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List of works by Elana J. Fertig

A 3'-UTR KRAS-variant is associated with cisplatin resistance in patients with recurrent and/or metastatic head and neck squamous cell carcinoma

scientific article

A Mechanism of Resistance to Antibody-Targeted Immune Attack

scientific article published on 18 December 2018

A Mentee's Baby Registry: Supporting New Academic Parents in 2020

scientific article published on 30 September 2020

A Phase 2 Study of Allogeneic GM-CSF Transfected Pancreatic Tumor Vaccine (GVAX) with Ipilimumab as Maintenance Treatment for Metastatic Pancreatic Cancer

scientific article published on 26 June 2020

A Software Application for Mining and Presenting Relevant Cancer Clinical Trials per Cancer Mutation

scientific article

A comparative study of 4D-VAR and a 4D Ensemble Kalman Filter: perfect model simulations with Lorenz-96

A comparative study of 4D-VAR and a 4D Ensemble Kalman Filter: perfect model simulations with Lorenz-96

article

A field guide to cultivating computational biology

scientific article published on 08 October 2021

A novel functional splice variant of AKT3 defined by analysis of alternative splice expression in HPV-positive oropharyngeal cancers

scientific article

A phase II study of temsirolimus and erlotinib in patients with recurrent and/or metastatic, platinum-refractory head and neck squamous cell carcinoma

scientific article published on 04 February 2013

A preliminary analysis of interleukin-1 ligands as potential predictive biomarkers of response to cetuximab

scientific article published on 16 July 2019

AGA: Interactive pipeline for reproducible gene expression and DNA methylation data analyses.

scientific article

Abstract 1493: The Twist box is required for Twist1-induced prostate cancer metastasis

Abstract 1889: Smad4 inactivation correlates with EMT and cetuximab resistance in head and neck squamous cell carcinoma

Abstract 2474: Smad4 loss induces cetuximab resistance and increased metastatic potential in head and neck squamous cell carcinoma

Abstract 2482: Key tumor suppressor genes inactivated by promoter methylation and somatic mutations in head and neck cancer

article

Abstract 2880: The discovery of novel GSN alternative splicing in head and neck squamous cell carcinoma

Abstract 2901: An integrated matrix factorization algorithm for DNA methylation and gene expression identi es HNSCC clinical subtypes and GLI1 signaling speci c to HPV-negative HNSCC

article

Abstract 3100: MicroRNA profiling reveals miR-205 upregulation is associated with head and neck squamous cell carcinoma and modulates E2F1 signaling

Abstract 3409: Transcription factor signature of head and neck squamous cell carcinoma

Abstract 3640: Validation of qBiomarker as an accurate and efficient mutation detection method in a comprehensive analysis of patient-derived tumor xenografts

Abstract 4807: Discovery of novel alternative splicing events in human papillomavirus-related oropharyngeal squamous cell carcinoma

Abstract 527: Analysis of the interaction between microRNAs and Notch pathway members in HNSCC (head and neck squamous cell carcinoma)

Abstract 5342: Hardwiring mechanism into predicting cancer phenotypes by computational learning

Abstract 633: Induction of ADCC resistance profoundly alters tumor cell phenotype and stress response

Abstract 777: The CoGAPS matrix factorization algorithm infers feedback mechanisms from therapeutic inhibition of EGFR that increases expression of growth factor receptors

Abstract B1-62: Bumphunting analysis identifies PAX5 promoter methylation and p53 somatic mutations in genomic instability pathways linked to very poor survival in head and neck cancer

Abstract B45: The Twist box domain is required for Twist1-induced metastasis of prostate cancer cells

Abstract LB-317: Interactive pipeline for reproducible genomics analyses

Activation of the NOTCH pathway in head and neck cancer

scientific article published on 18 December 2013

Aging-like Spontaneous Epigenetic Silencing Facilitates Wnt Activation, Stemness, and BrafV600E-Induced Tumorigenesis

scientific article published on 01 February 2019

An unbiased in vivo functional genomics screening approach in mice identifies novel tumor cell-based regulators of immune rejection

scientific article

Analysis of gene expression of secreted factors associated with breast cancer metastases in breast cancer subtypes

scientific article

Application of genomic and proteomic technologies in biomarker discovery

scientific article published on January 2012

Asporin Restricts Mesenchymal Stromal Cell Differentiation, Alters the Tumor Microenvironment, and Drives Metastatic Progression

scientific article published on 23 May 2019

Assimilating non-local observations with a local ensemble Kalman filter

Assimilating non-local observations with a local ensemble Kalman filter

Breast cancer cells condition lymphatic endothelial cells within pre-metastatic niches to promote metastasis

scientific article

Cancer Systems Biology

CancerInSilico: An R/Bioconductor package for combining mathematical and statistical modeling to simulate time course bulk and single cell gene expression data in cancer

scientific article published on 01 June 2018

Characterization of functionally active gene fusions in human papillomavirus related oropharyngeal squamous cell carcinoma

scientific article published on 7 March 2016

Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers

scientific article published on 16 May 2019

Chromatin structure regulates cancer-specific alternative splicing events in primary HPV-related oropharyngeal squamous cell carcinoma

scientific article published on 22 March 2020

CoGAPS 3: Bayesian non-negative matrix factorization for single-cell analysis with asynchronous updates and sparse data structures

scientific article published on 14 October 2020

CoGAPS matrix factorization algorithm identifies transcriptional changes in AP-2alpha target genes in feedback from therapeutic inhibition of the EGFR network

scientific article

CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data

scientific article

Comparative mutational landscape analysis of patient-derived tumour xenografts

scientific article published on 24 January 2017

Correction: Integrated single-cell and bulk gene expression and ATAC-seq reveals heterogeneity and early changes in pathways associated with resistance to cetuximab in HNSCC-sensitive cell lines

scientific article published on 21 July 2020

Cytokines secreted by stromal cells in TNBC microenvironment as potential targets for cancer therapy

scientific article published on 26 March 2020

DNA methylation regulates TMEM16A/ANO1 expression through multiple CpG islands in head and neck squamous cell carcinoma

scientific article published on 9 November 2017

Decomposing Cell Identity for Transfer Learning across Cellular Measurements, Platforms, Tissues, and Species

scientific article published on 01 May 2019

Decreased SMAD4 expression is associated with induction of epithelial-to-mesenchymal transition and cetuximab resistance in head and neck squamous cell carcinoma

scientific article

Differential Variation Analysis Enables Detection of Tumor Heterogeneity Using Single-Cell RNA-Sequencing Data

scientific article published on 23 July 2019

Differentially Methylated Super-Enhancers Regulate Target Gene Expression in Human Cancer

scientific article published on 21 October 2019

Digital Pathology Analysis Quantifies Spatial Heterogeneity of CD3, CD4, CD8, CD20, and FoxP3 Immune Markers in Triple-Negative Breast Cancer

scientific article published on 19 October 2020

Digitizing omics profiles by divergence from a baseline.

scientific article published on 16 April 2018

Discovery and development of differentially methylated regions in human papillomavirus-related oropharyngeal squamous cell carcinoma

scientific article published on 21 September 2018

Dynamics in hybrid complex systems of switches and oscillators

scientific article published on September 2013

Enter the Matrix: Factorization Uncovers Knowledge from Omics

scientific article published on 22 August 2018

Enter the matrix: factorization uncovers knowledge from omics

Epigenetic Regulation of Gene Expression in Cancer: Techniques, Resources, and Analysis

scientific article published on 8 March 2017

Epigenetic regulation of gene expression in cancer: techniques, resources and analysis.

scientific article

Epigenetic screening of salivary gland mucoepidermoid carcinoma identifies hypomethylation of CLIC3 as a common alteration

scientific article

Evaluation of Cyclophosphamide/GVAX Pancreas Followed by Listeria-mesothelin (CRS-207) With or Without Nivolumab in Patients with Pancreatic Cancer

scientific article published on 09 April 2020

Evaluation of a Strategy for the Assimilation of Satellite Radiance Observations with the Local Ensemble Transform Kalman Filter

Expression microarray analysis reveals alternative splicing of LAMA3 and DST genes in head and neck squamous cell carcinoma

scientific article

Extracellular Vesicles Released by Tumor Endothelial Cells Spread Immunosuppressive and Transforming Signals Through Various Recipient Cells

scientific article published on 09 September 2020

Functional characterization of alternatively spliced GSN in head and neck squamous cell carcinoma

scientific article published on 26 July 2018

Functional normalization of 450k methylation array data improves replication in large cancer studies

Functional normalization of 450k methylation array data improves replication in large cancer studies.

scientific article

Gene expression signatures modulated by epidermal growth factor receptor activation and their relationship to cetuximab resistance in head and neck squamous cell carcinoma

scientific article published on May 2012

HPV E2, E4, E5 drive alternative carcinogenic pathways in HPV positive cancers

scientific article published on 26 August 2020

Hybrid Modeling of Cell Signaling and Transcriptional Reprogramming and Its Application in C. elegans Development

scientific article published on 8 November 2011

Identification of methylated genes in salivary gland adenoid cystic carcinoma xenografts using global demethylation and methylation microarray screening

scientific article published on 18 May 2016

Identifying context-specific transcription factor targets from prior knowledge and gene expression data

scientific article

Identifying context-specific transcription factor targets from prior knowledge and gene expression data

article

Inferring causal molecular networks: empirical assessment through a community-based effort

scientific article

Inhibition of TGF-β enhances the in vivo antitumor efficacy of EGF receptor-targeted therapy

scientific article published on 27 August 2012

Inhibition of miR-21 regulates mutant KRAS effector pathways and intercepts pancreatic ductal adenocarcinoma development

scientific article published on 14 May 2020

Integrated analysis of whole-genome ChIP-Seq and RNA-Seq data of primary head and neck tumor samples associates HPV integration sites with open chromatin marks

scientific article published on 25 September 2017

Integrated immunological analysis of a successful conversion of locally advanced hepatocellular carcinoma to resectability with neoadjuvant therapy

scientific article published on 01 November 2020

Integrated single-cell and bulk gene expression and ATAC-seq reveals heterogeneity and early changes in pathways associated with resistance to cetuximab in HNSCC-sensitive cell lines

scientific article published on 04 May 2020

Integrated time course omics analysis distinguishes immediate therapeutic response from acquired resistance

Integrated time course omics analysis distinguishes immediate therapeutic response from acquired resistance.

scientific article

Integrative computational analysis of transcriptional and epigenetic alterations implicates DTX1 as a putative tumor suppressor gene in HNSCC

scientific article published on 27 January 2017

Key tumor suppressor genes inactivated by "greater promoter" methylation and somatic mutations in head and neck cancer

scientific article

Learning dysregulated pathways in cancers from differential variability analysis

scientific article

Loss of Trop2 causes ErbB3 activation through a neuregulin-1-dependent mechanism in the mesenchymal subtype of HNSCC.

scientific article

Matrix Factorization for Transcriptional Regulatory Network Inference

Matrix factorization and transfer learning uncover regulatory biology across multiple single-cell ATAC-seq data sets

scientific article published on 11 May 2020

Mechanistically detailed systems biology modeling of the HGF/Met pathway in hepatocellular carcinoma

scientific article published on 16 August 2019

Molecular Portrait of Hypoxia in Breast Cancer: A Prognostic Signature and Novel HIF-Regulated Genes

scientific article published on 23 July 2018

Morphology-guided transcriptomic analysis of human pancreatic cancer organoids reveals microenvironmental signals that enhance invasion

scientific article published in 2023

Multipanel mass cytometry reveals anti-PD-1 therapy-mediated B and T cell compartment remodeling in tumor-draining lymph nodes

scientific article published on 30 January 2020

NF-κB and stat3 transcription factor signatures differentiate HPV-positive and HPV-negative head and neck squamous cell carcinoma

scientific article

Newly identified members of fibroblast growth factor receptor 1 splice variants engage in crosstalk with the AXL/AKT axis in salivary adenoid cystic carcinoma

scientific article published on 06 January 2021

Observation bias correction with an ensemble Kalman filter

article by Elana J. Fertig et al published January 2009 in Tellus A

Observation bias correction with an ensemble Kalman filter

Pattern identification in time-course gene expression data with the CoGAPS matrix factorization

scientific article

PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF

PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF.

scientific article

Preferential activation of the hedgehog pathway by epigenetic modulations in HPV negative HNSCC identified with meta-pathway analysis

scientific article

Preserving biological heterogeneity with a permuted surrogate variable analysis for genomics batch correction

scientific article published on 6 June 2014

Programmed Cell Death Ligand-1 (PD-L1) and CD8 Expression Profiling Identify an Immunologic Subtype of Pancreatic Ductal Adenocarcinomas with Favorable Survival

scientific article published on 01 May 2019

Publisher Correction: Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers.

scientific article published on 29 May 2019

Quantifying the Dynamics of Coupled Networks of Switches and Oscillators

article

Quantifying the dynamics of coupled networks of switches and oscillators

scientific article (publication date: 2012)

SMAD4 Loss Is Associated with Cetuximab Resistance and Induction of MAPK/JNK Activation in Head and Neck Cancer Cells.

scientific article

Single-Cell Analysis of Human Retina Identifies Evolutionarily Conserved and Species-Specific Mechanisms Controlling Development

scientific article published on 28 April 2020

Single-Cell RNA-Seq Analysis of Retinal Development Identifies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specification

scientific article published on 22 May 2019

Splice Expression Variation Analysis (SEVA) for Inter-tumor Heterogeneity of Gene Isoform Usage in Cancer

scientific article published on 12 January 2018

StereoGene: Rapid Estimation of Genomewide Correlation of Continuous or Interval Feature Data

article

StereoGene: rapid estimation of genome-wide correlation of continuous or interval feature data

scientific article published in October 2017

Structure-function studies of the bHLH phosphorylation domain of TWIST1 in prostate cancer cells

scientific article

Synthesizer: Expediting synthesis studies from context-free data with information retrieval techniques

scientific article

Synthesizer: Expediting synthesis studies from context-free data with natural language processing

Systems Approaches to Cancer Biology

scientific article

Targeted sequencing reveals clonal genetic changes in the progression of early lung neoplasms and paired circulating DNA

scientific article

Ten quick tips for deep learning in biology

scientific article published on 24 March 2022

The estimation of dimensionality in gene expression data using Nonnegative Matrix Factorization

article

The twist box domain is required for Twist1-induced prostate cancer metastasis

scientific article published on 27 August 2013

Toward Signaling-Driven Biomarkers Immune to Normal Tissue Contamination

scientific article

Variation of Human Neural Stem Cells Generating Organizer States In Vitro before Committing to Cortical Excitatory or Inhibitory Neuronal Fates

scientific article published on 01 May 2020

Viral status, immune microenvironment and immunological response to checkpoint inhibitors in hepatocellular carcinoma

scientific article published on 01 April 2020

Whole-Genome Sequencing of Salivary Gland Adenoid Cystic Carcinoma

scientific article

p16 protein expression and human papillomavirus status as prognostic biomarkers of nonoropharyngeal head and neck squamous cell carcinoma

scientific article

projectR: An R/Bioconductor package for transfer learning via PCA, NMF, correlation, and clustering

scientific article published on 13 March 2020

shinyMethyl: interactive quality control of Illumina 450k DNA methylation arrays in R.

scientific article

switchBox: an R package for k-Top Scoring Pairs classifier development

scientific article