Lydia Freddolino

This study defines the pan-genome of Candidozyma auris and identifies essential genes, revealing organism-specific biology and potential antifungal targets.

Mu-seq maps long-range DNA-DNA contacts in E. coli without crosslinking, revealing new interaction patterns not detectable by Hi-C.

The paper predicts the structure and function of all proteins in uropathogenic E. coli UTI89 using computational methods and identifies novel host-microbe and microbe-phage interaction pathways.

This paper reports on the fourth CAFA challenge, showing improvements in Gene Ontology term prediction but highlighting challenges in new evaluation settings.

ShapeME discovers structural DNA motifs that improve prediction of protein-DNA binding beyond traditional PWMs using ChIP-seq data.

StarFunc combines deep learning with template information from multiple sources to improve protein function prediction, outperforming existing methods in benchmark tests.

The paper defines a 3D chromatin compartment blueprint that programs histone-to-protamine exchange during spermiogenesis using ATAC-seq, CUT&Tag, and Hi-C.

This paper introduces TARJIM, a method that infers sequence motifs from DNA-protein binding data by using reversible jump Metropolis Hastings to determine both the number and sequence of motifs.

This study examines how Enterococcus faecalis affects the transcriptome and metabolism of Escherichia coli in co-culture, revealing strain-specific responses and nutrient cross-feeding.

This study shows that the lac operon in uropathogenic E. coli enables host glycan utilization, enhancing intracellular growth and infection dissemination.

This study investigates how Lsr2 and LsrL regulate chromatin structure and biosynthetic gene clusters in Streptomyces venezuelae using multi-omics approaches.

StoPred predicts protein complex stoichiometry using protein language models and graph attention networks, achieving higher accuracy for both homomeric and heteromeric complexes than existing methods.

The paper maps the protein-DNA landscape of M. bovis BCG under iron starvation, revealing conserved heterochromatin-like structures and their role in stress response gene regulation.

This study shows DNA methylation in E. coli does not alter global chromatin structure but affects specific gene expression changes indirectly.

EZpred improves enzyme function prediction by using unlabeled sequence homologs, achieving higher F1-scores than existing methods.

The paper identifies nutrient stress response mechanisms in E. coli by integrating chromatin structure and small regulatory RNA data, revealing novel transcription factor-sRNA interactions.

The paper identifies polyphosphate as a scaffold for phase-separated condensates in bacteria and humans, showing its role in RNA turnover and translation.

InterLabelGO+ improves protein function prediction by combining deep learning and alignment-based methods with a novel loss function and dynamic weighting, achieving strong performance in the CAFA5 challenge.

This study shows that negative feedback of c-di-GMP levels in V. cholerae optimizes switching between sessile and motile lifestyles by regulating PDE expression through VpsR.

FURNA provides a database of functional annotations for experimental RNA structures, including Gene Ontology terms and ligand binding sites.

This study evaluates sequence database search tools for homology-based protein function prediction, finding that BLASTp and MMseqs2 outperform DIAMOND under default parameters, but DIAMOND can match their performance with proper settings.

The paper shows that H-NS and TsrA regulate horizontally acquired elements in a clinical isolate of V. cholerae, with TsrA modulating H-NS activity and independently affecting gene expression.

This study identifies novel Pumilio target genes and reveals how Pumilio and CCR4-NOT deadenylase regulate mRNA stability and translation efficiency in Drosophila.

This study examines the distinct roles of RNase HII and HIII in removing RNA:DNA hybrids and their impact on mutagenesis and DNA replication.

This study shows how the metabolic enzyme OGT regulates chromatin accessibility and transcription in Drosophila gustatory neurons to mediate sensory adaptations to a high sugar diet.

This paper introduces DRfold, a method that improves RNA tertiary structure prediction by integrating deep learning with geometric potentials, achieving significant performance gains over existing methods.

The paper shows that low GC-content flanking sequences and proximity to ribosomal RNA operons significantly reduce gene expression in E. coli, independent of regulatory elements.

PEPPI predicts protein-protein interactions using structural, sequence, and functional data, achieving higher accuracy than existing methods and identifying interactions relevant to SARS-CoV-2 infection.

TripletGO improves gene function annotations by integrating transcript expression, sequence alignment, and probability models across multiple species and proteins.

The paper uses IPOD-HR to globally map protein-DNA interactions in E. coli, revealing dynamic transcription factor occupancy and stable nucleoid factor domains, and develops computational models for transcription factor specificity.