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An O(n2) algorithm for signed translocation

Lusheng Wang, Daming Zhu, Xiaowen Liu, Shaohan Ma
2005 Journal of computer and system sciences (Print)  
The best known algorithm that can give the optimum sequence of translocation operations for signed translocation problem runs in O(n 2 log n) time. In this paper, we design an O(n 2 ) algorithm.  ...  A linear-time algorithm that computes the minimum number of translocation operations was given in a linear-time algorithm for computing translocation distance between signed genomes [16] .  ...  Acknowledgments We thank the referees for their helpful suggestions to improve the presentation of the paper.  ... 
doi:10.1016/j.jcss.2004.12.005 fatcat:n6mptpck7vdy7lbjxqlfb7q2zi


2005 Proceedings of the 3rd Asia-Pacific Bioinformatics Conference  
The best known algorithm that can give the optimum sequence of translocation operations for signed translocation problem runs in¨© time. In this paper, we design an¨© algorithm.  ...  Genome rearrangement is an important area in computational biology. There are three basic operations, reversal, translocation, and transposition. Here we study the translocation operations.  ...  However, it takes more time to give an optimal sequence of operations. For example, for the signed reversal distance, a lineartime algorithm that computes the reversal distance value was given in .  ... 
doi:10.1142/9781860947322_0035 fatcat:5ppa5funtnc6xdxijvmwejc5xe

Vaccinia virus protein N2 is a nuclear IRF3 inhibitor that promotes virulence

B. J. Ferguson, C. T. O. Benfield, H. Ren, V. H. Lee, G. L. Frazer, P. Strnadova, R. P. Sumner, G. L. Smith
2013 Journal of General Virology  
In summary, the N2 protein is an intracellular virulence factor that inhibits IRF3 activity in the nucleus.  ...  Consistent with its nuclear localization, N2 inhibits IRF3 downstream of the TANK-binding kinase (TBK)-1 and after IRF3 translocation into the nucleus.  ...  The conservation in many orthopoxviruses suggests an important function for N2.  ... 
doi:10.1099/vir.0.054114-0 pmid:23761407 pmcid:PMC3749055 fatcat:ouefwhyu5fcajd42d6f5alx5n4

On Sorting by Translocations

Anne Bergeron, Julia Mixtacki, Jens Stoye
2006 Journal of Computational Biology  
We give an elementary proof of the formula for computing the translocation distance in linear time, and we give a new algorithm for sorting by translocations, correcting an error in a previous algorithm  ...  The study of genome rearrangements is an important tool in comparative genomics.  ...  ACKNOWLEDGMENTS We wish to thank Michal Ozery-Flato for a very careful reading and for sharing with us a simple and elegant proof of Lemma 4.  ... 
doi:10.1089/cmb.2006.13.567 pmid:16597257 fatcat:4jq5fkcymnb5jf7qatdlbgic5e

Polynomial-time algorithm for computing translocation distance between genomes

Sridhar Hannenhalli
1996 Discrete Applied Mathematics  
This leads to an algorithm generating a most parsimonious (shortest) scenario, transforming one genome into another by translocations.  ...  The translocation distance problem was recently studied for the first time by Kececioglu and Ravi, who gave a 2-approximation algorithm for computing translocation distance.  ...  Acknowledgments The author is very thankful to Pave1 Pevzner for many helpful suggestions, and for pointing out a few mistakes in the earlier versions of this paper.  ... 
doi:10.1016/s0166-218x(96)00061-3 fatcat:n5hlapkwnfa27mvg7dqxb4ubwu

Reconstructing the pre-doubling genome

Nadia El-Mabrouk, David Bryant, David Sankoff
1999 Proceedings of the third annual international conference on Computational molecular biology - RECOMB '99  
We present an exact algorithm for reconstructing the ancestral pm-doubling genome in polynomial time, minimizing in key cases the number of translocations required to derive the observed order and orientation  ...  Genome duplication is an important source of new gene functions and novel physiological pathways.  ...  We present a polynomial algorithm for finding an exact solution to most of the interesting instances of the problem. 2 Genome halving of signed, ordered chromosomes.  ... 
doi:10.1145/299432.299475 dblp:conf/recomb/El-MabroukBS99 fatcat:nc66whfwajbyzlifnhhhx36nuy

The Reconstruction of Doubled Genomes

Nadia El-Mabrouk, David Sankoff
2003 SIAM journal on computing (Print)  
Somewhat different techniques are required for a translocations-only model, a translocations/reversals model, both of these in the multichromosomal context (eukaryotic nuclear genomes), and a reversals-only  ...  We present exact algorithms for reconstructing the ancestral doubled genome in linear time, minimizing the number of rearrangement mutations required to derive the observed order of genes along the present-day  ...  The authors are Scholar and Fellow of the Evolutionary Biology Program of the Canadian Institute for Advanced Research.  ... 
doi:10.1137/s0097539700377177 fatcat:ryegzmrfc5ca3pxkq6xvtrbrl4

Recursively Divided Pancake Graphs with a Small Network Cost

Jung-Hyun Seo, Hyeong-Ok Lee
2021 Symmetry  
, the degree is n − 1, and the network cost is O(n2). In an RDPn, the number of nodes is n!, the degree is 2log2n − 1, and the network cost is O(n(log2n)3).  ...  Because O(n(log2n)3) < O(n2), the RDP is superior to other pancake-like graphs. In this paper, we propose an RDPn and analyze its basic topological properties.  ...  n(n + 1)/2 O(3n/2) O(23n/14) ≒0.75n 3 ≒0.82n 3 restricted burnt pancake [6] 2 n × n! n/2 + 2 O(4.5n) ≒2.25n 2 signed permutation [8] [10] 2 n × n!  ... 
doi:10.3390/sym13050844 fatcat:eqp6ijczhvfuhp3s4px7jzlerq

Development of a human mitochondrial oligonucleotide microarray (h-MitoArray) and gene expression analysis of fibroblast cell lines from 13 patients with isolated F1Fo ATP synthase deficiency

Alena Čížková, Viktor Stránecký, Robert Ivánek, Hana Hartmannová, Lenka Nosková, Lenka Piherová, Markéta Tesařová, Hana Hansíková, Tomáš Honzík, Jiří Zeman, Petr Divina, Andrea Potocká (+6 others)
2008 BMC Genomics  
To strengthen research and differential diagnostics of mitochondrial disorders, we constructed and validated an oligonucleotide microarray (h-MitoArray) allowing expression analysis of 1632 human genes  ...  Using h-MitoArray we analyzed gene expression profiles in 9 control and 13 fibroblast cell lines from patients with F 1 F o ATP synthase deficiency consisting of 2 patients with mt9205∆TA microdeletion  ...  The N2 group showed neither signs of mitochondria response observed in the M group, nor signs of premature senescence observed in the N1 group.  ... 
doi:10.1186/1471-2164-9-38 pmid:18221507 pmcid:PMC2267714 fatcat:cvd6egp5j5bjtogru33w4o5kra

Exact and approximation algorithms for sorting by reversals, with application to genome rearrangement

J. Kececioglu, D. Sankoff
1995 Algorithmica  
For this problem, we develop two algorithms: a greedy approximation algorithm, that finds a solution provably close to optimal in O(n 2) time and O(n) space for n-element permutations, and a branch-and-bound  ...  exact algorithm, that finds an optimal solution in O(mL(n, n)) time and O(n 2) space, where m is the size of the branch-and-bound search tree, and L(n, n) is the time to solve a linear program of n variables  ...  For signed permutations, we observe an average difference, between the greedy approximation and a simplified lower bound, of less than one reversal, for n up to 10,000.  ... 
doi:10.1007/bf01188586 fatcat:qtuq5tysrrcp3gtdiujztnk5me

Adaptive Evolution under Extreme Genetic Drift in Oxidatively Stressed Caenorhabditis elegans

Stephen F Christy, Riana I Wernick, Michael J Lue, Griselda Velasco, Dana K Howe, Dee R Denver, Suzanne Estes
2017 Genome Biology and Evolution  
Further analysis revealed an enrichment of mutations in loci that occur in a gas-1-centric region of the C. elegans interactome, and could be classified into a small number of functional-genomic categories  ...  Our combined results suggest that selection favoring beneficial mutations can be powerful even under unfavorable population genetic conditions, and agree with fitness landscape theory predicting an inverse  ...  Sullins for laboratory support; and anonymous reviewers for thoughtful comments on the manuscript.  ... 
doi:10.1093/gbe/evx222 pmid:29069345 pmcid:PMC5714194 fatcat:nmwr5tu6kfcrxdwly2smgsh7ya

The genetic characterization of an isolated remnant population of an endangered rodent (Cricetus cricetus L.) using comparative data: implications for conservation

Iwona Melosik, Joanna Ziomek, Katarzyna Winnicka, Tobias Erik Reiners, Agata Banaszek, Kerstin Mammen, Ubbo Mammen, Adrian Marciszak
2017 Conservation Genetics  
habitats, has undergone a major decline in numbers to near-extinction in western Abstract Estimates of genetic diversity and phylogenetic affiliation represent an important resource for biodiversity assessment  ...  We recommend translocation of individuals as an effective management strategy, both at the level of Central phylogeographic group and at the species level, to overcome the negative consequences of inbreeding  ...  Acknowledgements The authors wish to acknowledge the anonymous reviewers for their detailed and constructive comments that help improve the manuscript.  ... 
doi:10.1007/s10592-017-0925-y fatcat:4wxvhfjhgjbnhet7mjkza62t2y

A novel PEX1 mutation in a Moroccan family with Zellweger spectrum disorders

Amale Bousfiha, Amina Bakhchane, Hicham Charoute, Zied Riahi, Khalid Snoussi, Hassan Rouba, Crystel Bonnet, Christine Petit, Abdelhamid Barakat
2017 Human Genome Variation  
ACKNOWLEDGEMENTS We thank all the patients and their families for their collaboration. This study was approved by the Ethics Committee of the Morocco Pasteur Institute.  ...  An informed written consent was signed by parents of patients to perform genetic testing before taking the blood of all the family members.  ...  The Pex1p contains two nucleotide-binding domains (D1 and D2) preceded by two N-terminal domains (N1 and N2). 3, 14 he D2 domain is highly conserved and contains an essential substrate-binding loop, and  ... 
doi:10.1038/hgv.2017.9 pmid:28446956 pmcid:PMC5390255 fatcat:4dfgdw7pyjhezautnuoez5r2wm

An All-Electric Single-Molecule Hybridisation Detector for short DNA Fragments [article]

Amelia Y.Y. Loh, Claire H. Burgess, Diana A. Tanase, Giorgio Ferrari, Martyn A. McLachlan, Anthony E.G. Cass, Tim Albrecht
2018 arXiv   pre-print
In combining DNA nanotechnology and high-bandwidth single-molecule detection in nanopipettes, we demonstrate an all-electric, label-free hybridisation sensor for short DNA sequences (< 100 nt).  ...  Such short fragments are known to occur as circulating cell-free DNA in various bodily fluids, such as blood plasma and saliva, and have been identified as disease markers for cancer and infectious diseases  ...  Themixture was incubated in the thermocycler at 37 o C for 2.5 hours and then heated to 65 o C for 20 min. to denature the RE.  ... 
arXiv:1808.01168v1 fatcat:rstdqquyh5hmbojzfhmuqxhxvm

Spectroscopy of Cu(II)-PcoC and the Multicopper Oxidase Function of PcoA, Two Essential Components ofEscherichia coli pcoCopper Resistance Operon†

David L. Huffman, Jennifer Huyett, F. Wayne Outten, Peter E. Doan, Lydia A. Finney, Brian M. Hoffman, Thomas V. O'Halloran
2002 Biochemistry  
The solvent accessibility of the Cu(II) in PcoC may allow for metal transfer to other plasmid and chromosomal factors and thus facilitate removal of Cu(II) from the cell envelope.  ...  We propose a model for the plasmid system in which Cu(I)-PcoC functions in this copper efflux pathway as a periplasmic copper binding protein that docks with the multiple repeats of Met-rich domains in  ...  Recalling that an ENDOR pattern collected at g | has the external field normal to the bond of an in-plane ligand, but parallel to the bond of an axial ligand, comparison with the data for [Cu(II)(H 2 O  ... 
doi:10.1021/bi0259960 pmid:12146969 fatcat:e7s6cyao7jfkjajl2ammcjpt5u
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