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jfr's profile

About me

Username:	jfr
Name:	James F. Reid
Job title:	Staff Scientist
Affiliation:	Istituto Nazionale Tumori (INT) and Istituto FIRC Oncologia Molecolare (IFOM)
Web page:	Not specified
Joined:	2005-08-14

What I do

Not specified

Interests

bioinformatics; functional genomics; microarrays; molecular tumor classification

Recent Activity

2009-11-08

23:34: posted Allelic imbalance sequencing reveals that single-nucleotide polymorphisms frequently alter microRNA-directed repression
23:32: posted The colorectal cancer risk at 18q21 is caused by a novel variant altering SMAD7 expression
23:21: posted Ten Simple Rules To Combine Teaching and Research
23:13: posted RGG: a general GUI Framework for R scripts.
23:11: posted Genome-wide massively parallel sequencing of formaldehyde fixed-paraffin embedded (FFPE) tumor tissues for copy-number- and mutation-analysis.
23:07: posted American Society of Clinical Oncology provisional clinical opinion: testing for KRAS gene mutations in patients with metastatic colorectal carcinoma to predict response to anti-epidermal growth factor receptor monoclonal antibody therapy.
23:03: posted Association of survival and disease progression with chromosomal instability: A genomic exploration of colorectal cancer
23:01: posted Combining chromosomal arm status and significantly aberrant genomic locations reveals new cancer subtypes.
22:58: posted Prediction of guide strand of microRNAs from its sequence and secondary structure
22:54: posted Properties of balanced permutations.
22:49: posted Recent advances in systemic therapy. Advances in adjuvant systemic chemotherapy of early breast cancer
22:48: posted Recent advances in systemic therapy. New diagnostics and biological predictors of outcome in early breast cancer
22:45: posted The breast cancer somatic 'muta-ome': tackling the complexity.
22:42: posted A dynamic network approach for the study of human phenotypes
22:39: posted Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples
22:37: posted Information flow analysis of interactome networks.
22:33: posted Genomic Grade Index Is Associated With Response to Chemotherapy in Patients With Breast Cancer
22:30: posted CloudBurst: highly sensitive read mapping with MapReduce
22:22: posted Molecular classification of solid tumours: towards pathway-driven therapeutics.
22:20: posted Identifying protein-coding genes in genomic sequences
22:18: posted Adventures in semantic publishing: exemplar semantic enhancements of a research article.
22:14: posted Small RNA: A Large Contributor to Carcinogenesis?
22:08: posted dbSMR: a novel resource of genome-wide SNPs affecting microRNA mediated regulation
22:06: posted Genetic Alterations and Oncogenic Pathways Associated with Breast Cancer Subtypes

2009-11-04

11:20: posted An introduction to artificial neural networks in bioinformatics--application to complex microarray and mass spectrometry datasets in cancer studies
11:17: posted A roadmap of clustering algorithms: finding a match for a biomedical application
11:15: posted Potential Bias in GO::TermFinder
11:09: posted Probes containing runs of guanines provide insights into the biophysics and bioinformatics of Affymetrix GeneChips
10:26: posted Redefining MicroRNA Targets
10:24: posted Metastatic gene signatures and emerging novel prognostic tests in the management of early stage breast cancer.
10:19: posted Evidence for Antisense Transcription Associated with MicroRNA Target mRNAs in Arabidopsis

2009-11-03

17:23: posted Identifying functional modules using expression profiles and confidence-scored protein interactions
17:22: posted MIST: Maximum Information Spanning Trees for dimension reduction of biological data sets
17:21: posted A modified hyperplane clustering algorithm allows for efficient and accurate clustering of extremely large datasets
17:20: posted Sparse linear discriminant analysis for simultaneous testing for the significance of a gene set/pathway and gene selection
17:17: posted Smoothing waves in array CGH tumor profiles
17:15: posted The use of gene ontology evidence codes in preventing classifier assessment bias
17:14: posted The tspair package for finding top scoring pair classifiers in R
17:11: posted Integrated functional, gene expression and genomic analysis for the identification of cancer targets.

2009-11-02

17:51: posted Gene expression profiles and breast cancer metastasis: a genetic perspective.
17:50: posted A validated gene expression profile for detecting clinical outcome in breast cancer using artificial neural networks.
17:48: posted Quantitative assessment of tissue biomarkers and construction of a model to predict outcome in breast cancer using multiple imputation.
17:43: posted Network-based support vector machine for classification of microarray samples.
17:27: posted Ultrasome: efficient aberration caller for copy number studies of ultra-high resolution.
17:25: posted gcExplorer: interactive exploration of gene clusters.
17:23: posted Human microRNAs co-silence in well-separated groups and have different predicted essentialities.
17:22: posted Tissue specificity and the human protein interaction network.
17:19: posted microPred: effective classification of pre-miRNAs for human miRNA gene prediction.
17:18: posted A flexible two-stage procedure for identifying gene sets that are differentially expressed.
17:16: posted Aurora-A expression is independently associated with chromosomal instability in colorectal cancer.
17:13: posted Personalizing medicine: a systems biology perspective.
17:11: posted Toward accurate reconstruction of functional protein networks.
17:09: posted Distinct genomic aberrations associated with ERG rearranged prostate cancer.
17:07: posted Interlaboratory and Interplatform Comparison of Microarray Gene Expression Analysis of HepG2 Cells Exposed to Benzo(a)pyrene.
17:06: posted A Two-Stage Feature Selection Method for Gene Expression Data.
17:02: posted The UCSC Cancer Genomics Browser.
17:01: posted New class of microRNA targets containing simultaneous 5'-UTR and 3'-UTR interaction sites.
16:58: posted Identification of copy number gain and overexpressed genes on chromosome arm 20q by an integrative genomic approach in cervical cancer: potential role in progression.
16:57: posted Copy number alterations that predict metastatic capability of human breast cancer.
16:41: posted Multivariate analysis of variance test for gene set analysis.
16:41: posted Identification of differential gene pathways with principal component analysis.
16:39: posted Integrated genomic profiling of endometrial carcinoma associates aggressive tumors with indicators of PI3 kinase activation.
16:34: posted Inferring clonal expansion and cancer stem cell dynamics from DNA methylation patterns in colorectal cancers.
16:32: posted Life sciences on the Semantic Web: the Neurocommons and beyond.
16:30: posted Semantic web for integrated network analysis in biomedicine.
16:29: posted Correlation of microRNA levels during hypoxia with predicted target mRNAs through genome-wide microarray analysis.
16:24: posted Scaling the walls of discovery: using semantic metadata for integrative problem solving.
16:23: posted Towards pharmacogenomics knowledge discovery with the semantic web.
16:22: posted Heterogeneity and power in clinical biomarker studies.
16:19: posted Linked data and provenance in biological data webs.
16:17: posted Building biomedical web communities using a semantically aware content management system.
16:15: posted Prediction of novel microRNA genes in cancer-associated genomic regions--a combined computational and experimental approach.
16:13: posted Semantic Web for Health Care and Life Sciences: a review of the state of the art.
16:06: posted Power of deep, all-exon resequencing for discovery of human trait genes.
16:01: posted Introducing molecular subtyping of breast cancer into the clinic?
15:57: posted New gene selection method for multiclass tumor classification by class centroid.
15:56: posted MicroRNAs preferentially target the genes with high transcriptional regulation complexity.
15:54: posted A genomic strategy to elucidate modules of oncogenic pathway signaling networks.
15:51: posted Combinatorial microRNAs: working together to make a difference.
15:49: posted MicroRNA detection and target prediction: integration of computational and experimental approaches.
15:46: posted Bio-informatic trends for the determination of miRNA-target interactions in mammals.
15:44: posted Biclustering sparse binary genomic data.
15:42: posted Bayesian inference of MicroRNA targets from sequence and expression data.
15:40: posted A bioinformatics tool for linking gene expression profiling results with public databases of microRNA target predictions.
15:38: posted PADGE: analysis of heterogeneous patterns of differential gene expression.
15:15: posted MADS: a new and improved method for analysis of differential alternative splicing by exon-tiling microarrays.
15:14: posted MicroRNomics: a newly emerging approach for disease biology.
15:12: posted A computational screen for mouse signaling pathways targeted by microRNA clusters.
15:10: posted miRDB: a microRNA target prediction and functional annotation database with a wiki interface.
15:04: posted Meta-analysis of age-related gene expression profiles identifies common signatures of aging
15:00: posted The DICS repository: module-assisted analysis of disease-related gene lists.
14:57: posted Parallelized prediction error estimation for evaluation of high-dimensional models.
14:55: posted Statistical methods of background correction for Illumina BeadArray data
14:54: posted A flexible rank-based framework for detecting copy number aberrations from array data
14:50: posted MSMAD: a computationally efficient method for the analysis of noisy array CGH data.