Vladimı́r Beneš

Lack of centrosomes limits the epithelial-to-mesenchymal transition in human mammary cells

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

Obligate cross-feeding of metabolites is common in soil microbial communities

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

Single-Cell Mapping of tRNA Expression Dynamics Across Human Hematopoiesis

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

Impact of low-calorie sweeteners on gut bacteria is modulated by common xenobiotics

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

Ubiquitin selective ribosome profiling reveals systematic principles of co-translational quality control

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.

Mapping the genomic and transcriptomic features associated with telomere maintenance mechanisms in complex karyotype sarcomas

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

Cancer pathway connectivity resolved by drug perturbation and RNA sequencing

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

Germline-restricted chromosome of songbirds has different centromere compared to regular chromosomes

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.

Integrative spatial and multi-omic profiling in bladder cancer links L1 retrotransposition to extrachromosomal DNA, genomic instability, and viral mimicry response

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.

Extensive PFAS accumulation by human gut bacteria

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.

Regulation of input excitability in human and mouse parvalbumin interneurons by Kir potassium channels

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

Glucocorticoid receptors mediate reprogramming of astrocytes in depression.

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

Embryonic Signatures of Intergenerational Inheritance across Paternal Environments and Genetic Backgrounds

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

Specialized axon initial segment enables low firing threshold and rapid action potential output in fast-spiking interneurons of the human neocortex

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.

A genome resource for the marine annelid Platynereis dumerilii

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

Transcriptional and epigenomic profiling identifies YAP signaling as a key regulator of intestinal epithelium maturation

Co-translational binding of importins to nascent proteins

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

Expanded FLP toolbox for spatiotemporal protein degradation and transcriptomic profiling in C. elegans

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.

Combi-Seq: Multiplexed transcriptome-based profiling of drug combinations using 1deterministic barcoding in single-cell droplets

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

Identification of LINE retrotransposons and long non-coding RNAs expressed in the octopus brain

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

Co-translational assembly counteracts promiscuous interactions

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.

Revealing genomic changes responsible for cannabinoid receptor loss in parrots: mechanism and functional effects

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

Patient-derived gene and protein expression signatures of NGLY1 deficiency

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

Single-cell transcriptomics reveals immune response of intestinal cell types to viral infection

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.

Extensive OMICS resource for Sf21 and Tni cell lines

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.

Single molecule occupancy patterns of transcription factors reveal determinants of cooperative binding in vivo

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.

Aberrant replication licensing drives Copy Number Gains across species

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.

Long-read only assembly of Drechmeria coniospora genomes reveals widespread chromosome plasticity and illustrates the limitations of current nanopore methods

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

Single-cell transcriptomics identifies CD44 as a new marker and regulator of haematopoietic stem cells development

The paper identifies CD44 as a marker and regulator of haematopoietic stem cell development through single-cell transcriptomics and functional experiments.

Single cell tri-channel-processing reveals structural variation landscapes and complex rearrangement processes

This paper introduces scTRIP, a method to detect structural variations in single cells, revealing new SV classes and mutational processes in cancer samples.