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FIXED SEQUENCE MULTIPLE TESTING By
, 2015
"... In this paper, we consider the problem of simultaneously testing many twosided hypotheses when rejections of null hypotheses are accompanied by claims of the direction of the alternative. The fundamental goal is to construct methods that control the mixed directional familywise error rate, which i ..."
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In this paper, we consider the problem of simultaneously testing many twosided hypotheses when rejections of null hypotheses are accompanied by claims of the direction of the alternative. The fundamental goal is to construct methods that control the mixed directional familywise error rate, which is the probability of making any type 1 or type 3 (directional) 1 error. In particular, attention is focused on cases where the hypotheses are ordered as H1; : : : ; Hn, so that Hi+1 is tested only if H1; : : : ; Hi have all been previously rejected. In this situation, one can control the usual familywise error rate under arbitrary dependence by the basic procedure which tests each hypothesis at level , and no other multiplicity adjustment is needed. However, we show that this is far too liberal if one also accounts for directional errors. But, by imposing certain dependence assumptions on the test statistics, one can retain the basic procedure. 1
Breaking and Fixing the NeedhamSchroeder PublicKey Protocol using FDR
, 1996
"... In this paper we analyse the well known NeedhamSchroeder PublicKey Protocol using FDR, a refinement checker for CSP. We use FDR to discover an attack upon the protocol, which allows an intruder to impersonate another agent. We adapt the protocol, and then use FDR to show that the new protocol is s ..."
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Cited by 716 (13 self)
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In this paper we analyse the well known NeedhamSchroeder PublicKey Protocol using FDR, a refinement checker for CSP. We use FDR to discover an attack upon the protocol, which allows an intruder to impersonate another agent. We adapt the protocol, and then use FDR to show that the new protocol is secure, at least for a small system. Finally we prove a result which tells us that if this small system is secure, then so is a system of arbitrary size. 1 Introduction In a distributed computer system, it is necessary to have some mechanism whereby a pair of agents can be assured of each other's identitythey should become sure that they really are talking to each other, rather than to an intruder impersonating the other agent. This is the role of an authentication protocol. In this paper we use the Failures Divergences Refinement Checker (FDR) [11, 5], a model checker for CSP, to analyse the NeedhamSchroeder PublicKey Authentication Protocol [8]. FDR takes as input two CSP processes, ...
A greedy algorithm for aligning DNA sequences
 J. COMPUT. BIOL
, 2000
"... For aligning DNA sequences that differ only by sequencing errors, or by equivalent errors from other sources, a greedy algorithm can be much faster than traditional dynamic programming approaches and yet produce an alignment that is guaranteed to be theoretically optimal. We introduce a new greedy a ..."
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Cited by 576 (16 self)
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For aligning DNA sequences that differ only by sequencing errors, or by equivalent errors from other sources, a greedy algorithm can be much faster than traditional dynamic programming approaches and yet produce an alignment that is guaranteed to be theoretically optimal. We introduce a new greedy
Maximum Likelihood Phylogenetic Estimation from DNA Sequences with Variable Rates over Sites: Approximate Methods
 J. Mol. Evol
, 1994
"... Two approximate methods are proposed for maximum likelihood phylogenetic estimation, which allow variable rates of substitution across nucleotide sites. Three data sets with quite different characteristics were analyzed to examine empirically the performance of these methods. The first, called ..."
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Cited by 540 (28 self)
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, and four such categories appear to be sufficient to produce both an optimum, or nearoptimum fit by the model to the data, and also an acceptable approximation to the continuous dis tribution. The second method, called "fixedrates mod el," classifies sites into several classes according
Basecalling of automated sequencer traces using phred. I. Accuracy Assessment
 GENOME RES
, 1998
"... The availability of massive amounts of DNA sequence information has begun to revolutionize the practice of biology. As a result, current largescale sequencing output, while impressive, is not adequate to keep pace with growing demand and, in particular, is far short of what will be required to obta ..."
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Cited by 1602 (4 self)
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The availability of massive amounts of DNA sequence information has begun to revolutionize the practice of biology. As a result, current largescale sequencing output, while impressive, is not adequate to keep pace with growing demand and, in particular, is far short of what will be required
Tandem repeats finder: a program to analyze DNA sequences
, 1999
"... A tandem repeat in DNA is two or more contiguous, approximate copies of a pattern of nucleotides. Tandem repeats have been shown to cause human disease, may play a variety of regulatory and evolutionary roles and are important laboratory and analytic tools. Extensive knowledge about pattern size, co ..."
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Cited by 946 (9 self)
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, copy number, mutational history, etc. for tandem repeats has been limited by the inability to easily detect them in genomic sequence data. In this paper, we present a new algorithm for finding tandem repeats which works without the need to specify either the pattern or pattern size. We model tandem
A Critical Point For Random Graphs With A Given Degree Sequence
, 2000
"... Given a sequence of nonnegative real numbers 0 ; 1 ; : : : which sum to 1, we consider random graphs having approximately i n vertices of degree i. Essentially, we show that if P i(i \Gamma 2) i ? 0 then such graphs almost surely have a giant component, while if P i(i \Gamma 2) i ! 0 the ..."
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Cited by 511 (8 self)
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Given a sequence of nonnegative real numbers 0 ; 1 ; : : : which sum to 1, we consider random graphs having approximately i n vertices of degree i. Essentially, we show that if P i(i \Gamma 2) i ? 0 then such graphs almost surely have a giant component, while if P i(i \Gamma 2) i ! 0
Insertion sequences
 Microbiol Mol. Biol. Rev
, 1998
"... These include: Receive: RSS Feeds, eTOCs, free email alerts (when new articles cite this article), more» Downloaded from ..."
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Cited by 426 (3 self)
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These include: Receive: RSS Feeds, eTOCs, free email alerts (when new articles cite this article), more» Downloaded from
Near Optimal Signal Recovery From Random Projections: Universal Encoding Strategies?
, 2004
"... Suppose we are given a vector f in RN. How many linear measurements do we need to make about f to be able to recover f to within precision ɛ in the Euclidean (ℓ2) metric? Or more exactly, suppose we are interested in a class F of such objects— discrete digital signals, images, etc; how many linear m ..."
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Cited by 1513 (20 self)
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measurements do we need to recover objects from this class to within accuracy ɛ? This paper shows that if the objects of interest are sparse or compressible in the sense that the reordered entries of a signal f ∈ F decay like a powerlaw (or if the coefficient sequence of f in a fixed basis decays like a power
Results 1  10
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