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List of works by Tim Hubbard

18th Sir Hans Krebs lecture. Knowledge-based protein modelling and design

scientific article published on March 1988

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis

scientific article

A browser for expression data

scientific article

A census of human cancer genes

scientific article

A comparison of peak callers used for DNase-Seq data

scientific article

A machine learning strategy to identify candidate binding sites in human protein-coding sequence

scientific article published on 26 September 2006

A new trade framework for global healthcare R&D;

scientific article

A physical map of the mouse genome

scientific article

A specification for defining and annotating regions of macromolecular structures

scientific article published on 01 January 1995

Accurate and sensitive peptide identification with Mascot Percolator

scientific article published on June 2009

Adding some SPICE to DAS.

scientific article published on September 2005

An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)

scientific article

An interactive genome browser of association results from the UK10K cohorts project

scientific article published on 26 August 2015

An overview of Ensembl

scientific article (publication date: May 2004)

Analysis and assessment of ab initio three-dimensional prediction, secondary structure, and contacts prediction

scientific article

Analysis of diagnoses extracted from electronic health records in a large mental health case register.

scientific article

AnnoTrack - a tracking system for genome annotation ⬇️

scientific article (publication date: 5 October 2010)

Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships

scientific article published on May 1998

Assessment of novel fold targets in CASP4: predictions of three-dimensional structures, secondary structures, and interresidue contacts.

scientific article

Assessment of transcript reconstruction methods for RNA-seq

scientific article

Automated PDF highlighting to support faster curation of literature for Parkinson's and Alzheimer's disease

scientific article

BioJava

scholarly article

Biological information: making it accessible and integrated (and trying to make sense of it).

scientific article published on January 2002

CASP5 target classification

scientific article published on January 2003

Cancer gene discovery in mouse and man.

scientific article

Characterisation of mental health conditions in social media using Informed Deep Learning

scientific article published on 22 March 2017

Characterizing genetic variants for clinical action

scientific article

Chromatin Accessibility Data Sets Show Bias Due to Sequence Specificity of the DNase I Enzyme ⬇️

scientific article published on July 26, 2013

Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome

scientific article

Comparative analysis of pseudogenes across three phyla

scientific article

Comparative analysis of the transcriptome across distant species

scientific article

Comparison of Mascot and X!Tandem performance for low and high accuracy mass spectrometry and the development of an adjusted Mascot threshold

scientific article

Comparison of solvent-inaccessible cores of homologous proteins: definitions useful for protein modelling

article

Computational detection and location of transcription start sites in mammalian genomic DNA

scientific article

Corrigendum: Characterisation of mental health conditions in social media using Informed Deep Learning

scientific article published on 16 May 2017

Critical assessment of methods of protein structure prediction (CASP)--round 6.

scientific article

Critical assessment of methods of protein structure prediction (CASP)-round V.

scientific article

Critical assessment of methods of protein structure prediction (CASP): Round II

scholarly article by John Moult published in January 1997

Critical assessment of methods of protein structure prediction (CASP): round II.

scientific article

Critical assessment of methods of protein structure prediction (CASP): round III.

scientific article

Critical assessment of methods of protein structure prediction (CASP): round IV.

scientific article

Critical assessment of methods of protein structure prediction-Round VII

scientific article

Current status and new features of the Consensus Coding Sequence database

scientific article

DNA sequence and analysis of human chromosome 9

scientific article

DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage

scientific article

Dalliance: interactive genome viewing on the web.

scientific article published on 19 January 2011

Data growth and its impact on the SCOP database: new developments

scientific article (publication date: 2008)

Databases and tools for browsing genomes

scientific article

Defining functional DNA elements in the human genome

scientific article

Developing and implementing an institute-wide data sharing policy ⬇️

scientific article (publication date: 28 September 2011)

Discovery of candidate disease genes in ENU-induced mouse mutants by large-scale sequencing, including a splice-site mutation in nucleoredoxin

scientific article

Domain insertions in protein structures

scientific article published on May 2004

EGASP: the human ENCODE Genome Annotation Assessment Project

scientific article

Ensembl 2002: accommodating comparative genomics

scientific article published on January 2003

Ensembl 2005

scientific article

Ensembl 2006.

scientific article

Ensembl 2007

scientific article

Ensembl 2008

scientific article

Ensembl 2009

scientific article (publication date: 2009)

Ensembl 2011

scientific article

Ensembl 2012

scientific article

Ensembl 2013

scientific article

Ensembl 2014

scientific article

Ensembl's 10th year

scientific article

Erratum to: Making sense of big data in health research: towards an EU action plan

scientific article

Erratum: The DNA sequence and biological annotation of human chromosome

scientific article published in Nature

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

scientific article

Evidence for transcript networks composed of chimeric RNAs in human cells

scientific article

First Protein Engineering Centres Meeting at CAPE/GBF on May 22–24, 1991

scientific article published on 01 March 1993

Fold recognition and ab initio structure predictions using hidden Markov models and beta-strand pair potentials

scientific article

From identification to validation to gene count.

scientific article

GENCODE reference annotation for the human and mouse genomes

scientific article published on 01 January 2019

GENCODE: Creating a Validated Manually Annotated Geneset for the Whole Human Genome

GENCODE: Creating a Validated Manually Annotated Geneset for the Whole Human Genome

GENCODE: producing a reference annotation for ENCODE

scientific article

GENCODE: the reference human genome annotation for The ENCODE Project

scientific article

GLASS: a tool to visualize protein structure prediction data in three dimensions and evaluate their consistency

scientific article

Gathering them in to the fold

scientific article

Gene duplications in H. influenzae

scientific article published in November 1995

Genome-wide end-sequenced BAC resources for the NOD/MrkTac() and NOD/ShiLtJ() mouse genomes

scientific article

Genomic anatomy of the Tyrp1 (brown) deletion complex

scholarly article

Global implementation of genomic medicine: We are not alone

scientific article

Heat-shock proteins during growth and sporulation of Bacillus subtilis

scientific article

ITFoM – The IT Future of Medicine

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

scientific article published in June 2007

Initial sequencing and analysis of the human genome

scientific article published on 15 February 2001

Initial sequencing and comparative analysis of the mouse genome

scientific article

Integrating biological data--the Distributed Annotation System

scientific article

Integrating sequence and structural biology with DAS

scientific article

Intermediate sequences increase the detection of homology between sequences

scientific article

Landscape of transcription in human cells

scientific article (publication date: 6 September 2012)

Large-scale discovery of promoter motifs in Drosophila melanogaster

scientific article

Large-scale mutagenesis in p19(ARF)- and p53-deficient mice identifies cancer genes and their collaborative networks

scientific article published on May 2008

Lessons learned from the initial sequencing of the pig genome: comparative analysis of an 8 Mb region of pig chromosome 17.

scientific article published on January 2007

Making sense of big data in health research: Towards an EU action plan

scientific article

MaxBench: evaluation of sequence and structure comparison methods

scientific article

Metamotifs--a generative model for building families of nucleotide position weight matrices

scientific article

Mining the draft human genome

scientific article

Modernizing reference genome assemblies

scientific article

NestedMICA: sensitive inference of over-represented motifs in nucleic acid sequence

scientific article

New horizons in sequence analysis

scientific article published on April 1997

New tools and expanded data analysis capabilities at the Protein Structure Prediction Center

scientific article

Novel candidate cancer genes identified by a large-scale cross-species comparative oncogenomics approach

scientific article

Numerical criteria for the evaluation of ab initio predictions of protein structure.

scientific article

Open annotation offers a democratic solution to genome sequencing

scientific article published in Nature

Petabyte-scale innovations at the European Nucleotide Archive

scientific article

Population statistics of protein structures: lessons from structural classifications

scientific article published on June 1997

Prediction of the structure of GroES and its interaction with GroEL.

scientific article

Prediction targets of CASP4

scientific article published on 01 January 2001

Prepublication data sharing

scientific article

Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database

scientific article (publication date: 2008)

Prizes for innovation of new medicines and vaccines.

scientific article published on January 2009

Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions

scientific article

Protein engineering and design

scientific article

Protein folds in the all-beta and all-alpha classes

scientific article

Protein structure prediction: playing the fold

scientific article

Pseudogenes in the mouse lineage: transcriptional activity and strain-specific history

RMS/coverage graphs: a qualitative method for comparing three-dimensional protein structure predictions.

scientific article

Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease

scientific article published on August 2014

SCOP database in 2002: refinements accommodate structural genomics ⬇️

scientific article published on January 1, 2002

SCOP database in 2004: refinements integrate structure and sequence family data

scientific article (publication date: 2004)

SCOP, Structural Classification of Proteins database: applications to evaluation of the effectiveness of sequence alignment methods and statistics of protein structural data

scientific article

SCOP: a Structural Classification of Proteins database

scientific article published in January 1999

SCOP: a Structural Classification of Proteins database

scientific article published on 01 January 1997

SCOP: a structural classification of proteins database

scientific article

SCOP: a structural classification of proteins database for the investigation of sequences and structures

scientific article (publication date: 7 April 1995)

SISYPHUS--structural alignments for proteins with non-trivial relationships

scientific article published in January 2007

SPEM: a parser for EMBL style flat file database entries

scientific article

Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods

scientific article

Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome

scientific article

Systematic evaluation of spliced alignment programs for RNA-seq data

scientific article

The 100 000 Genomes Project: bringing whole genome sequencing to the NHS

scientific article published in the British Medical Journal

The DNA sequence and analysis of human chromosome 13

scientific article

The DNA sequence and analysis of human chromosome 6

scientific article

The DNA sequence and biological annotation of human chromosome

scientific article

The DNA sequence and comparative analysis of human chromosome 10

scientific article

The DNA sequence and comparative analysis of human chromosome 20

scientific article

The DNA sequence of the human X chromosome

scientific article published on 17 March 2005

The Ensembl genome database project

scientific article

The GENCODE exome: sequencing the complete human exome

scientific article

The GENCODE human gene set

scientific article

The GENCODE human gene set

article

The GENCODE pseudogene resource

scientific article

The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression

scientific article

The Protein Feature Ontology: a tool for the unification of protein feature annotations

scientific article

The Vertebrate Genome Annotation (Vega) database

scientific article

The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes

scientific article

The origins, evolution, and functional potential of alternative splicing in vertebrates

scientific article

The role of heat-shock and chaperone proteins in protein folding: possible molecular mechanisms

scientific article published on October 1991

The significance of performance ranking in CASP--response to Marti-Renom et al.

scientific article

The solution structure of the S1 RNA binding domain: a member of an ancient nucleic acid-binding fold

scientific article

The vertebrate genome annotation (Vega) database

scientific article

The zebrafish reference genome sequence and its relationship to the human genome

scientific article (publication date: 25 April 2013)

Transcriptional activity and strain-specific history of mouse pseudogenes

scientific article published on 29 July 2020

Understanding protein structure: using scop for fold interpretation

scientific article

Update on protein structure prediction: results of the 1995 IRBM workshop

scientific article

Using neural networks for prediction of the subcellular location of proteins

scientific article

What can we learn from noncoding regions of similarity between genomes?

scientific article

ddbRNA: detection of conserved secondary structures in multiple alignments

scientific article published in September 2003

iMotifs: an integrated sequence motif visualization and analysis environment

scientific article

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