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Neutral network sizes of biological RNA molecules can be computed and are not atypically small
2008
BMC Bioinformatics
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We apply our method to the genotype-to-phenotype mapping of RNA molecules, and show that it can reliably measure neutral set sizes for molecules up to 100 bases. ...
Conclusions: The biological RNA structures we examined are more abundant than random structures. ...
Why are structures of biological molecules not atypically rare? ...
doi:10.1186/1471-2105-9-464
pmid:18973652
pmcid:PMC2639431
fatcat:ok34myaxyjd2nl5e2pkcpjomh4
QUANTIFYING SLOW EVOLUTIONARY DYNAMICS IN RNA FITNESS LANDSCAPES
2010
Journal of Bioinformatics and Computational Biology
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We re-examine the evolutionary dynamics of RNA secondary structures under directional selection towards an optimum RNA structure. ...
In addition, our study of the trajectories shows that the out-of-equilibrium effects due to the evolutionary process are very weak. ...
RNA structure and its fitness landscape For the purpose of this study, RNA molecules will be thought of as chains or strings of L nucleotides, taken from an alphabet of four possible nucleotides (A, C, ...
doi:10.1142/s0219720010005075
pmid:21121025
fatcat:nzchlzgshnh6xnarjmraixhl54
Evolvability and robustness in a complex signalling circuit
2011
Molecular Biosystems
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Two genotypes are neighbours in genotype space if they can be reached from each other by a single small genetic change. ...
Two genotypes are neighbours in genotype space if they can be reached from each other by a single small genetic change. ...
AW acknowledges support through Swiss National Science Foundation grants 315200-116814, 315200-119697, and 315230-129708. AW and KR are grateful for support through the YeastX project of SystemsX.ch. ...
doi:10.1039/c0mb00165a
pmid:21225054
fatcat:peklpfrksngilmmi64eh2baywu
Prebiotic Pathway from Ribose to RNA Formation
2021
International Journal of Molecular Sciences
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RNA could have come into being without the involvement of nucleotide precursors. ...
No satisfactory explanation was provided as to the missing link between the prebiotic synthesis of ribose and prebiotic RNA (preRNA). ...
Alternatively, RNA aptamers are supposed to control gene expression in response to small molecules in mammalian cells. ...
doi:10.3390/ijms22083857
pmid:33917807
fatcat:si2hbprorvfpniowmbxogfygvu
Molecular Dynamics and Quantum Mechanics of RNA: Conformational and Chemical Change We Can Believe In
2010
Accounts of Chemical Research
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The performance of force fields can be estimated by precise QM calculations on small model systems. Such calculations agree reasonably well with the Cornell et al. ...
Numerous techniques can elucidate the structural dynamics of RNA, but computational approaches based on experimental data arguably hold the promise of providing the most detail. ...
, counterions, and individual water molecules in imparting biological function to RNA. ...
doi:10.1021/ar900093g
pmid:19754142
pmcid:PMC2808146
fatcat:iigla6xdbngnrl3kihpzznisr4
Emergence of Hierarchical Modularity in Evolving Networks Uncovered by Phylogenomic Analysis
2019
Evolutionary Bioinformatics
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Remarkably, phylogenomic analyses uncover this emergence in the rewiring of metabolomic and transcriptome-informed metabolic networks, the nanosecond dynamics of proteins, and evolving networks of metabolism ...
In the first phase, parts are at first weakly linked and associate variously. As they diversify, they compete with each other and are often selected for performance. ...
As expected, the 7 RNA families that are universal include functional RNA that is known to be very ancient, including ribosomal RNA (rRNA) and transfer RNA (tRNA) molecules. ...
doi:10.1177/1176934319872980
pmid:31523127
pmcid:PMC6728656
fatcat:pundw72czjfwhc6gv2wnxktdvq
Experimental design and quantitative analysis of microbial community multiomics
2017
Genome Biology
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distribution patterns can be challenging when sample size is limited and/or signal is weak. ...
First, special care should be taken when applying any methods to small sample sizes (e.g., < 50) [98] . ...
• We accept pre-submission inquiries • Our selector tool helps you to find the most relevant journal Submit your next manuscript to BioMed Central and we will help you at every step: ...
doi:10.1186/s13059-017-1359-z
pmid:29187204
pmcid:PMC5708111
fatcat:vyhlrx5ejjflxoaxrp5i2heh4e
The role of noncoding RNAs in Parkinson's disease: biomarkers and associations with pathogenic pathways
2021
Journal of Biomedical Science
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AbstractThe discovery of various noncoding RNAs (ncRNAs) and their biological implications is a growing area in cell biology. ...
Increasing evidence has revealed canonical and noncanonical functions of long and small ncRNAs, including microRNAs, long ncRNAs (lncRNAs), circular RNAs, PIWI-interacting RNAs, and tRNA-derived fragments ...
With a mixture of small RNAs, since miRNAs (19-25 nt), piRNAs (25-31 nt) , and tRFs (14-36 nt) are all similar in size, they cannot be easily distinguished by examining their sizes. ...
doi:10.1186/s12929-021-00775-x
pmid:34794432
pmcid:PMC8603508
fatcat:nsrssgh7pfae3keg6j5e3zk3tu
Vision from next generation sequencing: Multi-dimensional genome-wide analysis for producing gene regulatory networks underlying retinal development, aging and disease
2015
Progress in retinal and eye research
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Computational biology and computational medicine are no longer intellectual domains of the chosen few. ...
We should emphasize that basic strategies for network construction and analyses can be transported to any tissue or cell type. ...
Acknowledgments We are grateful to Vijender Chaitanker for designing one of the figures and thank N-NRL colleagues, especially Alexis Boleda, Matthew Brooks, Linn Gieser, Koray Kaya, and Soo-Young Kim ...
doi:10.1016/j.preteyeres.2015.01.005
pmid:25668385
pmcid:PMC4402139
fatcat:4xzwqp3jorckxcsbp7pku3b7uu
Self-Referential Formation of the Genetic System
[chapter]
2008
Biosemiotics
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In one direction, proteins that are resistant to degradation and efficient RNA-binders stabilize the tRNAs that are specifically involved with their production; in the other direction, these tRNAs become ...
It is indicated that: (a) The Last Universal Common Ancestor populations could, at some early stages, be composed of lineages bearing similar genetic codes, due to the simple and highly deterministic character ...
The secondary structures are more varied in proteins, due to the small size and the diversity of amino acids. ...
doi:10.1007/978-1-4020-6340-4_5
fatcat:m737nov2ybdhhlnbkbehpbobyu
Beyond Mg 2+ : functional interactions between RNA and transition metals
2016
Current Opinion in Chemical Biology
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Novel reports that RNA can host Fe(II) in catalytic sites are relevant to early life in pre-oxygenic atmospheres. ...
It is well-known that RNA structure and function depend heavily on cations, and the ability of Mg 2+ to stabilize RNA structures has been emphasized. ...
Acknowledgements Work in the DeRose laboratory on Pt-RNA interactions is supported by the National Science Foundation (CHE-1153147 to VJD). ...
doi:10.1016/j.cbpa.2016.07.017
pmid:27616014
fatcat:vshk42xzcjftdeh4fbhkktwob4
Beyond Mg 2+ : functional interactions between RNA and transition metals
2016
Current Opinion in Chemical Biology
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Novel reports that RNA can host Fe(II) in catalytic sites are relevant to early life in pre-oxygenic atmospheres. ...
It is well-known that RNA structure and function depend heavily on cations, and the ability of Mg 2+ to stabilize RNA structures has been emphasized. ...
Acknowledgements Work in the DeRose laboratory on Pt-RNA interactions is supported by the National Science Foundation (CHE-1153147 to VJD). ...
doi:10.1016/j.cbpa.2016.02.015
pmid:27031926
fatcat:im2z53iatjb7dehzym6carz56i
Neutral evolution of model proteins: diffusion in sequence space and overdispersion
[article]
1998
arXiv
pre-print
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We prove the existence of extended neutral networks in sequence space -- sequences can evolve until their similarity with the starting point is almost the same as for random sequences. ...
This result is in contrast with the simplest model of neutral evolution, which assumes a Poisson process for substitutions, and in qualitative agreement with biological data. ...
Part of the work was made during the Euroconference on "Protein Folding and Structure Prediction" organized at the ISI Foundation, Torino, Italy, June [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [ ...
arXiv:cond-mat/9811267v1
fatcat:zzh6gd3fznaaxpqgdpvcpa4ebq
Ranking viruses: measures of positional importance within networks define core viruses for rational polyvalent vaccine development
2012
Computer applications in the biosciences : CABIOS
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Conclusion: Our approach relies on the network structure of PRRSV but applies to any diverse RNA virus because it identifies subsets of viral variants that are most important to overall viral diversity ...
No single viral variant can induce sufficiently broad immunity, and incorporating all known naturally circulating variants into one multivalent vaccine is not feasible. ...
Although existing computational methods to account for viral diversity are powerful when investigating small numbers of sequences, the size of potential tree space and computational complexity increases ...
doi:10.1093/bioinformatics/bts181
pmid:22495748
fatcat:t33iasruerehta5fvtehl66m2a
Structurally constrained protein evolution: results from a lattice simulation
2000
European Physical Journal B : Condensed Matter Physics
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2000 accepted arXiv:cond-mat/9912331v2 fatcat:tklcegwshrap7j7gavbjmq3pd4Other Versions
Typical pairs of sequences on a neutral network are nearly as different as randomly chosen sequences. ...
Thus we tentatively conjecture that neutral networks of different structures are typically well separated in sequence space. ...
Part of the work was made during the Euroconference on "Protein Folding and Structure Prediction" organized at the ISI Foundation, Torino, Italy, June [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [ ...
doi:10.1007/s100510051140
fatcat:6yk3axvu3bc4zela4quzqs2fhm
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