Published in Bioinformatics on January 29, 2004
Analyzing the antagonistic potential of the lichen microbiome against pathogens by bridging metagenomic with culture studies. Front Microbiol (2015) 0.90
Rhizobiales as functional and endosymbiontic members in the lichen symbiosis of Lobaria pulmonaria L. Front Microbiol (2015) 0.85
Type, density, and location of immune cells within human colorectal tumors predict clinical outcome. Science (2006) 24.54
Effector memory T cells, early metastasis, and survival in colorectal cancer. N Engl J Med (2005) 12.64
Genesis: cluster analysis of microarray data. Bioinformatics (2002) 10.50
ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics (2009) 8.60
Histopathologic-based prognostic factors of colorectal cancers are associated with the state of the local immune reaction. J Clin Oncol (2011) 5.63
In situ cytotoxic and memory T cells predict outcome in patients with early-stage colorectal cancer. J Clin Oncol (2009) 3.97
A survey of tools for variant analysis of next-generation genome sequencing data. Brief Bioinform (2013) 3.60
Spatiotemporal dynamics of intratumoral immune cells reveal the immune landscape in human cancer. Immunity (2013) 3.50
CARMAweb: comprehensive R- and bioconductor-based web service for microarray data analysis. Nucleic Acids Res (2006) 2.93
Coordination of intratumoral immune reaction and human colorectal cancer recurrence. Cancer Res (2009) 2.37
miR-17, miR-19b, miR-20a, and miR-106a are down-regulated in human aging. Aging Cell (2010) 2.31
MARS: microarray analysis, retrieval, and storage system. BMC Bioinformatics (2005) 2.14
PathwayExplorer: web service for visualizing high-throughput expression data on biological pathways. Nucleic Acids Res (2005) 2.12
Biomolecular network reconstruction identifies T-cell homing factors associated with survival in colorectal cancer. Gastroenterology (2009) 2.01
Gene expression profiling of human mesenchymal stem cells derived from bone marrow during expansion and osteoblast differentiation. BMC Genomics (2007) 1.90
Evolution of genomic instability in diethylnitrosamine-induced hepatocarcinogenesis in mice. Hepatology (2011) 1.56
Identification of small gains and losses in single cells after whole genome amplification on tiling oligo arrays. Nucleic Acids Res (2009) 1.37
Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy. Genome Biol (2015) 1.35
MASPECTRAS: a platform for management and analysis of proteomics LC-MS/MS data. BMC Bioinformatics (2007) 1.34
Oxytocin controls differentiation of human mesenchymal stem cells and reverses osteoporosis. Stem Cells (2008) 1.32
Activin a plays a critical role in proliferation and differentiation of human adipose progenitors. Diabetes (2010) 1.31
YPL.db: the Yeast Protein Localization database. Nucleic Acids Res (2002) 1.26
SIMPLEX: cloud-enabled pipeline for the comprehensive analysis of exome sequencing data. PLoS One (2012) 1.22
A quantization method based on threshold optimization for microarray short time series. BMC Bioinformatics (2005) 1.21
Mutations in ROGDI Cause Kohlschütter-Tönz Syndrome. Am J Hum Genet (2012) 1.21
Generic features of tertiary chromatin structure as detected in natural chromosomes. Mol Cell Biol (2004) 1.19
Proteomic analysis of human cataract aqueous humour: Comparison of one-dimensional gel LCMS with two-dimensional LCMS of unlabelled and iTRAQ®-labelled specimens. J Proteomics (2010) 1.18
Molecular processes during fat cell development revealed by gene expression profiling and functional annotation. Genome Biol (2005) 1.16
Identification of differential and functionally active miRNAs in both anaplastic lymphoma kinase (ALK)+ and ALK- anaplastic large-cell lymphoma. Proc Natl Acad Sci U S A (2010) 1.15
TAMEE: data management and analysis for tissue microarrays. BMC Bioinformatics (2007) 1.15
New trends in bioinformatics: from genome sequence to personalized medicine. Exp Gerontol (2003) 1.15
iLAP: a workflow-driven software for experimental protocol development, data acquisition and analysis. BMC Bioinformatics (2009) 1.14
Identification of evolutionarily conserved genetic regulators of cellular aging. Aging Cell (2010) 1.09
Comparative transcriptomics of human multipotent stem cells during adipogenesis and osteoblastogenesis. BMC Genomics (2008) 1.09
Differential transcriptional modulation of biological processes in adipocyte triglyceride lipase and hormone-sensitive lipase-deficient mice. Genomics (2008) 1.07
QPCR: Application for real-time PCR data management and analysis. BMC Bioinformatics (2009) 1.04
YPL.db2: the Yeast Protein Localization database, version 2.0. Yeast (2005) 1.01
The phosphatidylethanolamine level of yeast mitochondria is affected by the mitochondrial components Oxa1p and Yme1p. FEBS J (2007) 1.00
Client-server environment for high-performance gene expression data analysis. Bioinformatics (2003) 0.99
Java editor for biological pathways. Bioinformatics (2003) 0.98
Assessment of transcapillary glucose exchange in human skeletal muscle and adipose tissue. Am J Physiol Endocrinol Metab (2003) 0.96
Novel insights into adipogenesis from omics data. Curr Med Chem (2009) 0.95
Transcription factories. Front Genet (2012) 0.95
SPARQLGraph: a web-based platform for graphically querying biological Semantic Web databases. BMC Bioinformatics (2014) 0.95
Stathmin-like 2, a developmentally-associated neuronal marker, is expressed and modulated during osteogenesis of human mesenchymal stem cells. Biochem Biophys Res Commun (2008) 0.94
Organization of chromatin and histone modifications at a transcription site. J Cell Biol (2007) 0.93
MASPECTRAS 2: An integration and analysis platform for proteomic data. Proteomics (2010) 0.93
MEMOSys: Bioinformatics platform for genome-scale metabolic models. BMC Syst Biol (2011) 0.93
NAT8L (N-acetyltransferase 8-like) accelerates lipid turnover and increases energy expenditure in brown adipocytes. J Biol Chem (2013) 0.91
GPViz: dynamic visualization of genomic regions and variants affecting protein domains. Bioinformatics (2013) 0.90
Bioinformatics for cancer immunology and immunotherapy. Cancer Immunol Immunother (2012) 0.90
The role of intramyocellular lipids during hypoglycemia in patients with intensively treated type 1 diabetes. J Clin Endocrinol Metab (2005) 0.89
High STAT1 mRNA levels but not its tyrosine phosphorylation are associated with macrophage infiltration and bad prognosis in breast cancer. BMC Cancer (2014) 0.89
Arsenic trioxide induces apoptosis preferentially in B-CLL cells of patients with unfavourable prognostic factors including del17p13. J Mol Med (Berl) (2008) 0.87
Reconstruction of gene association network reveals a transmembrane protein required for adipogenesis and targeted by PPARγ. Cell Mol Life Sci (2010) 0.87
microRNAs in nociceptive circuits as predictors of future clinical applications. Front Mol Neurosci (2013) 0.85
Hypochlorite modification of sphingomyelin generates chlorinated lipid species that induce apoptosis and proteome alterations in dopaminergic PC12 neurons in vitro. Free Radic Biol Med (2010) 0.84
SeqBench: integrated solution for the management and analysis of exome sequencing data. BMC Res Notes (2014) 0.84
Cooperativity of stress-responsive transcription factors in core hypoxia-inducible factor binding regions. PLoS One (2012) 0.83
GOLD.db: genomics of lipid-associated disorders database. BMC Genomics (2004) 0.83
Analysis of DNA microarray data. Curr Top Med Chem (2004) 0.83
microRNAs in acute myeloid leukemia: expression patterns, correlations with genetic and clinical parameters, and prognostic significance. Genes Chromosomes Cancer (2010) 0.82
Identification of microRNA-mRNA functional interactions in UVB-induced senescence of human diploid fibroblasts. BMC Genomics (2013) 0.81
Co-expressed genes prepositioned in spatial neighborhoods stochastically associate with SC35 speckles and RNA polymerase II factories. Cell Mol Life Sci (2013) 0.81
Arxes: retrotransposed genes required for adipogenesis. Nucleic Acids Res (2010) 0.80
Information technology solutions for integration of biomolecular and clinical data in the identification of new cancer biomarkers and targets for therapy. Pharmacol Ther (2010) 0.79
LPL-mediated lipolysis of VLDL induces an upregulation of AU-rich mRNAs and an activation of HuR in endothelial cells. Atherosclerosis (2006) 0.78
Transcriptional regulatory program in wild-type and retinoblastoma gene-deficient mouse embryonic fibroblasts during adipocyte differentiation. BMC Res Notes (2011) 0.78
A new platform linking chromosomal and sequence information. Chromosome Res (2007) 0.78
Nr4a1 is required for fasting-induced down-regulation of Pparγ2 in white adipose tissue. Mol Endocrinol (2012) 0.78
Genome-scale model management and comparison. Methods Mol Biol (2013) 0.76
Data integration and exploration for the identification of molecular mechanisms in tumor-immune cells interaction. BMC Genomics (2010) 0.76
Adipose triglyceride lipase and hormone-sensitive lipase are involved in fat loss in JunB-deficient mice. Endocrinology (2011) 0.76
MEMOSys 2.0: an update of the bioinformatics database for genome-scale models and genomic data. Database (Oxford) (2014) 0.75
GiSAO.db: a database for ageing research. BMC Genomics (2011) 0.75
Insights into global mechanisms and disease by gene expression profiling. Methods Mol Biol (2011) 0.75
Information management systems for pharmacogenomics. Pharmacogenomics (2002) 0.75
Systems for the management of pharmacogenomic information. Methods Mol Biol (2005) 0.75