25344339
Pancyclic out-arcs of a Vertex in Tournaments
Abstract Thomassen (J. Combin. Theory Ser. B 28, 1980 , 142–163) proved that every strong tournament contains a vertex x such that each arc going out from x is contained in a Hamiltonian cycle. In this paper, we extend the result of Thomassen and prove that a strong tournament contains a vertex x such that every arc going out from x is pancyclic, and our proof yields a polynomial algorithm to find such a vertex. Furthermore, as another consequence of our main theorem, we get a result of Alspach (Canad. Math. Bull. 10, 1967 , 283–286) that states that every arc of a regular tournament is pancyclic.
15445426
An Ore-type Condition for Cyclability
A graph G is said to be cyclable if for each orientation D of G, there exists a set S(D) ?V(G) such that reversing all the arcs with one end in S results in a Hamiltonian digraph. Let G be a simple graph of even ordern? 8. In this paper, we show that if the degree sum of any two nonadjacent vertices is not less thann+ 1, then G is cyclable and the lower bound is sharp.
8284293
A note on list improper coloring planar graphs
A graph G is called (k, d)*-choosable if, for every list assignment L satisfying |L(v)| = k for all v ϵ V(G), there is an L-coloring of G such that each vertex of G has at most d neighbors colored with the same color as itself. In this note, we prove that every planar graph without 4-cycles and l-cycles for some l ϵ {5, 6, 7} is (3, 1)*-choosable.
29686713
A note on Ramsey numbers with two parameters
The Ramsey number R(G1, G2) is the smallest integer p such that for any graph G on p vertices either G contains G1 or G- contains G2, where G- denotes the complement of G. In this paper, some new bounds with two parameters for the Ramsey number R(G1, G2), under some assumptions, are obtained. Especially, we prove that R(K6 - e, K6) ≤ 116 and R(K6 - e, K7) ≤ 202, these improve the two upper bounds for the classical Ramsey number in [S.P. Radziszowski, Small Ramsey number, Electron. J. Combin. DSI (2002) 1-36].
5672527
Complementary cycles containing a fixed arc in diregular bipartite tournaments
Abstract Let ( x , y ) be a specified arc in a k -regular bipartite tournament B . We prove that there exists a cycle C of length four through ( x , y ) in B such that B − C is hamiltonian.
30370540
On (d, 2)-dominating numbers of binary undirected de Bruijn graphs
Abstract In this paper, we show that: (i) For n-dimensional undirected binary de Bruijn graphs, UB(n), n⩾4, there is a vertex x=x 1 x 1 x 1 ⋯ x 1 x 1 (x1=1 or 0) such that for any other vertex t there exist at least two internally disjoint paths of length at most n−1 between x and t in UB(n), i.e., the (n−1,2)-dominating number of UB(n) is equal to one. (ii) For n⩾5, let S={100⋯01,011⋯10}. For any other vertex t there exist at least two internally disjoint paths of length at most n−2 between t and S in UB(n), i.e., the (n−2,2)-dominating number of UB(n) is no more than 2.
901722
Dynamic programming algorithms for haplotype block partitioning: applications to human chromosome 21 haplotype data
Recent studies have shown that the human genome has a haplotype block structure such that it can be divided into discrete blocks of limited haplotype diversity. Patil et al. [6] and Zhang et al. [12] developed algorithms to partition haplotypes into blocks with minimum number of tag SNPs for the entire chromosome. However, it is not clear how to partition haplotypes into blocks with restricted number of SNPs when only limited resources are available. In this paper, we first formulated this problem as finding a block partition with a fixed number of tag SNPs that can cover the maximal percentage of a genome. Then we solved it by two dynamic programming algorithms, which are fairly flexible to take into account the knowledge of functional polymorphism. We applied our algorithms to the published SNP data of human chromosome 21 combining with the functional information of these SNPs and demonstrated the effectiveness of them. Statistical investigation of the relationship between the starting points of a block partition and the coding and non-coding regions illuminated that the SNPs at these starting points are not significantly enriched in coding regions. We also developed an efficient algorithm to find all possible long local maximal haplotypes across a subset of samples. After applying this algorithm to the human chromosome 21 haplotype data, we found that samples with long local haplotypes are not necessarily globally similar.
920164
Neuronal Tuning: To Sharpen or Broaden?
Sensory and motor variables are typically represented by a population of broadly tuned neurons. A coarser representation with broader tuning can often improve coding accuracy, but sometimes the accuracy may also improve with sharper tuning. The theoretical analysis here shows that the relationship between tuning width and accuracy depends crucially on the dimension of the encoded variable. A general rule is derived for how the Fisher information scales with the tuning width, regardless of the exact shape of the tuning function, the probability distribution of spikes, and allowing some correlated noise between neurons. These results demonstrate a universal dimensionality effect in neural population coding.
45668969
Efficient application migration under compiler guidance
9738891
Comparing multiple RNA secondary structures using tree comparisons
In a previous paper, an algorithm was presented for analyzing multiple RNA secondary structures utilizing a multiple string alignment algorithm. In this paper we present another approach to the problem of comparing many secondary structures by utilizing a very efficient tree-matching algorithm that will compare two trees in O([T1] X [T2] X L1 X L2) in the worst case and very close to O([T1] X [T2]) for average trees representing secondary structures. The result of the pairwise comparison algorithm is then used with a cluster algorithm to produce a multiple structure clustering which can be displayed in a taxonomy tree to show related structures.
11712321
HAPLORE: a program for haplotype reconstruction in general pedigrees without recombination
MOTIVATION
Haplotype reconstruction is an essential step in genetic linkage and association studies. Although many methods have been developed to estimate haplotype frequencies and reconstruct haplotypes for a sample of unrelated individuals, haplotype reconstruction in large pedigrees with a large number of genetic markers remains a challenging problem.


METHODS
We have developed an efficient computer program, HAPLORE (HAPLOtype REconstruction), to identify all haplotype sets that are compatible with the observed genotypes in a pedigree for tightly linked genetic markers. HAPLORE consists of three steps that can serve different needs in applications. In the first step, a set of logic rules is used to reduce the number of compatible haplotypes of each individual in the pedigree as much as possible. After this step, the haplotypes of all individuals in the pedigree can be completely or partially determined. These logic rules are applicable to completely linked markers and they can be used to impute missing data and check genotyping errors. In the second step, a haplotype-elimination algorithm similar to the genotype-elimination algorithms used in linkage analysis is applied to delete incompatible haplotypes derived from the first step. All superfluous haplotypes of the pedigree members will be excluded after this step. In the third step, the expectation-maximization (EM) algorithm combined with the partition and ligation technique is used to estimate haplotype frequencies based on the inferred haplotype configurations through the first two steps. Only compatible haplotype configurations with haplotypes having frequencies greater than a threshold are retained.


RESULTS
We test the effectiveness and the efficiency of HAPLORE using both simulated and real datasets. Our results show that, the rule-based algorithm is very efficient for completely genotyped pedigree. In this case, almost all of the families have one unique haplotype configuration. In the presence of missing data, the number of compatible haplotypes can be substantially reduced by HAPLORE, and the program will provide all possible haplotype configurations of a pedigree under different circumstances, if such multiple configurations exist. These inferred haplotype configurations, as well as the haplotype frequencies estimated by the EM algorithm, can be used in genetic linkage and association studies.


AVAILABILITY
The program can be downloaded from http://bioinformatics.med.yale.edu.