De novo mutational signature discovery in tumor genomes using SparseSignatures

The repertoire of mutational signatures in human cancer

(2020) Ludmil B. Alexandrov et al.   NATURE

The mutational signature profile of known and suspected human carcinogens in mice

(2020) Laura Riva et al.   NATURE GENETICS

Characterizing Mutational Signatures in Human Cancer Cell Lines Reveals Episodic APOBEC Mutagenesis

(2019) Mia Petljak et al.   CELL

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

(2018) Shixiang Wang et al.   ONCOGENE

SIMLR: A Tool for Large-Scale Genomic Analyses by Multi-Kernel Learning

(2018) Bo Wang et al.   PROTEOMICS

Somatic mutant clones colonize the human esophagus with age

(2018) Iñigo Martincorena et al.   SCIENCE

Multi-omic tumor data reveal diversity of molecular mechanisms that correlate with survival

(2018) Daniele Ramazzotti et al.   Nature Communications

Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning

(2017) Bo Wang et al.   NATURE METHODS

Exploring background mutational processes to decipher cancer genetic heterogeneity

(2017) Alexander Goncearenco et al.   NUCLEIC ACIDS RESEARCH

signeR: an empirical Bayesian approach to mutational signature discovery

(2016) Rafael A. Rosales et al.   BIOINFORMATICS

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

(2016) Serena Nik-Zainal et al.   NATURE

Tissue-specific mutation accumulation in human adult stem cells during life

(2016) Francis Blokzijl et al.   NATURE

Mutational signatures associated with tobacco smoking in human cancer

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

Clock-like mutational processes in human somatic cells

(2015) Ludmil B Alexandrov et al.   NATURE GENETICS

Exome sequencing of hepatocellular carcinomas identifies new mutational signatures and potential therapeutic targets

(2015) Kornelius Schulze et al.   NATURE GENETICS

A Simple Model-Based Approach to Inferring and Visualizing Cancer Mutation Signatures

(2015) Yuichi Shiraishi et al.   PLoS Genetics

Regularization Paths for Generalized Linear Models via Coordinate Descent

(2015) Jerome Friedman et al.   Journal of Statistical Software

Non-negative Matrix Factorization under equality constraints—a study of industrial source identification

(2014) A. Limem et al.   APPLIED NUMERICAL MATHEMATICS

Mechanisms underlying mutational signatures in human cancers

(2014) Thomas Helleday et al.   NATURE REVIEWS GENETICS

Heterogeneity of genomic evolution and mutational profiles in multiple myeloma

(2014) Niccolo Bolli et al.   Nature Communications

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

Exome and whole-genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity

(2013) Austin M Dulak et al.   NATURE GENETICS

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

A flexible R package for nonnegative matrix factorization

(2010) Renaud Gaujoux et al.   BMC BIOINFORMATICS