Veniamin Fishman

CTCF gradually acquires novel function modalities during bilaterian evolution

This study investigates how CTCF's functional properties evolved across bilaterian species, revealing gradual changes in its ability to regulate chromatin structure and transcription.

GENATATORs: ab initio Gene Annotation With DNA Language Models

The paper benchmarks gene annotation methods, showing fine-tuned DNA language models outperform existing tools and generalize across species and annotate non-coding transcripts.

Back to BERT in 2026: ModernGENA as a Strong, Efficient Baseline for DNA Foundation Models

This paper adapts a modernized BERT-style model to genomic sequence modeling, achieving strong efficiency and performance, and releases it as an open baseline.

The 3D genomics of lampbrush chromosomes highlights the role of active transcription in chromatin organization

This paper integrates single-cell Hi-C, RNA-seq, and microscopy to uncover how hypertranscription shapes lampbrush chromosome structure through transcription-dependent chromatin organization.

Zooming into rearranged genome: applying pipeline of cytological, genomic, and transcriptomic methods for structural variant interpretation

The paper demonstrates an integrative approach combining cytological, genomic, and transcriptomic methods to detect and characterize complex structural variants affecting specific genes and report a new neurodevelopmental phenotype.

A novel role for the CNTN6 locus in lumenization and radial glial cell fate determination during early human cortical development revealed in cerebral organoids

Direction and modality of transcription changes caused by TAD boundary disruption in Slc29a3/Unc5b locus depends on tissue-specific epigenetic context

The paper shows that disrupting TAD boundaries in the Slc29a3/Unc5b locus causes tissue-specific transcriptional changes in multiple genes.

Condensins-mediated mitotic folding persists as a structural echo in interphase chromatin

The paper investigates how condensins shape chromatin contacts in interphase nuclei using Hi-C data from mouse embryonic stem cells, showing structural memory of mitotic folding.

FOXM1 Inhibition Promotes Polyploidization and Metabolic Maturation in Human iPSC-Derived Hepatocytes by Modulating the Wnt/β-Catenin Pathway

This study shows that FOXM1 inhibition promotes terminal differentiation of human iPSC-derived hepatocytes by enhancing polyploidization and metabolic maturation through the Wnt/β-catenin pathway.

Charm is a flexible pipeline to simulate chromosomal rearrangements on Hi-C-like data.

Charm simulates Hi-C-like data with chromosomal rearrangements to benchmark SV detection tools and provides a dataset for future benchmarking.

GENA-LM: A Family of Open-Source Foundational DNA Language Models for Long Sequences

GENA-LM introduces transformer-based DNA language models for long sequences, capable of handling up to 36,000 base pairs and supporting multispecies and taxon-specific applications.

GENA-Web - GENomic Annotations Web Inference using DNA language models

GENA-Web is a web platform using DNA language models to annotate genomic elements, including promoter activity, splice sites, chromatin features, and enhancer activity in Drosophila.

A novel approach for simultaneous detection of structural and single-nucleotide variants based on a combination of chromosome conformation capture and exome sequencing

This paper introduces a method combining exome sequencing and chromosome conformation capture to detect both SNVs and SVs, demonstrating its effectiveness in identifying causative variants in rare disorders.

Expanding the list of sequence-agnostic enzymes for chromatin conformation capture assays with S1 nuclease

This paper introduces an S1 nuclease-based Hi-C method for chromatin conformation capture, offering improved chromatin fragmentation and library preparation compared to DNase I Hi-C.

Cell type-specific interpretation of noncoding variants using deep learning-based methods

The paper introduces DeepCT, a deep learning model that predicts cell type-specific effects of noncoding variants by learning from sparse epigenetic data.

Comparison and critical assessment of single-cell Hi-C protocols

This study compares two single-cell Hi-C protocols, showing that whole-genome amplification introduces more artifacts and noise than PCR-based amplification.

Derivation of ringed seal (Phoca hispida) induced multipotent stem cells

This study derives multipotent stem cells from ringed seal fibroblasts, which can differentiate into adipocytes and osteocytes but not into neuronal cells.

Anopheles mosquitoes revealed new principles of 3D genome organization in insects

This study profiles 3D genome organization in five Anopheles mosquito species, identifying long-range looping interactions conserved over 100 million years and distinct from known chromatin mechanisms.

Quantitative prediction of enhancer-promoter interactions

The paper shows that some chromatin interaction prediction algorithms overestimate their performance and proposes an alternative method using gene expression and CTCF-binding to predict enhancer-promoter interactions with high accuracy.

DNA barcoding reveals that injected transgenes are predominantly processed by homologous recombination in mouse zygote

The paper uses DNA barcoding to show that homologous recombination, specifically SDSA and DSBR, predominantly processes injected transgenes in mouse zygotes, with over 80% of copies undergoing recombination.

Targeted genomic integration of EGFP under tubulin beta 3 class III promoter and mEos2 under tryptophan hydroxylase 2 promoter does not produce sufficient levels of reporter gene expression

The paper tests targeted genomic integration of fluorescent reporters under specific promoters but finds insufficient expression levels for neuronal tracing.