Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562

Synergistic drug combinations for cancer identified in a CRISPR screen for pairwise genetic interactions

(2017) Kyuho Han et al.   NATURE BIOTECHNOLOGY

Genome-wide reconstruction of complex structural variants using read clouds

(2017) Noah Spies et al.   NATURE METHODS

Chromosome-scale mega-haplotypes enable digital karyotyping of cancer aneuploidy

(2017) John M. Bell et al.   NUCLEIC ACIDS RESEARCH

Linked read sequencing resolves complex genomic rearrangements in gastric cancer metastases

(2017) Stephanie U. Greer et al.   Genome Medicine

A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response

(2016) Britt Adamson et al.   CELL

A Genome-wide CRISPR Death Screen Identifies Genes Essential for Oxidative Phosphorylation

(2016) Jason D. Arroyo et al.   Cell Metabolism

Allele-specific transcription factor binding to common and rare variants associated with disease and gene expression

(2016) Marco Cavalli et al.   HUMAN GENETICS

Systematic comparison of CRISPR/Cas9 and RNAi screens for essential genes

(2016) David W Morgens et al.   NATURE BIOTECHNOLOGY

Haplotyping germline and cancer genomes with high-throughput linked-read sequencing

(2016) Grace X Y Zheng et al.   NATURE BIOTECHNOLOGY

CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells

(2016) S. John Liu et al.   SCIENCE

Mammalian Reverse Genetics without Crossing Reveals Nr3a as a Short-Sleeper Gene

(2016) Genshiro A. Sunagawa et al.   Cell Reports

MetaSV: an accurate and integrative structural-variant caller for next generation sequencing

(2015) Marghoob Mohiyuddin et al.   BIOINFORMATICS

Upregulation of NETO2 expression correlates with tumor progression and poor prognosis in colorectal carcinoma

(2015) Liang Hu et al.   BMC CANCER

An integrated map of structural variation in 2,504 human genomes

(2015) Peter H. Sudmant et al.   NATURE

De novo assembly of a haplotype-resolved human genome

(2015) Hongzhi Cao et al.   NATURE BIOTECHNOLOGY

Haplotype-resolved genome sequencing: experimental methods and applications

(2015) Matthew W. Snyder et al.   NATURE REVIEWS GENETICS

ENCODE data at the ENCODE portal

(2015) Cricket A. Sloan et al.   NUCLEIC ACIDS RESEARCH

Identification and characterization of essential genes in the human genome

(2015) T. Wang et al.   SCIENCE

Making the difference: integrating structural variation detection tools

(2014) Ke Lin et al.   BRIEFINGS IN BIOINFORMATICS

The FHIT gene product: tumor suppressor and genome “caretaker”

(2014) Catherine E. Waters et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Reducing INDEL calling errors in whole genome and exome sequencing data

(2014) Han Fang et al.   Genome Medicine

LUMPY: a probabilistic framework for structural variant discovery

(2014) Ryan M Layer et al.   GENOME BIOLOGY

A survey of tools for variant analysis of next-generation genome sequencing data

(2013) S. Pabinger et al.   BRIEFINGS IN BIOINFORMATICS

Human cell-based artificial antigen-presenting cells for cancer immunotherapy

(2013) Marcus O. Butler et al.   IMMUNOLOGICAL REVIEWS

The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line

(2013) Andrew Adey et al.   NATURE

RetroSeq: transposable element discovery from next-generation sequencing data

(2012) Thomas M. Keane et al.   BIOINFORMATICS

Paired-end sequencing of Fosmid libraries by Illumina

(2012) L. J. S. Williams et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Detecting and annotating genetic variations using the HugeSeq pipeline

(2012) Hugo Y K Lam et al.   NATURE BIOTECHNOLOGY

Three-Dimensional Genome Architecture Influences Partner Selection for Chromosomal Translocations in Human Disease

(2012) Jesse M. Engreitz et al.   PLoS One

Increase in NETO2 gene expression is a potential molecular genetic marker in renal and lung cancers

(2012) N. Yu. Oparina et al.   RUSSIAN JOURNAL OF GENETICS

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

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

(2011) Philip J. Stephens et al.   CELL

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

Characterizing complex structural variation in germline and somatic genomes

(2011) Aaron R. Quinlan et al.   TRENDS IN GENETICS

Haplotype-resolved genome sequencing of a Gujarati Indian individual

(2010) Jacob O Kitzman et al.   NATURE BIOTECHNOLOGY

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

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library

(2009) Hugo Y K Lam et al.   NATURE BIOTECHNOLOGY

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

(2009) Ken Chen et al.   NATURE METHODS

A Microhomology-Mediated Break-Induced Replication Model for the Origin of Human Copy Number Variation

(2009) P. J. Hastings et al.   PLoS Genetics

The Fine-Scale and Complex Architecture of Human Copy-Number Variation

(2008) George H. Perry et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE