Vladimı́r Beneš

The paper shows that centrosome absence inhibits cytoskeletal remodeling during EMT in breast cells, despite some nuclear changes and EMT marker upregulation.

The paper shows that many soil bacteria depend on metabolite supplementation from other community members, revealing widespread cross-feeding in soil microbial communities.

This study maps tRNA expression dynamics across human hematopoiesis using sc-STM-seq and identifies tRNAs linked to stemness, differentiation, and cell lineages.

This study investigates interactions between low-calorie sweeteners and xenobiotics on gut bacteria, finding synergistic effects that alter bacterial growth and host cell responses.

The paper introduces UbSeRP to map co-translational ubiquitination across the translatome, revealing RQC substrates, biophysical features predicting RQC, and aging-related changes in CTU.

The paper identifies genomic and transcriptomic features of telomere maintenance mechanisms in complex karyotype sarcomas, linking ALT status to therapeutic vulnerabilities.

The paper uses drug perturbations and RNA sequencing to map pathway connectivity in CLL, showing how genetic aberrations modulate drug responses and pathway interactions.

The paper identifies a centromeric satellite repeat in songbirds and shows it is absent from the germline-restricted chromosome (GRC), suggesting sequence changes underlie its programmed elimination.

This study integrates spatial and multi-omic data from bladder cancer patients to show L1 retrotransposition drives genomic instability, ecDNA formation, and a viral mimicry response.

This study characterizes the microbial community associated with Monocercomonoides exilis through metagenomic sequencing and metabolic analysis, revealing its reliance on bacterial partners for nutrient cycling.

This study shows human gut bacteria can accumulate PFAS, with some species like Bacteroides uniformis accumulating them to high concentrations, and identifies mechanisms involving transmembrane transport and efflux pumps.

This study shows that Kir potassium channels regulate input excitability in parvalbumin interneurons similarly in human and mouse, inhibiting them during postsynaptic potentials.

The paper identifies glucocorticoid receptor-mediated astrocyte reprogramming in depression using post-mortem samples and mouse models.

This study examines how paternal environments and genetic backgrounds affect early embryonic development and identifies molecular responses to paternal conditions.

The paper identifies structural and molecular differences in the axon initial segment of human fast-spiking interneurons that lower firing thresholds and reduce input-output delay compared to mice.

The paper presents genome assemblies for three Platynereis species to support comparative genomic studies and explore their biology.

This study shows aging impairs muscle regeneration by promoting fibro/fatty degeneration and inhibiting inflammation resolution through reduced Periostin in fibro/adipogenic progenitors.

The paper identifies importins that bind nascent proteins co-translationally in yeast, showing their role in preventing aggregation and integrating with ribosome-associated chaperones.

The paper expands the FLP toolkit in C. elegans by adding new driver lines and a protein degradation system, enabling precise gene inactivation and transcriptomic profiling.

The paper develops a method to screen drug combinations using single-cell transcriptome analysis, identifying synergistic and antagonistic pairs in K562 cells.

The paper identifies LINE retrotransposons and long non-coding RNAs in octopus brains, suggesting their role in cognitive evolution through germline and somatic activity.

The paper identifies co-translational assembly domains in proteins that facilitate interactions between nascent chains and fully synthesized subunits, revealing their role in regulating complex assembly pathways.

The paper investigates CNR2 pseudogenization in parrots, showing increased IL1B expression in the brain during inflammation, suggesting functional consequences of CNR2 loss.

The paper characterizes gene and protein expression changes in NGLY1 deficiency using patient-derived cells and provides a web resource for the data.

The paper uses single-cell RNA-Seq and imaging to study how intestinal cell types respond to viral infection, finding that each lineage has unique antiviral responses.

The paper presents genome assemblies and gene predictions for Sf21 and Tni cell lines using multi-omics data, enabling improved use in protein expression and genome engineering.

The paper uses single molecule footprinting to study transcription factor co-occupancy and cooperativity in mouse cis-regulatory elements, finding that high DNA co-occupancy can occur without direct physical interaction.

This study shows that aberrant replication licensing factors drive Copy Number Gains (CNGs) in fission yeast and mammalian cells, linking re-replication to cancer and evolution.

The paper uses nanopore sequencing to assemble Drechmeria coniospora genomes, revealing chromosome plasticity and highlighting the limitations of current long-read methods.