This study shows that non-optimal codon usage affects cell cycle progression and apoptosis by altering mRNA and protein stability in CDK1 and NUF2 genes.

bioRxiv · Nov 5, 2025 · PreprintMolecular Biology

Mutated Tumor Suppressors Follow Oncogenes Profile by the Gene Hypermethylation of Partners in the Protein Interaction Networks

Somnath Tagore, Milana Frenkel‐Morgenstern

The paper classifies tumor suppressors and oncogenes using network-based analysis and a novel preferential attachment score, showing mutated tumor suppressors integrate hyper-methylated partners like oncogenes.

bioRxiv · Mar 28, 2022 · PreprintSystems Biology

Improving patient survival by direct targeting of chimeric protein-protein interaction networks

Somnath Tagore, Milana Frenkel‐Morgenstern

The paper identifies drug targets by analyzing breakdown points in protein-protein interaction networks of cancer fusions, showing improved patient survival in specific cancer subtypes.

bioRxiv · Mar 24, 2022 · PreprintSystems Biology

Genomic footprints of activated telomere maintenance mechanisms in cancer

Lina Sieverling, Chen Hong, Sandra D. Koser, Philip Ginsbach, Kortine Kleinheinz, Barbara Hutter, Delia M. Braun, Isidro Cortés‐Ciriano, Ruibin Xi, Rolf Kabbe, Peter J. Park, Roland Eils, Matthias Schlesner, PCAWG-Structural Variation Working Group, Kadir C. Akdemir, , Rehan Akbani

The paper analyzes whole-genome sequencing data from cancer samples to identify genomic footprints of telomere maintenance mechanisms, finding specific telomere variant repeat patterns associated with ATRX/DAXX mutations.

Nature Communications · Feb 5, 2020Peer-reviewedGenomics

Spatial Genome Organization as a Framework for Somatic Alterations in Human Cancer

Kadir Caner Akdemir, Victoria T. Le, Sahaana Chandran, Yilong Li, Roel G.W. Verhaak, Rameen Beroukhim, Peter J. Campbell, Lynda Chin, Jesse R. Dixon, P. Andrew Futreal, PCAWG Structural Variation Working Group, Kadir C. Akdemir, Eva G. Álvarez, Adrian Baez‐Ortega, Paul C. Boutros, , Ludmil B. Alexandrov

The paper examines how somatic structural variations affect TAD boundaries and gene regulation in human cancers using whole genome sequencing data.

Nature Genetics · Feb 5, 2020Peer-reviewedGenomics

Whole genome and RNA sequencing of 1,220 cancers reveals hundreds of genes deregulated by rearrangement of cis-regulatory elements

Yiqun Zhang, Fengju Chen, Nuno A. Fonseca, Yao He, Masashi Fujita, Hidewaki Nakagawa, Zemin Zhang, Alvis Brāzma, PCAWG Transcriptome Working Group, Samirkumar B. Amin, Philip Awadalla, Peter J. Bailey, Alvis Brazma, Angela Norie Brooks, Claudia Calabrese, , Paul Alan Edwards

The paper identifies hundreds of genes deregulated by SVs in cancer, showing increased expression linked to SV breakpoints and enhancer elements.

Nature Communications · Feb 5, 2020Peer-reviewedGenomics

A Comprehensive Approach Characterizing Fusion Proteins and Their Interactions Using Biomedical Literature

Somnath Tagore, Alessandro Gorohovski, Lars Juhl Jensen, Milana Frenkel‐Morgenstern

The paper develops a text mining method to identify fusion proteins and their interactions from biomedical literature, achieving classification of 1817 fusions and 2908 interactions across 18 cancer types.

bioRxiv · Jul 17, 2018 · PreprintBioinformatics