List of works - Charlie Hodgman

A DEMETER-like DNA demethylase governs tomato fruit ripening

scientific article

A Transcriptomic Comparison of Two Bambara Groundnut Landraces under Dehydration Stress.

scientific article published on 18 April 2017

A historical perspective on gene/protein functional assignment

scientific article published on 01 January 2000

A machine learning heuristic to identify biologically relevant and minimal biomarker panels from omics data

scientific article

A methodology for elucidating regulatory mechanisms leading to changes in lipid profiles. ⬇️

scientific article

A new dynamic tool to perform assembly of Expressed Sequence Tags (ESTs) ⬇️

scientific article published on August 1, 1997

A new superfamily of replicative proteins

scientific article published in Nature

An Integrative Systems Perspective on Plant Phosphate Research

scientific article published on 13 February 2019

An analysis of the biological properties of monoclonal antibodies against glycoprotein D of herpes simplex virus and identification of amino acid substitutions that confer resistance to neutralization

scientific article published in June 1986

An information-flow model of the pharmaceutical industry

scientific article published on 01 December 2001

Analysis of Gene Regulatory Networks of Maize in Response to Nitrogen.

scientific article

Application of experimentally verified transcription factor binding sites models for computational analysis of ChIP-Seq data

scientific article

Assessing the functional coherence of modules found in multiple-evidence networks from Arabidopsis

scientific article

Author Correction: Rice auxin influx carrier OsAUX1 facilitates root hair elongation in response to low external phosphate ⬇️

scientific article published in May 2018

Automated management of gene discovery projects

article

Characterization of a Bacillus thuringiensis strain which is toxic to the housefly Musca domestica.

scientific article published on November 1993

Characterizing proteolytic cleavage site activity using bio-basis function neural networks

scientific article

Cloning and analysis of the first cry gene from Bacillus popilliae ⬇️

scientific article published on July 1, 1997

Comparison of functional annotation schemes for genomes

scientific article

Constructing an enzyme-centric view of metabolism.

scientific article

DNA Methylation and Chromatin Regulation during Fleshy Fruit Development and Ripening

scientific article

Editorial: The informatics of post-translational modification and its implications for systems biology

scientific article published on 01 June 2004

Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions.

scientific article

Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize

scientific article published on 21 July 2017

Growth-induced hormone dilution can explain the dynamics of plant root cell elongation.

scientific article

Gsmodutils: a python based framework for test-driven genome scale metabolic model development

scientific article published on 01 September 2019

INTERACT: an object oriented protein-protein interaction database.

scientific article

Identification of a cryptic gene associated with an insertion sequence not previously identified in Bacillus thuringiensis.

scientific article published in November 1993

Identification of the homologous beige and Chediak-Higashi syndrome genes

scientific article

Inference of gene regulatory networks using boolean-network inference methods.

scientific article published on December 2009

Inference of the genetic network regulating lateral root initiation in Arabidopsis thaliana

scientific article published in January 2013

Integrative biology--the way forward

scientific article published on 18 July 2007

Lipidomic analysis of plasma samples from women with polycystic ovary syndrome.

scientific article published on 17 August 2014

Mathematical simulation and analysis of cellular metabolism and regulation.

scientific article published in September 1999

Mechanical modelling quantifies the functional importance of outer tissue layers during root elongation and bending.

scientific article

Mechanistic insight into the role of AUXIN RESISTANCE4 in trafficking of AUXIN1 and LIKE AUX1-2

Metabolic differences in ripening of Solanum lycopersicum 'Ailsa Craig' and three monogenic mutants ⬇️

scientific article

Models for the structure and function of the Bacillus thuringiensis delta-endotoxins determined by compilational analysis

scientific article published in January 1990

Modulation of Arabidopsis and monocot root architecture by CLAVATA3/EMBRYO SURROUNDING REGION 26 peptide

scientific article published on 17 July 2015

Multi-omics analysis identifies genes mediating the extension of cell walls in the Arabidopsis thaliana root elongation zone. ⬇️

scientific article published on 20 February 2015

Network inference analysis identifies an APRR2-like gene linked to pigment accumulation in tomato and pepper fruits.

scientific article published on 4 January 2013

Occurrence of a Quadruplex Motif in a Unique Insert within Exon C of the Bovine Estrogen Receptor α Gene (ESR1)

article

OsCAND1 is required for crown root emergence in rice.

scientific article

Progress towards platform chemical production using

scientific article published on 17 April 2018

Reduction of off-flavor generation in soybean homogenates: a mathematical model.

scientific article published on 23 August 2010

Regulatory feedback response mechanisms to phosphate starvation in rice.

scientific article published on 8 January 2018

Reported sequence homology between Alzheimer amyloid770 and the MRC OX-2 antigen does not predict function

scientific article published on 01 January 1995

Repression of translation of human estrogen receptor alpha by G-quadruplex formation

scientific article

Rice auxin influx carrier OsAUX1 facilitates root hair elongation in response to low external phosphate ⬇️

scientific article published on 12 April 2018

Searching for discrimination rules in protease proteolytic cleavage activity using genetic programming with a min-max scoring function.

scientific article published in November 2003

Secondary structure analysis identifies a putative mouse protein demonstrating similarity to the repeat units found in CDC4, the G protein beta subunits and related proteins

scientific article published on January 1, 1992

Sequence variants in the bovine gonadotrophin releasing hormone receptor gene and their associations with fertility

scientific article published on 26 November 2009

Simultaneous modelling of metabolic, genetic and product-interaction networks.

scientific article published on September 2001

Statistical evaluation of transcriptomic data generated using the Affymetrix one-cycle, two-cycle and IVT-Express RNA labelling protocols with the Arabidopsis ATH1 microarray

scientific article (publication date: 15 March 2010)

Tackling drought stress: receptor-like kinases present new approaches

scientific article (publication date: June 2012)

The Beta-adrenergic agonist, Ractopamine, increases skeletal muscle expression of Asparagine Synthetase as part of an integrated stress response gene program

scientific article published in Scientific Reports

The herpes simplex virus type 2 equivalent of the herpes simplex virus type 1 US7 gene and its flanking sequences

scientific article

The logic of the floral transition: Reverse-engineering the switch controlling the identity of lateral organs

scientific article published on 20 September 2017

The successful application of systems approaches in plant biology.

scientific article

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models

scientific article (publication date: March 2003)

Unraveling the evolution of auxin signaling

scientific article

Validation of proteomic biomarkers previously found to be differentially expressed in women with polycystic ovary syndrome: a cross-sectional study.

scientific article published on 7 January 2014

Whole genome sequence and manual annotation of Clostridium autoethanogenum, an industrially relevant bacterium

scientific article

[Method SiteGA for the recognition of transcription factor binding sites]

scientific article published on 01 July 2006

pBR322 and other pSC101 derivatives have a gene fragment related to the mini-F plasmid resolvase.

scientific article

List of works by Charlie Hodgman

A DEMETER-like DNA demethylase governs tomato fruit ripening

A Transcriptomic Comparison of Two Bambara Groundnut Landraces under Dehydration Stress.

A historical perspective on gene/protein functional assignment

A machine learning heuristic to identify biologically relevant and minimal biomarker panels from omics data

A methodology for elucidating regulatory mechanisms leading to changes in lipid profiles. ⬇️

A new dynamic tool to perform assembly of Expressed Sequence Tags (ESTs) ⬇️

A new superfamily of replicative proteins

An Integrative Systems Perspective on Plant Phosphate Research

An analysis of the biological properties of monoclonal antibodies against glycoprotein D of herpes simplex virus and identification of amino acid substitutions that confer resistance to neutralization

An information-flow model of the pharmaceutical industry

Analysis of Gene Regulatory Networks of Maize in Response to Nitrogen.

Application of experimentally verified transcription factor binding sites models for computational analysis of ChIP-Seq data

Assessing the functional coherence of modules found in multiple-evidence networks from Arabidopsis

Author Correction: Rice auxin influx carrier OsAUX1 facilitates root hair elongation in response to low external phosphate ⬇️

Automated management of gene discovery projects

Characterization of a Bacillus thuringiensis strain which is toxic to the housefly Musca domestica.

Characterizing proteolytic cleavage site activity using bio-basis function neural networks

Cloning and analysis of the first cry gene from Bacillus popilliae ⬇️

Comparison of functional annotation schemes for genomes

Constructing an enzyme-centric view of metabolism.

DNA Methylation and Chromatin Regulation during Fleshy Fruit Development and Ripening

Editorial: The informatics of post-translational modification and its implications for systems biology

Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions.

Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize

Growth-induced hormone dilution can explain the dynamics of plant root cell elongation.

Gsmodutils: a python based framework for test-driven genome scale metabolic model development

INTERACT: an object oriented protein-protein interaction database.

Identification of a cryptic gene associated with an insertion sequence not previously identified in Bacillus thuringiensis.

Identification of the homologous beige and Chediak-Higashi syndrome genes

Inference of gene regulatory networks using boolean-network inference methods.

Inference of the genetic network regulating lateral root initiation in Arabidopsis thaliana

Integrative biology--the way forward

Lipidomic analysis of plasma samples from women with polycystic ovary syndrome.

Mathematical simulation and analysis of cellular metabolism and regulation.

Mechanical modelling quantifies the functional importance of outer tissue layers during root elongation and bending.

Mechanistic insight into the role of AUXIN RESISTANCE4 in trafficking of AUXIN1 and LIKE AUX1-2

Metabolic differences in ripening of Solanum lycopersicum 'Ailsa Craig' and three monogenic mutants ⬇️

Models for the structure and function of the Bacillus thuringiensis delta-endotoxins determined by compilational analysis

Modulation of Arabidopsis and monocot root architecture by CLAVATA3/EMBRYO SURROUNDING REGION 26 peptide

Multi-omics analysis identifies genes mediating the extension of cell walls in the Arabidopsis thaliana root elongation zone. ⬇️

Network inference analysis identifies an APRR2-like gene linked to pigment accumulation in tomato and pepper fruits.

Occurrence of a Quadruplex Motif in a Unique Insert within Exon C of the Bovine Estrogen Receptor α Gene (ESR1)

OsCAND1 is required for crown root emergence in rice.

Progress towards platform chemical production using

Reduction of off-flavor generation in soybean homogenates: a mathematical model.

Regulatory feedback response mechanisms to phosphate starvation in rice.

Reported sequence homology between Alzheimer amyloid770 and the MRC OX-2 antigen does not predict function

Repression of translation of human estrogen receptor alpha by G-quadruplex formation

Rice auxin influx carrier OsAUX1 facilitates root hair elongation in response to low external phosphate ⬇️

Searching for discrimination rules in protease proteolytic cleavage activity using genetic programming with a min-max scoring function.

Secondary structure analysis identifies a putative mouse protein demonstrating similarity to the repeat units found in CDC4, the G protein beta subunits and related proteins

Sequence variants in the bovine gonadotrophin releasing hormone receptor gene and their associations with fertility

Simultaneous modelling of metabolic, genetic and product-interaction networks.

Statistical evaluation of transcriptomic data generated using the Affymetrix one-cycle, two-cycle and IVT-Express RNA labelling protocols with the Arabidopsis ATH1 microarray

Tackling drought stress: receptor-like kinases present new approaches

The Beta-adrenergic agonist, Ractopamine, increases skeletal muscle expression of Asparagine Synthetase as part of an integrated stress response gene program

The herpes simplex virus type 2 equivalent of the herpes simplex virus type 1 US7 gene and its flanking sequences

The logic of the floral transition: Reverse-engineering the switch controlling the identity of lateral organs

The successful application of systems approaches in plant biology.

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models

Unraveling the evolution of auxin signaling

Validation of proteomic biomarkers previously found to be differentially expressed in women with polycystic ovary syndrome: a cross-sectional study.

Whole genome sequence and manual annotation of Clostridium autoethanogenum, an industrially relevant bacterium

[Method SiteGA for the recognition of transcription factor binding sites]

pBR322 and other pSC101 derivatives have a gene fragment related to the mini-F plasmid resolvase.