Erich Bornberg‐Bauer

How are evolutionarily young and old proteins distributed in sequence space?

The paper compares the distribution of young de novo proteins, old canonical proteins, and randomized sequences in sequence space using k-mer-based distances, finding distinct patterns and potential pathways between classes.

Reduced regulatory complexity associated with the evolutionary transition to sociality from cockroaches to termites despite evolutionary parallels with Hymenoptera

This study compares regulatory changes in transcription factors during the social transition from cockroaches to termites, finding reduced regulatory complexity despite similarities with Hymenoptera.

Structure can emerge from disorder under neutral evolution

The paper shows that neutral evolution can lead to increased structure in unstructured proteins and loss of structure in structured proteins, suggesting a diffuse sequence-structure landscape.

Orthologs of an essential orphan gene vary in their capacities for function and subcellular localization in Drosophila melanogaster

The paper investigates functional and localization differences among orthologs of the Drosophila melanogaster essential gene gdrd, finding that some orthologs can rescue fertility while others cannot due to structural and physicochemical differences.

Cryptocercus genomes expand knowledge of adaptations to xylophagy and termite sociality

The paper presents two new high-quality genomes from the cockroach genus Cryptocercus to study adaptations to xylophagy and subsociality, finding relaxed selection and positive selection in energy production pathways.

Studying the evolutionary potential of ancestral aryl sulfatases in the alkaline phosphatase family with droplet microfluidics

The paper uses droplet microfluidics to study the evolvability and robustness of ancestral and extant aryl sulfatases under varying mutation rates.

Pervasive translation of short open reading frames and de novo gene emergence in Arabidopsis

The paper identifies de novo translated regions in Arabidopsis by analyzing ribosome profiling data and genome comparisons, showing their role in novel gene emergence.

Convergent Evolutionary Traces of Genomic Innovations and Depletions in Socially Parasitic Ants

This study identifies convergent genomic changes in socially parasitic ants, showing gene loss, innovation, and network rewiring in parasites compared to hosts.

De novo ORFs are more likely to shrink than to elongate during neutral evolution.

The paper models ORF evolution as a Markov-jump process and shows that de novo ORFs are more likely to shrink than elongate in neutral evolution, supporting the idea that selection retains longer ORFs.

A functional landscape of human microproteins

This study identifies and characterizes the functional roles of microproteins (sPEPs) in three human tissues, revealing two distinct functional groups and their regulatory roles.

The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes

The paper produces gapless assemblies of ape sex chromosomes for five great apes and a lesser ape, revealing divergence in Y chromosomes and evolutionary dynamics.

Quantification and modeling of turnover dynamics of de novo transcripts in Drosophila melanogaster

The paper estimates de novo transcript turnover rates in Drosophila melanogaster using long and short reads, finding a high turnover rate suggesting frequent exploration of new genomic sequences.

DNA Transposons favour de novo transcript emergence through enrichment of transcription factor binding motifs

The paper identifies de novo transcripts in Drosophila melanogaster and shows they are associated with transposable elements and enriched transcription factor motifs.

Live-bearing cockroach genome reveals convergent evolutionary mechanisms linked to viviparity in insects and beyond

The paper identifies common genomic pathways involved in viviparity across insects, suggesting convergent evolution mechanisms shared with vertebrates.

Origin Matters: Using a Local Reference Genome Improves Measures in Population Genomics

This study shows that using a local reference genome improves mapping efficiency and genotyping accuracy in population genomics analyses of sticklebacks.

Population genomics reveals mechanisms and dynamics of de novo proto-gene emergence in Drosophila melanogaster

This study identifies proto-genes in Drosophila melanogaster, showing they arise rapidly, are frequently lost, and are driven by transposable elements and ORF formation.

Chaperones facilitate heterologous expression of naturally evolved putative de novo proteins

This study improves the expression of de novo proteins in E. coli by using chaperones and specific expression systems, increasing solubility from 30% to 62%.

New genomic signals underlying the emergence of human proto-genes

This study examines properties of human proto-genes, finding correlations between their genomic origin and features like introns, regulatory motifs, and domains.

Lifespan prolonging mechanisms and insulin upregulation without fat accumulation in long-lived reproductives of a higher termite

The paper investigates molecular mechanisms of longevity in termite reproductives, finding upregulated IIS pathway genes without fat accumulation.

Convergent loss of chemoreceptors across independent origins of slave-making in ants

This study identifies convergent loss of odorant receptors in slave-making ants, suggesting adaptive gene loss linked to parasitic lifestyle and reduced chemical perception.

A putative de novo evolved gene required for spermatid chromatin condensation in Drosophila melanogaster

This study identifies a de novo gene, atlas, essential for male fertility in Drosophila by facilitating chromatin condensation in spermatids, and reveals its complex evolutionary history.

A genetic variant alters the secondary structure of the lncRNA H19 and is associated with Dilated Cardiomyopathy

The paper identifies a SNP in lncRNA H19 that alters its secondary structure and is associated with Dilated Cardiomyopathy, suggesting structural changes in lncRNAs may explain hidden genetic variance.

Gene Content Evolution in the Arthropods

The paper analyzes gene and protein domain content changes across 76 arthropod genomes to understand evolutionary patterns and their association with phenotypic adaptations.

Higher-order epistatic networks underlie the evolutionary fitness landscape of a xenobiotic- degrading enzyme

This study identifies five mutations that enable the evolution of a xenobiotic-degrading enzyme and shows that higher-order epistasis shapes its adaptive landscape and substrate specificity.

De Novo Genes are "Frozen Accidents" whichEscaped Rapid Turnover of Pervasively TranscribedORFs

The paper investigates de novo gene emergence and finds that novel ORFs are rapidly lost, with only length and nucleotide composition changing over time, suggesting they are functional 'frozen accidents'.