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List of works by David R. Westhead

A PQM-1-Mediated Response Triggers Transcellular Chaperone Signaling and Regulates Organismal Proteostasis ⬇️

scientific article published on 01 June 2018

A comparative study of machine-learning methods to predict the effects of single nucleotide polymorphisms on protein function.

scientific article

A comparison of heuristic search algorithms for molecular docking.

scientific article published in May 1997

A computer system to perform structure comparison using TOPS representations of protein structure.

scientific article

A consensus algorithm to screen genomes for novel families of transmembrane beta barrel proteins

scientific article

A crucial role for the ubiquitously expressed transcription factor Sp1 at early stages of hematopoietic specification ⬇️

scientific article

A microarray platform-independent classification tool for cell of origin class allows comparative analysis of gene expression in diffuse large B-cell lymphoma

scientific article

A physiologically based mathematical model of dermal absorption in man.

scientific article published in January 1994

A primer on learning in Bayesian networks for computational biology

scientific article

A unique dual activity amino acid hydroxylase in Toxoplasma gondii

scientific article

A validated microRNA profile with predictive potential in glioblastoma patients treated with bevacizumab ⬇️

scientific article published on July 2016

AI-based algorithms for protein surface comparisons

scientific article published in December 2001

Active-site-directed 3D database searching: Pharmacophore extraction and validation of hits

scientific article published on 01 October 1996

Alio intuitu: the automated reconstruction of the metabolic networks of parasites

scientific article published on 28 August 2009

An atlas of protein topology cartoons available on the World-Wide Web.

scientific article

An extended set of PRDM1/BLIMP1 target genes links binding motif type to dynamic repression

scientific article published on 26 April 2010

Annotating the Plasmodium genome and the enigma of the shikimate pathway

scientific article published on February 2004

Arabidopsis Co-expression Tool (ACT): web server tools for microarray-based gene expression analysis

scientific article published on July 2006

Asymmetric mutation rates at enzyme-inhibitor interfaces: implications for the protein-protein docking problem

scientific article published on September 2003

Automated derivation and refinement of sequence length patterns for protein sequences using evolutionary computation

scientific article published in September 2005

BI-11 * PROGNOSTIC microRNAS IN MALIGNANT GLIOMA

Bayesian refinement of protein functional site matching

scientific article

Benchmarking pipelines for subclonal deconvolution of bulk tumour sequencing data

scientific article published on 04 November 2021

Beta edge strands in protein structure prediction and aggregation.

scientific article

Bioinformatic approaches to biological systems

scientific article published on January 2008

Calculation of helix packing angles in protein structures

scientific article published in July 2003

Cancer somatic mutations cluster in a subset of regulatory sites predicted from the ENCODE data ⬇️

scientific article

Cell-of-origin in diffuse large B-cell lymphoma: findings from the UK's population-based Haematological Malignancy Research Network ⬇️

scientific article published on 08 November 2018

Chromatin Accessibility-Based Characterization of the Gene Regulatory Network Underlying Plasmodium falciparum Blood-Stage Development. ⬇️

scientific article published in April 2018

Chronic FLT3-ITD Signaling in Acute Myeloid Leukemia Is Connected to a Specific Chromatin Signature. ⬇️

scientific article published on 23 July 2015

Combining the interactome and deleterious SNP predictions to improve disease gene identification

scientific article published in March 2009

Conservation, convergence, and divergence of light-responsive, circadian-regulated, and tissue-specific expression patterns during evolution of the Arabidopsis GATA gene family

scientific article published on 5 January 2007

Defining common principles of gene co-expression refines molecular stratification in cancer

article

Deleterious SNP prediction: be mindful of your training data!

scientific article

Depletion of RUNX1/ETO in t(8;21) AML cells leads to genome-wide changes in chromatin structure and transcription factor binding.

scientific article

Differential expression and extent of fungal/plant and fungal/bacterial chitinases of Aspergillus fumigatus

scientific article published on October 2005

Distinct genetic changes reveal evolutionary history and heterogeneous molecular grade of DLBCL with MYC/BCL2 double-hit

scientific article published on 16 December 2019

Dynamic Gene Regulatory Networks Drive Hematopoietic Specification and Differentiation. ⬇️

scientific article published on 18 February 2016

Dysregulation of the miR-30c/DLL4 axis by circHIPK3 is essential for KSHV lytic replication

scientific article published on 03 March 2022

Flexible docking using Tabu search and an empirical estimate of binding affinity

scientific article published in November 1998

Flexible model-based clustering of mixed binary and continuous data: application to genetic regulation and cancer ⬇️

scientific article

From gene expression to gene regulatory networks in Arabidopsis thaliana

scientific article

GENO-17AN 8-microRNA SIGNATURE PREDICTS RESPONSE TO BEVACIZUMAB IN GLIOBLASTOMA.

scientific article

GO-At: in silico prediction of gene function in Arabidopsis thaliana by combining heterogeneous data

scientific article

Gene expression meta-analysis reveals immune response convergence on the IFNγ-STAT1-IRF1 axis and adaptive immune resistance mechanisms in lymphoma ⬇️

scientific article

Gene function prediction using semantic similarity clustering and enrichment analysis in the malaria parasite Plasmodium falciparum

scientific article

Gene-expression profiling of bortezomib added to standard chemoimmunotherapy for diffuse large B-cell lymphoma (REMoDL-B): an open-label, randomised, phase 3 trial

article

Growth Factor-like Gene Regulation Is Separable from Survival and Maturation in Antibody-Secreting Cells ⬇️

article

Growth-factor like gene regulation is separable from survival and maturation in antibody secreting cells

article

Heat stress enhances the accumulation of polyadenylated mitochondrial transcripts in Arabidopsis thaliana

scientific article

Ibrutinib induces chromatin reorganisation of chronic lymphocytic leukaemia cells

scientific article published on 10 May 2019

Identification of a dynamic core transcriptional network in t(8;21) AML that regulates differentiation block and self-renewal ⬇️

scientific article published on 18 September 2014

Identification of gene specific cis-regulatory elements during differentiation of mouse embryonic stem cells: An integrative approach using high-throughput datasets

scientific article published on 04 November 2019

Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication ⬇️

scientific article published on 09 August 2006

Improved prediction of protein-protein binding sites using a support vector machines approach

scientific article published on 21 December 2004

In vitro generation of long-lived human plasma cells.

scientific article published on 16 November 2012

Inference in Bayesian networks

scientific article

Insights into protein-protein interfaces using a Bayesian network prediction method

scientific article published on 21 July 2006

Integrated analyses of chromatin accessibility and gene expression data for elucidating the transcriptional regulatory mechanisms during early hematopoietic development in mouse.

scientific article published on 18 March 2013

KvDB; mining and mapping sequence variants in voltage-gated potassium channels

scientific article published in August 2010

KvSNP: accurately predicting the effect of genetic variants in voltage-gated potassium channels

scientific article published on 17 June 2011

Ligand binding: functional site location, similarity and docking

scientific article

MetNetMaker: a free and open-source tool for the creation of novel metabolic networks in SBML format

scientific article published on 29 July 2010

Metabolic reconstruction and analysis for parasite genomes

scientific article published on 22 October 2007

Modelling the pH-dependent Properties of Kv1 Potassium Channels

scientific article published on 22 February 2007

Molecular High-Grade B-Cell Lymphoma: Defining a Poor-Risk Group That Requires Different Approaches to Therapy ⬇️

scientific article published on 03 December 2018

Motif-based searching in TOPS protein topology databases

scientific article

Multiple structural alignment for distantly related all beta structures using TOPS pattern discovery and simulated annealing.

scientific article

Natural antisense transcripts with coding capacity in Arabidopsis may have a regulatory role that is not linked to double-stranded RNA degradation ⬇️

scientific article

Network Analysis Identifies Proinflammatory Plasma Cell Polarization for Secretion of ISG15 in Human Autoimmunity. ⬇️

scientific article published on 29 June 2016

New tools and resources for analysing protein structures and their interactions

scientific article

PRO-LIGAND: an approach to de novo molecular design. 1. Application to the design of organic molecules

scientific article published on February 1995

PRO-LIGAND: an approach to de novo molecular design. 3. A genetic algorithm for structure refinement

scientific article published in April 1995

PRO_LIGAND: an approach to de novo molecular design. 2. Design of novel molecules from molecular field analysis (MFA) models and pharmacophores.

scientific article

PRO_LIGAND: an approach to de novo molecular design. 4. Application to the design of peptides

scientific article published on June 1995

Parsimonious Gene Correlation Network Analysis (PGCNA): a tool to define modular gene co-expression for refined molecular stratification in cancer

article

Petri Net representations in systems biology.

scientific article published on December 2003

PlasmoPredict: a gene function prediction website for Plasmodium falciparum

scientific article published on 19 January 2010

Predicting the effect of missense mutations on protein function: analysis with Bayesian networks ⬇️

scientific article

Prediction of clinical outcome in glioblastoma using a biologically relevant nine-microRNA signature ⬇️

scientific article published on 28 November 2014

Prediction of horizontal gene transfers in eukaryotes: approaches and challenges

scientific article published on August 2009

Prognostic microRNAs in high-grade glioma reveal a link to oligodendrocyte precursor differentiation.

scientific article

Protein fold recognition by threading: comparison of algorithms and analysis of results.

scientific article published on December 1995

Protein structural topology: Automated analysis and diagrammatic representation.

scientific article published on April 1999

Protein structure Prediction

article from 1998

Protein structure topological comparison, discovery and matching service.

scientific article

RUNX1 reshapes the epigenetic landscape at the onset of haematopoiesis.

scientific article

SPIB and BATF provide alternate determinants of IRF4 occupancy in diffuse large B-cell lymphoma linked to disease heterogeneity ⬇️

scientific article

Simple sequence-based kernels do not predict protein-protein interactions

scientific article published on 27 August 2010

Small RNA analysis in Petunia hybrida identifies unusual tissue-specific expression patterns of conserved miRNAs and of a 24mer RNA.

scientific article

System-wide studies of the transcriptional programming of chromatin during early hematopoietic development

scientific article published on 18 March 2013

TMB-Hunt: a web server to screen sequence sets for transmembrane beta-barrel proteins

scientific article

TMB-Hunt: an amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins

scientific article

TOPS: an enhanced database of protein structural topology

scientific article published on January 2004

The Arabidopsis co-expression tool (ACT): a WWW-based tool and database for microarray-based gene expression analysis.

scientific article published in April 2006

The fibril_one on-line database: mutations, experimental conditions, and trends associated with amyloid fibril formation

scientific article

The hematopoietic master regulator RUNX1 reshapes the epigenetic landscape at the onset of hematopoiesis

The transcriptional regulation of protein complexes; a cross-species perspective

scientific article published on 18 August 2009

The transferome of metabolic genes explored: analysis of the horizontal transfer of enzyme encoding genes in unicellular eukaryotes

scientific article published in 2009

TmaDB: a repository for tissue microarray data

scientific article

Transferring genomics to the clinic: distinguishing Burkitt and diffuse large B cell lymphomas ⬇️

scientific article published in July 2015

Two distinct auto-regulatory loops operate at the PU.1 locus in B cells and myeloid cells

scientific article

Using common variants to indicate cancer genes ⬇️

scientific article published on 14 May 2014

Whole genome expression profiling based on paraffin embedded tissue can be used to classify diffuse large B-cell lymphoma and predict clinical outcome

scientific article published on 13 September 2012

metaSHARK: a WWW platform for interactive exploration of metabolic networks

scientific article published on July 2006

metaSHARK: software for automated metabolic network prediction from DNA sequence and its application to the genomes of Plasmodium falciparum and Eimeria tenella ⬇️

scientific article

metaTIGER: a metabolic evolution resource

scientific article published on 25 October 2008

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