Anne‐Ruxandra Carvunis

Environmental stress and phenotypic tradeoff modulate the adaptive potential of novel coding sequences for de novo gene birth

The paper shows that environmental stress influences the phenotypic impact of de novo ORFs, with tradeoffs and stress-dependent growth effects observed in yeast.

The origin of taxonomically restricted genes in yeast

This study resolves the debate on the origin of taxonomically restricted genes in yeast by showing most are de novo genes while others derive from diverged ancestors.

High-quality peptide evidence for annotating non-canonical open reading frames as human proteins

The paper identifies 25% of 7,264 non-canonical open reading frames (ncORFs) as producing translated gene products, supported by over 3,000 peptides from 3.8 billion mass spectra.

An expanded reference catalog of translated open reading frames for biomedical research

The paper expands and refines a reference catalog of human non-canonical open reading frames (ncORFs) by incorporating more datasets and introducing a translation signature score framework to prioritize high-quality ncORFs.

Detection of human unannotated microproteins by mass spectrometry-based proteomics: a community assessment

The paper assesses MS-based identifications of unannotated human microproteins, finding large variation in reported proteins and PSM quality across studies.

Yeast de novo proteins integrate into cellular systems using ancient protein targeting and degradation pathways

This study investigates how de novo proteins in yeast integrate into cellular systems using ancient targeting and degradation pathways, revealing a conserved molecular signature that enables their ER localization and regulation.

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.

Biological Factors and Statistical Limitations Prevent Detection of Most Noncanonical Proteins by Mass Spectrometry

The paper investigates why noncanonical proteins are rarely detected by mass spectrometry in yeast, finding that their low abundance and small size, rather than instability, are the main factors.

A vast evolutionarily transient translatome contributes to phenotype and fitness

The paper identifies a large noncanonical translatome in yeast, showing most translated elements are not conserved genes and contribute to phenotype through fast-evolving mechanisms.

Massively integrated coexpression analysis reveals transcriptional regulation, evolution and cellular implications of the noncanonical translatome

The paper develops a coexpression analysis framework to study noncanonical open reading frames (nORFs) in yeast, revealing their transcriptional regulation, evolutionary patterns, and cellular roles.

A community-driven roadmap to advance research on translated open reading frames detected by Ribo-seq

This paper outlines a community-driven initiative to create a consolidated catalog of human Ribo-seq ORFs, addressing the lack of standardized annotation for these features.

RNF219 regulates CCR4-NOT function in mRNA translation and deadenylation

This study identifies RNF219 as an interacting partner of the CCR4-NOT complex that modulates its translational repression activity through deadenylation-independent mechanisms.

Elastic Network Modeling of Cellular Networks Unveils Sensor and Effector Genes that Control Information Flow

The paper uses elastic network modeling to identify sensor and effector genes in yeast that control information flow through long-range interactions.

On the illusion of auxotrophy: met15Δ yeast cells can grow on inorganic sulfur thanks to the previously uncharacterized homocysteine synthase Yll058w

The paper shows that yeast cells lacking Met15 can assimilate inorganic sulfur via Yll058w, but require exogenous methionine or hydrogen sulfide chelators to grow, challenging the traditional view of MET15 as essential for sulfur assimilation.

LI Detector: a framework for sensitive colony-based screens regardless of the distribution of fitness effects

The paper introduces LI Detector, a framework for sensitive colony-based fitness screens that does not assume normal distribution of fitness effects, enabling detection of both beneficial and deleterious effects.