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jfrs profile

About me

Username:	jfr
Name:	James F. Reid
Job title:	Not specified
Affiliation:	Not specified
Web page:	http://pierotti.group.ifom-ieo-campus.it/jreid/index.html
Joined:	2005-08-14

What I do

Not specified

Interests

bioinformatics; functional genomics; microarrays; molecular tumor classification

Recent Activity

2008-10-01

11:12: posted A stochastic carcinogenesis model incorporating multiple types of genomic instability fitted to colon cancer data.
11:10: posted Protein tyrosine phosphatase receptor-type O (PTPRO) is co-regulated by E2F1 and miR-17-92.
11:07: posted Comparison of molecular phenotypes of ductal carcinoma in situ and invasive breast cancer
11:06: posted Meta-analysis of gene-expression profiles in breast cancer: toward a unified understanding of breast cancer sub-typing and prognosis signatures
11:04: posted Molecular targeted therapies for breast cancer treatment
11:03: posted Oncogenic Ras and Transforming Growth Factor-{beta} Synergistically Regulate AU-Rich Element-Containing mRNAs during Epithelial to Mesenchymal Transition
09:58: posted Gene expression-based survival prediction in lung adenocarcinoma: a multi-site, blinded validation study.
09:56: posted Strategies for discovering novel cancer biomarkers through utilization of emerging technologies
09:55: posted Gene-expression profiling in epithelial ovarian cancer.
09:54: posted Latest discoveries and trends in translational cancer research: highlights of the 2008 Annual Meeting of the American Association for Cancer Research.
09:52: posted A comprehensive comparison of random forests and support vector machines for microarray-based cancer classification

2008-09-30

13:15: posted The public road to high-quality curated biological pathways.
13:14: posted The ontology of biological taxa.
13:11: posted Tissue-specific splicing factor gene expression signatures
11:16: posted A comparison of normalization techniques for microRNA microarray data.
11:13: posted Comparative 3'UTR analysis allows identification of regulatory clusters that drive Eph/ephrin expression in cancer cell lines.
11:11: posted MeV+R: using MeV as a graphical user interface for Bioconductor applications in microarray analysis
11:10: posted Analysis of gene expression in a developmental context emphasizes distinct biological leitmotifs in human cancers
11:09: posted A precisely regulated gene expression cassette potently modulates metastasis and survival in multiple solid cancers.

2008-09-29

2008-09-26

16:48: posted Strong position-dependent effects of sequence mismatches on signal ratios measured using long oligonucleotide microarrays
16:19: posted Estimation and testing for the effect of a genetic pathway on a disease outcome using logistic kernel machine regression via logistic mixed models
16:18: posted Literature-aided meta-analysis of microarray data: a compendium study on muscle development and disease
16:17: posted Between-groups within-gene heterogeneity of residual variances in microarray gene expression data
11:39: posted Seeded Bayesian Networks: constructing genetic networks from microarray data
11:38: posted MicroRNA prediction with a novel ranking algorithm based on random walks
11:37: posted PMC42, a breast progenitor cancer cell line, has normal-like mRNA and miRNA transcriptomes
11:35: posted The humoral immune system has a key prognostic impact in node-negative breast cancer.
11:31: posted Drug Target Identification Using Side-Effect Similarity
11:02: posted Towards the use of argumentation in bioinformatics: a gene expression case study.
11:00: posted Prediction of drug-target interaction networks from the integration of chemical and genomic spaces.
10:58: posted Identifying functional modules in protein-protein interaction networks: an integrated exact approach
10:56: posted Inferring differentiation pathways from gene expression.
10:55: posted Alignment and classification of time series gene expression in clinical studies.
10:53: posted Classification and feature selection algorithms for multi-class CGH data.
10:51: posted Differential variability analysis of gene expression and its application to human diseases.
10:48: posted Classification of arrayCGH data using fused SVM.

2008-09-24

14:52: posted The proto-oncogene LRF is under post-transcriptional control of MiR-20a: implications for senescence.
14:49: posted Unraveling Protein Networks with Power Graph Analysis
14:25: posted Keeping pace with the data: 2008 update on the Bioinformatics Links Directory.
14:24: posted FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology
14:23: posted Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping.
14:22: posted MYB function in normal and cancer cells
14:21: posted Multiple Loci With Different Cancer Specificities Within the 8q24 Gene Desert
14:18: posted The Systems Biology Research Tool: evolvable open-source software
14:15: posted A statistical framework for consolidating "sibling" probe sets for Affymetrix GeneChip data
14:08: posted Use and misuse of the gene ontology annotations.
14:07: posted Systems biology at the Institute for Systems Biology.
14:05: posted On correcting the overestimation of the permutation based false discovery rate estimator.
14:01: posted Dimension reduction with redundant gene elimination for tumor classification.
14:00: posted Systems biology driven software design for the research enterprise
13:58: posted The pairwise disconnectivity index as a new metric for the topological analysis of regulatory networks
13:54: posted Stability of gene contributions and identification of outliers in multivariate analysis of microarray data
13:51: posted Ten Simple Rules for Organizing a Scientific Meeting
13:49: posted Systematic reconstruction of TRANSPATH data into Cell System Markup Language
13:40: posted A weighted average difference method for detecting differentially expressed genes from microarray data
13:39: posted ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses.
13:36: posted Improving the power for detecting overlapping genes from multiple DNA microarray-derived gene lists.
13:32: posted A correction for estimating error when using the Local Pooled Error Statistical Test.
13:31: posted lumi: a pipeline for processing Illumina microarray.
13:30: posted RNA quality in frozen breast cancer samples and the influence on gene expression analysis - a comparison of three evaluation methods using microcapillary electrophoresis traces
13:27: posted Impact of RNA quality on reference gene expression stability.
13:25: posted Improved RNA quality and TaqMan(R) Pre-amplification method (PreAmp) to enhance expression analysis from formalin fixed paraffin embedded (FFPE) materials
13:24: posted Universal Reference RNA is Not a Representative Normal Sample for Oligonucleotide Microarray Studies.
13:20: posted Genome-scale cluster analysis of replicated microarrays using shrinkage correlation coefficient
11:43: posted Finding common genes in multiple cancer types through meta-analysis of microarray experiments: A rank aggregation approach.
11:42: posted Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends.
11:41: posted SMAD proteins control DROSHA-mediated microRNA maturation
11:33: posted On Gene Ranking Using Replicated Microarray Time Course Data.
11:32: posted Mathematical models of cancer stem cells.

2008-09-22

2008-09-19

15:34: posted I/NI-calls for the exclusion of non-informative genes: a highly effective filtering tool for microarray data
15:32: posted Knowledge - based Gene Expression Classification via Matrix Factorization.
15:17: posted TGFbeta primes breast tumors for lung metastasis seeding through angiopoietin-like 4.
15:16: posted Stromal gene expression predicts clinical outcome in breast cancer
14:57: posted Finding edging genes from microarray data.

2008-09-18

15:52: posted Mapping and quantifying mammalian transcriptomes by RNA-Seq.

2008-09-16

19:09: posted Pattern expression nonnegative matrix factorization: algorithm and applications to blind source separation.
19:08: posted MicroRNA Expression and Identification of Putative miRNA Targets in Ovarian Cancer
19:04: posted Evaluating Statistical Methods Using Plasmode Data Sets in the Age of Massive Public Databases: An Illustration Using False Discovery Rates
18:59: posted Development of a clinically feasible molecular assay to predict recurrence of stage II colon cancer.
18:57: posted Methods for evaluating gene expression from Affymetrix microarray datasets
18:56: posted Improving the prediction accuracy in classification using the combined data sets by ranks of gene expressions
18:55: posted Using the information embedded in the testing sample to break the limits caused by the small sample size in microarray-based classification
09:51: posted The impact of microRNAs on protein output
09:39: posted Widespread changes in protein synthesis induced by microRNAs
09:25: posted In Silico regulatory analysis for exploring human disease progression
09:21: posted Circulating microRNAs as stable blood-based markers for cancer detection.
09:16: posted Breast cancer: origins and evolution.
08:58: posted Dynamics of cancer progression

2008-09-15

17:52: posted The use of genomic tools for the molecular understanding of breast cancer and to guide personalized medicine.
17:03: posted NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways.
17:00: posted bioNMF: a web-based tool for nonnegative matrix factorization in biology
16:59: posted Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments.
16:56: posted CID-miRNA: a web server for prediction of novel miRNA precursors in human genome.
16:55: posted UCSC genome browser tutorial.
13:56: posted Public Databases and Software for the Pathway Analysis of Cancer Genomes.
12:49: posted Synergistic response to oncogenic mutations defines gene class critical to cancer phenotype
12:32: posted Hubba: hub objects analyzer--a framework of interactome hubs identification for network biology.
12:31: posted GEPAS, a web-based tool for microarray data analysis and interpretation
12:28: posted iTools: a framework for classification, categorization and integration of computational biology resources.
12:27: posted Mapping and sequencing of structural variation from eight human genomes
12:18: posted Inferring microRNA activities by combining gene expression with microRNA target prediction.
12:15: posted Estimation of relevant variables on high-dimensional biological patterns using iterated weighted kernel functions.
12:13: posted Comprehensive analysis of affymetrix exon arrays using BioConductor.
12:10: posted Comparison of normalization methods with microRNA microarray
11:53: posted Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers.
11:24: posted Transcription factor and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets.
10:51: posted Individual mRNA expression profiles reveal the effects of specific microRNAs
10:42: posted Characterization of microRNA-regulated protein-protein interaction network.
10:24: posted The "street light syndrome", or how protein taxonomy can bias experimental manipulations.