Mikhail Sergeevich Gelfand

The paper reanalyzes APOBEC3 mutagenesis in MPXV genomes, showing mutations are enriched at TC motifs in hairpin loops and downstream guanine-rich sequences, with structural and sequence context playing distinct roles at different genomic scales.

The paper analyzes Azospirillum genomes to characterize the organization and evolution of their secondary replicons, identifying gene composition, replication systems, and segregation mechanisms.

The paper identifies new hosts for the gammaproteobacterial genus 'Candidatus Endobugula' and describes distinct microbial communities in three marine bryozoan species.

This study analyzes short gene overlaps in bacterial genomes, finding they are evolutionarily dynamic and not strongly conserved, with limited functional associations.

The paper develops a kinetic theory of cohesin extrusion to explain loop statistics and fountain geometry, finding that cohesin crowding and roadblock dynamics determine loop lengths and arm coordination.

The paper identifies 'fountains' as enhancer-specific chromosome organization elements emerging during zygotic genome activation in zebrafish and mouse.

The paper shows that non-consensus nucleotides in transcription factor binding sites can be conserved due to epistatic interactions with other nucleotides in the same site.

This paper introduces Chimaera, a CNN that predicts Hi-C maps from DNA sequences, revealing chromatin structure features and evolutionary relationships across species.

The paper identifies gene expression modules linked to biofilm formation in E. coli by analyzing replicate-to-replicate variation across genetic backgrounds.

The paper reanalyzes MPXV mutation data and finds no statistically significant enrichment of APOBEC-signature mutations in cruciform structures formed by inverted repeats.

The paper analyzes MPXV RNA-seq data to determine if APOBEC3 enzymes edit viral RNA, concluding that observed mutations result from DNA-level mutagenesis, not RNA editing.

The paper analyzes transcriptomic dynamics during metamorphosis in two Drosophila species, revealing an inverted hourglass pattern of gene expression in pupae, contrasting with the traditional embryonic hourglass model.

The paper investigates chromatin looping in Dictyostelium discoideum, finding that convergent gene pairs act as directional barriers for chromatin extrusion during development.

The paper analyzes the evolution of secondary replicons in bacterial genomes, identifying two patterns: chromids with size correlated to the chromosome and megaplasmids with stable size.

The paper introduces optimalTAD, an algorithm for identifying TADs by maximizing chromatin mark enrichment differences between TADs and boundaries, showing it works across species and cell types.

The paper analyzes transcriptome data to show that pupal gene expression in holometabolous insects resembles embryonic patterns, suggesting a recapitulation of the embryonic transcriptional program during metamorphosis.

The paper identifies three types of A-to-I editing site clusters in cephalopods and describes structural features and mechanisms underlying their formation.

The paper reanalyzes human gut microbiome data using non-linear dimensionality reduction and finds no stable clusters, challenging the concept of enterotypes.

This study analyzes genome rearrangements in Shigella and E. coli strains, finding high rearrangement rates and specific E3 ubiquitin ligases linked to pathogenicity.

The paper identifies phospho-islands in mammals and shows they have distinct evolutionary and functional properties compared to individual phosphosites.

The paper annotates the Hirudo medicinalis genome and analyzes salivary transcriptomes of three leech species to identify salivary cell-specific genes and update knowledge on blood-sucking mechanisms.

The paper performs a pan-genomic analysis of Chlamydia species, showing genome stability with conserved core genes and evolvability in specific gene families due to host immune pressure.

The paper analyzes genome rearrangements and selection in Burkholderia species, finding non-random inversion patterns and potential phase variation mechanisms.

This paper analyzes the pan-genome structure and evolution of three Streptococcus species, finding dynamic open pan-genomes with strain-specific genes linked to virulence and adaptability.