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BMCBI
2010
137views more  BMCBI 2010»
13 years 11 months ago
Biana: a software framework for compiling biological interactions and analyzing networks
Background: The analysis and usage of biological data is hindered by the spread of information across multiple repositories and the difficulties posed by different nomenclature sy...
Javier Garcia-Garcia, Emre Guney, Ramon Aragues, J...
BMCBI
2010
69views more  BMCBI 2010»
13 years 11 months ago
BSSF: a fingerprint based ultrafast binding site similarity search and function analysis server
Bing Xiong, Jie Wu, David L. Burk, Mengzhu Xue, Hu...
BMCBI
2010
190views more  BMCBI 2010»
13 years 11 months ago
A parallel and incremental algorithm for efficient unique signature discovery on DNA databases
Background: DNA signatures are distinct short nucleotide sequences that provide valuable information that is used for various purposes, such as the design of Polymerase Chain Reac...
Hsiao Ping Lee, Tzu-Fang Sheu, Chuan Yi Tang
BMCBI
2010
150views more  BMCBI 2010»
13 years 11 months ago
Systematic calibration of a cell signaling network model
Background: Mathematical modeling is being applied to increasingly complex biological systems and datasets; however, the process of analyzing and calibrating against experimental ...
Kyoung Ae Kim, Sabrina L. Spencer, John G. Albeck,...
BMCBI
2010
133views more  BMCBI 2010»
13 years 11 months ago
New components of the Dictyostelium PKA pathway revealed by Bayesian analysis of expression data
Background: Identifying candidate genes in genetic networks is important for understanding regulation and biological function. Large gene expression datasets contain relevant info...
Anup Parikh, Eryong Huang, Christopher Dinh, Blaz ...
BMCBI
2010
132views more  BMCBI 2010»
13 years 11 months ago
dConsensus: a tool for displaying domain assignments by multiple structure-based algorithms and for construction of a consensus
Background: Partitioning of a protein into structural components, known as domains, is an important initial step in protein classification and for functional and evolutionary stud...
Kieran Alden, Stella Veretnik, Philip E. Bourne
BMCBI
2010
176views more  BMCBI 2010»
13 years 11 months ago
Bayesian statistical modelling of human protein interaction network incorporating protein disorder information
Background: We present a statistical method of analysis of biological networks based on the exponential random graph model, namely p2-model, as opposed to previous descriptive app...
Svetlana Bulashevska, Alla Bulashevska, Roland Eil...
BMCBI
2010
135views more  BMCBI 2010»
13 years 11 months ago
Delineation of amplification, hybridization and location effects in microarray data yields better-quality normalization
Background: Oligonucleotide arrays have become one of the most widely used high-throughput tools in biology. Due to their sensitivity to experimental conditions, normalization is ...
Marc Hulsman, Anouk Mentink, Eugene P. van Someren...
BMCBI
2010
100views more  BMCBI 2010»
13 years 11 months ago
Scaffold filling, contig fusion and comparative gene order inference
Background: There has been a trend in increasing the phylogenetic scope of genome sequencing without finishing the sequence of the genome. Increasing numbers of genomes are being ...
Adriana Muñoz, Chunfang Zheng, Qian Zhu, Vi...
BMCBI
2010
150views more  BMCBI 2010»
13 years 11 months ago
Evolutionary rates at codon sites may be used to align sequences and infer protein domain function
Background: Sequence alignments form part of many investigations in molecular biology, including the determination of phylogenetic relationships, the prediction of protein structu...
Pierre M. Durand, Scott Hazelhurst, Theresa L. Coe...