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YeastMine—an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit

Rama Balakrishnan, Julie Park, Kalpana Karra, Benjamin C. Hitz, Gail Binkley, Eurie L. Hong, Julie Sullivan, Gos Micklem, J. Michael Cherry
2012 Database: The Journal of Biological Databases and Curation  
Acknowledgements We wish to acknowledge Richard Smith at University of Cambridge, UK for valuable assistance; members of the growing collaboration of MODs implementing mines; and the Saccharomyces Genome  ...  Database project staff that has provided testing, development of tutorial videos and thoughtful discussions to expand our use of YeastMine.  ...  We chose to implement YeastMine, an integrated data warehouse with precomputed tables based on the InterMine platform.  ... 
doi:10.1093/database/bar062 pmid:22434830 pmcid:PMC3308152 fatcat:h2ydruct6nf55m6wxh2vvjtq34

BioJS InterMineTable Component: A BioJS component for displaying data from InterMine compatible webservice endpoints

Alexis Kalderimis, Radek Stepan, Julie Sullivan, Rachel Lyne, Michael Lyne, Gos Micklem
2014 F1000Research  
.: YeastMine-an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit. Database (Oxford). 2012; 2012: bar062.  ...  Chen YA, Tripathi LP, Mizuguchi K: TargetMine, an integrated data warehouse for candidate gene prioritisation and target discovery.  ...  In this way, the interoperability of these components makes them of increasing utility to developers, as more of them are published and integrated into third party applications.  ... 
doi:10.12688/f1000research.3-46.v1 fatcat:e7vyjr2ghzaeri73hgi5476mka

La levure à vin

Marie Filteau, Véronique Hamel, Christian R. Landry
2016 M S.Médecine Sciences  
YeastMine : an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit. Database (Oxford) 2012 ; 2012 : bar062. 11. Boeckstaens M.  ...  Complementation of yeast genes with human genes as an experimental platform for functional testing of human genetic variants. Genetics 2015 ; 201 : 1263-74. 9.  ... 
doi:10.1051/medsci/20163204007 pmid:27137687 fatcat:qsnmuxqxh5ghzbewi5cbawoykq

Transcriptional network of the industrial hybrid Saccharomyces pastorianus reveals temperature-dependent allele expression bias and preferential orthologous protein assemblies [article]

Soukaina Timouma, Laura Natalia Balarezo-Cisneros, Javier Pinto Aguirre, Roberto De la Cerda, Ursula M Bond, Jean-Marc Schwartz, Daniela Delneri
2021 bioRxiv   pre-print
Saccharomyces pastorianus is an industrial natural yeast evolved from different hybridisation events between the mesophilic S. cerevisiae and the cold-tolerant S. eubayanus.  ...  These characteristics lead to agonistic or antagonistic competition for substrates and a plethora of biochemical activities, resulting in a unique cellular metabolism.  ...  YeastMine--an 538 integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit. Database (Oxford). PJ, Liu WQ, Wang QM, Bai FY.  ... 
doi:10.1101/2021.04.07.438844 fatcat:n6jrlrobuzauvdntq5m5gwydza

SACCHAROMYCES CEREVISIAE VAR. BOULARDII PROBIOTIC YEASTS AS ETIOLOGICAL AGENTS OF OPORTUNISTIC INFECTIONS IN HUMANS

Katarzyna Roeske, Aleksandra Zasuń, Justyna Cieślik, Marta Wróblewska, Tomasz Jagielski
2020 Advancements of Microbiology  
Balakrishnan R., Park J., Karra K., Hitz B.C., Binkley G., Hong E.L., Sullivan J., Micklem G., Cherry J.M.: Yeast Mine-an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit  ...  Cherifi S., Robberecht J., Miendje Y.: Saccharomyces cerevisiae fungemia in an elderly patient with Clostridium difficile colitis. Acta Clin. Belg. 59, 223-224 (2004) 27.  ... 
doi:10.21307/pm-2020.59.3.21 fatcat:snvjqy7ntja27letsfc7piooki

Perturbations of transcription and gene expression-associated processes alter distribution of cell size values in Saccharomyces cerevisiae [article]

Nairita Maitra, Jayamani Anandhakumar, Heidi M. Blank, Craig D. Kaplan, Michael Polymenis
2018 bioRxiv   pre-print
Here, we show that cell size values of wild type Saccharomyces cerevisiae cells fit a gamma distribution, in haploid and diploid cells, and under different growth conditions.  ...  To identify genes that influence this pattern, we analyzed the cell size distributions of all single-gene deletion strains in Saccharomyces cerevisiae.  ...  Binkley et al., 2012 YeastMine--an integrated data 532 warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit. Database (Oxford) 533 2012:bar062. 534 Bjorklund, M., M. Taipale, M.  ... 
doi:10.1101/461210 fatcat:xzb2rexgy5db5aqae7as332xpu

Meiotic interactors of a mitotic gene TAO3 revealed by functional analysis of its rare variant [article]

Saumya Gupta, Aparna Radhakrishnan, Rachana Nitin, Pandu Raharja-Liu, Gen Lin, Lars M Steinmetz, Julien Gagneur, Himanshu Sinha
2015 bioRxiv   pre-print
Here we characterize the functional consequences of a rare coding variant of TAO3, previously reported to significantly contribute to sporulation efficiency variation in Saccharomyces cerevisiae.  ...  We thus uncover meiotic functions of TAO3, a mitotic gene and propose ERT1 and PIP2 as novel regulators of sporulation efficiency.  ...  Binkley et al., 2012 YeastMine -an 547 integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit. 548 Database (Oxford) 2012: bar062-bar062. 549 Baumgartner, U., B.  ... 
doi:10.1101/033167 fatcat:25rxuthfxzb5dmeh3v2vn7o74y

The Paf1 complex broadly impacts the transcriptome of Saccharomyces cerevisiae [article]

Mitchell A Ellison, Alex R Lederer, Marcie H Warner, Travis Mavrich, Elizabeth A Raupach, Lawrence E Heisler, Corey Nislow, Miler T Lee, Karen M. Arndt
2019 bioRxiv   pre-print
In this study, we investigated the extent to which the functions of Paf1C combine to regulate the Saccharomyces cerevisiae transcriptome.  ...  Together these data identify roles for Paf1C in controlling both coding and noncoding regions of the yeast genome.  ...  We are grateful to Frank Pugh and Stirling Churchman, and members of their labs, for assistance with analysis of published genomic data, and to Chenchen Zhu and Lars Steinmetz for advice on building a  ... 
doi:10.1101/567495 fatcat:je6hbtaxdfakvh4z64gdjpygve

Leveraging genetic interaction for adverse drug-drug interaction prediction [article]

Sheng Qian, Siqi Liang, Haiyuan Yu
2019 bioRxiv   pre-print
Leveraging genetic interaction features and a novel training scheme, we construct a gradient boosting-based classifier that achieves robust DDI prediction even for drugs whose interaction profiles are  ...  Here we demonstrate for the first time targets of adversely interacting drug pairs are significantly more likely to have synergistic genetic interactions than non-interacting drug pairs.  ...  Wierbowski for helpful discussions.  ... 
doi:10.1101/455006 fatcat:wwuifwc6pne7jlaup5zgnac4vm

Investigating Polyphosphate Biology: From Post-Translational Modification to Rare Disease [article]

Amanda Bentley-DeSousa, University, My
2021
In yeast, polyP is synthesized by the vacuolar transporter chaperone (VTC) complex as a translocation event into the vacuole lumen.  ...  In 2015, polyP chains were found to act as a post-translational modification termed polyphosphorylation on yeast proteins (Nsr1 and Top1).  ...  A. Mayer for yeast EcPPK1 expression constructs and Drs. C. Azevedo and A. Saiardi for sharing strains and for valuable advice. We thank Dr. T. Shiba for providing polyP standards.  ... 
doi:10.20381/ruor-26447 fatcat:ib6wr5rfj5bwzjfqqpsdged5sm