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86
Voted
BMCBI
2008
93views more  BMCBI 2008»
15 years 26 days ago
SlowFaster, a user-friendly program for slow-fast analysis and its application on phylogeny of Blastocystis
Background: Slow-fast analysis is a simple and effective method to reduce the influence of substitution saturation, one of the causes of phylogenetic noise and long branch attract...
Martin Kostka, Magdalena Uzlikova, Ivan Cepicka, J...
114
Voted
BMCBI
2008
102views more  BMCBI 2008»
15 years 26 days ago
Combining sequence-based prediction methods and circular dichroism and infrared spectroscopic data to improve protein secondary
Background: A number of sequence-based methods exist for protein secondary structure prediction. Protein secondary structures can also be determined experimentally from circular d...
Jonathan G. Lees, Robert W. Janes
87
Voted
BMCBI
2008
94views more  BMCBI 2008»
15 years 26 days ago
Conserved co-expression for candidate disease gene prioritization
Background: Genes that are co-expressed tend to be involved in the same biological process. However, co-expression is not a very reliable predictor of functional links between gen...
Martin Oti, Jeroen van Reeuwijk, Martijn A. Huynen...
BMCBI
2008
123views more  BMCBI 2008»
15 years 26 days ago
PocketMatch: A new algorithm to compare binding sites in protein structures
Background: Recognizing similarities and deriving relationships among protein molecules is a fundamental requirement in present-day biology. Similarities can be present at various...
Kalidas Yeturu, Nagasuma Chandra
BMCBI
2008
115views more  BMCBI 2008»
15 years 26 days ago
Systems biology driven software design for the research enterprise
Background: In systems biology, and many other areas of research, there is a need for the interoperability of tools and data sources that were not originally designed to be integr...
John Boyle, Christopher C. Cavnor, Sarah A. Killco...
82
Voted
BMCBI
2008
111views more  BMCBI 2008»
15 years 26 days ago
GENOMEPOP: A program to simulate genomes in populations
Background: There are several situations in population biology research where simulating DNA sequences is useful. Simulation of biological populations under different evolutionary...
Antonio Carvajal-Rodríguez
108
Voted
BMCBI
2008
172views more  BMCBI 2008»
15 years 26 days ago
Classification of drug molecules considering their IC50 values using mixed-integer linear programming based hyper-boxes method
Background: A priori analysis of the activity of drugs on the target protein by computational approaches can be useful in narrowing down drug candidates for further experimental t...
Pelin Armutlu, Muhittin Emre Ozdemir, Fadime Ü...
110
Voted
BMCBI
2008
124views more  BMCBI 2008»
15 years 26 days ago
Inferring modules of functionally interacting proteins using the Bond Energy Algorithm
Background: Non-homology based methods such as phylogenetic profiles are effective for predicting functional relationships between proteins with no considerable sequence or struct...
Ryosuke Watanabe, Enrique Morett, Edgar E. Vallejo
58
Voted
BMCBI
2008
77views more  BMCBI 2008»
15 years 26 days ago
A simple and robust method for connecting small-molecule drugs using gene-expression signatures
Background: Interaction of a drug or chemical with a biological system can result in a geneexpression profile or signature characteristic of the event. Using a suitably robust alg...
Shu-Dong Zhang, Timothy W. Gant
32
Voted
BMCBI
2008
63views more  BMCBI 2008»
15 years 26 days ago
Psiscan: a computational approach to identify H/ACA-like and AGA-like non-coding RNA in trypanosomatid genomes
Inna Myslyuk, Tirza Doniger, Yair Horesh, Avraham ...