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Gramene 2018: unifying comparative genomics and pathway resources for plant research

Marcela K Tello-Ruiz, Sushma Naithani, Joshua C Stein, Parul Gupta, Michael Campbell, Andrew Olson, Sharon Wei, Justin Preece, Matthew J Geniza, Yinping Jiao, Young Koung Lee, Bo Wang (+27 others)
<span title="2017-11-20">2017</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
Gramene (http://www.gramene.org) is a knowledgebase for comparative functional analysis in major crops and model plant species.  ...  gene trees, gene expression anatomograms, associated pathways, and external informatics resources.  ...  that have helped us to improve the overall quality of Gramene as a community resource.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkx1111">doi:10.1093/nar/gkx1111</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29165610">pmid:29165610</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5753211/">pmcid:PMC5753211</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/bxgarlrs6rab5lwpixua6gotgq">fatcat:bxgarlrs6rab5lwpixua6gotgq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190302084436/http://pdfs.semanticscholar.org/b295/9d978f7b3bfb90d28bd6309ebfd11e7638f1.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/b2/95/b2959d978f7b3bfb90d28bd6309ebfd11e7638f1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkx1111"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753211" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Biological Ontologies in Rice Databases. An Introduction to the Activities in Gramene and Oryzabase

Yukiko Yamazaki, Pankaj Jaiswal
<span title="2005-01-15">2005</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/qyzgzqbtjbd3xewtgies5bhl2e" style="color: black;">Plant and Cell Physiology</a> </i> &nbsp;
It is, however, time-consuming and laborious for individual researchers to collect information from individual original sites and to rearrange it for their own purpose.  ...  In this mini-review, we introduce activities in Gramene and Oryzabase, which provide biological ontologies for Oryza sativa (rice).  ...  David Mathews of Cornell University for critical reading of the manuscript. Reviewers of the paper provided helpful advice.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/pcp/pci505">doi:10.1093/pcp/pci505</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15659431">pmid:15659431</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/umxcazu6vbadrhfkjy6h6ujesm">fatcat:umxcazu6vbadrhfkjy6h6ujesm</a> </span>
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Current status of genomic resources on wild relatives of rice

Richa Kamboj, Balwant Singh, Tapan Kumar Mondal, Deepak Singh Bisht
<span title="2020-03-19">2020</span> <i title="Japanese Society of Breeding"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/bnksrlkmyjdw5hsswyaxwudwaa" style="color: black;">Breeding Science</a> </i> &nbsp;
Presently, there are several generic and specialized databases harboring genome-wide information on wild species of rice, and are acting as a useful resource for identification of novel genes and alleles  ...  , designing of molecular markers, comparative analysis and evolutionary biology studies.  ...  Acknowledgments The authors are grateful for the support given by Indian Council of Agricultural Research.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1270/jsbbs.19064">doi:10.1270/jsbbs.19064</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32523396">pmid:32523396</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7272243/">pmcid:PMC7272243</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/tn7j2ighmvaupmdiszssa5pzgy">fatcat:tn7j2ighmvaupmdiszssa5pzgy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201107025726/https://www.jstage.jst.go.jp/article/jsbbs/70/2/70_19064/_pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/3e/49/3e499d5d0b747239562fcd0804e96b3892338a8c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1270/jsbbs.19064"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7272243" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Multilevel comparative bioinformatics to investigate evolutionary relationships and specificities in gene annotations: an example for tomato and grapevine

Luca Ambrosino, Valentino Ruggieri, Hamed Bostan, Marco Miralto, Nicola Vitulo, Mohamed Zouine, Amalia Barone, Mondher Bouzayen, Luigi Frusciante, Mario Pezzotti, Giorgio Valle, Maria Luisa Chiusano
<span title="2018-11-30">2018</span> <i title="Springer (Biomed Central Ltd.)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
We presented here a multilevel comparative approach to investigate on genome evolutionary relationships and peculiarities of two fleshy fruit species of relevant agronomic interest, Solanum lycopersicum  ...  "Omics" approaches may provide useful information for a deeper understanding of speciation events, diversification and function innovation.  ...  features of the two plants species genomes and provides hints on possible applications which may be supported by this resource.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-018-2420-y">doi:10.1186/s12859-018-2420-y</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30497367">pmid:30497367</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6266932/">pmcid:PMC6266932</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/farhfomrm5cz7dne45jbbana3e">fatcat:farhfomrm5cz7dne45jbbana3e</a> </span>
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PLEXdb: gene expression resources for plants and plant pathogens

S. Dash, J. Van Hemert, L. Hong, R. P. Wise, J. A. Dickerson
<span title="2011-11-13">2011</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
The PLEXdb team also thanks Ethalinda Cannon of MaizeGDB for her work mapping expression probes to the maize v2 (5b.60) assembly.  ...  Grgic, Emmanuel Owusu, Akul Singhania, Ajani Thomas and Andrew Couch.  ...  SGN provides a unified resource with sequence, expression and pathway data but it is restricted to a single clade.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkr938">doi:10.1093/nar/gkr938</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22084198">pmid:22084198</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3245067/">pmcid:PMC3245067</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/udchdlk5nrbt7mkzlw2z3irzpq">fatcat:udchdlk5nrbt7mkzlw2z3irzpq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180728062508/https://watermark.silverchair.com/gkr938.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAaEwggGdBgkqhkiG9w0BBwagggGOMIIBigIBADCCAYMGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMs9uVhLboo0ojqgG3AgEQgIIBVDAOyMG2eWXwItg6wOHYEvmG3NHDnDk9Xw6tKfnEPt7ZIJ7YvCYPdOz3kP2CKFkqgrfawcva7f0xh0WhI1R4G66iq4UtM0CeOTMDVon8W0tkI9wv8DEQ6eZA0rICBpIKsTEv6Z2sfLHIxK4DOjpVVELCHWA2afbOApFl1A4z5iHR7hNJo0dHuFxevUAFMi15uD9C2gOAjDcWqDO6Xb9UbAlXjz5LHbq0OSPwY7X_dqIn1tbySrIzq45lo25jSEzQFVaXI8nxQQzOKYmo1SJCkwgMkt0e1_z3LjPtIzP9eQjnUuLVT25AD4jpxbXKcKYx6Emv6BHx9rmvF84gOlYCdXVY1GkUbX9BbzSctfzs3b3JNezcSw1VPLuAieKtz9fa4jXUhTdTajCAUHSr4-zKe7tZLE2vVxGW6zsxIcACtGbOhspxnAeYZ13RHG0vk1tRvtqU3NM" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/e3/7e/e37e38eb5db7ddd325d746e727dd8614d55692f0.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkr938"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245067" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Potentials, Challenges, and Genetic and Genomic Resources for Sugarcane Biomass Improvement

Ramkrishna Kandel, Xiping Yang, Jian Song, Jianping Wang
<span title="2018-02-16">2018</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/bbmitkj3efgeppizzjrx6w5emu" style="color: black;">Frontiers in Plant Science</a> </i> &nbsp;
Sugarcane (Saccharum spp. hybrids), a very efficient perennial C4 plant with a high polyploid level and complex genome, is considered a top-notch candidate for biomass production due to its salient features  ...  commercial cultivars, long breeding cycle, and non-synchronous flowering, (3) available genetic resources such as germplasm resources, and genomic and cell wall-related databases that facilitate biomass  ...  'Plant cell walls' is good resource for the scientific community interested in biofuel potential of cell wall whereas 'plant database of annotated cell wall genomes' is a huge resource for comparative  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fpls.2018.00151">doi:10.3389/fpls.2018.00151</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29503654">pmid:29503654</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5821101/">pmcid:PMC5821101</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ney4cm6iybc6hlws2lhr4wkdgm">fatcat:ney4cm6iybc6hlws2lhr4wkdgm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190302052625/http://pdfs.semanticscholar.org/9e42/8f8db80a0d6d89c4f7f6090bdba55d6b92b7.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/9e/42/9e428f8db80a0d6d89c4f7f6090bdba55d6b92b7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fpls.2018.00151"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> frontiersin.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5821101" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture

Lisa Harper, Jacqueline Campbell, Ethalinda K S Cannon, Sook Jung, Monica Poelchau, Ramona Walls, Carson Andorf, Elizabeth Arnaud, Tanya Z Berardini, Clayton Birkett, Steve Cannon, James Carson (+40 others)
<span title="2018-01-01">2018</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ejkvir3kzbdojf5kygupkidsca" style="color: black;">Database: The Journal of Biological Databases and Curation</a> </i> &nbsp;
Governmental agencies, publishers and science funders require data management plans for publicly funded research.  ...  Each section describes challenges and opportunities for these topics, along with recommendations and best practices.  ...  Acknowledgements We acknowledge with thanks The National Science Foundation Plant Genome Research Program Award # 1444573 for funding the AgBioData Workshop and development and hosting of the AgBio-Data  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/database/bay088">doi:10.1093/database/bay088</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30239679">pmid:30239679</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6146126/">pmcid:PMC6146126</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/spcxmd66qrgdnos4larqfvf6ai">fatcat:spcxmd66qrgdnos4larqfvf6ai</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190222082022/http://pdfs.semanticscholar.org/33a0/4f248af51477c64e0ace8022724f0a75bdaa.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/33/a0/33a04f248af51477c64e0ace8022724f0a75bdaa.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/database/bay088"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6146126" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

BioMart Central Portal: an open database network for the biological community

J. M. Guberman, J. Ai, O. Arnaiz, J. Baran, A. Blake, R. Baldock, C. Chelala, D. Croft, A. Cros, R. J. Cutts, A. Di Genova, S. Forbes (+49 others)
<span title="2011-09-18">2011</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ejkvir3kzbdojf5kygupkidsca" style="color: black;">Database: The Journal of Biological Databases and Curation</a> </i> &nbsp;
Gramene (15) ], Search by organism is subdivided into categories for bacteria, plants, protists, invertebrates and vertebrates.  ...  Database of proteome peptide identifications for investigating fragmentation patterns (27) Phytozome JGI/CIG, USA Comparative genomics of green plants (28) Potato Database CIP, Peru Potato  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/database/bar041">doi:10.1093/database/bar041</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21930507">pmid:21930507</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3263598/">pmcid:PMC3263598</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/sypgedelfncfbflx4d7skx2v6a">fatcat:sypgedelfncfbflx4d7skx2v6a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180728083041/https://watermark.silverchair.com/bar041.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAb4wggG6BgkqhkiG9w0BBwagggGrMIIBpwIBADCCAaAGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMNCPHWfQEJWDgvoKvAgEQgIIBcVTDIzAmRaTAWIM-E5vMkIl-Z0BJ_5L1TkCkUNCtL13lUl4Yg8Ob2hmxFLqdiPH6mBCbEFY71wQtJKXADWuqeoS4H0Nv6divqdgZoHl-bVJq4t8zSEfoomMLoz2JzdY9pMEMTrAPAtjOcF_Az6hgyMNCx1W8LowoyyHzNHHP_zfqrvQoUFIhTTaK4a5H34WjuTCPLqlDux-A1ELhN3qStmyhZOgZoPwv-v3K2fxAon51Phn9tlclUbPw0Tc6q_ID8Kik4rv-vFFwN7m-Mzf6-7bJvE0UE_2IqA2wu4hQVcd44Vc62tcYqXwAejNXBS6AmftUTeBtxKPh4-ceI2ZqrFiIgYX5zoiJMQJZP_LGL6SyUhPHAYHMAHwQuDzYtT-kt6Gw700983e-M99BK5S-Nd0NBRoVWz9i-3a7CjpPmeFMzu5ssfn-2iGWc2bReFoVzmmFPiFMC8szdvSS4FfS3aRQQrIEWTjikhhucr2FPVrLZA" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/e5/0c/e50cc51a19ab1ac1dca5e8e01817ffc535b6eaec.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/database/bar041"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3263598" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Cyberinfrastructure and resources to enable an integrative approach to studying forest trees

Jill L Wegrzyn, Taylor Falk, Emily Grau, Sean Buehler, Risharde Ramnath, Nic Herndon
<span title="2019-08-26">2019</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hnstxxau2bbjhkazfbxx7sdac4" style="color: black;">Evolutionary Applications</a> </i> &nbsp;
These data contribute to forest tree biology, but the associated sequence remains trapped in supplemental files that are poorly integrated in plant community databases and comparative genomic platforms  ...  Genomic data from these projects generates sequences that represent intermediate assemblies for transcriptomes and genomes.  ...  Other comparative genomic resources such as Gramene and Ensembl Plants provide ex-tensive resources for comparative genomics, pathway analysis, and variant data, but rely on high-quality reference genomes  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1111/eva.12860">doi:10.1111/eva.12860</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31892954">pmid:31892954</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6935593/">pmcid:PMC6935593</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/r2zcwfc7irdgdln4faunycp3ui">fatcat:r2zcwfc7irdgdln4faunycp3ui</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200509041543/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC6935593&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/59/ac/59ac3294b61b112e6dcec418c4df9da14e5925d2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1111/eva.12860"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6935593" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

PyRice: a Python package for querying Oryza Sativa functional databases [article]

Quan Hong DO, Hai Ho Bich, Pierre Larmande
<span title="2020-04-21">2020</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
The challenge is to collect information quickly from these applications and combine it logically, to facilitate scientific research.  ...  Moreover, methods of access are also diverse, mostly web-based and sometimes query APIs, which might not always be straightforward for domain experts.  ...  Funding This work has been supported by the CGIAR CRP RICE, IRD DIADE UNIT, The LMI RICE and ICTLab (USTH).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.04.20.049742">doi:10.1101/2020.04.20.049742</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/x4q3q4yeyzb75akf3zaxgchtiq">fatcat:x4q3q4yeyzb75akf3zaxgchtiq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201108073953/https://www.biorxiv.org/content/biorxiv/early/2020/07/26/2020.04.20.049742.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/df/4f/df4f982c5a662b8051769771313e7c5d7795eb04.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.04.20.049742"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Whole-Plant Growth Stage Ontology for Angiosperms and Its Application in Plant Biology

A. Pujar, P. Jaiswal, E. A. Kellogg, K. Ilic, L. Vincent, S. Avraham, P. Stevens, F. Zapata, L. Reiser, S. Y. Rhee, M. M. Sachs, M. Schaeffer (+3 others)
<span title="2006-08-11">2006</span> <i title="American Society of Plant Biologists (ASPB)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/lyouqq67dncvxgcbflq26svwta" style="color: black;">Plant Physiology</a> </i> &nbsp;
Information Resource, Gramene database, and MaizeGDB.  ...  This ontology represents a synthesis and integration of terms and concepts from a variety of species-specific vocabularies previously used for describing phenotypes and genomic information.  ...  We acknowledge the Gene Ontology Consortium for software support. We thank Drs. Dean Ravenscroft and Junjian Ni of Gramene database for reviewing the manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1104/pp.106.085720">doi:10.1104/pp.106.085720</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16905665">pmid:16905665</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC1586063/">pmcid:PMC1586063</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/yiujdunxozb2rjplqdzfxqnxcy">fatcat:yiujdunxozb2rjplqdzfxqnxcy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180723190350/http://www.plantphysiol.org/content/plantphysiol/142/2/414.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/e9/67/e96783d71b4d323c9924afc1ea0c7bcbec4603e5.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1104/pp.106.085720"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1586063" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

QTL Alignment for Seed Yield and Yield Related Traits in Brassica napus

Nadia Raboanatahiry, Hongbo Chao, Hou Dalin, Shi Pu, Wei Yan, Longjiang Yu, Baoshan Wang, Maoteng Li
<span title="2018-08-02">2018</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/bbmitkj3efgeppizzjrx6w5emu" style="color: black;">Frontiers in Plant Science</a> </i> &nbsp;
and high-quality protein for live stocks.  ...  Some yield-related traits, such as plant height, biomass yield, flowering time, and so on, also affect the SY indirectly.  ...  DISCUSSION Unified Seed Yield and Yield-Related QTLs in One Map Revealed Important Stable Loci for Yield Improvement In B. napus, SY depends on the number of PN or number of siliques per plant, the number  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fpls.2018.01127">doi:10.3389/fpls.2018.01127</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30116254">pmid:30116254</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6083399/">pmcid:PMC6083399</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/armotikdlvaobm6sgbl77qgk6i">fatcat:armotikdlvaobm6sgbl77qgk6i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190216162043/http://pdfs.semanticscholar.org/0266/66de3ea34afbb23fca92b82f05dcc7fe96f9.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/02/66/026666de3ea34afbb23fca92b82f05dcc7fe96f9.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fpls.2018.01127"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> frontiersin.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6083399" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Vision, challenges and opportunities for a Plant Cell Atlas

Plant Cell Atlas Consortium, Jahed Ahmed, Oluwafemi Alaba, Gazala Ameen, Vaishali Arora, Mario A Arteaga-Vazquez, Alok Arun, Julia Bailey-Serres, Laura E Bartley, George W Bassel, Dominique C Bergmann, Edoardo Bertolini (+137 others)
<span title="2021-09-07">2021</span> <i title="eLife Sciences Publications, Ltd"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/en4qj5ijrbf5djxx7p5zzpjyoq" style="color: black;">eLife</a> </i> &nbsp;
This framework, called the Plant Cell Atlas (PCA), will be critical for understanding and engineering plant development, physiology and environmental responses.  ...  With growing populations and pressing environmental problems, future economies will be increasingly plant-based.  ...  Acknowledgements The PCA community-building activities are funded in part by the National Science Foundation grant numbers MCB-1916797 and MCB-2052590  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.7554/elife.66877">doi:10.7554/elife.66877</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/34491200">pmid:34491200</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8423441/">pmcid:PMC8423441</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xq6vypwp4rbbjfkhtl5l2ty35q">fatcat:xq6vypwp4rbbjfkhtl5l2ty35q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210907181221/https://elifesciences.org/download/aHR0cHM6Ly9jZG4uZWxpZmVzY2llbmNlcy5vcmcvYXJ0aWNsZXMvNjY4NzcvZWxpZmUtNjY4NzctdjEucGRmP2Nhbm9uaWNhbFVyaT1odHRwczovL2VsaWZlc2NpZW5jZXMub3JnL2FydGljbGVzLzY2ODc3/elife-66877-v1.pdf?_hash=GyPtySZnG0grz6VPgWL5R%2Buw4PyWLwQC%2BRLWs93uJew%3D" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/b1/92/b192b158c993aa054636ec10d3a3fa3d109fd535.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.7554/elife.66877"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> elifesciences.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8423441" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Fertility of Pedicellate Spikelets in Sorghum is Controlled by a Jasmonic Acid Regulatory Module [article]

Nicholas P Gladman, Yinping Jiao, Young Koung Lee, Lifang Zhang, Ratan Chopra, Michael Regulski, Gloria Burow, Chad Hayes, Shawn A. Christensen, Lavanya Dampanaboina, Junping Chen, John Burke (+2 others)
<span title="2019-09-19">2019</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Further, we demonstrate that MSD1 binds to the promoters of MSD2 and other JA pathway genes.  ...  The findings advance our understanding of inflorescence development and could lead to new strategies for increasing GNP and grain yield in sorghum and other cereal crops.  ...  ., Gramene 2018: unifying comparative genomics and pathway 539 resources for plant research. Nucleic Acids Res 46, D1181-D1189 (2018). 68. R. F.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/773564">doi:10.1101/773564</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/d5wsaluzfra4je3e7oinynxxeq">fatcat:d5wsaluzfra4je3e7oinynxxeq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200324233312/https://www.biorxiv.org/content/biorxiv/early/2019/09/19/773564.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/a5/b1/a5b142895655935caa146646e3a37681fe8e98cc.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/773564"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Loss of premature stop codon in the Wall-Associated Kinase 91 (OsWAK91) gene confers sheath blight disease resistance in rice [article]

Noor Al-Bader, Austin Meier, Matthew Geniza, Yamid Sanabria Gongora, James Oard, Pankaj Jaiswal
<span title="2019-05-13">2019</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
The genetic arms race between pathogen and host plant is a tug of war that has been ongoing for millennia.  ...  The susceptible allele appears as a recent introduction found in the japonica subspecies reference genome and a majority of the tropical and temperate japonica lines sequenced by the 3000 rice genome project  ...  Gramene 2018: unifying comparative genomics and pathway 638 resources for plant research. Nucleic Acids Res. 46, D1181-D1189 (2018).639 45. Ram, T. et al.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/625509">doi:10.1101/625509</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4aibhsjpjbf2lmxwrvucy5osvm">fatcat:4aibhsjpjbf2lmxwrvucy5osvm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200324103234/https://www.biorxiv.org/content/biorxiv/early/2019/05/13/625509.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/a4/ed/a4ed0c50eb12ac794fb24cd257cad6b44508b81d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/625509"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>
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