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Mitochondrial phosphoproteomes are functionally specialized across tissuesThis study explores tissue-specific mitochondrial proteomes and phosphoproteomes in unprecedented depth, offering valuable insights into mitochondrial organization and specialization.
Performance and robustness analysis reveals phenotypic trade-offs in yeastThis study combines phenotypic data from yeast cultivations with quantification of robustness over a defined perturbation space, revealing trade-offs between performance and robustness.
MICA: a multi-omics method to predict gene regulatory networks in early human embryosOur comparative analysis of gene regulatory network predictions defines a pipeline to infer transcription factor–target gene regulatory interactions in early human embryos. Mutual information refined by chromatin accessibility allowed us to construct the first network during early human development.
Identification of biomarkers, pathways, and therapeutic targets for EGFR–TKI resistance in NSCLCThe exploration of the hub genes related to EGFR–TKI resistance in NSCLC through bioinformatics technologies can improve the understanding of the mechanisms of EGFR–TKI resistance and provide novel insights into therapeutics.
The highly improved genome of Ixodes scapularis with X and Y pseudochromosomesIxodes scapularis Gulia-Nuss (IscGN) genome assembly and gene set were obtained using DNA from eggs and male and female adult ticks. By combining Hi-C, PacBio HiFi, and Illumina sequencing technologies, we assembled 13 pseudoautosomes and sex chromosomes: X and Y.
Dissecting morphogenetic apoptosis through a genetic screen in DrosophilaThis genetic screen identifies elements of the “morphogenetic apoptosis pathway” potentially involved in the regulation, the orchestration or the impact of the apoptotic process on morphogenesis.
Comparative membrane proteomics reveals diverse cell regulators concentrated at the nuclear envelopeA cohort of low-abundance transmembrane proteins concentrated at the nuclear envelope has been identified, predicting diverse new functions for this membrane system.
Predictive data-driven modeling of C-terminal tyrosine function in the EGFR signaling networkThe site-specific function of EGFR’s C-terminal tyrosines is interrogated by phosphotyrosine phosphoproteomics to build a data-driven model that links cell response to signaling nodes and elucidates novel associations in the EGFR signaling network.
A practical comparison of the next-generation sequencing platform and assemblers using yeast genomeThis research analyzes the general and optimal de novo yeast assembly pipeline using the repetitive yeast genome assembly by benchmarking four different sequencing platforms and seven assembly programs.
Disease- and sex-specific differences in patients with heart valve disease: a proteome studyProteomics provide novel insights into molecular mechanisms and cardiac remodeling in heart failure because of pressure overload in aortic valve stenosis and volume overload in mitral valve regurgitation.