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Phylogenetic Reconstruction from Gene-Rearrangement Data with Unequal Gene Content [chapter]

Jijun Tang, Bernard M. E. Moret
2003 Lecture Notes in Computer Science  
In this paper, we present extensions to our GRAPPA approach that can handle limited numbers of duplications (one of the main requirements for analyzing genomic data from organelles) and a few deletions  ...  in high accuracy and fast running times.  ...  [2] later showed that this edit distance can be computed in linear time.  ... 
doi:10.1007/978-3-540-45078-8_4 fatcat:xf4j7inatjej7pouvlrhrxfhhm

Benchmarking access methods for time-evolving regional data

T Tzouramanis
2003 Data & Knowledge Engineering  
An extensive experimental space and time performance comparison of all the above access methods follows.  ...  Initially, we briefly review four temporal extensions of the Linear Region Quadtree: the Time-Split Linear Quadtree, the Multiversion Linear Quadtree, the Multiversion Access Structure for Evolving Raster  ...  It is a rather robust access method that can address time-interval queries with good average performance, using only minimal extra space (about 10-30% more space than OLQ) and comparable or minimal extra  ... 
doi:10.1016/j.datak.2003.08.002 fatcat:kz3j6tjisjdqnnyfzniazoy4wm

Query processing in main memory database management systems

Tobin J. Lehman, Michael J. Carey
1986 SIGMOD record  
-One can then design new data structures aid algorithms oriented towards making eflicient use of CPU cycles and memory space rather than minimizing disk accesses and &ing disk space efliciently.  ...  The primary goals for a disk-oriented index structure are to minimize the number of disk accesses and to minimize disk space.  ...  Separate chaining would waste at least half of the node's space on pointers, and open addressing would cause diflicuhies with delete by wasting either time or space to fill in holes left by deleted items  ... 
doi:10.1145/16856.16878 fatcat:aqhczp6glndhhljqxh3jgl4wsq

Benchmarking access methods for time-evolving regional data

Theodoros Tzouramanis, Michael Vassilakopoulos, Yannis Manolopoulos
2004 Data & Knowledge Engineering  
An extensive experimental space and time performance comparison of all the above access methods follows.  ...  Initially, we briefly review four temporal extensions of the Linear Region Quadtree: the Time-Split Linear Quadtree, the Multiversion Linear Quadtree, the Multiversion Access Structure for Evolving Raster  ...  It is a rather robust access method that can address time-interval queries with good average performance, using only minimal extra space (about 10-30% more space than OLQ) and comparable or minimal extra  ... 
doi:10.1016/j.datak.2003.08.008 fatcat:gz6sltta2faa5ipuh3tmyo4uli

Feed-Forward Loop Circuits as a Side Effect of Genome Evolution

Otto X. Cordero, Paulien Hogeweg
2006 Molecular biology and evolution  
For this, we design a model of stochastic duplications, deletions, and mutations of binding sites and genes and compare our results with yeast network data.  ...  The mechanism here proposed and the analysis of the yeast data show that regulator duplication could have played an important role in FFL evolution.  ...  For simplicity, both proteins and BSs are defined in a linear discrete space, separated by a mutational distance.  ... 
doi:10.1093/molbev/msl060 pmid:16840361 fatcat:ltewr2ui6baadc7rdsnva2sm3i

Invertible Bloom Lookup Tables [article]

Michael T. Goodrich, Michael Mitzenmacher
2015 arXiv   pre-print
If later entries are deleted to return the structure below the threshold, everything again functions appropriately.  ...  We present a version of the Bloom filter data structure that supports not only the insertion, deletion, and lookup of key-value pairs, but also allows a complete listing of its contents with high probability  ...  Space-Saving for an Invertible Bloom Lookup Table Up to this point, we have not been concerned with minimizing space for our IBLT structure, noting that it can be done in linear space.  ... 
arXiv:1101.2245v3 fatcat:dufwecnztrghlngsp7cixyuyku

Genome Archaeology: Detecting Ancient Polyploidy in Contemporary Genomes [chapter]

Todd J. Vision, Daniel G. Brown
2000 Comparative Genomics  
duplication events.  ...  After many generations of gene deletion, divergence of paralogous genes, and chromosomal rearrangements, an ancient polyploid comes to resemble a non-polyploid genome that has experienced multiple local  ...  We assume the form of the function to be linear until ÛÜ , the time at which the probability reaches 1 (Figure 2d ).  ... 
doi:10.1007/978-94-011-4309-7_41 fatcat:rnhqfc3auzdarfzeonawkdnuae

Reconstructing DNA copy number by penalized estimation and imputation

Zhongyang Zhang, Kenneth Lange, Roel Ophoff, Chiara Sabatti
2010 Annals of Applied Statistics  
Together these changes enable us to minimize the fused-lasso criterion in a highly effective way. We also reframe the reconstruction problem in terms of imputation via discrete optimization.  ...  optimization problem by the following: (a) changing the penalty terms slightly by substituting a smooth approximation to the absolute value function, (b) designing and implementing a new MM (majorization--minimization  ...  After normalization, the average of y i across individuals is 0. A large positive value suggests a duplication; a large negative value suggests a deletion.  ... 
doi:10.1214/10-aoas357 pmid:21572975 pmcid:PMC3092301 fatcat:ur7f6wtywrfura3uwpj6ke45ay

Circ-Tree: A B+-Tree Variant with Circular Design for Persistent Memory [article]

Chundong Wang, Gunavaran Brihadiswarn, Xingbin Jiang, Sudipta Chattopadhyay
2020 arXiv   pre-print
to minimize write amplifications.  ...  These pairs are shifted in a unidirectional fashion for insertions and deletions. Inserting and deleting one KV pair may inflict a large amount of write amplifications due to shifting KV pairs.  ...  Table 1 shows the average recovery time calculated in geometric mean. With a smaller node size, the recovery spent more time because much more INs were processed.  ... 
arXiv:1912.09783v2 fatcat:niety4734jhornc6qpgzjyc6re

Scaling laws in the functional content of genomes: Fundamental constants of evolution? [article]

Erik van Nimwegen
2004 arXiv   pre-print
rates of genes in category c, β(t) is the average duplication rate of all genes, δ c (t) is the average deletion rate of genes in category c, and δ(t) is the average deletion rate of all genes.  ...  averages of ρ c and ρ times the total time t.  ... 
arXiv:q-bio/0405022v1 fatcat:fuph3yrt5vcilau2ruvqsvknbq

Page 957 of Mathematical Reviews Vol. 55, Issue 3 [page]

1978 Mathematical Reviews  
relevant records is minimized under the constraint that no record is duplicated.  ...  The latter minimizes the retrieval time for the set of queries among all file organizations having no duplications, if each query is equally likely to be submitted and each block of consecutive records  ... 

Global objectives for standard cell placement

Mehmet Can Yildiz, Patrick H. Madden
2001 Proceedings of the 11th Great Lakes Symposium on VLSI - GLSVLSI '01  
These improvements are obtained with negligible impact to total run time.  ...  Experimental results show the effect of the approach; there is reduced variation in solution quality, in 8 of 11 benchmarks best case wire length is improved, and for 9 of 11 benchmarks, average wire length  ...  Feng Shui without iterative deletion is comparable to a Dunlop and Kernighan style approach. Run times are in seconds, and average per run.  ... 
doi:10.1145/368122.368801 dblp:conf/glvlsi/YildizM01a fatcat:ipwllwh2xbeulejst62egbhd7e

Bayesian Analysis of Nonlinear Autoregression Models Based on Neural Networks

A. Menchero, R. Montes Diez, D. Ríos Insua, P. Müller
2005 Neural Computation  
We consider a block based model building strategy to model linear and nonlinear features within the time series.  ...  Model identifiability problems arise when FFNN sigmoidal activation functions exhibit almost linear behaviour, or when there are almost duplicate or irrelevant neural network nodes.  ...  For example, we cannot delete a linear term when the current model is the linear model, nor can we delete duplicate nodes if we have just one node (see Figure 1 ).  ... 
doi:10.1162/0899766053011537 fatcat:ipi2tn2gqvexhifo33y3palxv4

On Approaching the One-Sided Exemplar Adjacency Number Problem [chapter]

Letu Qingge, Killian Smith, Sean Jungst, Binhai Zhu
2018 Lecture Notes in Computer Science  
Given one generic linear genome G with gene duplications (over n gene families), an exemplar genome G is a permutation obtained from G by deleting duplicated genes such that G contains exactly one gene  ...  Given G and one exemplar genome H over the same set of n gene families, the One-sided Exemplar Adjacency Number problem (One-sided EAN) is defined as follows: delete duplicated genes from the genome G  ...  On top of this, we use integer linear programming to efficiently delete extra gene duplications while computing the maximum number of adjacencies.  ... 
doi:10.1007/978-3-319-94968-0_27 fatcat:qnstygcucra67feizjojg5xs5a

Genomic Plasticity Enables Phenotypic Variation of Pseudomonas syringae pv. tomato DC3000

Zhongmeng Bao, Paul V. Stodghill, Christopher R. Myers, Hanh Lam, Hai-Lei Wei, Suma Chakravarthy, Brian H. Kvitko, Alan Collmer, Samuel W. Cartinhour, Peter Schweitzer, Bryan Swingle, Dawn Arnold
2014 PLoS ONE  
Deletion of one copy of the 165 kb region demonstrated that the duplication facilitated enhanced growth in some culture conditions, but did not affect pathogenic growth in host tomato plants.  ...  The average read depth coverage of Pst DC3000 whole genome sequencing results suggested that a 165 kb segment of the chromosome had doubled in copy number.  ...  could provide evidence of the mechanism of duplication.  ... 
doi:10.1371/journal.pone.0086628 pmid:24516535 pmcid:PMC3916326 fatcat:qula2u444rgkvhnpltmhzcgyzi
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