Conservation of mutation and recombination parameters between mammals and zebra finch.

Most of our understanding of the fundamental processes of mutation and recombination stems from a handful of disparate model organisms and pedigree studies of mammals, with little known about other vertebrates. To gain a broader comparative perspective, we focused on the zebra finch (), which, like other birds, differs from mammals in its karyotype (which includes many micro-chromosomes), in the mechanism by which recombination is directed to the genome, and in aspects of ontogenesis. We collected genome sequences from three generation pedigrees that provide information about 80 meioses, inferring 202 single-point mutations, 1,174 crossovers, and 275 non-crossovers.

Evaluating generalizability of artificial intelligence models for molecular datasets.

Deep learning has made rapid advances in modeling molecular sequencing data. Despite achieving high performance on benchmarks, it remains unclear to what extent deep learning models learn general principles and generalize to previously unseen sequences. Benchmarks traditionally interrogate model generalizability by generating metadata based (MB) or sequence-similarity based (SB) train and test splits of input data before assessing model performance.

Coordinated evolution at amino acid sites of SARS-CoV-2 spike.

SARS-CoV-2 has adapted in a stepwise manner, with multiple beneficial mutations accumulating in a rapid succession at origins of VOCs, and the reasons for this are unclear. Here, we searched for coordinated evolution of amino acid sites in the spike protein of SARS-CoV-2. Specifically, we searched for concordantly evolving site pairs (CSPs) for which changes at one site were rapidly followed by changes at the other site in the same lineage.

Landscape of allele-specific transcription factor binding in the human genome.

Sequence variants in gene regulatory regions alter gene expression and contribute to phenotypes of individual cells and the whole organism, including disease susceptibility and progression. Single-nucleotide variants in enhancers or promoters may affect gene transcription by altering transcription factor binding sites. Differential transcription factor binding in heterozygous genomic loci provides a natural source of information on such regulatory variants.

Immune Cell Induced Migration of Osteoprogenitor Cells Is Mediated by TGF-β Dependent Upregulation of NOX4 and Activation of Focal Adhesion Kinase.

The cytokines secreted by immune cells have a large impact on the tissue, surrounding a fracture, e.g., by attraction of osteoprogenitor cells.