A deep learning approach to automate refinement of somatic variant calling from cancer sequencing data

Somatic mutations in benign breast disease tissue and risk of subsequent invasive breast cancer

(2018) Thomas E. Rohan et al.   BRITISH JOURNAL OF CANCER

Standards and Guidelines for Validating Next-Generation Sequencing Bioinformatics Pipelines

(2018) Somak Roy et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Bioconda: sustainable and comprehensive software distribution for the life sciences

(2018) Björn Grüning et al.   NATURE METHODS

Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines

(2018) Kyle Ellrott et al.   Cell Systems

Mutation Clearance after Transplantation for Myelodysplastic Syndrome

(2018) Eric J. Duncavage et al.   NEW ENGLAND JOURNAL OF MEDICINE

Recurrent WNT pathway alterations are frequent in relapsed small cell lung cancer

(2018) Alex H. Wagner et al.   Nature Communications

Standard operating procedure for somatic variant refinement of sequencing data with paired tumor and normal samples

(2018) Erica K. Barnell et al.   GENETICS IN MEDICINE

Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer

(2017) Marilyn M. Li et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Recurrent and functional regulatory mutations in breast cancer

(2017) Esther Rheinbay et al.   NATURE

An immunogenic personal neoantigen vaccine for patients with melanoma

(2017) Patrick A. Ott et al.   NATURE

CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer

(2017) Malachi Griffith et al.   NATURE GENETICS

Biological and therapeutic implications of multisector sequencing in newly diagnosed glioblastoma

(2017) Tatenda Mahlokozera et al.   NEURO-ONCOLOGY

Spatial genomic heterogeneity in multiple myeloma revealed by multi-region sequencing

(2017) L. Rasche et al.   Nature Communications

Recurrent somatic mutations affecting B-cell receptor signaling pathway genes in follicular lymphoma

(2016) Kilannin Krysiak et al.   BLOOD

SNooPer: a machine learning-based method for somatic variant identification from low-pass next-generation sequencing

(2016) Jean-François Spinella et al.   BMC GENOMICS

Comprehensive genomic analysis reveals FLT3 activation and a therapeutic strategy for a patient with relapsed adult B-lymphoblastic leukemia

(2016) Malachi Griffith et al.   EXPERIMENTAL HEMATOLOGY

Dynamic changes in the clonal structure of MDS and AML in response to epigenetic therapy

(2016) G L Uy et al.   LEUKEMIA

Analysis of protein-coding genetic variation in 60,706 humans

(2016) Monkol Lek et al.   NATURE

TP53 and Decitabine in Acute Myeloid Leukemia and Myelodysplastic Syndromes

(2016) John S. Welch et al.   NEW ENGLAND JOURNAL OF MEDICINE

Truncating Prolactin Receptor Mutations Promote Tumor Growth in Murine Estrogen Receptor-Alpha Mammary Carcinomas

(2016) Obi L. Griffith et al.   Cell Reports

Current practices and guidelines for clinical next-generation sequencing oncology testing

(2016) Samuel P. Strom et al.   Cancer Biology & Medicine

A Phase I Trial of BKM120 (Buparlisib) in Combination with Fulvestrant in Postmenopausal Women with Estrogen Receptor-Positive Metastatic Breast Cancer

(2015) C. X. Ma et al.   CLINICAL CANCER RESEARCH

Association Between Mutation Clearance After Induction Therapy and Outcomes in Acute Myeloid Leukemia

(2015) Jeffery M. Klco et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas

(2015)   NEW ENGLAND JOURNAL OF MEDICINE

Genome Modeling System: A Knowledge Management Platform for Genomics

(2015) Malachi Griffith et al.   PLoS Computational Biology

Optimizing Cancer Genome Sequencing and Analysis

(2015) Malachi Griffith et al.   Cell Systems

Detection of Circulating Tumor DNA in Early- and Late-Stage Human Malignancies

(2014) C. Bettegowda et al.   Science Translational Medicine

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation

(2013) Maura Costello et al.   NUCLEIC ACIDS RESEARCH

Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs

(2012) Christopher T. Saunders et al.   BIOINFORMATICS

Feature-based classifiers for somatic mutation detection in tumour–normal paired sequencing data

(2011) Jiarui Ding et al.   BIOINFORMATICS

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Sniper: improved SNP discovery by multiply mapping deep sequenced reads

(2011) Daniel F Simola et al.   GENOME BIOLOGY

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

VarScan: variant detection in massively parallel sequencing of individual and pooled samples

(2009) Daniel C. Koboldt 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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS