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ORCIDMikhail S. Gelfand
Person information
- affiliation: Russian Academy of Science, A. A. Kharkevich Institute for Information Transmission Problems
- affiliation: M. V. Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics
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Journal Articles
- 2023
[j51]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)- 2021
- [j50]Aleksandra A. Galitsyna, Mikhail S. Gelfand:
Single-cell Hi-C data analysis: safety in numbers. Briefings Bioinform. 22(6) (2021) - [j49]Aleksey K. Fedorov, Mikhail S. Gelfand:
Towards practical applications in quantum computational biology. Nat. Comput. Sci. 1(2): 114-119 (2021) - [j48]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) - 2020
- [j47]Michal Rozenwald, Aleksandra A. Galitsyna, Grigory V. Sapunov, Ekaterina E. Khrameeva, Mikhail S. Gelfand:
A machine learning framework for the prediction of chromatin folding in Drosophila using epigenetic features. PeerJ Comput. Sci. 6: e307 (2020) - 2018
- [j46]Mikhail S. Gelfand:
Introduction to Papers Selected from MCCMB'17. J. Bioinform. Comput. Biol. 16(2): 1802002:1-1802002:2 (2018) - [j45]Evgeny E. Akkuratov, Mikhail S. Gelfand, Ekaterina Khrameeva:
Neanderthal and Denisovan ancestry in Papuans: A functional study. J. Bioinform. Comput. Biol. 16(2): 1840011:1-1840011:12 (2018) - 2016
- [j44]Mikhail S. Gelfand:
Introduction to selected papers from MCCMB 2015. J. Bioinform. Comput. Biol. 14(2): 1602003:1-1602003:2 (2016) - [j43]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): 1641001:1-1641001:12 (2016) - [j42]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): 1641002:1-1641002:12 (2016) - [j41]Sergey Pirogov, Alexander Rybko, Anastasia S. Kalinina, Mikhail S. Gelfand:
Recombination Processes and Nonlinear Markov Chains. J. Comput. Biol. 23(9): 711-717 (2016) - 2014
- [j40]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): 2360-2366 (2014) - [j39]Sylvia Rueda, Sana Fathima, Caroline L. Knight, Mohammad Yaqub, Aris T. 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): 797-813 (2014) - 2012
- [j38]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): S4 (2012) - 2010
- [j37]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: 29 (2010) - [j36]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): 163-183 (2010) - [j35]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): 111-118 (2010) - [j34]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): 299-307 (2010) - 2009
- [j33]Olga V. Kalinina, Mikhail S. Gelfand, Robert B. Russell:
Combining specificity determining and conserved residues improves functional site prediction. BMC Bioinform. 10 (2009) - 2008
- [j32]Natalia V. Sernova, Mikhail S. Gelfand:
Identification of replication origins in prokaryotic genomes. Briefings Bioinform. 9(5): 376-391 (2008) - 2007
- [j31]Ekaterina O. Ermakova, Ramil N. Nurtdinov, Mikhail S. Gelfand:
Overlapping Alternative donor splice Sites in the Human genome. J. Bioinform. Comput. Biol. 5(5): 991-1004 (2007) - [j30]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): 407-412 (2007) - 2006
- [j29]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): 981-998 (2006) - [j28]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): 1033-1056 (2006) - [j27]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) - 2005
- [j26]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): 2240-2245 (2005) - [j25]Irena I. Artamonova, Goar Frishman, Mikhail S. Gelfand, Dmitrij Frishman:
Mining sequence annotation databanks for association patterns. Bioinform. 21(S3): 57 (2005) - [j24]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: 266 (2005) - [j23]Anna V. Gerasimova, Mikhail S. Gelfand:
Evolution of the Nadr Regulon in Enterobacteriaceae. J. Bioinform. Comput. Biol. 3(4): 1007-1019 (2005) - [j22]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) - 2004
- [j21]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: 41 (2004) - [j20]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): 424-428 (2004) - 2003
- [j19]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): 3-15 (2003) - [j18]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): 33-47 (2003) - [j17]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): 197-204 (2003) - 2002
- [j16]M. V. Baytaluk, Mikhail S. Gelfand, Andrey A. Mironov:
Exact mapping of prokaryotic gene starts. Briefings Bioinform. 3(2): 181-194 (2002) - [j15]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): 195-199 (2002) - 2001
- [j14]Andrey A. Mironov, Pavel S. Novichkov, Mikhail S. Gelfand:
Pro-Frame: similarity-based gene recognition in eukaryotic DNA sequences with errors. Bioinform. 17(1): 13-15 (2001) - [j13]Pavel S. Novichkov, Mikhail S. Gelfand, Andrey A. Mironov:
Gene recognition in eukaryotic DNA by comparison of genomic sequences. Bioinform. 17(11): 1011-1018 (2001) - 2000
- [j12]Mikhail S. Gelfand, Pavel S. Novichkov, Elena S. Novichkova, Andrey A. Mironov:
Comparative Analysis of Regulatory Patterns in Bacterial Genomes. Briefings Bioinform. 1(4): 357-371 (2000) - [j11]I. Dralyuk, Michael Brudno, Mikhail S. Gelfand, Manfred Zorn, Inna Dubchak:
ASDB: database of alternatively spliced genes. Nucleic Acids Res. 28(1): 296-297 (2000) - 1999
- [j10]Leonid Peshkin, Mikhail S. Gelfand:
Segmentation of yeast DNA using hidden Markov models. Bioinform. 15(12): 980-986 (1999) - [j9]Mikhail S. Gelfand, Inna Dubchak, I. Dralyuk, Manfred Zorn:
ASDB: database of alternatively spliced genes. Nucleic Acids Res. 27(1): 301-302 (1999) - 1998
- [j8]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): 14-19 (1998) - 1997
- [j7]Mikhail A. Roytberg, Tatiana V. Astakhova, Mikhail S. Gelfand:
Combinatorial Approaches to Gene Recognition. Comput. Chem. 21(4): 229-235 (1997) - 1996
- [j6]Mikhail S. Gelfand, L. I. Podolsky, Tatiana V. Astakhova, Mikhail A. Roytberg:
Recognition of Genes in Human DNA Sequences. J. Comput. Biol. 3(2): 223-234 (1996) - 1995
- [j5]Mikhail S. Gelfand:
FANS-REF: a bibliography on statistics and functional analysis of nucleotide sequences. Comput. Appl. Biosci. 11(5): 541 (1995) - [j4]Mikhail S. Gelfand:
Prediction of Function in DNA Sequence. J. Comput. Biol. 2(1): 87-115 (1995) - [j3]Anatoly R. Rubinov, Mikhail S. Gelfand:
Reconstruction of a String from Substring Precedence Data. J. Comput. Biol. 2(2): 371-381 (1995) - [j2]Oleg Razgulyaev, Anatoly R. Rubinov, Mikhail S. Gelfand, Alexander Chetverin:
Sequencing Potential of Nested Strand Hybridization. J. Comput. Biol. 2(2): 383-395 (1995) - 1992
- [j1]Mikhail S. Gelfand, C. G. Kozhukhin, Pavel A. Pevzner:
Extendable words in nucleotide sequences. Comput. Appl. Biosci. 8(2): 129-135 (1992)
Conference and Workshop Papers
- 2020
- [c18]Nikolai S. Bykov, Olga M. Sigalova, Mikhail S. Gelfand, Aleksandra A. Galitsyna:
HiChew: a Tool for TAD Clustering in Embryogenesis. ISBRA 2020: 381-388 - 2018
- [c17]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: 2476 - [c16]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: 2482-2487 - [c15]Michal Rozenwald, Ekaterina Khrameeva, Grigory V. Sapunov, Mikhail S. Gelfand:
Prediction of 3D Chromatin Structure Using Recurrent Neural Networks. BIBM 2018: 2488 - [c14]Sergei Starikov, Ekaterina Khrameeva, Mikhail S. Gelfand:
Prediction of chromatin spatial structure characteristics using machine learning methods. BIBM 2018: 2489 - [c13]Olga Tsoy, Aleksandra A. Galitsyna, Ekaterina Khrameeva, Sergey V. Ulianov, Mikhail S. Gelfand, Sergey V. Razin:
The chromatin structure of Dictyostelium discoideum. BIBM 2018: 2492 - [c12]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: 2493 - 2016
- [c11]Andrey V. Zaika, Iakov I. Davydov, Mikhail S. Gelfand:
Selectoscope: A Modern Web-App for Positive Selection Analysis of Genomic Data. ISBRA 2016: 253-257 - 2012
- [c10]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: 199 - 2010
- [c9]Gennady G. Fedonin, Mikhail S. Gelfand:
Machine Learning Study of DNA Binding by Transcription Factors from the LacI Family. PRIB 2010: 15-26 - 2009
- [c8]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: 1-4 - 2003
- [c7]Eleazar Eskin, Uri Keich, Mikhail S. Gelfand, Pavel A. Pevzner:
Genome-Wide Analysis of Bacterial Promoter Regions. Pacific Symposium on Biocomputing 2003: 29-40 - 2002
- [c6]Sing-Hoi Sze, Mikhail S. Gelfand, Pavel A. Pevzner:
Finding Weak Motifs in DNA Sequences. Pacific Symposium on Biocomputing 2002: 235-246 - 2000
- [c5]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: 57-73 - 1998
- [c4]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 - 1996
- [c3]Mikhail S. Gelfand, Andrey A. Mironov, Pavel A. Pevzner:
Spliced Alignment: A New Approach to Gene Recognition. CPM 1996: 141-158 - 1992
- [c2]Mikhail S. Gelfand:
Computer Functional Analysis of Nucleotide Sequences: Problems and Approaches. Mathematical Methods Of Analysis Of Biopolymer Sequences 1992: 19-62 - [c1]Mikhail S. Gelfand:
Prediction of Protein-Coding Regions in DNA of Higher Eukaryotes. Mathematical Methods Of Analysis Of Biopolymer Sequences 1992: 87-98
Coauthor Index
Ekaterina Khrameeva
aka: Ekaterina E. Khrameeva
aka: Ekaterina E. Khrameeva
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