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BMCBI
2010
167views more  BMCBI 2010»
13 years 6 months ago
Creating PWMs of transcription factors using 3D structure-based computation of protein-DNA free binding energies
Background: Knowledge of transcription factor-DNA binding patterns is crucial for understanding gene transcription. Numerous DNA-binding proteins are annotated as transcription fa...
Denitsa Alamanova, Philip Stegmaier, Alexander E. ...
IMSCCS
2007
IEEE
14 years 1 months ago
Evolutionary Conservation of DNA-Contact residues in DNA-binding Domains
Background: DNA-binding proteins are of utmost importance to gene regulation. The identification of DNA-binding domains is useful for understanding the regulation mechanisms of DN...
Yao-Lin Chang, Huai-Kuang Tsai, Cheng-Yan Kao, Yun...
DNA
2006
Springer
146views Bioinformatics» more  DNA 2006»
13 years 10 months ago
On Times to Compute Shapes in 2D Tile Self-assembly
We study the times to grow structures within the tile self-assembly model proposed by Winfree, and the possible shapes that can be achieved. Our earlier work was confined to the g...
Yuliy M. Baryshnikov, Edward G. Coffman Jr., Boons...
ICALP
2005
Springer
14 years 7 days ago
Randomized Fast Design of Short DNA Words
We consider the problem of efficiently designing sets (codes) of equal-length DNA strings (words) that satisfy certain combinatorial constraints. This problem has numerous motivati...
Ming-Yang Kao, Manan Sanghi, Robert T. Schweller
RECOMB
2000
Springer
13 years 10 months ago
A compression algorithm for DNA sequences and its applications in genome comparison
We present a lossless compression algorithm, GenCompress, for genetic sequences, based on searching for approximate repeats. Our algorithm achieves the best compression ratios for...
Xin Chen, Sam Kwong, Ming Li