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Positional correlation analysis improves reconstruction of full-length transcripts and alternative isoforms from noisy array signals or short reads
2012
Computer applications in the biosciences : CABIOS
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Motivation: A reconstruction of full-length transcripts observed by next-generation sequencer or tiling arrays is an essential technique to know all phenomena of transcriptomes. ...
Moreover, the positional correlation and factor analysis embedded in ARTADE2 successfully detected regions at which alternative isoforms may exist, and thus are expected to be applied for discovering transcript ...
ACKNOWLEDGEMENTS We thank Junko Ishida, Maho Tanaka and Taeko Morosawa for the collection of tiling array experimental data of Arabidopsis. ...
doi:10.1093/bioinformatics/bts065
pmid:22332235
pmcid:PMC3315713
fatcat:fruzyipjgvhyxhgnwawvaghx2m
A survey of best practices for RNA-seq data analysis
2016
Genome Biology
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We review all of the major steps in RNA-seq data analysis, including experimental design, quality control, read alignment, quantification of gene and transcript levels, visualization, differential gene ...
expression, alternative splicing, functional analysis, gene fusion detection and eQTL mapping. ...
Research in PM's laboratory is supported by ERC starting grant Relieve-IMDs and by a core support grant from the Wellcome Trust and MRC to the Wellcome Trust-Medical Research Council Cambridge Stem Cell ...
doi:10.1186/s13059-016-0881-8
pmid:26813401
pmcid:PMC4728800
fatcat:pidog3wat5fgzirqpjxfd5nnta
Nanopore native RNA sequencing of a human poly(A) transcriptome
[article]
2018
bioRxiv
pre-print
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These native RNA sequence reads had an N50 length of 1334 bases, and a maximum length of 22,000 bases. ...
A total of 78,199 high-confidence isoforms were identified by combining long nanopore reads with short higher accuracy Illumina reads. Among these isoforms, over 50% are not present in GENCODE v24. ...
Daniel Garalde (ONT) provided early advice on use of the MinION for RNA sequencing. Nicholas Conrad gave insight into the correlation of intron retention and poly(A) tail length. ...
doi:10.1101/459529
fatcat:tducdoth5bhzpmxcttslrt2gxe
The study of eQTL variations by RNA-seq: from SNPs to phenotypes
2011
Trends in Genetics
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Several groups made inroads into the genomic analysis of splicing using exon arrays [21, 83] ; however, the analysis was complicated and the results noisy due to the limitations imposed by small probe ...
Paired-end reads: NGS targets are generally short sheared DNA fragments that can be sequenced from one or both ends of the fragment. ...
doi:10.1016/j.tig.2010.10.006
pmid:21122937
fatcat:quwu377pebdpvdrydmttwu3ehi
Transcriptome assembly from long-read RNA-seq alignments with StringTie2
2019
Genome Biology
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StringTie2 includes new methods to handle the high error rate of long reads and offers the ability to work with full-length super-reads assembled from short reads, which further improves the quality of ...
StringTie2 is more accurate and faster and uses less memory than all comparable short-read and long-read analysis tools. ...
Peer review information Barbara Cheifet was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team. ...
doi:10.1186/s13059-019-1910-1
pmid:31842956
pmcid:PMC6912988
fatcat:y236cn7ijjh4zpfdm7ekb456ii
Nanopore direct RNA sequencing reveals modification in full-length coronavirus genomes:
[article]
2018
bioRxiv
pre-print
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Although standard (short-read) sequencing technologies allow to readily determine consensus sequences for these quasispecies, it is far more difficult to reconstruct large numbers of full-length haplotypes ...
We also show how supplementary short-read sequencing (Illumina) can be used to reduce the error rate of nanopore sequencing. ...
We thank Ivonne Görlich and Marco Groth from the Core Facility DNA sequencing of the Leibniz Institute on Aging -Fritz Lipmann Institute in Jena for their help with Illumina sequencing. ...
doi:10.1101/483693
fatcat:esgv4gzzizdghifecxaf5menau
Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis
2019
Genome Research
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Standard (short-read) sequencing technologies are ill-suited to reconstruct large numbers of full-length haplotypes of (1) RNA virus genomes and (2) subgenome-length (sg) RNAs composed of noncontiguous ...
Also, the DRS approach, which circumvents reverse transcription and amplification of RNA, allowed us to detect methylation sites in viral RNAs. ...
We thank Ivonne Görlich and Marco Groth from the Core Facility DNA sequencing of the Leibniz Institute on Aging-Fritz Lipmann Institute in Jena for their help with Illumina sequencing. ...
doi:10.1101/gr.247064.118
pmid:31439691
pmcid:PMC6724671
fatcat:4tt5y2tpyvakfbbkdap4ggx5da
Transcriptome assembly from long-read RNA-seq alignments with StringTie2
[article]
2019
bioRxiv
pre-print
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It also offers the ability to work with full-length super-reads assembled from short reads, which further improves the quality of assemblies. ...
On 33 short-read datasets from humans and two plant species, StringTie2 is 47.3% more precise and 3.9% more sensitive than Scallop. ...
The "full length" and "not full length" PacBio
from Griebel, Zacher et al. 2012. ...
doi:10.1101/694554
fatcat:cco4k6bgpvhoxgdazhcw2mmll4
Computational solutions for omics data
2013
Nature reviews genetics
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Finally, efficient means for storing, searching and retrieving data are of foremost concern as they are necessary for any analysis to proceed. ...
Several software platforms and database systems have been developed for basic data analysis and integration 1-3 (BOX 1). ...
Acknowledgments The authors thank and L. Cowen for valuable feedback. B.B. thanks the US National Institutes of Health (NIH) for grant GM081871. ...
doi:10.1038/nrg3433
pmid:23594911
pmcid:PMC3966295
fatcat:b7n6xwzyc5gqzo7plgyoe257iq
Rational experiment design for sequencing-based RNA structure mapping
2014
RNA: A publication of the RNA Society
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Modifications are assayed via cDNA fragment analysis, using electrophoresis or next-generation sequencing (NGS). ...
and digital nature of NGS readouts. ...
This work is supported by National Institutes of Health (NIH) grants R00 HG006860 to S.A. and R01 HG006129 to L.P. Received December 8, 2013; accepted September 7, 2014. ...
doi:10.1261/rna.043844.113
pmid:25332375
pmcid:PMC4238353
fatcat:zkc7qukoxvbk5mndy3k5dze5cm
Evolutionary Convergence of Pathway-Specific Enzyme Expression Stoichiometry
2018
Cell
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Coexpression of proteins in response to pathway-inducing signals is the founding paradigm of gene regulation. ...
and architectures via remodeling of internal promoters and terminators. ...
Acknowledgments We thank BM Koo for providing B. subtilis single-gene deletion strains; M Laub, J Elf, and members of the GWL and A Grossman labs for discussions; A Amon, D Bartel, and V Siegel for comments ...
doi:10.1016/j.cell.2018.03.007
pmid:29606352
pmcid:PMC5978003
fatcat:upsrlxvf3zbwdhv47wu2udct2u
Recent advances in spatially resolved transcriptomics: challenges and opportunities
2022
BMB Reports
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However, cell dissociation from the tissue structure causes a loss of spatial information, which hinders the identification of intercellular communication networks and global transcriptional patterns present ...
In this review, we focus on the current state-of-the-art spatially resolved transcriptomic technologies, describe their applications in a variety of biological domains, and explore recent discoveries demonstrating ...
ACKNOWLEDGEMENTS The authors are grateful to Junho Song for critical reading of Trends in spatially resolved transcriptomics Jongwon Lee, et al. ...
doi:10.5483/bmbrep.2022.55.3.014
fatcat:jqiqjm7t2zftjofajn2hmdgnxq
Single-Cell Transcriptional Analysis
2017
Annual Review of Analytical Chemistry
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Consequently, this has fueled a virtuous cycle of even greater interest in the field and compelled development of further improved technical methodologies and approaches. ...
Despite being a relatively recent technological development, single-cell transcriptional analysis through high-throughput sequencing has already been used in hundreds of fruitful studies to make exciting ...
of transcript isoforms by alternative splicing. ...
doi:10.1146/annurev-anchem-061516-045228
pmid:28301747
fatcat:u3msit2eg5d6hlkhg43dao3tae
Nanopore sequencing and assembly of a human genome with ultra-long reads
2018
Nature Biotechnology
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This has necessitated development of de novo assembly algorithms and the use of long noisy data in conjunction with accurate short reads to produce high-quality reference genomes 10 . ...
We report sequencing and assembly of a reference human genome for GM12878 from the Utah/CEPH pedigree, using MinION R9.4 1D chemistry, including ultra-long reads up to 882 kb in length. ...
Akeson for his support and insight. We thank R. Poplawski and S. Thompson for technical assistance with configuring and using cloud-based file systems with millions of files on CLIMB. We thank W. ...
doi:10.1038/nbt.4060
pmid:29431738
pmcid:PMC5889714
fatcat:i7xbwk2smzeg3kj4ft6c6o5rmy
Integrative Biological Analysis For Neuropsychopharmacology
2013
Neuropsychopharmacology
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The brain is the most complex part of human anatomy from the standpoint of number and types of cells, their interconnections, and circuitry. ...
Published applications of an integrated approach to projects of neurological, psychiatric, and pharmacological natures are still few but show promise to provide deep biological knowledge derived from cells ...
Unbiased sequence methods can detect novel transcripts, alternatively spliced isoforms, SNPs, and fusion transcript, again in the absence of genome annotation. ...
doi:10.1038/npp.2013.156
pmid:23800968
pmcid:PMC3857644
fatcat:pkdind2ornd5zdazn2t76hwa5q
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