Find below a selection of recent papers. A full list can be found here.

Cancer genomes tolerate deleterious coding mutations through somatic copy number amplifications of wild-type regions

Alfieri et al. 2023. Nature Communications.

Location and condition based reconstruction of colon cancer microbiome from human RNA sequencing data

Sambruni et al. 2023. Genome Medicine.

Using protein-per-mRNA differences among human tissues in codon optimization

Hernandez-Alias et al. 2023. Genome Biology.

Regulation of protein complex partners as a compensatory mechanism in aneuploid tumors

Senger et al. 2022. eLife.

DNA methylation variation along the cancer epigenome and the identification of novel epigenetic driver events

Heery and Schaefer. 2021. Nucleic Acids Research

Protein Complex Organization Imposes Constraints on Proteome Dysregulation in Cancer

Senger and Schaefer. 2021. Frontiers in Bioinformatics.

Translational adaptation of human viruses to the tissues they infect

Hernandez-Alias et al. 2021. Cell Reports.

Silencing of SRRM4 suppresses microexon inclusion and promotes tumor growth across cancers

Head et al. 2021. Plos Biology.

Mutation bias within oncogene families is related to proliferation-specific codon usage

Benisty et al. 2020. PNAS.

Translational efficiency across healthy and tumor tissues is proliferation-related

Hernandez-Alias et al. 2020. Molecular Systems Biology.

Tissue-specific DNA methylation loss during ageing and carcinogenesis is linked to chromosome structure, replication timing and cell division rates

Dmitrijeva et al. 2018. NAR.

Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome

Zapata et al. 2018. Genome Biology.