N. Clark

Phylogenetic signal in primate tooth enamel proteins and its relevance for paleoproteomics

The paper evaluates the reliability of phylogenetic inference using primate enamel proteins by simulating sequence fragmentation and comparing results to a reference species tree.

Visualization of liquid-liquid phase transitions using a tiny G-quadruplex binding protein

The paper identifies SERF2 as a protein involved in stress granule formation and characterizes its interactions with G-quadruplex RNA structures to study liquid-liquid phase transitions.

Effects of protein G-quadruplex interactions on phase transitions and protein aggregation

This study shows Znf706 promotes protein aggregation but binds G-quadruplexes, which suppresses aggregation and affects mRNA levels.

Prediction of local convergent shifts in evolutionary rates with phyloConverge characterizes the phenotypic associations and modularity of regulatory elements

This paper introduces phyloConverge, a method to analyze local convergence in regulatory elements, showing it identifies rate-accelerated CNEs linked to ocular tissues in subterranean mammals.

Evolutionary rate covariation identifies SLC30A9 (ZnT9) as a mitochondrial zinc transporter.

The paper uses evolutionary rate covariation to predict the mitochondrial localization of SLC30A9, which is confirmed experimentally as a zinc exporter.

Complementary evolution of coding and noncoding sequence underlies mammalian hairlessness

The paper identifies coding and noncoding sequences that evolve differently in hairless mammals, revealing distinct evolutionary patterns between protein-coding genes and regulatory elements.

Activation by Cleavage of the Epithelial Na+ Channel α and γ Subunits Independently Coevolved with the Vertebrate Terrestrial Migration

The paper shows that ENaC subunit cleavage sites coevolved with vertebrate terrestrial migration and lung development, enabling Na+ conservation and gas exchange.

Phylogenetic Permulations: a statistically rigorous approach to measure confidence in associations between phenotypes and genetic elements in a phylogenetic context

This paper introduces phylogenetic permulations to calculate accurate p-values for phylogenetic analyses, improving statistical confidence in phenotype-genetic element associations.

Cancer control is a key functionality underlying evolution of extended lifespan in mammals

The paper uses comparative genomics to link evolutionary constraint on cancer-related pathways with extended lifespan in mammals, supporting the role of cancer control in longevity.

Microbial associations and spatial proximity predict North American moose (Alces alces) gastrointestinal community composition

The paper investigates how microbial associations and spatial proximity influence gut microbial community composition in North American moose.

TuxNet: A simple interface to process RNA sequencing data and infer gene regulatory networks

TuxNet provides a user-friendly platform to process RNA-seq data and infer gene regulatory networks using two different algorithms.

Systematic Discovery of the Functional Impact of Somatic Genome Alterations in Individual Tumors through Tumor-specific Causal Inference

This paper introduces a tumor-specific causal inference framework to identify causative somatic genome alterations and their impact on molecular phenotypes in individual tumors.

Cryptic, extensive and non-random chromosome reorganization revealed by a butterfly chromonome

The paper reveals extensive, non-random chromosome reorganization in the green-veined white butterfly through fission and fusion events, despite maintaining a standard haploid chromosome count and gene collinearity.

The integrated stress response pathway activates 4E-BP to bias mRNA translation and boost antimicrobial peptide synthesis in response to bacterial infection

This study shows that 4E-BP, induced by GCN2/ATF4 during bacterial infection, promotes cap-independent translation of antimicrobial peptides in Drosophila.