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Neutral network sizes of biological RNA molecules can be computed and are not atypically small

Thomas Jörg, Olivier C Martin, Andreas Wagner
2008 BMC Bioinformatics  
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

PETR ŠULC, ANDREAS WAGNER, OLIVIER C. MARTIN
2010 Journal of Bioinformatics and Computational Biology  
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

Karthik Raman, Andreas Wagner
2011 Molecular Biosystems  
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

Gaspar Banfalvi
2021 International Journal of Molecular Sciences  
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

Mark A. Ditzler, Michal Otyepka, Jiřì Šponer, Nils G. Walter
2010 Accounts of Chemical Research  
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

Gustavo Caetano-Anollés, M Fayez Aziz, Fizza Mughal, Frauke Gräter, Ibrahim Koç, Kelsey Caetano-Anollés, Derek Caetano-Anollés
2019 Evolutionary Bioinformatics  
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

Himel Mallick, Siyuan Ma, Eric A. Franzosa, Tommi Vatanen, Xochitl C. Morgan, Curtis Huttenhower
2017 Genome Biology  
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

Ming-Che Kuo, Sam Chi-Hao Liu, Ya-Fang Hsu, Ruey-Meei Wu
2021 Journal of Biomedical Science  
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

Hyun-Jin Yang, Rinki Ratnapriya, Tiziana Cogliati, Jung-Woong Kim, Anand Swaroop
2015 Progress in retinal and eye research  
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]

Romeu Cardoso Guimarães, Carlos Henrique Costa Moreira, Sávio Torres de Farias
2008 Biosemiotics  
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

Adam M Saunders, Victoria J DeRose
2016 Current Opinion in Chemical Biology  
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

Adam M Saunders, Victoria J DeRose
2016 Current Opinion in Chemical Biology  
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]

Ugo Bastolla, Michele Vendruscolo
1998 arXiv   pre-print
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

Tavis K. Anderson, William W. Laegreid, Francesco Cerutti, Fernando A. Osorio, Eric A. Nelson, Jane Christopher-Hennings, Tony L. Goldberg
2012 Computer applications in the biosciences : CABIOS  
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

U. Bastolla, M. Vendruscolo, H.E. Roman
2000 European Physical Journal B : Condensed Matter Physics  
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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