List of works - John Parkinson

200 000 nematode expressed sequence tags on the Net

scientific article published on 01 August 2001

400000 nematode ESTs on the Net.

scientific article

A comprehensive analysis of structural and sequence conservation in the TetR family transcriptional regulators

scientific article published on 2 June 2010

A family of diverse Kunitz inhibitors from Echinococcus granulosus potentially involved in host-parasite cross-talk.

scientific article

A family of secreted mucins from the parasitic nematode Toxocara canis bears diverse mucin domains but shares similar flanking six-cysteine repeat motifs.

scientific article

A systematic pipeline for classifying bacterial operons reveals the evolutionary landscape of biofilm machineries

scientific article published on 01 April 2020

A transcriptomic analysis of Echinococcus granulosus larval stages: implications for parasite biology and host adaptation

scientific article

A transcriptomic analysis of the phylum Nematoda

article

Accumulation of genetic variants associated with immunity in the selective breeding of broilers

scientific article published on 17 January 2020

Caenorhabditis elegans-applications to nematode genomics

scientific article

Cell++--simulating biochemical pathways

scientific article published on 11 October 2006

Central modules of the vaccinia virus complement control protein are not in extensive contact

scientific article published on November 1999

Centric diatom morphogenesis: a model based on a DLA algorithm investigating the potential role of microtubules.

scientific article published in October 1999

Characterization of the Arabidopsis thaliana exocyst complex gene families by phylogenetic, expression profiling, and subcellular localization studies

article

Chemogenetic Interrogation of a Brain-wide Fear Memory Network in Mice.

scientific article published in April 2017

Codon usage patterns in Nematoda: analysis based on over 25 million codons in thirty-two species

scientific article

Comparative Genomics and Evolutionary Modularity of Prokaryotes

scientific article

Comparative genomics of elastin: Sequence analysis of a highly repetitive protein

scientific article published on 25 May 2007

Comparative genomics of the apicomplexan parasites Toxoplasma gondii and Neospora caninum: Coccidia differing in host range and transmission strategy

scientific article published in 2012

Comparative transcriptomic analyses and single-cell RNA sequencing of the freshwater planarian Schmidtea mediterranea identify major cell types and pathway conservation

Comparison of assembly algorithms for improving rate of metatranscriptomic functional annotation

scientific article

Conditional Epistatic Interaction Maps Reveal Global Functional Rewiring of Genome Integrity Pathways in Escherichia coli.

scientific article

Conserved surface-exposed K/R-X-K/R motifs and net positive charge on poxvirus complement control proteins serve as putative heparin binding sites and contribute to inhibition of molecular interactions with human endothelial cells: a novel [...]

scientific article

Correction: Identification of Candidate Adherent-Invasive E. coli Signature Transcripts by Genomic/Transcriptomic Analysis

scientific article published on 28 July 2015

DAnCER: disease-annotated chromatin epigenetics resource

scientific article

DETECT--a density estimation tool for enzyme classification and its application to Plasmodium falciparum.

scientific article published on 30 May 2010

Design and application of a novel two-amplicon approach for defining eukaryotic microbiota

scientific article published in 2018

Discovery and characterization of a Gram-positive Pel polysaccharide biosynthetic gene cluster ⬇️

scientific article published on 01 April 2020

Discovery of novel and potent aryl diamines as leukotriene A4 hydrolase inhibitors

scientific article published on 18 June 2008

Dissecting Sites Important for Complement Regulatory Activity in Membrane Cofactor Protein (MCP; CD46)

scientific article published in Journal of Biological Chemistry

Draft genome of the filarial nematode parasite Brugia malayi

scientific article

E.coli Nissle increases transcription of flagella assembly and formate hydrogenlyase genes in response to colitis

publication published on 01 January 2021

Evolution and architecture of the inner membrane complex in asexual and sexual stages of the malaria parasite

scientific article (publication date: September 2012)

Expanding the landscape of chromatin modification (CM)-related functional domains and genes in human

scientific article

Expressed sequence tag survey of gene expression in the scab mite Psoroptes ovis--allergens, proteases and free-radical scavengers.

scientific article

Expressed sequence tags: an overview

scientific article

Generation and analysis of a mouse intestinal metatranscriptome through Illumina based RNA-sequencing

scientific article

Genetic interaction maps in Escherichia coli reveal functional crosstalk among cell envelope biogenesis pathways

scientific article

Genomic analysis of the causative agents of coccidiosis in domestic chickens

scientific article

Genomics of apicomplexan parasites.

scientific article

Global landscape of protein complexes in the yeast Saccharomyces cerevisiae

scientific article

Hyperscape: visualization for complex biological networks

scientific article

IDBA-MT: de novo assembler for metatranscriptomic data generated from next-generation sequencing technology.

scientific article

IL-4 dependent alternatively-activated macrophages have a distinctive in vivo gene expression phenotype

scientific article

Identification of Candidate Adherent-Invasive E. coli Signature Transcripts by Genomic/Transcriptomic Analysis

scientific article published on 30 June 2015

Identification of a functional connectome for long-term fear memory in mice

scientific article

Interaction network containing conserved and essential protein complexes in Escherichia coli

scientific article (publication date: 3 February 2005)

Large-scale modelling as a route to multiple surface comparisons of the CCP module family

article

Local admixture of amplified and diversified secreted pathogenesis determinants shapes mosaic Toxoplasma gondii genomes

scientific article published on 7 January 2016

Making sense of EST sequences by CLOBBing them

scientific article

Malaria parasites possess a telomere repeat-binding protein that shares ancestry with transcription factor IIIA

scientific article (publication date: 13 March 2017)

Metabolic reconstruction identifies strain-specific regulation of virulence in Toxoplasma gondii.

scientific article

Metabolomic Changes in Serum of Children with Different Clinical Diagnoses of Malnutrition

scientific article

Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality.

scientific article published on 12 January 2016

Modeling the metabolic interplay between a parasitic worm and its bacterial endosymbiont allows the identification of novel drug targets

scientific article published on 11 August 2020

Modelling the self-assembly of elastomeric proteins provides insights into the evolution of their domain architectures

scientific article

Mutations in NBEAL2, encoding a BEACH protein, cause gray platelet syndrome

scientific article (publication date: 17 July 2011)

New tricks for "old" domains: how novel architectures and promiscuous hubs contributed to the organization and evolution of the ECM

scientific article

Panorama of ancient metazoan macromolecular complexes

scientific article published on 07 September 2015

PartiGene--constructing partial genomes

scientific article published on 26 February 2004

PartiGeneDB--collating partial genomes

scientific article

Perilipin-2 modulates dietary fat-induced microbial global gene expression profiles in the mouse intestine

scientific article published on 6 September 2017

PhyloPro2.0: a database for the dynamic exploration of phylogenetically conserved proteins and their domain architectures across the Eukarya

scientific article published on 15 March 2016

PhyloPro: a web-based tool for the generation and visualization of phylogenetic profiles across Eukarya

scientific article published on 19 January 2011

Phylogenomic analysis of EST datasets

scientific article

Polymorphisms in the human tropoelastin gene modify in vitro self-assembly and mechanical properties of elastin-like polypeptides

scientific article

PopNet: A Markov Clustering Approach to Study Population Genetic Structure

scientific article published on 05 April 2017

Post-genomics resources and tools for studying apicomplexan metabolism

scientific article published on 08 December 2010

Proteome-wide dataset supporting the study of ancient metazoan macromolecular complexes

scientific article

Quantitative genome-wide genetic interaction screens reveal global epistatic relationships of protein complexes in Escherichia coli

scientific article

Self-assembly of rodlike particles in two dimensions: A simple model for collagen fibrillogenesis

article

Sequences and domain structures of mammalian, avian, amphibian and teleost tropoelastins: Clues to the evolutionary history of elastins

scientific article published on 12 August 2006

Sequencing and annotation of the Ophiostoma ulmi genome

scientific article

SimiTri--visualizing similarity relationships for groups of sequences

scientific article published in February 2003

Simple physical model of collagen fibrillogenesis based on diffusion limited aggregation

scientific article published on 01 April 1995

Simple physical model of collagen fibrillogenesis based on diffusion limited aggregation

article

SubSeqer: a graph-based approach for the detection and identification of repetitive elements in low-complexity sequences.

scientific article published on 26 February 2008

Synthesis of N-alkyl glycine amides as potent inhibitors of leukotriene A4 hydrolase

scientific article published on 18 June 2008

Systems-based analysis of the Sarcocystis neurona genome identifies pathways that contribute to a heteroxenous life cycle

scientific article

The Brugia malayi genome project: expressed sequence tags and gene discovery

scientific article

The Modular Organization of Protein Interactions in Escherichia coli

scientific article

The VPS33B-binding protein VPS16B is required in megakaryocyte and platelet α-granule biogenesis

scientific article published on 21 September 2012

The apicomplexan inner membrane complex

scientific article published on June 2013

The conservation and evolutionary modularity of metabolism

scientific article published on 12 June 2009

The evolutionary landscape of the chromatin modification machinery reveals lineage specific gains, expansions, and losses

scientific article

The genome of Onchocerca volvulus, agent of river blindness

scientific article published on 21 November 2016

The genomes of four tapeworm species reveal adaptations to parasitism

scientific article

The mechanical properties of simulated collagen fibrils

The origins of apicomplexan sequence innovation.

scientific article published on 10 April 2009

The role of palmitoylation for protein recruitment to the inner membrane complex of the malaria parasite

scientific article (publication date: 16 January 2015)

Toward a systems level view of the ECM and related proteins: a framework for the systematic definition and analysis of biological systems

article

Ubiquitination screen using protein microarrays for comprehensive identification of Rsp5 substrates in yeast

scientific article

List of works by John Parkinson

200 000 nematode expressed sequence tags on the Net

400000 nematode ESTs on the Net.

A comprehensive analysis of structural and sequence conservation in the TetR family transcriptional regulators

A family of diverse Kunitz inhibitors from Echinococcus granulosus potentially involved in host-parasite cross-talk.

A family of secreted mucins from the parasitic nematode Toxocara canis bears diverse mucin domains but shares similar flanking six-cysteine repeat motifs.

A systematic pipeline for classifying bacterial operons reveals the evolutionary landscape of biofilm machineries

A transcriptomic analysis of Echinococcus granulosus larval stages: implications for parasite biology and host adaptation

A transcriptomic analysis of the phylum Nematoda

Accumulation of genetic variants associated with immunity in the selective breeding of broilers

Caenorhabditis elegans-applications to nematode genomics

Cell++--simulating biochemical pathways

Central modules of the vaccinia virus complement control protein are not in extensive contact

Centric diatom morphogenesis: a model based on a DLA algorithm investigating the potential role of microtubules.

Characterization of the Arabidopsis thaliana exocyst complex gene families by phylogenetic, expression profiling, and subcellular localization studies

Chemogenetic Interrogation of a Brain-wide Fear Memory Network in Mice.

Codon usage patterns in Nematoda: analysis based on over 25 million codons in thirty-two species

Comparative Genomics and Evolutionary Modularity of Prokaryotes

Comparative genomics of elastin: Sequence analysis of a highly repetitive protein

Comparative genomics of the apicomplexan parasites Toxoplasma gondii and Neospora caninum: Coccidia differing in host range and transmission strategy

Comparative transcriptomic analyses and single-cell RNA sequencing of the freshwater planarian Schmidtea mediterranea identify major cell types and pathway conservation

Comparison of assembly algorithms for improving rate of metatranscriptomic functional annotation

Conditional Epistatic Interaction Maps Reveal Global Functional Rewiring of Genome Integrity Pathways in Escherichia coli.

Conserved surface-exposed K/R-X-K/R motifs and net positive charge on poxvirus complement control proteins serve as putative heparin binding sites and contribute to inhibition of molecular interactions with human endothelial cells: a novel [...]

Correction: Identification of Candidate Adherent-Invasive E. coli Signature Transcripts by Genomic/Transcriptomic Analysis

DAnCER: disease-annotated chromatin epigenetics resource

DETECT--a density estimation tool for enzyme classification and its application to Plasmodium falciparum.

Design and application of a novel two-amplicon approach for defining eukaryotic microbiota

Discovery and characterization of a Gram-positive Pel polysaccharide biosynthetic gene cluster ⬇️

Discovery of novel and potent aryl diamines as leukotriene A4 hydrolase inhibitors

Dissecting Sites Important for Complement Regulatory Activity in Membrane Cofactor Protein (MCP; CD46)

Draft genome of the filarial nematode parasite Brugia malayi

E.coli Nissle increases transcription of flagella assembly and formate hydrogenlyase genes in response to colitis

Evolution and architecture of the inner membrane complex in asexual and sexual stages of the malaria parasite

Expanding the landscape of chromatin modification (CM)-related functional domains and genes in human

Expressed sequence tag survey of gene expression in the scab mite Psoroptes ovis--allergens, proteases and free-radical scavengers.

Expressed sequence tags: an overview

Generation and analysis of a mouse intestinal metatranscriptome through Illumina based RNA-sequencing

Genetic interaction maps in Escherichia coli reveal functional crosstalk among cell envelope biogenesis pathways

Genomic analysis of the causative agents of coccidiosis in domestic chickens

Genomics of apicomplexan parasites.

Global landscape of protein complexes in the yeast Saccharomyces cerevisiae

Hyperscape: visualization for complex biological networks

IDBA-MT: de novo assembler for metatranscriptomic data generated from next-generation sequencing technology.

IL-4 dependent alternatively-activated macrophages have a distinctive in vivo gene expression phenotype

Identification of Candidate Adherent-Invasive E. coli Signature Transcripts by Genomic/Transcriptomic Analysis

Identification of a functional connectome for long-term fear memory in mice

Interaction network containing conserved and essential protein complexes in Escherichia coli

Large-scale modelling as a route to multiple surface comparisons of the CCP module family

Local admixture of amplified and diversified secreted pathogenesis determinants shapes mosaic Toxoplasma gondii genomes

Making sense of EST sequences by CLOBBing them

Malaria parasites possess a telomere repeat-binding protein that shares ancestry with transcription factor IIIA

Metabolic reconstruction identifies strain-specific regulation of virulence in Toxoplasma gondii.

Metabolomic Changes in Serum of Children with Different Clinical Diagnoses of Malnutrition

Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality.

Modeling the metabolic interplay between a parasitic worm and its bacterial endosymbiont allows the identification of novel drug targets

Modelling the self-assembly of elastomeric proteins provides insights into the evolution of their domain architectures

Mutations in NBEAL2, encoding a BEACH protein, cause gray platelet syndrome

New tricks for "old" domains: how novel architectures and promiscuous hubs contributed to the organization and evolution of the ECM

Panorama of ancient metazoan macromolecular complexes

PartiGene--constructing partial genomes

PartiGeneDB--collating partial genomes

Perilipin-2 modulates dietary fat-induced microbial global gene expression profiles in the mouse intestine

PhyloPro2.0: a database for the dynamic exploration of phylogenetically conserved proteins and their domain architectures across the Eukarya

PhyloPro: a web-based tool for the generation and visualization of phylogenetic profiles across Eukarya

Phylogenomic analysis of EST datasets

Polymorphisms in the human tropoelastin gene modify in vitro self-assembly and mechanical properties of elastin-like polypeptides

PopNet: A Markov Clustering Approach to Study Population Genetic Structure

Post-genomics resources and tools for studying apicomplexan metabolism

Proteome-wide dataset supporting the study of ancient metazoan macromolecular complexes

Quantitative genome-wide genetic interaction screens reveal global epistatic relationships of protein complexes in Escherichia coli

Self-assembly of rodlike particles in two dimensions: A simple model for collagen fibrillogenesis

Sequences and domain structures of mammalian, avian, amphibian and teleost tropoelastins: Clues to the evolutionary history of elastins

Sequencing and annotation of the Ophiostoma ulmi genome

SimiTri--visualizing similarity relationships for groups of sequences

Simple physical model of collagen fibrillogenesis based on diffusion limited aggregation

Simple physical model of collagen fibrillogenesis based on diffusion limited aggregation

SubSeqer: a graph-based approach for the detection and identification of repetitive elements in low-complexity sequences.

Synthesis of N-alkyl glycine amides as potent inhibitors of leukotriene A4 hydrolase

Systems-based analysis of the Sarcocystis neurona genome identifies pathways that contribute to a heteroxenous life cycle