Titlebook: Algorithms in Bioinformatics; 16th International W Martin‘Frith,Christian Nørgaard Storm Pedersen Conference proceedings 2016 Springer Inte

CAGE

Copy-Number Evolution Problems: Complexity and Algorithms, of mutations are copy number aberrations, which alter the number of copies of genomic regions. The number of copies of each position along a chromosome constitutes the chromosome’s copy-number profile. Understanding how such profiles evolve in cancer can assist in both diagnosis and prognosis. We m

语言学

,: A Fast and Memory-Efficient ,-mer Counter with GPU-Support,ome sequence. We present the open source .-mer counting software . that has been designed for the efficient counting of .-mers for .. Given the technology trend towards long reads of next-generation sequencers, support for large . becomes increasingly important. While existing .-mer counting tools s

影响

Genome Rearrangements on Both Gene Order and Intergenic Regions,ive genes, although it was recently shown decisive for the accuracy of the inference methods [., .]. In this line, we define a new genome rearrangement model called wDCJ, a generalization of the well-known Double Cut and Join (or DCJ) model that allows for modifying both the gene order . the interge

bromide

Better Identification of Repeats in Metagenomic Scaffolding,ng-read sequencing technologies, in metagenomic data intra-genome and, more importantly, inter-genome repeats continue to be a significant impediment to effective genome reconstruction. Detecting repeats in metagenomic samples is complicated by characteristic features of these data, primarily uneven

侵蚀

A Better Scoring Model for De Novo Peptide Sequencing: The Symmetric Difference Between Explained aasses. The inverse problem is the .: Given all prefix and suffix masses, determine the string of amino acids. In biological reality, the given masses are measured in a lab experiment, and measurements by necessity are noisy. The (real, noisy) . therefore has a noisy input: a few of the prefix and su

coddle

,,: Algorithms for Analyzing Coarse Grained RNA Dynamics Based on Markov Models of Connectivity-Grained from molecular dynamics simulations. RNA molecules are well-suited for this representation due to their composition which is mainly modular and assessable by the secondary structure alone. Each adjacency matrix represents the interactions of . nucleotides. We then define transitions between sta

fringe

Solving Generalized Maximum-Weight Connected Subgraph Problem for Network Enrichment Analysis, of such analysis is a reduction to a maximum-weight connected subgraph problem. In particular, in analysis of metabolic networks a generalized maximum-weight connected subgraph (GMWCS) problem, where both nodes and edges are scored, naturally arises. Here we present the first to our knowledge pract

Esalate

蒙太奇

rheumatism

https://doi.org/10.1007/978-3-663-09646-7reviously proposed greedy and approximation algorithms. We test our algorithm on real cancer data and show that our approach is viable and allows for the identification of subnetworks containing known cancer genes.