Mikhail S. Gelfand

Orcid: 0000-0003-4181-0846

Affiliations:
  • Russian Academy of Science, A. A. Kharkevich Institute for Information Transmission Problems
  • M. V. Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics


According to our database1, Mikhail S. Gelfand authored at least 69 papers between 1992 and 2023.

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Bibliography

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

2021
Perspectives for the reconstruction of 3D chromatin conformation using single cell Hi-C data.
PLoS Comput. Biol., 2021

Towards practical applications in quantum computational biology.
Nat. Comput. Sci., 2021

Single-cell Hi-C data analysis: safety in numbers.
Briefings Bioinform., 2021

2020
A machine learning framework for the prediction of chromatin folding in <i>Drosophila</i> using epigenetic features.
PeerJ Comput. Sci., 2020

HiChew: a Tool for TAD Clustering in Embryogenesis.
Proceedings of the Bioinformatics Research and Applications - 16th International Symposium, 2020

2018
Introduction to Papers Selected from MCCMB'17.
J. Bioinform. Comput. Biol., 2018

Neanderthal and Denisovan ancestry in Papuans: A functional study.
J. Bioinform. Comput. Biol., 2018

Nuclear lamina maintains global spatial organization of chromatin in Drosophila cultured cells.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2018

The chromatin structure of Dictyostelium discoideum.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2018

Prediction of chromatin spatial structure characteristics using machine learning methods.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2018

Prediction of 3D Chromatin Structure Using Recurrent Neural Networks.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2018

Clustering and Comparison of Hierarchies in the Spatial Organization of Chromatin.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2018

Reconstruction of the chromatin 3D conformation from single cell Hi-C data.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2018

2016
Recombination Processes and Nonlinear Markov Chains.
J. Comput. Biol., 2016

History of chromosome rearrangements reflects the spatial organization of yeast chromosomes.
J. Bioinform. Comput. Biol., 2016

Detection of homologous recombination in closely related strains.
J. Bioinform. Comput. Biol., 2016

Introduction to selected papers from MCCMB 2015.
J. Bioinform. Comput. Biol., 2016

Selectoscope: A Modern Web-App for Positive Selection Analysis of Genomic Data.
Proceedings of the Bioinformatics Research and Applications - 12th International Symposium, 2016

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

ANA HEp-2 cells image classification using number, size, shape and localization of targeted cell regions.
Pattern Recognit., 2014

2012
Biases in read coverage demonstrated by interlaboratory and interplatform comparison of 117 mRNA and genome sequencing experiments.
BMC Bioinform., 2012

Evidence for Widespread Association of Mammalian Splicing and Conserved Long-Range RNA Structures.
Proceedings of the Research in Computational Molecular Biology, 2012

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

RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes.
Nucleic Acids Res., 2010

Evolution of Regulatory Motifs of Bacterial Transcription Factors.
Silico Biol., 2010

An automated stochastic approach to the identification of the protein specificity determinants and functional subfamilies.
Algorithms Mol. Biol., 2010

Machine Learning Study of DNA Binding by Transcription Factors from the LacI Family.
Proceedings of the Pattern Recognition in Bioinformatics, 2010

2009
Combining specificity determining and conserved residues improves functional site prediction.
BMC Bioinform., 2009

Evolution of Regulatory Systems in Bacteria (Invited Keynote Talk).
Proceedings of the Bioinformatics Research and Applications, 5th International Symposium, 2009

2008
Identification of replication origins in prokaryotic genomes.
Briefings Bioinform., 2008

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

Overlapping Alternative donor splice Sites in the Human genome.
J. Bioinform. Comput. Biol., 2007

2006
Computational Reconstruction of Iron- and Manganese-Responsive Transcriptional Networks in α-Proteobacteria.
PLoS Comput. Biol., 2006

Recognition of Transmembrane Segments in Proteins: Review and Consistency-based Benchmarking of Internet Servers.
J. Bioinform. Comput. Biol., 2006

Comparative Genomics of Transcriptional Regulation in Yeasts and its Application to Identification of a Candidate Alpha-isopropylmalate Transporter.
J. Bioinform. Comput. Biol., 2006

2005
Dissimilatory Metabolism of Nitrogen Oxides in Bacteria: Comparative Reconstruction of Transcriptional Networks.
PLoS Comput. Biol., 2005

Evolution of the Nadr Regulon in Enterobacteriaceae.
J. Bioinform. Comput. Biol., 2005

Alternative splicing and protein function.
BMC Bioinform., 2005

A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length.
Bioinform., 2005

Mining sequence annotation databanks for association patterns.
Bioinform., 2005

2004
SDPpred: a tool for prediction of amino acid residues that determine differences in functional specificity of homologous proteins.
Nucleic Acids Res., 2004

No statistical support for correlation between the positions of protein interaction sites and alternatively spliced regions.
BMC Bioinform., 2004

2003
Bioinformatics classification and functional analysis of PhoH homologs.
Silico Biol., 2003

The channel in transporters is formed by residues that are rare in transmembrane helices.
Silico Biol., 2003

An algorithm for identification of regulatory signals in unaligned DNA sequences, its testing and parallel implementation.
Silico Biol., 2003

Genome-Wide Analysis of Bacterial Promoter Regions.
Proceedings of the 8th Pacific Symposium on Biocomputing, 2003

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.
Nucleic Acids Res., 2002

Exact mapping of prokaryotic gene starts.
Briefings Bioinform., 2002

Finding Weak Motifs in DNA Sequences.
Proceedings of the 7th Pacific Symposium on Biocomputing, 2002

2001
Gene recognition in eukaryotic DNA by comparison of genomic sequences.
Bioinform., 2001

Pro-Frame: similarity-based gene recognition in eukaryotic DNA sequences with errors.
Bioinform., 2001

2000
ASDB: database of alternatively spliced genes.
Nucleic Acids Res., 2000

Comparative Analysis of Regulatory Patterns in Bacterial Genomes.
Briefings Bioinform., 2000

Bayesian Approach to DNA Segmentation into Regions with Different Average Nucleotide Composition.
Proceedings of the Computational Biology, 2000

1999
ASDB: database of alternatively spliced genes.
Nucleic Acids Res., 1999

Segmentation of yeast DNA using hidden Markov models.
Bioinform., 1999

1998
Algorithms and software for support of gene identification experiments.
Bioinform., 1998

Combining diverse evidence for gene recognition in completely sequenced bacterial genomes.
Proceedings of the German Conference on Bioinformatics, 1998

1997
Combinatorial Approaches to Gene Recognition.
Comput. Chem., 1997

1996
Recognition of Genes in Human DNA Sequences.
J. Comput. Biol., 1996

Spliced Alignment: A New Approach to Gene Recognition.
Proceedings of the Combinatorial Pattern Matching, 7th Annual Symposium, 1996

1995
Reconstruction of a String from Substring Precedence Data.
J. Comput. Biol., 1995

Sequencing Potential of Nested Strand Hybridization.
J. Comput. Biol., 1995

Prediction of Function in DNA Sequence.
J. Comput. Biol., 1995

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

1992
Extendable words in nucleotide sequences.
Comput. Appl. Biosci., 1992

Prediction of Protein-Coding Regions in DNA of Higher Eukaryotes.
Proceedings of the Mathematical Methods Of Analysis Of Biopolymer Sequences, 1992

Computer Functional Analysis of Nucleotide Sequences: Problems and Approaches.
Proceedings of the Mathematical Methods Of Analysis Of Biopolymer Sequences, 1992


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