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The Rat Genome Database curation tool suite: a set of optimized software tools enabling efficient acquisition, organization, and presentation of biological data

S. J. F. Laulederkind, M. Shimoyama, G. T. Hayman, T. F. Lowry, R. Nigam, V. Petri, J. R. Smith, S.-J. Wang, J. de Pons, G. Kowalski, W. Liu, W. Rood (+4 others)
2011 Database: The Journal of Biological Databases and Curation  
Conflict of interest. None Declared.  ...  To perform that biocuration efficiently, the development of a suite of software tools was necessary.  ...  Many biological databases exist to organize and store either the sequencing data or associated biological data or both.  ... 
doi:10.1093/database/bar002 pmid:21321022 pmcid:PMC3041158 fatcat:gzoadgdnsre4vi7samk3flcjwu

TargetMine, an Integrated Data Warehouse for Candidate Gene Prioritisation and Target Discovery

Yi-An Chen, Lokesh P. Tripathi, Kenji Mizuguchi, Vladimir Uversky
2011 PLoS ONE  
It enables complicated searches that are difficult to perform with existing tools and it also offers integration of custom annotations and in-house experimental data.  ...  An integrated approach that combines results from multiple data types is best suited for optimal target selection. We developed TargetMine, a data warehouse for efficient target prioritisation.  ...  Acknowledgments We thank Mitsubishi Space Software Co., Ltd. for technical support. We gratefully acknowledge Dr. Tadashi Imanishi of Biomedicinal Information Author Contributions  ... 
doi:10.1371/journal.pone.0017844 pmid:21408081 pmcid:PMC3050930 fatcat:fvfqc77ymjfmlmviaqhb6wjkha

Computational dynamic approaches for temporal omics data with applications to systems medicine

Yulan Liang, Arpad Kelemen
2017 BioData Mining  
The most recent computing tools and software to analyze specific problem type, associated platform resources, and other potentials for the dynamic trajectory and interaction methods are also presented  ...  However, the delineation of the possible associations and causalities of genes, proteins, metabolites, cells and other biological entities from high throughput time course omics data is challenging for  ...  Availability of data and materials Data sharing not applicable to this article as no datasets were generated or analysed during the current study.  ... 
doi:10.1186/s13040-017-0140-x pmid:28638442 pmcid:PMC5473988 fatcat:rscvtjlpgrf53fbwlt6t4i22em

Whole Genome Annotation: In Silico Analysis [chapter]

Vasco Azevedo, Vinicius Abreu, Sintia Almeida, Anderson Santos, Siomar Soares, Amjad Ali, Anne Pinto, Aryane Magalhaes, Eudes Barbosa, Rommel Ramos, Louise Cerdeira, Adriana Carneiro (+3 others)
2011 Bioinformatics - Trends and Methodologies  
There are many web tools and softwares available to manage and efficiently extract data from genomes of various strains of the same species.  ...  Genomics A genome is the complete set of DNA sequences of a living organism; it consists of coding and non-coding sequences.  ...  This book suits young researchers who seek basic fundamentals of bioinformatic skills such as data mining, data integration, sequence analysis and gene expression analysis as well as scientists who are  ... 
doi:10.5772/23724 fatcat:of53q6bc4fbdxply64hl63sjqe

Next-Generation Bioinformatics Approaches and Resources for Coronavirus Vaccine Discovery and Development—A Perspective Review

Rahul Chatterjee, Mrinmoy Ghosh, Susrita Sahoo, Santwana Padhi, Namrata Misra, Visakha Raina, Mrutyunjay Suar, Young-Ok Son
2021 Vaccines  
Bioinformatics platforms and various computational tools and databases are also essential for the identification of promising vaccine targets making the best use of genomic resources, for further experimental  ...  The present review focuses on the various stages of the vaccine development process and the vaccines available for COVID-19.  ...  Acknowledgments: We would like to acknowledge Krishn Kumar Verma for his support of the scientific visualization; and the School of Biotechnology, Kalinga Institute of Industrial Technology, and KIIT Technology  ... 
doi:10.3390/vaccines9080812 pmid:34451937 pmcid:PMC8402397 fatcat:urw75khyavfqrozw4kwaryvwo4

Integration of Evidence across Human and Model Organism Studies: A Meeting Report

Rohan H C Palmer, Emma C Johnson, Hyejung Won, Renato Polimanti, Manav Kapoor, Apurva Chitre, Molly A Bogue, Chelsie E Benca-Bachman, Clarissa C Parker, Oana Ursu, Anurag Verma, Timothy Reynolds (+39 others)
2021 Genes, Brain and Behavior  
The National Institute on Drug Abuse and Joint Institute for Biological Sciences at the Oak Ridge National Laboratory hosted a meeting attended by a diverse group of scientists with expertise in substance  ...  Specific topics were to (a) evaluate the current state of substance use genetics and genomics research and fundamental gaps, (b) identify opportunities and challenges of integration and sharing across  ...  As with all large-scale data endeavors, the researchers recognized a limitation around encryption software that would enable accessibility of primary raw data and allow searches across databases without  ... 
doi:10.1111/gbb.12738 pmid:33893716 fatcat:h2ozonod25ax5ksurweizt3d5y

Integrated Omics: Tools, Advances, and Future Approaches

Biswapriya B Misra, Carl D Langefeld, Michael Olivier, Laura A Cox
2018 Journal of Molecular Endocrinology  
The ultimate goal is towards the holistic realization of a 'systems biology' understanding of the biological question in hand.  ...  With the rapid adoption of high-throughput omic approaches to analyze biological samples such as genomics, transcriptomics, proteomics, and metabolomics, each analysis can generate tera- to peta-byte sized  ...  Table 1 List of various tools, software, statistical approaches and databases available for integrated -omics approaches.  ... 
doi:10.1530/jme-18-0055 pmid:30006342 fatcat:62c6xglxcbhhnkxgqo5gt7garq

Proteomics for systems toxicology

Bjoern Titz, Ashraf Elamin, Florian Martin, Thomas Schneider, Sophie Dijon, Nikolai V. Ivanov, Julia Hoeng, Manuel C. Peitsch
2014 Computational and Structural Biotechnology Journal  
Current toxicology studies frequently lack measurements at molecular resolution to enable a more mechanismbased and predictive toxicological assessment.  ...  Overall, we provide the technical and conceptual foundation for the integration of proteomic measurements in a more comprehensive systems toxicology assessment framework.  ...  Software tools that match peptide masses to genome-based protein databases or spectra to spectral libraries directly can often be run in a parallelized mode to accelerate the data analysis.  ... 
doi:10.1016/j.csbj.2014.08.004 pmid:25379146 pmcid:PMC4212285 fatcat:jijc2r6xo5azriwbm7mn4wx5eu

A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism

Hooman Hefzi, Kok Siong Ang, Michael Hanscho, Aarash Bordbar, David Ruckerbauer, Meiyappan Lakshmanan, Camila A. Orellana, Deniz Baycin-Hizal, Yingxiang Huang, Daniel Ley, Veronica S. Martinez, Sarantos Kyriakopoulos (+28 others)
2016 Cell Systems  
MH curated human reconstruction content. DBH, GP, and MJB oversaw and generated metabolomic data for CHO-K1. DL, AML, and MRA constructed a reconstruction of amino acid metabolism in CHO.  ...  ZAK performed database checks and model transfer to the BiGG database. JSL validated asparagine auxotrophy predictions in CHO-K1 and CHO-S.  ...  Acknowledgments We acknowledge funding from the National Institutes of Health (R35 GM119850) and generous funding through  ... 
doi:10.1016/j.cels.2016.10.020 pmid:27883890 pmcid:PMC5132346 fatcat:5777qaqturbzbi7zxkgggyjimi

Unlocking Big Data for better health

Steven Munevar
2017 Nature Biotechnology  
We used our state-of-the-art orthologycalling software to identify homologous genes between the ferret and a set of 33 other organisms for which the complete genome sequence is known.  ...  Our curators will continue to map disease and dysregulation on Reactome pathways; the optimal presentation of modulation of complex pathways will be an active research topic.  ... 
doi:10.1038/nbt.3918 pmid:28700551 fatcat:oqiurm5cgzec7lfenvjvlemxoy

EMBnet.journal 18 Suppl. B

EMBnet Journal
2012 EMBnet journal  
National Research Council of Italy (CNR) and the Polish Academy of Sciences (PAN Acknowledgements This work is partial fulfillment of the research objective of "DM19410 -Laboratorio di Bioinformatica  ...  Segagni et al, presented at the DILS 2012 conference in Washington DC.  ...  Since the two schemas, of the software and the database, nearly overlap, data exchanges between these two components are fluid and efficient.  ... 
doi:10.14806/ej.18.b.592 fatcat:wlwsmbdlfzbjtk7vyhiabdov6q

Genome to Phenome: Improving Animal Health, Production, and Well-Being – A New USDA Blueprint for Animal Genome Research 2018–2027

Caird Rexroad, Jeffrey Vallet, Lakshmi Kumar Matukumalli, James Reecy, Derek Bickhart, Harvey Blackburn, Mark Boggess, Hans Cheng, Archie Clutter, Noelle Cockett, Catherine Ernst, Janet E. Fulton (+11 others)
2019 Frontiers in Genetics  
To develop a new, updated blueprint, ARS and NIFA, along with scientists in the animal genomics field, convened a workshop titled "Genome to Phenome: A USDA Blueprint for Improving Animal Production" in  ...  In the decade that followed, many of the goals set forth in the blueprint were accomplished. However, several other goals require further research.  ...  Institute of Food and Agriculture and support from the ARS Office of National Programs, and the National Agricultural Library.  ... 
doi:10.3389/fgene.2019.00327 pmid:31156693 pmcid:PMC6532451 fatcat:sl72idaubngs5bsj2ga7trdoaq

The rise of genomics

Jean Weissenbach
2016 Comptes rendus. Biologies  
, and David Vallenet for their help in preparing the tables and the figure.  ...  Acknowledgements I am indebted to Susan Cure, Claudine Mé digue, and Patrick Wincker for proposing numerous and thoughtful improvements to this manuscript and to Vé ronique de Berardinis, Sté phane Cruveiller  ...  Some of these, such as the protein databases, remain very general, whereas many other specialized databases focus on a limited set of objects or on a single species.  ... 
doi:10.1016/j.crvi.2016.05.002 pmid:27263360 fatcat:xnkq6y4pg5bf3m5x6fhs5fwgz4

Computational knowledge integration in biopharmaceutical research

D. Ficenec
2003 Briefings in Bioinformatics  
We also thank Carole Goble and Robert Stevens of the University of Manchester Department of Computer Science, and Peter Szolovits of the MIT Laboratory for  ...  Acknowledgments The authors are grateful for the support of Millennium's research scientists, and in particular Laura Rudolph-Owen, Robert Coopersmith and Harshwardhan Bal.  ...  In academia, frame-based representations of biological data have proven useful in several biological domains across a range of organisms.  ... 
doi:10.1093/bib/4.3.260 pmid:14582520 fatcat:s2oifpz3qfdttmflvvmm5q7h2u

EMBnet.journal 19 Suppl. A

EMBnet Journal
2013 EMBnet journal  
Michele Morgante: Structural variation and the plant pan genomes Infectious Diseases. identification from high-throughput sequencing data by joint Bayesian family calling. arrangement, DNA Methylation  ...  Leif Andersson: How domestic animal genomics can teach human medicine and medicine and evolutionary biology "down stream " bioinformatics analysis in order to meet the demands of the scientific community  ...  Oversight of the MAVEN project is provided by Genome Prairie and Dr. Reno Pontarollo.  ... 
doi:10.14806/ej.19.a.689 fatcat:2xs4bsifarfipopojjerizk3ce
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