Identification of cancer-related mutations in human pluripotent stem cells using RNA-seq analysis

Re-epithelialization and immune cell behaviour in an ex vivo human skin model

(2020) Ana Rakita et al.   Scientific Reports

Acquired genetic changes in human pluripotent stem cells: origins and consequences

(2020) Jason Halliwell et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Cancer-Related Mutations Are Not Enriched in Naive Human Pluripotent Stem Cells

(2020) Giuliano Giuseppe Stirparo et al.   Cell Stem Cell

Cancer-Related Mutations Identified in Primed Human Pluripotent Stem Cells

(2020) Yishai Avior et al.   Cell Stem Cell

Epigenetic aberrations in human pluripotent stem cells

(2019) Shiran Bar et al.   EMBO JOURNAL

RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues

(2019) Keren Yizhak et al.   SCIENCE

Self-organization of stem cells into embryos: A window on early mammalian development

(2019) Marta N. Shahbazi et al.   SCIENCE

The GATK joint genotyping workflow is appropriate for calling variants in RNA-seq experiments

(2019) Jean-Simon Brouard et al.   Journal of Animal Science and Biotechnology

Detection and benchmarking of somatic mutations in cancer genomes using RNA-seq data

(2018) Alexandre Coudray et al.   PeerJ

XenofilteR: computational deconvolution of mouse and human reads in tumor xenograft sequence data

(2018) Roelof J. C. Kluin et al.   BMC BIOINFORMATICS

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

COSMIC: the Catalogue Of Somatic Mutations In Cancer

(2018) John G Tate et al.   NUCLEIC ACIDS RESEARCH

Human pluripotent stem cells recurrently acquire and expand dominant negative P53 mutations

(2017) Florian T. Merkle et al.   NATURE

Nextflow enables reproducible computational workflows

(2017) Paolo Di Tommaso et al.   NATURE BIOTECHNOLOGY

Pluripotent stem cells in disease modelling and drug discovery

(2016) Yishai Avior et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Pluripotent stem cells progressing to the clinic

(2016) Alan Trounson et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Analysis of chromosomal aberrations and recombination by allelic bias in RNA-Seq

(2016) Uri Weissbein et al.   Nature Communications

Deletion of the Polycomb-Group Protein EZH2 Leads to Compromised Self-Renewal and Differentiation Defects in Human Embryonic Stem Cells

(2016) Adam Collinson et al.   Cell Reports

The safety of human pluripotent stem cells in clinical treatment

(2015) Oscar E Simonson et al.   ANNALS OF MEDICINE

Hallmarks of pluripotency

(2015) Alejandro De Los Angeles et al.   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Genome maintenance in pluripotent stem cells

(2014) Uri Weissbein et al.   JOURNAL OF CELL BIOLOGY

Pluripotent stem cells in regenerative medicine: challenges and recent progress

(2014) Viviane Tabar et al.   NATURE REVIEWS GENETICS

RADIA: RNA and DNA Integrated Analysis for Somatic Mutation Detection

(2014) Amie J. Radenbaugh et al.   PLoS One

Aneuploidy induces profound changes in gene expression, proliferation and tumorigenicity of human pluripotent stem cells

(2014) Uri Ben-David et al.   Nature Communications

Aneuploidy in pluripotent stem cells and implications for cancerous transformation

(2014) Jie Na et al.   Protein & Cell

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Predicting the Functional, Molecular, and Phenotypic Consequences of Amino Acid Substitutions using Hidden Markov Models

(2012) Hashem A. Shihab et al.   HUMAN MUTATION

Tabix: fast retrieval of sequence features from generic TAB-delimited files

(2011) H. Li   BIOINFORMATICS

Somatic coding mutations in human induced pluripotent stem cells

(2011) Athurva Gore et al.   NATURE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS