Detecting non-allelic homologous recombination from high-throughput sequencing data

Characterization of structural variants with single molecule and hybrid sequencing approaches

(2014) Anna Ritz et al.   BIOINFORMATICS

Resolving the complexity of the human genome using single-molecule sequencing

(2014) Mark J. P. Chaisson et al.   NATURE

High-resolution crystal structure of human Dim2/TXNL4B

(2013) Tengchuan Jin et al.   Acta Crystallographica Section F-Structural Biology and Crystallization Communications

Two Human Host Defense Ribonucleases against Mycobacteria, the Eosinophil Cationic Protein (RNase 3) and RNase 7

(2013) David Pulido et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Cytochrome P450 enzymes in drug metabolism: Regulation of gene expression, enzyme activities, and impact of genetic variation

(2013) Ulrich M. Zanger et al.   PHARMACOLOGY & THERAPEUTICS

pIRS: Profile-based Illumina pair-end reads simulator

(2012) Xuesong Hu et al.   BIOINFORMATICS

The link between the GBA gene and parkinsonism

(2012) Ellen Sidransky et al.   LANCET NEUROLOGY

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

Summarizing and correcting the GC content bias in high-throughput sequencing

(2012) Yuval Benjamini et al.   NUCLEIC ACIDS RESEARCH

Chapter 6: Structural Variation and Medical Genomics

(2012) Benjamin J. Raphael   PLoS Computational Biology

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

(2012) Suzanne S Sindi et al.   GENOME BIOLOGY

ANALYSIS OF CONTEXT-DEPENDENT ERRORS FOR ILLUMINA SEQUENCING

(2012) IRINA ABNIZOVA et al.   Journal of Bioinformatics and Computational Biology

Frequency of Nonallelic Homologous Recombination Is Correlated with Length of Homology: Evidence that Ectopic Synapsis Precedes Ectopic Crossing-Over

(2011) Pengfei Liu et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Identification and correction of systematic error in high-throughput sequence data

(2011) Frazer Meacham et al.   BMC BIOINFORMATICS

Addressing challenges in the production and analysis of illumina sequencing data

(2011) Martin Kircher et al.   BMC GENOMICS

PTEN genomic deletions that characterize aggressive prostate cancer originate close to segmental duplications

(2011) Maisa Yoshimoto et al.   GENES CHROMOSOMES & CANCER

Observation and prediction of recurrent human translocations mediated by NAHR between nonhomologous chromosomes

(2011) Z. Ou et al.   GENOME RESEARCH

CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing

(2011) A. Abyzov et al.   GENOME RESEARCH

Mapping copy number variation by population-scale genome sequencing

(2011) Ryan E. Mills et al.   NATURE

Genome structural variation discovery and genotyping

(2011) Can Alkan et al.   NATURE REVIEWS GENETICS

Homozygosity for the MTX1 c.184T>A (p.S63T) alteration modifies the age of onset in GBA-associated Parkinson's disease

(2011) Ziv Gan-Or et al.   NEUROGENETICS

Filaggrin Mutations Associated with Skin and Allergic Diseases

(2011) Alan D. Irvine et al.   NEW ENGLAND JOURNAL OF MEDICINE

Systematic bias in high-throughput sequencing data and its correction by BEADS

(2011) Ming-Sin Cheung et al.   NUCLEIC ACIDS RESEARCH

Structural variation of the human genome: mechanisms, assays, and role in male infertility

(2011) Claudia M.B. Carvalho et al.   Systems Biology in Reproductive Medicine

Context-based FISH localization of genomic rearrangements within chromosome 15q11.2q13 duplicons

(2011) Wahab A Khan et al.   Molecular Cytogenetics

Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems

(2011) André E Minoche et al.   GENOME BIOLOGY

Structural Variation in the Human Genome and its Role in Disease

(2010) Paweł Stankiewicz et al.   Annual Review of Medicine

Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery

(2010) Fereydoun Hormozdiari et al.   BIOINFORMATICS

A Human Genome Structural Variation Sequencing Resource Reveals Insights into Mutational Mechanisms

(2010) Jeffrey M. Kidd et al.   CELL

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

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

Detecting copy number variation with mated short reads

(2010) P. Medvedev et al.   GENOME RESEARCH

Eosinophil cationic protein (ECP) can bind heparin and other glycosaminoglycans through its RNase active site

(2010) Marc Torrent et al.   JOURNAL OF MOLECULAR RECOGNITION

RecA-Mediated Homology Search as a Nearly Optimal Signal Detection System

(2010) Yonatan Savir et al.   MOLECULAR CELL

DNA resection in eukaryotes: deciding how to fix the break

(2010) Pablo Huertas   NATURE STRUCTURAL & MOLECULAR BIOLOGY

COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer

(2010) S. A. Forbes et al.   NUCLEIC ACIDS RESEARCH

Diversity of Human Copy Number Variation and Multicopy Genes

(2010) Peter H. Sudmant et al.   SCIENCE

Genomic rearrangements in inherited disease and cancer

(2010) Jian-Min Chen et al.   SEMINARS IN CANCER BIOLOGY

STATISTICAL COMPARISON OF METHODS TO ESTIMATE THE ERROR PROBABILITY IN SHORT-READ ILLUMINA SEQUENCING

(2010) IRINA ABNIZOVA et al.   Journal of Bioinformatics and Computational Biology

A geometric approach for classification and comparison of structural variants

(2009) S. Sindi et al.   BIOINFORMATICS

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Sensitive and accurate detection of copy number variants using read depth of coverage

(2009) S. Yoon et al.   GENOME RESEARCH

Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes

(2009) F. Hormozdiari et al.   GENOME RESEARCH

Origins and functional impact of copy number variation in the human genome

(2009) Donald F. Conrad et al.   NATURE

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

(2009) Ken Chen et al.   NATURE METHODS

Continuous base identification for single-molecule nanopore DNA sequencing

(2009) James Clarke et al.   Nature Nanotechnology

Mechanisms of change in gene copy number

(2009) P. J. Hastings et al.   NATURE REVIEWS GENETICS

Advances in visual perceptual learning and plasticity

(2009) Yuka Sasaki et al.   NATURE REVIEWS NEUROSCIENCE

Genomic disorders ten years on

(2009) James R Lupski   Genome Medicine

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

Mechanism of homologous recombination from the RecA–ssDNA/dsDNA structures

(2008) Zhucheng Chen et al.   NATURE

Mapping and sequencing of structural variation from eight human genomes

(2008) Jeffrey M. Kidd et al.   NATURE

Centroid estimation in discrete high-dimensional spaces with applications in biology

(2008) L. E. Carvalho et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE