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Empirical estimation of the reliability of ribosomal RNA alignments

E. A. O'Brien, D. G. Higgins
1998 Bioinformatics  
Results: We show how to use a simple jack-knife procedure to derive an estimate of the reliability that is to be expected at each position of a large alignment of eukaryotic rRNA sequences.  ...  We examine the use of empirical methods for the identification of regions of an alignment of a new sequence with an existing large alignment which can confidently be predicted to be correctly aligned.  ...  Acknowledgement This work was supported by a grant (BIO4-CT95-0130) from the EU Biotechnology programme.  ... 
doi:10.1093/bioinformatics/14.10.830 pmid:9927711 fatcat:7yj3p6xkfbh75md62h7lxyaeti

RiboDiff: Detecting Changes of Translation Efficiency from Ribosome Footprints [article]

Yi Zhong, Theofanis Karaletsos, Philipp Drewe, Vipin Thankam T Sreedharan, David Kuo, Kamini Singh, Hans-Guido Wendel, Gunnar Rätsch
2015 bioRxiv   pre-print
RiboDiff uses generalized linear models to estimate the over-dispersion of RNA-Seq and ribosome profiling measurements separately, and performs a statistical test for differential translation efficiency  ...  Motivation: Deep sequencing based ribosome footprint profiling can provide novel insights into the regulatory mechanisms of protein translation.  ...  It demonstrates the deviation of the empirical dispersion of RNA-Seq and ribosome footprint data in this experimental setting.  ... 
doi:10.1101/017111 fatcat:jm4dxiegrnasbhbw5lq6pwndge

Potential pitfalls of modelling ribosomal RNA data in phylogenetic tree reconstruction: Evidence from case studies in the Metazoa

Harald O Letsch, Karl M Kjer
2011 BMC Evolutionary Biology  
Failure to account for covariation patterns in helical regions of ribosomal RNA (rRNA) genes has the potential to misdirect the estimation of the phylogenetic signal of the data.  ...  Here, we explore the potentials of RNA substitution models and the interactions of specific model setups with the inherent pattern of covariation in rRNA stems and substitution rate variation among loop  ...  Stamatakis, Heidelberg Institute for Theoretical Studies, for comments on the implementation of RNA models in RAxML.  ... 
doi:10.1186/1471-2148-11-146 pmid:21619604 pmcid:PMC3123606 fatcat:vaeiwzqbjfduhfjhnfua3vyji4

The Impact of rRNA Secondary Structure Consideration in Alignment and Tree Reconstruction: Simulated Data and a Case Study on the Phylogeny of Hexapods

Harald O. Letsch, Patrick Kück, Roman R. Stocsits, Bernhard Misof
2010 Molecular biology and evolution  
The use of secondary structures has been advocated to improve both the alignment and the tree reconstruction processes of ribosomal RNA (rRNA) data sets.  ...  As empirical data, we used a hexapod rRNA data set to study the influence of nucleotide interdependencies in sequence alignment and tree reconstruction.  ...  Acknowledgments Thanks to Arndt von Haeseler, Karl Kjer, and an anonymous reviewer for comments and suggestions, which clearly helped to improve the manuscript. We would further like to  ... 
doi:10.1093/molbev/msq140 pmid:20530152 fatcat:mm5zxma4jvczbjnb5bisxtq57m

RiboDiff: detecting changes of mRNA translation efficiency from ribosome footprints

Yi Zhong, Theofanis Karaletsos, Philipp Drewe, Vipin T. Sreedharan, David Kuo, Kamini Singh, Hans-Guido Wendel, Gunnar Rätsch
2016 Bioinformatics  
RiboDiff uses generalized linear models to estimate the over-dispersion of RNA-Seq and ribosome profiling measurements separately, and performs a statistical test for differential translation efficiency  ...  Motivation: Deep sequencing based ribosome footprint profiling can provide novel insights into the regulatory mechanisms of protein translation.  ...  This technology can be leveraged by combining the measurements from RNA-Seq estimates in order to determine a gene's translation efficiency (TE), which is the ratio of the abundances of translated mRNA  ... 
doi:10.1093/bioinformatics/btw585 pmid:27634950 pmcid:PMC5198522 fatcat:u2db5p3usndehawqlnftgapzh4

Identification and analysis of ribosome-associated lncRNAs using ribosome profiling data

Chao Zeng, Tsukasa Fukunaga, Michiaki Hamada
2018 BMC Genomics  
Although the number of discovered long non-coding RNAs (lncRNAs) has increased dramatically, their biological roles have not been established.  ...  Many recent studies have used ribosome profiling data to assess the protein-coding capacity of lncRNAs.  ...  Efforts that focus on the identification of reliable ribosome-associated lncRNAs are insufficient.  ... 
doi:10.1186/s12864-018-4765-z pmid:29843593 pmcid:PMC5975437 fatcat:yic3mubyv5fi3i45ofpnbuewqi

Computational RNA Structure Prediction

Marc Marti-Renom, Emidio Capriotti
2008 Current Bioinformatics  
Finally, we assess the impact of the current coverage of the RNA structural space on comparative modeling RNA structures.  ...  The view of RNA as simple information transfer molecule has been continuously challenged since the discovery of ribozymes, a class of RNA molecules with enzyme-like function.  ...  RRNADIST, RRNAML and RNAML: programs for modeling empirical substitutions for Ribosomal RNA. http://www.uhnresearch.ca/labs/tillier/rRNA/rna.html.  ... 
doi:10.2174/157489308783329823 fatcat:rpo3hjt2nzgkzdgkhumwz7kmou

A statistical test for conserved RNA structure shows lack of evidence for structure in lncRNAs

Elena Rivas, Jody Clements, Sean R Eddy
2016 Nature Methods  
The first manual covariation analyses of small numbers of aligned RNA sequences used rules of thumb to infer conserved structures from a few compensatory base pair substitutions 2;6 .  ...  Many functional RNAs have an evolutionarily conserved secondary structure. Conservation of RNA base pairing induces pairwise covariations in sequence alignments.  ...  Egnor for suggesting the name R-scape, and the Centro de Ciencias de Benasque Pedro Pascual in Spain, where part of this manuscript was drafted.  ... 
doi:10.1038/nmeth.4066 pmid:27819659 pmcid:PMC5554622 fatcat:t4yf5dpcpne53iblheq4w24ky4

Accurate quantification of circular RNAs identifies extensive circular isoform switching events

Jinyang Zhang, Shuai Chen, Jingwen Yang, Fangqing Zhao
2020 Nature Communications  
By constructing pseudo-circular reference for re-alignment of RNA-seq reads and employing sophisticated statistical models to correct RNase R treatment biases, CIRIquant can provide more accurate expression  ...  We apply CIRIquant to RNA-seq datasets of hepatocellular carcinoma, and characterize two important groups of linear-circular switching and circular transcript usage switching events, which demonstrate  ...  All these RNA-seq datasets were aligned to their reference genomes and the ribosomal RNA (rRNA) sequences using HISAT2 23 to assess the mapping rate and rRNA sequence fraction.  ... 
doi:10.1038/s41467-019-13840-9 pmid:31900416 pmcid:PMC6941955 fatcat:5dwudwpqgndgvcfrz3lxww54ue

Variant ribosomal RNA alleles are conserved and exhibit tissue-specific expression

Matthew M. Parks, Chad M. Kurylo, Randall A. Dass, Linda Bojmar, David Lyden, C. Theresa Vincent, Scott C. Blanchard
2018 Science Advances  
Together with the 5S rRNA, the 18S, 5.8S, and 28S rRNAs form the RNA core of the ribosome. tRNA, transfer RNA. (B) Per-individual rDNA copy number estimation in humans, grouped by population.  ...  GC content-specific fragmentation rates l g as defined by Benjamini and Speed (36) were empirically computed for each possible GC content g = 0, …, L using all properly aligned reads on the autosomes,  ... 
doi:10.1126/sciadv.aao0665 pmid:29503865 pmcid:PMC5829973 fatcat:76mihuztuzay5gtafsrphqdxii

Post-translational buffering leads to convergent protein expression levels between primates

Sidney H. Wang, Chiaowen Joyce Hsiao, Zia Khan, Jonathan K. Pritchard
2018 Genome Biology  
Results: To gain a comprehensive view of gene regulation, we surveyed genome-wide ribosome occupancy, which reflects levels of protein translation, in lymphoblastoid cell lines derived from human, chimpanzee  ...  Inter-species divergence in transcription is generally propagated to the level of protein translation.  ...  Availability of data and materials The sequencing data supporting the conclusions of this article are available at Gene Expression Omnibus (accession number GSE71808, data uploaded on 6 Aug 2015) [67]  ... 
doi:10.1186/s13059-018-1451-z pmid:29950183 pmcid:PMC6020354 fatcat:d6w7numqozhu7iscfaq555xy5i

Assessing the measurement transfer function of single-cell RNA sequencing [article]

Hannah R. Dueck, Rizi Ai, Adrian Camarena, Bo Ding, Reymundo Dominguez, Oleg V. Evgrafov, Jian-Bing Fan, Stephen A. Fisher, Jennifer S. Herstein, Tae Kyung Kim, Jae Mun (Hugo) Kim, Ming-Yi Lin (+19 others)
2016 bioRxiv   pre-print
Methods for single-cell RNA sequencing (scRNA-seq) have received considerable attention, but the broad reliability of single cell methods and the factors governing their performance are still poorly known  ...  Measurement reliability increased with expression level for all methods and we conservatively estimate the measurement transfer functions to be linear above ~5-10 molecules.  ...  RSEM expression level estimates based on ribosomal and mitochondrial RNA depleted samples were used as "truth" throughout.  ... 
doi:10.1101/045450 fatcat:dutpbu2zojcg5mpnpw3ajhsk5i

Assessing characteristics of RNA amplification methods for single cell RNA sequencing

Hannah R. Dueck, Rizi Ai, Adrian Camarena, Bo Ding, Reymundo Dominguez, Oleg V. Evgrafov, Jian-Bing Fan, Stephen A. Fisher, Jennifer S. Herstein, Tae Kyung Kim, Jae Mun Kim, Ming-Yi Lin (+19 others)
2016 BMC Genomics  
Methods for single-cell RNA sequencing (scRNA-seq) have received considerable attention, but the broad reliability of single cell methods and the factors governing their performance are still poorly known  ...  Measurement reliability increased with expression level for all methods and we conservatively estimate measurements to be quantitative at an expression level greater than~5-10 molecules.  ...  Accuracy and robustness of expression estimates across library preparation methods: ribosomal-depletion (combined n = 3 samples per HBR and UHR) and poly-A RNA selection (combined n = 4 samples per source  ... 
doi:10.1186/s12864-016-3300-3 pmid:27881084 pmcid:PMC5122016 fatcat:luwxeg2ni5gzjbnphoq7vewiym

Advantages and disadvantages of molecular phylogenetics: a case study of ascaridoid nematodes

S A Nadler
1995 Journal of nematology  
Based on partial ribosomal RNA sequences, tree topologies inconsistent with monophyly of the Ascaridinae were significantly worse by maximum likelihood inference.  ...  Statistical methods for comparing phylogenetic hypotheses have been used to assess the reliability of alternative trees for ascaridoid nematodes.  ...  By contrast, partial sequences of 18S and 28S ribosomal RNA have been shown to have utility for estimating phylogenetic relationships for representative ascaridoid taxa (18) .  ... 
pmid:19277308 pmcid:PMC2619635 fatcat:d2ydq7d4tvc73eikz4fkqkmvva

Post-transcriptional regulation across human tissues [article]

Alexander Franks, Edoardo Airoldi, Nikolai Slavov
2015 bioRxiv   pre-print
The reliable quantification of the latter estimate is limited by substantial measurement noise.  ...  Estimates of the factors determining protein levels in human tissues do not distinguish between (i) the factors determining the variability between the abundances of different proteins, i.e., mean-level-variability  ...  The reliability of RNA and protein are estimated as the correlations between estimates from different datasets.  ... 
doi:10.1101/020206 fatcat:rkreuvsukrhxre35pse65pc4fy
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