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» BAG: a graph theoretic sequence clustering algorithm
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FOCS
2007
IEEE
14 years 1 months ago
Adaptive Simulated Annealing: A Near-optimal Connection between Sampling and Counting
We present a near-optimal reduction from approximately counting the cardinality of a discrete set to approximately sampling elements of the set. An important application of our wo...
Daniel Stefankovic, Santosh Vempala, Eric Vigoda
BIOCOMP
2008
13 years 9 months ago
GIPSCo: A Method for Comparison of Protein Structures Based on Geometric Invariants
Protein structure comparison is important for elucidation of evolutionary relationships, function and functionally important amino acid residues. We propose Geometric Invariant bas...
Sandeep Deshmukh, Aniket Dalal, Pramod Wangikar
BIBM
2010
IEEE
286views Bioinformatics» more  BIBM 2010»
13 years 5 months ago
Evaluation of short read metagenomic assembly
Advances in sequencing technologies have equipped researchers with the ability to sequence the collective genome of entire microbial communities commonly referred to as metagenomi...
Anveshi Charuvaka, Huzefa Rangwala
DAM
2011
13 years 2 months ago
On minimal Sturmian partial words
Partial words, which are sequences that may have some undefined positions called holes, can be viewed as sequences over an extended alphabet A = A ∪ { }, where stands for a hol...
Francine Blanchet-Sadri, John Lensmire
BMCBI
2007
86views more  BMCBI 2007»
13 years 7 months ago
Tandem mass spectrometry data quality assessment by self-convolution
Background: Many algorithms have been developed for deciphering the tandem mass spectrometry (MS) data sets. They can be essentially clustered into two classes. The first performs...
Keng Wah Choo, Wai Mun Tham