101 research outputs found

    Gene Ontology: Pitfalls, Biases, and Remedies.

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    The Gene Ontology (GO) is a formidable resource, but there are several considerations about it that are essential to understand the data and interpret it correctly. The GO is sufficiently simple that it can be used without deep understanding of its structure or how it is developed, which is both a strength and a weakness. In this chapter, we discuss some common misinterpretations of the ontology and the annotations. A better understanding of the pitfalls and the biases in the GO should help users make the most of this very rich resource. We also review some of the misconceptions and misleading assumptions commonly made about GO, including the effect of data incompleteness, the importance of annotation qualifiers, and the transitivity or lack thereof associated with different ontology relations. We also discuss several biases that can confound aggregate analyses such as gene enrichment analyses. For each of these pitfalls and biases, we suggest remedies and best practices

    Resolving the Ortholog Conjecture: Orthologs Tend to Be Weakly, but Significantly, More Similar in Function than Paralogs

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    The function of most proteins is not determined experimentally, but is extrapolated from homologs. According to the “ortholog conjecture”, or standard model of phylogenomics, protein function changes rapidly after duplication, leading to paralogs with different functions, while orthologs retain the ancestral function. We report here that a comparison of experimentally supported functional annotations among homologs from 13 genomes mostly supports this model. We show that to analyze GO annotation effectively, several confounding factors need to be controlled: authorship bias, variation of GO term frequency among species, variation of background similarity among species pairs, and propagated annotation bias. After controlling for these biases, we observe that orthologs have generally more similar functional annotations than paralogs. This is especially strong for sub-cellular localization. We observe only a weak decrease in functional similarity with increasing sequence divergence. These findings hold over a large diversity of species; notably orthologs from model organisms such as E. coli, yeast or mouse have conserved function with human proteins

    Volume 06

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    Introduction from Dean Dr. Charles Ross Caught Between Folklore and the Cold War: The Americanization of Russian Children\u27s Literature by Kristen Gains Graphic Design by Amanda Willis Graphic Design by Holly Backer Prejudices in Swiss German Accents by Monika Gutierrez Photography by Cara O\u27Neal Photography by Sara Nelson Edmund Tyrone\u27s Long Journey through Night by Sasha Silberman Photography by Jessica Beardsley Photography by Jamie Gardner and Edward Peeples The Republican Razor: The Guillotine as a Symbol of Equality by Jamie Clift Graphic Design by Matthew Sakach Genocide: The Lasting Effects of Gender Stratification in Rwanda By Tess Lione and Emily Wilkins Photography by Kelsey Holt and Jessica Page Morocco and the 20 February Movement by Charles Vancampen, Gilbert Hall, Jenny Nehrt, Kasey Dye, Amanda Tharp, Jamie Leeawrik, & Ashley McGee Photography by Emily Poulin Photography by Michael Kropf Improving Performance of Arbitrary Precision Arithmetic Using SIMD Assembly Code Instructions by Nick Pastore Art by Austin Polasky and Morgan Glasco Art by Laura L. Kahler The Effects of the Neutral Response Option on the Extremeness of Participant Responses by Melinda L. Edwards and Brandon C. Smith Graphic Design by Mariah Asbell Graphic Design by Cabell Edmunds College Bullying: An Exploratory Analysis by Amelia D. Perry Photography by Alyssa Hayes Death-Related Crime: Applying Bryant\u27s Conceptual Paradigm of Thanatological Crime to Military Settings by Irina Boothe Graphic Design by Perry Bason Graphic Design by James Earl

    Which Green Matters for Whom? Greening and Firm Performance across Age and Size Distribution of Firms.

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    A growing body of literature links firm performance with sustainability efforts.We contribute to this literature by developing a novel framework for contextualising greening through the lens of tangibility and visibility of greening activities and examine the impact of different types of greening on firm performance along the age and size distribution of firms. The empirical results based on a large-scale database suggest that rewards to different types of greening differ across age and size distributions

    The Ranking of Masters Programs In International Business

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    Several years ago Donald Ball and Wendell McCulloch carried out an opinion survey of members of the Academy of International Business as to the ranking of international programs in U.S. business schools (JIBS, Spring/Summer 1984). It included 79 schools in the results.This author carried out a survey of the leading 47 schools (plus 5 others) to gather factual data about the masters programs I.B. in those schools, about the students and about the faculty who teach the I.B. courses.Usable responses were received from 42 schools, of which it was found that 12 did not offer a major or concentration in I.B. Using 18 criteria, the I.B. programs of the remaining 30 schools were ranked, assuming an equal weight to each criterion.The major purpose of the survey was to rank the programs based on data furnished by an AIB member at each school. In addition, the data gathered informs the reader as to the facts about the leading masters programs in I.B., beyond what one can gain from the official AIB Curriculum Survey.© 1987 JIBS. Journal of International Business Studies (1987) 18, 91–99
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