List of works - Andrew D. Smith

A geometric interpretation for local alignment-free sequence comparison

scientific article published on July 2013

A transition probability model for amino acid substitutions from blocks

scientific article published in January 2003

An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1)-target genes that form the core response to hypoxia.

scientific article published on 02 June 2009

Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome

scientific article

Before It Gets Started: Regulating Translation at the 5' UTR.

scientific article

Challenges in Understanding Genome-Wide DNA Methylation

scientific article

Computational prediction of novel components of lung transcriptional networks

scientific article published on 18 October 2006

DNA motifs in human and mouse proximal promoters predict tissue-specific expression

scholarly article

DWE: discriminating word enumerator

scientific article published on 27 August 2004

De novo DNA demethylation and noncoding transcription define active intergenic regulatory elements.

scientific article published on 28 June 2013

Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment

scientific article

Diverse endonucleolytic cleavage sites in the mammalian transcriptome depend upon microRNAs, Drosha, and additional nucleases

scientific article

Empirical Models for Substitution in Ribosomal RNA

scientific article

Gene set-based module discovery in the breast cancer transcriptome

scientific article

Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs

scientific article

Genomic analyses of the RNA-binding protein Hu antigen R (HuR) identify a complex network of target genes and novel characteristics of its binding sites

scientific article

Genomic analyses reveal broad impact of miR-137 on genes associated with malignant transformation and neuronal differentiation in glioblastoma cells

scientific article published on 22 January 2014

Genomic landscape of human allele-specific DNA methylation.

scientific article

High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing

scientific article published on 06 July 2009

Identifying dispersed epigenomic domains from ChIP-Seq data ⬇️

scientific article published on February 16, 2011

Identifying tissue-selective transcription factor binding sites in vertebrate promoters

scientific article

Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum

scientific article published in January 2013

Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells

scientific article

Mining ChIP-chip data for transcription factor and cofactor binding sites

scientific article

Molecular hierarchy of mammary differentiation yields refined markers of mammary stem cells.

scientific article published on 11 April 2013

Multiple sequence assembly from reads alignable to a common reference genome

scientific article published in September 2011

On the complexity of finding common approximate substrings

scientific article

RNA-Binding Protein Musashi1 Is a Central Regulator of Adhesion Pathways in Glioblastoma

scientific article

Regionally specific and genome-wide analyses conclusively demonstrate the absence of CpG methylation in human mitochondrial DNA.

scientific article published on 13 May 2013

SIMPROT: using an empirically determined indel distribution in simulations of protein evolution

scientific article

Site identification in high-throughput RNA-protein interaction data

scientific article

Sperm methylation profiles reveal features of epigenetic inheritance and evolution in primates

scientific article

Statistical significance of cis-regulatory modules

scientific article

The RNA-binding protein Musashi1 affects medulloblastoma growth via a network of cancer-related genes and is an indicator of poor prognosis

scientific article

The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA.

scientific article

The oncogenic RNA-binding protein Musashi1 is regulated by tumor suppressor miRNAs

scientific article

Tissue-specific regulatory elements in mammalian promoters

scientific article published on 16 January 2007

Transcription start site evolution in Drosophila.

scientific article published on 06 May 2013

Updates to the RMAP short-read mapping software

scientific article

Using quality scores and longer reads improves accuracy of Solexa read mapping

scientific article

List of works by Andrew D. Smith

A geometric interpretation for local alignment-free sequence comparison

A transition probability model for amino acid substitutions from blocks

An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1)-target genes that form the core response to hypoxia.

Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome

Before It Gets Started: Regulating Translation at the 5' UTR.

Challenges in Understanding Genome-Wide DNA Methylation

Computational prediction of novel components of lung transcriptional networks

DNA motifs in human and mouse proximal promoters predict tissue-specific expression

DWE: discriminating word enumerator

De novo DNA demethylation and noncoding transcription define active intergenic regulatory elements.

Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment

Diverse endonucleolytic cleavage sites in the mammalian transcriptome depend upon microRNAs, Drosha, and additional nucleases

Empirical Models for Substitution in Ribosomal RNA

Gene set-based module discovery in the breast cancer transcriptome

Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs

Genomic analyses of the RNA-binding protein Hu antigen R (HuR) identify a complex network of target genes and novel characteristics of its binding sites

Genomic analyses reveal broad impact of miR-137 on genes associated with malignant transformation and neuronal differentiation in glioblastoma cells

Genomic landscape of human allele-specific DNA methylation.

High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing

Identifying dispersed epigenomic domains from ChIP-Seq data ⬇️

Identifying tissue-selective transcription factor binding sites in vertebrate promoters

Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum

Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells

Mining ChIP-chip data for transcription factor and cofactor binding sites

Molecular hierarchy of mammary differentiation yields refined markers of mammary stem cells.

Multiple sequence assembly from reads alignable to a common reference genome

On the complexity of finding common approximate substrings

RNA-Binding Protein Musashi1 Is a Central Regulator of Adhesion Pathways in Glioblastoma

Regionally specific and genome-wide analyses conclusively demonstrate the absence of CpG methylation in human mitochondrial DNA.

SIMPROT: using an empirically determined indel distribution in simulations of protein evolution

Site identification in high-throughput RNA-protein interaction data

Sperm methylation profiles reveal features of epigenetic inheritance and evolution in primates

Statistical significance of cis-regulatory modules

The RNA-binding protein Musashi1 affects medulloblastoma growth via a network of cancer-related genes and is an indicator of poor prognosis

The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA.

The oncogenic RNA-binding protein Musashi1 is regulated by tumor suppressor miRNAs

Tissue-specific regulatory elements in mammalian promoters

Transcription start site evolution in Drosophila.

Updates to the RMAP short-read mapping software

Using quality scores and longer reads improves accuracy of Solexa read mapping