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The Incremental Group Testing Model for Gap Closing in Sequencing Long Molecules

Frank K. Hwang, Wen-Dar Lin
2003 Journal of combinatorial optimization  
In this paper, we propose the incremental group testing model for the gap closing problem, which assumes that we can tell the difference between the outcome of testing a subset S, and the outcome of testing  ...  We also give improvements over currently best results in literature for some other models.  ...  With the fact that Q(k, 1) ≥ 0.78 for k = 1, 2, . . . , we conclude that averagely more than 78% of unidentified edges are identified in each looping of Step 2 for edges internal to the p 2 blocks of size  ... 
doi:10.1023/b:joco.0000017381.11696.c6 fatcat:ymqwme4efjfbdmwdbvrzl5hr5u

A Structure-Based Mechanism for Arf1-Dependent Recruitment of Coatomer to Membranes

Xinchao Yu, Marianna Breitman, Jonathan Goldberg
2012 Cell  
A bivalent GTP-dependent binding mode has implications for the dynamics of coatomer interaction with the Golgi and for the selection of cargo molecules.  ...  Structure-guided biochemical analysis reveals that a second Arf1-GTP molecule binds to bd-COP at a site common to the g-and b-COP subunits.  ...  ACKNOWLEDGMENTS We thank staff at beamline X-29 of the NSLS for access to synchrotron facilities. We thank Changwook Lee and Romina Mancusso for assistance with protein studies.  ... 
doi:10.1016/j.cell.2012.01.015 pmid:22304919 pmcid:PMC3285272 fatcat:fxu3y5potjbhthbqx6euxsraqq

Elastic energy storage in unmineralized and mineralized extracellular matrices (ECMs): A comparison between molecular modeling and experimental measurements

Joseph W. Freeman, Frederick H. Silver
2004 Journal of Theoretical Biology  
We hypothesize that these increases in slope are due to a change from the stretching of flexible regions of the collagen molecule to the stretching of less flexible regions.  ...  In this study the energy stored in unmineralized and mineralized collagen fibers was measured and compared to the amount of energy stored in molecular models.  ...  Acknowledgements The authors wish to thank the ABD Program of Virginia Polytechnic Institute and State University for financial support for this study and the Engineering Science and Mechanics Department  ... 
doi:10.1016/j.jtbi.2004.04.018 pmid:15234204 fatcat:pbmpk3t5hbdw5jsoljwdu6tk6e

Collagen as a scaffold for biomimetic mineralization of vertebrate tissues

William J. Landis, Frederick H. Silver, Joseph W. Freeman
2006 Journal of Materials Chemistry  
In its mineralized form, collagen potentially can be utilized as a biomimetic material for a variety of applications, including, for example, the augmentation and repair of damaged, congenitally defective  ...  In order to effect an optimal response in this regard, the manner in which collagen becomes mineralized is critically important to understand.  ...  Acknowledgements This work has been supported by grant AR41452 from the National Institutes of Health (to WJL).  ... 
doi:10.1039/b505706j fatcat:akqrlb73kzdlrkp4bv7xcpnvje

RNAslider: a faster engine for consecutive windows folding and its application to the analysis of genomic folding asymmetry

Yair Horesh, Ydo Wexler, Ilana Lebenthal, Michal Ziv-Ukelson, Ron Unger
2009 BMC Bioinformatics  
We also present results from calculating the MFE landscape of a mouse chromosome 1, characterizing the MFE of the long ncRNA molecules that reside in this chromosome.  ...  Conclusion: The efficient consecutive windows folding engine described in this paper allows for genome wide scans for ncRNA molecules as well as large-scale statistics.  ...  We are indebted to the anonymous referees for suggesting the dinucleotide shuffling experiment and many other valuable suggestions.  ... 
doi:10.1186/1471-2105-10-76 pmid:19257906 pmcid:PMC2682796 fatcat:d4l5dkr64fe3xmg6zmvqo26xmm

Building and Improving Reference Genome Assemblies

Karyn Meltz Steinberg, Valerie A. Schneider, Can Alkan, Michael J. Montague, Wesley C. Warren, Deanna M. Church, Richard K. Wilson
2017 Proceedings of the IEEE  
| A genome sequence assembly provides the foundation for studies of genotypic and phenotypic variation, genome structure, and evolution of the target organism.  ...  In the past four decades, there has been a surge of new sequencing technologies, and with these developments, computational scientists have developed new algorithms to improve genome assembly.  ...  Larson for reading the manuscript and providing comments.  ... 
doi:10.1109/jproc.2016.2645402 fatcat:6mm2qx33fjecxhcbrxnhaebfji

A computer simulation of free-volume distributions and related structural properties in a model lipid bilayer

T.X. Xiang
1993 Biophysical Journal  
The mean cavity shape is described in terms of a probability distribution for the angle at which the test permeant is in contact with one of and does not overlap with anyone of the chain segments in the  ...  The model bilayer consists of 2 x 100 chain molecules with each chain molecule having 15 carbon segments and one head group and subject to forces restricting bond stretching, bending, and torsional motions  ...  ACKNOWLEDGMENTS I would like to thank the staffs of the Utah Supercomputing Institute for the assistance in the optimization of the computer program used in this work in the early phase of this work.  ... 
doi:10.1016/s0006-3495(93)81156-1 pmid:8241390 pmcid:PMC1225828 fatcat:pksj3llcn5g2bakwoohizxsgxu

LinearFold: linear-time approximate RNA folding by 5'-to-3' dynamic programming and beam search

2019 Bioinformatics  
Inspired by incremental parsing for context-free grammars in computational linguistics, our alternative dynamic programming algorithm scans the sequence in a left-to-right (5'-to-3') direction rather than  ...  More interestingly, it leads to significantly more accurate predictions on the longest sequence families in that database (16S and 23S Ribosomal RNAs), as well as improved accuracies for long-range base  ...  Acknowledgements We would like to thank the reviewers for suggestions, Rhiju Das for encouragement and early adoption of LinearFold into the EteRNA game, James Cross for help in algorithm design, Juneki  ... 
doi:10.1093/bioinformatics/btz375 pmid:31510672 pmcid:PMC6681470 fatcat:5eybu4l76zdsvfcyaixk6roeva

ESSA: an integrated and interactive computer tool for analysing RNA secondary structure

F Chetouani
1997 Nucleic Acids Research  
This computer program is organized around the display of folding models produced by two complementary methods suitable to draw long RNA molecules.  ...  The potentialities of ESSA are illustrated by the identification of a possible tertiary motif in the LSU rRNA and the visualization of a pseudoknot in S15 mRNA.  ...  In (d) and (e), when a set of sequences are compared, '#' stand for gaps, 'Y' is for pyrimidines, 'R' for purines and 'O' for any base, according to the input value for consensus.  ... 
doi:10.1093/nar/25.17.3514 pmid:9254713 pmcid:PMC146922 fatcat:zs4qnjamdrcrzouyfih7r47agq

LongStitch: High-quality genome assembly correction and scaffolding using long reads [article]

Lauren Coombe, Janet X Li, Theodora Lo, Johnathan Wong, Vladimir Nikolic, René L Warren, Inanc Birol
2021 bioRxiv   pre-print
In recent years, long-read sequencing has greatly benefited genome assembly and scaffolding, a process by which assembled sequences are ordered and oriented through the use of long-range information.  ...  Results LongStitch incorporates multiple tools developed by our group and runs in up to three stages, which includes initial assembly correction (Tigmint-long), followed by two incremental scaffolding  ...  Acknowledgements We thank Justin Chu for his valuable contributions to brainstorming discussions early in the project, which helped drive the development of the algorithms.  ... 
doi:10.1101/2021.06.17.448848 fatcat:uo4bug3ii5awpchbj6zr6piyca

Read Length and Repeat Resolution: Exploring Prokaryote Genomes Using Next-Generation Sequencing Technologies

Matt J. Cahill, Claudio U. Köser, Nicholas E. Ross, John A. C. Archer, Wenjun Li
2010 PLoS ONE  
thus predict the number of gaps that would need to be closed to produce a complete sequence.  ...  Methodology/Principal Findings: Using a simple model of repeat assembly, we develop and test a technique that, for any read length, can estimate the occurrence of unresolvable repeats in a genome, and  ...  Using a simple model of repeat assembly, we develop and test a technique that, for any read length, can estimate the occurrence of unresolvable repeats in a sequenced genome and thus predict assembly results  ... 
doi:10.1371/journal.pone.0011518 pmid:20634954 pmcid:PMC2902515 fatcat:3q3bzx3adfhpvhgf6yg4lpkdme

Molecular level detection and localization of mechanical damage in collagen enabled by collagen hybridizing peptides

Jared L. Zitnay, Yang Li, Zhao Qin, Boi Hoa San, Baptiste Depalle, Shawn P. Reese, Markus J. Buehler, S. Michael Yu, Jeffrey A. Weiss
2017 Nature Communications  
In the case of mechanical subfailure damage, no apparent macroscale damage can be detected, yet this damage initiates and potentiates in pathological processes.  ...  Mechanical injury to connective tissue causes changes in collagen structure and material behaviour, but the role and mechanisms of molecular damage have not been established.  ...  We thank Matthew Converse for assistance in acquisition of collagen SHG signal. We thank Nathan Galli for the schematic drawings.  ... 
doi:10.1038/ncomms14913 pmid:28327610 pmcid:PMC5364439 fatcat:nmiukprfgjbftktfyljwythdbq

Multiple Sequence Alignment Using a Genetic Algorithm and GLOCSA

Helga Ochoterena
2009 Journal of Artificial Evolution and Applications  
In this paper, we thoroughly present a Global Criterion for Sequence Alignment (GLOCSA) that uses a scoring function to globally rate multiple alignments aiming to produce matrices that minimize the number  ...  We show that in the example cases our GLOCSA-guided Genetic Algorithm (GGGA) does improve the GLOCSA values, resulting in alignments that imply less putative synapomorphies.  ...  Acknowledgments The authors would like to thank CONACYT under the project 61507 and SIBA-UNIBIO (UNAM) for the funding that made this work possible.  ... 
doi:10.1155/2009/963150 fatcat:75rhpnxfpzgfdixbq2pril7dwy

Connexin32 gap junction channels in stably transfected cells. Equilibrium and kinetic properties

A.P. Moreno, B. Eghbali, D.C. Spray
1991 Biophysical Journal  
Transitions between open and closed states in response to transjunctional voltages of either polarity are single order processes; transitions from one closed state to the other involve passage through  ...  Communication-deficient cells (the SKHepl cell line) were stably transfected with a plasmid containing cDNA which encodes the major gap junction protein of rat liver, connexin32.  ...  In this region of the molecule, charged amino acid residues align when the sequence is modeled as ac-helical, and a consensual feature of all connexins is that the charged residues are flanked by bulky  ... 
doi:10.1016/s0006-3495(91)82160-9 pmid:1722120 pmcid:PMC1260180 fatcat:qogvbdp2bzahnkzbnjg6cchrv4

Role of sialyloligosaccharide binding in Theiler's virus persistence

L Zhou, X Lin, T J Green, H L Lipton, M Luo
1997 Journal of Virology  
Comparisons among the known GDVII, BeAn, and DA structures as well as the predicted models for the TMEV chimeras suggested that a gap on the capsid surface next to the putative receptor binding site, composed  ...  This persistent central nervous system infection with demyelination resembles multiple sclerosis (MS) in humans and has thus become an important model for studying MS.  ...  Zhang and Lily Yang for technical assistance. This work was supported by grants from NIH to M.L. (NS23349) and to H.L.L. (NS21913).  ... 
pmid:9371636 pmcid:PMC230280 fatcat:wtgawix4i5gnjka6bk24clqkgm
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