List of works - Laura Elnitski

A Case of IL-7R Deficiency Caused by a Novel Synonymous Mutation and Implications for Mutation Screening in SCID Diagnosis.

scientific article published on 27 October 2016

A Systems Biology Comparison of Ovarian Cancers Implicates Putative Somatic Driver Mutations through Protein-Protein Interaction Models

scientific article

Aberrant DNA methylation defines isoform usage in cancer, with functional implications

scientific article published on 22 July 2019

Ascertaining regions affected by GC-biased gene conversion through weak-to-strong mutational hotspots

scientific article published on 13 April 2014

Bidirectional promoters as important drivers for the emergence of species-specific transcripts

scientific article

CAGI experiments: modeling sequence variant impact on gene splicing using predictions from computational tools

article

Characterization and clustering of kinase isoform expression in metastatic melanoma

scientific article published on 13 May 2022

Comparative analyses of bidirectional promoters in vertebrates

scientific article

Computational analysis reveals a correlation of exon-skipping events with splicing, transcription and epigenetic factors

scientific article published on 24 December 2013

Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution

scientific article

CpG island methylator phenotype in adenocarcinomas from the digestive tract: Methods, conclusions, and controversies

scientific article published on March 2017

Cross-species mapping of bidirectional promoters enables prediction of unannotated 5' UTRs and identification of species-specific transcripts

scientific article

Cross-species sequence comparisons: a review of methods and available resources

scientific article

DNA methylation profiles unique to Kalahari KhoeSan individuals

scientific article published on 06 September 2020

Detection and characterization of silencers and enhancer-blockers in the greater CFTR locus

scientific article published on 24 April 2008

Differential analysis of ovarian and endometrial cancers identifies a methylator phenotype

scientific article

Discovering Gene Regulatory Elements Using Coverage-based Heuristics

scientific article published on 30 October 2015

Distinguishing regulatory DNA from neutral sites

scientific article published on January 2003

Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences

scientific article

Finding Occurrences of Relevant Functional Elements in Genomic Signatures

scientific article

Functional analysis of a novel cis-acting regulatory region within the human ankyrin gene (ANK-1) promoter

scientific article

Functional analysis of synonymous substitutions predicted to affect splicing of the CFTR gene

scientific article

GALA, a database for genomic sequence alignments and annotations

scientific article

Galaxy: a platform for interactive large-scale genome analysis

scientific article

Generation and comparative analysis of approximately 3.3 Mb of mouse genomic sequence orthologous to the region of human chromosome 7q11.23 implicated in Williams syndrome

scientific article

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

scientific article

Genome-wide detection of a TFIID localization element from an initial human disease mutation

scientific article

Genomic features defining exonic variants that modulate splicing

scientific article

Identification of human silencers by correlating cross-tissue epigenetic profiles and gene expression

article

Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results

scientific article

Initial sequencing and comparative analysis of the mouse genome

scientific article

Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques

scientific article

MethylToSNP: identifying SNPs in Illumina DNA methylation array data

scientific article published on 20 December 2019

Molecular determinants of NOTCH4 transcription in vascular endothelium

scientific article

Multi-species sequence comparison reveals dynamic evolution of the elastin gene that has involved purifying selection and lineage-specific insertions/deletions

scientific article

MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences

scientific article

Orthology-driven mapping of bidirectional promoters in human and mouse genomes

scientific article

Pan-cancer stratification of solid human epithelial tumors and cancer cell lines reveals commonalities and tissue-specific features of the CpG island methylator phenotype

scientific article published on 17 April 2015

PhenCode: connecting ENCODE data with mutations and phenotype

scientific article

Recurrent patterns of DNA methylation in the ZNF154, CASP8, and VHL promoters across a wide spectrum of human solid epithelial tumors and cancer cell lines

scientific article published on 22 October 2013

Regulatory potential scores from genome-wide three-way alignments of human, mouse, and rat

scientific article published on April 2004

Robust Detection of DNA Hypermethylation of ZNF154 as a Pan-Cancer Locus with in Silico Modeling for Blood-Based Diagnostic Development

scientific article published on 30 January 2016

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

scientific article

SigSeeker: a peak-calling ensemble approach for constructing epigenetic signatures

scientific article published on 25 April 2017

Significant associations between driver gene mutations and DNA methylation alterations across many cancer types.

scientific article published on 10 November 2017

The Emergence of Pan-Cancer CIMP and Its Elusive Interpretation

scientific article

The functional relevance of somatic synonymous mutations in melanoma and other cancers

scientific article published on 24 August 2015

The genome sequence of taurine cattle: a window to ruminant biology and evolution

scientific article

The hypothesis of ultraconserved enhancer dispensability overturned.

scientific article published on 8 May 2018

Tissue-specific and ubiquitous expression patterns from alternative promoters of human genes

scientific article

Unique alterations of an ultraconserved non-coding element in the 3'UTR of ZIC2 in holoprosencephaly

scientific article

Word-based characterization of promoters involved in human DNA repair pathways

scientific article

WordSeeker: concurrent bioinformatics software for discovering genome-wide patterns and word-based genomic signatures

scientific article

List of works by Laura Elnitski

A Case of IL-7R Deficiency Caused by a Novel Synonymous Mutation and Implications for Mutation Screening in SCID Diagnosis.

A Systems Biology Comparison of Ovarian Cancers Implicates Putative Somatic Driver Mutations through Protein-Protein Interaction Models

Aberrant DNA methylation defines isoform usage in cancer, with functional implications

Ascertaining regions affected by GC-biased gene conversion through weak-to-strong mutational hotspots

Bidirectional promoters as important drivers for the emergence of species-specific transcripts

CAGI experiments: modeling sequence variant impact on gene splicing using predictions from computational tools

Characterization and clustering of kinase isoform expression in metastatic melanoma

Comparative analyses of bidirectional promoters in vertebrates

Computational analysis reveals a correlation of exon-skipping events with splicing, transcription and epigenetic factors

Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution

CpG island methylator phenotype in adenocarcinomas from the digestive tract: Methods, conclusions, and controversies

Cross-species mapping of bidirectional promoters enables prediction of unannotated 5' UTRs and identification of species-specific transcripts

Cross-species sequence comparisons: a review of methods and available resources

DNA methylation profiles unique to Kalahari KhoeSan individuals

Detection and characterization of silencers and enhancer-blockers in the greater CFTR locus

Differential analysis of ovarian and endometrial cancers identifies a methylator phenotype

Discovering Gene Regulatory Elements Using Coverage-based Heuristics

Distinguishing regulatory DNA from neutral sites

Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences

Finding Occurrences of Relevant Functional Elements in Genomic Signatures

Functional analysis of a novel cis-acting regulatory region within the human ankyrin gene (ANK-1) promoter

Functional analysis of synonymous substitutions predicted to affect splicing of the CFTR gene

GALA, a database for genomic sequence alignments and annotations

Galaxy: a platform for interactive large-scale genome analysis

Generation and comparative analysis of approximately 3.3 Mb of mouse genomic sequence orthologous to the region of human chromosome 7q11.23 implicated in Williams syndrome

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

Genome-wide detection of a TFIID localization element from an initial human disease mutation

Genomic features defining exonic variants that modulate splicing

Identification of human silencers by correlating cross-tissue epigenetic profiles and gene expression

Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results

Initial sequencing and comparative analysis of the mouse genome

Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques

MethylToSNP: identifying SNPs in Illumina DNA methylation array data

Molecular determinants of NOTCH4 transcription in vascular endothelium

Multi-species sequence comparison reveals dynamic evolution of the elastin gene that has involved purifying selection and lineage-specific insertions/deletions

MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences

Orthology-driven mapping of bidirectional promoters in human and mouse genomes

Pan-cancer stratification of solid human epithelial tumors and cancer cell lines reveals commonalities and tissue-specific features of the CpG island methylator phenotype

PhenCode: connecting ENCODE data with mutations and phenotype

Recurrent patterns of DNA methylation in the ZNF154, CASP8, and VHL promoters across a wide spectrum of human solid epithelial tumors and cancer cell lines

Regulatory potential scores from genome-wide three-way alignments of human, mouse, and rat

Robust Detection of DNA Hypermethylation of ZNF154 as a Pan-Cancer Locus with in Silico Modeling for Blood-Based Diagnostic Development

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

SigSeeker: a peak-calling ensemble approach for constructing epigenetic signatures

Significant associations between driver gene mutations and DNA methylation alterations across many cancer types.

The Emergence of Pan-Cancer CIMP and Its Elusive Interpretation

The functional relevance of somatic synonymous mutations in melanoma and other cancers

The genome sequence of taurine cattle: a window to ruminant biology and evolution

The hypothesis of ultraconserved enhancer dispensability overturned.

Tissue-specific and ubiquitous expression patterns from alternative promoters of human genes

Unique alterations of an ultraconserved non-coding element in the 3'UTR of ZIC2 in holoprosencephaly

Word-based characterization of promoters involved in human DNA repair pathways

WordSeeker: concurrent bioinformatics software for discovering genome-wide patterns and word-based genomic signatures