1,721,147 research outputs found
Additional file 3 of Profiling conserved transcription factor binding motifs in Phaseolus vulgaris through comparative genomics
No full textSupplementary Material 3: Supplementary Table 2. List of conserved motifs on P. vulgaris v1.0 promoters.NSFPeer reviewe
SQANTI-SIM: a simulator of controlled transcript novelty for lrRNA-seq benchmark
No full text<p>In this repository, we present the PacBio and ONT simulated datasets used for benchmarking transcriptome reconstruction tools, as evaluated in the manuscript titled "<i>SQANTI-SIM: a simulator of controlled transcript novelty for lrRNA-seq benchmark</i>". The dataset includes simulated long reads, short reads, CAGE peaks, and a reduced reference annotation. Additionally, we have included reconstructed transcriptomes from each method, along with SQANTI3 output files. The SQANTI-SIM software can be accessed on GitHub at the following URL: <a href="https://github.com/ConesaLab/SQANTI-SIM">https://github.com/ConesaLab/SQANTI-SIM</a>.</p><p>- Please ensure to cite the original publication (listed below) when using these datasets.</p>
Profiling conserved transcription factor binding motifs in Phaseolus vulgaris through comparative genomics
No full textAbstract Common bean (Phaseolus vulgaris), a staple food in Latin America and Africa, serves as a vital source of energy, protein, and essential minerals for millions of people. However, genomics knowledge that breeders could leverage for improvement of this crop is scarce. We have developed and validated a comparative genomics approach to predict conserved transcription factor binding sites (TFBS) in common bean and studied gene regulatory networks. We analyzed promoter regions and identified TFBS for 12,631 bean genes with an average of 6 conserved motifs per gene. Moreover, we discovered a statistically significant relationship between the number of conserved motifs and amount of available experimental evidence of gene regulation. Notably, ERF, MYB, and bHLH transcription factor families dominated conserved motifs, with implications for starch biosynthesis regulation. Furthermore, we provide gene regulatory data as a resource that can be interrogated for the regulatory landscape of any set of genes. Our results underscore the significance of TFBS conservation in legumes and aligns with the notion that core genes often exhibit a more conserved regulatory makeup. The study demonstrates the effectiveness of a comparative genomics approach for addressing genome information gaps in non-model organisms and provides valuable insights into the regulatory networks governing starch biosynthesis genes that can support crop improvement programs
SQANTI-SIM: a simulator of controlled transcript novelty for lrRNA-seq benchmark
Full text linkSQANTI-SIM is available at https://github.com/ConesaLab/SQANTI-SIM under GNU GPLv3 license. The human reference genome sequence (primary assembly, GRCh38) and gene annotation v43 from GENCODE can be obtained from https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_43. The long-read sequencing data obtained from the human WTC11 cell line is available at ENCODE (https://www.encodeproject.org/search): the cDNA ONT FASTQ file can be found under accession ENCFF263YFG, the dRNA ONT sample under file accession ENCFF155CFF, and the cDNA PacBio data under experiment accession ENCSR507JOF. Short-read sequencing data can be retrieved from accession number ENCSR673UKZ. The CAGE-Seq data is available at NCBI Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/geo/) under the accession number GSE185917. The simulated datasets generated and analyzed during the current study can be reproduced using the code provided in the SQANTI-SIM v0.2 software repository and supplementary materials. Additionally, the processed data and the SQANTI-SIM source code used in this study are also accessible on Zenodo (https://doi.org/10.5281/zenodo.10160381) [37].Long-read RNA sequencing has emerged as a powerful tool for transcript discovery, even in well-annotated organisms. However, assessing the accuracy of different methods in identifying annotated and novel transcripts remains a challenge. Here, we present SQANTI-SIM, a versatile tool that wraps around popular long-read simulators to allow precise management of transcript novelty based on the structural categories defined by SQANTI3. By selectively excluding specific transcripts from the reference dataset, SQANTI-SIM effectively emulates scenarios involving unannotated transcripts. Furthermore, the tool provides customizable features and supports the simulation of additional types of data, representing the first multi-omics simulation tool for the lrRNA-seq field.Open Access funding provided thanks to the CRUE-CSIC agreement with Springer Nature.This work has been funded by NIH grant R21HG011280 and by the Spanish Ministry of Science grant PID2020-119537RB-100.Peer reviewe
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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