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BMCBI
2010
140views more  BMCBI 2010»
9 years 7 months ago
An improved machine learning protocol for the identification of correct Sequest search results
Background: Mass spectrometry has become a standard method by which the proteomic profile of cell or tissue samples is characterized. To fully take advantage of tandem mass spectr...
Morten Kallberg, Hui Lu
BMCBI
2010
154views more  BMCBI 2010»
9 years 7 months ago
Knowledge-based matrix factorization temporally resolves the cellular responses to IL-6 stimulation
Background: External stimulations of cells by hormones, cytokines or growth factors activate signal transduction pathways that subsequently induce a re-arrangement of cellular gen...
Andreas Kowarsch, Florian Blöchl, Sebastian B...
BMCBI
2010
218views more  BMCBI 2010»
9 years 7 months ago
A hybrid blob-slice model for accurate and efficient detection of fluorescence labeled nuclei in 3D
Background: To exploit the flood of data from advances in high throughput imaging of optically sectioned nuclei, image analysis methods need to correctly detect thousands of nucle...
Anthony Santella, Zhuo Du, Sonja Nowotschin, Anna-...
BMCBI
2010
161views more  BMCBI 2010»
9 years 7 months ago
Addressing the Challenge of Defining Valid Proteomic Biomarkers and Classifiers
Background: The purpose of this manuscript is to provide, based on an extensive analysis of a proteomic data set, suggestions for proper statistical analysis for the discovery of ...
Mohammed Dakna, Keith Harris, Alexandros Kalousis,...
BMCBI
2010
108views more  BMCBI 2010»
9 years 7 months ago
Prediction of RNA secondary structure by maximizing pseudo-expected accuracy
Background: Recent studies have revealed the importance of considering the entire distribution of possible secondary structures in RNA secondary structure predictions; therefore, ...
Michiaki Hamada, Kengo Sato, Kiyoshi Asai
BMCBI
2010
143views more  BMCBI 2010»
9 years 7 months ago
A genome alignment algorithm based on compression
Background: Traditional genome alignment methods consider sequence alignment as a variation of the string edit distance problem, and perform alignment by matching characters of th...
Minh Duc Cao, Trevor I. Dix, Lloyd Allison
BMCBI
2010
155views more  BMCBI 2010»
9 years 7 months ago
BrEPS: a flexible and automatic protocol to compute enzyme-specific sequence profiles for functional annotation
Background: Models for the simulation of metabolic networks require the accurate prediction of enzyme function. Based on a genomic sequence, enzymatic functions of gene products a...
Constantin Bannert, A. Welfle, C. aus dem Spring, ...
BMCBI
2010
97views more  BMCBI 2010»
9 years 7 months ago
Preprocessing of gene expression data by optimally robust estimators
Background: The preprocessing of gene expression data obtained from several platforms routinely includes the aggregation of multiple raw signal intensities to one expression value...
Matthias Kohl, Hans-Peter Deigner
BMCBI
2010
162views more  BMCBI 2010»
9 years 7 months ago
SNPexp - A web tool for calculating and visualizing correlation between HapMap genotypes and gene expression levels
Background: Expression levels for 47294 transcripts in lymphoblastoid cell lines from all 270 HapMap phase II individuals, and genotypes (both HapMap phase II and III) of 3.96 mil...
Kristian Holm, Espen Melum, Andre Franke, Tom H. K...
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