bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protein homology detection using string alignment kernels
Authors: Saigo Hiroto , Vert Jean-Philippe , Ueda Nobuhisa , Akutsu Tatsuya 
Published: March 2004

Abstract
Motivation: Remote homology detection between protein sequences is a central problem in computational biology. Discriminative methods involving support vector machines (SVMs) are currently the most effective methods for the problem of superfamily recognition in the Structural Classification Of Proteins (SCOP) database. The performance of SVMs depends critically on the kernel function used to quantify the similarity between sequences.
Results: We propose new kernels for strings adapted to biological sequences, which we call local alignment kernels. These kernels measure the similarity between two sequences by summing up scores obtained from local alignments with gaps of the sequences. When tested in combination with SVM on their ability to recognize SCOP superfamilies on a benchmark dataset, the new kernels outperform state-of-the-art methods for remote homology detection.
Availability: Software and data available upon request.
Fuzzy J-Means and VNS methods for clustering genes from microarray data
Authors: Belacel Nabil , Čuperlović-Culf Miroslava , Laflamme Mark , Ouellette Rodney 
Published: March 2004

Abstract
Motivation: In the interpretation of gene expression data from a group of microarray experiments that include samples from either different patients or conditions, special consideration must be given to the pleiotropic and epistatic roles of genes, as observed in the variation of gene coexpression patterns. Crisp clustering methods assign each gene to one cluster, thereby omitting information about the multiple roles of genes.
Results: Here, we present the application of a local search heuristic, Fuzzy J-Means, embedded into the variable neighborhood search metaheuristic for the clustering of microarray gene expression data. We show that for all the datasets studied this algorithm outperforms the standard Fuzzy C-Means heuristic. Different methods for the utilization of cluster membership information in determining gene coregulation are presented. The clustering and data analyses were performed on simulated datasets as well as experimental cDNA microarray data for breast cancer and human blood from the Stanford Microarray Database.
Availability: The source code of the clustering software (C programming language) is freely available from Nabil.Belacel@nrc-cnrc.gc.ca
Why neural networks should not be used for HIV-1 protease cleavage site prediction
Authors: Rögnvaldsson Thorsteinn , You Liwen 
Published: March 2004

Abstract
Summary: Several papers have been published where nonlinear machine learning algorithms, e.g. artificial neural networks, support vector machines and decision trees, have been used to model the specificity of the HIV-1 protease and extract specificity rules. We show that the dataset used in these studies is linearly separable and that it is a misuse of nonlinear classifiers to apply them to this problem. The best solution on this dataset is achieved using a linear classifier like the simple perceptron or the linear support vector machine, and it is straightforward to extract rules from these linear models. We identify key residues in peptides that are efficiently cleaved by the HIV-1 protease and list the most prominent rules, relating them to experimental results for the HIV-1 protease.
Motivation: Understanding HIV-1 protease specificity is important when designing HIV inhibitors and several different machine learning algorithms have been applied to the problem. However, little progress has been made in understanding the specificity because nonlinear and overly complex models have been used.
Results: We show that the problem is much easier than what has previously been reported and that linear classifiers like the simple perceptron or linear support vector machines are at least as good predictors as nonlinear algorithms. We also show how sets of specificity rules can be generated from the resulting linear classifiers.
Availability: The datasets used are available at http://www.hh.se/staff/bioinf/
‘Harvester’: a fast meta search engine of human protein resources
Authors: Liebel Urban , Kindler Bjoern , Pepperkok Rainer 
Published: March 2004

Abstract
Summary: We have developed a Web-based tool named ‘Harvester’ that bulk-collects bioinformatic data on human proteins from various databases and prediction servers. The information on every single protein is assembled on a single HTML page as a combination of database screen-shots and plain text. A full text meta search engine, similar to Google™, allows screening of the whole genome proteome for current protein functions and predictions in a few seconds. With Harvester it is now possible to compare and check the quality of different database entries and prediction algorithms on a single page. A feedback forum allows users to comment on Harvester and to report database inconsistencies.
Availability: The service is freely available to the academic community at http://harvester.embl.de.
Primer design using genetic algorithm
Authors: Wu Jain-Shing , Lee Chungnan , Wu Chien-Chang , Shiue Yow-Ling 
Published: March 2004

Abstract
Motivation: Before performing a polymerase chain reaction experiment, a pair of primers to clip the target DNA subsequence is required. However, this is a tedious task as too many constraints need to be satisfied. Various kinds of approaches for designing a primer have been proposed in the last few decades, but most of them do not have restriction sites on the designed primers and do not satisfy the specificity constraint.
Results: The proposed algorithm imitates nature's process of evolution and genetic operations on chromosomes in order to achieve optimal solutions, and is a best fit for DNA behavior. Experimental results indicate that the proposed algorithm can find a pair of primers that not only obeys the design properties but also has a specific restriction site and specificity. Gel electrophoresis verifies that the proposed method really can clip out the target sequence.
Availability: A public version of the software is available on request from the authors.
Haplotypes histories as pathways of recombinations
Authors: El-Mabrouk Nadia , Labuda Damian 
Published: March 2004

Abstract
Motivation: The diversity of a haplotype, represented as a string of polymorphic sites along a DNA sequence, increases exponentially with the number of sites if recombinations are taking place. Reconstructing the history of recombinations compared with that of the polymorphic sites is thus extremely difficult. However, in the human genome, because of the relatively simple pattern of haplotype diversity dominated by a few ancestral haplotypes, the complexity of the recombinational network can be reduced, thus making its reconstruction feasible. We focus on the problem of inferring the recombination pathways starting with putative ancestral haplotypes and leading to new rare recombinant haplotypes.
Results: We describe classes of recombinations that represent the whole set of minimal recombination pathways leading to a new haplotype. We present an O(n2) algorithm that outputs such representative recombination pathways. We apply it to haplotypes of the 8 kb dystrophin gene segment dys44.
Availability: A software implementing the algorithm and some other extentions has been developed on a Java platform (JDK 1.3.1). It is freely available at http://www.iro.umontreal.ca/~mabrouk/
Haplotype reconstruction from genotype data using Imperfect Phylogeny
Authors: Halperin Eran , Eskin Eleazar 
Published: March 2004

Abstract
Critical to the understanding of the genetic basis for complex diseases is the modeling of human variation. Most of this variation can be characterized by single nucleotide polymorphisms (SNPs) which are mutations at a single nucleotide position. To characterize the genetic variation between different people, we must determine an individual's haplotype or which nucleotide base occurs at each position of these common SNPs for each chromosome. In this paper, we present results for a highly accurate method for haplotype resolution from genotype data. Our method leverages a new insight into the underlying structure of haplotypes that shows that SNPs are organized in highly correlated ‘blocks’. In a few recent studies, considerable parts of the human genome were partitioned into blocks, such that the majority of the sequenced genotypes have one of about four common haplotypes in each block. Our method partitions the SNPs into blocks, and for each block, we predict the common haplotypes and each individual's haplotype. We evaluate our method over biological data. Our method predicts the common haplotypes perfectly and has a very low error rate (&lt;2% over the data) when taking into account the predictions for the uncommon haplotypes. Our method is extremely efficient compared with previous methods such as PHASE and HAPLOTYPER. Its efficiency allows us to find the block partition of the haplotypes, to cope with missing data and to work with large datasets.
Availability: The algorithm is available via a Web server at http://www.calit2.net/compbio/hap/
Sight: automating genomic data-mining without programming skills
Authors: Meskauskas Audrius , Lehmann-Horn Frank , Jurkat-Rott Karin 
Published: March 2004

Abstract
Summary: We created and tested Sight, a Java-based package that provides a user-friendly interface to generate and connect agents for automatic genomic data-mining for individual requirements without requiring programming skills from the user.
Availability: http://physiologie.uni-ulm.de//Seiten/Arbeitsgruppe/Jurkat-Rott/Jurkat-Rott.htm. The system does not require additional components and runs on IBM PCs under Windows (NT 4.0, 2000 and XP) or Linux (Phat 4.0 and Mandrake 9.0).
An a posteriori strategy for enhancing gene discovery in anonymous cDNA microarray experiments
Authors: Anderssen R. S. , Wu Y. , Dolferus R. , Saunders I. 
Published: March 2004

Abstract
Motivation: Because of the high cost of sequencing, the bulk of gene discovery is performed using anonymous cDNA microarrays. Though the clones on such arrays are easier and cheaper to construct and utilize than unigene and oligonucleotide arrays, they are there in proportion to their corresponding gene expression activity in the tissue being examined. The associated redundancy will be there in any pool of possibly interesting differentially expressed clones identified in a microarray experiment for subsequent sequencing and investigation. An a posteriori sampling strategy is proposed to enhance gene discovery by reducing the impact of the redundancy in the identified pool.
Results: The proposed strategy exploits the fact that individual genes that are highly expressed in a tissue are more likely to be present as a number of spots in an anonymous library and, as a direct consequence, are also likely to give higher fluorescence intensity responses when present in a probe in a cDNA microarray experiment. Consequently, spots that respond with low intensities will have a lower redundancy and so should be sequenced in preference to those with the highest intensities. The proposed method, which formalizes how the fluorescence intensity of a spot should be assessed, is validated using actual microarray data, where the sequences of all the clones in the identified pool had been previously determined. For such validations, the concept of a repeat plot is introduced. It is also utilized to visualize and examine different measures for the characterization of fluorescence intensity. In addition, as confirmatory evidence, sequencing from the lowest to the highest intensities in a pool, with all the sequences known, is compared graphically with their random sequencing. The results establish that, in general, the opportunity for gene discovery is enhanced by avoiding the pooling of different biological libraries (because their construction will have involved different hybridization episodes) and concentrating on the clones with lower fluorescence intensities.
Multiple-sequence functional annotation and the generalized hidden Markov phylogeny
Authors: McAuliffe Jon D. , Pachter Lior , Jordan Michael I. 
Published: March 2004

Abstract
Motivation: Phylogenetic shadowing is a comparative genomics principle that allows for the discovery of conserved regions in sequences from multiple closely related organisms. We develop a formal probabilistic framework for combining phylogenetic shadowing with feature-based functional annotation methods. The resulting model, a generalized hidden Markov phylogeny (GHMP), applies to a variety of situations where functional regions are to be inferred from evolutionary constraints.
Results: We show how GHMPs can be used to predict complete shared gene structures in multiple primate sequences. We also describe shadower, our implementation of such a prediction system. We find that shadower outperforms previously reported ab initio gene finders, including comparative human–mouse approaches, on a small sample of diverse exonic regions. Finally, we report on an empirical analysis of shadower's performance which reveals that as few as five well-chosen species may suffice to attain maximal sensitivity and specificity in exon demarcation.
Availability: A Web server is available at http://bonaire.lbl.gov/shadower
Genomic data visualization on the Web
Authors: Wu Wei , Noble William S. 
Published: March 2004

Abstract
Many types of genomic data can be represented in matrix format, with rows corresponding to genes and columns corresponding to gene features. The heat map is a popular technique for visualizing such data, plotting the data on a two-dimensional grid and using a color scale to represent the magnitude of each matrix entry. Prism is a Web-based software tool for generating annotated heat map visualizations of genome-wide data quickly. The tool provides a selection of genome-specific annotation catalogs as well as a catalog upload capability. The heat maps generated are clickable, allowing the user to drill down to examine specific matrix entries, and gene annotations are linked to relevant genomic databases.
Availability: http://noble.gs.washington.edu/prism
GenAlyzer: interactive visualization of sequence similarities between entire genomes
Authors: Choudhuri Jomuna V. , Schleiermacher Chris , Kurtz Stefan , Giegerich Robert 
Published: March 2004

Abstract
Summary: Genalyzer is a software tool designed for the interactive visualization of sequence matches between DNA or protein sequences. It provides visualizations on different levels of granularity, from complete overviews via zoomed regions to alignments of particular matching substrings. Genalyzer can efficiently handle very large datasets, allowing to display tens of thousands of matches between sequences of tens of millions of bases.
Availability: Genalyzer is available free of charge for non-commercial research institutions. For more details, see http://www.genalyzer.de
Spatial and temporal variation in patch occupancy and population density in a model system of an arctic Collembola species assemblage
Authors: Ims Rolf A. , Petter Leinaas Hans , Coulson Steve 
Published: March 2004

We employed an experimental model system to investigate the mechanisms underlying patterns of patch occupancy and population density in a high arctic assemblage of Collembola species inhabiting a sedge tussock landscape on Svalbard. The replicate model systems consisted of 5 cores of the tussocks (habitat patches) imbedded in a barren matrix. Four of the patches were open so that animals could migrate between them, while there was one closed patch per system to test the effect of migration on extinction rate. There were model systems of two types: one with long and one with short inter‐patch distances to test the effect of patch isolation on colonisation and extinction rates. Each of the four most common collembolan species at the field site were introduced to two open patches per system (source patches), with the other two functioning as colonisation patches for the species. The experiment was run in an ecotrone over three identical, simulated arctic summers separated by winters of 3 weeks. Six replicates of systems with short and long inter‐patch distances were sampled at the end of each summer. The species varied markedly in their performance in both open arenas and closed patches, indicating differential responses to patch humidity, consistent with their differential distribution along the moisture gradient in the field site.The extinction – colonisation dynamics differed markedly between species as predicted from our field studies. This could partly be ascribed to differential dispersal and colonisation ability, but also to different tolerance to spatially variable patch quality and/or tendency for aggregative behaviour. Three of the species exhibited dynamics that superficially resemble what could be expected from classical metapopulation dynamics. However, there was a striking discrepancy between what would be expected from the effect of migration on the extinction rate of isolated patches (in particular closed patches) and the observed rates. Thus, metapopulation processes, such as stochastic colonisation and extinction events due to demographic stochasticity, were relatively unimportant compared to other sources of spatial variability among which subtle differences in patch quality are probably most important. We discuss the value of combining field studies with model system experiments, in particular when habitat quality cannot easily be measured in the field. However, our field and laboratory studies also emphasise the need for a thorough knowledge of species‐specific life history traits for making biologically sound interpretations based on both observational and experimental data.
Scale‐dependence of movement rates in stream invertebrates
Authors: Englund Göran , Hambäck Peter A. 
Published: March 2004

We used analytical models and random walk simulations in a one‐dimensional habitat to study the scale‐dependence of migration rates in stream invertebrates. Our models predict that per capita migration rate is inversely proportional to patch length when patches are large compared to the scale of movements. When patches are small the scale‐dependence is weaker and primarily determined by the length of individual movements (steps) relative to patch size. Laboratory experiments using isopods (Asellus aquaticus L.) and mayfly nymphs (Baetis sp.) confirmed that the strength of the scale‐dependence decreased with increasing step length.For the case when step length distributions follow an exponential probability distribution, which is often the case for stream organisms, we provide a simple model that allows the scale‐dependence to be predicted from the mean step length. We fitted this model to published field data on drift densities at different downstream distances from a net that blocks the drift from upstream areas. Agreement between model and data was excellent in most cases. We then used already published data on the length of induced drift movements to predict the scale‐dependence that was observed in block experiments performed in the same system. Predicted and observed scale‐dependence showed very close agreement.We conclude that our models and published data on drift distances can be used to calculate the expected scale‐dependence of per capita emigration rates for a large number of taxa under a wide range of environmental conditions.
Profile Parsimony (PP): an analysis under Implied Weights (IW)
Authors: Arias J. Salvador , Miranda‐Esquivel Daniel Rafael 
Published: March 2004

Abstract Faith and Trueman [Syst. Biol. (2001) 331] recently proposed “Profile Parsimony” (PP) as a new form of phylogenetic analysis, but it is equivalent to the Implied Weights (IW) method when certain functions are used. The PP method cannot accommodate missing/inapplicable cells and/or multistate characters. Finally we demonstrate that, as defined, PP scores are not random, and there is no need to generate random trees as proposed by Faith and Trueman.
Abstracts of the 22nd Annual Meeting of the Willi Hennig Society
Authors: Stevenson Dennis Wm. 
Published: March 2004

The 22nd annual meeting of the Willi Hennig Society was held at the New York Botanical Garden in the Bronx, New York from July 20–24. There were 154 participants representing 15 countries and a total of 65 talks, 16 posters, and four software presentations. There were five symposia ranging from sequence alignment to worm biology to biogeography. As with Hennig 21 at Helsinki, there was strong student participation. Student posters represented 13 of the total 16 posters and 23 of 65 oral presentations were by students. Student presentations were part of all symposia. The strength and future of the Willi Hennig Society resides in the students and recent meetings indicate a healthy society for the future.The Student Awards Committee consisted of Jonathan A. Coddington, Arnold G. Kluge and Gunilla Ståhls. The winners were Taran Grant, the Hennig Prize ($1000) for “Insertions and deletions in the evolution of equal‐length DNA fragments”; Johannes Bergsten, the Brundin Prize ($500) for “Acilius Phylogeny (Coleoptera: Dytiscidae), Problems with Long‐branch attraction and Morphological Intersexual Coevolution”; and A. R. Lindgren, the Rosen Prize ($250) for “A New Phylogeny of the Cephalopoda Using Total Evidence”.
Investigations into the phylogenetic position of Micrognathozoa using four molecular loci
Authors: Giribet Gonzalo , Sørensen Martin V. , Funch Peter , Kristensen Reinhardt Møbjerg , Sterrer Wolfgang 
Published: March 2004

AbstractMicrognathozoa is the most recently discovered higher metazoan lineage. The sole known species of the group, Limnognathia maerski, was originally reported from running freshwater in Disko Island (Greenland), and has recently been recorded from the subantarctic region. Because of the presence of a particular type of jaws formed of special cuticularized rods, similar to those of gnathostomulids and rotifers, the three metazoan lineages were considered closely related, and assigned to the clade Gnathifera. A phylogenetic comparison of four molecular loci for Limnognathia maerski and other newly generated sequences of mainly acoelomate animals showed that Micrognathozoa may constitute an independent lineage from those of Gnathostomulida and Rotifera. However, the exact position of Micrognathozoa could not be determined due to the lack of support for any given relationships and due to the lack of stability in the position of Limnognathia maerski under analysis of different loci and of different parameter sets for sequence comparison. Nuclear loci tend to place Micrognathozoa with the syndermatan/cycliophoran taxa, but the addition of the mitochondrial gene cytochrome c oxidase subunit I favors a relationship of Micrognathozoa to Entoprocta.
Total evidence phylogeny of Gasterosteidae: combining molecular, morphological and behavioral data
Authors: Mattern Michelle Y. , McLennan Deborah A. 
Published: March 2004

AbstractGenealogical relationships among Gasterosteidae (Teleostei: Gasterosteiformes) were tested with 84 morphological, 48 behavioral, and 2879 molecular characters. Phylogenetic analysis of the combined data set identified a single (CI = 0.735) best‐supported hypothesis (Spinachia(Apeltes((Pungitius+Culaea)(Gasterosteus aculeatus+G.wheatlandi)))). This hypothesis is identical to previous phylogenetic propositions proposed on the basis of behavioral, and behavioral plus morphological data. Our hypothesis, however, differed from a molecular‐based phylogeny in the placement ofApeltes. This analysis highlights the importance of combining all available evidence in order to produce the best‐supported proposition of genealogical relationships.