2,189 research outputs found
Stable Feature Selection for Biomarker Discovery
Feature selection techniques have been used as the workhorse in biomarker
discovery applications for a long time. Surprisingly, the stability of feature
selection with respect to sampling variations has long been under-considered.
It is only until recently that this issue has received more and more attention.
In this article, we review existing stable feature selection methods for
biomarker discovery using a generic hierarchal framework. We have two
objectives: (1) providing an overview on this new yet fast growing topic for a
convenient reference; (2) categorizing existing methods under an expandable
framework for future research and development
Undisclosed, unmet and neglected challenges in multi-omics studies
[EN] Multi-omics approaches have become a reality in both large genomics projects and small laboratories. However, the multi-omics research community still faces a number of issues that have either not been sufficiently discussed or for which current solutions are still limited. In this Perspective, we elaborate on these limitations and suggest points of attention for future research. We finally discuss new opportunities and challenges brought to the field by the rapid development of single-cell high-throughput molecular technologies.This work has been funded by the Spanish Ministry of Science and Innovation with grant
number BES-2016-076994 to A.A.-L.Tarazona, S.; Arzalluz-Luque, Á.; Conesa, A. (2021). Undisclosed, unmet and neglected challenges in multi-omics studies. Nature Computational Science. 1(6):395-402. https://doi.org/10.1038/s43588-021-00086-z3954021
Voices in methods development
To mark the 15th anniversary of Nature Methods, we asked scientists from across diverse fields of basic biology research for their views on the most exciting and essential methodological challenges that their communities are poised to tackle in the near future
A note on retrodiction and machine evolution
Biomolecular communication demands that interactions between parts of a
molecular system act as scaffolds for message transmission. It also requires an
evolving and organized system of signs - a communicative agency - for creating
and transmitting meaning. Here I explore the need to dissect biomolecular
communication with retrodiction approaches that make claims about the past
given information that is available in the present. While the passage of time
restricts the explanatory power of retrodiction, the use of molecular structure
in biology offsets information erosion. This allows description of the gradual
evolutionary rise of structural and functional innovations in RNA and proteins.
The resulting chronologies can also describe the gradual rise of molecular
machines of increasing complexity and computation capabilities. For example,
the accretion of rRNA substructures and ribosomal proteins can be traced in
time and placed within a geological timescale. Phylogenetic, algorithmic and
theoretical-inspired accretion models can be reconciled into a congruent
evolutionary model. Remarkably, the time of origin of enzymes, functional RNA,
non-ribosomal peptide synthetase (NRPS) complexes, and ribosomes suggest they
gradually climbed Chomsky's hierarchy of formal grammars, supporting the
gradual complexification of machines and communication in molecular biology.
Future retrodiction approaches and in-depth exploration of theoretical models
of computation will need to confirm such evolutionary progression.Comment: 7 pages, 1 figur
Voices in methods development
To mark the 15th anniversary of Nature Methods, we asked scientists from across diverse fields of basic biology research for their views on the most exciting and essential methodological challenges that their communities are poised to tackle in the near future
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