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List of works by Elaine Mardis

143 Identification of Neoantigen-specific CD8+ T Cells in Two Murine Orthotopic Glioblastoma Models Using Cancer Immunogenomics

scientific article

A 50-gene intrinsic subtype classifier for prognosis and prediction of benefit from adjuvant tamoxifen

scientific article published on 18 June 2012

A Drosophila model of multiple endocrine neoplasia type 2.

scientific article

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

scientific article published on 12 November 2015

A Phase II Trial of Neoadjuvant MK-2206, an AKT Inhibitor, with Anastrozole in Clinical Stage II or III PIK3CA-Mutant ER-Positive and HER2-Negative Breast Cancer.

scientific article published on 5 September 2017

A Vaccine for Cancer?

scientific article

A burst of segmental duplications in the genome of the African great ape ancestor

scientific article published on February 2009

A central support system can facilitate implementation and sustainability of a Classroom-based Undergraduate Research Experience (CURE) in Genomics

scientific article

A comparison of PAM50 intrinsic subtyping with immunohistochemistry and clinical prognostic factors in tamoxifen-treated estrogen receptor-positive breast cancer

scientific article

A course-based research experience: how benefits change with increased investment in instructional time

scientific article published on January 2014

A decade's perspective on DNA sequencing technology

scientific article

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

scientific article

A focus on personal genomics

article published in 2009

A glimpse at tumor genome evolution.

scientific article published on 19 September 2011

A high-resolution map of human evolutionary constraint using 29 mammals

scientific article

A luminal breast cancer genome atlas: progress and barriers

scientific article

A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms

scientific article (publication date: 15 February 2001)

A multiple myeloma-specific capture sequencing platform discovers novel translocations and frequent, risk-associated point mutations in IGLL5.

scientific article

A novel retinoblastoma therapy from genomic and epigenetic analyses

scientific article published on 11 January 2012

A physical map of the chicken genome

scientific article

A physical map of the human genome

scientific article

A pilot study of high-throughput, sequence-based mutational profiling of primary human acute myeloid leukemia cell genomes.

scientific article

A precise reconstruction of the emergence and constrained radiations of Escherichia coli O157 portrayed by backbone concatenomic analysis

scholarly article

A sequence motif within chromatin entry sites directs MSL establishment on the Drosophila X chromosome

scientific article published on August 2008

A surprising cross-species conservation in the genomic landscape of mouse and human oral cancer identifies a transcriptional signature predicting metastatic disease.

scientific article published on 25 March 2014

A vertebrate case study of the quality of assemblies derived from next-generation sequences

scientific article

AACR Cancer Progress Report 2013.

scientific article published on 16 September 2013

AACR Cancer Progress Report 2014

scientific article

Abstract S1-04: Exome sequencing of post-menopausal ER+ breast cancer (BC) treated pre-surgically with aromatase inhibitors (AIs) in the POETIC trial (CRUK/07/015)

Accounting for proximal variants improves neoantigen prediction

scientific article published on 03 December 2018

Acquired copy number alterations in adult acute myeloid leukemia genomes

scholarly article

Activating HER2 mutations in HER2 gene amplification negative breast cancer

scientific article

Advances in genome biology and technology

scientific article

Agarose Gel Size Selection for DNA Sequencing Libraries

scientific article

Age-related mutations associated with clonal hematopoietic expansion and malignancies

scientific article

An Inv(16)(p13.3q24.3)-encoded CBFA2T3-GLIS2 fusion protein defines an aggressive subtype of pediatric acute megakaryoblastic leukemia

scientific article published on November 2012

An mRNA Gene Expression-Based Signature to Identify FGFR1-Amplified Estrogen Receptor-Positive Breast Tumors

scientific article

An obesity-associated gut microbiome with increased capacity for energy harvest

scientific article (publication date: 21 December 2006)

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome

scientific article published in June 2007

Analysis of next-generation genomic data in cancer: accomplishments and challenges ⬇️

scientific article published on September 15, 2010

Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach.

scientific article published on 29 September 2006

Ancestry estimation and control of population stratification for sequence-based association studies

scientific article

Anticipating the 1,000 dollar genome

scientific article

Application of a superword array in genome assembly

scientific article

Applications of Immunogenomics to Cancer

scientific article published on February 2017

Applying next-generation sequencing to pancreatic cancer treatment ⬇️

scientific article published on July 3, 2012

Aromatase inhibition remodels the clonal architecture of estrogen-receptor-positive breast cancers

scientific article published on 09 August 2016

Assessing telomeric DNA content in pediatric cancers using whole-genome sequencing data

scientific article

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

scientific article

Association of Somatic Mutations of ADAMTS Genes With Chemotherapy Sensitivity and Survival in High-Grade Serous Ovarian Carcinoma

scientific article

Association of Tumor Microenvironment T-cell Repertoire and Mutational Load with Clinical Outcome after Sequential Checkpoint Blockade in Melanoma

scientific article published on 11 January 2019

Association of age at diagnosis and genetic mutations in patients with neuroblastoma.

scientific article

Assuring the quality of next-generation sequencing in clinical laboratory practice

scientific article

Author Correction: Comparative and demographic analysis of orang-utan genomes

correction of a scholarly article

Author Correction: The prognostic effects of somatic mutations in ER-positive breast cancer

scientific article published in Nature Communications

Automated Library Preparation for DNA Sequencing

scientific article

Background Mutations in Parental Cells Account for Most of the Genetic Heterogeneity of Induced Pluripotent Stem Cells ⬇️

scientific article published on April 26, 2012

Biome representational in silico karyotyping

scientific article

Blinded comparison of repetitive-sequence PCR and multilocus sequence typing for genotyping methicillin-resistant Staphylococcus aureus isolates from a children's hospital in St. Louis, Missouri

scientific article published on June 2006

Body Mass Index, PAM50 Subtype, and Outcomes in Node-Positive Breast Cancer: CALGB 9741 (Alliance).

scientific article

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation

scientific article

BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data

scientific article

BreakTrans: uncovering the genomic architecture of gene fusions

scientific article

Breast Cancer Neoantigens Can Induce CD8+ T-Cell Responses and Antitumor Immunity

scientific article published on 15 June 2017

Brief Report: The Role of Rare Protein-Coding Variants in Anti-Tumor Necrosis Factor Treatment Response in Rheumatoid Arthritis.

scientific article

C11ORF95-RELA FUSIONS DRIVE ONCOGENIC NF-KB SIGNALING IN EPENDYMOMA.

scientific article published in July 2014

C11orf95-RELA fusions drive oncogenic NF-κB signalling in ependymoma

scientific article

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

scientific article (publication date: 31 January 2017)

CIViC: A knowledgebase for expert-crowdsourcing the clinical interpretation of variants in cancer

CMDS: a population-based method for identifying recurrent DNA copy number aberrations in cancer from high-resolution data

scientific article

CREST maps somatic structural variation in cancer genomes with base-pair resolution.

scientific article

Caenorhabditis elegans glp-4 Encodes a Valyl Aminoacyl tRNA Synthetase

scientific article

California Dreamin': the Future of Genomic Medicine

scientific article published on March 2016

Cancer Genomics

scientific article published on 28 October 2015

Cancer Genomics: Large-Scale Projects Translate into Therapeutic Advances

scientific article published on 27 December 2016

Cancer Immunogenomics: Computational Neoantigen Identification and Vaccine Design.

scientific article published on 7 April 2017

Cancer exome analysis reveals a T-cell-dependent mechanism of cancer immunoediting

scientific article published on 08 February 2012

Cancer genome sequencing and its implications for personalized cancer vaccines

scientific article

Cancer genome sequencing: a review

scientific article published on October 2009

Cancer genomics identifies determinants of tumor biology

scientific article

Cancer immunotherapy. A dendritic cell vaccine increases the breadth and diversity of melanoma neoantigen-specific T cells

scientific article published on 2 April 2015

Caspase-9 is required for normal hematopoietic development and protection from alkylator-induced DNA damage in mice

scientific article

ChIP-seq: welcome to the new frontier

scientific article

Challenges of sequencing human genomes

scientific article

Characterizing the cancer genome in lung adenocarcinoma

scientific article

Checkpoint blockade cancer immunotherapy targets tumour-specific mutant antigens

scientific article

Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content

scientific article published on 13 January 2010

Clinical and Genetic Risk Factors for Acute Pancreatitis in Patients With Acute Lymphoblastic Leukemia

scientific article published on 25 April 2016

Clinical and Genomic Insights from Metastatic Cancers

scientific article published on 4 January 2018

Clinical significance of CTNNB1 mutation and Wnt pathway activation in endometrioid endometrial carcinoma

scientific article

Clonal architecture of secondary acute myeloid leukemia

scientific article published on 14 March 2012

Clonal architecture of secondary acute myeloid leukemia defined by single-cell sequencing

scientific article

Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa

scientific article

Comparative and demographic analysis of orang-utan genomes

scientific article

Comparison of dot chromosome sequences from D. melanogaster and D. virilis reveals an enrichment of DNA transposon sequences in heterochromatic domains

scientific article

Complete Khoisan and Bantu genomes from southern Africa

scientific article

Complete characterization of the microRNAome in a patient with acute myeloid leukemia ⬇️

scientific article published on September 28, 2010

Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients

article

Comprehensive Characterization of Cancer Driver Genes and Mutations

article

Comprehensive discovery of noncoding RNAs in acute myeloid leukemia cell transcriptomes

scientific article

Comprehensive gene expression meta-analysis identifies signature genes that distinguish microglia from peripheral monocytes/macrophages in health and glioma

scientific article published on 14 February 2019

Comprehensive genetic variant discovery in the surfactant protein B gene

scientific article published on August 2007

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

scientific article

Comprehensive genomic studies: emerging regulatory, strategic, and quality assurance challenges for biorepositories

scientific article

Conifers have a unique small RNA silencing signature

scientific article (publication date: August 2008)

Contribution of systemic and somatic factors to clinical response and resistance in urothelial cancer: an exploratory multi-omic analysis

Contribution of systemic and somatic factors to clinical response and resistance to PD-L1 blockade in urothelial cancer: An exploratory multi-omic analysis.

scientific article

Convergent evolution of chicken Z and human X chromosomes by expansion and gene acquisition

scientific article

Convergent loss of PTEN leads to clinical resistance to a PI(3)Kα inhibitor

scientific article

Correction to: Comprehensive gene expression meta-analysis identifies signature genes that distinguish microglia from peripheral monocytes/macrophages in health and glioma

scientific article published on 08 January 2020

Correction: Tumor Evolution in Two Patients with Basal-like Breast Cancer: A Retrospective Genomics Study of Multiple Metastases

scientific article

Cycle-Sequencing Reactions

scientific article published in November 2016

DGIdb 2.0: mining clinically relevant drug-gene interactions.

scientific article

DGIdb: mining the druggable genome

scientific article published on 13 October 2013

DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome

scientific article

DNA sequencing technologies: 2006-2016.

scientific article published on 05 January 2017

DNMT3A Mutations in Acute Myeloid Leukemia

scientific article (publication date: 16 December 2010)

De Novo Gene Disruptions in Children on the Autistic Spectrum

scientific article (publication date: April 2012)

De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data

scientific article

De novo primary central nervous system pure erythroid leukemia/sarcoma with t(1;16)(p31;q24) NFIA/CBFA2T3 translocation

scientific article published on 16 January 2020

Deregulation of DUX4 and ERG in acute lymphoblastic leukemia

scientific article published on 24 October 2016

Design and implementation of a generalized laboratory data model

scientific article

Detection of neoantigen-specific T cells following a personalized vaccine in a patient with glioblastoma

scientific article published on 25 January 2019

Development and verification of the PAM50-based Prosigna breast cancer gene signature assay

scientific article published on 22 August 2015

Direct genomic selection.

scientific article

Disease-Associated Mosaic Variation in Clinical Exome Sequencing: A Two Year Pediatric Tertiary Care Experience

scientific article published on 05 May 2020

Distinct patterns of mutations occurring in de novo AML versus AML arising in the setting of severe congenital neutropenia

scientific article

DoCM: a database of curated mutations in cancer.

scientific article

Drosophila Muller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution

scientific article

EGF receptor gene mutations are common in lung cancers from "never smokers" and are associated with sensitivity of tumors to gefitinib and erlotinib

scientific article

Endocrine-therapy-resistant ESR1 variants revealed by genomic characterization of breast-cancer-derived xenografts

scientific article

Endogenous Neoantigen-Specific CD8 T Cells Identified in Two Glioblastoma Models Using a Cancer Immunogenomics Approach

scientific article published on 31 October 2016

Erratum: A burst of segmental duplications in the genome of the African great ape ancestor

scientific article published in Nature

Erratum: Corrigendum: C11orf95–RELA fusions drive oncogenic NF-κB signalling in ependymoma

scholarly article published in Nature

Estrogen receptor expression is high but is of lower intensity in tubular carcinoma than in well-differentiated invasive ductal carcinoma.

scientific article

Evolution of a distinct genomic domain in Drosophila: comparative analysis of the dot chromosome in Drosophila melanogaster and Drosophila virilis

scientific article

Evolutionary and Biomedical Insights from the Rhesus Macaque Genome

scientific article

Exome sequencing implicates an increased burden of rare potassium channel variants in the risk of drug-induced long QT interval syndrome

scientific article

Exome sequencing of case-unaffected-parents trios reveals recessive and de novo genetic variants in sporadic ALS.

scientific article

Expanding the clinical history associated with syndromic Klippel-Feil: A unique case of comorbidity with medulloblastoma

scientific article published on 10 June 2019

Exploiting Oxytricha trifallax nanochromosomes to screen for non-coding RNA genes

scientific article

Expression of a bcr-1 isoform of RARalpha-PML does not affect the penetrance of acute promyelocytic leukemia or the acquisition of an interstitial deletion on mouse chromosome 2

scientific article published on 28 September 2006

Extending assembly of short DNA sequences to handle error.

scientific article published on 24 September 2007

F11R is a novel monocyte prognostic biomarker for malignant glioma

scientific article

Finding the missing heritability of complex diseases

scientific article

Fosmid-based physical mapping of the Histoplasma capsulatum genome

scientific article published in August 2004

Fourteen-genome comparison identifies DNA markers for severe-disease-associated strains of Clostridium difficile

scientific article

From "N of 1" to N of more

scientific article published on October 2015

Frontiers in cancer immunotherapy-a symposium report

scientific article published on 13 November 2020

Functional heterogeneity of genetically defined subclones in acute myeloid leukemia

scientific article published on 06 March 2014

Future cancer research priorities in the USA: a Lancet Oncology Commission

scientific article published on 31 October 2017

Gallus GBrowse: a unified genomic database for the chicken

scientific article

Generation and analysis of 280,000 human expressed sequence tags

scientific article

Generation and annotation of the DNA sequences of human chromosomes 2 and 4

scientific article

Genetic Characterization of Pediatric Sarcomas by Targeted RNA Sequencing

scientific article published on 31 July 2020

Genetic alterations in uncommon low-grade neuroepithelial tumors: BRAF, FGFR1, and MYB mutations occur at high frequency and align with morphology.

scientific article published on 25 January 2016

Genetic risk factors for the development of osteonecrosis in children under age 10 treated for acute lymphoblastic leukemia

scientific article published on 20 November 2015

Genome Modeling System: A Knowledge Management Platform for Genomics

scientific article published on 9 July 2015

Genome analysis of the platypus reveals unique signatures of evolution

scientific article

Genome analysis of the platypus reveals unique signatures of evolution

scientific article published in Nature

Genome remodelling in a basal-like breast cancer metastasis and xenograft

scientific article

Genome science: a video tour of the Washington University Genome Sequencing Center for high school and undergraduate students

scientific article

Genome sequencing and cancer ⬇️

scientific article published on April 23, 2012

Genome sequencing identifies somatic BRAF duplication c.1794_1796dupTAC;p.Thr599dup in pediatric patient with low-grade ganglioglioma

scientific article published on 6 February 2018

Genome-wide diversity and selective pressure in the human rhinovirus

scientific article published on 3 May 2007

Genomic analysis to define molecular basis of aggressiveness in a mouse model of oral cancer

scientific article

Genomic impact of transient low-dose decitabine treatment on primary AML cells

scientific article published on 7 January 2013

Genomic landscape of Ewing sarcoma defines an aggressive subtype with co-association of STAG2 and TP53 mutations

scientific article

Genomic landscape of non-small cell lung cancer in smokers and never-smokers

scientific article published on September 2012

Genomic landscape of paediatric adrenocortical tumours

scientific article

Genomic profiling of murine mammary tumors identifies potential personalized drug targets for p53-deficient mammary cancers.

scientific article published on 05 May 2016

Genomics of acute myeloid leukemia

scientific article

Germline Genetic IKZF1 Variation and Predisposition to Childhood Acute Lymphoblastic Leukemia

scientific article published on 16 April 2018

Germline Mutations in Predisposition Genes in Pediatric Cancer

scientific article published on 18 November 2015

Germline genetic variation in ETV6 and risk of childhood acute lymphoblastic leukaemia: a systematic genetic study

scientific article

HGV2009 meeting: bigger and better studies provide more answers and more questions

scientific article published on July 2010

Histidine protects against zinc and nickel toxicity in Caenorhabditis elegans

scientific article (publication date: March 2011)

INTEGRATE-neo: a pipeline for personalized gene fusion neoantigen discovery

scientific article

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

scientific article published in June 2007

Identification of Therapeutic Targets in Rhabdomyosarcoma through Integrated Genomic, Epigenomic, and Proteomic Analyses

scientific article published on 23 August 2018

Identification of a novel TP53 cancer susceptibility mutation through whole-genome sequencing of a patient with therapy-related AML.

scientific article

Identification of a rare coding variant in complement 3 associated with age-related macular degeneration

scientific article published on 15 September 2013

Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: a comparative genomics approach.

scholarly article

Identification of somatic JAK1 mutations in patients with acute myeloid leukemia

scientific article published on 26 December 2007

Immune Activity and Response Differences of Oncolytic Viral Therapy in Recurrent Glioblastoma: Gene Expression Analyses of a Phase IB Study

scientific article published on 01 February 2022

Immunogenomics of Hypermutated Glioblastoma: A Patient with Germline POLE Deficiency Treated with Checkpoint Blockade Immunotherapy

scientific article published on 28 September 2016

Immunological ignorance is an enabling feature of the oligo-clonal T cell response to melanoma neoantigens

scientific article published on 04 November 2019

Immunotherapeutic Challenges for Pediatric Cancers

scientific article published on 28 August 2019

Impact of mutational profiles on response of primary oestrogen receptor-positive breast cancers to oestrogen deprivation

scientific article

Infantile fibrosarcoma-like tumor driven by novel RBPMS-MET fusion consolidated with cabozantinib

scientific article published on 07 October 2020

Inherited coding variants at the CDKN2A locus influence susceptibility to acute lymphoblastic leukaemia in children

scientific article

Initial sequencing and analysis of the human genome

scientific article published on 15 February 2001

Initial sequencing and comparative analysis of the mouse genome

scientific article

Integrated Analysis of RNA and DNA from the Phase III Trial CALGB 40601 Identifies Predictors of Response to Trastuzumab-Based Neoadjuvant Chemotherapy in HER2-Positive Breast Cancer

scientific article published on 23 July 2018

Integrated RNA and DNA sequencing reveals early drivers of metastatic breast cancer

scientific article published on 26 February 2018

Integrated analysis of germline and somatic variants in ovarian cancer.

scientific article

Integrated and sequence-ordered BAC- and YAC-based physical maps for the rat genome

scientific article published in April 2004

Integrated genomic characterization of endometrial carcinoma ⬇️

scientific article published on May 2, 2013

Integrating Genetic and Genomic Testing Into Oncology Practice

scientific article published on 01 May 2020

Integration of sequence data from a Consanguineous family with genetic data from an outbred population identifies PLB1 as a candidate rheumatoid arthritis risk gene

scientific article

Landscape of somatic single nucleotide variants and indels in colorectal cancer and impact on survival

scientific article published on 20 July 2020

Large-scale sequencing and analytical processing of ESTs

scientific article

Library Quantification Using PicoGreen Fluorometry

scientific article

Library Quantification Using SYBR Green-Quantitative Polymerase Chain Reaction (qPCR).

scientific article

Library Quantification: Fluorometric Quantitation of Double-Stranded or Single-Stranded DNA Samples Using the Qubit System

scientific article

Long non-coding RNA RAMS11 promotes metastatic colorectal cancer progression

scientific article published on 01 May 2020

MYCN amplification and ATRX mutations are incompatible in neuroblastoma

scientific article published on 14 February 2020

Many mutations in one clinical-trial basket

scientific article published in February 2018

Melorheostosis: Exome sequencing of an associated dermatosis implicates postzygotic mosaicism of mutated KRAS.

scientific article published on 20 April 2017

Modernizing reference genome assemblies

scientific article

Molecular refinement of gibbon genome rearrangements

scientific article published on 21 December 2006

MuSiC: identifying mutational significance in cancer genomes

scientific article

Mutational analysis of EGFR and related signaling pathway genes in lung adenocarcinomas identifies a novel somatic kinase domain mutation in FGFR4

scientific article

Neoantigen Discovery in Human Cancers

scientific article published on March 2017

Neoantigens and genome instability: impact on immunogenomic phenotypes and immunotherapy response

scientific article published on 20 November 2019

New additions to the cancer precision medicine toolkit

scientific article published on 13 April 2018

New strategies and emerging technologies for massively parallel sequencing: applications in medical research

scientific article

Next-Generation Sequencing Technologies

scientific article published on 01 November 2019

Next-generation DNA sequencing methods

scientific article

Next-generation cancer genomics.

scientific article

Next-generation sequencing identifies the natural killer cell microRNA transcriptome.

scientific article

Next-generation sequencing of cancer genomes: back to the future.

scientific article

Next-generation sequencing platforms

scientific article published on January 2013

Next-generation sequencing, cancer and molecular diagnostics: an interview with Elaine Mardis

scientific article

No evidence that G6PD deficiency affects the efficacy or safety of daunorubicin in acute lymphoblastic leukemia induction therapy

scientific article published on 07 March 2019

Novel MEK1 mutation identified by mutational analysis of epidermal growth factor receptor signaling pathway genes in lung adenocarcinoma

scientific article published on July 2008

Novel mutations target distinct subgroups of medulloblastoma.

scientific article

Novel venom gene discovery in the platypus.

scientific article published on 29 September 2010

Optimizing cancer genome sequencing and analysis

scientific article published in September 2015

Oral Cavity Squamous Cell Carcinoma Xenografts Retain Complex Genotypes and Intertumor Molecular Heterogeneity.

scientific article published in August 2018

Orthotopic patient-derived xenografts of paediatric solid tumours

scientific article published on 30 August 2017

PAM50 gene signatures and breast cancer prognosis with adjuvant anthracycline- and taxane-based chemotherapy: correlative analysis of C9741 (Alliance).

scientific article

PGRNseq: a targeted capture sequencing panel for pharmacogenetic research and implementation

scientific article published on 05 January 2016

Panton-Valentine Leukocidin-positive methicillin-resistant Staphylococcus aureus lung infection in patients with cystic fibrosis

scientific article

PathScan: a tool for discerning mutational significance in groups of putative cancer genes

scientific article

Patterns and functional implications of rare germline variants across 12 cancer types

scientific article

Pediatric cancer: case studies illustrate mechanisms to address significant challenges

scientific article published on 23 October 2019

PolyScan: an automatic indel and SNP detection approach to the analysis of human resequencing data

scientific article

Precision oncogenomics.

scientific article published in April 2019

Predicting response and survival in chemotherapy-treated triple-negative breast cancer.

scientific article

Preparation of a 3-kb Mate-Pair Library for Illumina Sequencing

scientific article

Preparation of an 8-kb Mate-Pair Library for Illumina Sequencing

scientific article

Preparing Plasmid Subclones for Capillary Sequencing

scientific article

Preparing Polymerase Chain Reaction (PCR) Products for Capillary Sequencing

scientific article published in November 2016

RB1 gene inactivation by chromothripsis in human retinoblastoma

scientific article published on January 2014

RNA Sequencing of Tumor-Associated Microglia Reveals Ccl5 as a Stromal Chemokine Critical for Neurofibromatosis-1 Glioma Growth.

scientific article

RNA-Seq: RNA Conversion to cDNA and Amplification

scientific article

RNA-sequencing reveals oligodendrocyte and neuronal transcripts in microglia relevant to central nervous system disease

scientific article

Rapid expansion of preexisting nonleukemic hematopoietic clones frequently follows induction therapy for de novo AML.

scientific article published on 2 December 2015

Rare Variation in TET2 Is Associated with Clinically Relevant Prostate Carcinoma in African Americans

scientific article published on 2 August 2016

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

scientific article published in Nature Communications

Recurrent mutations in the U2AF1 splicing factor in myelodysplastic syndromes

scientific article published on 11 December 2011

Recurrent somatic structural variations contribute to tumorigenesis in pediatric osteosarcoma.

scientific article

Recurring mutations found by sequencing an acute myeloid leukemia genome

scientific article

Reduced PU.1 expression causes myeloid progenitor expansion and increased leukemia penetrance in mice expressing PML-RARalpha.

scientific article

Research-based PAM50 signature and long-term breast cancer survival

scientific article published on 21 September 2019

Resistance promoting effects of ependymoma treatment revealed through genomic analysis of multiple recurrences in a single patient

scientific article published on 13 February 2018

Retrotransposons Are the Major Contributors to the Expansion of the Drosophila ananassae Muller F Element.

scientific article published on 30 June 2017

Revolutionizing cancer care with next-generation sequencing: an interview with Elaine Mardis

scientific article published on March 2014

Role of TP53 mutations in the origin and evolution of therapy-related acute myeloid leukaemia.

scientific article

Samovar: Single-Sample Mosaic Single-Nucleotide Variant Calling with Linked Reads

scientific article published on 29 May 2019

SciClone: inferring clonal architecture and tracking the spatial and temporal patterns of tumor evolution

scientific article (publication date: August 2014)

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

scientific article

Sequencing a mouse acute promyelocytic leukemia genome reveals genetic events relevant for disease progression

scientific article

Sequencing human-gibbon breakpoints of synteny reveals mosaic new insertions at rearrangement sites

scientific article

Sequencing the AML genome, transcriptome, and epigenome

scientific article

Solution-Phase Exome Capture

scientific article

Somatic SLC35A2 mosaicism correlates with clinical findings in epilepsy brain tissue

scientific article published on 17 June 2020

Somatic histone H3 alterations in pediatric diffuse intrinsic pontine gliomas and non-brainstem glioblastomas

scientific article

Somatic mutations affect key pathways in lung adenocarcinoma

scientific article

Somatic mutations and germline sequence variants in the expressed tyrosine kinase genes of patients with de novo acute myeloid leukemia

scientific article published on 12 February 2008

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

scientific article published on 6 June 2018

Somatic neurofibromatosis type 1 (NF1) inactivation characterizes NF1-associated pilocytic astrocytoma

scientific article published on 5 December 2012

Somatic variation as an incidental finding in the pediatric next-generation sequencing era

scientific article published on 29 October 2021

SomaticSniper: identification of somatic point mutations in whole genome sequencing data ⬇️

scientific article published on December 6, 2011

TP53 Germline Variations Influence the Predisposition and Prognosis of B-Cell Acute Lymphoblastic Leukemia in Children

scientific article published on 4 January 2018

TYK2 protein-coding variants protect against rheumatoid arthritis and autoimmunity, with no evidence of major pleiotropic effects on non-autoimmune complex traits

scientific article

Targetable kinase-activating lesions in Ph-like acute lymphoblastic leukemia

scientific article

Targeting oxidative stress in embryonal rhabdomyosarcoma.

scientific article published on December 2013

Temporally Distinct PD-L1 Expression by Tumor and Host Cells Contributes to Immune Escape

scientific article published on 10 January 2017

The $1,000 genome, the $100,000 analysis?

scientific article (publication date: 26 November 2010)

The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma

article

The Clonal Evolution of Metastatic Osteosarcoma as Shaped by Cisplatin Treatment

scientific article published on 16 January 2019

The DNA sequence of human chromosome 7

scientific article

The Dynamic Epigenetic Landscape of the Retina During Development, Reprogramming, and Tumorigenesis.

scientific article published in May 2017

The Dynamic Genome and Transcriptome of the Human Fungal Pathogen Blastomyces and Close Relative Emmonsia

scientific article published on 6 October 2015

The Impact of Next-Generation Sequencing on Cancer Genomics: From Discovery to Clinic

scientific article published on 03 September 2019

The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes

scientific article

The Oxytricha trifallax mitochondrial genome

scientific article

The Pediatric Cancer Genome Project ⬇️

scientific article published on May 29, 2012

The challenges of big data

scientific article

The chromosome 3p21.3-encoded gene, LIMD1, is a critical tumor suppressor involved in human lung cancer development

scholarly article

The clonal evolution of metastatic colorectal cancer

scientific article published on 10 June 2020

The complete genome sequence of a chronic atrophic gastritis Helicobacter pylori strain: evolution during disease progression

scientific article

The draft genome of the parasitic nematode Trichinella spiralis

scientific article

The emerging clinical relevance of genomics in cancer medicine

scientific article

The era of precision oncogenomics.

scientific article published on 2 April 2018

The functional spectrum of low-frequency coding variation ⬇️

scientific article published on September 14, 2011

The genetic basis of early T-cell precursor acute lymphoblastic leukaemia

scientific article

The genome of a songbird

scientific article

The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics

scientific article published in November 2003

The genomic landscape of childhood and adolescent melanoma.

scientific article published on 30 September 2014

The genomic landscape of core-binding factor acute myeloid leukemias

scientific article

The genomic landscape of diffuse intrinsic pontine glioma and pediatric non-brainstem high-grade glioma

scientific article

The genomic landscape of hypodiploid acute lymphoblastic leukemia

scientific article published on 20 January 2013

The genomics education partnership: successful integration of research into laboratory classes at a diverse group of undergraduate institutions.

scientific article

The impact of next-generation sequencing technology on genetics

scientific article

The landscape of somatic mutations in epigenetic regulators across 1,000 paediatric cancer genomes.

scientific article

The landscape of somatic mutations in infant MLL-rearranged acute lymphoblastic leukemias

scientific article

The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes

scientific article by Lucinda Fulton and Elaine Mardis

The next-generation sequencing revolution and its impact on genomics

scientific article published on September 2013

The prognostic effects of somatic mutations in ER-positive breast cancer

scientific article published in Nature Communications

The repetitive landscape of the chicken genome

scientific article published on 15 July 2004

The translation of cancer genomics: time for a revolution in clinical cancer care

scientific article

The value of avian genomics to the conservation of wildlife

scientific article (publication date: 14 July 2009)

The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage.

scientific article

Transcriptome analysis for Caenorhabditis elegans based on novel expressed sequence tags

scientific article

Transcriptome-wide identification of novel imprinted genes in neonatal mouse brain

scientific article

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

scientific article published on September 2016

Tumor Evolution in Two Patients with Basal-like Breast Cancer: A Retrospective Genomics Study of Multiple Metastases

scientific article

Tumor heterogeneity: next-generation sequencing enhances the view from the pathologist's microscope

scientific article

Tumor neoantigens: building a framework for personalized cancer immunotherapy

scientific article

Use of whole-genome sequencing to diagnose a cryptic fusion oncogene

scientific article

VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing

scientific article

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

scientific article

Viral Discovery and Sequence Recovery Using DNA Microarrays ⬇️

scientific article published on November 17, 2003

Visualizing tumor evolution with the fishplot package for R

scientific article

What is finished, and why does it matter

scientific article

What is the future of electrophoresis in large-scale genomic sequencing?

scientific article published on October 2006

What's different about women's health?

scientific article

Where Next for Genetics and Genomics?

scientific article

Whole genome analyses reveal no pathogenetic single nucleotide or structural differences between monozygotic twins discordant for amyotrophic lateral sclerosis.

scientific article

Whole-Genome Sequencing: Automated, Indexed Library Preparation

scientific article

Whole-Genome Sequencing: Automated, Nonindexed Library Preparation

scientific article

Whole-Genome Sequencing: Manual Library Preparation

scientific article

Whole-exome sequencing identifies rare, functional CFH variants in families with macular degeneration

scientific article

Whole-genome analysis informs breast cancer response to aromatase inhibition

scientific article

Whole-genome sequencing and variant discovery in C. elegans.

scientific article

Whole-genome sequencing identifies genetic alterations in pediatric low-grade gliomas

scientific article published on 14 April 2013

Xenografts as models of clonal selection and acquired resistance to therapy

scientific article

YAP1-FAM118B Fusion Defines a Rare Subset of Childhood and Young Adulthood Meningiomas

scientific article published on 16 October 2020

cDNA hybrid capture improves transcriptome analysis on low-input and archived samples

scientific article

contribution of genetically restricted, methicillin-susceptible strains to the ongoing epidemic of community-acquired Staphylococcus aureus infections.

scientific article

miRNAs and Long-term Breast Cancer Survival: Evidence from the WHEL Study

scientific article published on 11 June 2019

pVAC-Seq: A genome-guided in silico approach to identifying tumor neoantigens

scientific article published on 29 January 2016

pVACtools: A Computational Toolkit to Identify and Visualize Cancer Neoantigens

scientific article published on 06 January 2020

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