Geoffrey J. Barton

Geoffrey J. Barton's AcademicInfluence.com Rankings

Geoffrey J. Barton

Biology

#8557

World Rank

#11654

Historical Rank

Bioinformatics

#92

World Rank

#94

Historical Rank

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Biology

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Geoffrey J. Barton's Published Works

Number of citations in a given year to any of this author's works

Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author

Published Works

Jalview Version 2—a multiple sequence alignment editor and analysis workbench (2009) (7580)
The Jpred 3 secondary structure prediction server (2008) (1589)
The Jalview Java alignment editor (2004) (1544)
JPred4: a protein secondary structure prediction server (2015) (1439)
ALSCRIPT: a tool to format multiple sequence alignments. (1993) (1091)
JPred: a consensus secondary structure prediction server (1998) (1039)
Application of multiple sequence alignment profiles to improve protein secondary structure prediction (2000) (832)
Draft Genome Sequence of the Sexually Transmitted Pathogen Trichomonas vaginalis (2007) (739)
Evaluation and improvement of multiple sequence methods for protein secondary structure prediction (1999) (683)
Multiple protein sequence alignment from tertiary structure comparison: Assignment of global and residue confidence levels (1992) (680)
Identification of multiple distinct Snf2 subfamilies with conserved structural motifs (2006) (661)
Draft Genome of the Filarial Nematode Parasite Brugia malayi (2007) (639)
Protein sequence alignments: a strategy for the hierarchical analysis of residue conservation (1993) (578)
Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs. (2009) (549)
Emerging roles of pseudokinases. (2006) (523)
A strategy for the rapid multiple alignment of protein sequences. Confidence levels from tertiary structure comparisons. (1987) (503)
How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use? (2016) (478)
System-Wide Changes to SUMO Modifications in Response to Heat Shock (2009) (478)
Prediction of protein secondary structure and active sites using the alignment of homologous sequences. (1987) (451)
Crystal structure of isopenicillin N synthase is the first from a new structural family of enzymes (1995) (389)
A Quantitative Spatial Proteomics Analysis of Proteome Turnover in Human Cells* (2011) (357)
High-Resolution Whole-Genome Sequencing Reveals That Specific Chromatin Domains from Most Human Chromosomes Associate with Nucleoli (2010) (284)
A Role for Snf2-Related Nucleosome-Spacing Enzymes in Genome-Wide Nucleosome Organization (2011) (274)
GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes (2004) (259)
PIPs: human protein–protein interaction prediction database (2008) (232)
OXBench: A benchmark for evaluation of protein multiple sequence alignment accuracy (2003) (227)
Regulation of the miR-212/132 locus by MSK1 and CREB in response to neurotrophins. (2010) (216)
Protein multiple sequence alignment and flexible pattern matching. (1990) (205)
PGE2 Induces Macrophage IL-10 Production and a Regulatory-like Phenotype via a Protein Kinase A–SIK–CRTC3 Pathway (2013) (200)
Human miRNA Precursors with Box H/ACA snoRNA Features (2009) (193)
Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification (2019) (189)
Structural features can be unconserved in proteins with similar folds. An analysis of side-chain to side-chain contacts secondary structure and accessibility. (1994) (173)
Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics (2021) (172)
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. (1994) (166)
Continuous and discontinuous domains: An algorithm for the automatic generation of reliable protein domain definitions (1995) (165)
Classification and functional annotation of eukaryotic protein kinases (2007) (163)
Characterization and prediction of protein nucleolar localization sequences (2010) (157)
Direct Sequencing of Arabidopsis thaliana RNA Reveals Patterns of Cleavage and Polyadenylation (2012) (151)
E-MSD: an integrated data resource for bioinformatics (2004) (151)
Probabilistic prediction and ranking of human protein-protein interactions (2007) (147)
14-3-3-Pred: improved methods to predict 14-3-3-binding phosphopeptides (2015) (140)
Amino acid sequence analysis of the annexin super-gene family of proteins. (1991) (140)
A structural analysis of phosphate and sulphate binding sites in proteins. Estimation of propensities for binding and conservation of phosphate binding sites. (1994) (139)
Protein fold recognition by mapping predicted secondary structures. (1996) (138)
Tmem79/Matt is the matted mouse gene and is a predisposing gene for atopic dermatitis in human subjects (2013) (135)
Identification of human miRNA precursors that resemble box C/D snoRNAs (2011) (132)
Structural similarity between the p17 matrix protein of HIV-1 and interferon-γ (1994) (132)
Flexible protein sequence patterns. A sensitive method to detect weak structural similarities. (1990) (128)
NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins (2011) (125)
The structure of serine palmitoyltransferase; gateway to sphingolipid biosynthesis. (2007) (122)
The Scottish Structural Proteomics Facility: targets, methods and outputs (2010) (121)
Live imaging of nascent RNA dynamics reveals distinct types of transcriptional pulse regulation (2012) (120)
Evaluation and improvements in the automatic alignment of protein sequences. (1987) (118)
Filaggrin-stratified transcriptomic analysis of pediatric skin identifies mechanistic pathways in patients with atopic dermatitis (2014) (115)
PTEN Protein Phosphatase Activity Correlates with Control of Gene Expression and Invasion, a Tumor-Suppressing Phenotype, But Not with AKT Activity (2012) (110)
Conservation analysis and structure prediction of the SH2 family of phosphotyrosine binding domains (1992) (109)
TarO: a target optimisation system for structural biology (2008) (105)
Distinct donor and acceptor specificities of Trypanosoma brucei oligosaccharyltransferases (2009) (105)
Erratum: How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use? (2016) (97)
SCANPS: a web server for iterative protein sequence database searching by dynamic programing, with display in a hierarchical SCOP browser (2008) (95)
Java bioinformatics analysis web services for multiple sequence alignment—JABAWS:MSA (2011) (94)
Kinomer v. 1.0: a database of systematically classified eukaryotic protein kinases (2008) (91)
Proteotoxic stress reprograms the chromatin landscape of SUMO modification (2015) (85)
Scop: structural classification of proteins. (1994) (83)
Visualization of multiple alignments, phylogenies and gene family evolution (2010) (83)
Statistical models for RNA-seq data derived from a two-condition 48-replicate experiment (2015) (83)
The limits of protein secondary structure prediction accuracy from multiple sequence alignment. (1993) (80)
Human box C/D snoRNA processing conservation across multiple cell types (2011) (79)
The complement of protein kinases of the microsporidium Encephalitozoon cuniculi in relation to those of Saccharomyces cerevisiae and Schizosaccharomyces pombe (2007) (77)
Mutational analysis of human papillomavirus E4 proteins: identification of structural features important in the formation of cytoplasmic E4/cytokeratin networks in epithelial cells (1994) (73)
SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein–Protein Interactions (2007) (73)
ParCrys: a Parzen window density estimation approach to protein crystallization propensity prediction (2008) (70)
Haploinsufficiency for AAGAB causes clinically heterogeneous forms of punctate palmoplantar keratoderma (2012) (69)
Identification of functional residues and secondary structure from protein multiple sequence alignment. (1996) (67)
The kinomes of apicomplexan parasites. (2012) (64)
PDBe-KB: a community-driven resource for structural and functional annotations (2019) (63)
Ambisonic Decoders for HDTV (1992) (63)
Transcription Termination and Chimeric RNA Formation Controlled by Arabidopsis thaliana FPA (2013) (59)
A normalised scale for structural genomics target ranking: The OB‐Score (2006) (56)
The RNA-binding protein FPA regulates flg22-triggered defense responses and transcription factor activity by alternative polyadenylation (2013) (56)
Quantification of the variation in percentage identity for protein sequence alignments (2006) (56)
Quantitative proteomics in resected renal cancer tissue for biomarker discovery and profiling (2014) (56)
3Dee: a database of protein structural domains (2001) (56)
Protein secondary structure prediction. (1995) (55)
MACSIMS : multiple alignment of complete sequences information management system (2006) (54)
Major transcriptome re-organisation and abrupt changes in signalling, cell cycle and chromatin regulation at neural differentiation in vivo (2014) (52)
The SWI/SNF complex acts to constrain distribution of the centromeric histone variant Cse4 (2011) (48)
Analysis of Human Small Nucleolar RNAs (snoRNA) and the Development of snoRNA Modulator of Gene Expression Vectors (2010) (47)
Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework (2017) (46)
Alignment of Biological Sequences with Jalview. (2020) (46)
An efficient algorithm to locate all locally optimal alignments between two sequences allowing for gaps (1993) (45)
The contrasting properties of conservation and correlated phylogeny in protein functional residue prediction (2008) (45)
Elevated O‐GlcNAc Levels Activate Epigenetically Repressed Genes and Delay Mouse ESC Differentiation Without Affecting Naïve to Primed Cell Transition (2014) (44)
Genome Analysis of the Unicellular Green Alga Chlamydomonas reinhardtii Indicates an Ancient Evolutionary Origin for Key Pattern Recognition and Cell-Signaling Protein Families (2008) (44)
Global network analysis of drug tolerance, mode of action and virulence in methicillin-resistant S. aureus (2011) (43)
AIDS vaccine predictions (1987) (40)
Prediction of domain organisation and secondary structure of thyroid peroxidase, a human autoantigen involved in destructive thyroiditis (1990) (37)
Proteus: an R package for downstream analysis of MaxQuant output (2018) (36)
Identification of a glycosylphosphatidylinositol anchor‐modifying β1‐3 N‐acetylglucosaminyl transferase in Trypanosoma brucei (2009) (35)
Estimation of P-values for global alignments of protein sequences (2001) (34)
Protein structural domains: Analysis of the 3Dee domains database (2001) (33)
Biological units and their effect upon the properties and prediction of protein-protein interactions. (2006) (30)
Protein Sequence Alignment and Database Scanning (2001) (29)
An SH2—SH3 domain hybrid (1993) (28)
Improved Annotation of 3′ Untranslated Regions and Complex Loci by Combination of Strand-Specific Direct RNA Sequencing, RNA-Seq and ESTs (2013) (26)
XANNpred: Neural nets that predict the propensity of a protein to yield diffraction-quality crystals (2010) (25)
Secondary structure prediction for modelling by homology. (1993) (24)
LOPAL and SCAMP: techniques for the comparison and display of protein structures (1988) (23)
ProtEST: protein multiple sequence alignments from expressed sequence tags (2000) (23)
Prediction of antigenic determinants and secondary structures of the major AIDS virus proteins (1987) (23)
PDBe-KB: collaboratively defining the biological context of structural data (2021) (22)
A new family of transcription factors (2008) (22)
JABAWS 2.2 distributed web services for Bioinformatics: protein disorder, conservation and RNA secondary structure (2018) (21)
A knowledge-based architecture for protein sequence analysis and structure prediction. (1990) (21)
Chromosome evolution and the genetic basis of agronomically important traits in greater yam (2021) (20)
Protein structure prediction (1993) (20)
Protein sequence alignment techniques. (1998) (19)
Widespread premature transcription termination of Arabidopsis thaliana NLR genes by the spen protein FPA (2020) (19)
Secondary structure prediction from multiple sequence data: blood clotting factor XIII and Yersinia protein-tyrosine phosphatase. (2009) (18)
E-MSD: an integrated data resource for bioinformatics. (2004) (18)
Identifying plant genes shaping microbiota composition in the barley rhizosphere (2021) (18)
Missense variants in ACE2 are predicted to encourage and inhibit interaction with SARS-CoV-2 Spike and contribute to genetic risk in COVID-19 (2020) (18)
Adenylate cyclase A acting on PKA mediates induction of stalk formation by cyclic diguanylate at the Dictyostelium organizer (2017) (17)
Scanning protein sequence databanks using a distributed processing workstation network (1991) (16)
Relative Abundance of Transcripts ( RATs): Identifying differential isoform abundance from RNA-seq (2019) (15)
Nanopore direct RNA sequencing maps an Arabidopsis N6 methyladenosine epitranscriptome (2019) (15)
Deposition of macromolecular structures. (1998) (14)
Yanocomp: robust prediction of m6A modifications in individual nanopore direct RNA reads (2021) (13)
A comparison of SCOP and CATH with respect to domain–domain interactions (2007) (13)
Computer speed and sequence comparison. (1992) (12)
Detection and Mitigation of Spurious Antisense Reads with RoSA (2018) (12)
The AMPS package for multiple protein sequence alignment. (1994) (12)
Increased Coverage Obtained by Combination of Methods for Protein Sequence Database Searching (2003) (11)
The Dundee Resource for Sequence Analysis and Structure Prediction (2019) (11)
Jalview: Visualization and Analysis of Molecular Sequences, Alignments, and Structures (2005) (11)
Identifying differential isoform abundance with RATs: a universal tool and a warning (2017) (10)
PNAC: a protein nucleolar association classifier (2011) (9)
Detection and mitigation of spurious antisense expression with RoSA (2019) (9)
Ambisonic Surround-Sound Mixing for Multitrack Studios (1984) (9)
Sequence alignment for molecular replacement (2007) (9)
Interaction of synthetic peptides from annexin I and uteroglobin with lipid monolayers and their effect on phospholipase A2 activity. (1990) (8)
Computational approaches to selecting and optimising targets for structural biology (2011) (8)
2passtools: two-pass alignment using machine-learning-filtered splice junctions increases the accuracy of intron detection in long-read RNA sequencing (2020) (8)
PIMS sequencing extension: a laboratory information management system for DNA sequencing facilities (2011) (8)
Human protein-protein interaction prediction (2010) (7)
A study of the structural properties of sites modified by the O-linked 6-N-acetylglucosamine transferase (2017) (7)
How well do RNA-Seq differential gene expression tools perform in higher eukaryotes? (2016) (7)
Protein fold recognition from secondary structure assignments (1995) (7)
How well do RNA-Seq differential gene expression tools perform in a complex eukaryote? A case study in Arabidopsis thaliana (2019) (7)
Human Missense Variation is Constrained by Domain Structure and Highlights Functional and Pathogenic Residues (2017) (7)
How well do RNA-Seq differential gene expression tools perform in a eukaryote with a complex transcriptome? (2017) (6)
Missense variants in human ACE2 strongly affect binding to SARS-CoV-2 Spike providing a mechanism for ACE2 mediated genetic risk in Covid-19: A case study in affinity predictions of interface variants (2022) (6)
A PROLOG approach to analysing protein structure (1990) (6)
Web of intrigue (1996) (6)
Improved annotation with de novo transcriptome assembly in four social amoeba species (2017) (6)
Purification, crystallization and data collection of methicillin-resistant Staphylococcus aureus Sar2676, a pantothenate synthetase. (2007) (6)
Creation and analysis of protein multiple sequence alignments. (2001) (5)
Disease related single point mutations alter the global dynamics of a tetratricopeptide (TPR) α-solenoid domain (2019) (5)
AlmostSignificant: simplifying quality control of high-throughput sequencing data (2016) (5)
Visual Representation of Database Search Results: The RHIMS Plot (2003) (4)
Ankyrin repeats in context with human population variation (2021) (4)
Expression, purification, crystallization, data collection and preliminary biochemical characterization of methicillin-resistant Staphylococcus aureus Sar2028, an aspartate/tyrosine/phenylalanine pyridoxal-5'-phosphate-dependent aminotransferase. (2007) (4)
Missense variants in human ACE2 modify binding to SARS-CoV-2 Spike (2021) (3)
Structural and Functional Analysis of the S-Layer Protein from Bacillus stearothermophilus (1993) (3)
m6A modification of U6 snRNA modulates usage of two major classes of pre-mRNA 5’ splice site (2022) (3)
Activity Expression and Invasion , a Tumor-Suppressing Phenotype , But Not with PTEN Protein Phosphatase Activity Correlates with Control of Gene ` (2012) (3)
Elevated O-GlcNAc levels activate epigenetically repressed genes and delay mouse ES cell differentiation without affecting naive to primed cell transition (2014) (3)
The relationship between domain-domain interaction orientation and sequence similarity (2007) (2)
Generation and interpretation of protein sequence and structural multiple alignments (1992) (2)
A Dictyostelium SH2 adaptor protein required for correct DIF-1 signaling and pattern formation (2011) (2)
Multiple Sequence Alignment and Flexible Pattern Matching (1992) (2)
The RNA-binding protein FPA regulates flg22-triggered defense responses and transcription factor activity by alternative (2013) (1)
java2script/SwingJS for bioinformatics: Reintroducing Jalview on the Web as JalviewJS (2019) (1)
New developments to SCANPS : High performance parallel iterated protein sequence searching with full dynamic programming and onthe-fly statistics (1)
Correction: A study of the structural properties of sites modified by the O-linked 6-N-acetylglucosamine transferase (2017) (1)
Correction to: Alignment of Biological Sequences with Jalview. (2021) (1)
Detection and mitigation of spurious antisense expression with RoSA [version 1; peer review: 2 approved with reservations] (2021) (1)
Dicer-dependent small RNAs derived from tRNAs Filtering of deep sequencing data reveals the existence of abundant Material Supplemental (2009) (1)
Continuous and discontinuous domains : An algorithm for the automatic generation of protein domain definitionsreliable (2006) (0)
Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework (2017) (0)
Large knowledge based applications in molecular biology and genetics (1990) (0)
1 The kinomes of apicomplexan parasites (2013) (0)
Prediction of Protein Structure from Multiple Sequence Alignment (1993) (0)
Detecting Structural Similarity from Protein Sequence Comparison (2006) (0)
Visualising Variants on Structure with Jalview (2019) (0)
Transcriptome analysis of skin reveals differences between atopic eczema cases stratified for filaggrin genotype (2012) (0)
2passtools: two-pass alignment using machine-learning-filtered splice junctions increases the accuracy of intron detection in long-read RNA sequencing (2021) (0)
Distributed Web services for bioinformatics: Multiple sequence alignment, conservation and protein disorder (2011) (0)
Development of a Computational Pipeline For Automated Prediction of Bacterial Transcription Factor Binding Sites (2006) (0)
A K for and nowledge-based architecture protein sequence analysis structure prediction (2006) (0)
HIGH RESOLUTION STRUCTURE OF SPT WITH PLP INTERNAL ALDIMINE (2007) (0)
A tool and a warning: differential isoform usage with RATs (2017) (0)
Prediction of transcription factor binding sites in bacterial genomes : case study with Pectobacterium atrosepticum (2006) (0)
Simple jury predicts protein secondary structure best (2003) (0)
Improved annotation with de novo transcriptome assembly in four social amoeba species (2016) (0)
1 1 m 6 A modification of U 6 snRNA modulates 2 usage of two major classes of pre-mRNA 5 ’ 3 splice site 4 5 (0)
Helicos direct RNA sequencing of FPA mutants and overexpressors (2020) (0)
Re: letter to the editor regarding deposition of 3D structural studies of biological macromolecules. (1998) (0)
Low resolution structure of SPT (2007) (0)
BIOINFORMATICS The Jalview Java alignment editor (2004) (0)
Electronic publishing and the biochemist (1995) (0)
Artificial Intelligence and Molecular Biology.Lawrence Hunter (1995) (0)
Getting to grips with sequences. Computational Molecular Biology‐Sources and Methods for Sequence Analysis (1989). Edited by Arthur Lesk. Oxford University Press. Oxford, Pp. 254. £25.00 (1989) (0)
Text-Translat ion Al ignment : Three Languages Are Bet ter Than Two * (2002) (0)
Single-molecule transcriptomics of atopic eczema in human skin (2012) (0)
RESEARCH INTO METABOLIC DISEASES (1997) (0)
DEV112623 3266..3276 (2014) (0)
Prediction and ranking of human protein-protein interactions within a Bayesian framework (2007) (0)
Crystallization and X-ray diffraction studies of recombinant human platelet-derived endothelial cell growth factor (1993) (0)
Digital Analysis of Quantisation Errors in Digital Signal Processing (1985) (0)
ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (MANGANESE COMPLEX) (1998) (0)

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Other Resources About Geoffrey J. Barton

www.lifesci.dundee.ac.uk

What Schools Are Affiliated With Geoffrey J. Barton?

Geoffrey J. Barton is affiliated with the following schools: