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Which craft is best in bioinformatics?
2001
Computers and Chemistry
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we do not fully understand the rules of protein folding, so we cannot predict protein structure; and we cannot invariably diagnose protein function, given knowledge only of its sequence or structure in ...
Our use of computers to model such concepts is limited by, and must be placed in the context of, the current limits of our understanding of these biological processes. ...
Many automatic analysis systems have operated on the assumption that it is sufficient to transfer the annotation from the best-matching hit. ...
doi:10.1016/s0097-8485(01)00069-9
pmid:11459349
fatcat:erbjkntftnd5xpb443uuqvxtmm
The metaRbolomics Toolbox in Bioconductor and beyond
2019
Metabolites
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A major benefit of such an environment is the possibility of connecting different tools into more complex workflows. ...
This review provides an extensive overview of existing packages in R for different steps in a typical computational metabolomics workflow, including data processing, biostatistics, metabolite annotation ...
It utilises the
knowledge of known metabolites, as well as robust
machine learning. ...
doi:10.3390/metabo9100200
pmid:31548506
pmcid:PMC6835268
fatcat:3b2gnq6qdrcfbcq6hewgoobdce
PageRank Beyond the Web
2015
SIAM Review
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Google's PageRank method was developed to evaluate the importance of web-pages via their link structure. ...
The mathematics of PageRank, however, are entirely general and apply to any graph or network in any domain. ...
The anonymous referees were also critical to improving this manuscript. ...
doi:10.1137/140976649
fatcat:odab3aoaqbfddidyh653kn4oem
Best practices for bioinformatic characterization of neoantigens for clinical utility
2019
Genome Medicine
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Finally, we outline necessary areas of development, including the need to improve HLA class II typing accuracy, to expand software support for diverse neoantigen sources, and to incorporate clinical response ...
To create a personalized cancer vaccine, neoantigens must be computationally predicted from matched tumor-normal sequencing data, and then ranked according to their predicted capability in stimulating ...
We also thank Joshua McMichael for guidance on the creation of Fig. 1 . ...
doi:10.1186/s13073-019-0666-2
pmid:31462330
pmcid:PMC6714459
fatcat:gk5n5kfisrhmxca4b62bvtgjg4
Beyond cells – The virome in the human holobiont
2019
Microbial Cell
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It has strong foundations rooted in over a century of discoveries in the field of virology and recent advances in molecular biology and sequencing technologies. ...
Yet, most of this uncanny viral world remains vastly unexplored to date, greatly hindered by the bewildering complexity inherent to such studies and the methodological and conceptual limitations. ...
In fact, basic machine learning algorithms are now routinely applied to metagenomics, as is the case of supervised learning with random forests [211] . ...
doi:10.15698/mic2019.09.689
pmid:31528630
pmcid:PMC6717880
fatcat:ykcgicvsu5cp7bathi6i2w2fmm
PubMed and beyond: a survey of web tools for searching biomedical literature
2011
Database: The Journal of Biological Databases and Curation
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However, the acquisition of such information is becoming increasingly difficult due to its large volume and rapid growth. ...
The past decade has witnessed the modern advances of high-throughput technology and rapid growth of research capacity in producing large-scale biological data, both of which were concomitant with an exponential ...
Acknowledgements The author is grateful to the helpful discussion with John Wilbur, Minlie Huang and Natalie Xie. Conflict of interest: None declared. ...
doi:10.1093/database/baq036
pmid:21245076
pmcid:PMC3025693
fatcat:fvxvidxs7fhphfp62xpvcijuui
Beyond mass spectrometry, the next step in proteomics
2020
Science Advances
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The need to identify these critical actors was recognized early (1951) by Sanger; the first biopolymer sequenced was a peptide, insulin. ...
Proteins can be the root cause of a disease, and they can be used to cure it. ...
The pattern of drops in fluorescence intensity is interpreted to provide a partial sequence annotation for each peptide, which can be matched and scored against a protein sequence database to infer the ...
doi:10.1126/sciadv.aax8978
pmid:31950079
pmcid:PMC6954058
fatcat:7pqcw4s62rdr5gzzzwpjgp4kcm
BioExcel-2 Deliverable D3.5 – Best Practice Guides
2020
Zenodo
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This document describes the best practice guides developed by BioExcel for our core codes and workflow engines. ...
machines available to EU researchers through PRACE, and best practices for molecular docking with HADDOCK. ...
This article aims for a wider view on the different workflow and provenance standards (see also our white-paper The role of metadata in reproducible computational research https://arxiv.org/abs/2006.08589 ...
doi:10.5281/zenodo.5511703
fatcat:c5xsxxsauvdxlgtntrvmob3yqy
The Evolving Role of Tissue Biospecimens in the Treatment of Cancer
[chapter]
2011
Current Cancer Treatment - Novel Beyond Conventional Approaches
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The detection of these mutations can be accomplished by a number of different methods, the common denominator being that they evaluated the DNA sequence of the KRAS gene within tumor cells. ...
In another study, gene expression values differed by a value greater than two fold in almost 20% of the genes studied between matched FFPE and frozen tissue samples (Mojica, 2007) . ...
doi:10.5772/24740
fatcat:tonoc7lewjgm3ksudht6x24h4e
Learning From Limited Data: Towards Best Practice Techniques for Antimicrobial Resistance Prediction From Whole Genome Sequencing Data
2021
Frontiers in Cellular and Infection Microbiology
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Despite significant reductions in sequencing cost, the availability and sampling diversity of WGS data with matched antimicrobial susceptibility testing (AST) profiles required for training of WGS-AST ...
Limited data restricts the choice of machine learning training and evaluation methods and can result in overestimation of model performance. ...
ACKNOWLEDGMENTS We thank Thomas Weinmaier for help with data retrieval, Michael Ante for fruitful discussion of the statistical analysis of results, and Anna Yuwen for critical reading of the manuscript ...
doi:10.3389/fcimb.2021.610348
pmid:33659219
pmcid:PMC7917081
fatcat:okrshed6gjcw3mgq4lcv4evm6y
Beyond the Exome: The Non-coding Genome and Enhancers in Neurodevelopmental Disorders and Malformations of Cortical Development
2019
Frontiers in Cellular Neuroscience
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Even though functional annotation of non-coding regions is still lagging behind that of protein-coding genes, tremendous progress has been made in the field of gene regulation. ...
regions beyond the exome. ...
ACKNOWLEDGMENTS We thank Grazia Mancini, Tjakko van Ham, and Gerben Schaaf for the critical reading of the manuscript. ...
doi:10.3389/fncel.2019.00352
pmid:31417368
pmcid:PMC6685065
fatcat:5szds4kghze2pkjgpiw4qkc7z4
Prophossi: automating expert validation of phosphopeptide–spectrum matches from tandem mass spectrometry
2010
Computer applications in the biosciences : CABIOS
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the spectra by an experienced analyst. ...
putative phosphorylation sites in 74 proteins of the Trypanosoma brucei proteome. ...
N.A.M. provided guidance on construction of the analytical rules and critical assessment of the software. ...
doi:10.1093/bioinformatics/btq341
pmid:20651112
pmcid:PMC2922888
fatcat:6hrlhl7pxva7dotbewqqwgucry
A Survey of Computational Methods for Protein Function Prediction
[chapter]
2016
Big Data Analytics in Genomics
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The latter are related to the different sources of data exploited to predict function, as well as different choices in representing and integrating heterogeneous data. ...
Automated protein function annotation or prediction is a prime problem for computational methods to tackle in the post-genomic era of big molecular data. ...
Acknowledgements Funding for this work is provided in part by NSF-IIS1144106.
References ...
doi:10.1007/978-3-319-41279-5_7
fatcat:pejwmwpoarhyjhulevmkbavocm
High-precision high-coverage functional inference from integrated data sources
2008
BMC Bioinformatics
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Information obtained from diverse data sources can be combined in a principled manner using various machine learning methods to increase the reliability and range of knowledge about protein function. ...
FLN via machine learning techniques (2) development of a decision rule for the constructed FLN to optimize functional annotation. ...
Acknowledgements We thank the three anonymous reviewers for their constructive comments. YX is supported by a Research Starter Grant in Informatics from the PhRMA Foundation. ...
doi:10.1186/1471-2105-9-119
pmid:18298847
pmcid:PMC2292694
fatcat:kpwqxkqbwzew5okuo2rsz76euq
Graph-based Text Representation and Matching: A Review of the State of the Art and Future Challenges
2020
IEEE Access
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The graph-based methods focus on how to represent text documents in the shape of a graph to exploit the best features of their characteristics. ...
In this review, we conduct an inclusive survey of the state of the art in graph-based text representation and learning. ...
ACKNOWLEDGMENTS This work was funded by the Deanship of Scientific Research (DSR) at King Abdulaziz University, Jeddah, under grant no. DF-681-830-1441. ...
doi:10.1109/access.2020.2993191
fatcat:wkss6xzzcneujfe6ynnmbydhsa
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