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List of works by Chip Stewart

<i>ZBTB33</i> is mutated in clonal hematopoiesis and myelodysplastic syndromes and impacts RNA splicing

scientific article published on 14 July 2021

A (fire)cloud-based DNA methylation data preprocessing and quality control platform

A comprehensive map of mobile element insertion polymorphisms in humans

scientific article

A remarkably simple genome underlies highly malignant pediatric rhabdoid cancers

scientific article

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

scientific article published on 05 February 2020

Author Correction: Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes

article

Clonal evolution in patients with chronic lymphocytic leukaemia developing resistance to BTK inhibition

scientific article published on 20 May 2016

Clonal hematopoiesis is associated with adverse outcomes in multiple myeloma patients undergoing transplant

scientific article published on 12 June 2020

Combined tumor and immune signals from genomes or transcriptomes predict outcomes of checkpoint inhibition in melanoma

scientific article published in 2022

Comment on “DNA damage is a pervasive cause of sequencing errors, directly confounding variant identification”

scientific article published in Science

Copy Number Variation detection from 1000 Genomes project exon capture sequencing data ⬇️

scientific article published on November 17, 2012

DNA defects, epigenetics, and gene expression in cancer-adjacent breast: a study from The Cancer Genome Atlas

scientific article

DeTiN: overcoming tumor-in-normal contamination

scientific article published on 25 June 2018

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

scientific article

Electroporation of a multicellular system: asymptotic model analysis

scientific article published on 01 January 2004

Erratum: Corrigendum: The genomic landscape of juvenile myelomonocytic leukemia

article

Evolution and impact of subclonal mutations in chronic lymphocytic leukemia

scientific article published on February 2013

Exome and whole-genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity

scientific article published on 24 March 2013

Exome sequencing identifies BRAF mutations in papillary craniopharyngiomas

scientific article

Exome sequencing of lymphomas from three dog breeds reveals somatic mutation patterns reflecting genetic background

scientific article published on 16 September 2015

Expression divergence measured by transcriptome sequencing of four yeast species ⬇️

scientific article published on December 29, 2011

GE-05EXOME SEQUENCING REVEALS BRAF MUTATIONS IN PAPILLARY CRANIOPHARYNGIOMAS.

scientific article

Genetic and clonal dissection of murine small cell lung carcinoma progression by genome sequencing

scientific article

Genetic subtypes of smoldering multiple myeloma are associated with distinct pathogenic phenotypes and clinical outcomes

scientific article published on 01 January 2022

Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma

scientific article published on 14 April 2016

Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma

scientific article published on October 2016

Genomic Evolutionary Patterns of Leiomyosarcoma and Liposarcoma

scientific article published on 04 June 2019

Genomic Profiling of Smoldering Multiple Myeloma Identifies Patients at a High Risk of Disease Progression

scientific article published on 22 May 2020

Genomic analyses of PMBL reveal new drivers and mechanisms of sensitivity to PD-1 blockade

scientific article published on 01 December 2019

Genomic analyses of flow-sorted Hodgkin Reed-Sternberg cells reveal complementary mechanisms of immune evasion

scientific article published on 01 December 2019

Growth dynamics in naturally progressing chronic lymphocytic leukaemia

scientific article published on 29 May 2019

Identification of heart rate-associated loci and their effects on cardiac conduction and rhythm disorders

scientific article published on 14 April 2013

Integrated Molecular Characterization of Uterine Carcinosarcoma

scientific article

Integrative Molecular Characterization of Malignant Pleural Mesothelioma

scientific article published on 15 October 2018

Integrative and comparative genomic analysis of lung squamous cell carcinomas in East Asian patients

scientific article

Lack of transgenerational effects of ionizing radiation exposure from the Chernobyl accident

scientific article published in 2021

Landscape of genomic alterations in cervical carcinomas

scientific article

MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping

scientific article

Mapping copy number variation by population-scale genome sequencing

scientific article

Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes

article

Mutational heterogeneity in cancer and the search for new cancer-associated genes

scientific article

Mutations driving CLL and their evolution in progression and relapse

scientific article published on 14 October 2015

Paired exome analysis of Barrett's esophagus and adenocarcinoma

scientific article

Prospective derivation of a living organoid biobank of colorectal cancer patients.

scientific article published on May 2015

Publisher Correction: Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes

article

RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues

scientific article published on 01 June 2019

Recurrent and functional regulatory mutations in breast cancer

scientific article published on 28 June 2017

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

Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors.

scientific article published on 6 November 2017

Scotty: a web tool for designing RNA-Seq experiments to measure differential gene expression ⬇️

scientific article published on January 12, 2013

Selective and mechanistic sources of recurrent rearrangements across the cancer genome

Sequence Analysis and Characterization of Active Human Alu Subfamilies Based on the 1000 Genomes Pilot Project

scientific article

Somatic rearrangements across cancer reveal classes of samples with distinct patterns of DNA breakage and rearrangement-induced hypermutability

scientific article published on 2 November 2012

Somatic retrotransposition in human cancer revealed by whole-genome and exome sequencing

scientific article

Sporadic Early-Onset Diffuse Gastric Cancers Have High Frequency of Somatic CDH1 Alterations, but Low Frequency of Somatic RHOA Mutations Compared With Late-Onset Cancers.

scientific article published on 15 May 2017

Sporadic hemangioblastomas are characterized by cryptic VHL inactivation

scientific article

SvABA: genome-wide detection of structural variants and indels by local assembly.

scientific article published on 13 March 2018

Targetable genetic features of primary testicular and primary central nervous system lymphomas

scientific article published on 23 December 2015

The functional spectrum of low-frequency coding variation ⬇️

scientific article published on September 14, 2011

The genetic landscape of high-risk neuroblastoma

scientific article published on 20 January 2013

The genomic landscape of juvenile myelomonocytic leukemia

scientific article

The genomic landscape of pediatric Ewing sarcoma

scientific article

Widespread Chromosomal Losses and Mitochondrial DNA Alterations as Genetic Drivers in Hürthle Cell Carcinoma

scientific article published on 01 August 2018

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