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Comparative Genomics of Chlamydomonas
No full textFiles for "Comparative genomics of Chlamydomonas" manuscript.See README.
Please note information on two provisionally accepted file formats in the deposit:
* GFF3 is General Feature Format 3. It is plain text, and is the standard file format used for gene annotations (gene coordinates, exon-intron structure, etc.). The format is described by NCBI here: https://www.ncbi.nlm.nih.gov/datasets/docs/about-ncbi-gff3/
* hal is hierarchical alignment format. It is an HDF5 file used for storing genome alignments. The format is described here (https://github.com/ComparativeGenomicsToolkit/hal) and in this publication (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3654707/)
transposable elements
No full textFiles from the PhD thesis "The Evolutionary Genomics of Chlamydomonas" by Rory Craig.
Appendix C:
Supplementary Material for Chapter 3:
Note S1. High molecular weight DNA extraction protocol for Chlamydomonas.
Dataset S1: Annotation notes for curated transposable elements from Chlamydomonas incerta, Chlamydomonas schloesseri, Edaphochlamys debaryana, Eudorina sp. and Volvox carteri. See Appendix E, Dataset S1 for Chlamydomonas reinhardtii transposable element annotation notes.
Dataset S2: Assembly metrics for genome assemblies of all available Reinhardtinia species and selected outgroups.
Dataset S3: Gene model annotation metrics for all available Reinhardtinia species and selected outgroups.
Dataset S4. List of contigs terminating in telomeric repeats.
Dataset S5. Orthogroup and InterPro domain annotation for Chlamydomonas-specific orthogroups with annotated domains.
Dataset S6: Orthogroup and InterPro domain annotation for E. debaryana gene family expansions (log2-transformed ratios >1) and contractions (ratios <-1) .
Dataset S7: Presence-absence of C. reinhardtii MT– genes in C. incerta, C. schloesseri and E. debaryana.
Dataset S8: New genes identified with significant blastp homology to proteins from the C. reinhardtii v4.3 annotation.
Dataset S9: Core-Reinhardtinia ultraconserved elements (elements >=50 bp, 100% conservation within Chlamydomonas and >=95% conservation across eight core-Reinhardtinia species).
Appendix D: Supplementary Material for Chapter 4:
Dataset S1: Metrics and sequence context of all CC-503 v6 assembly gaps.
Dataset S2: Curated structural mutations unique to the CC-503 v6 assembly.
Dataset S3: Curated structural mutations unique to the CC-4532 v6 assembly.
Dataset S4. Metrics and sequence context of all CC-4532 v6 assembly gaps.
Dataset S5. Curated TE transposition events unique to the CC-503 v6 assembly.
Dataset S6: Curated TE transposition events unique to the CC-4452 v6 assembly.
Appendix E: Supplementary Material for Chapter 5:
Dataset S1: Annotation notes for the updated transposable element library for Chlamydomonas reinhardtii.
Dataset S2: Chlamys annotation notes.
Dataset S3: Naiad annotation notes.
Dataset S4. Chlamys-like annotation notes.
Dataset S5. Hydra annotation notes
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
Author-wise bibliometric analysis based on entropy.
No full textAuthor-wise bibliometric analysis based on entropy.</p
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