Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Algorithmic Methods to Infer the Evolutionary Trajectories in Cancer
  Progression   The genomic evolution inherent to cancer relates directly to a renewed focus
on the voluminous next generation sequencing (NGS) data, and machine learning
for the inference of explanatory models of how the (epi)genomic events are
choreographed in cancer initiation and development. However, despite the
increasing availability of multiple additional -omics data, this quest has been
frustrated by various theoretical and technical hurdles, mostly stemming from
the dramatic heterogeneity of the disease. In this paper, we build on our
recent works on "selective advantage" relation among driver mutations in cancer
progression and investigate its applicability to the modeling problem at the
population level. Here, we introduce PiCnIc (Pipeline for Cancer Inference), a
versatile, modular and customizable pipeline to extract ensemble-level
progression models from cross-sectional sequenced cancer genomes. The pipeline
has many translational implications as it combines state-of-the-art techniques
for sample stratification, driver selection, identification of
fitness-equivalent exclusive alterations and progression model inference. We
demonstrate PiCnIc's ability to reproduce much of the current knowledge on
colorectal cancer progression, as well as to suggest novel experimentally
verifiable hypotheses.

5
The categories of this paper are: gr-qc
25
The categories of this paper are: patt-sol
8
The categories of this paper are: hep-ex
26
The categories of this paper are: bayes-an
20
The categories of this paper are: acc-phys
1
The categories of this paper are: cs
31
The categories of this paper are: ao-sci
13
The categories of this paper are: quant-ph
4
The categories of this paper are: cond-mat
9
The categories of this paper are: nlin
17
The categories of this paper are: q-fin
34
The categories of this paper are: chem-ph
15
The categories of this paper are: nucl-ex
29
The categories of this paper are: funct-an
0
The categories of this paper are: hep-ph
12
The categories of this paper are: nucl-th