Author
University of OttawaORCID 0000-0002-5827-3154Unclaimed ORCID profile · follow to get notified of new preprints
8 papers
Recent·Most cited
The paper investigates mutagenesis in yeast linked to glycolytic sugar metabolism and protonation of single-stranded DNA, showing increased mutation rates with higher glucose concentrations and pH changes.
Mutation research. Fundamental and molecular mechanisms of mutagenesis · Jan 1, 2023Peer-reviewedGenetics
Suzana P. Gelova, Kassidy N. Doherty, Salma Alasmar, Kin Chan
The paper analyzes base substitution patterns across species and finds they align with cancer mutational signatures, linking metabolism to DNA damage and mutation generation.
Genetics · Sep 23, 2022Peer-reviewedGenomics
Mahanish J. Thapa, Reena Michelle Fabros, Salma Alasmar, Kin Chan
This study analyzes mutational patterns induced by formaldehyde and acetaldehyde, revealing similarities to a known mutational signature and distinguishing features between the two compounds.
G3 Genes Genomes Genetics · Sep 8, 2022Peer-reviewedGenomics
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
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
Isidro Cortés-Ciriano, Jake June-Koo Lee, Ruibin Xi, Dhawal S. Jain, Youngsook Lucy Jung, Lixing Yang, Dmitry A. Gordenin, Leszek J. Klimczak, Cheng‐Zhong Zhang, David S. Pellman, PCAWG Structural Variation Working Group, Kadir Caner Akdemir, Eva G. Álvarez, Adrian Baez‐Ortega, Rameen Beroukhim, , Kenneth Aldape
This study analyzes chromothripsis in 2,658 cancers using whole-genome sequencing, finding it prevalent across multiple cancer types with complex structural alterations.
Nature Genetics · Feb 5, 2020Peer-reviewedGenomics
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
Kadir Caner Akdemir, Victoria T. Le, Sarah Killcoyne, Devin A. King, Ya-Ping Li, Yanyan Tian, Akira Inoue, Samirkumar B. Amin, Frederick Scott Robinson, Rafael E. Herrera, Erica J. Lynn, Kin Chan, Sahil Seth, Leszek J. Klimczak, Moritz Gerstung, , P. Andrew Futreal
The paper examines how somatic mutation distributions vary across chromatin folding domains in cancer genomes, revealing distinct patterns associated with different mutational processes.
bioRxiv · Oct 14, 2018 · PreprintGenomics