcriptional Networks in α-Proteobacteria. PLoS Comput. Biol. 2 (12) (2006)
Galina Yu. Kovaleva, Georgii A. Bazykin, Michael Brudno, Mikhail S. Gelfand
Comparative Genomics of Transcriptional Regulation in Yeasts and its Application to Identification of a Candidate Alpha-isopropylmalate Transporter. J. Bioinform. Comput. Biol. 4 (5) (2006)
Nataliya S. Sadovskaya, Roman A. Sutormin, Mikhail S. Gelfand
Recognition of Transmembrane Segments in Proteins: Review and Consistency-based Benchmarking of Internet Servers. J. Bioinform. Comput. Biol. 4 (5) (2006)
Dmitry A. Rodionov, Inna Dubchak, Adam P. Arkin, Eric J. Alm, Mikhail S. Gelfand
Dissimilatory Metabolism of Nitrogen Oxides in Bacteria: Comparative Reconstruction of Transcriptional Networks. PLoS Comput. Biol. 1 (5) (2005)
A. D. Neverov, Irena I. Artamonova, Ramil N. Nurtdinov, Dmitrij Frishman, Mikhail S. Gelfand, Andrey A. Mironov
Alternative splicing and protein function. BMC Bioinform. 6 (2005)
Anna V. Gerasimova, Mikhail S. Gelfand
Evolution of the Nadr Regulon in Enterobacteriaceae. J. Bioinform. Comput. Biol. 3 (4) (2005)
Alexander V. Favorov, Mikhail S. Gelfand, Anna V. Gerasimova, Dmitry A. Ravcheev, Andrey A. Mironov, Vsevolod J. Makeev
A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length. Bioinform. 21 (10) (2005)
Irena I. Artamonova, Goar Frishman, Mikhail S. Gelfand, Dmitrij Frishman
Mining sequence annotation databanks for association patterns. Bioinform. 21 (S3) (2005)
Olga V. Kalinina, Pavel S. Novichkov, Andrey A. Mironov, Mikhail S. Gelfand, Aleksandra B. Rakhmaninova
SDPpred: a tool for prediction of amino acid residues that determine differences in functional specificity of homologous proteins. Nucleic Acids Res. 32 (Web-Server-Issue) (2004)
Marc N. Offman, Ramil N. Nurtdinov, Mikhail S. Gelfand, Dmitrij Frishman
No statistical support for correlation between the positions of protein interaction sites and alternatively spliced regions. BMC Bioinform. 5 (2004)
Alexei E. Kazakov, Olga Vassieva, Mikhail S. Gelfand, Andrei Osterman, Ross A. Overbeek
Bioinformatics classification and functional analysis of PhoH homologs. Silico Biol. 3 (1-2) (2003)
Olga V. Kalinina, Vsevolod J. Makeev, Roman A. Sutormin, Mikhail S. Gelfand, Aleksandra B. Rakhmaninova
The channel in transporters is formed by residues that are rare in transmembrane helices. Silico Biol. 3 (1-2) (2003)
Eleazar Eskin, Uri Keich, Mikhail S. Gelfand, Pavel A. Pevzner
Genome-Wide Analysis of Bacterial Promoter Regions. Pacific Symposium on Biocomputing (2003)
Ludmila V. Danilova, Vassily A. Lyubetsky, Mikhail S. Gelfand
An algorithm for identification of regulatory signals in unaligned DNA sequences, its testing and parallel implementation. Silico Biol. 3 (1-2) (2003)
Julia V. Ponomarenko, Galina Orlova, Anatoly S. Frolov, Mikhail S. Gelfand, Mikhail P. Ponomarenko
SELEX_DB: a database on in vitro selected oligomers adapted for recognizing natural sites and for analyzing both SNPs and site-directed mutagenesis data. Nucleic Acids Res. 30 (1) (2002)
Sing-Hoi Sze, Mikhail S. Gelfand, Pavel A. Pevzner
Finding Weak Motifs in DNA Sequences. Pacific Symposium on Biocomputing (2002)
M. V. Baytaluk, Mikhail S. Gelfand, Andrey A. Mironov
Exact mapping of prokaryotic gene starts. Briefings Bioinform. 3 (2) (2002)
Andrey A. Mironov, Pavel S. Novichkov, Mikhail S. Gelfand
Pro-Frame: similarity-based gene recognition in eukaryotic DNA sequences with errors. Bioinform. 17 (1) (2001)
Pavel S. Novichkov, Mikhail S. Gelfand, Andrey A. Mironov
Gene recognition in eukaryotic DNA by comparison of genomic sequences. Bioinform. 17 (11) (2001)
Vsevolod J. Makeev, Vasily Ramensky, Mikhail S. Gelfand, Mikhail A. Roytberg, Vladimir G. Tumanyan
Bayesian Approach to DNA Segmentation into Regions with Different Average Nucleotide Composition. JOBIM (2000)
Mikhail S. Gelfand, Pavel S. Novichkov, Elena S. Novichkova, Andrey A. Mironov
Comparative Analysis of Regulatory Patterns in Bacterial Genomes. Briefings Bioinform. 1 (4) (2000)
I. Dralyuk, Michael Brudno, Mikhail S. Gelfand, Manfred Zorn, Inna Dubchak
ASDB: database of alternatively spliced genes. Nucleic Acids Res. 28 (1) (2000)
Leonid Peshkin, Mikhail S. Gelfand
Segmentation of yeast DNA using hidden Markov models. Bioinform. 15 (12) (1999)
Mikhail S. Gelfand, Inna Dubchak, I. Dralyuk, Manfred Zorn
ASDB: database of alternatively spliced genes. Nucleic Acids Res. 27 (1) (1999)
Sing-Hoi Sze, Mikhail A. Roytberg, Mikhail S. Gelfand, Andrey A. Mironov, Tatiana V. Astakhova, Pavel A. Pevzner
Algorithms and software for support of gene identification experiments. Bioinform. 14 (1) (1998)
Dmitrij Frishman, Andrey A. Mironov, Hans-Werner Mewes, Mikhail S. Gelfand
Combining diverse evidence for gene recognition in completely sequenced bacterial genomes. German Conference on Bioinformatics (1998)
Mikhail A. Roytberg, Tatiana V. Astakhova, Mikhail S. Gelfand
Combinatorial Approaches to Gene Recognition. Comput. Chem. 21 (4) (1997)
Mikhail S. Gelfand, Andrey A. Mironov, Pavel A. Pevzner
Spliced Alignment: A New Approach to Gene Recognition. CPM (1996)
Mikhail S. Gelfand, L. I. Podolsky, Tatiana V. Astakhova, Mikhail A. Roytberg
Recognition of Genes in Human DNA Sequences. J. Comput. Biol. 3 (2) (1996)
Mikhail S. Gelfand
Prediction of Function in DNA Sequence. J. Comput. Biol. 2 (1) (1995)
Mikhail S. Gelfand
FANS-REF: a bibliography on statistics and functional analysis of nucleotide sequences. Comput. Appl. Biosci. 11 (5) (1995)
Oleg Razgulyaev, Anatoly R. Rubinov, Mikhail S. Gelfand, Alexander Chetverin
Sequencing Potential of Nested Strand Hybridization. J. Comput. Biol. 2 (2) (1995)
Anatoly R. Rubinov, Mikhail S. Gelfand
Reconstruction of a String from Substring Precedence Data. J. Comput. Biol. 2 (2) (1995)
Mikhail S. Gelfand, C. G. Kozhukhin, Pavel A. Pevzner
Extendable words in nucleotide sequences. Comput. Appl. Biosci. 8 (2) (1992)
Mikhail S. Gelfand
Computer Functional Analysis of Nucleotide Sequences: Problems and Approaches. Mathematical Methods Of Analysis Of Biopolymer Sequences (1992)
Mikhail S. Gelfand
Prediction of Protein-Coding Regions in DNA of Higher Eukaryotes. Mathematical Methods Of Analysis Of Biopolymer Sequences (1992)