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66
Prediction of complete gene structures in human genomic DNA
 J. Mol. Biol
, 1997
"... The problem of identifying genes in genomic DNA sequences by computational methods has attracted considerable research attention in recent years. From one point of view, the problem is closely ..."
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Cited by 1160 (9 self)
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The problem of identifying genes in genomic DNA sequences by computational methods has attracted considerable research attention in recent years. From one point of view, the problem is closely
Current methods of gene prediction, their strengths and weaknesses
, 2002
"... While the genomes of many organisms have been sequenced over the last few years, transforming such raw sequence data into knowledge remains a hard task. A great number of prediction programs have been developed that try to address one part of this problem, which consists of locating the genes along ..."
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Cited by 93 (6 self)
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While the genomes of many organisms have been sequenced over the last few years, transforming such raw sequence data into knowledge remains a hard task. A great number of prediction programs have been developed that try to address one part of this problem, which consists of locating the genes along a genome. This paper reviews the existing approaches to predicting genes in eukaryotic genomes and underlines their intrinsic advantages and limitations. The main mathematical models and computational algorithms adopted are also briefly described and the resulting software classified according to both the method and the type of evidence used. Finally, the several difficulties and pitfalls encountered by the programs are detailed, showing that improvements are needed and that new directions must be considered.
Evaluation of genefinding programs on mammalian sequences
 Genome Res
, 2001
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Identification of Genes in Human Genomic DNA
, 1997
"... A general probabilistic model of the gene structural and compositional properties of human genomic DNA is introduced and applied to the problem of identifying genes in unannotated human genomic sequences. The model uses a \Hidden semiMarkov" or semiMarkov source architecture which incorpo ..."
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Cited by 37 (1 self)
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A general probabilistic model of the gene structural and compositional properties of human genomic DNA is introduced and applied to the problem of identifying genes in unannotated human genomic sequences. The model uses a \Hidden semiMarkov&quot; or semiMarkov source architecture which incorporates probabilistic descriptions of fundamental transcriptional, translational and splicing signals, as well as length distributions and compositional features of exons, introns and intergenic regions. Distinct sets of model parameters are derived which account for many of the substantial di erences in gene density and structure observed in distinct C+G compositional regions (\isochores&quot;) of the human genome. A novel model building procedure, termed Maximal Dependence Decomposition, is introduced which captures potentially important dependencies between nonadjacent aswell as adjacent positions in a biological signal. Application of this model to the donor splice signal not only gives better discrimination of potential donor sites than previous probabilistic models, but also reveals subtle properties of this signal which suggest aspects of its biochemical function. Acceptor
Nature and structure of human genes that generate retropseudogenes
 Genome Res
, 2000
"... The human genome is estimated to contain 23,000 to 33,000 retropseudogenes. To study the properties of genes giving rise to these retroelements, we compared the structure and expression of genes with or without known retropseudogenes. Four main features have emerged from the analysis of 181 genes as ..."
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Cited by 31 (4 self)
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The human genome is estimated to contain 23,000 to 33,000 retropseudogenes. To study the properties of genes giving rise to these retroelements, we compared the structure and expression of genes with or without known retropseudogenes. Four main features have emerged from the analysis of 181 genes associated to retropseudogenes: Reversetranscribed genes are (1) widely expressed, (2) highly conserved, (3) short, and (4) GCpoor. The first two properties probably reflect the fact that genes giving rise to retropseudogenes have to be expressed in the germline. The two latter points suggest that reversetranscription and transposition is more efficient for short GCpoor mRNAs. In addition, this analysis allowed us to reject previous hypotheses that widely expressed genes are GC rich. Rather, globally, genes with a wide tissue distribution are GC poor. Retropseudogenes arise in evolution by reverse transcription of processed mRNAs and incorporation of the resulting cDNAs back into the genome (Vanin 1985). Hence, retropseudogenes can be distinguished from other types of pseudogenes by the fact that they lack introns, possess relics of the poly(A) tail at their 38 ends, and are flanked by targetsite duplications. Gen
An optimal algorithm for the maximumdensity segment problem
 SIAM Journal on Computing
"... We address a fundamental problem arising from analysis of biomolecular sequences. The input consists of two numbers wmin and wmax and a sequence S of n number pairs (ai, wi) with wi> 0. Let segment S(i, j) of S be the consecutive subsequence of S between indices i and j. The density of S(i, j) is ..."
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Cited by 22 (1 self)
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We address a fundamental problem arising from analysis of biomolecular sequences. The input consists of two numbers wmin and wmax and a sequence S of n number pairs (ai, wi) with wi> 0. Let segment S(i, j) of S be the consecutive subsequence of S between indices i and j. The density of S(i, j) is d(i, j) = (ai+ai+1+ · · ·+aj)/(wi+wi+1+ · · ·+wj). The maximumdensity segment problem is to find a maximumdensity segment over all segments S(i, j) with wmin ≤ wi + wi+1 + · · · + wj ≤ wmax. The best previously known algorithm for the problem, due to Goldwasser, Kao, and Lu, runs in O(n log(wmax−wmin+1)) time. In the present paper, we solve the problem in O(n) time. Our approach bypasses the complicated rightskew decomposition, introduced by Lin, Jiang, and Chao. As a result, our algorithm has the capability to process the input sequence in an online manner, which is an important feature for dealing with genomescale sequences. Moreover, for a type of input sequences S representable in O(m) space, we show how to exploit the sparsity of S and solve the maximumdensity segment problem for S in O(m) time. 1
LinearTime Algorithms for Computing MaximumDensity Sequence Segments with Bioinformatics Applications
"... We study an abstract optimization problem arising from biomolecular sequence analysis. For a sequence A of pairs (a i ; w i ) for i = 1; : : : ; n and w i > 0, a segment A(i; j) is a consecutive subsequence of A starting with index i and ending with index j. The width of A(i; j) is w(i; j) = ..."
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Cited by 21 (3 self)
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We study an abstract optimization problem arising from biomolecular sequence analysis. For a sequence A of pairs (a i ; w i ) for i = 1; : : : ; n and w i > 0, a segment A(i; j) is a consecutive subsequence of A starting with index i and ending with index j. The width of A(i; j) is w(i; j) = w k , and the density is ( ikj a k )=w(i; j): The maximumdensity segment problem takes A and two values L and U as input and asks for a segment of A with the largest possible density among those of width at least L and at most U . When U is unbounded, we provide a relatively simple, O(n)time algorithm, improving upon the O(n log L)time algorithm by Lin, Jiang and Chao. When both L and U are speci ed, there are no previous nontrivial results. We solve the problem in O(n) time if w i = 1 for all i, and more generally in O(n + n log(U L + 1)) time when w i 1 for all i.
Statistical Properties of Open Reading Frames in Complete Genome Sequences
, 1999
"... Some statistical properties of open reading frames in all currently available complete genome sequences are analyzed (seventeen prokatyotic genomes, and 16 chromosome sequences from the yeast genome). The size distribution of open reading frames is characterized by various techniques, such as quanti ..."
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Cited by 15 (2 self)
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Some statistical properties of open reading frames in all currently available complete genome sequences are analyzed (seventeen prokatyotic genomes, and 16 chromosome sequences from the yeast genome). The size distribution of open reading frames is characterized by various techniques, such as quantile tables, QQplots, ranksize plots (Zipf's plots), and spatial densities. The issue of the influence of CG% on the size distribution is addressed. When yeast chromosomes are compared with archaeal and eubacterial genomes, they tend to have more long open reading frames. There is little or no evidence to reject the null hypothesis that open reading frames on six different reading frames and two strands distribute similarly. A topic of current interest, the base composition asymmetry in open reading frames between the two strands, is studied using regression analysis. The base composition asymmetry at three codon positions is analyzed separately. It was shown in these genome sequences that the first codon position is G and Arich (i.e. purinerich); there is a coexistence of A and Trich branches at the second codon position; and the third codon position is weakly Trich.
Interview by author
, 2008
"... Abstract—For a Hausdorff space X, we denote by 2X the collection of all closed subsets of X. In this paper, we discuss the connectedness and locally connectedness of hyperspace 2X endowed with the vietoris topology. Further path connectedness is investigated. The results generalize some theorems of ..."
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Cited by 11 (1 self)
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Abstract—For a Hausdorff space X, we denote by 2X the collection of all closed subsets of X. In this paper, we discuss the connectedness and locally connectedness of hyperspace 2X endowed with the vietoris topology. Further path connectedness is investigated. The results generalize some theorems of E. Micheal. Keywordsconnectedness; locally connectedness; path connectedness; vietoris topology; hyperspace I.
Posttranscriptional regulation of gene expression in plants during abiotic stress. Int J Mol Sci 10: 316885. 111 3 : Rôles des canaux potassiques en réponse à l’ozone Posttranscriptional regulation of the GORK channel by O2 • participate to outward re
, 2009
"... Abstract: Land plants are anchored in one place for most of their life cycle and therefore must constantly adapt their growth and metabolism to abiotic stresses such as light intensity, temperature and the availability of water and essential minerals. Thus, plants’ subsistence depends on their abili ..."
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Cited by 8 (1 self)
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Abstract: Land plants are anchored in one place for most of their life cycle and therefore must constantly adapt their growth and metabolism to abiotic stresses such as light intensity, temperature and the availability of water and essential minerals. Thus, plants’ subsistence depends on their ability to regulate rapidly gene expression in order to adapt their physiology to their environment. Recent studies indicate that posttranscriptional regulations of gene expression play an important role in how plants respond to abiotic stresses. We will review the different mechanisms of posttranscriptional regulation of nuclear genes expression including messenger RNA (mRNA) processing, stability, localization and protein translation, and discuss their relative importance for plant adaptation to abiotic stress.