Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Efficient Algorithms for de novo Assembly of Alternative Splicing Events
  from RNA-seq Data   In this thesis, we address the problem of identifying and quantifying
variants (alternative splicing and genomic polymorphism) in RNA-seq data when
no reference genome is available, without assembling the full transcripts.
Based on the fundamental idea that each variant corresponds to a recognizable
pattern, a bubble, in a de Bruijn graph constructed from the RNA-seq reads, we
propose a general model for all variants in such graphs. We then introduce an
exact method, called KisSplice, to extract alternative splicing events.
Finally, we show that it enables to identify more correct events than general
purpose transcriptome assemblers.
  In order to deal with ever-increasing volumes of NGS data, we put an extra
effort to make KisSplice as scalable as possible. First, to improve its running
time, we propose a new polynomial delay algorithm to enumerate bubbles. We show
that it is several orders of magnitude faster than previous approaches. Then,
to reduce its memory consumption, we propose a new compact way to build and
represent a de Bruijn graph. We show that our approach uses 30% to 40% less
memory than the state of the art, with an insignificant impact on the
construction time.
  Additionally, we apply the same techniques developed to list bubbles in two
classical problems: cycle enumeration and the K-shortest paths problem. We give
the first optimal algorithm to list cycles in undirected graphs, improving over
Johnson's algorithm. This is the first improvement to this problem in almost 40
years. We then consider a different parameterization of the classical
K-shortest (simple) paths problem: instead of bounding the number of st-paths,
we bound the weight of the st-paths. We present new algorithms with the same
time complexities but using exponentially less memory than previous approaches.

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The categories of this paper are: dg-ga
16
The categories of this paper are: stat
27
The categories of this paper are: comp-gas
31
The categories of this paper are: ao-sci
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The categories of this paper are: q-alg
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The categories of this paper are: chao-dyn
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The categories of this paper are: math-ph
15
The categories of this paper are: nucl-ex
0
The categories of this paper are: hep-ph
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The categories of this paper are: cmp-lg
5
The categories of this paper are: gr-qc
3
The categories of this paper are: physics
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The categories of this paper are: plasm-ph
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The categories of this paper are: adap-org
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The categories of this paper are: nlin
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The categories of this paper are: hep-th