A Deterministic Analysis of Genome Integrity during Neoplastic Growth in Drosophila

Pathways involved in Drosophila and human cancer development: the Notch, Hedgehog, Wingless, Runt, and Trithorax pathway

(2012) Klaus Geissler et al.   ANNALS OF HEMATOLOGY

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

(2012) Anne-Katrin Emde et al.   BIOINFORMATICS

CLEVER: clique-enumerating variant finder

(2012) Tobias Marschall et al.   BIOINFORMATICS

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

(2012) T. Rausch et al.   BIOINFORMATICS

Mutational Processes Molding the Genomes of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Impact of genomic structural variation in Drosophila melanogaster based on population-scale sequencing

(2012) T. Zichner et al.   GENOME RESEARCH

SOAPindel: Efficient identification of indels from short paired reads

(2012) S. Li et al.   GENOME RESEARCH

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Mixture models and wavelet transforms reveal high confidence RNA-protein interaction sites in MOV10 PAR-CLIP data

(2012) Cem Sievers et al.   NUCLEIC ACIDS RESEARCH

Aneuploidy-induced delaminating cells drive tumorigenesis in Drosophila epithelia

(2012) A. Dekanty et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

AGE: defining breakpoints of genomic structural variants at single-nucleotide resolution, through optimal alignments with gap excision

(2011) Alexej Abyzov et al.   BIOINFORMATICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer Development

(2011) Philip J. Stephens et al.   CELL

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

Cancer epigenetics: linking basic biology to clinical medicine

(2011) Hsing-Chen Tsai et al.   CELL RESEARCH

Modeling tumor invasion and metastasis in Drosophila

(2011) W. O. Miles et al.   Disease Models & Mechanisms

Silencing chromatin: comparing modes and mechanisms

(2011) Christian Beisel et al.   NATURE REVIEWS GENETICS

Genome structural variation discovery and genotyping

(2011) Can Alkan et al.   NATURE REVIEWS GENETICS

Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion

(2011) R. Xi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data

(2010) Bruno Zeitouni et al.   BIOINFORMATICS

A Combined Ex Vivo and In Vivo RNAi Screen for Notch Regulators in Drosophila Reveals an Extensive Notch Interaction Network

(2010) Abil Saj et al.   DEVELOPMENTAL CELL

The Hippo Signaling Pathway in Development and Cancer

(2010) Duojia Pan   DEVELOPMENTAL CELL

Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome

(2010) A. R. Quinlan et al.   GENOME RESEARCH

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS

About Combs, Notches, and Tumors: Epigenetics Meets Signaling

(2009) Gunter Merdes et al.   DEVELOPMENTAL CELL

Computational methods for discovering structural variation with next-generation sequencing

(2009) Paul Medvedev et al.   NATURE METHODS

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation

(2009) Ken Chen et al.   NATURE METHODS

PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data

(2009) Jan O Korbel et al.   GENOME BIOLOGY