1,721,047 research outputs found
Application of genome assembly methods to human and non-human primate genomics
Get PDFGenomic analyses are at the center of contemporary biology. These studies heavily rely on reference genome assemblies, yet those are typically highly fragmented. Having accurate representations of complex genomes, or parts thereof, is crucial to study human and primate evolution and disease. Here, we develop and apply new sequencing strategies and technologies to improve reference assemblies. We first explore the combinatorial potential of different datasets to generate a highly improved reference for the chimpanzee, a crucial species for the study of human origins. We are able to close 77% of the over 159.000 remaining gaps in the previous iteration of this species’ assembly and increase continuity by more than 750%. We then go on to develop a workflow to assemble the first human Y chromosome of African ancestry, using native flow-sorted chromosomes sequenced on a Nanopore device. We are able to assemble the Y chromosome to a reference grade quality and achieve unprecedented sequence resolution across structurally complex regions. These results open new avenues for comparative studies including the chimpanzee genome or human Y chromosomes.Els anàlisis genòmics són el centre de la biologia contemporània. Aquests estudis depenen molt de l’assemblatge de genomes de referència, tot i que aquets en general estan molt fragmentats. Tenir representacions precises de genomes complexos, o parts d’aquests, és crucial per estudiar les malalties i l’evolució en humans i primats. En els estudis següents, desenvolupem i apliquem noves estratègies i tecnologies de seqüenciació per millorar els assemblatges de referència. En primer lloc, explorem el potencial de combinar diferents conjunts de dades per generar una referència substancialment millorada per al ximpanzé, una espècie crucial per a l'estudi dels orígens humans. Som capaços de tancar el 77% dels més de 159,000 buits que hi havia a la iteració prèvia de l’assemblatge d'aquesta espècie, i augmentar la continuïtat en més del 750%. A continuació, desenvolupem un protocol per assemblar el primer cromosoma Y humà d’ascendència africana, utilitzant cromosomes nadius aïllats per citometria de flux i seqüenciats mitjançant un dispositiu Nanopore. D’aquesta manera, aconseguim assemblar el cromosoma Y a una qualitat de referència i una resolució de seqüències sense precedents en regions estructuralment complexes. Aquests resultats obren noves vies per a estudis comparatius que inclouen el genoma del ximpanzé o els cromosomes Y humans.Programa de doctorat en Biomedicin
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
Identification of constrained sequence elements across 239 primate genomes
No full textAbstract Noncoding DNA is central to our understanding of human gene regulation and complex diseases 1,2 , and measuring the evolutionary sequence constraint can establish the functional relevance of putative regulatory elements in the human genome 3–9 . Identifying the genomic elements that have become constrained specifically in primates has been hampered by the faster evolution of noncoding DNA compared to protein-coding DNA 10 , the relatively short timescales separating primate species 11 , and the previously limited availability of whole-genome sequences 12 . Here we construct a whole-genome alignment of 239 species, representing nearly half of all extant species in the primate order. Using this resource, we identified human regulatory elements that are under selective constraint across primates and other mammals at a 5% false discovery rate. We detected 111,318 DNase I hypersensitivity sites and 267,410 transcription factor binding sites that are constrained specifically in primates but not across other placental mammals and validate their cis -regulatory effects on gene expression. These regulatory elements are enriched for human genetic variants that affect gene expression and complex traits and diseases. Our results highlight the important role of recent evolution in regulatory sequence elements differentiating primates, including humans, from other placental mammals
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
Complex Evolutionary History With Extensive Ancestral Gene Flow in an African Primate Radiation
No full textAbstract Understanding the drivers of speciation is fundamental in evolutionary biology, and recent studies highlight hybridization as an important evolutionary force. Using whole-genome sequencing data from 22 species of guenons (tribe Cercopithecini), one of the world's largest primate radiations, we show that rampant gene flow characterizes their evolutionary history and identify ancient hybridization across deeply divergent lineages that differ in ecology, morphology, and karyotypes. Some hybridization events resulted in mitochondrial introgression between distant lineages, likely facilitated by cointrogression of coadapted nuclear variants. Although the genomic landscapes of introgression were largely lineage specific, we found that genes with immune functions were overrepresented in introgressing regions, in line with adaptive introgression, whereas genes involved in pigmentation and morphology may contribute to reproductive isolation. In line with reports from other systems that hybridization might facilitate diversification, we find that some of the most species-rich guenon clades are of admixed origin. This study provides important insights into the prevalence, role, and outcomes of ancestral hybridization in a large mammalian radiation
Application of genome assembly methods to human and non-human primate genomics
No full textGenomic analyses are at the center of contemporary biology. These studies heavily rely on reference genome assemblies, yet those are typically highly fragmented. Having accurate representations of complex genomes, or parts thereof, is crucial to study human and primate evolution and disease. Here, we develop and apply new sequencing strategies and technologies to improve reference assemblies. We first explore the combinatorial potential of different datasets to generate a highly improved reference for the chimpanzee, a crucial species for the study of human origins. We are able to close 77% of the over 159.000 remaining gaps in the previous iteration of this species’ assembly and increase continuity by more than 750%. We then go on to develop a workflow to assemble the first human Y chromosome of African ancestry, using native flow-sorted chromosomes sequenced on a Nanopore device. We are able to assemble the Y chromosome to a reference grade quality and achieve unprecedented sequence resolution across structurally complex regions. These results open new avenues for comparative studies including the chimpanzee genome or human Y chromosomes.Els anàlisis genòmics són el centre de la biologia contemporània. Aquests estudis depenen molt de l’assemblatge de genomes de referència, tot i que aquets en general estan molt fragmentats. Tenir representacions precises de genomes complexos, o parts d’aquests, és crucial per estudiar les malalties i l’evolució en humans i primats. En els estudis següents, desenvolupem i apliquem noves estratègies i tecnologies de seqüenciació per millorar els assemblatges de referència. En primer lloc, explorem el potencial de combinar diferents conjunts de dades per generar una referència substancialment millorada per al ximpanzé, una espècie crucial per a l'estudi dels orígens humans. Som capaços de tancar el 77% dels més de 159,000 buits que hi havia a la iteració prèvia de l’assemblatge d'aquesta espècie, i augmentar la continuïtat en més del 750%. A continuació, desenvolupem un protocol per assemblar el primer cromosoma Y humà d’ascendència africana, utilitzant cromosomes nadius aïllats per citometria de flux i seqüenciats mitjançant un dispositiu Nanopore. D’aquesta manera, aconseguim assemblar el cromosoma Y a una qualitat de referència i una resolució de seqüències sense precedents en regions estructuralment complexes. Aquests resultats obren noves vies per a estudis comparatius que inclouen el genoma del ximpanzé o els cromosomes Y humans.Programa de doctorat en Biomedicin
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
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