Mapping DNA by stochastic relaxation: a new approach to fragment sizes. - A. V. Grigorjev; Andrey A. Mironov (Comput. Appl. Biosci., 1990)

DNASUN: a package of computer programs for the biotechnology laboratory. - Andrey A. Mironov; N. N. Alexandrov; N. Yu. Bogodarova; A. Grigorjev; V. F. Lebedev; L. V. Lunovskaya; M. E. Truchan; Pavel A. Pevzner (Comput. Appl. Biosci., 1995)

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

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)

SST versus EST in Gene Recognition (Invited Paper). - Andrey A. Mironov; Pavel A. Pevzner (SPIRE, 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)

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

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

Two genetic algorithms for identification of regulatory signals. - Elena D. Stavrovskaya; Andrey A. Mironov (Silico Biol., 2003)

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)

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)

Rnakinetics: a Web Server that Models Secondary Structure Kinetics of an Elongating RNA. - Ludmila V. Danilova; Dmitri D. Pervouchine; Alexander V. Favorov; Andrey A. Mironov (J. Bioinform. Comput. Biol., 2006)

An Overview of the Algorithmic Session of MCCMB'05. - Gregory Kucherov; Andrey A. Mironov; Mikhail A. Roytberg (J. Bioinform. Comput. Biol., 2006)

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)

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)

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)

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)

A Generalized Hidden Markov Model for Prediction of Cis-regulatory Modules in Eukaryote Genomes and Description of Their Internal Structure. - Anna A. Nilulova; Alexander V. Favorov; Vsevolod J. Makeev; Andrey A. Mironov (BIOINFORMATICS, 2012)

Automated Regulon Content Prediction and Estimation of PWM Quality. - Elena D. Stavrovskaya; Andrey A. Mironov; Dmitry A. Rodionov; Inna Dubchak; Pavel S. Novichkov (BIOINFORMATICS, 2012)

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)

Exploring Massive, Genome Scale Datasets with the GenometriCorr Package. - Alexander V. Favorov; Loris Mularoni; Leslie M. Cope; Yulia A. Medvedeva; Andrey A. Mironov; Vsevolod J. Makeev; Sarah J. Wheelan (PLoS Comput. Biol., 2012)

Fast assessment of the correlation between coverage-like genomic features and its statistical significance. - Elena D. Stavrovskaya; Andrey A. Mironov; Alexander V. Favorov (IWBBIO, 2013)

RNASurface: fast and accurate detection of locally optimal potentially structured RNA segments. - Ruslan A. Soldatov; Svetlana V. Vinogradova; Andrey A. Mironov (Bioinform., 2014)

StereoGene: rapid estimation of genome-wide correlation of continuous or interval feature data. - Elena D. Stavrovskaya; Tejasvi Niranjan; Elana J. Fertig; Sarah J. Wheelan; Alexander V. Favorov; Andrey A. Mironov (Bioinform., 2017)

Coloc-stats: a unified web interface to perform colocalization analysis of genomic features. - Boris Simovski; Chakravarthi Kanduri; Sveinung Gundersen; Dmytro Titov; Diana Domanska; Christoph Bock; Lara Bossini-Castillo; Maria Chikina; Alexander V. Favorov; Ryan M. Layer; Andrey A. Mironov; Aaron R. Quinlan; et al. (Nucleic Acids Res., 2018)

An extended catalogue of tandem alternative splice sites in human tissue transcriptomes. - Andrey A. Mironov; Stepan Denisov; Alexander Greß; Olga V. Kalinina; Dmitri D. Pervouchine (PLoS Comput. Biol., 2021)

RNA-Chrom: a manually curated analytical database of RNA-chromatin interactome. - Grigory Ryabykh; S. V. Kuznetsov; Y. D. Korostelev; A. I. Sigorskikh; A. A. Zharikova; Andrey A. Mironov (Database J. Biol. Databases Curation, 2023)

Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale. - Asia Mendelevich; Saumya Gupta; Aleksei Pakharev; Athanasios Teodosiadis; Andrey A. Mironov; Alexander A. Gimelbrant (Bioinform., 2023)