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CSB
2005
IEEE
125views Bioinformatics» more  CSB 2005»
14 years 5 months ago
On Optimizing Distance-Based Similarity Search for Biological Databases
Similarity search leveraging distance-based index structures is increasingly being used for both multimedia and biological database applications. We consider distance-based indexi...
Rui Mao, Weijia Xu, Smriti R. Ramakrishnan, Glen N...
CSB
2005
IEEE
130views Bioinformatics» more  CSB 2005»
14 years 5 months ago
TreeRefiner: A Tool for Refining a Multiple Alignment on a Phylogenetic Tree
We present TreeRefiner, a tool for refining multiple alignments of biological sequences. Given a multiple alignment, a phylogenetic tree, and scoring parameters as input, TreeRefi...
Aswath Manohar, Serafim Batzoglou
CSB
2005
IEEE
166views Bioinformatics» more  CSB 2005»
14 years 5 months ago
Automated Validation of Polymerase Chain Reactions Using Amplicon Melting Curves
PCR, the polymerase chain reaction, is a fundamental tool of molecular biology. Quantitative PCR is the goldstandard methodology for determination of DNA copy numbers, quantitatin...
Tobias P. Mann, Richard Humbert, John A. Stamatoya...
CSB
2005
IEEE
116views Bioinformatics» more  CSB 2005»
14 years 5 months ago
DockingShop: a Tool for Interactive Protein Docking
The molecular docking problem is to determine how molecules interact with other molecules and plays a key role in understanding how cells function. DockingShop is an integrated en...
Ting-Cheng Lu, Jinhui Ding, Silvia N. Crivelli
CSB
2005
IEEE
135views Bioinformatics» more  CSB 2005»
14 years 5 months ago
Relating transcription factors, modules of genes and cultivation conditions in Saccharomyces cerevisiae
Usually, the functionality of a module of co-expressed genes is derived from enrichment within the module of a particular gene annotation category. The systematic setup of the che...
Theo A. Knijnenburg, Marcel J. T. Reinders, J. M. ...
CSB
2005
IEEE
125views Bioinformatics» more  CSB 2005»
14 years 5 months ago
Discriminative Discovery of Transcription Factor Binding Sites from Location Data
Motivation: The availability of genome-wide location analyses based on chromatin immunoprecipitation (ChIP) data gives a new insight for in silico analysis of transcriptional regu...
Yuji Kawada, Yasubumi Sakakibara
CSB
2005
IEEE
129views Bioinformatics» more  CSB 2005»
14 years 5 months ago
Deformable Modeling for Improved Calculation of Molecular Velocities from Single-Particle Tracking
Single-particle tracking provides a powerful technique for measuring dynamic cellular processes on the level of individual molecules. Much recent work has been devoted to using si...
Peter M. Kasson, Mark M. Davis, Axel T. Brüng...
CSB
2005
IEEE
125views Bioinformatics» more  CSB 2005»
14 years 5 months ago
Pathway Logic Helping Biologists Understand and Organize Pathway Information
Merrill Knapp, Linda Briesemeister, Steven Eker, P...