Publications

Free full text or preprint of each paper via links below, where available.

Gelova SP, Chan K. (2023) Mutagenesis induced by protonation of single-stranded DNA is linked to glycolytic sugar metabolism. Mutat Res. 826:111814.
Thapa MJ, Fabros RM, Alasmar S, Chan K. (2022) Analyses of Mutational Patterns Induced by Formaldehyde and Acetaldehyde Reveal Similarity to a Common Mutational Signature in Cancers. G3 (Bethesda). 12:jkac238. Full text available.
Gelova SP, Doherty KN, Alasmar S, Chan K. (2022) Intrinsic base substitution patterns in diverse species reveal links to cancer and metabolism. Genetics. 222(3):iyac144. Full text available.
Campbell PJ, Getz G, Korbel JO, Stuart JM, Jennings JL, Stein LD, et al. Pan-cancer analysis of whole genomes. Nature. 2020 Feb 1;578(7793):82–93. Full text available.
Alexandrov LB, Kim J, Haradhvala NJ, Huang MN, Tian Ng AW, Wu Y, et al. The repertoire of mutational signatures in human cancer. Nature. 2020 Feb 1;578(7793):94–101. Full text available.
Rheinbay E, Nielsen MM, Abascal F, Wala JA, Shapira O, Tiao G, et al. Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature. 2020 Feb 1;578(7793):102–11. Full text available.
Li Y, Roberts ND, Wala JA, Shapira O, Schumacher SE, Kumar K, et al. Patterns of somatic structural variation in human cancer genomes. Nature. 2020 Feb 1;578(7793):112–21. Full text available.
Sakofsky CJ, Saini N, Klimczak LJ, Chan K, Malc EP, et al. Repair of multiple simultaneous double-strand breaks causes bursts of genome-wide clustered hypermutation. (2019) PLoS Biology. 17:9, e3000464. https://journals.plos.org/plosbiology/article?rev=1&id=10.1371/journal.pbio.3000464
Chan K. (2018) Molecular Genetic Characterization of Mutagenesis Using a Highly Sensitive Single-Stranded DNA Reporter System in Budding Yeast. In Genome Instability: Methods and Protocols. Methods Mol Biol. 1672, 33-42. doi: 10.1007/978-1-4939-7306-4_4. PMID: 29043615.
Waszak SM, Tiao G, Zhu B, Rausch T, Muyas F, Rodriguez-Martin B, et al. Germline determinants of the somatic mutation landscape in 2,642 cancer genomes. bioRxiv [Internet]. 2017 Nov 1; Available from: http://biorxiv.org/content/early/2017/11/01/208330.abstract
Wala JA, Shapira O, Li Y, Craft D, Schumacher SE, Imielinski M, et al. Selective and mechanistic sources of recurrent rearrangements across the cancer genome. bioRxiv [Internet]. 2017 Sep 14; Available from: http://biorxiv.org/content/early/2017/09/14/187609.abstract
The Cancer Genome Atlas Research Network. (2017) Integrated genomic and molecular characterization of cervical cancer. Nature. 543:378-84. https://www.ncbi.nlm.nih.gov/pubmed/28112728
Saini N, Roberts SA, Klimczak LJ, Chan K, Grimm SA, Dai S, Fargo DC, Boyer JC, Kaufmann WK, Taylor JA, Lee E, Cortes-Ciriano I, Park PJ, Schurman SH, Malc EP, Mieczkowski PA, Gordenin DA. (2016) The Impact of Environmental and Endogenous Damage on Somatic Mutation Load in Human Skin Fibroblasts. PLOS Genetics. 12(10): e1006385. https://www.ncbi.nlm.nih.gov/pubmed/27788131
Chan K, Gordenin DA. (2015) Clusters of Multiple Mutations: Incidence and Molecular Mechanisms. Annual Review of Genetics. 49:243-67. https://www.ncbi.nlm.nih.gov/pubmed/26631512
Chan K, Roberts SA, Klimczak LJ, Sterling JF, Saini N, Malc EP, Kim Jaegil, Kwiatkowski DJ, Fargo DC, Mieczkowski PA, Getz G, and Gordenin DA. (2015) An APOBEC3A hypermutation signature is distinguishable from the signature of background mutagenesis by APOBEC3B in human cancers. Nature Genetics. 47(9):1067-72. https://www.ncbi.nlm.nih.gov/pubmed/26258849
Chan K, Resnick MA, and Gordenin DA. (2013) The choice of nucleotide inserted opposite abasic sites formed within chromosomal DNA reveals the polymerase activities participating in translesion DNA synthesis. DNA Repair. 12(11):878-89. https://www.ncbi.nlm.nih.gov/pubmed/23988736
Chan K, Sterling JF, Roberts SA, Bhagwat AS, Resnick MA, and Gordenin DA. (2012) Base Damage within Single-Strand DNA Underlies In Vivo Hypermutability Induced by a Ubiquitous Environmental Agent. PLOS Genetics. 8(12): e1003149. https://www.ncbi.nlm.nih.gov/pubmed/23271983
Chan K, Goldmark JP, and Roth MB. (2010) Suspended animation extends survival limits of Caenorhabditis elegans and Saccharomyces cerevisiae at low temperature. Molecular Biology of the Cell. 21(13): 2161-71. https://www.ncbi.nlm.nih.gov/pubmed/20462960
Chan K, Roth MB. (2008) Anoxia-induced suspended animation in budding yeast as an experimental paradigm for studying oxygen-regulated gene expression. Eukaryotic Cell. 7(10): 1795-808. https://www.ncbi.nlm.nih.gov/pubmed/18708563

Free full text or preprint of each paper via links below, where available.

Gelova SP, Chan K. (2023) Mutagenesis induced by protonation of single-stranded DNA is linked to glycolytic sugar metabolism. Mutat Res. 826:111814.

Thapa MJ, Fabros RM, Alasmar S, Chan K. (2022) Analyses of Mutational Patterns Induced by Formaldehyde and Acetaldehyde Reveal Similarity to a Common Mutational Signature in Cancers. G3 (Bethesda). 12:jkac238. Full text available.

Gelova SP, Doherty KN, Alasmar S, Chan K. (2022) Intrinsic base substitution patterns in diverse species reveal links to cancer and metabolism. Genetics. 222(3):iyac144. Full text available.

Campbell PJ, Getz G, Korbel JO, Stuart JM, Jennings JL, Stein LD, et al. Pan-cancer analysis of whole genomes. Nature. 2020 Feb 1;578(7793):82–93. Full text available.

Alexandrov LB, Kim J, Haradhvala NJ, Huang MN, Tian Ng AW, Wu Y, et al. The repertoire of mutational signatures in human cancer. Nature. 2020 Feb 1;578(7793):94–101. Full text available.

Rheinbay E, Nielsen MM, Abascal F, Wala JA, Shapira O, Tiao G, et al. Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature. 2020 Feb 1;578(7793):102–11. Full text available.

Li Y, Roberts ND, Wala JA, Shapira O, Schumacher SE, Kumar K, et al. Patterns of somatic structural variation in human cancer genomes. Nature. 2020 Feb 1;578(7793):112–21. Full text available.

Sakofsky CJ, Saini N, Klimczak LJ, Chan K, Malc EP, et al. Repair of multiple simultaneous double-strand breaks causes bursts of genome-wide clustered hypermutation. (2019) PLoS Biology. 17:9, e3000464. https://journals.plos.org/plosbiology/article?rev=1&id=10.1371/journal.pbio.3000464

Chan K. (2018) Molecular Genetic Characterization of Mutagenesis Using a Highly Sensitive Single-Stranded DNA Reporter System in Budding Yeast. In Genome Instability: Methods and Protocols. Methods Mol Biol. 1672, 33-42. doi: 10.1007/978-1-4939-7306-4_4. PMID: 29043615.

Waszak SM, Tiao G, Zhu B, Rausch T, Muyas F, Rodriguez-Martin B, et al. Germline determinants of the somatic mutation landscape in 2,642 cancer genomes. bioRxiv [Internet]. 2017 Nov 1; Available from: http://biorxiv.org/content/early/2017/11/01/208330.abstract

Wala JA, Shapira O, Li Y, Craft D, Schumacher SE, Imielinski M, et al. Selective and mechanistic sources of recurrent rearrangements across the cancer genome. bioRxiv [Internet]. 2017 Sep 14; Available from: http://biorxiv.org/content/early/2017/09/14/187609.abstract

The Cancer Genome Atlas Research Network. (2017) Integrated genomic and molecular characterization of cervical cancer. Nature. 543:378-84. https://www.ncbi.nlm.nih.gov/pubmed/28112728

Chan K, Gordenin DA. (2015) Clusters of Multiple Mutations: Incidence and Molecular Mechanisms. Annual Review of Genetics. 49:243-67. https://www.ncbi.nlm.nih.gov/pubmed/26631512

Chan K, Resnick MA, and Gordenin DA. (2013) The choice of nucleotide inserted opposite abasic sites formed within chromosomal DNA reveals the polymerase activities participating in translesion DNA synthesis. DNA Repair. 12(11):878-89. https://www.ncbi.nlm.nih.gov/pubmed/23988736

Chan K, Sterling JF, Roberts SA, Bhagwat AS, Resnick MA, and Gordenin DA. (2012) Base Damage within Single-Strand DNA Underlies In Vivo Hypermutability Induced by a Ubiquitous Environmental Agent. PLOS Genetics. 8(12): e1003149. https://www.ncbi.nlm.nih.gov/pubmed/23271983

Chan K, Goldmark JP, and Roth MB. (2010) Suspended animation extends survival limits of Caenorhabditis elegans and Saccharomyces cerevisiae at low temperature. Molecular Biology of the Cell. 21(13): 2161-71. https://www.ncbi.nlm.nih.gov/pubmed/20462960

Chan K, Roth MB. (2008) Anoxia-induced suspended animation in budding yeast as an experimental paradigm for studying oxygen-regulated gene expression. Eukaryotic Cell. 7(10): 1795-808. https://www.ncbi.nlm.nih.gov/pubmed/18708563