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Complete probabilistic analysis of RNA shapes

Björn Voss, Robert Giegerich, Marc Rehmsmeier
2006 BMC Biology  
From these results, and the fact that we use a complete and exact analysis of the folding space, we conclude that this approach opens up new and promising routes for investigating and understanding RNA  ...  An in-depth analysis of the folding space as a whole appeared necessary to deduce the structural properties of a given RNA molecule reliably.  ...  Acknowledgements The authors thank an anonymous reviewer for pointing out the mathematical reason for the sequence length independence of the sample size M.  ... 
doi:10.1186/1741-7007-4-5 pmid:16480488 pmcid:PMC1479382 fatcat:m4n2c6ltazgdxlhait6bn7qmxy

Probabilistic Methods in Cancer Biology

Mathukumalli Vidyasagar
2011 European Journal of Control  
gene regulatory networks, analyzing the significance of expression levels for collections of genes, and discriminating between drivers (mutations that cause cancer) and passengers (mutations that are  ...  For persons trained in control theory, there is now a significant opportunity to work with biologists to create a virtuous cycle of hypothesis generation and experimental validation.  ...  I would also like to thank Tamer Başar, Aniruddha Datta, Vibhav Gogate, Steve Marcus and Roberto Tempo for  ... 
doi:10.3166/ejc.17.483-511 fatcat:rqvf2p6xrbc7da5jmt3kss3owe

Probabilistic analysis of the human transcriptome with side information [article]

Leo Lahti
2011 arXiv   pre-print
Statistical learning and probabilistic models provide a natural framework for such modeling tasks.  ...  The key contributions of the thesis are general exploratory tools for high-throughput data analysis that have provided new insights to cell-biological networks, cancer mechanisms and other aspects of genome  ...  , ribosomal RNA and transfer-RNA molecules (Carninci, 2009; Johnson et al., 2005) .  ... 
arXiv:1102.5509v1 fatcat:zlwxrob7c5hapgje2v2tstx6uy

Probabilistic and Flux Landscapes of the Phage λ Genetic Switch [article]

Nathan Borggren
2012 arXiv   pre-print
In this work, a dynamical model of the non-equilibrium statistical mechanics is revisited and generalized.  ...  To this end, general integral forms for advection-diffusion equations have been developed and numerically solved for a variety of mutants and assumptions about the state of the cells.  ...  Mistake, seemed to have already been taken, though time has now evolved sufficiently long to have absorbed enough contribution from elsewhere to break this continuity sufficiently to warrant a new name and  ... 
arXiv:1204.1953v1 fatcat:do4vjinaojadphxoe3vowb54oe

Evaluation of a sophisticated SCFG design for RNA secondary structure prediction

Markus E. Nebel, Anika Scheid
2011 Theory in biosciences  
on probabilistic RNA models.  ...  relevant for biologists) yield the conclusion that the Boltzmann distribution of the PF sampling approach is more centered than the ensemble distribution induced by the sophisticated SCFG model, which  ...  Acknowledgements The authors wish to thank two anonymous reviewers for their careful and helpful remarks and suggestions made for a previous version of this article.  ... 
doi:10.1007/s12064-011-0139-7 pmid:22135038 fatcat:a7p4b62w4nedxewvuuranz5r2q

MGcount: a total RNA-seq quantification tool to address multi-mapping and multi-overlapping alignments ambiguity in non-coding transcripts

Andrea Hita, Gilles Brocart, Ana Fernandez, Marc Rehmsmeier, Anna Alemany, Sol Schvartzman
2022 BMC Bioinformatics  
Consequently, reads from total-RNA-seq libraries may cause ambiguous genomic alignments, demanding for flexible quantification approaches.  ...  Results Here we present Multi-Graph count (MGcount), a total-RNA-seq quantification tool combining two strategies for handling ambiguous alignments.  ...  Acknowledgements We would like to thank Professor Martin Simon for contributing to the improvement of our work with interesting discussions on small-RNA-seq and for providing with the mouse liver and nematode  ... 
doi:10.1186/s12859-021-04544-3 pmid:35030988 pmcid:PMC8760670 fatcat:akduthfdtfdwbnzplilphpvday

Identifying differentially expressed transcripts from RNA-seq data with biological variation

Peter Glaus, Antti Honkela, Magnus Rattray
2012 Computer applications in the biosciences : CABIOS  
The analysis of transcriptome expression levels and differential expression estimation requires a probabilistic approach to properly account for ambiguity caused by shared exons and finite read sampling  ...  We demonstrate the advantages of our method using simulated data as well as an RNA-seq dataset with technical and biological replication for both studied conditions.  ...  Graphical representation of the RNA-seq data probabilistic model.  ... 
doi:10.1093/bioinformatics/bts260 pmid:22563066 pmcid:PMC3381971 fatcat:awexp7n36fcbhgnkb5f2cht2ni

Research on folding diversity in statistical learning methods for RNA secondary structure prediction

Yu Zhu, ZhaoYang Xie, YiZhou Li, Min Zhu, Yi-Ping Phoebe Chen
2018 International Journal of Biological Sciences  
The existing prediction methods for a single sequence do not fully consider the folding diversity which may occur among RNAs with different functions or sources.  ...  This paper explores the relationship between folding diversity and prediction accuracy, and puts forward a new method to improve the prediction accuracy of RNA secondary structure.  ...  energy on structure and fits the nested branching structure of RNA molecules.  ... 
doi:10.7150/ijbs.24595 pmid:29989089 pmcid:PMC6036747 fatcat:kzyc7yxkdjb7tgtvvg7h7h3opu

Self-organization versus Watchmaker: ambiguity of molecular recognition and design charts of cellular circuitry

Alexei Kurakin
2007 Journal of Molecular Recognition  
pathways are inherently probabilistic, ambiguous, and context-dependent.  ...  usefulness of the mechanistic assumptions and inferences embodied in the design charts of cellular circuitry.  ...  Veronica Galvan (Buck Institute) for critical reading of the manuscript and Dr. Dale E. Bredesen (Buck Institute) for support and encouragement.  ... 
doi:10.1002/jmr.839 pmid:17847050 fatcat:ypynzncp7ndyfobdwaif6yslca

Bioinformatics---an introduction for computer scientists

Jacques Cohen
2004 ACM Computing Surveys  
The topics covered include: descriptions of the current software especially developed for biologists, computer and mathematical cell models, and areas of computer science that play an important role in  ...  The underlying motivation for many of the bioinformatics approaches is the evolution of organisms and the complexity of working with incomplete and noisy data.  ...  ACKNOWLEDGMENTS The author wishes to express his gratitude to Mark Gerstein, Nathan Goodman and the reviewers who provided many suggestions to improve the original manuscript.  ... 
doi:10.1145/1031120.1031122 fatcat:i5au72xpujffrgryx3vnyiyeyy

Large-scale allosteric switch in the 7SK RNA regulates transcription in response to growth and stress [article]

Samuel W Olson, Anne-Marie W Turner, J Winston Arney, Irfana Saleem, Chase A Weidmann, David M Margolis, Kevin M Weeks, Anthony M Mustoe
2021 bioRxiv   pre-print
as a powerful strategy for comprehensively defining RNA structure and dynamics in cells.  ...  ) direct base pairing interactions, and (iii) tertiary and higher-order interactions for each conformation of multi-state RNA structural ensembles, all from a single experiment.  ...  Acknowledgements We thank Khoa Dhoa (Baylor College of Medicine, BCM) for exploratory analyses, and Calla Olson (BCM), Kristen Karlin (BCM), and David Price (University of Iowa) for helpful discussions  ... 
doi:10.1101/2021.09.16.460563 fatcat:3blpx5jefjhsvhpkmu3azv7sly

Evaluating the effect of disturbed ensemble distributions on SCFG based statistical sampling of RNA secondary structures

Anika Scheid, Markus E Nebel
2012 BMC Bioinformatics  
Recently, a novel probabilistic method for the prediction of RNA secondary structures from a single sequence has been studied which is based on generating statistically representative and reproducible  ...  The key results of this paper are crucial for the design of an efficient and competitive heuristic prediction method based on the increasingly accepted and attractive statistical sampling approach.  ...  All authors wish to thank an anonymous reviewer for careful reading and helpful remarks and suggestions made for a previous version of this article.  ... 
doi:10.1186/1471-2105-13-159 pmid:22776037 pmcid:PMC3871765 fatcat:jxixc6iyqngovhlvxcnyakdxom

Knotify: An Efficient Parallel Platform for RNA Pseudoknot Prediction Using Syntactic Pattern Recognition

Christos Andrikos, Evangelos Makris, Angelos Kolaitis, Georgios Rassias, Christos Pavlatos, Panayiotis Tsanakas
2022 Methods and Protocols  
Obtaining valuable clues for noncoding RNA (ribonucleic acid) subsequences remains a significant challenge, acknowledging that most of the human genome transcribes into noncoding RNA parts related to unknown  ...  The methodology achieved a F1-score equal to 0.774 and MCC equal 0.543 in discovering all the stems of an RNA sequence, outperforming the particular task.  ...  Thermodynamic methods incorporate a biologically oriented, energy-driven model for RNA folding and obtain their parameters from experiments on specific short RNA molecules.  ... 
doi:10.3390/mps5010014 pmid:35200530 pmcid:PMC8876629 fatcat:ao2zvmqlrfc2dkhbljheqyweoa

The emerging role of physical modeling in the future of structure determination [article]

Kari Gaalswyk, Mir Ishruna Muniyat, Justin MacCallum
2017 bioRxiv   pre-print
However, recent efforts to model conformational ensembles and to make sense of sparse, ambiguous, and noisy data have revealed the value of detailed, quantitative physical models in structure determination  ...  We review these two key challenges, describe different approaches to physical modeling in structure determination, and illustrate several successes and emerging technologies enabled by physical modeling  ...  Acknowledgements This work was supported by funding from the Natural Sciences and Engineering Research Council of Canada. JLM is a Tier 2 Canada Research Chair.  ... 
doi:10.1101/228247 fatcat:yqxphotgvngwpapl4xsqx6esz4

Predictions of RNA secondary structure by combining homologous sequence information

Michiaki Hamada, Kengo Sato, Hisanori Kiryu, Toutai Mituyama, Kiyoshi Asai
2009 Computer applications in the biosciences : CABIOS  
Results: In this article, we propose a new method for secondary structure predictions of individual RNA sequences by taking the information of their homologous sequences into account without assuming the  ...  In our computational experiments, the proposed method provides better predictions than those performed only on the basis of the formation of individual RNA sequences and those performed by using methods  ...  Carvalho and C. E. Lawrence for valuable comments. The authors are also grateful to our colleagues at the Computational Biology Research Center (CBRC) for fruitful discussions.  ... 
doi:10.1093/bioinformatics/btp228 pmid:19478007 pmcid:PMC2687982 fatcat:bx56bl5gtrd5zodipfxeg6yubi
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