Geoffrey Barton

Publications

• Transcription Termination and Chimeric RNA Formation Controlled by Arabidopsis thaliana FPA DOI: 10.1371/journal.pgen.1003867
• Tmem79/Matt is the matted mouse gene and is a predisposing gene for atopic dermatitis in human subjects DOI: 10.1016/j.jaci.2013.08.046
• The RNA-binding protein FPA regulates flg22-triggered defense responses and transcription factor activity by alternative polyadenylation DOI: 10.1038/srep02866
• PGE2 induces macrophage IL-10 production and a regulatory-like phenotype via a protein kinase A-SIK-CRTC3 pathway DOI: 10.4049/jimmunol.1202462
• The kinomes of apicomplexan parasites DOI: 10.1016/j.micinf.2012.04.007
• PTEN protein phosphatase activity correlates with control of gene expression and invasion, a tumor-suppressing phenotype, but not with AKT activity DOI: 10.1126/scisignal.2002138
• Live imaging of nascent RNA dynamics reveals distinct types of transcriptional pulse regulation DOI: 10.1073/pnas.1117603109
• Human box C/D snoRNA processing conservation across multiple cell types DOI: 10.1093/nar/gkr1233
• Haploinsufficiency for AAGAB causes clinically heterogeneous forms of punctate palmoplantar keratoderma DOI: 10.1038/ng.2444
• Direct sequencing of Arabidopsis thaliana RNA reveals patterns of cleavage and polyadenylation DOI: 10.1038/nsmb.2345
• A quantitative spatial proteomics analysis of proteome turnover in human cells DOI: 10.1074/mcp.M111.011429
• XANNpred: Neural nets that predict the propensity of a protein to yield diffraction-quality crystals DOI: 10.1002/prot.22914
• The SWI/SNF complex acts to constrain distribution of the centromeric histone variant Cse4 DOI: 10.1038/emboj.2011.112
• PNAC: A protein nucleolar association classifier DOI: 10.1186/1471-2164-12-74
• PIMS sequencing extension: A laboratory information management system for DNA sequencing facilities DOI: 10.1186/1756-0500-4-48
• NoD: A Nucleolar localization sequence detector for eukaryotic and viral proteins DOI: 10.1186/1471-2105-12-317
• Java bioinformatics analysis web services for multiple sequence alignment-JABAWS:MSA DOI: 10.1093/bioinformatics/btr304
• Identification of human miRNA precursors that resemble box C/D snoRNAs DOI: 10.1093/nar/gkq1355
• Global network analysis of drug tolerance, mode of action and virulence in methicillin-resistant S. aureus DOI: 10.1186/1752-0509-5-68
• Computational approaches to selecting and optimising targets for structural biology DOI: 10.1016/j.ymeth.2011.08.014
• A role for Snf2-related nucleosome-spacing enzymes in genome-wide nucleosome organization DOI: 10.1126/science.1206097
• A Dictyostelium SH2 adaptor protein required for correct DIF-1 signaling and pattern formation DOI: 10.1016/j.ydbio.2011.03.003
• Visualization of multiple alignments, phylogenies and gene family evolution DOI: 10.1038/nmeth.1434
• The scottish structural proteomics facility: Targets, methods and outputs DOI: 10.1007/s10969-010-9090-y
• Regulation of the miR-212/132 locus by MSK1 and CREB in response to neurotrophins DOI: 10.1042/BJ20100024
• Characterization and prediction of protein nucleolar localization sequences DOI: 10.1093/nar/gkq653
• Analysis of human small nucleolar RNAs (snoRNA) and the development of snoRNA modulator of gene expression vectors DOI: 10.1091/mbc.E10-01-0078
• System-wide changes to sumo modifications in response to heat shock DOI: 10.1126/scisignal.2000282
• PIPs: Human protein-protein interaction prediction database DOI: 10.1093/nar/gkn870
• Kinomer v. 1.0: A database of systematically classified eukaryotic protein kinases DOI: 10.1093/nar/gkn834
• Jalview Version 2-A multiple sequence alignment editor and analysis workbench DOI: 10.1093/bioinformatics/btp033
• Identification of a glycosylphosphatidylinositol anchor-modifying β1-3 N-acetylglucosaminyl transferase in Trypanosoma brucei DOI: 10.1111/j.1365-2958.2008.06542.x
• Human miRNA precursors with box H/ACA snoRNA features DOI: 10.1371/journal.pcbi.1000507
• Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs DOI: 10.1261/rna.1738409
• Distinct donor and acceptor specificities of Trypanosoma brucei oligosaccharyltransferases DOI: 10.1038/emboj.2009.203
• The Jpred 3 secondary structure prediction server. DOI: 10.1093/nar/gkn238
• The contrasting properties of conservation and correlated phylogeny in protein functional residue prediction DOI: 10.1186/1471-2105-9-51
• TarO: a target optimisation system for structural biology. DOI: 10.1093/nar/gkn141
• SCANPS: a web server for iterative protein sequence database searching by dynamic programing, with display in a hierarchical SCOP browser. DOI: 10.1093/nar/gkn320
• ParCrys: A Parzen window density estimation approach to protein crystallization propensity prediction DOI: 10.1093/bioinformatics/btn055
• Genome analysis of the unicellular green alga Chlamydomonas reinhardtii indicates an ancient evolutionary origin for key pattern recognition and cell-signaling protein families DOI: 10.1534/genetics.107.085936
• A new family of transcription factors DOI: 10.1242/dev.026377
• A comparison of SCOP and CATH with respect to domain-domain interactions DOI: 10.1002/prot.21496
• The Structure of Serine Palmitoyltransferase; Gateway to Sphingolipid Biosynthesis DOI: 10.1016/j.jmb.2007.04.086
• The complement of protein kinases of the microsporidium Encephalitozoon cuniculi in relation to those of Saccharomyces cerevisiae and Schizosaccharomyces pombe DOI: 10.1186/1471-2164-8-309
• SNAPPI-DB: A database and API of structures, iNterfaces and Alignments for Protein-Protein Interactions DOI: 10.1093/nar/gkl836
• Sequence alignment for molecular replacement DOI: 10.1107/S0907444907046343
• Purification, crystallization and data collection of methicillin-resistant Staphylococcus aureus Sar2676, a pantothenate synthetase DOI: 10.1107/S1744309107020362
• Probabilistic prediction and ranking of human protein-protein interactions DOI: 10.1186/1471-2105-8-239
• Expression, purification, crystallization, data collection and preliminary biochemical characterization of methicillin-resistant Staphylococcus aureus Sar2028, an aspartate/tyrosine/phenylalanine pyridoxal-5′-phosphate- dependent aminotransferase DOI: 10.1107/S1744309107019562
• Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis DOI: 10.1126/science.1132894
• Draft genome of the filarial nematode parasite Brugia malayi DOI: 10.1126/science.1145406
• Classification and functional annotation of eukaryotic protein kinases DOI: 10.1002/prot.21444
• Quantification of the variation in percentage identity for protein sequence alignments DOI: 10.1186/1471-2105-7-415
• MACSIMS : Multiple alignment of complete sequences information management system DOI: 10.1186/1471-2105-7-318
• Identification of multiple distinct Snf2 subfamilies with conserved structural motifs DOI: 10.1093/nar/gkl295
• Emerging roles of pseudokinases DOI: 10.1016/j.tcb.2006.07.003
• Biological Units and their Effect upon the Properties and Prediction of Protein-Protein Interactions DOI: 10.1016/j.jmb.2006.09.042
• A normalised scale for structural genomics target ranking: The OB-Score DOI: 10.1016/j.febslet.2006.06.015
• The Jalview Java alignment editor DOI: 10.1093/bioinformatics/btg430
• GOtcha: A new method for prediction of protein function assessed by the annotation of seven genomes DOI: 10.1186/1471-2105-5-178
• E-MSD: An integrated data resource for bioinformatics
• Visual representation of database search results: The RHIMS plot DOI: 10.1093/bioinformatics/btg116
• OXBench: A benchmark for evaluation of protein multiple sequence alignment accuracy DOI: 10.1186/1471-2105-4-47
• Increased coverage obtained by combination of methods for protein sequence database searching DOI: 10.1093/bioinformatics/btg156
• Estimation of p-values for global alignments of protein sequences
• Protein structural domains: Analysis of the 3dee domains database DOI: 10.1002/1097-0134(20010215)42:3<332::AID-PROT40>3.0.CO;2-S
• Creation and analysis of protein multiple sequence alignments
• 3Dee: A database of protein structural domains
• ProtEST: Protein multiple sequence alignments from expressed sequence tags
• Application of multiple sequence alignment profiles to improve protein secondary structure prediction DOI: 10.1002/1097-0134(20000815)40:3<502::AID-PROT170>3.0.CO;2-Q
• Evaluation and improvement of multiple sequence methods for protein secondary structure prediction DOI: 10.1002/(SICI)1097-0134(19990301)34:4<508::AID-PROT10>3.0.CO;2-4
• Protein sequence alignment techniques DOI: 10.1107/S0907444998008324
• JPred: A consensus secondary structure prediction server DOI: 10.1093/bioinformatics/14.10.892
• Deposition of macromolecular structures DOI: 10.1107/S0907444998008464
• Protein fold recognition by mapping predicted secondary structures DOI: 10.1006/jmbi.1996.0325
• Conservation of amino acids in multiple alignments: Aspartic acid has unexpected conservation DOI: 10.1016/S0014-5793(96)01181-7
• [29] Identification of functional residues and secondary structure from protein multiple sequence alignment
• Protein secondary structure prediction DOI: 10.1016/0959-440X(95)80099-9
• Crystal structure of isopenicillin N synthase is the first from a new structural family of enzymes
• Continuous and discontinuous domains: An algorithm for the automatic generation of reliable protein domain definitions
• The AMPS package for multiple protein sequence alignment.
• Structural similarity between the p17 matrix protein of HIV-1 and interferon-γ DOI: 10.1038/370666a0
• Structural features can be unconserved in proteins with similar folds. An analysis of side-chain to side-chain contacts secondary structure and accessibility DOI: 10.1006/jmbi.1994.1733
• Secondary structure prediction from multiple sequence data: Blood clotting factor XIII and Yersinia protein-tyrosine phosphatase
• scop: Structural classification of proteins DOI: 10.1016/0968-0004(94)90060-4
• Conservation analysis and structure prediction of the protein serine/threonine phosphatases. Sequence similarity with diadenosine tetraphosphatase from Escherichia coli suggests homology to the protein phosphatases
• A structural analysis of phosphate and sulphate binding sites in proteins estimation of propensities for binding and conservation of phosphate binding sites
• The limits of protein secondary structure prediction accuracy from multiple sequence alignment DOI: 10.1006/jmbi.1993.1649
• Secondary structure prediction for modelling by homology
• Protein structure prediction [11]
• Protein sequence alignments: A strategy for the hierarchical analysis of residue conservation
• An SH2-SH3 domain hybrid [10] DOI: 10.1038/364765a0
• An efficient algorithm to locate all locally optimal alignments between two sequences allowing for gaps
• ALSCRIPT: A tool to format multiple sequence alignments
• Multiple protein sequence alignment from tertiary structure comparison: Assignment of global and residue confidence levels
• Human platelet-derived endothelial cell growth factor is homologous to Escherichia coli thymidine phosphorylase
• Generation and interpretation of protein sequence and structural multiple alignments DOI: 10.1007/BF01673746
• Conservation analysis and structure prediction of the SH2 family of phosphotyrosine binding domains DOI: 10.1016/0014-5793(92)80579-6
• Computer speed and sequence comparison [1]
• Scanning protein sequence databanks using a distributed processing workstation network
• Amino acid sequence analysis of the annexin super-gene family of proteins
• Protein multiple sequence alignment and flexible pattern matching
• Prediction of domain organisation and secondary structure of thyroid peroxidase, a human autoantigen involved in destructive thyroiditis DOI: 10.1016/0014-5793(90)81524-R
• Large knowledge based applications in molecular biology and genetics
• Interaction of synthetic peptides from annexin I and uteroglobin with lipid monolayers and their effect on phospholipase A2 activity
• Flexible protein sequence patterns: a sensitive method to detect weak structural similarities
• A PROLOG approach to analysing protein structure
• A knowledge-based architecture for protein sequence analysis and structure prediction
• LOPAL and SCAMP: techniques for the comparison and display of protein structures
• Prediction of protein secondary structure and active sites using the alignment of homologous sequences
• Prediction of antigenic determinants and secondary structures of the major AIDS virus proteins
• Evaluation and improvements in the automatic alignment of protein sequences
• AIDS vaccine predictions
• A strategy for the rapid multiple alignment of protein sequences. Confidence levels from tertiary structure comparisons