R-loops and regulatory changes in chronologically ageing fission yeast cells drive non-random patterns of genome rearrangements

Barcode sequencing and a high-throughput assay for chronological lifespan uncover ageing-associated genes in fission yeast

(2021) Catalina A. Romila et al.   Microbial Cell

Long non-coding RNA repertoire and targeting by nuclear exosome, cytoplasmic exonuclease and RNAi in fission yeast

(2018) Sophie Atkinson et al.   RNA

Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast

(2017) Daniel C. Jeffares et al.   Nature Communications

RNA metabolism is the primary target of formamide in vivo

(2017) Rafael Hoyos-Manchado et al.   Scientific Reports

Transcription as a Threat to Genome Integrity

(2016) Hélène Gaillard et al.   Annual Review of Biochemistry

A Life Investigating Pathways That Repair Broken Chromosomes

(2016) James E. Haber   Annual Review of Genetics

Long Neural Genes Harbor Recurrent DNA Break Clusters in Neural Stem/Progenitor Cells

(2016) Pei-Chi Wei et al.   CELL

Do DNA Double-Strand Breaks Drive Aging?

(2016) Ryan R. White et al.   MOLECULAR CELL

DNA double strand break repair, aging and the chromatin connection

(2016) Vera Gorbunova et al.   MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS

Quantitative detection of low-abundance somatic structural variants in normal cells by high-throughput sequencing

(2016) Wilber Quispe-Tintaya et al.   NATURE METHODS

Analysis of genomic rearrangements by using the Burrows-Wheeler transform of short-read data

(2015) Kouichi Kimura et al.   BMC BIOINFORMATICS

Elimination of Unfit Cells Maintains Tissue Health and Prolongs Lifespan

(2015) Marisa M. Merino et al.   CELL

Bulk Segregant Analysis Reveals the Genetic Basis of a Natural Trait Variation in Fission Yeast

(2015) Wen Hu et al.   Genome Biology and Evolution

The genomic and phenotypic diversity of Schizosaccharomyces pombe

(2015) Daniel C Jeffares et al.   NATURE GENETICS

R loops: new modulators of genome dynamics and function

(2015) José M. Santos-Pereira et al.   NATURE REVIEWS GENETICS

Role of Ccr4-Not complex in heterochromatin formation at meiotic genes and subtelomeres in fission yeast

(2015) Cristina Cotobal et al.   Epigenetics & Chromatin

AnGeLi: A Tool for the Analysis of Gene Lists from Fission Yeast

(2015) Danny A. Bitton et al.   Frontiers in Genetics

Gustaf: Detecting and correctly classifying SVs in the NGS twilight zone

(2014) K. Trappe et al.   BIOINFORMATICS

RECQL5 Controls Transcript Elongation and Suppresses Genome Instability Associated with Transcription Stress

(2014) Marco Saponaro et al.   CELL

Nucleosome loss leads to global transcriptional up-regulation and genomic instability during yeast aging

(2014) Z. Hu et al.   GENES & DEVELOPMENT

A double-edged sword: R loops as threats to genome integrity and powerful regulators of gene expression

(2014) K. Skourti-Stathaki et al.   GENES & DEVELOPMENT

Natural genetic variation impacts expression levels of coding, non-coding, and antisense transcripts in fission yeast

(2014) M. Clement-Ziza et al.   Molecular Systems Biology

PomBase 2015: updates to the fission yeast database

(2014) Mark D. McDowall et al.   NUCLEIC ACIDS RESEARCH

Ribosomal RNA gene repeats, their stability and cellular senescence

(2014) Takehiko KOBAYASHI   PROCEEDINGS OF THE JAPAN ACADEMY SERIES B-PHYSICAL AND BIOLOGICAL SCIENCES

The role of microhomology in genomic structural variation

(2014) Diego Ottaviani et al.   TRENDS IN GENETICS

Systematic Analysis of the Role of RNA-Binding Proteins in the Regulation of RNA Stability

(2014) Ayesha Hasan et al.   PLoS Genetics

Knock-In Reporter Mice Demonstrate that DNA Repair by Non-homologous End Joining Declines with Age

(2014) Amita Vaidya et al.   PLoS Genetics

Is Non-Homologous End-Joining Really an Inherently Error-Prone Process?

(2014) Mireille Bétermier et al.   PLoS Genetics

LUMPY: a probabilistic framework for structural variant discovery

(2014) Ryan M Layer et al.   GENOME BIOLOGY

TORC1 signaling inhibition by rapamycin and caffeine affect lifespan, global gene expression, and cell proliferation of fission yeast

(2013) Charalampos Rallis et al.   AGING CELL

Causes of Genome Instability

(2013) Andrés Aguilera et al.   Annual Review of Genetics

Genome Instability and Aging

(2013) Jan Vijg et al.   Annual Review of Physiology

The Hallmarks of Aging

(2013) Carlos López-Otín et al.   CELL

Lifespan of neurons is uncoupled from organismal lifespan

(2013) Lorenzo Magrassi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ultra-Sensitive Sequencing Reveals an Age-Related Increase in Somatic Mitochondrial Mutations That Are Inconsistent with Oxidative Damage

(2013) Scott R. Kennedy et al.   PLoS Genetics

Somatic mtDNA Mutation Spectra in the Aging Human Putamen

(2013) Siôn L. Williams et al.   PLoS Genetics

Alternative end-joining mechanisms: a historical perspective

(2013) Anabelle Decottignies   Frontiers in Genetics

Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS

(2012) Anne-Katrin Emde et al.   BIOINFORMATICS

PRISM: Pair-read informed split-read mapping for base-pair level detection of insertion, deletion and structural variants

(2012) Yue Jiang et al.   BIOINFORMATICS

DELLY: structural variant discovery by integrated paired-end and split-read analysis

(2012) T. Rausch et al.   BIOINFORMATICS

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Detectable clonal mosaicism and its relationship to aging and cancer

(2012) Kevin B Jacobs et al.   NATURE GENETICS

Detectable clonal mosaicism from birth to old age and its relationship to cancer

(2012) Cathy C Laurie et al.   NATURE GENETICS

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

High Resolution Genome Wide Binding Event Finding and Motif Discovery Reveals Transcription Factor Spatial Binding Constraints

(2012) Yuchun Guo et al.   PLoS Computational Biology

Microhomology Directs Diverse DNA Break Repair Pathways and Chromosomal Translocations

(2012) Diana D. Villarreal et al.   PLoS Genetics

An integrative probabilistic model for identification of structural variation in sequencing data

(2012) Suzanne S Sindi et al.   GENOME BIOLOGY

ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information

(2011) Shin Suzuki et al.   BMC BIOINFORMATICS

RNase H and Multiple RNA Biogenesis Factors Cooperate to Prevent RNA:DNA Hybrids from Generating Genome Instability

(2011) Lamia Wahba et al.   MOLECULAR CELL

CREST maps somatic structural variation in cancer genomes with base-pair resolution

(2011) Jianmin Wang et al.   NATURE METHODS

PomBase: a comprehensive online resource for fission yeast

(2011) V. Wood et al.   NUCLEIC ACIDS RESEARCH

A Geographically Diverse Collection of Schizosaccharomyces pombe Isolates Shows Limited Phenotypic Variation but Extensive Karyotypic Diversity

(2011) William R. A. Brown et al.   G3-Genes Genomes Genetics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Lessons on longevity from budding yeast

(2010) Matt Kaeberlein   NATURE

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

(2009) K. Ye et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Pro-Aging Effects of Glucose Signaling through a G Protein-Coupled Glucose Receptor in Fission Yeast

(2009) Antoine E. Roux et al.   PLoS Genetics

Rising from the RecQ-age: the role of human RecQ helicases in genome maintenance

(2008) V BOHR   TRENDS IN BIOCHEMICAL SCIENCES