jfr's profile

Recent Activity

• 14:14: posted Predictive signatures for chemotherapy sensitivity in breast cancer: are they ready for use in the clinic?
• 14:03: posted A HUPO test sample study reveals common problems in mass spectrometry-based proteomics.
• 13:58: posted Validation of gene signatures that predict the response of breast cancer to neoadjuvant chemotherapy: a substudy of the EORTC 10994/BIG 00-01 clinical trial.
• 13:25: posted The functions of animal microRNAs
• 13:23: posted Basal-like breast carcinoma: from expression profiling to routine practice.
• 13:06: posted Evaluation of next generation sequencing platforms for population targeted sequencing studies.
• 12:54: posted Predicting microRNA targets and functions: traps for the unwary.

• 13:36: posted Inter-observer reproducibility of HER2 immunohistochemical assessment and concordance with fluorescent in situ hybridization (FISH): pathologist assessment compared to quantitative image analysis.
• 11:28: posted Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
• 11:26: posted ABySS: a parallel assembler for short read sequence data.
• 11:25: posted Exploring the human genome with functional maps
• 10:30: posted Getting started in computational mass spectrometry-based proteomics.

• 14:51: posted A Classifier-based approach to identify genetic similarities between diseases
• 14:50: posted Model-based clustering of array CGH data
• 14:49: posted From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations
• 14:48: posted Probabilistic retrieval and visualization of biologically relevant microarray experiments
• 14:45: posted Fewer permutations, more accurate P-values
• 14:43: posted Cross species analysis of microarray expression data
• 14:42: posted Application and evaluation of automated semantic annotation of gene expression experiments.
• 14:26: posted PTEN Expression and KRAS Mutations on Primary Tumors and Metastases in the Prediction of Benefit From Cetuximab Plus Irinotecan for Patients With Metastatic Colorectal Cancer
• 14:25: posted Genetic analysis of radiation-induced changes in human gene expression
• 14:23: posted Chromosomal instability determines taxane response.
• 14:21: posted Automated high-dimensional flow cytometric data analysis
• 14:20: posted Constrained mixture estimation for analysis and robust classification of clinical time series
• 14:09: posted Local recurrence after breast-conserving therapy in relation to gene expression patterns in a large series of patients.
• 13:26: posted Choosing the right path: enhancement of biologically relevant sets of genes or proteins using pathway structure
• 13:21: posted Evaluation of microarray preprocessing algorithms based on concordance with RT-PCR in clinical samples.
• 13:14: posted Data driven derivation of cutoffs from a pool of 3,030 Affymetrix arrays to stratify distinct clinical types of breast cancer.
• 13:10: posted MicroRNA-92a controls angiogenesis and functional recovery of ischemic tissues in mice.
• 13:06: posted SHRiMP: Accurate Mapping of Short Color-space Reads

• 14:42: posted MicroRNAs: Novel regulators in the hallmarks of human cancer

• 13:43: posted Gradient lasso for Cox proportional hazards model
• 13:34: posted Reverse transcription-quantitative polymerase chain reaction: description of a RIN-based algorithm for accurate data normalization.
• 13:18: posted The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments.
• 13:15: posted DIANA-mirPath: Integrating human and mouse microRNAs in pathways.
• 13:14: posted Hierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data.
• 13:11: posted A global meta-analysis of microarray expression data to predict unknown gene functions and estimate the literature-data divide.

• 16:26: posted Prediction of qualitative outcome of oligonucleotide microarray hybridization by measurement of RNA integrity using the 2100 Bioanalyzer capillary electrophoresis system.
• 16:22: posted KEGGgraph: a graph approach to KEGG PATHWAY in R and bioconductor.
• 16:20: posted ViaComplex: software for landscape analysis of gene expression networks in genomic context
• 16:18: posted FDR made easy in differential feature discovery and correlation analyses
• 16:16: posted SBML2L(A)T(E)X: conversion of SBML files into human-readable reports.
• 16:09: posted Data structures and algorithms for analysis of genetics of gene expression with Bioconductor: GGtools 3.x
• 15:57: posted BioconductorBuntu - A Linux Distribution that Implements a Web-Based DNA Microarray Analysis Server
• 15:51: posted ProbeMatch: rapid alignment of oligonucleotides to genome allowing both gaps and mismatches.
• 15:50: posted Biopython: freely available Python tools for computational molecular biology and bioinformatics
• 15:01: posted Variable slope normalization of reverse phase protein arrays
• 14:57: posted Multicenter validation of a 1,550-gene expression profile for identification of tumor tissue of origin.
• 14:54: posted Correlation of expression profiles between microRNAs and mRNA targets using NCI-60 data
• 14:43: posted Ki67 index, HER2 status, and prognosis of patients with luminal B breast cancer.
• 14:37: posted Data-driven normalization strategies for high-throughput quantitative RT-PCR.
• 14:36: posted A transcriptional sketch of a primary human breast cancer by 454 deep sequencing.
• 14:34: posted Intra-Platform Repeatability and Inter-Platform Comparability of MicroRNA Microarray Technology
• 14:30: posted Unsupervised selection of highly coexpressed and noncoexpressed genes using a consensus clustering approach.
• 14:27: posted A gene expression predictor of response to EGFR-targeted therapy stratifies progression-free survival to cetuximab in KRAS wild-type metastatic colorectal cancer.
• 14:24: posted Modeling and managing experimental data using FuGE.
• 14:22: posted Mining metastasis related genes by primary-secondary tumor comparisons from large-scale databases.

• 12:09: posted Cloud computing
• 11:46: posted MicroRNA signatures predict oestrogen receptor, progesterone receptor and HER2/neu receptor status in breast cancer.
• 11:43: posted MicroRNA identification in plasma and serum: a new tool to diagnose and monitor diseases
• 11:27: posted Reliability and reproducibility of a RNA preamplification method for low-density array analysis from formalin-fixed paraffin-embedded breast cancer samples.
• 11:25: posted Selection of REFERENCE genes for normalization of qRT-PCR data derived from FFPE breast tumors.

• 17:38: posted Mining subspace clusters from DNA microarray data using large itemset techniques.
• 17:37: posted A Regularized Method for Selecting Nested Groups of Relevant Genes from Microarray Data
• 17:34: posted Genes that mediate breast cancer metastasis to the brain
• 17:28: posted How to map billions of short reads onto genomes
• 17:15: posted The apoptotic machinery as a biological complex system: analysis of its omics and evolution, identification of candidate genes for fourteen major types of cancer, and experimental validation in CML and neuroblastoma

• 14:49: posted A single-molecule method for the quantitation of microRNA gene expression
• 14:45: posted High-throughput stem-loop RT-qPCR miRNA expression profiling using minute amounts of input RNA.
• 14:42: posted mRNA-Seq whole-transcriptome analysis of a single cell
• 14:39: posted Visualization of genomic data with the Hilbert curve
• 14:37: posted Joint estimation of copy number variation and reference intensities on multiple DNA arrays using GADA.
• 14:36: posted Aneuploidy prediction and tumor classification with heterogeneous hidden conditional random fields
• 13:42: posted Statistical comparison framework and visualization scheme for ranking-based algorithms in high-throughput genome-wide studies.
• 13:38: posted Target discovery from data mining approaches.
• 13:36: posted Breast Cancer Subtypes and Response to Docetaxel in Node-Positive Breast Cancer: Use of an Immunohistochemical Definition in the BCIRG 001 Trial
• 13:32: posted PAnnBuilder: An R Package for Assembling Proteomic Annotation Data.
• 13:31: posted Integrated analysis of breast cancer cell lines reveals unique signaling pathways
• 11:39: posted Adaptable gene-specific dye bias correction for two-channel DNA microarrays.
• 10:33: posted Targeted proteomics for validation of biomarkers in clinical samples

• 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