Lars A. Eicholt

A discrete protein subset drives structure prediction discordance in orphan proteins

The paper identifies a subset of proteins that causes discordance between structure and disorder predictors, showing that this subset is compositionally distinct and not a general sequence-class artefact.

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.

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.

DeNoFo: a file format and toolkit for standardised, comparable de novo gene annotation

DeNoFo provides a standardised format and toolkit for reproducible de novo gene annotation, enabling consistent documentation and comparison across studies.

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.

Sequence, Structure and Functional space of Drosophila de novo proteins

The paper identifies and characterizes functional de novo proteins in Drosophila using machine learning tools, finding some adopt known folds and participate in cellular processes.

Random, de novo and conserved proteins: How structure and disorder predictors perform differently

This study evaluates how structure prediction tools perform on de novo, random, and conserved proteins, finding differences in prediction accuracy and disorder correlations.

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%.