Computer Functional Analysis of Nucleotide Sequences: Problems and Approaches. - Mikhail S. Gelfand (Mathematical Methods Of Analysis Of Biopolymer Sequences, 1992)

Prediction of Protein-Coding Regions in DNA of Higher Eukaryotes. - Mikhail S. Gelfand (Mathematical Methods Of Analysis Of Biopolymer Sequences, 1992)

Extendable words in nucleotide sequences. - Mikhail S. Gelfand; C. G. Kozhukhin; Pavel A. Pevzner (Comput. Appl. Biosci., 1992)

FANS-REF: a bibliography on statistics and functional analysis of nucleotide sequences. - Mikhail S. Gelfand (Comput. Appl. Biosci., 1995)

Prediction of Function in DNA Sequence. - Mikhail S. Gelfand (J. Comput. Biol., 1995)

Sequencing Potential of Nested Strand Hybridization. - Oleg Razgulyaev; Anatoly R. Rubinov; Mikhail S. Gelfand; Alexander Chetverin (J. Comput. Biol., 1995)

Reconstruction of a String from Substring Precedence Data. - Anatoly R. Rubinov; Mikhail S. Gelfand (J. Comput. Biol., 1995)

Spliced Alignment: A New Approach to Gene Recognition. - Mikhail S. Gelfand; Andrey A. Mironov; Pavel A. Pevzner (CPM, 1996)

Recognition of Genes in Human DNA Sequences. - Mikhail S. Gelfand; L. I. Podolsky; Tatiana V. Astakhova; Mikhail A. Roytberg (J. Comput. Biol., 1996)

Combinatorial Approaches to Gene Recognition. - Mikhail A. Roytberg; Tatiana V. Astakhova; Mikhail S. Gelfand (Comput. Chem., 1997)

Combining diverse evidence for gene recognition in completely sequenced bacterial genomes. - Dmitrij Frishman; Andrey A. Mironov; Hans-Werner Mewes; Mikhail S. Gelfand (German Conference on Bioinformatics, 1998)

Algorithms and software for support of gene identification experiments. - Sing-Hoi Sze; Mikhail A. Roytberg; Mikhail S. Gelfand; Andrey A. Mironov; Tatiana V. Astakhova; Pavel A. Pevzner (Bioinform., 1998)

Segmentation of yeast DNA using hidden Markov models. - Leonid Peshkin; Mikhail S. Gelfand (Bioinform., 1999)

ASDB: database of alternatively spliced genes. - Mikhail S. Gelfand; Inna Dubchak; I. Dralyuk; Manfred Zorn (Nucleic Acids Res., 1999)

Bayesian Approach to DNA Segmentation into Regions with Different Average Nucleotide Composition. - Vsevolod J. Makeev; Vasily Ramensky; Mikhail S. Gelfand; Mikhail A. Roytberg; Vladimir G. Tumanyan (JOBIM, 2000)

Comparative Analysis of Regulatory Patterns in Bacterial Genomes. - Mikhail S. Gelfand; Pavel S. Novichkov; Elena S. Novichkova; Andrey A. Mironov (Briefings Bioinform., 2000)

ASDB: database of alternatively spliced genes. - I. Dralyuk; Michael Brudno; Mikhail S. Gelfand; Manfred Zorn; Inna Dubchak (Nucleic Acids Res., 2000)

Pro-Frame: similarity-based gene recognition in eukaryotic DNA sequences with errors. - Andrey A. Mironov; Pavel S. Novichkov; Mikhail S. Gelfand (Bioinform., 2001)

Gene recognition in eukaryotic DNA by comparison of genomic sequences. - Pavel S. Novichkov; Mikhail S. Gelfand; Andrey A. Mironov (Bioinform., 2001)

Finding Weak Motifs in DNA Sequences. - Sing-Hoi Sze; Mikhail S. Gelfand; Pavel A. Pevzner (Pacific Symposium on Biocomputing, 2002)

Exact mapping of prokaryotic gene starts. - M. V. Baytaluk; Mikhail S. Gelfand; Andrey A. Mironov (Briefings Bioinform., 2002)

SELEX_DB: a database on in vitro selected oligomers adapted for recognizing natural sites and for analyzing both SNPs and site-directed mutagenesis data. - Julia V. Ponomarenko; Galina Orlova; Anatoly S. Frolov; Mikhail S. Gelfand; Mikhail P. Ponomarenko (Nucleic Acids Res., 2002)

Genome-Wide Analysis of Bacterial Promoter Regions. - Eleazar Eskin; Uri Keich; Mikhail S. Gelfand; Pavel A. Pevzner (Pacific Symposium on Biocomputing, 2003)

An algorithm for identification of regulatory signals in unaligned DNA sequences, its testing and parallel implementation. - Ludmila V. Danilova; Vassily A. Lyubetsky; Mikhail S. Gelfand (Silico Biol., 2003)

The channel in transporters is formed by residues that are rare in transmembrane helices. - Olga V. Kalinina; Vsevolod J. Makeev; Roman A. Sutormin; Mikhail S. Gelfand; Aleksandra B. Rakhmaninova (Silico Biol., 2003)

Bioinformatics classification and functional analysis of PhoH homologs. - Alexei E. Kazakov; Olga Vassieva; Mikhail S. Gelfand; Andrei Osterman; Ross A. Overbeek (Silico Biol., 2003)

No statistical support for correlation between the positions of protein interaction sites and alternatively spliced regions. - Marc N. Offman; Ramil N. Nurtdinov; Mikhail S. Gelfand; Dmitrij Frishman (BMC Bioinform., 2004)

SDPpred: a tool for prediction of amino acid residues that determine differences in functional specificity of homologous proteins. - Olga V. Kalinina; Pavel S. Novichkov; Andrey A. Mironov; Mikhail S. Gelfand; Aleksandra B. Rakhmaninova (Nucleic Acids Res., 2004)

Mining sequence annotation databanks for association patterns. - Irena I. Artamonova; Goar Frishman; Mikhail S. Gelfand; Dmitrij Frishman (Bioinform., 2005)

A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length. - Alexander V. Favorov; Mikhail S. Gelfand; Anna V. Gerasimova; Dmitry A. Ravcheev; Andrey A. Mironov; Vsevolod J. Makeev (Bioinform., 2005)

Alternative splicing and protein function. - A. D. Neverov; Irena I. Artamonova; Ramil N. Nurtdinov; Dmitrij Frishman; Mikhail S. Gelfand; Andrey A. Mironov (BMC Bioinform., 2005)

Evolution of the Nadr Regulon in Enterobacteriaceae. - Anna V. Gerasimova; Mikhail S. Gelfand (J. Bioinform. Comput. Biol., 2005)

Dissimilatory Metabolism of Nitrogen Oxides in Bacteria: Comparative Reconstruction of Transcriptional Networks. - Dmitry A. Rodionov; Inna Dubchak; Adam P. Arkin; Eric J. Alm; Mikhail S. Gelfand (PLoS Comput. Biol., 2005)

Comparative Genomics of Transcriptional Regulation in Yeasts and its Application to Identification of a Candidate Alpha-isopropylmalate Transporter. - Galina Yu. Kovaleva; Georgii A. Bazykin; Michael Brudno; Mikhail S. Gelfand (J. Bioinform. Comput. Biol., 2006)

Recognition of Transmembrane Segments in Proteins: Review and Consistency-based Benchmarking of Internet Servers. - Nataliya S. Sadovskaya; Roman A. Sutormin; Mikhail S. Gelfand (J. Bioinform. Comput. Biol., 2006)

Computational Reconstruction of Iron- and Manganese-Responsive Transcriptional Networks in α-Proteobacteria. - Dmitry A. Rodionov; Mikhail S. Gelfand; Jonathan D. Todd; Andrew R. J. Curson; Andrew W. B. Johnston (PLoS Comput. Biol., 2006)

Overlapping Alternative donor splice Sites in the Human genome. - Ekaterina O. Ermakova; Ramil N. Nurtdinov; Mikhail S. Gelfand (J. Bioinform. Comput. Biol., 2007)

RegTransBase - a database of regulatory sequences and interactions in a wide range of prokaryotic genomes. - 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 (Nucleic Acids Res., 2007)

Identification of replication origins in prokaryotic genomes. - Natalia V. Sernova; Mikhail S. Gelfand (Briefings Bioinform., 2008)

Evolution of Regulatory Systems in Bacteria (Invited Keynote Talk). - 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 (ISBRA, 2009)

Combining specificity determining and conserved residues improves functional site prediction. - Olga V. Kalinina; Mikhail S. Gelfand; Robert B. Russell (BMC Bioinform., 2009)

Machine Learning Study of DNA Binding by Transcription Factors from the LacI Family. - Gennady G. Fedonin; Mikhail S. Gelfand (PRIB, 2010)

An automated stochastic approach to the identification of the protein specificity determinants and functional subfamilies. - Pavel V. Mazin; Mikhail S. Gelfand; Andrey A. Mironov; Aleksandra B. Rakhmaninova; Anatoly R. Rubinov; Robert B. Russell; Olga V. Kalinina (Algorithms Mol. Biol., 2010)

Evolution of Regulatory Motifs of Bacterial Transcription Factors. - Konstantin Yu. Gorbunov; Olga N. Laikova; Dmitry A. Rodionov; Mikhail S. Gelfand; Vassily A. Lyubetsky (Silico Biol., 2010)

RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes. - Pavel S. Novichkov; Olga N. Laikova; Elena S. Novichkova; Mikhail S. Gelfand; Adam P. Arkin; Inna Dubchak; Dmitry A. Rodionov (Nucleic Acids Res., 2010)

RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach. - 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 (Nucleic Acids Res., 2010)

Evidence for Widespread Association of Mammalian Splicing and Conserved Long-Range RNA Structures. - Dmitri D. Pervouchine; Ekaterina Khrameeva; Marina Pichugina; Olexii Nikolaienko; Mikhail S. Gelfand; Petr Rubtsov; Andrey A. Mironov (RECOMB, 2012)

Biases in read coverage demonstrated by interlaboratory and interplatform comparison of 117 mRNA and genome sequencing experiments. - Ekaterina Khrameeva; Mikhail S. Gelfand (BMC Bioinform., 2012)

ANA HEp-2 cells image classification using number, size, shape and localization of targeted cell regions. - Gennady V. Ponomarev; Vladimir L. Arlazarov; Mikhail S. Gelfand; Marat D. Kazanov (Pattern Recognit., 2014)

Evaluation and Comparison of Current Fetal Ultrasound Image Segmentation Methods for Biometric Measurements: A Grand Challenge. - 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; et al. (IEEE Trans. Medical Imaging, 2014)

Selectoscope: A Modern Web-App for Positive Selection Analysis of Genomic Data. - Andrey V. Zaika; Iakov I. Davydov; Mikhail S. Gelfand (ISBRA, 2016)

Introduction to selected papers from MCCMB 2015. - Mikhail S. Gelfand (J. Bioinform. Comput. Biol., 2016)

Detection of homologous recombination in closely related strains. - Anastasia S. Kalinina; Alexandra L. Suvorikova; Vladimir G. Spokoiny; Mikhail S. Gelfand (J. Bioinform. Comput. Biol., 2016)

History of chromosome rearrangements reflects the spatial organization of yeast chromosomes. - Ekaterina Khrameeva; Geoffrey Fudenberg; Mikhail S. Gelfand; Leonid A. Mirny (J. Bioinform. Comput. Biol., 2016)

Recombination Processes and Nonlinear Markov Chains. - Sergey Pirogov; Alexander Rybko; Anastasia S. Kalinina; Mikhail S. Gelfand (J. Comput. Biol., 2016)

Reconstruction of the chromatin 3D conformation from single cell Hi-C data. - Pavel I. Kos; Aleksandra A. Galitsyna; Sergey V. Ulianov; Mikhail S. Gelfand; Sergey V. Razin; Alexander V. Chertovich (BIBM, 2018)

Clustering and Comparison of Hierarchies in the Spatial Organization of Chromatin. - Olga Pushkareva; Alexander Kurashenko; Uliana Moskvina; Anatoly R. Rubinov; Mikhail S. Gelfand (BIBM, 2018)

Prediction of 3D Chromatin Structure Using Recurrent Neural Networks. - Michal Rozenwald; Ekaterina Khrameeva; Grigory V. Sapunov; Mikhail S. Gelfand (BIBM, 2018)

Prediction of chromatin spatial structure characteristics using machine learning methods. - Sergei Starikov; Ekaterina Khrameeva; Mikhail S. Gelfand (BIBM, 2018)

The chromatin structure of Dictyostelium discoideum. - Olga Tsoy; Aleksandra A. Galitsyna; Ekaterina Khrameeva; Sergey V. Ulianov; Mikhail S. Gelfand; Sergey V. Razin (BIBM, 2018)

Nuclear lamina maintains global spatial organization of chromatin in Drosophila cultured cells. - 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 (BIBM, 2018)

Neanderthal and Denisovan ancestry in Papuans: A functional study. - Evgeny E. Akkuratov; Mikhail S. Gelfand; Ekaterina Khrameeva (J. Bioinform. Comput. Biol., 2018)

Introduction to Papers Selected from MCCMB'17. - Mikhail S. Gelfand (J. Bioinform. Comput. Biol., 2018)

HiChew: a Tool for TAD Clustering in Embryogenesis. - Nikolai S. Bykov; Olga M. Sigalova; Mikhail S. Gelfand; Aleksandra A. Galitsyna (ISBRA, 2020)

A machine learning framework for the prediction of chromatin folding in Drosophila using epigenetic features. - Michal Rozenwald; Aleksandra A. Galitsyna; Grigory V. Sapunov; Ekaterina E. Khrameeva; Mikhail S. Gelfand (PeerJ Comput. Sci., 2020)

Single-cell Hi-C data analysis: safety in numbers. - Aleksandra A. Galitsyna; Mikhail S. Gelfand (Briefings Bioinform., 2021)

Towards practical applications in quantum computational biology. - Aleksey K. Fedorov; Mikhail S. Gelfand (Nat. Comput. Sci., 2021)

Perspectives for the reconstruction of 3D chromatin conformation using single cell Hi-C data. - Pavel I. Kos; Aleksandra A. Galitsyna; Sergey V. Ulianov; Mikhail S. Gelfand; Sergey V. Razin; Alexander V. Chertovich (PLoS Comput. Biol., 2021)

HiConfidence: a novel approach uncovering the biological signal in Hi-C data affected by technical biases. - 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 (Briefings Bioinform., 2023)

On "Bioinformatics in Russia: history and present-day landscape" by M.A. Nawaz, I.E. Pamirsky, and K.S. Golokhvast. - Mikhail S. Gelfand (Briefings Bioinform., 2025)