8 papers · ranked by Valyu relevance
Rudolph Pienaar, Christian Hasselgrove, Kiho Im, David Kennedy + 4 more
We present a description of a system that uses a compact binary representation to describe and trace sulci on a reconstructed human cortical surface, based on a set of human-generated targets. The inputs to the system were manually created on a training set of 20 normal subjects (11 females, 9 males) with ages 22 – 40…
Jing Xie, Qi Duan
Biological pathway analysis often requires identifying interventions that block reachability to an undesirable state, such as a disease-associated module, toxic byproduct, or adverse phenotype, while preserving reachability among essential biological functions. Motivated by this setting, we study the Reachability…
Pesho Ivanov, Benjamin Bichsel, Harun Mustafa, André Kahles + 2 more
We present an algorithm for the optimal alignment of sequences to genome graphs. It works by phrasing the edit distance minimization task as finding a shortest path on an implicit alignment graph. To find a shortest path, we instantiate the A^⋆^ paradigm with a novel domain-specific heuristic function that accounts for…
Ragnar Groot Koerkamp, Pesho Ivanov
Sequence alignment has been at the core of computational biology for half a century. Still, it is an open problem to design a practical algorithm for exact alignment of a pair of related sequences in linear-like time (25). We solve exact global pairwise alignment with respect to edit distance by using the A shortest…
Xian Chang, Jordan Eizenga, Adam M. Novak, Jouni Sirén + 1 more
Graph representations of genomes are capable of expressing more genetic variation and can therefore better represent a population than standard linear genomes. However, due to the greater complexity of genome graphs relative to linear genomes, some functions that are trivial on linear genomes become more difficult in…
Mikko Rautiainen, Tobias Marschall
Graphs are commonly used to represent sets of sequences. Either edges or nodes can be labeled by sequences, so that each path in the graph spells a concatenated sequence. Examples include graphs to represent genome assemblies, such as string graphs and de Bruijn graphs, and graphs to represent a pan-genome and hence…
Mikko Rautiainen, Veli Mäkinen, Tobias Marschall
Graphs are commonly used to represent sets of sequences. Either edges or nodes can be labeled by sequences, so that each path in the graph spells a concatenated sequence. Examples include graphs to represent genome assemblies, such as string graphs and de Bruijn graphs, and graphs to represent a pan-genome and hence…
Francisco Sena, Eliel Ingervo, Shahbaz Khan, Andrey Prjibelski + 2 more
A decomposition of a network flow is a set of weighted paths whose superposition equals the flow. The problem of characterising and computing safe walks for flow decompositions has so far seen only a partial solution by restricting the flow decomposition to consist of paths, and the graph to be directed and acyclic…