40339335
Algorithms to Distinguish the Role of Gene-Conversion from Single-Crossover Recombination in the Derivation of SNP Sequences in Populations
Meiotic recombination is a fundamental biological event and one of the principal evolutionary forces responsible for shaping genetic variation within species. In addition to its fundamental role, recombination is central to several critical applied problems. The most important example is “association mapping” in populations, which is widely hoped to help find genes that influence genetic diseases [3, 4]. Hence, a great deal of recent attention has focused on problems of inferring the historical derivation of sequences in populations when both mutations and recombinations have occurred. In the algorithms literature, most of that recent work has been directed to single-crossover recombination. However, gene-conversion is an important, and more common, form of (two-crossover) recombination which has been much less investigated in the algorithms literature. 
 
In this paper we explicitly incorporate gene-conversion into discrete methods to study historical recombination. We are concerned with algorithms for identifying and locating the extent of historical crossing-over and gene-conversion (along with single-nucleotide mutation), and problems of constructing full putative histories of those events. The novel technical issues concern the incorporation of gene-conversion into recently developed discrete methods [20, 26] that compute lower and upper-bound information on the amount of needed recombination without gene-conversion. We first examine the most natural extension of the lower bound methods from [20], showing that the extension can be computed efficiently, but that this extension can only yield weak lower bounds. We then develop additional ideas that lead to higher lower bounds, and show how to solve, via integer-linear programming, a more biologically realistic version of the lower bound problem. We also show how to compute effective upper bounds on the number of needed single-crossovers and gene-conversions, along with explicit networks showing a putative history of mutations, single-crossovers and gene-conversions. 
 
We validate the significance of these methods by showing that they can be effectively used to distinguish simulation-derived sequences generated without gene-conversion from sequences that were generated with gene-conversion. We apply the methods to recently studied sequences of Arabidopsis thaliana, identifying many more regions in the sequences than were previously identified [22], where gene-conversion may have played a significant role. Demonstration software is available at www.cs. ucdavis.edu/~gusfield.
23745644
Parsimonious Reconstruction of Sequence Evolution and Haplotype Blocks
Under the infinite-sites model of mutation, we consider the problem of finding the minimum number of recombination events which must have occurred in the evolutionary history of sampled DNA sequences. Our approach is deterministic and is based on the combinatorics of leaf-labelled rooted trees. In contrast to previously known approaches, which only yield estimated lower bounds, our approach always gives the exact minimum number of recombination events. Furthermore, our method can be used to reconstruct explicitly evolutionary histories with the minimum number of recombination events. As an additional application, we discuss how our work can be used to define haplotype blocks.
14072276
An Efficient Algorithm for Statistical Multiple Alignment on Arbitrary Phylogenetic Trees
We present an efficient algorithm for statistical multiple alignment based on the TKF91 model of Thorne, Kishino, and Felsenstein (1991) on an arbitrary k-leaved phylogenetic tree. The existing algorithms use a hidden Markov model approach, which requires at least O( radical 5(k)) states and leads to a time complexity of O(5(k)L(k)), where L is the geometric mean sequence length. Using a combinatorial technique reminiscent of inclusion/exclusion, we are able to sum away the states, thus improving the time complexity to O(2(k)L(k)) and considerably reducing memory requirements. This makes statistical multiple alignment under the TKF91 model a definite practical possibility in the case of a phylogenetic tree with a modest number of leaves.
11425513
Graceful degradation of loss-tolerant QoS using (m, k)-firm constraints in guaranteed rate networks
The Weighted Fair Queueing (WFQ) scheduling algorithm and its variants can be used to provide real-time guarantees by making bandwidth reservation. However, while hard guarantees are based on a peak workload model that leads to underutilize network resources, soft guarantees, based on average workload model, are not always sufficient to maintain acceptable Quality-of-Service (QoS) since consecutive packet losses or deadline misses may occur, which are not suitable for real-time applications. In this paper, we propose a trade-off between hard and soft real-time guarantees to maintain an acceptable QoS in overload conditions and efficiently maximize the utilization of network resources. The key to our solution is based on the fact that many real-time applications, such as voice and video, are loss-tolerant. The loss profile must be well defined, and such a profile can be easily specified using the (m,k)-firm model. Therefore, we propose the (m,k)-WFQ algorithm to take into account (m,k)-firm timing constraints to provide delay guarantees of at least m packets out of any k consecutive packets without violating bandwidth fairness or misusing network resources. Using the Network Calculus theory, an analytic study gives the deterministic delay bound provided by the (m,k)-WFQ algorithm for upper bounded arrival curve traffic. We extend our analytic results for guaranteed-rate networks, such as the IntServ QoS model and ATM networks, and the DiffServ QoS model. Analytic results and simulations show a noticeable improvement in delay guarantee made by (m,k)-WFQ compared to WFQ without much degradation of bandwidth fairness.
564335
Automatic organization for digital photographs with geographic coordinates
2647804
Extended DBP for (m, k)-Firm Based QoS
In this paper, an extended DBP (E_DBP) scheme is studied for (m,k)-firm constraint. The basic idea of the proposed algorithm takes into account the distance to exit a failure state, which is a symmetrical notion of distance to fall into a failure state in DBP. Quality of Service (QoS) in terms of dynamic failure and delay is evaluated. Simulation results reveal the effectiveness of E_DBP to provide better QoS.
28755708
Automatically generating metadata for digital photographs with geographic coordinates
Given location information on digital photographs, we can automatically generate an abundance of photo-related metadata using off-the-shelf and web-based data sources. These metadata can serve as additional memory cues and filters when browsing a personal or global collection of photos.
7144496
Loss-tolerant QoS using firm constraints in guaranteed rate networks
We propose a trade-off between hard and soft real-time guarantees to maintain an acceptable QoS guarantee in overload condition and maximize efficiently the utilization of network resources. The key of our solution is that many real-time applications are loss-tolerant, but the loss profile must be well defined since successive packet losses are not suitable. We use the concept of (m,k)-firm timing constraints to define a novel guaranteed loss-tolerant QoS. Therefore, we extend the basic WFQ algorithm to take into account the firm timing constraints to provide lower delay guarantees without violating bandwidth fairness or misusing network resources. The proposal is called (m,k)-WFQ. Using network calculus formalism, analytic study gives the deterministic delay bound provided by the (m,k)-WFQ algorithm for upper bounded arrival curve traffic. Theoretical results and simulations show a noticeable improvement on delay guarantee made by (m,k)-WFQ compared to standard WFQ algorithm without much degrading bandwidth fairness.