Published in Genome Res on May 25, 2012
Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution. Nature (2014) 2.85
Targeted gene correction minimally impacts whole-genome mutational load in human-disease-specific induced pluripotent stem cell clones. Cell Stem Cell (2014) 2.24
Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data. Ann Oncol (2014) 2.08
PAM50 breast cancer subtyping by RT-qPCR and concordance with standard clinical molecular markers. BMC Med Genomics (2012) 2.01
SciClone: inferring clonal architecture and tracking the spatial and temporal patterns of tumor evolution. PLoS Comput Biol (2014) 1.88
Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing. Blood (2013) 1.84
TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data. Genome Res (2014) 1.45
High-definition reconstruction of clonal composition in cancer. Cell Rep (2014) 1.45
Single cell sequencing reveals low levels of aneuploidy across mammalian tissues. Proc Natl Acad Sci U S A (2014) 1.34
Computational methods for detecting copy number variations in cancer genome using next generation sequencing: principles and challenges. Oncotarget (2013) 1.15
Robust high-performance nanoliter-volume single-cell multiple displacement amplification on planar substrates. Proc Natl Acad Sci U S A (2016) 1.10
Systems biology: personalized medicine for the future? Curr Opin Pharmacol (2012) 1.04
Whole-genome mutational landscape and characterization of noncoding and structural mutations in liver cancer. Nat Genet (2016) 1.02
Inferring copy number and genotype in tumour exome data. BMC Genomics (2014) 1.01
Genome-wide identification of somatic aberrations from paired normal-tumor samples. PLoS One (2014) 0.98
MBASED: allele-specific expression detection in cancer tissues and cell lines. Genome Biol (2014) 0.93
Novel insights into breast cancer genetic variance through RNA sequencing. Sci Rep (2013) 0.92
Deciphering clonality in aneuploid breast tumors using SNP array and sequencing data. Genome Biol (2014) 0.92
CLImAT: accurate detection of copy number alteration and loss of heterozygosity in impure and aneuploid tumor samples using whole-genome sequencing data. Bioinformatics (2014) 0.91
Genomic Complexity Profiling Reveals That HORMAD1 Overexpression Contributes to Homologous Recombination Deficiency in Triple-Negative Breast Cancers. Cancer Discov (2015) 0.90
Genome-Wide Profiles of Extra-cranial Malignant Rhabdoid Tumors Reveal Heterogeneity and Dysregulated Developmental Pathways. Cancer Cell (2016) 0.89
Mutated tumor alleles are expressed according to their DNA frequency. Sci Rep (2014) 0.85
MiR-27a modulates radiosensitivity of triple-negative breast cancer (TNBC) cells by targeting CDC27. Med Sci Monit (2015) 0.85
Scalable whole-genome single-cell library preparation without preamplification. Nat Methods (2017) 0.85
The relative timing of mutations in a breast cancer genome. PLoS One (2013) 0.84
Cancer genomics: why rare is valuable. J Mol Med (Berl) (2015) 0.80
Assessment of megabase-scale somatic copy number variation using single-cell sequencing. Genome Res (2016) 0.80
Genomic and transcriptional alterations in lung adenocarcinoma in relation to EGFR and KRAS mutation status. PLoS One (2013) 0.79
Vasculogenic mimicry in small cell lung cancer. Nat Commun (2016) 0.77
Putative BRAF activating fusion in a medullary thyroid cancer. Cold Spring Harb Mol Case Stud (2016) 0.77
Network insights into the genes regulated by hepatocyte nuclear factor 4 in response to drug induced perturbations: a review. Curr Drug Discov Technol (2013) 0.77
Copy number alterations detected by whole-exome and whole-genome sequencing of esophageal adenocarcinoma. Hum Genomics (2015) 0.77
Identifying putative breast cancer-associated long intergenic non-coding RNA loci by high density SNP array analysis. Front Genet (2012) 0.77
Massive interstitial copy-neutral loss-of-heterozygosity as evidence for cancer being a disease of the DNA-damage response. BMC Med Genomics (2015) 0.77
Prognostic relevance of acquired uniparental disomy in serous ovarian cancer. Mol Cancer (2015) 0.77
Personalized oncogenomics in the management of gastrointestinal carcinomas-early experiences from a pilot study. Curr Oncol (2016) 0.75
An Integrated Approach for RNA-seq Data Normalization. Cancer Inform (2016) 0.75
Molecular etiology of an indolent lymphoproliferative disorder determined by whole-genome sequencing. Cold Spring Harb Mol Case Stud (2016) 0.75
CLImAT-HET: detecting subclonal copy number alterations and loss of heterozygosity in heterogeneous tumor samples from whole-genome sequencing data. BMC Med Genomics (2017) 0.75
Identification of medium-sized copy number alterations in whole-genome sequencing. Cancer Inform (2015) 0.75
Segmentum: a tool for copy number analysis of cancer genomes. BMC Bioinformatics (2017) 0.75
ENVE: a novel computational framework characterizes copy-number mutational landscapes in colorectal cancers from African American patients. Genome Med (2015) 0.75
TAFFYS: An Integrated Tool for Comprehensive Analysis of Genomic Aberrations in Tumor Samples. PLoS One (2015) 0.75
Reassessing the Evolutionary History of the 17q21 Inversion Polymorphism. Genome Biol Evol (2015) 0.75
Exceptional Durable Response to Everolimus in a Patient with Biphenotypic Breast Cancer Harboring an STK11 Variant. Cold Spring Harb Mol Case Stud (2017) 0.75
Kronos: a workflow assembler for genome analytics and informatics. Gigascience (2017) 0.75
Secondary Somatic Mutations Restoring RAD51C and RAD51D Associated with Acquired Resistance to the PARP Inhibitor Rucaparib in High-grade Ovarian Carcinoma. Cancer Discov (2017) 0.75
Genomic profiling of pelvic genital type leiomyosarcoma in a woman with a germline CHEK2:c.1100delC mutation and a concomitant diagnosis of metastatic invasive ductal breast carcinoma. Cold Spring Harb Mol Case Stud (2017) 0.75
The Sequence Alignment/Map format and SAMtools. Bioinformatics (2009) 232.39
Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics (2009) 190.94
The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res (2010) 97.51
Integrated genomic analyses of ovarian carcinoma. Nature (2011) 47.72
Somatic mutations affect key pathways in lung adenocarcinoma. Nature (2008) 30.02
Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics (2010) 26.76
A comprehensive catalogue of somatic mutations from a human cancer genome. Nature (2009) 24.27
The cancer genome. Nature (2009) 23.13
The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature (2012) 20.47
Tumour evolution inferred by single-cell sequencing. Nature (2011) 19.13
A small-cell lung cancer genome with complex signatures of tobacco exposure. Nature (2009) 18.39
Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature (2009) 18.08
The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature (2012) 11.91
QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data. Nucleic Acids Res (2007) 10.08
Allele-specific copy number analysis of tumors. Proc Natl Acad Sci U S A (2010) 7.70
dChipSNP: significance curve and clustering of SNP-array-based loss-of-heterozygosity data. Bioinformatics (2004) 6.78
Enrichment map: a network-based method for gene-set enrichment visualization and interpretation. PLoS One (2010) 6.61
Single-cell exome sequencing reveals single-nucleotide mutation characteristics of a kidney tumor. Cell (2012) 5.62
Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV. Bioinformatics (2011) 5.45
Single-cell exome sequencing and monoclonal evolution of a JAK2-negative myeloproliferative neoplasm. Cell (2012) 5.16
A human functional protein interaction network and its application to cancer data analysis. Genome Biol (2010) 4.73
Cis-acting regulatory variation in the human genome. Science (2004) 4.47
Paxillin and focal adhesion signalling. Nat Cell Biol (2000) 4.37
PICNIC: an algorithm to predict absolute allelic copy number variation with microarray cancer data. Biostatistics (2009) 4.31
The genesis and evolution of high-grade serous ovarian cancer. Nat Rev Cancer (2010) 4.06
SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors. Bioinformatics (2010) 4.02
A continuum model for tumour suppression. Nature (2011) 3.48
Inferring loss-of-heterozygosity from unpaired tumors using high-density oligonucleotide SNP arrays. PLoS Comput Biol (2006) 3.39
JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data. Bioinformatics (2012) 3.21
High-resolution DNA analysis of human embryonic stem cell lines reveals culture-induced copy number changes and loss of heterozygosity. Nat Biotechnol (2010) 3.21
Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data. Bioinformatics (2011) 2.86
Allele-specific amplification in cancer revealed by SNP array analysis. PLoS Comput Biol (2005) 2.84
PLASQ: a generalized linear model-based procedure to determine allelic dosage in cancer cells from SNP array data. Biostatistics (2006) 2.82
A statistical approach for detecting genomic aberrations in heterogeneous tumor samples from single nucleotide polymorphism genotyping data. Genome Biol (2010) 2.72
Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios. BMC Bioinformatics (2008) 2.66
Feature-based classifiers for somatic mutation detection in tumour-normal paired sequencing data. Bioinformatics (2011) 2.26
Cancer genome sequencing: a review. Hum Mol Genet (2009) 2.15
Single nucleotide polymorphism arrays: a decade of biological, computational and technological advances. Nucleic Acids Res (2009) 1.98
Estimation of rearrangement phylogeny for cancer genomes. Genome Res (2011) 1.91
GPHMM: an integrated hidden Markov model for identification of copy number alteration and loss of heterozygosity in complex tumor samples using whole genome SNP arrays. Nucleic Acids Res (2011) 1.75
TumorBoost: normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays. BMC Bioinformatics (2010) 1.70
Single nucleotide polymorphism array analysis of cancer. Curr Opin Oncol (2007) 1.66
The mammalian XRCC genes: their roles in DNA repair and genetic stability. DNA Repair (Amst) (2003) 1.26
Genomic imprinting and cancer. Exp Cell Res (1999) 1.07
Haploinsufficiency of RAD51B causes centrosome fragmentation and aneuploidy in human cells. Cancer Res (2006) 1.03
Systematic detection of putative tumor suppressor genes through the combined use of exome and transcriptome sequencing. Genome Biol (2010) 1.01
Calling amplified haplotypes in next generation tumor sequence data. Genome Res (2011) 0.95
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods (2007) 45.04
Circos: an information aesthetic for comparative genomics. Genome Res (2009) 40.02
Signatures of mutational processes in human cancer. Nature (2013) 21.63
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proc Natl Acad Sci U S A (2002) 20.48
The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature (2012) 20.47
International network of cancer genome projects. Nature (2010) 20.35
Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N Engl J Med (2013) 19.87
Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature (2009) 18.08
Evolutionary and biomedical insights from the rhesus macaque genome. Science (2007) 16.21
The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol (2010) 13.99
The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLoS Biol (2003) 13.32
Analysis of circulating tumor DNA to monitor metastatic breast cancer. N Engl J Med (2013) 13.22
ARID1A mutations in endometriosis-associated ovarian carcinomas. N Engl J Med (2010) 13.07
The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature (2012) 11.91
The landscape of cancer genes and mutational processes in breast cancer. Nature (2012) 11.24
Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin. Nat Genet (2010) 10.97
Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res (2008) 10.18
Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing. Biotechniques (2008) 10.02
Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature (2010) 9.81
Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature (2011) 9.71
De novo assembly and analysis of RNA-seq data. Nat Methods (2010) 9.69
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res (2004) 9.18
Tumor-associated macrophages and survival in classic Hodgkin's lymphoma. N Engl J Med (2010) 8.74
Loss of acetylation at Lys16 and trimethylation at Lys20 of histone H4 is a common hallmark of human cancer. Nat Genet (2005) 8.45
De novo transcriptome assembly with ABySS. Bioinformatics (2009) 8.38
The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science (2009) 8.23
Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature (2007) 7.91
A tiling resolution DNA microarray with complete coverage of the human genome. Nat Genet (2004) 7.68
Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA. Nature (2013) 7.42
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res (2007) 7.05
Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol (2010) 7.00
Applications of next-generation sequencing technologies in functional genomics. Genomics (2008) 6.50
Next-generation tag sequencing for cancer gene expression profiling. Genome Res (2009) 6.50
The genome of the sea urchin Strongylocentrotus purpuratus. Science (2006) 6.41
MicroRNA expression profiling of human breast cancer identifies new markers of tumor subtype. Genome Biol (2007) 6.41
Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation. PLoS Biol (2008) 5.88
Differential oestrogen receptor binding is associated with clinical outcome in breast cancer. Nature (2012) 5.84
Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. N Engl J Med (2015) 5.71
Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA. Sci Transl Med (2012) 5.69
Molecular classification and molecular forecasting of breast cancer: ready for clinical application? J Clin Oncol (2005) 5.63
Mutation of FOXL2 in granulosa-cell tumors of the ovary. N Engl J Med (2009) 5.63
Genetic unmasking of an epigenetically silenced microRNA in human cancer cells. Cancer Res (2007) 5.62
Driver mutations in TP53 are ubiquitous in high grade serous carcinoma of the ovary. J Pathol (2010) 5.23
Alternative expression analysis by RNA sequencing. Nat Methods (2010) 5.02
The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans. Science (2005) 4.74