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The challenge of constructing, classifying, and representing metabolic pathways

Ron Caspi, Kate Dreher, Peter D. Karp
<span title="2013-06-27">2013</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tribqhktongz5aerkes5pty26q" style="color: black;">FEMS Microbiology Letters</a> </i> &nbsp;
Scientists, educators, and students benefit from having free and centralized access to the wealth of metabolic information that has been gathered over the decades. Curators of the MetaCyc database work to present this information in an easily understandable pathway-based framework. MetaCyc is used not only as an encyclopedic resource for metabolic information but also as a template for the pathway prediction software that generates pathway/genome databases for thousands of organisms with
more &raquo; ... ed genomes (available at www.biocyc. org). Curators need to define pathway boundaries and classify pathways within a broader pathway ontology to maximize the utility of the pathways to both users and the pathway prediction software. These seemingly simple tasks pose several challenges. This review describes these challenges as well as the criteria that need to be considered, and the rules that have been developed by MetaCyc curators as they make decisions regarding the representation and classification of metabolic pathway information in MetaCyc. The functional consequences of these decisions in regard to pathway prediction in new species are also discussed.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1111/1574-6968.12194">doi:10.1111/1574-6968.12194</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23746312">pmid:23746312</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4026850/">pmcid:PMC4026850</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3qsy54kfmncojlvzalp46gmeja">fatcat:3qsy54kfmncojlvzalp46gmeja</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180729205500/https://watermark.silverchair.com/345-2-85.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAaowggGmBgkqhkiG9w0BBwagggGXMIIBkwIBADCCAYwGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQM1XLNKC7P3Zldts68AgEQgIIBXRYXRQoKfVIHNVyki-2Hl4Apq8OdHYrwZaE0e6dO8MvF0ItxpB0XeIlzGAauGB_FxpJ8QxEulCibwzx5nf0TzpPCzCRsY5gfBDSmnMfIFjMcCGbCzI-MnIZbaorQRW6RdS4_xaXkbUTzjzSn664qyMYBd30ZWuG-fz_BfcViCYHjH6BRP97mAjt-51H_JAusdPSNW_abeEwrcS3L1fG1XHXdmhGi81hKjjFzzhPrJrNod3XSAeBchwVW_-fwmjB-ri4ugRdZBafXOail6czId-mwxyzfvt1BqJCVkNZtK70itLbz-mW3ZpFsG8iGiaM0tPQYRUs4iT_dp-BuVWF2_B8vP1aVeqYPkw-2gUGN_rF7goV2QMMQev9U6Pr8zFP0cr0OtlIVd2ip8FnOEg4r95je0RmPDmUcU6BtspWcUY11bEp4IDE4WmOPAXIROWEaJzUMfr3Nf2JRqQBHhtw" 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/4e/f8/4ef849131c10a9a7d7ea9e4cba73a03089f5c1d5.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1111/1574-6968.12194"> <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/PMC4026850" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Cycloheximide Assays to Measure Protein Degradation in vivo in Plants

Jonathan Gilkerson, Raymond Tam, Aimee Zhang, Kate Dreher, Judy Callis
<span title="">2016</span> <i title="Bio-Protocol, LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/e55uzv62bnf5rmy6y62tsamtoq" style="color: black;">Bio-protocol</a> </i> &nbsp;
The half-life of a protein is a characteristic property, and can be modulated by posttranslational modifications, changes in subcellular localization, and/or interaction with other proteins or ligands. As one determinant of its steady-state level, a protein's degradation represents an important distinguishing attribute relevant to its biological function. Because protein longevity cannot be elucidated from bioinformatics analyses, it must be determined empirically. Here we describe two
more &raquo; ... s for in vivo half-life determination in plants: 1. pooled-seedling degradation assays monitoring either tagged versions of the protein (luciferase fusions or other epitope tags) or following the endogenous protein; 2. single-seedling degradation assays using luciferase fusion proteins. The advantages of these approaches are their simplicity and low cost. Materials and Reagents 1. 60 x 15 mm sterile Petri dishes (Corning, Falcon ® , catalog number: 353002) 2. Microfuge tubes 3. Pipet tips 4. White polystyrene flat-bottom 96-well plates (Thermo Fisher Scientific, Fisher Scientific, catalog number: 12-566-619) 5. PVDF (polyvinylidene fluoride) Western protein blotting membrane (Sigma-Aldrich, Amersham Hybond TM , catalog number: GE10600023) 6. Clear adhesive plate film (USA-Scientific, catalog number: 2921-7810) 7. X-ray film (Thermo Fisher Scientific, Thermo Scientific TM , catalog number: 34091) 8. Plant lines expressing protein of interest, either from transgene or from endogenous locus 9. Cycloheximide (CHX) (Sigma-Aldrich, catalog number: C1988) 10. Primary antibody [example, anti-HA-HRP (3F10) (Sigma-Aldrich, Roche, catalog number: 12158167001)] 11. Secondary antibody (horseradish peroxidase-linked) (Bio-Rad Laboratories, catalog number: 1662408EDU) 12. Tween-20 (Sigma-Aldrich, catalog number: P9416)
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.21769/bioprotoc.1919">doi:10.21769/bioprotoc.1919</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3hdurynqfvfkdh7u5xra3kvroa">fatcat:3hdurynqfvfkdh7u5xra3kvroa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210812023507/https://bio-protocol.org/pdf/Bio-protocol1919.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/17/7b/177bdb683ed78865418ec1d35464532a5ec84e9b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.21769/bioprotoc.1919"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Empirical Comparison of Tropical Maize Hybrids Selected Through Genomic and Phenotypic Selections

Yoseph Beyene, Manje Gowda, Michael Olsen, Kelly R. Robbins, Paulino Pérez-Rodríguez, Gregorio Alvarado, Kate Dreher, Star Yanxin Gao, Stephen Mugo, Boddupalli M. Prasanna, Jose Crossa
<span title="2019-11-22">2019</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;
Genomic selection predicts the genomic estimated breeding values (GEBVs) of individuals not previously phenotyped. Several studies have investigated the accuracy of genomic predictions in maize but there is little empirical evidence on the practical performance of lines selected based on phenotype in comparison with those selected solely on GEBVs in advanced testcross yield trials. The main objectives of this study were to (1) empirically compare the performance of tropical maize hybrids
more &raquo; ... d through phenotypic selection (PS) and genomic selection (GS) under well-watered (WW) and managed drought stress (WS) conditions in Kenya, and (2) compare the cost-benefit analysis of GS and PS. For this study, we used two experimental maize data sets (stage I and stage II yield trials). The stage I data set consisted of 1492 doubled haploid (DH) lines genotyped with rAmpSeq SNPs. A subset of these lines (855) representing various DH populations within the stage I cohort was crossed with an individual single-cross tester chosen to complement each population. These testcross hybrids were evaluated in replicated trials under WW and WS conditions for grain yield and other agronomic traits, while the remaining 637 DH lines were predicted using the 855 lines as a training set. The second data set (stage II) consists of 348 DH lines from the first data set. Among these 348 best DH lines, 172 lines selected were solely based on GEBVs, and 176 lines were selected based on phenotypic performance. Each of the 348 DH lines were crossed with three common testers from complementary heterotic groups, and the resulting 1042 testcross hybrids and six commercial checks were evaluated in four to five WW locations and one WS condition in Kenya. For stage I trials, the cross-validated prediction accuracy for grain yield was 0.67 and 0.65 under WW and WS conditions, respectively. We found similar responses to selection using PS and GS for grain yield other agronomic traits under WW and WS conditions. The top 15% of hybrids advanced through GS and PS gave 21%-23% higher grain yield under WW and 51%-52% more grain yield under WS than the mean of the checks. The GS reduced the cost by 32% over the PS with similar selection gains. We concluded that the use of GS for yield under WW and WS conditions in maize can produce selection candidates with similar performance as those generated from conventional PS, but at a lower cost, and therefore, should be incorporated into maize breeding pipelines to increase breeding program efficiency.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fpls.2019.01502">doi:10.3389/fpls.2019.01502</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31824533">pmid:31824533</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6883373/">pmcid:PMC6883373</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/y4dgnwuqqvczpac4yvwj5mqs5a">fatcat:y4dgnwuqqvczpac4yvwj5mqs5a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200207235404/https://fjfsdata01prod.blob.core.windows.net/articles/files/491039/pubmed-zip/.versions/1/.package-entries/fpls-10-01502.pdf?sv=2015-12-11&amp;sr=b&amp;sig=eya8jupyCHoVrmHoA9LipVdvH%2Bni8iVrjdDt22QYamI%3D&amp;se=2020-02-07T23%3A54%3A34Z&amp;sp=r&amp;rscd=attachment%3B%20filename%2A%3DUTF-8%27%27fpls-10-01502.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/3d/4b/3d4ba4d1456c8f96628116457deac447a98cc47f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fpls.2019.01502"> <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/PMC6883373" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants

Pascal Schläpfer, Peifen Zhang, Chuan Wang, Taehyong Kim, Michael Banf, Lee Chae, Kate Dreher, Arvind K. Chavali, Ricardo Nilo-Poyanco, Thomas Bernard, Daniel Kahn, Seung Y. Rhee
<span title="2017-02-22">2017</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;
Plant metabolism underpins many traits of ecological and agronomic importance. Plants produce numerous compounds to cope with their environments but the biosynthetic pathways for most of these compounds have not yet been elucidated. To engineer and improve metabolic traits, we need comprehensive and accurate knowledge of the organization and regulation of plant metabolism at the genome scale. Here, we present a computational pipeline to identify metabolic enzymes, pathways, and gene clusters
more &raquo; ... m a sequenced genome. Using this pipeline, we generated metabolic pathway databases for 22 species and identified metabolic gene clusters from 18 species. This unified resource can be used to conduct a wide array of comparative studies of plant metabolism. Using the resource, we discovered a widespread occurrence of metabolic gene clusters in plants: 11,969 clusters from 18 species. The prevalence of metabolic gene clusters offers an intriguing possibility of an untapped source for uncovering new metabolite biosynthesis pathways. For example, more than 1,700 clusters contain enzymes that could generate a specialized metabolite scaffold (signature enzymes) and enzymes that modify the scaffold (tailoring enzymes). In four species with sufficient gene expression data, we identified 43 highly coexpressed clusters that contain signature and tailoring enzymes, of which eight were characterized previously to be functional pathways. Finally, we identified patterns of genome organization that implicate local gene duplication and, to a lesser extent, single gene transposition as having played roles in the evolution of plant metabolic gene clusters.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1104/pp.16.01942">doi:10.1104/pp.16.01942</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28228535">pmid:28228535</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5373064/">pmcid:PMC5373064</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4i3cpgroiffpbb3ba7epqqpd6y">fatcat:4i3cpgroiffpbb3ba7epqqpd6y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190221010426/http://pdfs.semanticscholar.org/3124/6a550631a8a6ae292ffd4030e1f8415ad6ca.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/31/24/31246a550631a8a6ae292ffd4030e1f8415ad6ca.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1104/pp.16.01942"> <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/PMC5373064" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Germinate 3: Development of a Common Platform to Support the Distribution of Experimental Data on Crop Wild Relatives

Paul D. Shaw, Sebastian Raubach, Sarah J. Hearne, Kate Dreher, Glenn Bryan, Gaynor McKenzie, Iain Milne, Gordon Stephen, David F. Marshall
<span title="">2017</span> <i title="Crop Science Society of America"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6pvja7nupvd7rph3vskg3rmju4" style="color: black;">Crop science</a> </i> &nbsp;
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2135/cropsci2016.09.0814">doi:10.2135/cropsci2016.09.0814</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/iio7y4mcuvbbhnebhqxm6jfu6y">fatcat:iio7y4mcuvbbhnebhqxm6jfu6y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180719151945/https://dl.sciencesocieties.org/publications/cs/pdfs/57/3/1259" 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/88/e0/88e0ee48fa0acc0df2d9d6af02ec945452addef2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2135/cropsci2016.09.0814"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Maximizing efficiency of genomic selection in CIMMYT's tropical maize breeding program

Sikiru Adeniyi Atanda, Michael Olsen, Juan Burgueño, Jose Crossa, Daniel Dzidzienyo, Yoseph Beyene, Manje Gowda, Kate Dreher, Xuecai Zhang, Boddupalli M. Prasanna, Pangirayi Tongoona, Eric Yirenkyi Danquah (+2 others)
<span title="2020-10-10">2020</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/uujcme4xu5f5np4ytlgfenn5nm" style="color: black;">Theoretical and Applied Genetics</a> </i> &nbsp;
Key message Historical data from breeding programs can be efficiently used to improve genomic selection accuracy, especially when the training set is optimized to subset individuals most informative of the target testing set. Abstract The current strategy for large-scale implementation of genomic selection (GS) at the International Maize and Wheat Improvement Center (CIMMYT) global maize breeding program has been to train models using information from full-sibs in a "test-half-predict-half
more &raquo; ... ach." Although effective, this approach has limitations, as it requires large full-sib populations and limits the ability to shorten variety testing and breeding cycle times. The primary objective of this study was to identify optimal experimental and training set designs to maximize prediction accuracy of GS in CIMMYT's maize breeding programs. Training set (TS) design strategies were evaluated to determine the most efficient use of phenotypic data collected on relatives for genomic prediction (GP) using datasets containing 849 (DS1) and 1389 (DS2) DH-lines evaluated as testcrosses in 2017 and 2018, respectively. Our results show there is merit in the use of multiple bi-parental populations as TS when selected using algorithms to maximize relatedness between the training and prediction sets. In a breeding program where relevant past breeding information is not readily available, the phenotyping expenditure can be spread across connected bi-parental populations by phenotyping only a small number of lines from each population. This significantly improves prediction accuracy compared to within-population prediction, especially when the TS for within full-sib prediction is small. Finally, we demonstrate that prediction accuracy in either sparse testing or "test-half-predict-half" can further be improved by optimizing which lines are planted for phenotyping and which lines are to be only genotyped for advancement based on GP.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s00122-020-03696-9">doi:10.1007/s00122-020-03696-9</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33037897">pmid:33037897</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7813723/">pmcid:PMC7813723</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ggagwgrsebejpljrhddwgdxj7e">fatcat:ggagwgrsebejpljrhddwgdxj7e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210429014655/https://link.springer.com/content/pdf/10.1007/s00122-020-03696-9.pdf?error=cookies_not_supported&amp;code=277697a0-dd25-41f9-afe5-57a5ce6aa817" 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/14/ba/14ba9ea9fbf1d3c9dfa6c06abc4d56fe2a9952e9.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s00122-020-03696-9"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7813723" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Improved quality of life and reduced depressive symptoms in medical students after a single-session intervention

Mariane B. Bermudez, Monise Costanzi, Malu Joyce A. Macedo, Tiago Tatton-Ramos, Alice C.M. Xavier, Ygor A. Ferrão, Kate H. Bentley, Gisele G. Manfro, Carolina B. Dreher
<span title="2019-12-20">2019</span> <i title="FapUNIFESP (SciELO)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/cy6q3tapnvh5fpfytdllgx7yd4" style="color: black;">Revista Brasileira de Psiquiatria</a> </i> &nbsp;
Anxiety and depression are prevalent among medical students. Brazilian medical students have higher levels of depression and lower quality of life than their U.S. counterparts, and no preventive intervention exists for this risk group in Brazil. The Unified Protocol for Transdiagnostic Treatment of Emotional Disorders (UP), a cognitive-behavioral treatment protocol for neuroticism, was recently adapted into a single-session, preventive intervention. This study tested the impact of this protocol
more &raquo; ... on psychiatric symptoms and quality of life in Brazilian medical students. In this open trial, the intervention protocol was translated and adapted to Brazilian Portuguese. Medical students over 18 years of age without psychotic symptoms, severe depressive episodes, or acute psychiatric risk were included, undergoing a psychiatric clinical interview (Mini-International Neuropsychiatric Interview [MINI]) and evaluation at baseline and at 7 and 30 days after a single-session UP that included experimental avoidance, quality of life, self-esteem, empathy, and anxiety symptom scales. A new evaluation was performed 90 days after the intervention. Sixty-two students participated. Ninety days after the intervention, there were significant reductions in the number of students who met the criteria for social anxiety disorder (p = 0.013) or panic disorder (p = 0.001). There were also significant improvements in depressive symptoms (Beck Depression Inventory, p < 0.001) and quality of life (Quality of Life Enjoyment and Satisfaction Questionnaire, p < 0.001). UP improved anxiety and depressive symptoms in medical students. The single-session group format could reduce costs and facilitate application. Future placebo-controlled studies are necessary to confirm these findings.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1590/1516-4446-2019-0526">doi:10.1590/1516-4446-2019-0526</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31859792">pmid:31859792</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hpuvoc2kmzdubiftsprvfp7vuq">fatcat:hpuvoc2kmzdubiftsprvfp7vuq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200507210424/https://www.scielo.br/pdf/rbp/v42n2/1516-4446-rbp-1516444620190526.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/30/d0/30d08499b4ca29bcb874d3700df5af691fe42acf.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1590/1516-4446-2019-0526"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> scielo.br </button> </a>

Patterns of Metabolite Changes Identified from Large-Scale Gene Perturbations in Arabidopsis Using a Genome-Scale Metabolic Network

Taehyong Kim, Kate Dreher, Ricardo Nilo-Poyanco, Insuk Lee, Oliver Fiehn, Bernd Markus Lange, Basil J. Nikolau, Lloyd Sumner, Ruth Welti, Eve S. Wurtele, Seung Y. Rhee
<span title="2015-02-10">2015</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;
Metabolomics enables quantitative evaluation of metabolic changes caused by genetic or environmental perturbations. However, little is known about how perturbing a single gene changes the metabolic system as a whole and which network and functional properties are involved in this response. To answer this question, we investigated the metabolite profiles from 136 mutants with single gene perturbations of functionally diverse Arabidopsis (Arabidopsis thaliana) genes. Fewer than 10 metabolites
more &raquo; ... changed significantly relative to the wild type in most of the mutants, indicating that the metabolic network was robust to perturbations of single metabolic genes. These changed metabolites were closer to each other in a genome-scale metabolic network than expected by chance, supporting the notion that the genetic perturbations changed the network more locally than globally. Surprisingly, the changed metabolites were close to the perturbed reactions in only 30% of the mutants of the well-characterized genes. To determine the factors that contributed to the distance between the observed metabolic changes and the perturbation site in the network, we examined nine network and functional properties of the perturbed genes. Only the isozyme number affected the distance between the perturbed reactions and changed metabolites. This study revealed patterns of metabolic changes from large-scale gene perturbations and relationships between characteristics of the perturbed genes and metabolic changes.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1104/pp.114.252361">doi:10.1104/pp.114.252361</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25670818">pmid:25670818</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lumkjwqknvaangusaaievr7uoi">fatcat:lumkjwqknvaangusaaievr7uoi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190501141538/http://www.plantphysiol.org/content/plantphysiol/167/4/1685.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/36/76/36761ad7e69a7f65f1b73165bb5da605efd5e260.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1104/pp.114.252361"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools

Philippe Lamesch, Tanya Z. Berardini, Donghui Li, David Swarbreck, Christopher Wilks, Rajkumar Sasidharan, Robert Muller, Kate Dreher, Debbie L. Alexander, Margarita Garcia-Hernandez, Athikkattuvalasu S. Karthikeyan, Cynthia H. Lee (+5 others)
<span title="2011-12-02">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 Arabidopsis Information Resource (TAIR, http://arabidopsis.org) is a genome database for Arabidopsis thaliana, an important reference organism for many fundamental aspects of biology as well as basic and applied plant biology research. TAIR serves as a central access point for Arabidopsis data, annotates gene function and expression patterns using controlled vocabulary terms, and maintains and updates the A. thaliana genome assembly and annotation. TAIR also provides researchers with an
more &raquo; ... nsive set of visualization and analysis tools. Recent developments include several new genome releases (TAIR8, TAIR9 and TAIR10) in which the A. thaliana assembly was updated, pseudogenes and transposon genes were re-annotated, and new data from proteomics and next generation transcriptome sequencing were incorporated into gene models and splice variants. Other highlights include progress on functional annotation of the genome and the release of several new tools including Textpresso for Arabidopsis which provides the capability to carry out full text searches on a large body of research literature.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkr1090">doi:10.1093/nar/gkr1090</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22140109">pmid:22140109</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3245047/">pmcid:PMC3245047</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4pxvtzrfxbgcnju46s4gfh5uhy">fatcat:4pxvtzrfxbgcnju46s4gfh5uhy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170811212814/http://rna.igmors.u-psud.fr/X-fer/FALR/3a.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/d7/dd/d7ddc069220757720415659aa81911159c0f38b3.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkr1090"> <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/PMC3245047" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The City Under COVID‐19: Podcasting As Digital Methodology

Dallas Rogers, Miles Herbert, Carolyn Whitzman, Eugene McCann, Paul J. Maginn, Beth Watts, Ashraful Alam, Madeleine Pill, Roger Keil, Tanja Dreher, Matt Novacevski, Jason Byrne (+11 others)
<span title="2020-06-09">2020</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/adxgsqohrbd67ddis32kfpjb3q" style="color: black;">Tijdschrift voor economische en sociale geografie</a> </i> &nbsp;
(Kate Murray, Melbourne, Australia.  ...  (Kate Murray, Melbourne, Australia.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1111/tesg.12426">doi:10.1111/tesg.12426</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32836481">pmid:32836481</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7300694/">pmcid:PMC7300694</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4xjqdxzwhfhnjlgjr5w2n6k7xy">fatcat:4xjqdxzwhfhnjlgjr5w2n6k7xy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200910122231/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC7300694&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/ca/8d/ca8d03525dc043c46ca48997bd1b6cff46b31958.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1111/tesg.12426"> <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/PMC7300694" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

Ron Caspi, Tomer Altman, Joseph M. Dale, Kate Dreher, Carol A. Fulcher, Fred Gilham, Pallavi Kaipa, Athikkattuvalasu S. Karthikeyan, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Lukas A. Mueller (+6 others)
<span title="2009-10-22">2009</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 MetaCyc database (MetaCyc.org) is a comprehensive and freely accessible resource for metabolic pathways and enzymes from all domains of life. The pathways in MetaCyc are experimentally determined, small-molecule metabolic pathways and are curated from the primary scientific literature. With more than 1400 pathways, MetaCyc is the largest collection of metabolic pathways currently available. Pathways reactions are linked to one or more well-characterized enzymes, and both pathways and
more &raquo; ... are annotated with reviews, evidence codes, and literature citations. BioCyc (BioCyc.org) is a collection of more than 500 organism-specific Pathway/Genome Databases (PGDBs). Each BioCyc PGDB contains the full genome and predicted metabolic network of one organism. The network, which is predicted by the Pathway Tools software using MetaCyc as a reference, consists of metabolites, enzymes, reactions and metabolic pathways. BioCyc PGDBs also contain additional features, such as predicted operons, transport systems, and pathway holefillers. The BioCyc Web site offers several tools for the analysis of the PGDBs, including Omics Viewers that enable visualization of omics datasets on two different genome-scale diagrams and tools for comparative analysis. The BioCyc PGDBs generated by SRI are offered for adoption by any party interested in curation of metabolic, regulatory, and genomerelated information about an organism.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkp875">doi:10.1093/nar/gkp875</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19850718">pmid:19850718</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2808959/">pmcid:PMC2808959</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3mdlecp47rbszcro7wmgktztqi">fatcat:3mdlecp47rbszcro7wmgktztqi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180730125628/https://watermark.silverchair.com/gkp875.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAaowggGmBgkqhkiG9w0BBwagggGXMIIBkwIBADCCAYwGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMTrG7TcGi32pzHT0DAgEQgIIBXaCJG635ckmO8mr9rV7C0Tff0KxdTOUXfLRPDW_jBF9Rr2IvBXqTe7JVFiAwaXYbX6OuNTxD_t3gulO93FTc-ykLKZRTEu3ZMPFK_b2e_-89KOhrhMLhK51IJRtleE5jxiCLaALLyTE9Bw92qDPApqjVP9jwhOfwcRdbUMPDd6m8o_NUFMowIVClF9RNcasRsHoRwa8hxYxwrGv8Zpc_9sgGuQSNARrgd67gYs2pjpHwai4jTHW_BtypDjf8-RpDkefDxfJq56entEtvu5HX0PI1Nb_mADJ9zpb0P2nBSI1DPlQASfmgXtT2-VjAcEYyAAiI2K1x7wtrfdTJpmSaTXsIClQSXIn_ujInwRNMuWz2wL9biXO-v0Vy5WsM-TnHvLcALbQh-Zp6UzyFAL29NW1faDg2N4UpiVY4p1hIWZhsk_p3AmoGeSY0NjIrG0-HzG7kQGxjL_NkRI4rRkM" 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/be/e3/bee3b113e8415bd3ec25607bb4d5ff3ad80567e9.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkp875"> <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/PMC2808959" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Strategies for Effective Use of Genomic Information in Crop Breeding Programs Serving Africa and South Asia

Nicholas Santantonio, Sikiru Adeniyi Atanda, Yoseph Beyene, Rajeev K. Varshney, Michael Olsen, Elizabeth Jones, Manish Roorkiwal, Manje Gowda, Chellapilla Bharadwaj, Pooran M. Gaur, Xuecai Zhang, Kate Dreher (+7 others)
<span title="2020-03-27">2020</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;
Copyright © 2020 Santantonio, Atanda, Beyene, Varshney, Olsen, Jones, Roorkiwal, Gowda, Bharadwaj, Gaur, Zhang, Dreher, Ayala-Hernández, Crossa, Pérez-Rodríguez, Rathore, Gao, McCouch and Robbins.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fpls.2020.00353">doi:10.3389/fpls.2020.00353</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32292411">pmid:32292411</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7119190/">pmcid:PMC7119190</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lrdk76gezbcujdjowcdi55moma">fatcat:lrdk76gezbcujdjowcdi55moma</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210715113511/https://researchrepository.murdoch.edu.au/id/eprint/60179/2/serving%20Africa.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/91/38/9138d044e51f52c8d2f6388c00a5f0556a2a54df.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fpls.2020.00353"> <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/PMC7119190" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

Ron Caspi, Tomer Altman, Richard Billington, Kate Dreher, Hartmut Foerster, Carol A. Fulcher, Timothy A. Holland, Ingrid M. Keseler, Anamika Kothari, Aya Kubo, Markus Krummenacker, Mario Latendresse (+8 others)
<span title="2013-11-12">2013</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 MetaCyc database (MetaCyc.org) is a comprehensive and freely accessible database describing metabolic pathways and enzymes from all domains of life. MetaCyc pathways are experimentally determined, mostly small-molecule metabolic pathways and are curated from the primary scientific literature. MetaCyc contains >2100 pathways derived from >37 000 publications, and is the largest curated collection of metabolic pathways currently available. BioCyc (BioCyc.org) is a collection of >3000
more &raquo; ... specific Pathway/Genome Databases (PGDBs), each containing the full genome and predicted metabolic network of one organism, including metabolites, enzymes, reactions, metabolic pathways, predicted operons, transport systems and pathway-hole fillers. Additions to BioCyc over the past 2 years include YeastCyc, a PGDB for Saccharomyces cerevisiae, and 891 new genomes from the Human Microbiome Project. The BioCyc Web site offers a variety of tools for querying and analysis of PGDBs, including Omics Viewers and tools for comparative analysis. New developments include atom mappings in reactions, a new representation of glycan degradation pathways, improved compound structure display, better coverage of enzyme kinetic data, enhancements of the Web Groups functionality, improvements to the Omics viewers, a new representation of the Enzyme Commission system and, for the desktop version of the software, the ability to save display states.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkt1103">doi:10.1093/nar/gkt1103</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24225315">pmid:24225315</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3964957/">pmcid:PMC3964957</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mfa4okdnxvhwrgf27kguvrss2q">fatcat:mfa4okdnxvhwrgf27kguvrss2q</a> </span>
<a target="_blank" rel="noopener" href="https://archive.org/download/pubmed-PMC3964957/PMC3964957-gkt1103.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> File Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ba/f0/baf03356bf3403f0fc111e1b348a77a01ef48899.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkt1103"> <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/PMC3964957" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Diversity analysis of 80,000 wheat accessions reveals consequences and opportunities of selection footprints

Carolina Sansaloni, Jorge Franco, Bruno Santos, Lawrence Percival-Alwyn, Sukhwinder Singh, Cesar Petroli, Jaime Campos, Kate Dreher, Thomas Payne, David Marshall, Benjamin Kilian, Iain Milne (+17 others)
<span title="2020-09-11">2020</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/a4wan6l5o5dfzn767kyz7jqevi" style="color: black;">Nature Communications</a> </i> &nbsp;
Undomesticated wild species, crop wild relatives, and landraces represent sources of variation for wheat improvement to address challenges from climate change and the growing human population. Here, we study 56,342 domesticated hexaploid, 18,946 domesticated tetraploid and 3,903 crop wild relatives in a massive-scale genotyping and diversity analysis. Using DArTseqTM technology, we identify more than 300,000 high-quality SNPs and SilicoDArT markers and align them to three reference maps: the
more &raquo; ... SC RefSeq v1.0 genome assembly, the durum wheat genome assembly (cv. Svevo), and the DArT genetic map. On average, 72% of the markers are uniquely placed on these maps and 50% are linked to genes. The analysis reveals landraces with unexplored diversity and genetic footprints defined by regions under selection. This provides fertile ground to develop wheat varieties of the future by exploring specific gene or chromosome regions and identifying germplasm conserving allelic diversity missing in current breeding programs.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41467-020-18404-w">doi:10.1038/s41467-020-18404-w</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32917907">pmid:32917907</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fpdcdg5hcvdall6sfk2lphtjze">fatcat:fpdcdg5hcvdall6sfk2lphtjze</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210427130957/https://discovery.dundee.ac.uk/ws/files/52249969/s41467_020_18404_w.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/0f/cd/0fcde0dd045f5a26753c3543df61e702a0cb2beb.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41467-020-18404-w"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> nature.com </button> </a>

From bits to bites: advancement of the germinate platform to support genetic resources collections and pre‐breeding informatics for crop wild relatives

Sebastian Raubach, Benjamin Kilian, Kate Dreher, Ahmed Amri, Filippo M. Bassi, Ousmane Boukar, Douglas Cook, Alan Cruickshank, Christian Fatokun, Noureddine El Haddad, Alan Humphries, David Jordan (+23 others)
<span title="2020-06-30">2020</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6pvja7nupvd7rph3vskg3rmju4" style="color: black;">Crop science</a> </i> &nbsp;
Dreher has contributed to this manuscript and is responsible for deployment of Germinate for the CIMMYT maize and wheat collections and has provided technical feedback on features. D. F.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/csc2.20248">doi:10.1002/csc2.20248</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ptp7d2ekjjg4bkxdnw2a6tru54">fatcat:ptp7d2ekjjg4bkxdnw2a6tru54</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210715164318/https://mel.cgiar.org/reporting/download/hash/d507b280fe84b26ec1d478c242391429" 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/ec/82/ec8268bea85342b3363d5dfc2f3569a2c8edb3e7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/csc2.20248"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> wiley.com </button> </a>
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