Published in Nucleic Acids Res on May 27, 2011
Integrated genomic characterization reveals novel, therapeutically relevant drug targets in FGFR and EGFR pathways in sporadic intrahepatic cholangiocarcinoma. PLoS Genet (2014) 1.60
The landscape and therapeutic relevance of cancer-associated transcript fusions. Oncogene (2014) 1.49
Folate receptor-α (FOLR1) expression and function in triple negative tumors. PLoS One (2015) 1.47
SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data. Genome Biol (2013) 1.47
De novo assembly and characterization of the root transcriptome of Aegilops variabilis during an interaction with the cereal cyst nematode. BMC Genomics (2012) 1.40
Identification of kinase fusion oncogenes in post-Chernobyl radiation-induced thyroid cancers. J Clin Invest (2013) 1.27
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Identification of recurrent SMO and BRAF mutations in ameloblastomas. Nat Genet (2014) 1.20
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Gene expression, single nucleotide variant and fusion transcript discovery in archival material from breast tumors. PLoS One (2013) 1.07
Recurrent read-through fusion transcripts in breast cancer. Breast Cancer Res Treat (2014) 1.05
Reanalysis of RNA-sequencing data reveals several additional fusion genes with multiple isoforms. PLoS One (2012) 1.04
Pharmacologic reversion of epigenetic silencing of the PRKD1 promoter blocks breast tumor cell invasion and metastasis. Breast Cancer Res (2013) 1.03
Exploration of the gene fusion landscape of glioblastoma using transcriptome sequencing and copy number data. BMC Genomics (2013) 1.01
Recurrent PAX3-MAML3 fusion in biphenotypic sinonasal sarcoma. Nat Genet (2014) 0.99
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RNA-Seq mapping and detection of gene fusions with a suffix array algorithm. PLoS Comput Biol (2012) 0.95
Long-range transcriptome sequencing reveals cancer cell growth regulatory chimeric mRNA. Neoplasia (2012) 0.94
Discovery, Annotation, and Functional Analysis of Long Noncoding RNAs Controlling Cell-Cycle Gene Expression and Proliferation in Breast Cancer Cells. Mol Cell (2015) 0.94
High EVI1 expression is associated with MLL rearrangements and predicts decreased survival in paediatric acute myeloid leukaemia: a report from the children's oncology group. Br J Haematol (2013) 0.93
Comparative assessment of methods for the fusion transcripts detection from RNA-Seq data. Sci Rep (2016) 0.92
Comprehensive evaluation of fusion transcript detection algorithms and a meta-caller to combine top performing methods in paired-end RNA-seq data. Nucleic Acids Res (2015) 0.92
Integrated mate-pair and RNA sequencing identifies novel, targetable gene fusions in peripheral T-cell lymphoma. Blood (2016) 0.88
FUSIM: a software tool for simulating fusion transcripts. BMC Bioinformatics (2013) 0.88
Recurrent chimeric fusion RNAs in non-cancer tissues and cells. Nucleic Acids Res (2016) 0.87
RNA sequencing identifies multiple fusion transcripts, differentially expressed genes, and reduced expression of immune function genes in BRAF (V600E) mutant vs BRAF wild-type papillary thyroid carcinoma. J Clin Endocrinol Metab (2013) 0.86
Novel CSF1-S100A10 fusion gene and CSF1 transcript identified by RNA sequencing in tenosynovial giant cell tumors. Int J Oncol (2014) 0.86
Discovering and understanding oncogenic gene fusions through data intensive computational approaches. Nucleic Acids Res (2016) 0.85
Direct Transcriptional Consequences of Somatic Mutation in Breast Cancer. Cell Rep (2016) 0.84
BreakTrans: uncovering the genomic architecture of gene fusions. Genome Biol (2013) 0.83
Dissect: detection and characterization of novel structural alterations in transcribed sequences. Bioinformatics (2012) 0.82
Impact of library preparation on downstream analysis and interpretation of RNA-Seq data: comparison between Illumina PolyA and NuGEN Ovation protocol. PLoS One (2013) 0.82
Fusion transcriptome profiling provides insights into alveolar rhabdomyosarcoma. Proc Natl Acad Sci U S A (2016) 0.82
Common Oncogene Mutations and Novel SND1-BRAF Transcript Fusion in Lung Adenocarcinoma from Never Smokers. Sci Rep (2015) 0.82
RVboost: RNA-seq variants prioritization using a boosting method. Bioinformatics (2014) 0.80
Open-access synthetic spike-in mRNA-seq data for cancer gene fusions. BMC Genomics (2014) 0.78
Transcriptome Profiling of Pediatric Core Binding Factor AML. PLoS One (2015) 0.77
Recurrent rearrangements of the Myb/SANT-like DNA-binding domain containing 3 gene (MSANTD3) in salivary gland acinic cell carcinoma. PLoS One (2017) 0.75
Identifying fusion transcripts using next generation sequencing. Wiley Interdiscip Rev RNA (2016) 0.75
Impact of RNA degradation on fusion detection by RNA-seq. BMC Genomics (2016) 0.75
Recurrent hormone-binding domain truncated ESR1 amplifications in primary endometrial cancers suggest their implication in hormone independent growth. Sci Rep (2016) 0.75
Gene Fusion Markup Language: a prototype for exchanging gene fusion data. BMC Bioinformatics (2012) 0.75
An integrated genomic analysis of Tudor domain-containing proteins identifies PHD finger protein 20-like 1 (PHF20L1) as a candidate oncogene in breast cancer. Mol Oncol (2015) 0.75
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol (2009) 235.12
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
Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science (2005) 39.06
Identification of the transforming EML4-ALK fusion gene in non-small-cell lung cancer. Nature (2007) 37.09
A census of human cancer genes. Nat Rev Cancer (2004) 36.20
Transcriptome sequencing to detect gene fusions in cancer. Nature (2009) 11.63
Chimeric transcript discovery by paired-end transcriptome sequencing. Proc Natl Acad Sci U S A (2009) 5.30
FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data. Genome Biol (2010) 2.79
Distinct mammalian SWI/SNF chromatin remodeling complexes with opposing roles in cell-cycle control. EMBO J (2007) 2.75
Identification of fusion genes in breast cancer by paired-end RNA-sequencing. Genome Biol (2011) 2.64
Transcriptome-guided characterization of genomic rearrangements in a breast cancer cell line. Proc Natl Acad Sci U S A (2009) 2.57
Association of the human papillomavirus type 16 E7 oncoprotein with the 600-kDa retinoblastoma protein-associated factor, p600. Proc Natl Acad Sci U S A (2005) 2.51
Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing. Genome Res (2010) 2.50
A transcriptional sketch of a primary human breast cancer by 454 deep sequencing. BMC Genomics (2009) 2.27
Integrated analysis of gene expression, CpG island methylation, and gene copy number in breast cancer cells by deep sequencing. PLoS One (2011) 2.16
Cloning of BCAS3 (17q23) and BCAS4 (20q13) genes that undergo amplification, overexpression, and fusion in breast cancer. Genes Chromosomes Cancer (2002) 2.04
An integrative approach to reveal driver gene fusions from paired-end sequencing data in cancer. Nat Biotechnol (2009) 1.47
Association of genetic variation in mitotic kinases with breast cancer risk. Breast Cancer Res Treat (2009) 1.02
Establishment of two new cell lines derived from human breast carcinomas with HER-2/neu amplification. Br J Cancer (1991) 1.01
Interaction of TRAF6 with MAST205 regulates NF-kappaB activation and MAST205 stability. J Biol Chem (2004) 1.00
Accurate whole human genome sequencing using reversible terminator chemistry. Nature (2008) 90.20
Alternative isoform regulation in human tissue transcriptomes. Nature (2008) 52.76
Trastuzumab plus adjuvant chemotherapy for operable HER2-positive breast cancer. N Engl J Med (2005) 33.60
The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol (2006) 30.90
American Society of Clinical Oncology/College of American Pathologists guideline recommendations for human epidermal growth factor receptor 2 testing in breast cancer. J Clin Oncol (2006) 25.12
Paclitaxel plus bevacizumab versus paclitaxel alone for metastatic breast cancer. N Engl J Med (2007) 20.19
A randomized trial of letrozole in postmenopausal women after five years of tamoxifen therapy for early-stage breast cancer. N Engl J Med (2003) 13.81
Recommendations for human epidermal growth factor receptor 2 testing in breast cancer: American Society of Clinical Oncology/College of American Pathologists clinical practice guideline update. J Clin Oncol (2013) 12.57
High density DNA methylation array with single CpG site resolution. Genomics (2011) 10.35
Prognostic and predictive value of the 21-gene recurrence score assay in postmenopausal women with node-positive, oestrogen-receptor-positive breast cancer on chemotherapy: a retrospective analysis of a randomised trial. Lancet Oncol (2009) 9.39
Carrier testing for severe childhood recessive diseases by next-generation sequencing. Sci Transl Med (2011) 8.20
American Society of Clinical Oncology/College of American Pathologists guideline recommendations for human epidermal growth factor receptor 2 testing in breast cancer. Arch Pathol Lab Med (2007) 8.02
Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells. Nat Biotechnol (2012) 7.37
Mammalian microRNAs: experimental evaluation of novel and previously annotated genes. Genes Dev (2010) 7.14
A highly annotated whole-genome sequence of a Korean individual. Nature (2009) 6.91
Pharmacogenetics of tamoxifen biotransformation is associated with clinical outcomes of efficacy and hot flashes. J Clin Oncol (2005) 6.90
Adjuvant exemestane with ovarian suppression in premenopausal breast cancer. N Engl J Med (2014) 6.76
Weekly paclitaxel in the adjuvant treatment of breast cancer. N Engl J Med (2008) 6.54
Estrogen-receptor status and outcomes of modern chemotherapy for patients with node-positive breast cancer. JAMA (2006) 6.45
High-resolution analysis of parent-of-origin allelic expression in the mouse brain. Science (2010) 5.91
Adjuvant chemotherapy in older women with early-stage breast cancer. N Engl J Med (2009) 5.68
Prognostic value of tumor-infiltrating lymphocytes in triple-negative breast cancers from two phase III randomized adjuvant breast cancer trials: ECOG 2197 and ECOG 1199. J Clin Oncol (2014) 5.61
Prospective Validation of a 21-Gene Expression Assay in Breast Cancer. N Engl J Med (2015) 5.57
Randomized trial of letrozole following tamoxifen as extended adjuvant therapy in receptor-positive breast cancer: updated findings from NCIC CTG MA.17. J Natl Cancer Inst (2005) 5.55
Longer therapy, iatrogenic amenorrhea, and survival in early breast cancer. N Engl J Med (2010) 5.17
Estrogen- and progesterone-receptor status in ECOG 2197: comparison of immunohistochemistry by local and central laboratories and quantitative reverse transcription polymerase chain reaction by central laboratory. J Clin Oncol (2008) 5.10
FKBP51 affects cancer cell response to chemotherapy by negatively regulating Akt. Cancer Cell (2009) 4.48
PRG-1 and 21U-RNAs interact to form the piRNA complex required for fertility in C. elegans. Mol Cell (2008) 4.48
Prognostic utility of the 21-gene assay in hormone receptor-positive operable breast cancer compared with classical clinicopathologic features. J Clin Oncol (2008) 4.42
The impact of cytochrome P450 2D6 metabolism in women receiving adjuvant tamoxifen. Breast Cancer Res Treat (2006) 4.35
Treatment of HER2-positive breast cancer: current status and future perspectives. Nat Rev Clin Oncol (2011) 4.12
Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver. Genome Res (2009) 4.11
Genome, epigenome and RNA sequences of monozygotic twins discordant for multiple sclerosis. Nature (2010) 3.90
Genetic variants and risk of lung cancer in never smokers: a genome-wide association study. Lancet Oncol (2010) 3.49
Late extended adjuvant treatment with letrozole improves outcome in women with early-stage breast cancer who complete 5 years of tamoxifen. J Clin Oncol (2008) 3.40
Phenotypic reversion or death of cancer cells by altering signaling pathways in three-dimensional contexts. J Natl Cancer Inst (2002) 3.39
A gene expression signature predicts survival of patients with stage I non-small cell lung cancer. PLoS Med (2006) 3.37
Concordance between local and central laboratory HER2 testing in the breast intergroup trial N9831. J Natl Cancer Inst (2002) 3.34
Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq). Proc Natl Acad Sci U S A (2011) 3.30
Exemestane versus anastrozole in postmenopausal women with early breast cancer: NCIC CTG MA.27--a randomized controlled phase III trial. J Clin Oncol (2013) 3.24
Transcriptome-wide regulation of pre-mRNA splicing and mRNA localization by muscleblind proteins. Cell (2012) 3.20
Mutations in DNMT1 cause hereditary sensory neuropathy with dementia and hearing loss. Nat Genet (2011) 3.16
Whole-genome sequencing of multiple myeloma from diagnosis to plasma cell leukemia reveals genomic initiating events, evolution, and clonal tides. Blood (2012) 2.98
Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia. PLoS Genet (2012) 2.94
Prevalence of CXCR4 tropism among antiretroviral-treated HIV-1-infected patients with detectable viremia. J Infect Dis (2006) 2.74
Using synthetic templates to design an unbiased multiplex PCR assay. Nat Commun (2013) 2.72
Molecular Evidence of Sexual Transmission of Ebola Virus. N Engl J Med (2015) 2.71
Oral clodronate for adjuvant treatment of operable breast cancer (National Surgical Adjuvant Breast and Bowel Project protocol B-34): a multicentre, placebo-controlled, randomised trial. Lancet Oncol (2012) 2.65
Phase II randomized study of trastuzumab emtansine versus trastuzumab plus docetaxel in patients with human epidermal growth factor receptor 2-positive metastatic breast cancer. J Clin Oncol (2013) 2.61
Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument. Nat Biotechnol (2011) 2.60
Akt interacts directly with Smad3 to regulate the sensitivity to TGF-beta induced apoptosis. Nat Cell Biol (2004) 2.59
A multigene expression assay to predict local recurrence risk for ductal carcinoma in situ of the breast. J Natl Cancer Inst (2013) 2.56
Recommendations for human epidermal growth factor receptor 2 testing in breast cancer: American Society of Clinical Oncology/College of American Pathologists clinical practice guideline update. Arch Pathol Lab Med (2013) 2.54
Cohesin-mediated interactions organize chromosomal domain architecture. EMBO J (2013) 2.48
Noncanonical compensation of zygotic X transcription in early Drosophila melanogaster development revealed through single-embryo RNA-seq. PLoS Biol (2011) 2.43
Fulvestrant in women with advanced breast cancer after progression on prior aromatase inhibitor therapy: North Central Cancer Treatment Group Trial N0032. J Clin Oncol (2006) 2.28
Characterization of human plasma-derived exosomal RNAs by deep sequencing. BMC Genomics (2013) 2.27
A two-gene expression ratio of homeobox 13 and interleukin-17B receptor for prediction of recurrence and survival in women receiving adjuvant tamoxifen. Clin Cancer Res (2006) 2.27
From single-cell to cell-pool transcriptomes: stochasticity in gene expression and RNA splicing. Genome Res (2013) 2.23
Brain expression genome-wide association study (eGWAS) identifies human disease-associated variants. PLoS Genet (2012) 2.23
Genomic convergence analysis of schizophrenia: mRNA sequencing reveals altered synaptic vesicular transport in post-mortem cerebellum. PLoS One (2008) 2.22
Integrated analysis of gene expression, CpG island methylation, and gene copy number in breast cancer cells by deep sequencing. PLoS One (2011) 2.16
HER2 testing in breast cancer: NCCN Task Force report and recommendations. J Natl Compr Canc Netw (2006) 2.15
3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer. BMC Genomics (2009) 2.12
mRNA-seq with agnostic splice site discovery for nervous system transcriptomics tested in chronic pain. Genome Res (2010) 2.12
Novel late-onset Alzheimer disease loci variants associate with brain gene expression. Neurology (2012) 2.08
Six cycles of doxorubicin and cyclophosphamide or Paclitaxel are not superior to four cycles as adjuvant chemotherapy for breast cancer in women with zero to three positive axillary nodes: Cancer and Leukemia Group B 40101. J Clin Oncol (2012) 2.07
Progress against solid tumors in danger: the metastatic breast cancer example. J Clin Oncol (2012) 2.05
Atypical protein kinase Ciota plays a critical role in human lung cancer cell growth and tumorigenicity. J Biol Chem (2005) 2.05
Phase III evaluation of fluoxetine for treatment of hot flashes. J Clin Oncol (2002) 1.97
Genome-wide analysis reveals recurrent structural abnormalities of TP63 and other p53-related genes in peripheral T-cell lymphomas. Blood (2012) 1.96
Efficacy of letrozole extended adjuvant therapy according to estrogen receptor and progesterone receptor status of the primary tumor: National Cancer Institute of Canada Clinical Trials Group MA.17. J Clin Oncol (2007) 1.93
Exome sequencing and systems biology converge to identify novel mutations in the L-type calcium channel, CACNA1C, linked to autosomal dominant long QT syndrome. Circ Cardiovasc Genet (2013) 1.93
Zoledronic acid inhibits adjuvant letrozole-induced bone loss in postmenopausal women with early breast cancer. J Clin Oncol (2006) 1.92
NCCN Task Force Report: Adjuvant Therapy for Breast Cancer. J Natl Compr Canc Netw (2006) 1.88
Radiation pharmacogenomics: a genome-wide association approach to identify radiation response biomarkers using human lymphoblastoid cell lines. Genome Res (2010) 1.87
Neuropathy is not associated with clinical outcomes in patients receiving adjuvant taxane-containing therapy for operable breast cancer. J Clin Oncol (2012) 1.85
Batch effect correction for genome-wide methylation data with Illumina Infinium platform. BMC Med Genomics (2011) 1.84
Fine mapping of chromosome 6q23-25 region in familial lung cancer families reveals RGS17 as a likely candidate gene. Clin Cancer Res (2009) 1.83
Radiotherapy and adjuvant trastuzumab in operable breast cancer: tolerability and adverse event data from the NCCTG Phase III Trial N9831. J Clin Oncol (2009) 1.80
Zoledronic acid effectively prevents aromatase inhibitor-associated bone loss in postmenopausal women with early breast cancer receiving adjuvant letrozole: Z-FAST study 36-month follow-up results. Clin Breast Cancer (2009) 1.78
Integrated analysis of zoledronic acid for prevention of aromatase inhibitor-associated bone loss in postmenopausal women with early breast cancer receiving adjuvant letrozole. Oncologist (2008) 1.77
Phase III randomized, placebo-controlled, double-blind trial of risedronate for the prevention of bone loss in premenopausal women undergoing chemotherapy for primary breast cancer. J Clin Oncol (2008) 1.77
Estrogen receptor alpha controls a gene network in luminal-like breast cancer cells comprising multiple transcription factors and microRNAs. Am J Pathol (2010) 1.73
Adjuvant trastuzumab: a milestone in the treatment of HER-2-positive early breast cancer. Oncologist (2006) 1.65
Protein kinase Ciota is required for Ras transformation and colon carcinogenesis in vivo. J Cell Biol (2004) 1.63
Choosing the best trastuzumab-based adjuvant chemotherapy regimen: should we abandon anthracyclines? J Clin Oncol (2012) 1.62
Mayo Genome Consortia: a genotype-phenotype resource for genome-wide association studies with an application to the analysis of circulating bilirubin levels. Mayo Clin Proc (2011) 1.62
Quality of life after breast cancer surgery: What have we learned and where should we go next? J Surg Oncol (2009) 1.60
Comparative methylome analysis of benign and malignant peripheral nerve sheath tumors. Genome Res (2011) 1.60