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Which craft is best in bioinformatics?

T.K. Attwood, C.J. Miller
2001 Computers and Chemistry  
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

Jan Stanstrup, Corey D. Broeckling, Rick Helmus, Nils Hoffmann, Ewy Mathé, Thomas Naake, Luca Nicolotti, Kristian Peters, Johannes Rainer, Reza M. Salek, Tobias Schulze, Emma L. Schymanski (+7 others)
2019 Metabolites  
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

David F. Gleich
2015 SIAM Review  
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

Megan M. Richters, Huiming Xia, Katie M. Campbell, William E. Gillanders, Obi L. Griffith, Malachi Griffith
2019 Genome Medicine  
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

Rodrigo García-López, Vicente Pérez-Brocal, Andrés Moya
2019 Microbial Cell  
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

Z. Lu
2011 Database: The Journal of Biological Databases and Curation  
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

Winston Timp, Gregory Timp
2020 Science Advances  
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

Sarah Butcher, Ania Niewelska, Vera Matser, Marta Lloret Llinares, Ian Harrow, Yvonne Westermaier, Christian Blau, Alexandre Bonvin
2020 Zenodo  
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]

Wilfrido D.
2011 Current Cancer Treatment - Novel Beyond Conventional Approaches  
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

Lukas Lüftinger, Peter Májek, Stephan Beisken, Thomas Rattei, Andreas E. Posch
2021 Frontiers in Cellular and Infection Microbiology  
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

Elena Perenthaler, Soheil Yousefi, Eva Niggl, Tahsin Stefan Barakat
2019 Frontiers in Cellular Neuroscience  
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

David M.A. Martin, Isabelle R.E. Nett, Franck Vandermoere, Jonathan D. Barber, Nicholas A. Morrice, Michael A.J. Ferguson
2010 Computer applications in the biosciences : CABIOS  
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]

Amarda Shehu, Daniel Barbará, Kevin Molloy
2016 Big Data Analytics in Genomics  
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

Bolan Linghu, Evan S Snitkin, Dustin T Holloway, Adam M Gustafson, Yu Xia, Charles DeLisi
2008 BMC Bioinformatics  
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

Ahmed Hamza Osman, Omar Mohammed Barukub
2020 IEEE Access  
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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