An Integrated Model of the Transcriptome of HER2-Positive Breast Cancer

Abstract PD10-04: Predictive genomic markers to chemotherapy and adjuvant trastuzumab via whole genome expression DASL profiling in the N9831 adjuvant study

(2014) EA Perez et al.   CANCER RESEARCH

RNA sequencing of cancer reveals novel splicing alterations

(2013) Jeyanthy Eswaran et al.   Scientific Reports

Detection of Redundant Fusion Transcripts as Biomarkers or Disease-Specific Therapeutic Targets in Breast Cancer

(2012) Y. W. Asmann et al.   CANCER RESEARCH

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

(2012) Jordi Barretina et al.   NATURE

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

Deep Sequence Analysis of Non-Small Cell Lung Cancer: Integrated Analysis of Gene Expression, Alternative Splicing, and Single Nucleotide Variations in Lung Adenocarcinomas with and without Oncogenic KRAS Mutations

(2012) Krishna R. Kalari et al.   Frontiers in Oncology

Sequential Versus Concurrent Trastuzumab in Adjuvant Chemotherapy for Breast Cancer

(2011) Edith A. Perez et al.   JOURNAL OF CLINICAL ONCOLOGY

Four-Year Follow-Up of Trastuzumab Plus Adjuvant Chemotherapy for Operable Human Epidermal Growth Factor Receptor 2–Positive Breast Cancer: Joint Analysis of Data From NCCTG N9831 and NSABP B-31

(2011) Edith A. Perez et al.   JOURNAL OF CLINICAL ONCOLOGY

Predictability of Adjuvant Trastuzumab Benefit in N9831 Patients Using the ASCO/CAP HER2-Positivity Criteria

(2011) Edith A. Perez et al.   JNCI-Journal of the National Cancer Institute

SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors

(2010) Rodrigo Goya et al.   BIOINFORMATICS

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

Proteomic Characterization of Novel Alternative Splice Variant Proteins in Human Epidermal Growth Factor Receptor 2/neu–Induced Breast Cancers

(2010) Rajasree Menon et al.   CANCER RESEARCH

Exon-Level Microarray Analyses Identify Alternative Splicing Programs in Breast Cancer

(2010) A. Lapuk et al.   MOLECULAR CANCER RESEARCH

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Trastuzumab Beyond Progression in Human Epidermal Growth Factor Receptor 2–Positive Advanced Breast Cancer: A German Breast Group 26/Breast International Group 03-05 Study

(2009) Gunter von Minckwitz et al.   JOURNAL OF CLINICAL ONCOLOGY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Reactome knowledgebase of human biological pathways and processes

(2008) L. Matthews et al.   NUCLEIC ACIDS RESEARCH