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Research Highlights

John Doe
2015 The Plant Genome  
These methods can be used successfully to characterize and select events but do not provide sequence-level information or take advantage of the significant advances in the next-generation sequencing (NGS  ...  Hovav et al. performed global gene expression analyses of cotton seed development using next generation sequencing and four developmental time-points.  ... 
doi:10.3835/plantgenome2015.10.0001rh pmid:33228283 fatcat:nwvs7feltfgwlgbewpirwi5w74

AnsNGS: An Annotation System to Sequence Variations of Next Generation Sequencing Data for Disease-Related Phenotypes

Young-Ji Na, Yonglae Cho, Ju Han Kim
2013 Healthcare Informatics Research  
AnsNGS (annotation system of sequence variations for next generation sequencing data) is a new tool for annotating detected variants using disease-associated variants. II.  ...  NGS: next-generation sequencing.  ... 
doi:10.4258/hir.2013.19.1.50 pmid:23626918 pmcid:PMC3633172 fatcat:lcpo3iptx5hetmojftlmgq76h4

Fast-evolving microRNAs are highly expressed in the early embryo of Drosophila virilis

M. Ninova, M. Ronshaugen, S. Griffiths-Jones
2014 RNA: A publication of the RNA Society  
We then generated small RNA sequencing data sets covering D. virilis development and explored the relationship between microRNA conservation and expression in a developmental context.  ...  We determined the evolutionary origins of extant Drosophila microRNAs and estimated the sequence divergence between the 130 orthologous microRNAs in Drosophila melanogaster and Drosophila virilis, separated  ...  MicroRNA sequence divergence and evolutionary age D. melanogaster microRNA sequences from miRBase (v18) were used as a query for sequence similarity searches using BLASTN (w = 4, r = 2, q = −3, e = 0.01  ... 
doi:10.1261/rna.041657.113 pmid:24448446 pmcid:PMC3923130 fatcat:zht6crvzdne4xdv7u6euc7m2ry

Evolutionary flux of canonical microRNAs and mirtrons in Drosophila

Eugene Berezikov, Na Liu, Alex S Flynt, Emily Hodges, Michelle Rooks, Gregory J Hannon, Eric C Lai
2010 Nature Genetics  
They also showed that partially methylated domains (PMDs), in evolutionary flux of canonical micrornAs and mirtrons in Drosophila To the Editor: Next-generation sequencing technologies generate vast catalogs  ...  We instead identified a distinct and smaller set of new miRNAs supported by high-confidence cloning signatures, which included a high proportion of evolutionarily nascent mirtrons.  ...  They also showed that partially methylated domains (PMDs), in evolutionary flux of canonical micrornAs and mirtrons in Drosophila To the Editor: Next-generation sequencing technologies generate vast  ... 
doi:10.1038/ng0110-6 pmid:20037610 pmcid:PMC4136759 fatcat:b2gbnjgqcraxdg56xgdvsmuk6a

Unlimited Thirst for Genome Sequencing, Data Interpretation, and Database Usage in Genomic Era: The Road towards Fast-Track Crop Plant Improvement

Arun Prabhu Dhanapal, Mahalingam Govindaraj
2015 Genetics Research International  
The number of sequenced crop genomes and associated genomic resources is growing rapidly with the advent of inexpensive next generation sequencing methods.  ...  The databases and associated web portals provide at a minimum a uniform set of tools and automated analysis across a wide range of crop plant genomes.  ...  Advancement in next-generation sequencing (NGS) technology coupled with many reference genomes sequence data allows us to discover variations among many crop plants.  ... 
doi:10.1155/2015/684321 pmid:25874133 pmcid:PMC4383144 fatcat:kl7tgs6zx5dy7cyy2tisqfmjxi

Identification and Characterization of Microsatellite Loci in Maqui (Aristotelia chilensis [Molina] Stunz) Using Next-Generation Sequencing (NGS)

Adriana Bastías, Francisco Correa, Pamela Rojas, Rubén Almada, Carlos Muñoz, Boris Sagredo, Yuepeng Han
2016 PLoS ONE  
This results, including partial sequences of genes, some miRNAs and SSR markers from high throughput next generation sequencing (NGS) of maqui genomic DNA, constitute the first platform to undertake genetic  ...  Reads were assembled into 4,832 contigs, while 98,546 reads remained as singletons, generating a total of 103,378 consensus genomic sequences. A total of 24,494 SSR maqui markers were identified.  ...  Acknowledgments Thanks to CONAF and the staff of the Río Los Cipreses National Reserve, as well as A. Lara and R. Contreras for help in sampling.  ... 
doi:10.1371/journal.pone.0159825 pmid:27459734 pmcid:PMC4961369 fatcat:3gpdqorzcvcwhi2trlfqd7r634

Insect phylogenomics

S. K. Behura
2015 Insect molecular biology (Print)  
With the advent of next-generation sequencing methods, phylogenetics has taken a new turn in the recent years.  ...  The next-generation sequencing methods are now increasingly used by entomologists to generate genomic and transcript sequences of various insect species and strains.  ...  Acknowledgments My effort to prepare this article was partly supported by a grant (R21 AI101345-A1) from National Institutes of Health (NIH), USA.  ... 
doi:10.1111/imb.12174 pmid:25963452 pmcid:PMC4503476 fatcat:hvwuete53bc57az5wnjjsf6h2q

Bichir microRNA repertoire suggests a ray-finned fish affinity of Polypteriforme

Liandong Yang, Zhaolei Zhang, Shunping He
2015 Gene  
In this study, we applied a third independent source of datasets, the presence versus absence of microRNAs, to re-investigate the phylogenetic relationship of bichirs.  ...  Through deep sequencing of small RNA library, we showed that bichirs should be grouped into ray-finned fishes rather than lobe-finned fishes.  ...  Acknowledgments We are grateful to Zaixuan Zhong and Lihong Guan for their help with the experiments and Weitao Chen for his help in using BEAST.  ... 
doi:10.1016/j.gene.2015.04.058 pmid:25917619 fatcat:y5cfc3utrncwvjo5lfzdvjifce

Genomics - from Neanderthals to high-throughput sequencing

Matthew John Wakefield
2006 Genome Biology  
After a long incubation, the first effects of the next-generation sequencing platforms are now being felt. Two new high-throughput platforms for ultrarapid DNA sequencing were in evidence.  ...  Next-generation DNA sequencing Genomics is still driven and directed by advancements and limitations of sequencing technology.  ... 
doi:10.1186/gb-2006-7-8-326 pmid:16934106 pmcid:PMC1779599 fatcat:7423lsghdne3dmfu2llzu4avfe

Non-coding yet non-trivial: a review on the computational genomics of lincRNAs

Travers Ching, Jayson Masaki, Jason Weirather, Lana X. Garmire
2015 BioData Mining  
Thanks to next generation sequencing (NGS) technology and its applications, we have recently witnessed a surge in non-coding RNA research, including lincRNA research.  ...  Some of these challenges have been addressed by the revolutionary inventions of next generation sequencing (NGS) and its applications, such as RNA-Seq, which captures whole transcriptome data, including  ...  Downstream target prediction through directed graphs Reverse engineering of gene regulatory networks has been an area of research before the explosion of next generation sequencing and lincRNA research  ... 
doi:10.1186/s13040-015-0075-z pmid:26697116 pmcid:PMC4687140 fatcat:6adlfaqsuzblri4w66mqrdl6rq

Editorial: Genetics, Evolution, and Conservation of Neotropical Fishes

Rodrigo Augusto Torres, Roberto Ferreira Artoni
2019 Frontiers in Genetics  
While a good beginning, bioinformatics use in the selection of satellite DNA markers and their chromosome localization is still growing (Utsunomia et al.) .  ...  With integration of cytogenetics and molecular markers, a new cycle of methodological developments has come to pass, especially with the inclusion of dates that became available through massive sequencing  ...  No use, distribution or reproduction is permitted which does not comply with these terms.  ... 
doi:10.3389/fgene.2019.01124 pmid:31749844 pmcid:PMC6844201 fatcat:hvwlyc2lcjd5hlb66hqc6wb5qe

Classification of Precursor MicroRNAs from Different Species Based on K-mer Distance Features

Malik Yousef, Jens Allmer
2021 Algorithms  
With this line of research, we support the differentiation between true and false miRNAs detected from next-generation sequencing data, provide an additional viewpoint for confirming miRNAs when the species  ...  of origin is known, and open up a new strategy for analyzing miRNA evolution.  ...  Availability and Implementation: We performed all analysis using the KNIME platform and have made the analysis workflow available at GitHub: https://github.com/malikyousef/microRNAsbased-on-K-mer-Distance-Features  ... 
doi:10.3390/a14050132 doaj:ef01af41922545cc878e3a182b36b050 fatcat:74ejw4ia7faxfgcduorginrige

The singing genome

H Ellegren
2010 Heredity  
Genome sequencing is now gradually turning to assemblies based on next-generation sequencing (NGS) technology.  ...  Zebra finch genome sequencing was done in the 'standard way', using Sanger technology and by integrating sequence assembly data and information on the physical map via BAC clones.  ... 
doi:10.1038/hdy.2010.109 pmid:20823906 pmcid:PMC3183893 fatcat:ue2efao7hrd3dfe545nzmspdha

An overview of wheat genome sequencing and its implications for crop improvement

MEHANATHAN MUTHAMILARASAN, MANOJ PRASAD
2014 Journal of Genetics  
Muthamilarasan M. and Prasad M. 2014 An overview of wheat genome sequencing and its implication for crop improvement. J. Genet. 93, 619-622]  ...  Acknowledgement Mehanathan Muthamilarasan acknowledges University Grants Commission, New Delhi, India for providing Research Fellowship.  ...  , predicting novel useful haplotypes and also facilitate the development of allele-specific markers for use in marker-assisted selection.  ... 
doi:10.1007/s12041-014-0455-z pmid:25572220 fatcat:k5h3ljecujhibmy2rzw6jxzhbu

Signatures of genetic variation in human microRNAs point to processes of positive selection related to population-specific disease risks [article]

Pablo Villegas Mirón, Alicia Gallego, Jaume Bertranpetit, Hafid Laayouni, Yolanda Espinosa-Parrilla
2021 bioRxiv   pre-print
We show by means of the in silico analysis of noncoding variation of microRNAs that the level of evolutionary constraint of these sequences is governed by the interplay of different factors, like their  ...  a pattern of higher genetic diversity that appears to be caused by the dramatic frequency shifts of a fraction of human microRNAs.  ...  selection that generate frequency shifts at population level.  ... 
doi:10.1101/2021.05.24.445417 fatcat:zs4sxmoh25hubavrqmlwkwd74u
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