Network-based approaches elucidate differences within APOBEC and clock-like signatures in breast cancer

Hidden Markov models lead to higher resolution maps of mutation signature activity in cancer

(2019) Damian Wojtowicz et al.   Genome Medicine

APOBEC3B and APOBEC mutational signature as potential predictive markers for immunotherapy response in non-small cell lung cancer

(2018) Shixiang Wang et al.   ONCOGENE

The effects of mutational processes and selection on driver mutations across cancer types

(2018) Daniel Temko et al.   Nature Communications

Invasive lobular and ductal breast carcinoma differ in immune response, protein translation efficiency and metabolism

(2018) Tian Du et al.   Scientific Reports

Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas

(2018) Theo A. Knijnenburg et al.   Cell Reports

The therapeutic significance of mutational signatures from DNA repair deficiency in cancer

(2018) Jennifer Ma et al.   Nature Communications

Cdh1 and Pik3ca Mutations Cooperate to Induce Immune-Related Invasive Lobular Carcinoma of the Breast

(2018) Yeji An et al.   Cell Reports

Analysis of 7,815 cancer exomes reveals associations between mutational processes and somatic driver mutations

(2018) Rebecca C. Poulos et al.   PLoS Genetics

A mutational signature reveals alterations underlying deficient homologous recombination repair in breast cancer

(2017) Paz Polak et al.   NATURE GENETICS

HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures

(2017) Helen Davies et al.   NATURE MEDICINE

p53 controls expression of the DNA deaminase APOBEC3B to limit its potential mutagenic activity in cancer cells

(2017) Manikandan Periyasamy et al.   NUCLEIC ACIDS RESEARCH

Exploring background mutational processes to decipher cancer genetic heterogeneity

(2017) Alexander Goncearenco et al.   NUCLEIC ACIDS RESEARCH

BeWith: A Between-Within method to discover relationships between cancer modules via integrated analysis of mutual exclusivity, co-occurrence and functional interactions

(2017) Phuong Dao et al.   PLoS Computational Biology

A Specific Mutational Signature Associated with DNA 8-Oxoguanine Persistence in MUTYH-defective Colorectal Cancer

(2017) Alessandra Viel et al.   EBioMedicine

APOBEC3A damages the cellular genome during DNA replication

(2016) Abby M. Green et al.   CELL CYCLE

CDH1 germline mutations and hereditary lobular breast cancer

(2016) Giovanni Corso et al.   Familial Cancer

APOBEC-induced mutations in human cancers are strongly enriched on the lagging DNA strand during replication

(2016) Vladimir B. Seplyarskiy et al.   GENOME RESEARCH

Landscape of somatic mutations in 560 breast cancer whole-genome sequences

(2016) Serena Nik-Zainal et al.   NATURE

Somatic ERCC2 mutations are associated with a distinct genomic signature in urothelial tumors

(2016) Jaegil Kim et al.   NATURE GENETICS

Mutational signatures associated with tobacco smoking in human cancer

(2016) L. B. Alexandrov et al.   SCIENCE

The topography of mutational processes in breast cancer genomes

(2016) Sandro Morganella et al.   Nature Communications

Genomic landscape of DNA repair genes in cancer

(2016) Young Kwang Chae et al.   Oncotarget

Understanding Genotype-Phenotype Effects in Cancer via Network Approaches

(2016) Yoo-Ah Kim et al.   PLoS Computational Biology

MEMCover: integrated analysis of mutual exclusivity and functional network reveals dysregulated pathways across multiple cancer types

(2015) Yoo-Ah Kim et al.   BIOINFORMATICS

Clock-like mutational processes in human somatic cells

(2015) Ludmil B Alexandrov et al.   NATURE GENETICS

Hereditary Diffuse Gastric Cancer Syndrome

(2015) Samantha Hansford et al.   JAMA Oncology

Mutational signatures: the patterns of somatic mutations hidden in cancer genomes

(2014) Ludmil B Alexandrov et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Association of a germline copy number polymorphism of APOBEC3A and APOBEC3B with burden of putative APOBEC-dependent mutations in breast cancer

(2014) Serena Nik-Zainal et al.   NATURE GENETICS

Mechanisms underlying mutational signatures in human cancers

(2014) Thomas Helleday et al.   NATURE REVIEWS GENETICS

Apc and p53 interaction in DNA damage and genomic instability in hepatocytes

(2014) V Méniel et al.   ONCOGENE

CHK2 kinase in the DNA damage response and beyond

(2014) L. Zannini et al.   Journal of Molecular Cell Biology

APOBEC3B Upregulation and Genomic Mutation Patterns in Serous Ovarian Carcinoma

(2013) B. Leonard et al.   CANCER RESEARCH

Lessons from the Cancer Genome

(2013) Levi A. Garraway et al.   CELL

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

Evidence for APOBEC3B mutagenesis in multiple human cancers

(2013) Michael B Burns et al.   NATURE GENETICS

Network-based stratification of tumor mutations

(2013) Matan Hofree et al.   NATURE METHODS

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

Deciphering Signatures of Mutational Processes Operative in Human Cancer

(2013) Ludmil B. Alexandrov et al.   Cell Reports

EMu: probabilistic inference of mutational processes and their localization in the cancer genome

(2013) Andrej Fischer et al.   GENOME BIOLOGY

Oxidative DNA Damage and Nucleotide Excision Repair

(2012) Joost P.M. Melis et al.   ANTIOXIDANTS & REDOX SIGNALING

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

A novel function of adenomatous polyposis coli (APC) in regulating DNA repair

(2008) Aruna S. Jaiswal et al.   CANCER LETTERS

Truncation mutations abolish chromatin-associated activities of adenomatous polyposis coli

(2008) A P Kouzmenko et al.   ONCOGENE

The PTEN–PI3K pathway: of feedbacks and cross-talks

(2008) A Carracedo et al.   ONCOGENE