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List of works by David E Root

( R )-2-Hydroxyglutarate Is Sufficient to Promote Leukemogenesis and Its Effects Are Reversible ⬇️

scientific article published on 07 February 2013

A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines

scientific article published on 3 October 2017

A Compendium of Genetic Modifiers of Mitochondrial Dysfunction Reveals Intra-organelle Buffering

scientific article published on 01 November 2019

A Functional Landscape of Resistance to MEK1/2 and CDK4/6 Inhibition in NRAS-Mutant Melanoma

scientific article published on 28 February 2019

A Genome-wide CRISPR Death Screen Identifies Genes Essential for Oxidative Phosphorylation

scientific article published on 9 September 2016

A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles.

scientific article published in November 2017

A comprehensive platform for highly multiplexed mammalian functional genetic screens

scientific article

A dominant-negative effect drives selection of TP53 missense mutations in myeloid malignancies

scientific article published on 01 August 2019

A flexible data analysis tool for chemical genetic screens.

scientific article

A functional landscape of resistance to ALK inhibition in lung cancer

scientific article

A genome-scale CRISPR screen identifies the ERBB and mTOR signalling networks as key determinants of response to PI3K inhibition in pancreatic cancer

scientific article published on 05 May 2020

A genome-scale RNA interference screen implicates NF1 loss in resistance to RAF inhibition

scientific article

A genome-wide RNAi screen identifies multiple RSK-dependent regulators of cell migration

scientific article

A genome-wide gain-of-function screen identifies CDKN2C as a HBV host factor

scientific article published on 01 June 2020

A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen

scientific article (publication date: 24 March 2006)

A melanocyte lineage program confers resistance to MAP kinase pathway inhibition

scientific article published on 3 November 2013

A molecular network of the aging human brain provides insights into the pathology and cognitive decline of Alzheimer’s disease

article

A physical and regulatory map of host-influenza interactions reveals pathways in H1N1 infection

scientific article

A public genome-scale lentiviral expression library of human ORFs

scientific article

A targeted RNA interference screen reveals novel epigenetic factors that regulate herpesviral gene expression

scientific article published on 04 February 2014

AKT-independent signaling downstream of oncogenic PIK3CA mutations in human cancer

scientific article

ATARiS: computational quantification of gene suppression phenotypes from multisample RNAi screens

scientific article

Acquired FGFR and FGF alterations confer resistance to estrogen receptor (ER) targeted therapy in ER+ metastatic breast cancer

scientific article published on 28 July 2020

Agreement between two large pan-cancer CRISPR-Cas9 gene dependency data sets

scientific article published on 20 December 2019

Aire-dependent genes undergo Clp1-mediated 3'UTR shortening associated with higher transcript stability in the thymus

scientific article published on 27 April 2020

Amplification of CRKL induces transformation and epidermal growth factor receptor inhibitor resistance in human non-small cell lung cancers

scientific article

An RNAi screen for Aire cofactors reveals a role for Hnrnpl in polymerase release and Aire-activated ectopic transcription

scientific article published on 16 January 2014

An alternative splicing switch in FLNB promotes the mesenchymal cell state in human breast cancer

scientific article published on 30 July 2018

An epigenetic mechanism of resistance to targeted therapy in T cell acute lymphoblastic leukemia

scientific article

BAF Complex Maintains Glioma Stem Cells in Pediatric H3K27M Glioma

scientific article published in 2022

BIOL-04. INTEGRATED COPY-NUMBER AND CANCER DEPENDENCY ANALYSIS REVEALS ALTERED SPLICEOSOME STOICHIOMETRY AS A NOVEL VULNERABILITY IN GENOMICALLY DISRUPTED CANCERS.

scientific article published on 31 May 2017

Biological Mechanism Profiling Using an Annotated Compound Library ⬇️

scientific article published on September 1, 2003

Bromodomain Inhibitors Correct Bioenergetic Deficiency Caused by Mitochondrial Disease Complex I Mutations

scientific article published on 15 September 2016

CDK8 is a colorectal cancer oncogene that regulates beta-catenin activity

scientific article

CK1epsilon is required for breast cancers dependent on beta-catenin activity

scientific article

COT drives resistance to RAF inhibition through MAP kinase pathway reactivation

scientific article (publication date: 16 December 2010)

CREB5 Promotes Resistance to Androgen-Receptor Antagonists and Androgen Deprivation in Prostate Cancer

scientific article published on 01 November 2019

CRISPR-Cas9 screen reveals a MYCN-amplified neuroblastoma dependency on EZH2.

scientific article published on 4 December 2017

CRISPR/Cas9 Screens Reveal Epstein-Barr Virus-Transformed B Cell Host Dependency Factors

scientific article published on May 2017

Cancer vulnerabilities unveiled by genomic loss

scientific article

Cells Lacking the RB1 Tumor Suppressor Gene are Hyperdependent on Aurora B Kinase for Survival

article

Combined Pan-RAF and MEK Inhibition Overcomes Multiple Resistance Mechanisms to Selective RAF Inhibitors.

scientific article

Complementary information derived from CRISPR Cas9 mediated gene deletion and suppression

scientific article published on 23 May 2017

Computational correction of copy number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells.

scientific article

Conserved pathways within bacteria and yeast as revealed by global protein network alignment

scientific article

Control of cyclin D1 and breast tumorigenesis by the EglN2 prolyl hydroxylase

scientific article

Copy-number and gene dependency analysis reveals partial copy loss of wild-type SF3B1 as a novel cancer vulnerability.

scientific article

Correction: Mitochondrial and nuclear genomic responses to loss of LRPPRC expression

scientific article published on 01 April 2020

Corrigendum: PARP3 is a promoter of chromosomal rearrangements and limits G4 DNA.

scientific article published on 13 June 2017

Creation of Novel Protein Variants with CRISPR/Cas9-Mediated Mutagenesis: Turning a Screening By-Product into a Discovery Tool

scientific article

Csnk1a1 inhibition has p53-dependent therapeutic efficacy in acute myeloid leukemia.

scientific article

DOT1L inhibits SIRT1-mediated epigenetic silencing to maintain leukemic gene expression in MLL-rearranged leukemia.

scientific article

DYNLL1 binds to MRE11 to limit DNA end resection in BRCA1-deficient cells

scientific article published in Nature

Defining a Cancer Dependency Map.

scientific article

Defining the landscape of ATP-competitive inhibitor resistance residues in protein kinases

scientific article published on 10 January 2020

Detecting Spatial Patterns in Biological Array Experiments ⬇️

scientific article published on August 1, 2003

Electronic absorption spectroscopy of copper proteins

scientific article

Evaluation of RNAi and CRISPR technologies by large-scale gene expression profiling in the Connectivity Map.

scientific article

Functional Genomics Identifies Metabolic Vulnerabilities in Pancreatic Cancer

scientific article published on 28 October 2020

Functional genomics identifies negative regulatory nodes controlling phagocyte oxidative burst

scientific article

Functional genomics reveal that the serine synthesis pathway is essential in breast cancer

scientific article

Functional proteogenomics reveals biomarkers and therapeutic targets in lymphomas.

scientific article published on 12 June 2017

Functional screen of MSI2 interactors identifies an essential role for SYNCRIP in myeloid leukemia stem cells

scientific article

Gene sets identified with oncogene cooperativity analysis regulate in vivo growth and survival of leukemia stem cells.

scientific article

Gene-centric functional dissection of human genetic variation uncovers regulators of hematopoiesis

Gene-centric functional dissection of human genetic variation uncovers regulators of hematopoiesis

scientific article published on 09 May 2019

Genetic and Proteomic Interrogation of Lower Confidence Candidate Genes Reveals Signaling Networks in β-Catenin-Active Cancers

scientific article published on September 2016

Genetic modifiers of EGFR dependence in non-small cell lung cancer

scientific article

Genome-scale CRISPR-Cas9 knockout screening in human cells

scientific article (publication date: 3 January 2014)

Genome-scale loss-of-function screening with a lentiviral RNAi library

scientific article published in September 2006

Genomic Copy Number Dictates a Gene-Independent Cell Response to CRISPR/Cas9 Targeting

scientific article published on 3 June 2016

Global analysis of large-scale chemical and biological experiments.

scientific article

HDAC5 controls MEF2C-driven sclerostin expression in osteocytes

scientific article

HIF activation causes synthetic lethality between the VHL tumor suppressor and the EZH1 histone methyltransferase.

scientific article published in July 2017

High content image analysis identifies novel regulators of synaptogenesis in a high-throughput RNAi screen of primary neurons

scientific article (publication date: 2014)

High-Throughput Platform for Identifying Molecular Factors Involved in Phenotypic Stabilization of Primary Human Hepatocytes In Vitro.

scientific article

High-throughput Phenotyping of Lung Cancer Somatic Mutations

scientific article published on 28 July 2016

High-throughput Phenotyping of Lung Cancer Somatic Mutations

scientific article published in December 2017

Highly parallel identification of essential genes in cancer cells

scholarly article

Identification of RPS14 as a 5q- syndrome gene by RNA interference screen

scientific article

Identification of an oncogenic RAB protein

scientific article published on 3 September 2015

Identification of regulators of polyploidization presents therapeutic targets for treatment of AMKL

scientific article

Improved estimation of cancer dependencies from large-scale RNAi screens using model-based normalization and data integration

scientific article published in Nature Communications

In Vivo RNAi screening identifies a leukemia-specific dependence on integrin beta 3 signaling

scientific article published on 13 June 2013

In vivo CRISPR screening identifies Ptpn2 as a cancer immunotherapy target.

scientific article published on 19 July 2017

In vivo discovery of immunotherapy targets in the tumour microenvironment

scientific article

In vivo multiplexed interrogation of amplified genes identifies GAB2 as an ovarian cancer oncogene

scientific article published on 02 January 2014

Indoprofen upregulates the survival motor neuron protein through a cyclooxygenase-independent mechanism

scientific article

Inducible RNAi in vivo reveals that the transcription factor BATF is required to initiate but not maintain CD8+ T-cell effector differentiation

scientific article

Integrated genetic and pharmacologic interrogation of rare cancers

scientific article

Integrative genomic approaches identify IKBKE as a breast cancer oncogene

scientific article

KRAS and YAP1 converge to regulate EMT and tumor survival

scientific article

MTAP deletion confers enhanced dependency on the PRMT5 arginine methyltransferase in cancer cells

scientific article published on 11 February 2016

Malaria. A forward genetic screen identifies erythrocyte CD55 as essential for Plasmodium falciparum invasion ⬇️

scientific article published on May 2015

Metabolic and functional genomic studies identify deoxythymidylate kinase as a target in LKB1-mutant lung cancer

scientific article published on 28 May 2013

MicroSCALE screening reveals genetic modifiers of therapeutic response in melanoma

scientific article

Minimizing the risk of reporting false positives in large-scale RNAi screens

article

Morphological Profiles of RNAi-Induced Gene Knockdown Are Highly Reproducible but Dominated by Seed Effects

scientific article published on 21 July 2015

Mutational processes shape the landscape of TP53 mutations in human cancer.

scientific article

Neuronal differentiation and cell-cycle programs mediate response to BET-bromodomain inhibition in MYC-driven medulloblastoma

scientific article published on 03 June 2019

Nitric Oxide Engages an Anti-inflammatory Feedback Loop Mediated by Peroxiredoxin 5 in Phagocytes

scientific article published on 01 July 2018

Noncanonical open reading frames encode functional proteins essential for cancer cell survival

scientific article published on 28 January 2021

Optimized libraries for CRISPR-Cas9 genetic screens with multiple modalities

scientific article published in Nature Communications

Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9.

scientific article published on 18 January 2016

Orthologous CRISPR-Cas9 enzymes for combinatorial genetic screens.

scientific article

PARP3 is a promoter of chromosomal rearrangements and limits G4 DNA.

scientific article

PIK3CA mutant tumors depend on oxoglutarate dehydrogenase

scientific article published on 10 April 2017

PPM1D mutations are oncogenic drivers of de novo diffuse midline glioma formation

scientific article published on 01 February 2022

Parallel genome-scale loss of function screens in 216 cancer cell lines for the identification of context-specific genetic dependencies

scientific article published on 30 September 2014

Parallel genome-scale loss of function screens in 216 cancer cell lines for the identification of context-specific genetic dependencies

scientific article published on 11 November 2014

Phenotypic Characterization of a Comprehensive Set of MAPK1/ERK2 Missense Mutants

scientific article published on October 2016

Pooled Lentiviral-Delivery Genetic Screens

scientific article published on 16 January 2018

Progression signature underlies clonal evolution and dissemination of multiple myeloma

scientific article published on 04 November 2020

Proteomic and genetic approaches identify Syk as an AML target

scientific article

Rational design of highly active sgRNAs for CRISPR-Cas9-mediated gene inactivation.

scientific article

Receptor tyrosine kinases fall into distinct classes based on their inferred signaling networks

scientific article (publication date: 16 July 2013)

Regulated ADAM17-dependent EGF family ligand release by substrate-selecting signaling pathways ⬇️

scientific article published on May 29, 2013

Regulation of Cellular Heterogeneity and Rates of Symmetric and Asymmetric Divisions in Triple-Negative Breast Cancer

scientific article published on 01 September 2018

Renal medullary carcinomas depend upon loss and are sensitive to proteasome inhibition

scientific article published on 12 March 2019

Requirement for CDK6 in MLL-rearranged acute myeloid leukemia

scientific article

Resources for the design of CRISPR gene editing experiments

scientific article

SQSTM1 is a pathogenic target of 5q copy number gains in kidney cancer

scientific article published on December 2013

Scoring diverse cellular morphologies in image-based screens with iterative feedback and machine learning

scientific article

Selective Modulation of a Pan-Essential Protein as a Therapeutic Strategy in Cancer

publication published on 21 April 2021

Selective gene dependencies in MYCN-amplified neuroblastoma include the core transcriptional regulatory circuitry

article

Small-Molecule and CRISPR Screening Converge to Reveal Receptor Tyrosine Kinase Dependencies in Pediatric Rhabdoid Tumors

scientific article published on 01 August 2019

Small-molecule targeting of brachyury transcription factor addiction in chordoma

scientific article published on 21 January 2019

Subtype-specific genomic alterations define new targets for soft-tissue sarcoma therapy

scientific article

Synergistic interactions with PI3K inhibition that induce apoptosis.

scientific article

Synthetic Lethal Interaction between the ESCRT Paralog Enzymes VPS4A and VPS4B in Cancers Harboring Loss of Chromosome 18q or 16q

scientific article published on 01 December 2020

Synthetic Lethal Interaction of SHOC2 Depletion with MEK Inhibition in RAS-Driven Cancers

scientific article published on 01 October 2019

Synthetic lethal interaction between oncogenic KRAS dependency and STK33 suppression in human cancer cells

scientific article

Synthetic lethal screening in the mammalian central nervous system identifies Gpx6 as a modulator of Huntington's disease

scientific article

Systematic Functional Interrogation of Rare Cancer Variants Identifies Oncogenic Alleles

scientific article

Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1

scientific article (publication date: 5 November 2009)

Systematic discovery of TLR signaling components delineates viral-sensing circuits

scientific article

Systematic investigation of genetic vulnerabilities across cancer cell lines reveals lineage-specific dependencies in ovarian cancer

scientific article

Targetable vulnerabilities in T- and NK-cell lymphomas identified through preclinical models.

scientific article published on 22 May 2018

Targeted shRNA screening identified critical roles of pleckstrin-2 in erythropoiesis.

scientific article

Targeted tumor-penetrating siRNA nanocomplexes for credentialing the ovarian cancer oncogene ID4

scientific article published on August 2012

The Canonical Wnt Pathway Drives Macropinocytosis in Cancer

scientific article published on 05 June 2018

The JAK2/STAT3 signaling pathway is required for growth of CD44+CD24– stem cell–like breast cancer cells in human tumors ⬇️

scientific article published on July 1, 2011

The bromodomain protein Brd4 insulates chromatin from DNA damage signalling

scientific article

The landscape of cancer cell line metabolism

scientific article published on 08 May 2019

The master regulator of the cellular stress response (HSF1) is critical for orthopoxvirus infection

scientific article (publication date: February 2014)

The receptor TREML4 amplifies TLR7-mediated signaling during antiviral responses and autoimmunity

scientific article

Towards patient-based cancer therapeutics

scientific article

Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses

scientific article

WRN helicase is a synthetic lethal target in microsatellite unstable cancers

scientific article published on 10 April 2019

Wilms tumor 1 (WT1) regulates KRAS-driven oncogenesis and senescence in mouse and human models.

scientific article

ZFHX4 interacts with the NuRD core member CHD4 and regulates the glioblastoma tumor-initiating cell state

scientific journal article

lincRNAs act in the circuitry controlling pluripotency and differentiation

scientific article (publication date: 28 August 2011)

miRNA-embedded shRNAs for Lineage-specific BCL11A Knockdown and Hemoglobin F Induction

scientific article published on 17 June 2015

β-Catenin-driven cancers require a YAP1 transcriptional complex for survival and tumorigenesis

scientific article

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