1,720,969 research outputs found
Significant change in element length and substitution rate in overlapping CNEs upstream of and
No full text<p><b>Copyright information:</b></p><p>Taken from "Comparative genomics using reveals insights into regulatory subfunctionalization"</p><p>Genome Biology 2007;8(4):R53-R53.</p><p>Published online 11 Apr 2007</p><p>PMCID:PMC1896008.</p><p></p> CNEs (filled blue boxes) were identified around each co-ortholog (A1, top) and (A2, bottom) (gene exons are shown in the coding sequence (CDS) track as filled red boxes). The scale at the top represents positions along the sequence used in the multiple alignment. Two CNEs, highlighted in pink boxes, one upstream of (CRCNEAC00031954 [53], referred to as CNE_A1) and one upstream of (CRCNEAC00032205 [53], referred to as CNE_A2) are conserved to part of the same sequence in human upstream of . The overlap region is 126 bp in length and encompasses all of the CNE_A2 but only 35% of CNE_A1 (which is 360 bp long), indicating a significant loss of element length in CNE_A2. A relative rate test of the CNEs across the overlapping region using human as the outgroup reveals a highly significant number of independent substitutions (26) in CNE_A2 with no independent substitutions in CNE_A1 (< 0.001). This suggests CNE_A1 is likely to have retained the ancestral function while CNE_A2 may have evolved to have a different function
Proportion of CNEs around each co-ortholog that overlap or are distinct to sequences in mammals compared to CNEs identified in its counterpart co-ortholog
No full text<p><b>Copyright information:</b></p><p>Taken from "Comparative genomics using reveals insights into regulatory subfunctionalization"</p><p>Genome Biology 2007;8(4):R53-R53.</p><p>Published online 11 Apr 2007</p><p>PMCID:PMC1896008.</p><p></p> Each bar represents the total number of CNEs identified around each co-ortholog with a proportion of that total colored as overlapping (light purple) or distinct (maroon) CNEs
Proportion of each CNE sequence that overlaps the counterpart co-ortholog CNE
No full text<p><b>Copyright information:</b></p><p>Taken from "Comparative genomics using reveals insights into regulatory subfunctionalization"</p><p>Genome Biology 2007;8(4):R53-R53.</p><p>Published online 11 Apr 2007</p><p>PMCID:PMC1896008.</p><p></p> Main graph: for each overlapping pair of co-orthologous CNEs (involving just two sequences), the proportion of the full length of each CNE (P1-P2) made up by the overlap was calculated using the human sequence as the reference. The larger of the two proportions was always plotted as P1 to simplify analysis. Inset bar chart: summary of the number of overlapping CNE pairs falling into three main proportion categories: P1 ≥ 0.8, P2 ≥ 0.8 - pairs that overlapped over the majority of both elements, suggesting little evolution of element length since duplication; P1 ≥ 0.8, P2 < 0.8 - pairs that have undergone significant degeneration in element length in one of the copies compared to its counterpart; P1 < 0.8, P2 < 0.8 - pairs that have undergone a level of degeneration in element length in both copies at their edges
Genomic environment around co-orthologs in comparison to the human ortholog
No full text<p><b>Copyright information:</b></p><p>Taken from "Comparative genomics using reveals insights into regulatory subfunctionalization"</p><p>Genome Biology 2007;8(4):R53-R53.</p><p>Published online 11 Apr 2007</p><p>PMCID:PMC1896008.</p><p></p> Diagrammatic representation of the genomic environment around co-orthologs and human orthologs of: , , , , , and . For each gene, the top two lines represent the genic environment around each of the co-orthologs whilst the third line represents the genic environment around the human ortholog. Regions are not drawn to scale and are representative only. Human chromosome locations and scaffold IDs are stated to the left of each graphic. scaffold IDs can be cross-referenced for their exact location through Table 1. All annotation was retrieved from Ensembl (v36.4) and Human (v.36.35i). Only genes that are conserved in both and human are shown. Reference genes are colored in red and are always orientated in 5'→3' orientation. Surrounding genes in are marked in blue and in human in green. The names of neighboring homologs that share conserved synteny with human (but not necessarily the same relative order or orientation) are highlighted in an orange box. Genes orientated in the same direction as the reference gene are located above the line and those orientated in the opposite direction are below the line. Yellow triangles represent the positions of the furthest CNEs upstream and downstream in each genomic sequence and delineate the region in which CNEs were identified
VISTA plot of an MLAGAN alignment of orthologous regions surrounding two co-orthologs in (Fr) and in chicken (Gg), rat (Rn) and human
No full text<p><b>Copyright information:</b></p><p>Taken from "Comparative genomics using reveals insights into regulatory subfunctionalization"</p><p>Genome Biology 2007;8(4):R53-R53.</p><p>Published online 11 Apr 2007</p><p>PMCID:PMC1896008.</p><p></p> The baseline is 268 kb of human sequence. Conservation between human and each sequence is shown as a peak. Peaks that represent conservation in a non-coding region of at least 65% over 40 bp are shaded pink with coding exons shaded purple and peaks located within untranslated regions shaded light-blue. All CNEs conserved in at least one of the co-orthologs are color-coded. CNEs in both co-orthologs that overlap the same region in human are shaded yellow while CNEs that are 'distinct' (or conserved solely) in are shaded red and CNEs distinct to are shaded green. Peaks marked with a double-headed arrow are conserved in in the opposite orientation (and therefore do not show up in the VISTA plot). A number of the CNEs around are also duplicated CNEs (dCNEs) that are located elsewhere in the genome in the vicinity of paralogs. CNEs marked with an orange box have another dCNE family member in the vicinity of and the CNE marked with a blue box has a dCNE family member conserved upstream of
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe 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
Full text link“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
Full text linkWe 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
Full text linkWe 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
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