Recent advances in algorithmic techniques and statistics of sequence alignment have
helped to make near-optimal alignments an important tool in the delineation of biologically …

We give algorithms for finding the k shortest paths (not required to be simple) connecting a
pair of vertices in a digraph. Our algorithms output an implicit representation of these paths …

In one of the first major texts in the emerging field of computational molecular biology, Pavel
Pevzner covers a broad range of algorithmic and combinatorial topics and shows how they …

The question of multiple sequence alignment quality has received much attention from
developers of alignment methods. Less forthcoming, however, are practical measures for …

The accuracy of a homology model based on the structure of a distant relative or other
topologically equivalent protein is primarily limited by the quality of the alignment. Here we …

We propose an algorithm for enumerating solutions to the Lasso regression problem. In
ordinary Lasso regression, one global optimum is obtained and the resulting features are …

We present a new algorithm for enumerating all near‐shortest simple (loopless) s‐t paths in
a graph G=(V, E) with nonnegative edge lengths. Letting n=| V| and m=| E|, the time per path …

The standard method of applying hidden Markov models to biological problems is to find a
Viterbi (maximal weight) path through the HMM graph. The Viterbi algorithm reduces the …

arxiv:1412.5075v1 [cs.DS] 16 Dec 2014 Page 1 arxiv:1412.5075v1 [cs.DS] 16 Dec 2014 K-Best
Enumeration David Eppstein∗ Abstract We survey k-best enumeration problems and the …

Background To develop protein therapeutics from exogenous sources, it is necessary to
mitigate the risks of eliciting an anti-biotherapeutic immune response. A key aspect of the …