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Get ready to GO! A biologist's guide to the Gene Ontology

J. Lomax
2005 Briefings in Bioinformatics  
To group your genes into the GO categories listed in your GO slim, the GO Consortium provides a script, map2slim.pl. 29 The input for this script is an annotation file in the Gene Ontology format, 30  ...  By making annotations to a common, shared set of vocabularies, the Gene Ontology (GO) resource provides a powerful way to capture, query and analyse this information in a way that is independent of species  ... 
doi:10.1093/bib/6.3.298 pmid:16212777 fatcat:2eeoshktlffkvmvcgakvholjxm

Computational protein function prediction: Are we making progress?

A. Godzik, M. Jambon, I. Friedberg
2007 Cellular and Molecular Life Sciences (CMLS)  
M. and Sherlock, G. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25, 25 — 29. Lomax, J. (2005) Get ready to GO!  ...  A biologist’s guide to the Gene Ontology. Brief. Bioinform. 6, 298 — 304. Soro, S. and Tramontano, A. (2005) The prediction of protein function at CASP6. Proteins 61 Suppl. 7, 201 - 213.  ... 
doi:10.1007/s00018-007-7211-y pmid:17611711 fatcat:kwptig2eufczdbnm62ykqfbipe

Bacterial cultures: ontologies of bacteria and engineering expertise at the nexus of synthetic biology and water services

Andrew S. Balmer, Susan Molyneux-Hodgson
2013 Engineering Studies  
Am I going to die here in the lab, or get super powers? Am I going to cure cholera or just screw everything up? I feel like I'm less of a risk now though.  ...  , so like a new way of detecting leakage with noise, takes ten years to get to industry. … [with Synthetic Biology] we're talking about a total re-think, re-change of what they're going to do!  ... 
doi:10.1080/19378629.2013.766198 fatcat:z3a4gmprwvguxbuneiqy4jgkei

Bias tradeoffs in the creation and analysis of protein–protein interaction networks

Jesse Gillis, Sara Ballouz, Paul Pavlidis
2014 Journal of Proteomics  
We analyze interaction studies over time with respect to data in the Gene Ontology and find that reproducibly observed interactions are less likely to favor multifunctional proteins.  ...  We determine the degree to which selection bias in favor of biologically interesting bait proteins goes down with study size, while we also find that promiscuity in prey contributes more substantially  ...  Acknowledgments We thank Adriana Sedeño for assistance with the Gene Ontology data. We thank an anonymous reviewer for valuable comments.  ... 
doi:10.1016/j.jprot.2014.01.020 pmid:24480284 pmcid:PMC3972268 fatcat:7raqtw2hffdcnc3e6mmhnku4pm

Three Roles of Empirical Information in Philosophy: Intuitions on Mathematics do Not Come for Free

Deborah Kant, José Antonio Pérez-Escobar, Deniz Sarikaya
2021 Kriterion - Journal of Philosophy  
This is a shift of focus from the source of the information towards its use by philosophers.  ...  for non-mathematicians (since they are sometimes hard to grasp even for mathematicians).  ...  All authors are very thankful for the advice and helpful comments by D. A. King, S. Nagler, H. Pillin, and R. Wagner and the financial aid to cover the OA-fees by the University of Konstanz.  ... 
doi:10.1515/krt-2021-0025 fatcat:hqoi6bk5onc5jjncgaokkkplw4

Twelve quick steps for genome assembly and annotation in the classroom

Hyungtaek Jung, Tomer Ventura, J. Sook Chung, Woo-Jin Kim, Bo-Hye Nam, Hee Jeong Kong, Young-Ok Kim, Min-Seung Jeon, Seong-il Eyun, Francis Ouellette
2020 PLoS Computational Biology  
This paper also includes information on how to build a wide community for a genome project, the importance of data management, and how to make the data and results Findable, Accessible, Interoperable,  ...  and Reusable (FAIR) by submitting them to a public repository and sharing them with the research community.  ...  Acknowledgments The authors are grateful to their colleagues, collaborators, and field/technical specialists from each company for their valuable comments.  ... 
doi:10.1371/journal.pcbi.1008325 pmid:33180771 fatcat:43xebbok6repzjevew4eajxqmm

The Claims of Generalized Darwinism

Rod Thomas
2017 Philosophy of Management  
Generalized Darwinism (GD) claims to be a conceptual and theoretical framework for researching evolutionary change processes in organizations. This paper examines the claims of GD.  ...  But in considering the applicability of the two schemata to organizational evolution, criticism reveals one to be problematic, whereas the other one, to which the GD programme collapses if the problematical  ...  A shortened version of the paper, with the present title, was presented to faculty of the Newcastle Business School, Northumbria University on 30 th June 2016.  ... 
doi:10.1007/s40926-017-0060-3 fatcat:3wivo3zy5za6pkgf7nz34xvpme

A two-phase framework for quality-aware Web service selection

Qi Yu, Manjeet Rege, Athman Bouguettaya, Brahim Medjahed, Mourad Ouzzani
2010 Service Oriented Computing and Applications  
We conduct a set of experiments to assess the performance of the proposed algorithms.  ...  The framework incorporates a service query model and a two-phase optimization strategy.  ...  The mutation operator helps guide the evolution process to find the optimal solution.  ... 
doi:10.1007/s11761-010-0055-6 fatcat:dt5ydnf7urd6fjyro5qmiawxw4

BioSilicoSystems – A Multipronged Approach Towards Analysis and Representation of Biological Data (PhD Thesis)

Sridhar Hariharaputran, Sridhar Hariharaputran
2010 Nature Precedings  
It is provided by parseable flat files by most of the databases, whereas Gene Ontology (GO) is supplied via a SQL dump file.  ...  The keyword databases of many gene and protein are linked to each node in the GO ontologies along with other kind of information.  ...  Appendix I Appendix III As explained in the SBML web pages the following enzymatic reaction will be represented by SBML as <?xml version="1.0" encoding="UTF-8"?  ... 
doi:10.1038/npre.2010.5164.1 fatcat:bo3ri2crajb5xk7kukxhe6affa

BioSilicoSystems – A Multipronged Approach Towards Analysis and Representation of Biological Data (PhD Thesis)

Sridhar Hariharaputran, Sridhar Hariharaputran
2010 Nature Precedings  
It is provided by parseable flat files by most of the databases, whereas Gene Ontology (GO) is supplied via a SQL dump file.  ...  The keyword databases of many gene and protein are linked to each node in the GO ontologies along with other kind of information.  ...  Appendix I Appendix III As explained in the SBML web pages the following enzymatic reaction will be represented by SBML as <?xml version="1.0" encoding="UTF-8"?  ... 
doi:10.1038/npre.2010.5164 fatcat:72ufu6ycfba55gi6bvhatcld3e

How Does Strategic Communication Shape Transdisciplinary Collaboration? A Focus on Definitions, Audience, Expertise, and Ethical Praxis

Bridie McGreavy, Kaitlyn Haynal, Jennifer Smith-Mayo, Jessica Reilly-Moman, Michael T. Kinnison, Darren Ranco, Heather M. Leslie
2022 Frontiers in Communication  
Identifying relationships among strategic communication, knowledge co-production, and power enables the development of strategic collaborative practices, including asking questions as a means to identify  ...  In this paper, we share results from an engaged and ethnographic research project focused on strategic communication in a large-scale transdisciplinary collaboration to develop environmental-DNA (eDNA)  ...  I'm trying to think from [a biologist's] perspective.  ... 
doi:10.3389/fcomm.2022.831727 fatcat:ztel6vfqc5evbn4cp2nc5dnnx4

The Gaggle: an open-source software system for integrating bioinformatics software and data sources

Paul T Shannon, David J Reiss, Richard Bonneau, Nitin S Baliga
2006 BMC Bioinformatics  
A crucial challenge is to combine the capabilities of these (and other forthcoming) data resources and tools to create a data exploration and analysis environment that does justice to the variety and complexity  ...  We highlight some capabilities of the Gaggle with an exploration of Helicobacter pylori pathogenesis genes, in which we identify a putative ricin-like protein -a discovery made possible by simultaneous  ...  The work was funded through grants from NSF (EF-0313754) and DoE (DAAD13-03-O-0057) to NSB.  ... 
doi:10.1186/1471-2105-7-176 pmid:16569235 pmcid:PMC1464137 fatcat:wcucwxamejb3tdzpmdywlimjle

Globalizing Genomics: The Origins of the International Nucleotide Sequence Database Collaboration

Hallam Stevens
2017 Journal of the History of Biology  
The "transnationalism" of nucleotide sequence was critical to their ontology -what DNA sequences came to be during the Human Genome Project was deeply influenced by international exchange.  ...  Genomics is increasingly considered a global enterprise -the fact that biological information can flow rapidly around the planet is taken to be important to what genomics is and what it can achieve.  ...  The National Institute of Genetics in Mishima, Japan also provided support that enabled me to present a version of this paper there.  ... 
doi:10.1007/s10739-017-9490-y pmid:28986915 fatcat:panniideznbnhfelfspeygb6v4

A biologist's guide to statistical thinking and analysis

David S. Fay
2013 WormBook  
A gene ontology (GO) search reveals that 13 of these genes encode proteins with a RING domain.  ...  Then its name has to reflect the statistic in question; so, for A biologist's guide to statistical thinking and analysis 9 example, .  ...  The Cartoon Guide to Statistics (New York: HarperPerennial). Don't let the name fool you. This book is quite dense and contains the occasional calculus equation.  ... 
doi:10.1895/wormbook.1.159.1 pmid:23908055 pmcid:PMC3880567 fatcat:pngovbsdqjgcpg6e4aupf7dji4

Evolution for whom?

David J. Hosken
2012 Trends in Ecology & Evolution  
(a characterisation of "niche-space") we may be able to use such a theory as a basis for formulating new more precisely defined concepts with which to articulate less ambiguous questions about the space  ...  If we can find a general theory of the variety of possible architectures (a characterisation of "design-space") and the variety of environments, tasks and roles to which such architectures are well suited  ...  Acknowledgements and Notes This work was supported by the UK Joint Council Initiative, the Renaissance Trust, and a grant from the University of Birmingham.  ... 
doi:10.1016/j.tree.2011.10.003 fatcat:5xwy4ytwcnfpfgtwqtvk4zivy4
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