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The UCSC Genome Browser Database: 2008 update

D. Karolchik, R. M. Kuhn, R. Baertsch, G. P. Barber, H. Clawson, M. Diekhans, B. Giardine, R. A. Harte, A. S. Hinrichs, F. Hsu, K. M. Kober, W. Miller (+13 others)
2007 Nucleic Acids Research  
Since its 2001 debut, the University of California, Santa Cruz (UCSC) Genome Browser (http://genome. ucsc.edu/) team has provided continuous support to the international genomics and biomedical communities  ...  The browser's publicly accessible databases are the backbone of a rich, integrated bioinformatics tool suite that includes a graphical interface for data queries and downloads, alignment programs, command-line  ...  Several UCSC-hosted tracks use multiple related tables in the SQL Nucleic Acids Research, 2017, Vol. 45, Database issue D631 Multi-Region display in the UCSC Genome Browser.  ... 
doi:10.1093/nar/gkm966 pmid:18086701 pmcid:PMC2238835 fatcat:zdlffcr2vvhpdhn5epwzsneyky

The UCSC SARS-CoV-2 Genome Browser [article]

Jason D Fernandes, Angie S Hinrichs, Hiram Clawson, Jairo Navarro Gonzales, Brian T Lee, Luis R Nassar, Brian J Raney, Kate R Rosenbloom, Santrupti Nerli, Arjun A Rao, Daniel Schmelter, Ann S Zweig (+6 others)
2020 bioRxiv   pre-print
Results: The UCSC Genome Browser for SARS-CoV-2 (https://genome.ucsc.edu/covid19.html) provides continuously updated access to the mutations in the many thousands of SARS-CoV-2 genomes deposited in GISAID  ...  We adapted our genome browser visualization tool to the viral genome for this purpose.  ...  Armenta, Phil Berman, Nik Sgourakis and the rest of the scientists at UCSC and across the world for making these tracks of molecular information possible.  ... 
doi:10.1101/2020.05.04.075945 fatcat:yqmldbtnwbe43mb4yftpzy4ubi

The Pancreatic Expression Database: 2018 update

Jacek Marzec, Abu Z. Dayem Ullah, Stefano Pirrò, Emanuela Gadaleta, Tatjana Crnogorac-Jurcevic, Nicholas R. Lemoine, Hemant M. Kocher, Claude Chelala
2017 Nucleic Acids Research  
The Pancreatic Expression Database (PED, http:// www.pancreasexpression.org) continues to be a major resource for mining pancreatic -omics data a decade after its initial release.  ...  The literature-mining module has been improved with a redesigned web appearance, restructured query platforms and updated annotations.  ...  We also thank our colleagues who contributed data for previous versions of the database, especially Professor Stephan A Hahn.  ... 
doi:10.1093/nar/gkx955 pmid:29059374 pmcid:PMC5753364 fatcat:iqpxown4jrf6ho76cydzaemnka

ABCMdb reloaded: updates on mutations in ATP binding cassette proteins

Hedvig Tordai, Kristóf Jakab, Gergely Gyimesi, Kinga András, Anna Brózik, Balázs Sarkadi, Tamás Hegedűs
2017 Database: The Journal of Biological Databases and Curation  
In the new version of the database we aimed to collect the effect of mutations from databases including ClinVar.  ...  Database URL: http://abcm2.hegelab.org V C The Author(s)  ...  For example, the DECODE (DECipherment Of DNA Elements) database, which combines ABiosciences' proprietary database, QIAGEN's Text Mining Application, and also data from the UCSC Genome Browser, does not  ... 
doi:10.1093/database/bax023 pmid:28365738 pmcid:PMC5467578 fatcat:xhqszoljp5djbhbhxtqvyutyry

MiRIAD update: using alternative polyadenylation, protein interaction network analysis and additional species to enhance exploration of the role of intragenic miRNAs and their host genes

Ludwig C. Hinske, Felipe R. C. dos Santos, Daniel T. Ohara, Lucila Ohno-Machado, Simone Kreth, Pedro A. F. Galante
2017 Database: The Journal of Biological Databases and Curation  
MiRIAD is a database with an interactive and user-friendly online interface that has been facilitating research on intragenic miRNAs. In this article, we present a major update.  ...  Although the previous version solely reported protein interactions, the update features a separate network analysis view that can either be accessed V C The Author(s) through the submission of a list of  ...  Acknowledgements The authors thank Gustavo S. Franc¸a for working on the previous miRIAD version as well as Anamaria A. Camargo and Luiz F. L. Reis for their valuable suggestions.  ... 
doi:10.1093/database/bax053 pmid:29220447 pmcid:PMC5569676 fatcat:j6h6gfuwgbezfa2r2mlyjsucca

GWIPS-viz: 2018 update

Audrey M Michel, Stephen J Kiniry, Patrick B F O'Connor, James P Mullan, Pavel V Baranov
2017 Nucleic Acids Research  
The GWIPS-viz browser (http://gwips.ucc.ie/) is an on-line genome browser which is tailored for exploring ribosome profiling (Ribo-seq) data.  ...  To improve the power of the signal, we aggregate Ribo-seq data from several studies into Global aggregate tracks for each genome.  ...  We also wish to thank the UCSC Genome Browser Development team who have always been so generous with their help.  ... 
doi:10.1093/nar/gkx790 pmid:28977460 pmcid:PMC5753223 fatcat:yb2jqbjmnrhsdd7ceyynsqvceq

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

Aziz Khan, Oriol Fornes, Arnaud Stigliani, Marius Gheorghe, Jaime A Castro-Mondragon, Robin van der Lee, Adrien Bessy, Jeanne Chèneby, Shubhada R Kulkarni, Ge Tan, Damir Baranasic, David J Arenillas (+7 others)
2017 Nucleic Acids Research  
ACKNOWLEDGEMENTS We thank the scientific community for performing experimental assays of TF-DNA interactions and for publicly releasing the data.  ...  We thank Rachelle Farkas for proofreading the manuscript.  ...  The predicted TFBSs are publicly available through a UCSC Genome Browser data hub (47) containing tracks for the human genome assemblies hg19 and hg38 (http://jaspar.genereg.net/genome-tracks/).  ... 
doi:10.1093/nar/gkx1126 pmid:29140473 pmcid:PMC5753243 fatcat:bzfitmkui5e4fihzspdn2roula

ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments

Jeanne Chèneby, Marius Gheorghe, Marie Artufel, Anthony Mathelier, Benoit Ballester
2017 Nucleic Acids Research  
Additionally, the updated database includes new search features for TR names as well as aliases, including cell line names and the ability to navigate the data directly within genome browsers via public  ...  ReMap 2018 provides a significant update of the ReMap database, providing an in depth view of the complexity of the regulatory landscape in human.  ...  The content of the ReMap database can be browsed through four options: (i) across two mirror sites of the UCSC Genome Browser (22) where a public session has been created ( Figure 2 and Supplementary  ... 
doi:10.1093/nar/gkx1092 pmid:29126285 pmcid:PMC5753247 fatcat:4z7rimsipjhv7lvgrir4nhgzdq

An update on sORFs.org: a repository of small ORFs identified by ribosome profiling

Volodimir Olexiouk, Wim Van Criekinge, Gerben Menschaert
2017 Nucleic Acids Research  
This update elaborates on the major improvements implemented since its initial release. sORFs.org now additionally supports three more species (zebrafish, rat and Caenorhabditis elegans) and currently  ...  The inclusion of other species also led to the development of an inner BLAST pipeline, assessing sequence similarity between sORFs in the repository.  ...  ACKNOWLEDGEMENTS We want acknowledge Kenneth Verheggen and Lennart Martens for their contribution in creating and improving the parameter extraction pipeline for PRIDE-ReSpin.  ... 
doi:10.1093/nar/gkx1130 pmid:29140531 pmcid:PMC5753181 fatcat:vami7rpgcrgfrawzebwmz3msaa

The 2018 Nucleic Acids Research database issue and the online molecular biology database collection

Daniel J Rigden, Xosé M Fernández
2017 Nucleic Acids Research  
This issue also contains reports on genomics resources including Ensembl, the UCSC Genome Browser and ENCODE.  ...  The NAR online Molecular Biology Database Collection has been updated, reviewing 138 entries, adding 88 new resources and eliminating 47 discontinued URLs, bringing the current total to 1737 databases.  ...  The authors' opinions do not necessarily reflect the views of their respective institutions.  ... 
doi:10.1093/nar/gkx1235 pmid:29316735 pmcid:PMC5753253 fatcat:ftpcgajkxbfstmn7rh37q7foyi

PCSD: a plant chromatin state database

Yue Liu, Tian Tian, Kang Zhang, Qi You, Hengyu Yan, Nannan Zhao, Xin Yi, Wenying Xu, Zhen Su
2017 Nucleic Acids Research  
The self-organization mapping (SOM) results for these different chromatin signatures and UCSC Genome Browser for visualization were also integrated into the PCSD database.  ...  Genome-wide maps of chromatin states have become a powerful representation of genome annotation and regulatory activity.  ...  Visualization in UCSC Genome Browser In PCSD, visualization of chromatin states and associations with genes and epigenetic marks in the genome are shown in the UCSC Genome Browser ( Figure 1C , Figure  ... 
doi:10.1093/nar/gkx919 pmid:29040761 pmcid:PMC5753246 fatcat:xd7zmlpfvvguxek3pfslppi2v4

VerSeDa: vertebrate secretome database

Ana R. Cortazar, José A. Oguiza, Ana M. Aransay, José L. Lavín
2017 Database: The Journal of Biological Databases and Curation  
at the NCBI, UCSC and ENSEMBL sites.  ...  To our knowledge, VerSeDa is the only state-of-the-art database designed to store secretome data from multiple vertebrate genomes, thus, saving an important amount of time spent in the prediction of protein  ...  Sutherland for critical reading of the manuscript and English language revision.  ... 
doi:10.1093/database/baw171 pmid:28365718 pmcid:PMC5467544 fatcat:aud6bozqinahdokup5m53e3hfi

Xenbase: a genomic, epigenomic and transcriptomic model organism database

Kamran Karimi, Joshua D Fortriede, Vaneet S Lotay, Kevin A Burns, Dong Zhou Wang, Malcom E Fisher, Troy J Pells, Christina James-Zorn, Ying Wang, V G Ponferrada, Stanley Chu, Praneet Chaturvedi (+2 others)
2017 Nucleic Acids Research  
These include new genomes for both supported species (each with chromosome scale assemblies), new genome annotations, genome segmentation, dynamic and interactive visualization for RNA-Seq data, updated  ...  Over the past two years many new types of content have been added along with new tools and functionalities to reflect the impact of high-throughput sequencing.  ...  The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.  ... 
doi:10.1093/nar/gkx936 pmid:29059324 pmcid:PMC5753396 fatcat:yrmnbwipgffc5c5ncaqi2bc2bi

Protein Bioinformatics Databases and Resources [chapter]

Chuming Chen, Hongzhan Huang, Cathy H. Wu
2017 Msphere  
As an update to our previously contributed MiMB series chapter [8], we now focus on databases that are aligned with the content of this book and emphasize the types of data stored and related data access  ...  , gene expression databases, genome annotation databases, organism specific databases, phylogenomic databases, polymorphism and mutation databases, protein-protein interaction databases, proteomic databases  ...  Acknowledgments This work was supported by grants from the National Institutes of Health: U41HG007822 and Delaware-INBRE (P20GM103446).  ... 
doi:10.1007/978-1-4939-6783-4_1 pmid:28150231 pmcid:PMC5506686 fatcat:rrclcq47p5hqrlffz2v2xexjoy

HEDD: Human Enhancer Disease Database

Zhen Wang, Quanwei Zhang, Wen Zhang, Jhih-Rong Lin, Ying Cai, Joydeep Mitra, Zhengdong D Zhang
2017 Nucleic Acids Research  
Despite recent systematic identification of them in the human genome, currently there is an urgent need for comprehensive annotation databases of human enhancers with a focus on their disease connections  ...  In response, we built the Human Enhancer Disease Database (HEDD) to facilitate studies of enhancers and their potential roles in human complex diseases.  ...  Rosenfeld for their expert advice on the biology of enhancers.  ... 
doi:10.1093/nar/gkx988 pmid:29077884 pmcid:PMC5753236 fatcat:sig4jqzi6zgnbporro6wzvhvdu
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