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The Genome Sequence Archive Family: Towards Explosive Data Growth and Diverse Data Types [article]

Tingting Chen, Xu Chen, Sisi Zhang, Junwei Zhu, Bixia Tang, Anke Wang, Lili Dong, Zhewen Zhang, Caixia Yu, Yanling Sun, Lianjiang Chi, Huanxin Chen (+9 others)
2021 bioRxiv   pre-print
Considering explosive data growth with diverse data types, here we present the GSA family by expanding into a set of resources for raw data archive with different purposes, namely, GSA (  ...  Together, all these resources form a family of resources dedicated to archiving explosive data with diverse types, accept data submissions from all over the world and provide free open access to all publicly  ...  Jingchu Luo and Prof. Weimin Zhu for their valuable suggestions and a number of users for their contributions to the data submission.  ... 
doi:10.1101/2021.06.29.449849 fatcat:bbeo35mucfexvhixv56ditoa2y

The InterPro protein families database: the classification resource after 15 years

Alex Mitchell, Hsin-Yu Chang, Louise Daugherty, Matthew Fraser, Sarah Hunter, Rodrigo Lopez, Craig McAnulla, Conor McMenamin, Gift Nuka, Sebastien Pesseat, Amaia Sangrador-Vegas, Maxim Scheremetjew (+24 others)
2014 Nucleic Acids Research  
The InterPro database ( interpro/) is a freely available resource that can be used to classify sequences into protein families and to predict the presence of important domains and  ...  to classify protein families and domains.  ...  We also discuss the challenges faced by the resource given the explosive growth in sequence data in recent years.  ... 
doi:10.1093/nar/gku1243 pmid:25428371 pmcid:PMC4383996 fatcat:4asvzb32obgwhlvdkrfhiokvme

The prokaryotic complex iron–sulfur molybdoenzyme family

Richard A. Rothery, Gregory J. Workun, Joel H. Weiner
2008 Biochimica et Biophysica Acta - Biomembranes  
Bacterial genomes encode an extensive range of respiratory enzymes that enable respiratory metabolism with a diverse group of reducing and oxidizing substrates under both aerobic and anaerobic growth conditions  ...  We have used genome sequence data to establish that there is a bias against the presence of soluble periplasmic molybdoenzymes in bacteria lacking an outer membrane.  ...  We also wish to thank the following for critical reading of the manuscript: Victor Cheng and Kamila Moquin.  ... 
doi:10.1016/j.bbamem.2007.09.002 pmid:17964535 fatcat:zxu2c6ym4zbklc7drmh3useovu

Biological Databases for Human Research

Dong Zou, Lina Ma, Jun Yu, Zhang Zhang
2015 Genomics, Proteomics & Bioinformatics  
With the explosive growth of biological data, there is an increasing number of biological databases that have been developed in aid of human-related research.  ...  Here we present a collection of humanrelated biological databases and provide a mini-review by classifying them into different categories according to their data types.  ...  Method of biocuration As a consequence of the explosive growth of data, curation increasingly requires collective intelligence for collaborative data integration and annotation.  ... 
doi:10.1016/j.gpb.2015.01.006 pmid:25712261 pmcid:PMC4411498 fatcat:dubusegmv5gi5gcjxfrcaqhmvy

Insights from 20 years of bacterial genome sequencing

Miriam Land, Loren Hauser, Se-Ran Jun, Intawat Nookaew, Michael R. Leuze, Tae-Hyuk Ahn, Tatiana Karpinets, Ole Lund, Guruprased Kora, Trudy Wassenaar, Suresh Poudel, David W. Ussery
2015 Functional & Integrative Genomics  
Using third-generation DNA sequencing, it is possible to completely sequence a bacterial genome in a few hours and identify some types of methylation sites along the genome as well.  ...  The diversity of bacterial communities is extensive as is evident from the genome sequences available from 50 different bacterial phyla and 11 different archaeal phyla.  ...  Acknowledgments We gratefully acknowledge funding support for this research by the Genomic Science Program, US Department of Energy (DOE), Office of Science, Biological and Environmental Research (BER)  ... 
doi:10.1007/s10142-015-0433-4 pmid:25722247 pmcid:PMC4361730 fatcat:l6adp44wbjbvbh5j6t2qqioatm

Dealing with the Data Deluge – New Strategies in Prokaryotic Genome Analysis [chapter]

Leonid Zaslavsky, Stacy Ciufo, Boris Fedorov, Boris Kiryutin, Igor Tolstoy, Tatiana Tatusova
2016 Next Generation Sequencing - Advances, Applications and Challenges  
New strategies have been designed to bring an order to this genome sequence shockwave and improve the usability of associated data.  ...  Protein distance measures dissimilarity between markers of the same type and the subsequent genomic distance averages over the majority of marker-distances, ignoring the outliers.  ...  Wolf for productive discussions and to Vyacheslav Brover for the database support. Author details  ... 
doi:10.5772/62125 fatcat:cxwvhwsxwrc7nk7a2qqdczlaem

Deep resequencing reveals excess rare recent variants consistent with explosive population growth

Alex Coventry, Lara M. Bull-Otterson, Xiaoming Liu, Andrew G. Clark, Taylor J. Maxwell, Jacy Crosby, James E. Hixson, Thomas J. Rea, Donna M. Muzny, Lora R. Lewis, David A. Wheeler, Aniko Sabo (+18 others)
2010 Nature Communications  
Here, we applied sanger sequencing of genomic PCR amplicons to resequence the diabetesassociated genes KCNJ11 and HHEX in 13,715 people (10,422 European Americans and 3,293 African Americans) and validated  ...  variants, and that disease risk and the burden of disease in contemporary populations may be heavily influenced by the distribution of rare variants.  ...  , Tim Connallon, Alon Keinan, Richard Meisel and Margarida Cardoso Moreira for helpful comments on the manuscript; Greg Dyson for useful discussions; and Lawrence S Shimmin, Clement Chow and Peter Schweitzer  ... 
doi:10.1038/ncomms1130 pmid:21119644 pmcid:PMC3060603 fatcat:fwbe7d2eordq5lxp4f5uprbbue

From Nehemiah Grew to Genomics: The Emerging Field of Evo-Devo Research for Woody Plants

Andrew Groover, Quentin Cronk
2013 International journal of plant sciences  
JSTOR is a not-for-profit service that helps scholars, researchers, and students discover, use, and build upon a wide range of content in a trusted digital archive.  ...  The University of Chicago Press is collaborating with JSTOR to digitize, preserve and extend access to International Journal of Plant Sciences.  ...  Cronk's laboratory is provided by the National Science and Engineering Research Council, Canada (NSERC), and Genome Canada.  ... 
doi:10.1086/671569 fatcat:i6wmkvi6h5gxjg67v4gw7lufi4

Design and development of portal for biological database in agriculture

Shashi Bhushan Lal, Pankaj Kumar Pandey, Punit K Rai, Anil Rai, Anu Sharma, Krishna Kumar Chaturvedi
2013 Bioinformation  
The application of novel and modern techniques in genetic engineering and genomics has resulted in information explosion in genomics.  ...  These scientists are dependent on NCBI, EMBL, DDBJ and other portals for their sequence submissions, analysis and other data mining tasks.  ...  The recent genomic era has seen a massive explosion in the amount of biological information and data arising from the rapid research and unprecedented progress in molecular biology and genome sequencing  ... 
doi:10.6026/97320630009588 pmid:23888101 pmcid:PMC3717188 fatcat:6rlbp4cjszb3bnqz43acdlv3ha

Evidence-Based Annotation of Gene Function in Shewanella oneidensis MR-1 Using Genome-Wide Fitness Profiling across 121 Conditions

Adam Deutschbauer, Morgan N. Price, Kelly M. Wetmore, Wenjun Shao, Jason K. Baumohl, Zhuchen Xu, Michelle Nguyen, Raquel Tamse, Ronald W. Davis, Adam P. Arkin, Paul M. Richardson
2011 PLoS Genetics  
Given the great diversity of bacteria and the ease of genome sequencing, high-throughput approaches to identify gene function experimentally are needed.  ...  Here, we use pools of tagged transposon mutants in the metal-reducing bacterium Shewanella oneidensis MR-1 to probe the mutant fitness of 3,355 genes in 121 diverse conditions including different growth  ...  Acknowledgments We thank Marcin Joachimiak and Keith Keller for computational assistance, Jennifer Reed for sharing results from the MR-1 flux balance model, and Jeff Skerker for comments on the manuscript  ... 
doi:10.1371/journal.pgen.1002385 pmid:22125499 pmcid:PMC3219624 fatcat:abapzordkfgrha6bcdz7flwbjy

The digital code of DNA

Leroy Hood, David Galas
2003 Nature  
DNA research is therefore crucial to a new generation of immunologists, from those striving towards the development of novel vaccines to those seeking to understand and control autoimmune diseases, allergy  ...  , allergy and transplantation.  ...  This exponential growth has been a driver for the explosive growth of information technology.  ... 
doi:10.1038/nature01410 pmid:12540920 fatcat:qolmdqgogjhhnpg2awbtfshqdy

Unlocking Big Data for better health

Steven Munevar
2017 Nature Biotechnology  
Ensembl collaborates with genome sequencing centres and annotation groups around the world. Ensembl Genomes The falling costs of DNA sequencing have led to an explosion of reference genome  ...  Rfam families are created from ENA sequence data and experimental evidence in the literature.  ... 
doi:10.1038/nbt.3918 pmid:28700551 fatcat:oqiurm5cgzec7lfenvjvlemxoy

Bacterial genomic epidemiology, from local outbreak characterization to species-history reconstruction

Stefano Gaiarsa, Leone De Marco, Francesco Comandatore, Piero Marone, Claudio Bandi, Davide Sassera
2015 Pathogens and Global Health  
Bacteriology has embraced the next-generation sequencing revolution, swiftly moving from the time of single genome sequencing to the age of genomic epidemiology.  ...  Hundreds and now even thousands of genomes are being sequenced for single bacterial species, allowing unprecedented levels of resolution and insight in the evolution and epidemic diffusion of the main  ...  The authors selected and sequenced 324 isolates from archives and databases, in order to represent the global diversity of the two species, choosing among different genomic variants, location and sources  ... 
doi:10.1080/20477724.2015.1103503 pmid:26878934 pmcid:PMC4768628 fatcat:2igqa2hv6vhfdbv7hp5gulhh3e

National Institute of Allergy and Infectious Diseases Bioinformatics Resource Centers: New Assets for Pathogen Informatics

J. M. Greene, F. Collins, E. J. Lefkowitz, D. Roos, R. H. Scheuermann, B. Sobral, R. Stevens, O. White, V. Di Francesco
2007 Infection and Immunity  
Each BRC is adopting its own approaches for dealing with the upcoming explosion in the number of sequenced microbial genomes.  ...  and archiving.  ... 
doi:10.1128/iai.00105-07 pmid:17420237 pmcid:PMC1932942 fatcat:ywmscqywenflnlxo7frpehvnii

Genetic Testing and Tissue Banking for Personalized Oncology: Analytical and Institutional Factors

George Miles, James Rae, Suresh S. Ramalingam, John Pfeifer
2015 Seminars in Oncology  
Unique challenges and opportunities accompany the rapidly evolving interplay between tissue banking and genomic sequencing, and are the driving forces underlying the revolution in precision medicine.  ...  Comprehensive screening of tumors by DNA sequencing and the ability to mine and interpret these large data sets from well-organized tissue banks have defined molecular subtypes of cancer.  ...  Sequencing data from genomic profiling can also be misleading since the genomic profile of the most abundant cell type within a given tumor specimen may not necessarily reflect the biological activity  ... 
doi:10.1053/j.seminoncol.2015.07.013 pmid:26433552 pmcid:PMC4705034 fatcat:ochsrojurnfopesdkngf2wwf5m
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