Search filters

List of works by Christian J Stoeckert

A Coordinated Approach by Public Domain Bioinformatics Resources to Aid the Fight Against Alzheimer's Disease Through Expert Curation of Key Protein Targets

scientific article published on 20 July 2020

A Framework for Global Collaborative Data Management for Malaria Research

scientific article

A molecular profile of a hematopoietic stem cell niche

scientific article

A practical false discovery rate approach to identifying patterns of differential expression in microarray data

scientific article

A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB

scientific article

AmoebaDB and MicrosporidiaDB: functional genomic resources for Amoebozoa and Microsporidia species

scientific article

An object model and database for functional genomics

scientific article published on 14 May 2004

An open letter on microarray data from the MGED Society

scientific article published on November 2004

Analysis and management of microarray gene expression data.

scientific article

AnnotCompute: annotation-based exploration and meta-analysis of genomics experiments ⬇️

scientific article published on December 21, 2011

Annotare--a tool for annotating high-throughput biomedical investigations and resulting data

scientific article

ApiDB: integrated resources for the apicomplexan bioinformatics resource center

scientific article

ApiEST-DB: analyzing clustered EST data of the apicomplexan parasites

scientific article

Arterial endothelial methylome: differential DNA methylation in athero-susceptible disturbed flow regions in vivo

scientific article

Assessing the significance of conserved genomic aberrations using high resolution genomic microarrays

scientific article

CLO: The cell line ontology

scientific article

Chronic endoplasmic reticulum stress activates unfolded protein response in arterial endothelium in regions of susceptibility to atherosclerosis.

scientific article published on 6 August 2009

ClinEpiDB: an open-access clinical epidemiology database resource encouraging online exploration of complex studies

scientific article published on 25 November 2019

Clustering of genes into regulons using integrated modeling-COGRIM.

scientific article published on January 2007

Coexisting proinflammatory and antioxidative endothelial transcription profiles in a disturbed flow region of the adult porcine aorta.

scholarly article

Common objects: think global, act local

scientific article published on 01 January 2003

Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM).

scientific article

Comparative genomics of the neglected human malaria parasite Plasmodium vivax

scientific article

Comparison of different labeling methods for two-channel high-density microarray experiments

scientific article

Computational Methods and Bioinformatic Tools

Computational analysis of constraints on noncoding regions, coding regions and gene expression in relation to Plasmodium phenotypic diversity

scientific article

Computational modeling of the Plasmodium falciparum interactome reveals protein function on a genome-wide scale

scientific article

Conservation and divergence of known apicomplexan transcriptional regulons

scientific article

Coronary artery endothelial transcriptome in vivo: identification of endoplasmic reticulum stress and enhanced reactive oxygen species by gene connectivity network analysis

scientific article

Data standards for Omics data: the basis of data sharing and reuse

scientific article (publication date: 2011)

Defining the mammalian CArGome

scientific article

Design and implementation of microarray gene expression markup language (MAGE-ML)

scientific article

Development of FuGO: an ontology for functional genomics investigations

scientific article published on January 2006

Development of the Minimum Information Specification for In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE).

scientific article published on January 2006

Discovery approaches to UPR in athero-susceptible endothelium in vivo.

scientific article published on January 2011

Dual lineage-specific expression of Sox17 during mouse embryogenesis.

scientific article published on October 2012

EPConDB: a web resource for gene expression related to pancreatic development, beta-cell function and diabetes

scientific article published on 27 October 2006

Emerging topic: flow-related epigenetic regulation of endothelial phenotype through DNA methylation.

scientific article published on 27 May 2014

EuPathDB: a portal to eukaryotic pathogen databases

scientific article

EuPathDB: the eukaryotic pathogen database

scientific article

EuPathDB: the eukaryotic pathogen genomics database resource

scientific article

Expansion of adult beta-cell mass in response to increased metabolic demand is dependent on HNF-4alpha

scientific article published on April 2007

Fidelity and enhanced sensitivity of differential transcription profiles following linear amplification of nanogram amounts of endothelial mRNA.

scientific article published on 16 April 2003

Functional genomics databases on the web.

scientific article

Functional genomics of the beta-cell: short-chain 3-hydroxyacyl-coenzyme A dehydrogenase regulates insulin secretion independent of K+ currents.

scientific article

Functional genomics of the endocrine pancreas: the pancreas clone set and PancChip, new resources for diabetes research

scientific article published in July 2002

FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes.

scientific article published on 20 March 2018

Gene discovery in the apicomplexa as revealed by EST sequencing and assembly of a comparative gene database

scientific article

GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis

scientific article

Insm1 promotes endocrine cell differentiation by modulating the expression of a network of genes that includes Neurog3 and Ripply3

scientific journal article

Integrated Regional Cardiac Hemodynamic Imaging and RNA Sequencing Reveal Corresponding Heterogeneity of Ventricular Wall Shear Stress and Endocardial Transcriptome

scientific article

Integrating computationally assembled mouse transcript sequences with the Mouse Genome Informatics (MGI) database

scientific article

LKB1 regulates pancreatic beta cell size, polarity, and function

scientific article published on October 2009

Large scale transcriptome data integration across multiple tissues to decipher stem cell signatures

scientific article

Microarray databases: standards and ontologies

scientific article

MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments

scientific article

Minimum information about a microarray experiment (MIAME)-toward standards for microarray data

scientific article (publication date: December 2001)

Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE)

scientific article

Modeling biomedical experimental processes with OBI

scientific article

Modelling kidney disease using ontology: insights from the Kidney Precision Medicine Project

scientific article published on 16 September 2020

Much room for improvement in deposition rates of expression microarray datasets

scientific article

Neuron-specific mRNA complexity responses during hippocampal apoptosis after traumatic brain injury.

scientific article published in March 2004

Novel genes identified by manual annotation and microarray expression analysis in the pancreas

article

OBIB-a novel ontology for biobanking

scientific article published on 2 May 2016

OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies

scientific article published on 13 October 2021

Ontodog: a web-based ontology community view generation tool

scientific article published on 09 January 2014

Ontogeny of erythroid gene expression

scientific article

OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups

scientific article

OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes

scientific article (publication date: September 2003)

PPARgamma and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scale

scientific article published on November 2008

Pancreatic Inflammation Redirects Acinar to β Cell Reprogramming.

scientific article published on November 2016

Phospho-PTM proteomic discovery of novel EPO- modulated kinases and phosphatases, including PTPN18 as a positive regulator of EPOR/JAK2 Signaling

scientific article published on 03 February 2020

Phospho-proteomic discovery of novel signal transducers including thioredoxin-interacting protein as mediators of erythropoietin-dependent human erythropoiesis

scientific article published on 04 April 2020

PlasmoDB v5: new looks, new genomes

scientific article published on 6 October 2006

PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data

scientific article

PlasmoDB: the Plasmodium genome resource. An integrated database providing tools for accessing, analyzing and mapping expression and sequence data (both finished and unfinished).

scientific article

Plasmodium research in the postgenomic era.

scientific article

Predicting gene ontology functions from ProDom and CDD protein domains

scientific article

Prelesional arterial endothelial phenotypes in hypercholesterolemia: universal ABCA1 upregulation contrasts with region-specific gene expression in vivo

scientific article

Promoter features related to tissue specificity as measured by Shannon entropy

scientific article

Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project

scientific article (publication date: August 2008)

Propagation of adipogenic signals through an epigenomic transition state.

scientific article

Regional determinants of arterial endothelial phenotype dominate the impact of gender or short-term exposure to a high-fat diet.

scientific article published in June 2005

Renal gene and protein expression signatures for prediction of kidney disease progression

scientific article

STAC: A method for testing the significance of DNA copy number aberrations across multiple array-CGH experiments

scientific article

Spatial phenotyping of the endocardial endothelium as a function of intracardiac hemodynamic shear stress

scientific article published on 16 November 2016

Standardization of assay representation in the Ontology for Biomedical Investigations

scientific article published on 16 June 2021

Standardized metadata for human pathogen/vector genomic sequences

scientific article (publication date: 2014)

Standards for microarray data

scientific article

Standards for microarray data: an open letter

scientific article

Stat and interferon genes identified by network analysis differentially regulate primitive and definitive erythropoiesis

scientific article

Synaptotagmin 4 Regulates Pancreatic β Cell Maturation by Modulating the Ca2+ Sensitivity of Insulin Secretion Vesicles

scientific article published on 12 April 2018

Systems biology-defined NF-kappaB regulons, interacting signal pathways and networks are implicated in the malignant phenotype of head and neck cancer cell lines differing in p53 status

scientific article published on 11 March 2008

The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics

article

The MGED Ontology: a resource for semantics-based description of microarray experiments

scientific article published on 21 January 2006

The MGED ontology: a framework for describing functional genomics experiments

scientific article published on January 2003

The Ontology for Biomedical Investigations

scientific article

The Ontology for Parasite Lifecycle (OPL): towards a consistent vocabulary of lifecycle stages in parasitic organisms

scientific article

The Plasmodium genome database

scientific article published in Nature

The SOFG Anatomy Entry List (SAEL): an annotation tool for functional genomics data

scientific article

The Strategies WDK: a graphical search interface and web development kit for functional genomics databases

scientific article

The underlying principles of scientific publication.

scientific article published in November 2002

Top-down standards will not serve systems biology

scientific article published in Nature

ToxoDB: an integrated Toxoplasma gondii database resource

scientific article

Transcriptional program of the endocrine pancreas in mice and humans.

scientific article

TriTrypDB: a functional genomic resource for the Trypanosomatidae

scientific article

Using OrthoMCL to assign proteins to OrthoMCL-DB groups or to cluster proteomes into new ortholog groups

scientific article

Using ontologies to annotate microarray experiments

scientific article published on January 2006

Wrestling with SUMO and bio-ontologies

scientific article

Paulina is supported by:

About Paulina

Help