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List of works by Ernest Fraenkel

A Multi-Omics Interpretable Machine Learning Model Reveals Modes of Action of Small Molecules

scientific article published on 22 January 2020

A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data.

scientific article

A multi-omic analysis of MCF10A cells provides a resource for integrative assessment of ligand-mediated molecular and phenotypic responses

scientific article published in 2022

A quantitative model of transcriptional regulation reveals the influence of binding location on expression

scientific article

A small domain of CBP/p300 binds diverse proteins: solution structure and functional studies

scientific article

APOE4 is Associated with Differential Regional Vulnerability to Bioenergetic Deficits in Aged APOE Mice

scientific article published on 09 March 2020

Aberrant Development Corrected in Adult-Onset Huntington's Disease iPSC-Derived Neuronal Cultures via WNT Signaling Modulation

scientific article published on 27 February 2020

An improved map of conserved regulatory sites for Saccharomyces cerevisiae

scientific article

Analysis of in vitro insulin-resistance models and their physiological relevance to in vivo diet-induced adipose insulin resistance

scientific article published on 03 October 2013

Answer ALS, a large-scale resource for sporadic and familial ALS combining clinical and multi-omics data from induced pluripotent cell lines

scientific article published on 03 February 2022

Aromatic-aromatic interactions in the zinc finger motif. Analysis of the two-dimensional nuclear magnetic resonance structure of a mutant domain

scientific article published on June 1992

Assembly of a functional beta interferon enhanceosome is dependent on ATF-2-c-jun heterodimer orientation

scientific article

Bmi1 promotes erythroid development through regulating ribosome biogenesis

scientific article published on March 2015

Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity

scientific article

Cell freezing protocol suitable for ATAC-Seq on motor neurons derived from human induced pluripotent stem cells.

scientific article published on 5 May 2016

Comparative proteomic analysis highlights metabolic dysfunction in α-synucleinopathy

scientific article published on 11 December 2020

Comparison of X-ray and NMR structures for the Antennapedia homeodomain-DNA complex

scientific article

Compounds from an unbiased chemical screen reverse both ER-to-Golgi trafficking defects and mitochondrial dysfunction in Parkinson's disease models

scientific article

Computational discovery of gene modules and regulatory networks

scientific article published on 12 October 2003

Control of pancreas and liver gene expression by HNF transcription factors

scientific article

Core transcriptional regulatory circuitry in human hepatocytes

scientific article published on 2 May 2006

DiSCoVERing Innovative Therapies for Rare Tumors: Combining Genetically Accurate Disease Models with In Silico Analysis to Identify Novel Therapeutic Targets

scientific article published on 24 March 2016

Direct recruitment of polycomb repressive complex 1 to chromatin by core binding transcription factors.

scientific article

Discovering Altered Regulation and Signaling Through Network-based Integration of Transcriptomic, Epigenomic, and Proteomic Tumor Data.

scientific article published in January 2018

Elucidating MicroRNA Regulatory Networks Using Transcriptional, Post-transcriptional, and Histone Modification Measurements

scientific article published on 30 December 2015

Engrailed homeodomain-DNA complex at 2.2 A resolution: a detailed view of the interface and comparison with other engrailed structures

scientific article

Extensive changes in DNA methylation are associated with expression of mutant huntingtin.

scientific article published on 22 January 2013

Foxp3 occupancy and regulation of key target genes during T-cell stimulation

scientific article

Functional Genomics Approach Identifies Novel Signaling Regulators of TGFα Ectodomain Shedding

scientific article published on 10 October 2017

Genome-Scale Networks Link Neurodegenerative Disease Genes to α-Synuclein through Specific Molecular Pathways

scientific article

Genome-wide Analyses Identify KIF5A as a Novel ALS Gene

scientific article published in March 2018

Genome-wide profiling of H3K56 acetylation and transcription factor binding sites in human adipocytes

scientific article (publication date: 2011)

Genomic characterization of Wilms' tumor suppressor 1 targets in nephron progenitor cells during kidney development.

scientific article

HSF1 drives a transcriptional program distinct from heat shock to support highly malignant human cancers

scientific article

Hepatic Dysfunction Caused by Consumption of a High-Fat Diet.

scientific article published in December 2017

High-resolution computational models of genome binding events.

scientific article published on August 2006

Huntington's Disease iPSC-Derived Brain Microvascular Endothelial Cells Reveal WNT-Mediated Angiogenic and Blood-Brain Barrier Deficits

scientific article published in May 2017

Hyper- and hypo- nutrition studies of the hepatic transcriptome and epigenome suggest that PPARα regulates anaerobic glycolysis

scientific article

Identifying patterns in amyotrophic lateral sclerosis progression from sparse longitudinal data

scientific article published on 08 September 2022

Identifying therapeutic targets by combining transcriptional data with ordinal clinical measurements.

scientific article published on 20 September 2017

Insights into GATA-1-mediated gene activation versus repression via genome-wide chromatin occupancy analysis

scientific article

Integrated network analyses for functional genomic studies in cancer

scientific article published on 27 June 2013

Integrating proteomic, transcriptional, and interactome data reveals hidden components of signaling and regulatory networks

scientific article

Linking proteomic and transcriptional data through the interactome and epigenome reveals a map of oncogene-induced signaling

scientific article

MB-103DiSCoVERing INNOVATIVE THERAPIES: COMBINING GENETICALLY ACCURATE DISEASE MODELS OF MEDULLOBLASTOMA WITH ADVANCED IN SILICO ANALYSIS TO IDENTIFY NOVEL THERAPEUTIC TARGETS.

scientific article published on 30 May 2016

Multiplexed barcoded CRISPR-Cas9 screening enabled by CombiGEM.

scientific article published on 10 February 2016

Network Modeling Identifies Patient-specific Pathways in Glioblastoma.

scientific article published on 29 June 2016

Network modeling of kinase inhibitor polypharmacology reveals pathways targeted in chemical screens.

scientific article published on 12 October 2017

Network-Based Interpretation of Diverse High-Throughput Datasets through the Omics Integrator Software Package

scientific article

PCSF: An R-package for network-based interpretation of high-throughput data.

scientific article

Pathway-based network modeling finds hidden genes in shRNA screen for regulators of acute lymphoblastic leukemia

scientific article published on 17 June 2016

Poly-glutamine expanded huntingtin dramatically alters the genome wide binding of HSF1.

scientific article published on January 2012

Practical strategies for discovering regulatory DNA sequence motifs

scientific article published in April 2006

Proteomics, Post-translational Modifications, and Integrative Analyses Reveal Molecular Heterogeneity within Medulloblastoma Subgroups

scientific article published on 01 September 2018

ResponseNet: revealing signaling and regulatory networks linking genetic and transcriptomic screening data

scientific article

Revealing disease-associated pathways by network integration of untargeted metabolomics.

scientific article published on August 2016

SAMNet: a network-based approach to integrate multi-dimensional high throughput datasets ⬇️

scientific article published on November 1, 2012

SAMNetWeb: identifying condition-specific networks linking signaling and transcription

scientific article

SOX2 co-occupies distal enhancer elements with distinct POU factors in ESCs and NPCs to specify cell state

scientific article

Sequence analysis of chromatin immunoprecipitation data for transcription factors.

scientific article

Shallow Sparsely-Connected Autoencoders for Gene Set Projection

article

Sharing information to reconstruct patient-specific pathways in heterogeneous diseases

scientific article published on January 2014

Simultaneous reconstruction of multiple signaling pathways via the prize-collecting steiner forest problem

scientific article published on February 2013

SteinerNet: a web server for integrating 'omic' data to discover hidden components of response pathways.

scientific article

Structural basis of DNA recognition by the heterodimeric cell cycle transcription factor E2F-DP

scientific article

Swimming upstream: identifying proteomic signals that drive transcriptional changes using the interactome and multiple "-omics" datasets

scientific article published on January 2012

Synthesizing Signaling Pathways from Temporal Phosphoproteomic Data

scientific article published on 01 September 2018

TAMO: a flexible, object-oriented framework for analyzing transcriptional regulation using DNA-sequence motifs

scientific article published on 19 May 2005

Targeting H3K4 trimethylation in Huntington disease

scientific article published on 19 July 2013

The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations

scientific article published on 24 November 2017

The whole-genome landscape of medulloblastoma subtypes

scientific article published in July 2017

Tissue and cellular rigidity and mechanosensitive signaling activation in Alexander disease

scientific article published on 15 May 2018

Tissue-specific transcriptional regulation has diverged significantly between human and mouse

scientific article published on 21 May 2007

Transcriptional regulatory code of a eukaryotic genome

scientific article

Transcriptional regulatory networks in Saccharomyces cerevisiae

scientific article

Treatment with JQ1, a BET bromodomain inhibitor, is selectively detrimental to R6/2 Huntington's disease mice

scientific article published on 01 January 2020

Turning omics data into therapeutic insights

scientific article published on 24 August 2018

Unbiased, Genome-Wide In Vivo Mapping of Transcriptional Regulatory Elements Reveals Sex Differences in Chromatin Structure Associated with Sex-Specific Liver Gene Expression

article

Unbiased, genome-wide in vivo mapping of transcriptional regulatory elements reveals sex differences in chromatin structure associated with sex-specific liver gene expression

scientific article

Unexpected similarities between C9ORF72 and sporadic forms of ALS/FTD suggest a common disease mechanism

scientific article published on 13 July 2018

WebMOTIFS: automated discovery, filtering and scoring of DNA sequence motifs using multiple programs and Bayesian approaches

scientific article published on 21 June 2007

Zfp281 (ZBP-99) plays a functionally redundant role with Zfp148 (ZBP-89) during erythroid development

scientific article published on 01 August 2019

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