Mikhail S. Gelfand

70 papers B 2Misc 2Journal 52Unranked 14

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	On "Bioinformatics in Russia: history and present-day landscape" by M.A. Nawaz, I.E. Pamirsky, and K.S. Golokhvast. Briefings Bioinform. Mikhail S. Gelfand
2023	J	`jnl`	HiConfidence: a novel approach uncovering the biological signal in Hi-C data affected by technical biases. Briefings Bioinform. 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
2021	J	`jnl`	Perspectives for the reconstruction of 3D chromatin conformation using single cell Hi-C data. PLoS Comput. Biol. Pavel I. Kos, Aleksandra A. Galitsyna, Sergey V. Ulianov, Mikhail S. Gelfand, Sergey V. Razin, Alexander V. Chertovich
2021	J	`jnl`	Single-cell Hi-C data analysis: safety in numbers. Briefings Bioinform. Aleksandra A. Galitsyna, Mikhail S. Gelfand
2021	J	`jnl`	Towards practical applications in quantum computational biology. Nat. Comput. Sci. Aleksey K. Fedorov, Mikhail S. Gelfand
2020	J	`jnl`	A machine learning framework for the prediction of chromatin folding in PeerJ Comput. Sci. Michal Rozenwald, Aleksandra A. Galitsyna, Grigory V. Sapunov, Ekaterina E. Khrameeva, Mikhail S. Gelfand
2020	—	`conf`	HiChew: a Tool for TAD Clustering in Embryogenesis. ISBRA Nikolai S. Bykov, Olga M. Sigalova, Mikhail S. Gelfand, Aleksandra A. Galitsyna
2018	—	`conf`	Clustering and Comparison of Hierarchies in the Spatial Organization of Chromatin. BIBM Olga Pushkareva, Alexander Kurashenko, Uliana Moskvina, Anatoly R. Rubinov, Mikhail S. Gelfand
2018	J	`jnl`	Introduction to Papers Selected from MCCMB'17. J. Bioinform. Comput. Biol. Mikhail S. Gelfand
2018	J	`jnl`	Neanderthal and Denisovan ancestry in Papuans: A functional study. J. Bioinform. Comput. Biol. Evgeny E. Akkuratov, Mikhail S. Gelfand, Ekaterina Khrameeva
2018	—	`conf`	Nuclear lamina maintains global spatial organization of chromatin in Drosophila cultured cells. BIBM 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
2018	—	`conf`	Prediction of 3D Chromatin Structure Using Recurrent Neural Networks. BIBM Michal Rozenwald, Ekaterina Khrameeva, Grigory V. Sapunov, Mikhail S. Gelfand
2018	—	`conf`	Prediction of chromatin spatial structure characteristics using machine learning methods. BIBM Sergei Starikov, Ekaterina Khrameeva, Mikhail S. Gelfand
2018	—	`conf`	Reconstruction of the chromatin 3D conformation from single cell Hi-C data. BIBM Pavel I. Kos, Aleksandra A. Galitsyna, Sergey V. Ulianov, Mikhail S. Gelfand, Sergey V. Razin, Alexander V. Chertovich
2018	—	`conf`	The chromatin structure of Dictyostelium discoideum. BIBM Olga Tsoy, Aleksandra A. Galitsyna, Ekaterina Khrameeva, Sergey V. Ulianov, Mikhail S. Gelfand, Sergey V. Razin
2016	J	`jnl`	Detection of homologous recombination in closely related strains. J. Bioinform. Comput. Biol. Anastasia S. Kalinina, Alexandra L. Suvorikova, Vladimir G. Spokoiny, Mikhail S. Gelfand
2016	J	`jnl`	History of chromosome rearrangements reflects the spatial organization of yeast chromosomes. J. Bioinform. Comput. Biol. Ekaterina Khrameeva, Geoffrey Fudenberg, Mikhail S. Gelfand, Leonid A. Mirny
2016	J	`jnl`	Introduction to selected papers from MCCMB 2015. J. Bioinform. Comput. Biol. Mikhail S. Gelfand
2016	J	`jnl`	Recombination Processes and Nonlinear Markov Chains. J. Comput. Biol. Sergey Pirogov, Alexander Rybko, Anastasia S. Kalinina, Mikhail S. Gelfand
2016	—	`conf`	Selectoscope: A Modern Web-App for Positive Selection Analysis of Genomic Data. ISBRA Andrey V. Zaika, Iakov I. Davydov, Mikhail S. Gelfand
2014	J	`jnl`	ANA HEp-2 cells image classification using number, size, shape and localization of targeted cell regions. Pattern Recognit. Gennady V. Ponomarev, Vladimir L. Arlazarov, Mikhail S. Gelfand, Marat D. Kazanov
2014	J	`jnl`	Evaluation and Comparison of Current Fetal Ultrasound Image Segmentation Methods for Biometric Measurements: A Grand Challenge. IEEE Trans. Medical Imaging 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
2012	J	`jnl`	Biases in read coverage demonstrated by interlaboratory and interplatform comparison of 117 mRNA and genome sequencing experiments. BMC Bioinform. Ekaterina Khrameeva, Mikhail S. Gelfand
2012	B	`conf`	Evidence for Widespread Association of Mammalian Splicing and Conserved Long-Range RNA Structures. RECOMB Dmitri D. Pervouchine, Ekaterina Khrameeva, Marina Pichugina, Olexii Nikolaienko, Mikhail S. Gelfand, Petr Rubtsov, Andrey A. Mironov
2010	J	`jnl`	An automated stochastic approach to the identification of the protein specificity determinants and functional subfamilies. Algorithms Mol. Biol. Pavel V. Mazin, Mikhail S. Gelfand, Andrey A. Mironov, Aleksandra B. Rakhmaninova, Anatoly R. Rubinov, Robert B. Russell, Olga V. Kalinina
2010	J	`jnl`	Evolution of Regulatory Motifs of Bacterial Transcription Factors. Silico Biol. Konstantin Yu. Gorbunov, Olga N. Laikova, Dmitry A. Rodionov, Mikhail S. Gelfand, Vassily A. Lyubetsky
2010	—	`conf`	Machine Learning Study of DNA Binding by Transcription Factors from the LacI Family. PRIB Gennady G. Fedonin, Mikhail S. Gelfand
2010	J	`jnl`	RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes. Nucleic Acids Res. Pavel S. Novichkov, Olga N. Laikova, Elena S. Novichkova, Mikhail S. Gelfand, Adam P. Arkin, Inna Dubchak, Dmitry A. Rodionov
2010	J	`jnl`	RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach. Nucleic Acids Res. 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
2009	J	`jnl`	Combining specificity determining and conserved residues improves functional site prediction. BMC Bioinform. Olga V. Kalinina, Mikhail S. Gelfand, Robert B. Russell
2009	—	`conf`	Evolution of Regulatory Systems in Bacteria (Invited Keynote Talk). ISBRA 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
2008	J	`jnl`	Identification of replication origins in prokaryotic genomes. Briefings Bioinform. Natalia V. Sernova, Mikhail S. Gelfand
2007	J	`jnl`	Overlapping Alternative donor splice Sites in the Human genome. J. Bioinform. Comput. Biol. Ekaterina O. Ermakova, Ramil N. Nurtdinov, Mikhail S. Gelfand
2007	J	`jnl`	RegTransBase - a database of regulatory sequences and interactions in a wide range of prokaryotic genomes. Nucleic Acids Res. 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
2006	J	`jnl`	Comparative Genomics of Transcriptional Regulation in Yeasts and its Application to Identification of a Candidate Alpha-isopropylmalate Transporter. J. Bioinform. Comput. Biol. Galina Yu. Kovaleva, Georgii A. Bazykin, Michael Brudno, Mikhail S. Gelfand
2006	J	`jnl`	Computational Reconstruction of Iron- and Manganese-Responsive Transcriptional Networks in α-Proteobacteria. PLoS Comput. Biol. Dmitry A. Rodionov, Mikhail S. Gelfand, Jonathan D. Todd, Andrew R. J. Curson, Andrew W. B. Johnston
2006	J	`jnl`	Recognition of Transmembrane Segments in Proteins: Review and Consistency-based Benchmarking of Internet Servers. J. Bioinform. Comput. Biol. Nataliya S. Sadovskaya, Roman A. Sutormin, Mikhail S. Gelfand
2005	J	`jnl`	A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length. Bioinform. Alexander V. Favorov, Mikhail S. Gelfand, Anna V. Gerasimova, Dmitry A. Ravcheev, Andrey A. Mironov, Vsevolod J. Makeev
2005	J	`jnl`	Alternative splicing and protein function. BMC Bioinform. A. D. Neverov, Irena I. Artamonova, Ramil N. Nurtdinov, Dmitrij Frishman, Mikhail S. Gelfand, Andrey A. Mironov
2005	J	`jnl`	Dissimilatory Metabolism of Nitrogen Oxides in Bacteria: Comparative Reconstruction of Transcriptional Networks. PLoS Comput. Biol. Dmitry A. Rodionov, Inna Dubchak, Adam P. Arkin, Eric J. Alm, Mikhail S. Gelfand
2005	J	`jnl`	Evolution of the Nadr Regulon in Enterobacteriaceae. J. Bioinform. Comput. Biol. Anna V. Gerasimova, Mikhail S. Gelfand
2005	J	`jnl`	Mining sequence annotation databanks for association patterns. Bioinform. Irena I. Artamonova, Goar Frishman, Mikhail S. Gelfand, Dmitrij Frishman
2004	J	`jnl`	No statistical support for correlation between the positions of protein interaction sites and alternatively spliced regions. BMC Bioinform. Marc N. Offman, Ramil N. Nurtdinov, Mikhail S. Gelfand, Dmitrij Frishman
2004	J	`jnl`	SDPpred: a tool for prediction of amino acid residues that determine differences in functional specificity of homologous proteins. Nucleic Acids Res. Olga V. Kalinina, Pavel S. Novichkov, Andrey A. Mironov, Mikhail S. Gelfand, Aleksandra B. Rakhmaninova
2003	J	`jnl`	An algorithm for identification of regulatory signals in unaligned DNA sequences, its testing and parallel implementation. Silico Biol. Ludmila V. Danilova, Vassily A. Lyubetsky, Mikhail S. Gelfand
2003	J	`jnl`	Bioinformatics classification and functional analysis of PhoH homologs. Silico Biol. Alexei E. Kazakov, Olga Vassieva, Mikhail S. Gelfand, Andrei Osterman, Ross A. Overbeek
2003	Misc	`conf`	Genome-Wide Analysis of Bacterial Promoter Regions. Pacific Symposium on Biocomputing Eleazar Eskin, Uri Keich, Mikhail S. Gelfand, Pavel A. Pevzner
2003	J	`jnl`	The channel in transporters is formed by residues that are rare in transmembrane helices. Silico Biol. Olga V. Kalinina, Vsevolod J. Makeev, Roman A. Sutormin, Mikhail S. Gelfand, Aleksandra B. Rakhmaninova
2002	J	`jnl`	Exact mapping of prokaryotic gene starts. Briefings Bioinform. M. V. Baytaluk, Mikhail S. Gelfand, Andrey A. Mironov
2002	Misc	`conf`	Finding Weak Motifs in DNA Sequences. Pacific Symposium on Biocomputing Sing-Hoi Sze, Mikhail S. Gelfand, Pavel A. Pevzner
2002	J	`jnl`	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. Julia V. Ponomarenko, Galina Orlova, Anatoly S. Frolov, Mikhail S. Gelfand, Mikhail P. Ponomarenko
2001	J	`jnl`	Gene recognition in eukaryotic DNA by comparison of genomic sequences. Bioinform. Pavel S. Novichkov, Mikhail S. Gelfand, Andrey A. Mironov
2001	J	`jnl`	Pro-Frame: similarity-based gene recognition in eukaryotic DNA sequences with errors. Bioinform. Andrey A. Mironov, Pavel S. Novichkov, Mikhail S. Gelfand
2000	J	`jnl`	ASDB: database of alternatively spliced genes. Nucleic Acids Res. I. Dralyuk, Michael Brudno, Mikhail S. Gelfand, Manfred Zorn, Inna Dubchak
2000	—	`conf`	Bayesian Approach to DNA Segmentation into Regions with Different Average Nucleotide Composition. JOBIM Vsevolod J. Makeev, Vasily Ramensky, Mikhail S. Gelfand, Mikhail A. Roytberg, Vladimir G. Tumanyan
2000	J	`jnl`	Comparative Analysis of Regulatory Patterns in Bacterial Genomes. Briefings Bioinform. Mikhail S. Gelfand, Pavel S. Novichkov, Elena S. Novichkova, Andrey A. Mironov
1999	J	`jnl`	ASDB: database of alternatively spliced genes. Nucleic Acids Res. Mikhail S. Gelfand, Inna Dubchak, I. Dralyuk, Manfred Zorn
1999	J	`jnl`	Segmentation of yeast DNA using hidden Markov models. Bioinform. Leonid Peshkin, Mikhail S. Gelfand
1998	J	`jnl`	Algorithms and software for support of gene identification experiments. Bioinform. Sing-Hoi Sze, Mikhail A. Roytberg, Mikhail S. Gelfand, Andrey A. Mironov, Tatiana V. Astakhova, Pavel A. Pevzner
1998	—	`conf`	Combining diverse evidence for gene recognition in completely sequenced bacterial genomes. German Conference on Bioinformatics Dmitrij Frishman, Andrey A. Mironov, Hans-Werner Mewes, Mikhail S. Gelfand
1997	J	`jnl`	Combinatorial Approaches to Gene Recognition. Comput. Chem. Mikhail A. Roytberg, Tatiana V. Astakhova, Mikhail S. Gelfand
1996	J	`jnl`	Recognition of Genes in Human DNA Sequences. J. Comput. Biol. Mikhail S. Gelfand, L. I. Podolsky, Tatiana V. Astakhova, Mikhail A. Roytberg
1996	B	`conf`	Spliced Alignment: A New Approach to Gene Recognition. CPM Mikhail S. Gelfand, Andrey A. Mironov, Pavel A. Pevzner
1995	J	`jnl`	FANS-REF: a bibliography on statistics and functional analysis of nucleotide sequences. Comput. Appl. Biosci. Mikhail S. Gelfand
1995	J	`jnl`	Prediction of Function in DNA Sequence. J. Comput. Biol. Mikhail S. Gelfand
1995	J	`jnl`	Reconstruction of a String from Substring Precedence Data. J. Comput. Biol. Anatoly R. Rubinov, Mikhail S. Gelfand
1995	J	`jnl`	Sequencing Potential of Nested Strand Hybridization. J. Comput. Biol. Oleg Razgulyaev, Anatoly R. Rubinov, Mikhail S. Gelfand, Alexander Chetverin
1992	—	`conf`	Computer Functional Analysis of Nucleotide Sequences: Problems and Approaches. Mathematical Methods Of Analysis Of Biopolymer Sequences Mikhail S. Gelfand
1992	J	`jnl`	Extendable words in nucleotide sequences. Comput. Appl. Biosci. Mikhail S. Gelfand, C. G. Kozhukhin, Pavel A. Pevzner
1992	—	`conf`	Prediction of Protein-Coding Regions in DNA of Higher Eukaryotes. Mathematical Methods Of Analysis Of Biopolymer Sequences Mikhail S. Gelfand