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The Cancer Omics Atlas: an integrative resource for cancer omics annotations

Qingrong Sun, Mengyuan Li, Xiaosheng Wang
2018 BMC Medical Genomics  
The Cancer Genome Atlas (TCGA) is an important data resource for cancer biologists and oncologists.  ...  Methods: We developed a new web-based tool The Cancer Omics Atlas (TCOA, http://tcoa.cpu.edu.cn) for fast and straightforward querying of TCGA "omics" data.  ...  We also downloaded six immune-related gene sets from the InnateDB database [26] , and selected the genes that were included in at least two of the six gene sets.  ... 
doi:10.1186/s12920-018-0381-7 pmid:30089500 pmcid:PMC6083503 fatcat:xt5ngsqrvzcwlgghsuzac6uvzy

Transcriptome database resource and gene expression atlas for the rose

Annick Dubois, Sebastien Carrere, Olivier Raymond, Benjamin Pouvreau, Ludovic Cottret, Aymeric Roccia, Jean-Paul Onesto, Soulaiman Sakr, Rossitza Atanassova, Sylvie Baudino, Fabrice Foucher, Manuel Bris (+2 others)
2012 BMC Genomics  
Transcriptome database resource and gene expression atlas for the rose ] http://okina.univ-angers.fr/publications?f[author]=12288 [8] http://okina.univ-angers.fr/publications?  ...  f[author]=12290 [11] http://okina.univ-angers.fr/f.foucher/publications Submitted by Emmanuel Lemoine on Thu, 02/12/2015 -13:07 Titre Transcriptome database resource and gene expression atlas for the  ... 
doi:10.1186/1471-2164-13-638 pmid:23164410 pmcid:PMC3518227 fatcat:npawg2bwnbdq5jwuhocmvqi7ee

The mitochondrial genomes of Atlas Geckos (Quedenfeldtia): mitogenome assembly from transcriptomes and anchored hybrid enrichment datasets

Mariana L. Lyra, Ulrich Joger, Ulrich Schulte, Tahar Slimani, El Hassan El Mouden, Abdellah Bouazza, Sven Künzel, Alan R. Lemmon, Emily Moriarty Lemmon, Miguel Vences
2017 Mitochondrial DNA Part B: Resources  
The nearly complete mitogenomes of the two species of North African Atlas geckos, Quedenfeldtia moerens and Q. trachyblepharus were assembled from anchored hybrid enrichment data and RNAseq data.  ...  We recovered the 13 protein-coding genes, 22 tRNA genes, and two rRNA genes for both species, including partial control region. The order of genes agrees with that of other geckos.  ...  The authors report no conflicts of interest.  ... 
doi:10.1080/23802359.2017.1339212 pmid:33473826 pmcid:PMC7800026 fatcat:lldymzx3mrasdf3frtpgugbnh4

The complete chloroplast genome of a new candidate cultivar, Sang Jae, of Abeliophyllum distichum Nakai (Oleaceae): initial step of A. distichum intraspecies variations atlas

Juhyeon Min, Yongsung Kim, Hong Xi, Taewon Jang, Gwanho Kim, Jongsun Park, Jae-Ho Park
2019 Mitochondrial DNA Part B: Resources  
Chloroplast genome of Sang Jae, new candidate cultivar of Abeliophyllum distichum Nakai, has been sequenced to reveal infraspecific relationship of wildtypes and cultivars.  ...  Only one INDEL was found in the comparison of another natural isolate (MF407183).  ...  It is identical to that of Ok-Hwang-1-ho because this cultivar was rescued from the same region.  ... 
doi:10.1080/23802359.2019.1679678 pmid:33366157 pmcid:PMC7707604 fatcat:bpixuxzhdjemflrt2dafs5suhu

General resources in Genetics and/or Oncology

Etienne De Braekeleer, Jean Loup Huret, Hossain Mossafa, Katriina Hautaviita, Philippe Dessen
2017 Atlas of Genetics and Cytogenetics in Oncology and Haematology  
This "Deep Insight" is a detailed subchapter of a general review article and summary on Internet databases for cytogeneticists: Internet databases and resources for cytogenetics and cytogenomics.  ...  The International Genome Sample Resource (IGSR) is maintaining and extending the 1000 Genomes Project data.  ...  In continuation of the 1000 Genome project (sequencing 1000 human genome as exomes or whole genomes), the International Genome Sample Resource (IGSR) aims to expand information to new populations, a better  ... 
doi:10.4267/2042/62946 fatcat:ogpkbnstcnbrnm6pawmf32npua

General resources in Genetics and/or Oncology

Etienne De Braekeleer, Jean Loup Huret, Hossain Mossafa, Katriina Hautaviita, Philippe Dessen
2017 Atlas of Genetics and Cytogenetics in Oncology and Haematology  
This "Deep Insight" is a detailed subchapter of a general review article and summary on Internet databases for cytogeneticists: Internet databases and resources for cytogenetics and cytogenomics.  ...  The International Genome Sample Resource (IGSR) is maintaining and extending the 1000 Genomes Project data.  ...  In continuation of the 1000 Genome project (sequencing 1000 human genome as exomes or whole genomes), the International Genome Sample Resource (IGSR) aims to expand information to new populations, a better  ... 
doi:10.4267/2042/62779 fatcat:j3jbmjapd5b3ndhz2xsf7mgaki

Model organisms

1998 Current Biology  
Pretty much the best online source of Arabidopsis information is the well-designed Stanford Genomic Resources Arabidopsis thaliana Database.  ...  The Arabinet collection of links will connect you with genomics, informatics, genetics and mapping resources.  ... 
doi:10.1016/s0960-9822(07)00495-2 fatcat:pnq7xofsxfai5hebw2bztwwede

GWAS Atlas: a curated resource of genome-wide variant-trait associations in plants and animals

2019 Nucleic Acids Research  
GWAS Atlas (https://bigd.big.ac.cn/gwas/) is a manually curated resource of genome-wide variant-trait associations for a wide range of species.  ...  valuable resource for genetic research of important traits and breeding application.  ...  ACKNOWLEDGEMENTS We thank members of the National Genomics Data Center for reporting bugs and sending comments.  ... 
doi:10.1093/nar/gkz828 pmid:31566222 pmcid:PMC6943065 fatcat:g6ajjbniffdc7en3u4hb2agl4e

Colorectal cancer atlas: An integrative resource for genomic and proteomic annotations from colorectal cancer cell lines and tissues

David Chisanga, Shivakumar Keerthikumar, Mohashin Pathan, Dinuka Ariyaratne, Hina Kalra, Stephanie Boukouris, Nidhi Abraham Mathew, Haidar Al Saffar, Lahiru Gangoda, Ching-Seng Ang, Oliver M. Sieber, John M. Mariadason (+3 others)
2015 Nucleic Acids Research  
Here, we have developed Colorectal Cancer Atlas (http://www.colonatlas. org), an integrated web-based resource that catalogues the genomic and proteomic annotations identified in CRC tissues and cell lines  ...  Overall, Colorectal Cancer Atlas has been designed to serve as a central resource to facilitate research in CRC.  ...  Here, we describe Colorectal Cancer Atlas (http://www. colonatlas.org), an integrated web-based resource which catalogues genomic and proteomic data from CRC tissues and cell lines.  ... 
doi:10.1093/nar/gkv1097 pmid:26496946 pmcid:PMC4702801 fatcat:zav42smdurfsrbm3py7nehrcuu

Gramene database: Navigating plant comparative genomics resources

Parul Gupta, Sushma Naithani, Marcela Karey Tello-Ruiz, Kapeel Chougule, Peter D'Eustachio, Antonio Fabregat, Yinping Jiao, Maria Keays, Young Koung Lee, Sunita Kumari, Joseph Mulvaney, Andrew Olson (+10 others)
2016 Current Plant Biology  
Gramene (http://www.gramene.org) is an online, open source, curated resource for plant comparative genomics and pathway analysis designed to support researchers working in plant genomics, breeding, evolutionary  ...  Here we briefly describe the functions and uses of the Gramene database.  ...  of the resources and tools.  ... 
doi:10.1016/j.cpb.2016.12.005 pmid:28713666 pmcid:PMC5509230 fatcat:gmdx6rggmjgpbptvme75fmf7d4

An Accelerating Two-Layer Anchor Search With Application to the Resource-Constrained Project Scheduling Problem

Reza Zamani
2010 IEEE Transactions on Evolutionary Computation  
To test the effectiveness of the method, it has been applied to the resource-constrained project scheduling problem.  ...  To test the effectiveness of the method, it has been applied to the resource-constrained project scheduling problem.  ...  ATLAS The ATLAS starts with constructing two local optimal solutions. The encoding of one of the solutions is called "base genome" and that of the other is called "transient genome."  ... 
doi:10.1109/tevc.2010.2047861 fatcat:2xebv5rzbfhe5kahr5qh22aowa

Atlas of Genetics and Cytogenetics in Oncology and Haematology, year 2003

J.-L. Huret
2003 Nucleic Acids Research  
The Atlas is part of the genome project and it participates in research on cancer epidemiology.  ...  The 'Atlas of Genetics and Cytogenetics in Oncology and Haematology' (http://www.infobiogen.fr/services/ chromcancer) contains concise and updated cards on genes involved in cancer, cytogenetics and clinical  ...  ACKNOWLEDGEMENTS The Atlas is funded by: Ministère de la Recherche, Ministère de l'Education Nationale, Département de la Vienne, Communauté d' Agglomération de Poitiers, Ligue Nationale contre le Cancer  ... 
doi:10.1093/nar/gkg126 pmid:12520000 pmcid:PMC165573 fatcat:i7xywqanw5blbemp3znf3eclxm

Integration of Russian Tier-1 Grid Center with High Performance Computers at NRC-KI for LHC experiments and beyond HENP

A Belyaev, A Berezhnaya, L Betev, P Buncic, K De, D Drizhuk, A Klimentov, Y Lazin, I Lyalin, R Mashinistov, A Novikov, D Oleynik (+6 others)
2015 Journal of Physics, Conference Series  
To meet this challenge the integration of the opportunistic resources into LHC computing model is highly important.  ...  The delegation of even a fraction of supercomputing resources to the LHC Computing will notably increase total capacity.  ...  This work was funded in part by the U.S.  ... 
doi:10.1088/1742-6596/664/9/092018 fatcat:lkw2kwzecfbavbwiw2mxjpr46u

An Atlas of annotations of Hydra vulgaris transcriptome

Daniela Evangelista, Kumar Parijat Tripathi, Mario Rosario Guarracino
2016 BMC Bioinformatics  
Web resource URL: www-labgtp.na.icar.cnr.it/Atlas.  ...  In order to provide to the users an advantageous resource that include the whole functional annotated transcriptome of Hydra vulgaris water polyp, we implemented the Atlas web-tool contains 31.988 accesible  ...  the genome is not yet well annotated.  ... 
doi:10.1186/s12859-016-1172-9 pmid:28185543 pmcid:PMC5046195 fatcat:mqvded26ifbzzgd2l2peawxame

Update of the FANTOM web resource: expansion to provide additional transcriptome atlases

Marina Lizio, Imad Abugessaisa, Shuhei Noguchi, Atsushi Kondo, Akira Hasegawa, Chung Chau Hon, Michiel de Hoon, Jessica Severin, Shinya Oki, Yoshihide Hayashizaki, Piero Carninci, Takeya Kasukawa (+1 others)
2018 Nucleic Acids Research  
Here, we report the recent updates of both data and interfaces in the FANTOM web resource.  ...  The CAGE data obtained from human and mouse were reprocessed to make them available on the latest genome assemblies.  ...  ACKNOWLEDGMENTS The authors would like to thank Dr A.R.R. Forrest for scientific coordination of the FANTOM5 collaboration, Dr C. Plessy for helping the manuscript preparation, J. Harsh-  ... 
doi:10.1093/nar/gky1099 pmid:30407557 pmcid:PMC6323950 fatcat:xc6iffwzbngsdcqsrm7aptzgxa
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