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List of works by Malachi Griffith

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 Spontaneous Aggressive ERα+ Mammary Tumor Model Is Driven by Kras Activation

scientific article published on 01 August 2019

A case of acute myeloid leukemia with promyelocytic features characterized by expression of a novel RARG-CPSF6 fusion

scientific article published on 01 June 2018

A common founding clone with TP53 and PTEN mutations gives rise to a concurrent germ cell tumor and acute megakaryoblastic leukemia

scientific article

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

scientific article

A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer

scientific article published on 03 April 2020

ALEXA: a microarray design platform for alternative expression analysis

article

Abstract 2608: Global integration of knowledgebases for clinical interpretation of cancer variants

Accounting for proximal variants improves neoantigen prediction

scientific article published on 03 December 2018

Adapting crowdsourced clinical cancer curation in CIViC to the ClinGen minimum variant level data community-driven standards

scientific article published on 01 November 2018

Alternative expression analysis by RNA sequencing

scientific article published on 12 September 2010

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

scientific article published on 29 September 2006

Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells

scientific article

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

scientific article published on 09 August 2016

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

scientific article

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

scientific article published in Nature Communications

Author response: Wikidata as a knowledge graph for the life sciences

scholarly article, peer review and author response published on 24 January 2020

Best practices for bioinformatic characterization of neoantigens for clinical utility

scientific article published on 28 August 2019

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

CIViCpy: A Python Software Development and Analysis Toolkit for the CIViC Knowledgebase

scientific article published on 01 March 2020

Cancer Immunogenomics: Computational Neoantigen Identification and Vaccine Design.

scientific article published on 7 April 2017

ClinGen Cancer Somatic Working Group - standardizing and democratizing access to cancer molecular diagnostic data to drive translational research

scientific article published in January 2018

Clinical implications of neoepitope landscapes for adult and pediatric cancers

scientific article published on 31 August 2017

Clonal architectures and driver mutations in metastatic melanomas

scientific article

Collaborative, Multidisciplinary Evaluation of Cancer Variants Through Virtual Molecular Tumor Boards Informs Local Clinical Practices

scientific article published on 01 July 2020

Comprehensive discovery of noncoding RNAs in acute myeloid leukemia cell transcriptomes

scientific article

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

scientific article

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

scientific article

Correction: Neoadjuvant and Adjuvant Pembrolizumab in Resectable Locally Advanced, Human Papillomavirus-unrelated Head and Neck Cancer: A Multicenter, Phase II Trial

scientific article published on 01 January 2021

DGIdb 3.0: a redesign and expansion of the drug-gene interaction database

scientific article published on 16 November 2017

DGIdb 5.0: rebuilding the drug–gene interaction database for precision medicine and drug discovery platforms

scientific article published on 11 November 2023

DGIdb: mining the druggable genome

scientific article published on 13 October 2013

De novo assembly and analysis of RNA-seq data.

scientific article

DoCM: a database of curated mutations in cancer.

scientific article

Donor-Derived Follicular Lymphoma After Kidney Transplantation: A Case Report

scientific article published in September 2023

Epigenetic and transcriptional determinants of the human breast

scientific article

Epigenomic regulation of human T-cell leukemia virus by chromatin-insulator CTCF

scientific article published on 21 May 2021

Erratum to: Modeling precision treatment of breast cancer

scientific article published on 12 May 2015

Escherichia coli endA deletion strain for use in two-hybrid shuttle vector selection

scientific article published on 01 August 2003

Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors

scientific article

Extensive relationship between antisense transcription and alternative splicing in the human genome.

scientific article

F11R is a novel monocyte prognostic biomarker for malignant glioma

scientific article

Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma

scientific article

Functional heterogeneity of genetically defined subclones in acute myeloid leukemia

scientific article published on 06 March 2014

GA4GH: International policies and standards for data sharing across genomic research and healthcare

scientific article published on 10 November 2021

GenVisR: Genomic Visualizations in R

scientific article published on 10 June 2016

GenVisR: Genomic Visualizations in R

scholarly article published 15 March 2016

Genetic Ancestry Correlations with Driver Mutations Suggest Complex Interactions between Somatic and Germline Variation in Cancer

scientific article published in March 2021

Genome Modeling System: A Knowledge Management Platform for Genomics

scientific article published on 9 July 2015

Genomic analysis of a rare human tumor

scientific article published on 23 July 2010

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

scientific article published on September 2012

Hippo signaling influences HNF4A and FOXA2 enhancer switching during hepatocyte differentiation

scientific article

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

scientific article published on 04 November 2019

Impact of whole genome amplification on analysis of copy number variants

scientific article

In-depth characterization of the microRNA transcriptome in a leukemia progression model

scientific article published on 10 October 2008

Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud

scientific article

Integration of the Drug-Gene Interaction Database (DGIdb 4.0) with open crowdsource efforts

scientific article published on 25 November 2020

Interaction of cyclin-dependent kinase 12/CrkRS with cyclin K1 is required for the phosphorylation of the C-terminal domain of RNA polymerase II

scientific article

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

scientific article published on 20 April 2017

Modeling precision treatment of breast cancer

scientific article published on January 2013

Mutant U2AF1 Expression Alters Hematopoiesis and Pre-mRNA Splicing In Vivo

scientific article published on May 2015

NeoPalAna: Neoadjuvant Palbociclib, a Cyclin-Dependent Kinase 4/6 Inhibitor, and Anastrozole for Clinical Stage 2 or 3 Estrogen Receptor-Positive Breast Cancer

scientific article published on 7 March 2017

Neoadjuvant and Adjuvant Pembrolizumab in Resectable Locally Advanced, Human Papillomavirus-Unrelated Head and Neck Cancer: A Multicenter, Phase 2 Trial

scientific article published on 14 July 2020

Neoantigen-targeted CD8+ T cell responses with PD-1 blockade therapy

scientific article published on 08 March 2023

Neoantigens in immunotherapy and personalized vaccines: Implications for head and neck squamous cell carcinoma

scientific article published on 14 October 2016

Noninvasive Detection of High-Risk Adenomas Using Stool-Derived Eukaryotic RNA Sequences as Biomarkers

scientific article published on 30 May 2019

Normalization of drug and therapeutic concepts with Thera-Py

scientific article published on 4 October 2023

Novel avian influenza H7N3 strain outbreak, British Columbia

scientific article

Novel mRNA isoforms and mutations of uridine monophosphate synthetase and 5-fluorouracil resistance in colorectal cancer

scientific article published on 17 January 2012

ORegAnno 3.0: a community-driven resource for curated regulatory annotation

scientific article

ORegAnno: an open-access community-driven resource for regulatory annotation

scientific article

Open-Sourced CIViC Annotation Pipeline to Identify and Annotate Clinically Relevant Variants Using Single-Molecule Molecular Inversion Probes

scientific article published on 01 October 2019

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

Personalized oncogenomics.

scientific article

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

scientific article

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

scientific article

Rapid progression of adult T-cell leukemia/lymphoma as tumor-infiltrating Tregs after PD-1 blockade

scientific article published on 01 October 2019

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

scientific article published in Nature Communications

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

scientific article

Reply

scientific article published on 16 November 2019

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

scientific article (publication date: August 2014)

Sequencing and analysis of 10,967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis reveals post-tetraploidization transcriptome remodeling

scientific article published on 3 May 2006

Single exon-resolution targeted chromosomal microarray analysis of known and candidate intellectual disability genes

scientific article

Single-agent ibrutinib in relapsed or refractory follicular lymphoma: a phase 2 consortium trial.

scientific article published on 26 October 2017

Splicing factor SF3B1 promotes endometrial cancer progression via regulating KSR2 RNA maturation

scientific article published on 10 October 2020

Spontaneous aggressive ERα+ mammary tumor model is driven by Kras activation

Standard operating procedure for curation and clinical interpretation of variants in cancer

scientific article published on 29 November 2019

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

scientific article published on 05 October 2018

Standard operating procedure for somatic variant refinement of tumor sequencing data

Standardizing And Democratizing Access To Cancer Molecular Diagnostic Test Data From Patients To Drive Translational Research.

scientific article

Systematic recovery and analysis of full-ORF human cDNA clones

scientific article

Text-mining clinically relevant cancer biomarkers for curation into the CIViC database

scientific article published on 03 December 2019

The GA4GH Variation Representation Specification: A computational framework for variation representation and federated identification

scientific article published on 10 November 2021

The clonal and mutational evolution spectrum of primary triple-negative breast cancers

scientific article (publication date: 4 April 2012)

The clonal evolution of metastatic colorectal cancer

scientific article published on 10 June 2020

The completion of the Mammalian Gene Collection (MGC).

scientific article published on 18 September 2009

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

scientific article published in Nature Communications

The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)

scientific article

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

scientific article published on September 2016

Wikidata as a FAIR knowledge graph for the life sciences

scholarly article posted as a preprint in BioRxiv on 11 February 2020

Wikidata as a knowledge graph for the life sciences ⬇️

scientific article published on 17 March 2020

Yap1 Mediates Trametinib Resistance in Head and Neck Squamous Cell Carcinomas

scientific article published on 05 February 2021

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

scientific article

deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data

scientific article

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

scientific article published on 29 January 2016

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