List of works by Nathan D Price

A CD133-related gene expression signature identifies an aggressive glioblastoma subtype with excessive mutations.

scientific article

A blood-based proteomic classifier for the molecular characterization of pulmonary nodules.

scientific article

A candidate regulatory variant at the TREM gene cluster associates with decreased Alzheimer's disease risk and increased TREML1 and TREM2 brain gene expression

scientific article published on 8 December 2016

A community-driven global reconstruction of human metabolism. ⬇️

scientific article

A comprehensive map of genome-wide gene regulation in Mycobacterium tuberculosis.

scientific article published on 31 March 2015

A refined genome-scale reconstruction of Chlamydomonas metabolism provides a platform for systems-level analyses

scientific article

A synthesis of bacterial and archaeal phenotypic trait data

scientific article published on 05 June 2020

A systems approach to clinical oncology uses deep phenotyping to deliver personalized care

scientific article published on 16 October 2019

A systems approach to prion disease

scientific article

A wellness study of 108 individuals using personal, dense, dynamic data clouds

scientific article published on 17 July 2017

AUREA: an open-source software system for accurate and user-friendly identification of relative expression molecular signatures.

scientific article

Accomplishments in genome-scale in silico modeling for industrial and medical biotechnology

scientific article

Aggression is associated with aerobic glycolysis in the honey bee brain(1)

scientific article

An argument for mechanism-based statistical inference in cancer.

scientific article

Atlas of Transcription Factor Binding Sites from ENCODE DNase Hypersensitivity Data Across 27 Tissue Types

Atlas of Transcription Factor Binding Sites from ENCODE DNase Hypersensitivity Data across 27 Tissue Types

scientific article published on 01 August 2020

Big biomedical data as the key resource for discovery science

scientific article published on 21 July 2015

Blood metabolome predicts gut microbiome α-diversity in humans

scientific article published on 02 September 2019

Candidate metabolic network states in human mitochondria. Impact of diabetes, ischemia, and diet.

scientific article published on 30 November 2004

Candidate states of Helicobacter pylori's genome-scale metabolic network upon application of "loop law" thermodynamic constraints.

scientific article

Combining inferred regulatory and reconstructed metabolic networks enhances phenotype prediction in yeast

scientific article

Comparative Analysis of Yeast Metabolic Network Models Highlights Progress, Opportunities for Metabolic Reconstruction

scientific article

Comparative analysis of gene expression in maternal peripheral blood and monocytes during spontaneous preterm labor.

scientific article published on 2 January 2018

Comparative transcriptomic analysis of human placentae at term and preterm delivery.

scientific article published on 4 December 2017

Comparison of network-based pathway analysis methods

scientific article

Conserved brain myelination networks are altered in Alzheimer's and other neurodegenerative diseases

scientific article published on 26 October 2017

Corrigendum: Motivational, proteostatic and transcriptional deficits precede synapse loss, gliosis and neurodegeneration in the B6.HttQ111/+ model of Huntington's disease.

scientific article published on 28 March 2017

Crops In Silico: Generating Virtual Crops Using an Integrative and Multi-scale Modeling Platform

scientific article

Data-driven integration of genome-scale regulatory and metabolic network models

scientific article

Deep phenotyping during pregnancy for predictive and preventive medicine

scientific article published on 01 January 2020

Demystifying disease, democratizing health care

scientific article published on 01 February 2014

Detection of 1α,25-dihydroxyvitamin D-regulated miRNAs in zebrafish by whole transcriptome sequencing

scientific article

Determination of redundancy and systems properties of the metabolic network of Helicobacter pylori using genome-scale extreme pathway analysis.

scientific article published on May 2002

Development of a gene knockout system using mobile group II introns (Targetron) and genetic disruption of acid production pathways in Clostridium beijerinckii

scientific article (publication date: October 2013)

Development of network-based pathway definitions: the need to analyze real metabolic networks

article

Digitizing omics profiles by divergence from a baseline.

scientific article published on 16 April 2018

Distinct communication patterns of trophoblastic miRNA among the maternal-placental-fetal compartments

scientific article published on 22 October 2018

Divergent brain gene expression patterns associate with distinct cell-specific tau neuropathology traits in progressive supranuclear palsy

article

Do genome-scale models need exact solvers or clearer standards?

scientific article published on 14 October 2015

Editorial overview: Systems biology: Data, discovery, delivery

scientific article published on 01 June 2018

Editorial: Systems biology for biotech applications

scientific article published on 01 July 2010

Emerging Proteomic Technologies Provide Enormous and Underutilized Potential for Brain Cancer Research.

scientific article published on 25 September 2015

Enhanced retinal responses in Huntington's disease patients.

scientific article published in January 2017

Exploring Hydrogenotrophic Methanogenesis: a Genome Scale Metabolic Reconstruction of Methanococcus maripaludis

scientific article

Extreme pathway lengths and reaction participation in genome-scale metabolic networks

scientific article

Fostering synergy between cell biology and systems biology.

scientific article published on 23 May 2015

Gene expression, methylation and neuropathology correlations at progressive supranuclear palsy risk loci.

scientific article published on 26 April 2016

Genetic Predisposition Impacts Clinical Changes in a Lifestyle Coaching Program

article

Genetic co-occurrence network across sequenced microbes

scientific article

Genome-Scale Transcriptional Regulatory Network Models of Psychiatric and Neurodegenerative Disorders

scientific article published on 13 February 2019

Genome-scale consequences of cofactor balancing in engineered pentose utilization pathways in Saccharomyces cerevisiae

scientific article (publication date: 2011)

Genome-scale metabolic model of the rat liver predicts effects of diet restriction

scientific article published on 08 July 2019

Genome-scale metabolic reconstruction and hypothesis testing in the methanogenic archaeon Methanosarcina acetivorans C2A.

scientific article published on 2 December 2011

Genome-scale microbial in silico models: the constraints-based approach.

scientific article

Genome-scale modeling for metabolic engineering.

scientific article published on 13 January 2015

Genome-scale models of microbial cells: evaluating the consequences of constraints

scientific article (publication date: November 2004)

Genome-wide pleiotropy analysis of neuropathological traits related to Alzheimer's disease

scientific article published on 20 February 2018

Genomic, Transcriptional, and Phenotypic Analysis of the Glucose Derepressed Clostridium beijerinckii Mutant Exhibiting Acid Crash Phenotype

scientific article published in August 2017

Genomically and biochemically accurate metabolic reconstruction of Methanosarcina barkeri Fusaro, iMG746

scientific article published on 26 March 2013

Gut microbiome pattern reflects healthy ageing and predicts survival in humans

scientific article published on 18 February 2021

Halomonas sulfidaeris-dominated microbial community inhabits a 1.8 km-deep subsurface Cambrian Sandstone reservoir.

scientific article

Health and disease markers correlate with gut microbiome composition across thousands of people

scientific article published on 15 October 2020

Heterogeneity in protein expression induces metabolic variability in a modeled Escherichia coli population.

scientific article published on August 2013

Human whole genome genotype and transcriptome data for Alzheimer's and other neurodegenerative diseases

scientific article

IFPA meeting 2016 workshop report I: Genomic communication, bioinformatics, trophoblast biology and transport systems

scientific article published on 11 January 2017

IL-10 alters immunoproteostasis in APP mice, increasing plaque burden and worsening cognitive behavior.

scientific article published on 22 January 2015

ITEP: an integrated toolkit for exploration of microbial pan-genomes

scientific article

In silico models of cancer ⬇️

scientific article published on July 1, 2010

Integrated Modeling of Gene Regulatory and Metabolic Networks in Mycobacterium tuberculosis

scientific article (publication date: November 2015)

Integrated proteomics and genomics analysis reveals a novel mesenchymal to epithelial reverting transition in leiomyosarcoma through regulation of slug

scientific article

Ion channel expression patterns in glioblastoma stem cells with functional and therapeutic implications for malignancy

scientific article

Isoforms of RNA-Editing Enzyme ADAR1 Independently Control Nucleic Acid Sensor MDA5-Driven Autoimmunity and Multi-organ Development.

scientific article published on November 2015

Label-free proteomics and systems biology analysis of mycobacterial phagosomes in dendritic cells and macrophages.

scientific article published on 30 March 2011

Likelihood-based gene annotations for gap filling and quality assessment in genome-scale metabolic models

scientific article

Long-range periodic patterns in microbial genomes indicate significant multi-scale chromosomal organization.

scientific article

Longitudinal analysis reveals transition barriers between dominant ecological states in the gut microbiome

scientific article published on 29 May 2020

MEMOTE for standardized genome-scale metabolic model testing

scientific article published on 01 March 2020

Macroscopic kinetic effect of cell-to-cell variation in biochemical reactions

scientific article published on 08 April 2010

Measurement of Organ-Specific and Acute-Phase Blood Protein Levels in Early Lyme Disease

scientific article published on 01 November 2019

Measuring the effect of inter-study variability on estimating prediction error.

scientific article

MediaDB: a database of microbial growth conditions in defined media

scientific article

Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite

Metabolic constraint-based refinement of transcriptional regulatory networks

scientific article (publication date: 2013)

Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052.

scientific article

Metabolite coupling in genome-scale metabolic networks

scientific article

MicroRNAs and lipid metabolism.

scientific article published on 22 March 2017

Motivational, proteostatic and transcriptional deficits precede synapse loss, gliosis and neurodegeneration in the B6.HttQ111/+ model of Huntington's disease

scientific article

Motor neuron loss and neuroinflammation in a model of α-synuclein-induced neurodegeneration

scientific article published on 06 September 2018

Multi-omic biomarker identification and validation for diagnosing warzone-related post-traumatic stress disorder

scientific article published on 10 September 2019

Multi-study integration of brain cancer transcriptomes reveals organ-level molecular signatures

scientific article

Multiscale Analysis of Independent Alzheimer’s Cohorts Finds Disruption of Molecular, Genetic, and Clinical Networks by Human Herpesvirus

article

Network reconstruction and systems analysis of plant cell wall deconstruction by Neurospora crassa.

scientific article published on 21 September 2017

Network-based analysis of metabolic regulation in the human red blood cell

scientific article (publication date: 21 November 2003)

Network-level analysis of metabolic regulation in the human red blood cell using random sampling and singular value decomposition

scientific article

OptRAM: In-silico strain design via integrative regulatory-metabolic network modeling

scientific article published on 08 March 2019

P4 medicine: how systems medicine will transform the healthcare sector and society

scientific article

Peripheral huntingtin silencing does not ameliorate central signs of disease in the B6.HttQ111/+ mouse model of Huntington's disease

scientific article

Personalized nutrition through big data.

scientific article

Predictive Big Data Analytics: A Study of Parkinson's Disease Using Large, Complex, Heterogeneous, Incongruent, Multi-Source and Incomplete Observations

scientific article

ProbAnnoWeb and ProbAnnoPy: probabilistic annotation and gap-filling of metabolic reconstructions.

scientific article published on 18 December 2017

Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis.

scientific article

Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing

scientific article published on 01 April 2020

Quantitative proteomic analysis reveals effects of epidermal growth factor receptor (EGFR) on invasion-promoting proteins secreted by glioblastoma cells

scientific article

Rare coding variants in PLCG2, ABI3, and TREM2 implicate microglial-mediated innate immunity in Alzheimer's disease

scientific article

Rare variants in neuronal excitability genes influence risk for bipolar disorder

scientific article

Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE

scientific article

Relative expression analysis for identifying perturbed pathways.

scientific article published on January 2009

Relative expression analysis for molecular cancer diagnosis and prognosis

scientific article

Relative stability of network states in Boolean network models of gene regulation in development.

scientific article published on 07 March 2016

Reply

Reply to "Precision medicine in the clouds"

scientific article published on 01 August 2018

Reproducible big data science: A case study in continuous FAIRness

scientific article published on 11 April 2019

Serum from calorie-restricted animals delays senescence and extends the lifespan of normal human fibroblasts in vitro.

scientific article

Single-Cell Proteomics Reveal that Quantitative Changes in Co-expressed Lineage-Specific Transcription Factors Determine Cell Fate

scientific article published on 14 March 2019

Systems approach to neurodegenerative disease biomarker discovery.

scientific article

Systems cancer medicine: towards realization of predictive, preventive, personalized and participatory (P4) medicine

scientific article

Systems pharmacology modeling: an approach to improving drug safety

scientific article

TLR5 decoy receptor as a novel anti-amyloid therapeutic for Alzheimer's disease

scientific article published on 01 September 2018

Taking Systems Medicine to Heart.

scientific article published in April 2018

Targeting TWIST1 through loss of function inhibits tumorigenicity of human glioblastoma.

scientific article

Temporal Transcriptomic Analysis of Metabolic Genes in Maternal Organs and Placenta During Murine Pregnancy

article

The DNA-binding network of Mycobacterium tuberculosis

scientific article

The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models

scientific article

The building blocks of successful translation of proteomics to the clinic.

scientific article published on 6 February 2018

The genome-scale metabolic extreme pathway structure in Haemophilus influenzae shows significant network redundancy.

scientific article published in March 2002

The limits of de novo DNA motif discovery.

scientific article published on 7 November 2012

Transcriptional analysis of aggressiveness and heterogeneity across grades of astrocytomas

scientific article

Transcriptional program for nitrogen starvation-induced lipid accumulation in Chlamydomonas reinhardtii

scientific article

Transparency in metabolic network reconstruction enables scalable biological discovery

scientific article published on 3 January 2015

Uniform sampling of steady-state flux spaces: means to design experiments and to interpret enzymopathies.

scientific article

Version 6 of the consensus yeast metabolic network refines biochemical coverage and improves model performance.

scientific article published on 9 August 2013

iREAD: a tool for intron retention detection from RNA-seq data

scientific article published on 06 February 2020

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