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Positional correlation analysis improves reconstruction of full-length transcripts and alternative isoforms from noisy array signals or short reads

Shuji Kawaguchi, Kei Iida, Erimi Harada, Kousuke Hanada, Akihiro Matsui, Masanori Okamoto, Kazuo Shinozaki, Motoaki Seki, Tetsuro Toyoda
2012 Computer applications in the biosciences : CABIOS  
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

Ana Conesa, Pedro Madrigal, Sonia Tarazona, David Gomez-Cabrero, Alejandra Cervera, Andrew McPherson, Michał Wojciech Szcześniak, Daniel J. Gaffney, Laura L. Elo, Xuegong Zhang, Ali Mortazavi
2016 Genome Biology  
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]

Rachael E Workman, Alison Tang, Paul S. Tang, Miten Jain, John R Tyson, Philip C Zuzarte, Timothy Gilpatrick, Roham Razaghi, Joshua Quick, Norah Sadowski, Nadine Holmes, Jaqueline Goes de Jesus (+10 others)
2018 bioRxiv   pre-print
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

Jacek Majewski, Tomi Pastinen
2011 Trends in Genetics  
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

Sam Kovaka, Aleksey V. Zimin, Geo M. Pertea, Roham Razaghi, Steven L. Salzberg, Mihaela Pertea
2019 Genome Biology  
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]

Adrian Viehweger, Sebastian Krautwurst, Kevin Lamkiewicz, Ramakanth Madhugiri, John Ziebuhr, Martin Hölzer, Manja Marz
2018 bioRxiv   pre-print
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

Adrian Viehweger, Sebastian Krautwurst, Kevin Lamkiewicz, Ramakanth Madhugiri, John Ziebuhr, Martin Hölzer, Manja Marz
2019 Genome Research  
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]

Sam Kovaka, Aleksey V Zimin, Geo M Pertea, Roham Razaghi, Steven L Salzberg, Mihaela Pertea
2019 bioRxiv   pre-print
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

Bonnie Berger, Jian Peng, Mona Singh
2013 Nature reviews genetics  
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

Sharon Aviran, Lior Pachter
2014 RNA: A publication of the RNA Society  
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

Jean-Benoît Lalanne, James C. Taggart, Monica S. Guo, Lydia Herzel, Ariel Schieler, Gene-Wei Li
2018 Cell  
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

Jongwon Lee, Minsu Yoo, Jungmin Choi
2022 BMB Reports  
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

Angela R. Wu, Jianbin Wang, Aaron M. Streets, Yanyi Huang
2017 Annual Review of Analytical Chemistry  
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

Miten Jain, Sergey Koren, Karen H Miga, Josh Quick, Arthur C Rand, Thomas A Sasani, John R Tyson, Andrew D Beggs, Alexander T Dilthey, Ian T Fiddes, Sunir Malla, Hannah Marriott (+14 others)
2018 Nature Biotechnology  
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

Mark R Emmett, Roger A Kroes, Joseph R Moskal, Charles A Conrad, Waldemar Priebe, Fernanda Laezza, Anke Meyer-Baese, Carol L Nilsson
2013 Neuropsychopharmacology  
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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