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https://www.readbyqxmd.com/read/30418570/efficient-and-accurate-detection-of-splice-junctions-from-rna-seq-with-portcullis
#1
Daniel Mapleson, Luca Venturini, Gemy Kaithakottil, David Swarbreck
Next generation sequencing (NGS) technologies enable rapid and cheap genome-wide transcriptome analysis, providing vital information about gene structure, transcript expression and alternative splicing. Key to this is the the accurate identification of exon-exon junctions from RNA sequenced (RNA-Seq) reads. A number of RNA-Seq aligners capable of splitting reads across these splice junctions (SJs) have been developed, however, it has been shown that while they correctly identify most genuine SJs available in a given sample, they also often produce large numbers of incorrect SJs...
November 12, 2018: GigaScience
https://www.readbyqxmd.com/read/30418578/comprehensive-evaluation-of-rna-seq-analysis-pipelines-in-diploid-and-polyploid-species
#2
Miriam Payá-Milans, James W Olmstead, Gerardo Nunez, Timothy A Rinehart, Margaret Staton
Background: The usual analysis of RNA-Seq reads is based on an existing reference genome and annotated gene models. However, when a reference for the sequenced species is not available, alternatives include using a reference genome from a related species or reconstructing transcript sequences with de novo assembly. In addition, researchers are faced with many options for RNA-Seq data processing and limited information on how their decisions will impact the final outcome. Using both a diploid and polyploid species with a distant reference genome, we have tested the influence of different tools at various steps of a typical RNA-Seq analysis workflow on the recovery of useful processed data available for downstream analysis...
November 10, 2018: GigaScience
https://www.readbyqxmd.com/read/30418576/an-open-source-high-speed-infrared-videography-database-to-study-the-principles-of-active-sensing-in-freely-navigating-rodents
#3
Alireza Azarfar, Yiping Zhang, Artoghrul Alishbayli, Stéphanie Miceli, Lara Kepser, Daan van der Wielen, Mike van de Moosdijk, Judith Homberg, Dirk Schubert, Rémi Proville, Tansu Celikel
Background: Active sensing is crucial for navigation. It is characterized by self-generated motor action controlling the accessibility and processing of sensory information. In rodents, active sensing is commonly studied in the whisker system. As rats and mice modulate their whisking contextually, they employ frequency and amplitude modulation. Understanding the development, mechanisms and plasticity of adaptive motor control will require precise behavioral measurements of whisker position...
November 10, 2018: GigaScience
https://www.readbyqxmd.com/read/30418564/nat-ncs2-hound-a-webserver-for-the-detection-and-evolutionary-classification-of-prokaryotic-and-eukaryotic-nucleobase-cation-symporters-of-the-nat-ncs2-family
#4
A Chaliotis, P Vlastaridis, C Ntountoumi, M Botou, V Yalelis, P Lazou, E Tatsaki, D Mossialos, S Frillingos, G D Amoutzias
Nucleobase transporters are important for supplying the cell with purines and/or pyrimidines, for controlling the intracellular pool of nucleotides and for obtaining exogenous nitrogen/carbon sources for the metabolism. Nucleobase transporters are also evaluated as potential targets for antimicrobial therapies, since several pathogenic microorganisms rely on purine/pyrimidine salvage from their hosts. The majority of known nucleobase transporters belong to the evolutionarily conserved and ubiquitous NAT/NCS2 protein family...
November 10, 2018: GigaScience
https://www.readbyqxmd.com/read/30395218/transfer-learning-improves-resting-state-functional-connectivity-pattern-analysis-using-convolutional-neural-networks
#5
Pál Vakli, Regina J Deák-Meszlényi, Petra Hermann, Zoltán Vidnyánszky
Background: Deep learning is gaining importance in the prediction of cognitive states and brain pathology based on neuroimaging data. Including multiple hidden layers in artificial neural networks enables unprecedented predictive power; however, the proper training of deep neural networks requires thousands of exemplars. Collecting this amount of data is not feasible in typical neuroimaging experiments. A handy solution to this problem, which has largely fallen outside the scope of deep learning applications in neuroimaging, is to repurpose deep networks that have already been trained on large datasets by fine-tuning them to target datasets/tasks with fewer exemplars...
November 5, 2018: GigaScience
https://www.readbyqxmd.com/read/30395211/aequatus-an-open-source-homology-browser
#6
Anil S Thanki, Nicola Soranzo, Javier Herrero, Wilfried Haerty, Robert P Davey
Background: Phylogenetic information inferred from the study of homologous genes helps us to understand the evolution of genes and gene families, including the identification of ancestral gene duplication events as well as regions under positive or purifying selection within lineages. Gene family and orthogroup characterisation enables the identification of syntenic blocks, which can then be visualised with various tools. Unfortunately, currently available tools display only an overview of syntenic regions as a whole, limited to the gene level, and none provide further details about structural changes within genes, such as the conservation of ancestral exon boundaries amongst multiple genomes...
November 5, 2018: GigaScience
https://www.readbyqxmd.com/read/30395209/a-parasite-s-perspective-on-data-sharing
#7
YoSon Park, Casey S Greene
Data generation is expensive in terms of both time and money. Sharing data enables the rapid replication, validation and application of discoveries, increasing the pace and accuracy of research. As research parasites, or users of other people's data, we recognize that a strong science ecosystem requires those who share best to be recognized. We find that widely accessible benchmark datasets have provided outsized benefits, and we hope that the benefits of sharing will also begin to accrue to individual investigators who share well...
November 5, 2018: GigaScience
https://www.readbyqxmd.com/read/30351383/imaging-tissues-and-cells-beyond-the-diffraction-limit-with-structured-illumination-microscopy-and-bayesian-image-reconstruction
#8
Jakub Pospíšil, Tomáš Lukeš, Justin Bendesky, Karel Fliegel, Kathrin Spendier, Guy M Hagen
Background: Structured illumination microscopy (SIM) is a family of methods in optical fluorescence microscopy that can achieve both optical sectioning and super-resolution effects. SIM is a valuable method for high-resolution imaging of fixed cells or tissues labeled with conventional fluorophores, as well as for imaging the dynamics of live cells expressing fluorescent protein constructs. In SIM, one acquires a set of images with shifting illumination patterns. This set of images is subsequently treated with image analysis algorithms to produce an image with reduced out-of-focus light (optical sectioning) and/or with improved resolution (super-resolution)...
October 23, 2018: GigaScience
https://www.readbyqxmd.com/read/30346553/cost-effective-assembly-of-the-african-wild-dog-lycaon-pictus-genome-using-linked-reads
#9
Ellie E Armstrong, Ryan W Taylor, Stefan Prost, Peter Blinston, Esther van der Meer, Hillary Madzikanda, Olivia Mufute, Roseline Mandisodza-Chikerema, John Stuelpnagel, Claudio Sillero-Zubiri, Dmitri Petrov
Background: A high-quality reference genome assembly is a valuable tool for the study of non-model organisms. Genomic techniques can provide important insights about past population sizes, local adaptation, and aid in the development of breeding management plans. This information is important for fields like conservation genetics, where endangered species require critical and immediate attention. However, funding for genomic-based methods can be sparse for conservation projects, as costs for general species management can consume budgets...
October 22, 2018: GigaScience
https://www.readbyqxmd.com/read/30346548/a-benchmark-study-of-k-mer-counting-methods-for-high-throughput-sequencing
#10
Swati C Manekar, Shailesh R Sathe
The rapid development of high-through sequencing technologies means that hundreds of gigabytes of sequencing data can be produced in a single study. Many bioinformatics tools require counts of substrings of length k in DNA/RNA sequencing reads obtained for applications such as genome and transcriptome assembly, error correction, multiple sequence alignment, and repeat detection. Recently, several techniques have been developed to count k-mers in large sequencing datasets, with a trade-off between the time and memory required to perform this function...
October 22, 2018: GigaScience
https://www.readbyqxmd.com/read/30277534/we-need-to-talk-about-authorship
#11
Hans Zauner, Nicole A Nogoy, Scott C Edmunds, Hongling Zhou, Laurie Goodman
In our day-to-day editorial work at GigaScience, time and again we see issues cropping up that make us worry whether everyone understands good scientific practice when it comes to listing author names on the title page. There are many issues that underlie inappropriate authorship designations, but there are also guidelines to help potential authors determine when and how a researcher should be placed on a manuscript. Here we help clarify this, and also provide a clear statement of our expectations around how authors are assigned to manuscripts submitted to GigaScience...
October 2, 2018: GigaScience
https://www.readbyqxmd.com/read/30277499/metapgn-a-pipeline-for-construction-and-graphical-visualization-of-annotated-pangenome-networks
#12
Ye Peng, Shanmei Tang, Dan Wang, Huanzi Zhong, Huijue Jia, Xianghang Cai, Zhaoxi Zhang, Minfeng Xiao, Huanming Yang, Jian Wang, Karsten Kristiansen, Xun Xu, Junhua Li
Pangenome analyses facilitate the interpretation of genetic diversity and evolutionary history of a taxon. However, there is an urgent and unmet need to develop new tools for advanced pangenome construction and visualization, especially for metagenomic data. Here we present an integrated pipeline, named MetaPGN, for construction and graphical visualization of pangenome network from either microbial genomes or metagenomes. Given either isolated genomes or metagenomic assemblies coupled with a reference genome of the targeted taxon, MetaPGN generates a pangenome in a topological network, consisting of genes (nodes) and gene-gene genomic adjacencies (edges) of which biological information can be easily updated and retrieved...
October 2, 2018: GigaScience
https://www.readbyqxmd.com/read/30277498/pigx-reproducible-genomics-analysis-pipelines-with-gnu-guix
#13
Ricardo Wurmus, Bora Uyar, Brendan Osberg, Vedran Franke, Alexander Gosdschan, Katarzyna Wreczycka, Jonathan Ronen, Altuna Akalin
In bioinformatics, as well as other computationally-intensive research fields, there is a need for workflows that can reliably produce consistent output, from known sources, independent of the software environment or configuration settings of the machine on which they are executed. Indeed, this is essential for controlled comparison between different observations or for the wider dissemination of workflows. Providing this type of reproducibility and traceability, however, is often complicated by the need to accommodate the myriad dependencies included in a larger body of software, each of which generally come in various versions...
October 2, 2018: GigaScience
https://www.readbyqxmd.com/read/30256939/chromosomal-level-assembly-of-yellow-catfish-genome-using-third-generation-dna-sequencing-and-hi-c-analysis
#14
Gaorui Gong, Cheng Dan, Shijun Xiao, Wenjie Guo, Peipei Huang, Yang Xiong, Junjie Wu, Yan He, Jicheng Zhang, Xiaohui Li, Nansheng Chen, Jian-Fang Gui, Jie Mei
Background: The yellow catfish, Pelteobagrus fulvidraco, belonging to Siluriformes order, is an economically important freshwater aquaculture fish species in Asia, especially in Southern China. The aquaculture industry has recently been facing tremendous challenges in germplasm degeneration and poor diseases resistance. As the yellow catfish exhibits notable sex dimorphism in growth, with adult males about two to three fold bigger than females, how aquaculture industry takes advantage of such sex dimorphism is another challenge...
September 25, 2018: GigaScience
https://www.readbyqxmd.com/read/30256935/the-genome-of-common-long-arm-octopus-octopus-minor
#15
Bo-Mi Kim, Seunghyun Kang, Do-Hwan Ahn, Seung-Hyun Jung, Hwanseok Rhee, Jong Su Yoo, Jong-Eun Lee, SeungJae Lee, Yong-Hee Han, Kyoung-Bin Ryu, Sung-Jin Cho, Hyun Park, Hye Suck An
Background: The common long-arm octopus (Octopus minor) is found in mudflats of subtidal zones and faces numerous environmental challenges. The ability to adapt its morphology and behavioural repertoire to diverse environmental conditions makes the species a promising model to understand genomic adaptation and evolution in cephalopods. Findings: The final genome assembly of O. minor is 5.09 Gb, with a contig N50 size of 197 kb and longest size of 3.027 Mb, from a total of 419 Gb raw reads generated using PacBio RS II platform...
September 25, 2018: GigaScience
https://www.readbyqxmd.com/read/30239706/single-cell-rna-seq-reveals-dynamic-transcriptome-profiling-in-human-early-neural-differentiation
#16
Zhouchun Shang, Dongsheng Chen, Quanlei Wang, Shengpeng Wang, Qiuting Deng, Liang Wu, Chuanyu Liu, Xiangning Ding, Shiyou Wang, Jixing Zhong, Doudou Zhang, Xiaodong Cai, Shida Zhu, Huanming Yang, Longqi Liu, J Lynn Fink, Fang Chen, Xiaoqing Liu, Zhengliang Gao, Xun Xu
Background: Investigating cell fate decision and subpopulation specification in the context of the neural lineage is fundamental to understanding neurogenesis and neurodegenerative diseases. The differentiation process of neural-tube-like rosettes in vitro is representative of neural tube structures, which are composed of radially organized, columnar epithelial cells and give rise to functional neural cells. However, the underlying regulatory network of cell fate commitment during early neural differentiation remains elusive...
September 18, 2018: GigaScience
https://www.readbyqxmd.com/read/30239704/extensive-evaluation-of-the-generalized-relevance-network-approach-to-inferring-gene-regulatory-networks
#17
Vladimir Kuzmanovski, Ljupco Todorovski, Sašo Džeroski
Background: The generalized relevance network approach to network inference reconstructs network links based on the strength of associations between data in individual network nodes. It can reconstruct undirected networks, i.e. relevance networks, sensu stricto, as well as directed networks, referred to as causal relevance networks. The generalized approach allows the use of an arbitrary measure of pairwise association between nodes, an arbitrary scoring scheme that transforms the associations into weights of the network links, and a method for inferring the directions of the links...
September 18, 2018: GigaScience
https://www.readbyqxmd.com/read/30239684/chromosome-level-genome-assembly-of-the-spotted-sea-bass-lateolabrax-maculatus
#18
Changwei Shao, Chang Li, Na Wang, Yating Qin, Wenteng Xu, Qun Liu, Qian Zhou, Yong Zhao, Xihong Li, Shanshan Liu, Xiaowu Chen, Shahid Mahboob, Xin Liu, Songlin Chen
Background: The spotted sea bass (Lateolabrax maculatus) is a valuable commercial fish that is widely cultured in China. While analyses using molecular markers and population genetics have been conducted, genomic resources are lacking. Finding: Here, we report a chromosome-scale assembly of the spotted sea bass genome by high-depth genome sequencing, assembly and annotation. The genome scale was 0.62 Gb with contig and scaffold N50 length to be 31 Kb and 1,040 Kb, respectively...
September 18, 2018: GigaScience
https://www.readbyqxmd.com/read/30192951/sequana-coverage-detection-and-characterization-of-genomic-variations-using-running-median-and-mixture-models
#19
Dimitri Desvillechabrol, Christiane Bouchier, Sean Kennedy, Thomas Cokelaer
Background: In addition to mapping quality information, the Genome coverage contains valuable biological information like the presence of repetitive regions, deleted genes or copy number variations. It is essential to take into consideration atypical regions, trends (e.g., origin of replication) or known and unknown biases that influence coverage. It is also important that reported events have robust statistics (e.g. z-score) associated with their detections as well as precise location...
September 6, 2018: GigaScience
https://www.readbyqxmd.com/read/30165633/genome-wide-definition-of-selective-sweeps-reveals-molecular-evidence-of-trait-driven-domestication-among-elite-goat-capra-species-breeds-for-the-production-of-dairy-cashmere-and-meat
#20
Bao Zhang, Liao Chang, Yong Xian Lan, Nadeem Asif, Fang Lin Guan, Ke Dong Fu, Bo Li, Xia Chun Yan, Bo Hong Zhang, Yan Xiao Zhang, Zhen Yong Huang, Hong Chen, Jun Yu, Bin Sheng Li
Background: The domestication of wild goats and subsequent intensive trait-driven crossing, inbreeding, and selection have led to dramatic phenotypic purification and intermediate breeds for the high-quality production of dairy, cashmere, and meat. Genomic re-sequencing provides a powerful means for the direct identification of trait-associated sequence variations that underlie molecular mechanisms of domestication. Results: Here, we report our effort to define such variations based on data from domestic goat breeds (Capra aegagrus hircus; 5 each) selected for dairy, cashmere, and meat production in referencing to their wild ancestors, the Sindh ibex (Capra aegagrus blythi; 2) and the Markhor (Capra falconeri; 2)...
August 27, 2018: GigaScience
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