bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vegetative Compatibility Among Isolates of Colletotrichum gloeosporioides from Yam (Dioscorea spp.) in Nigeria
Authors: Abang M. M. , Hoffmann P. , Winter S. , Green K. R. , Wolf G. A. 
Published: January 2004

AbstractIsolates of Colletotrichum gloeosporioides obtained from yam‐based cropping systems in Nigeria, previously characterized on the basis of morphology, virulence and rDNA internal transcribed spacer (ITS) sequence variation were further compared for vegetative compatibility (VC). Chlorate‐resistant nitrate non‐utilizing (nit) mutants were generated from the isolates and used in complementation (heterokaryon) tests. Tests of VC between complementary mutants from different isolates indicated the presence of several genotypes within a single field, suggesting limited clonal spread. In some cases, isolates obtained from the same lesion were observed to belong to different vegetative compatibility groups (VCGs). No compatibility was observed between isolates of the highly virulent slow‐growing grey (SGG), the moderately virulent fast‐growing salmon (FGS) and the avirulent/weakly virulent fast‐growing grey (FGG) strains. Forty‐one C. gloeosporioides isolates belonged to 28 VCGs, giving a genotype diversity estimate of 0.68. This diversity confirmed the high variability of the pathogen population as revealed by previous characterization studies, however, a correlation between VCGs and isolate groupings based on morphology and virulence was not found. The finding that an isolate from weed was compatible with yam isolates indicated that transfer of important traits, such as virulence, may take place between isolates from yam and non‐yam hosts. The VCG diversity revealed by this study suggests that in addition to asexual reproduction, sexual reproduction may play an important role in the epidemiology of anthracnose on yam.
Occurrence of Antimicrobial Serin‐Proteinases in Sunflower Seeds
Authors: Mendieta J. R. , Giudici A. M. , de la Canal L. 
Published: January 2004

AbstractUsing an experimental approach directed to the isolation of antimicrobial proteins, we have detected the presence of a trypsin inhibitor (TI) with associated antifungal activity in sunflower seeds. Purification of the isolated protein by affinity chromatography on a trypsin‐agarose matrix confirmed that a trypsin inhibitor was responsible for the inhibition of spore germination of the fungal pathogen Sclerotinia sclerotiorum. The protein is a potent antifungal compound as it can completely inhibit the germination of S. sclerotiorum ascospores at a concentration of 14 μg/ml. The putative contribution of this TI to control fungal invasion is discussed.
Hypovirulence of Didymella bryoniae Associated with dsRNA
Authors: Urs R. R. , Mayhew D. E. , Roberts P. D. 
Published: January 2004

Abstract Didymella bryoniae, isolate 98–18, recovered from watermelon seedlings with symptoms of gummy stem blight, showed abnormal growth, mycelial lysis, sectoring, barrage and limited production of fruiting bodies in culture. A dsRNA (approximately 6.5 kbp) was associated with isolate 98–18 and other isolates showing abnormal mycelial growth. Transfer of dsRNA from 98–18 to virulent isolates Tk659 and TK671 via hyphal anastamosis was achieved only by consecutive exposure to 98–18, but not to virulent isolates RJ1 and RJ2. Transfer of dsRNA via infiltration through growth media to virulent isolates RJ1, RJ2, TK659 and TK671 was unsuccessful. The disease severity index of isolate 98–18 was reduced 53% on watermelon, 32% on cataloupe and 26% on yellow squash compared with isolate RJ2, suggesting that the presence of the dsRNA is associated with reduced virulence of D. bryoniae isolate 98–18. Zucchini and yellow squash were resistant to both isolates when tested.
Prediction of locally stable RNA secondary structures for genome-wide surveys
Authors: Hofacker I. L. , Priwitzer B. , Stadler P. F. 
Published: January 2004

Abstract
Motivation: Recently novel classes of functional RNAs, most prominently the miRNAs have been discovered, strongly suggesting that further types of functional RNAs are still hidden in the recently completed genomic DNA sequences. Only few techniques are known, however, to survey genomes for such RNA genes. When sufficiently similar sequences are not available for comparative approaches the only known remedy is to search directly for structural features.
Results: We present here efficient algorithms for computing locally stable RNA structures at genome-wide scales. Both the minimum energy structure and the complete matrix of base pairing probabilities can be computed in 𝒪(N × L2) time and 𝒪(N + L2) memory in terms of the length N of the genome and the size L of the largest secondary structure motifs of interest. In practice, the 100 Mb of the complete genome of Caenorhabditis elegans can be folded within about half a day on a modern PC with a search depth of L = 100. This is sufficient example for a survey for miRNAs.
Availability: The software described in this contribution will be available for download at http://www.tbi.univie.ac.at/~ivo/RNA/ as part of the Vienna RNA Package.
Shared relationship analysis: ranking set cohesion and commonalities within a literature-derived relationship network
Authors: Wren Jonathan D. , Garner Harold R. 
Published: January 2004

Abstract
Motivation: There is a general scientific need to be able to identify and evaluate what any given set of ‘objects’ (e.g. genes, phenotypes, chemicals, diseases) has in common. Whether it is to classify, expand upon or identify commonalities and functional groupings, informational needs can be diverse and the best source to identify relationships among a potentially heterogeneous set of objects is the scientific literature.
Results: We first establish a network of related objects by their co-occurrence within MEDLINE records. A set of objects within this network can then be queried to identify shared relationships, and a method is presented to score their statistical relevance by comparing observed frequencies with what would be expected in a random network model. Using Gene Ontology (GO) categories, we demonstrate that this method enables a quantitative ranking of the ‘cohesiveness’ of a set of objects and, importantly, allows other objects related to this set to be identified and evaluated for their ‘cohesion’ to it.
Supplemental information: A list of ranked genes related to each GO category analyzed can be found at http://innovation.swmed.edu/IRIDESCENT/GO_relationships.htm
Comparative evaluation of word composition distances for the recognition of SCOP relationships
Authors: Vinga Susana , Gouveia-Oliveira Rodrigo , Almeida Jonas S. 
Published: January 2004

Abstract
Motivation: Alignment-free metrics were recently reviewed by the authors, but have not until now been object of a comparative study. This paper compares the classification accuracy of word composition metrics therein reviewed. It also presents a new distance definition between protein sequences, the W-metric, which bridges between alignment metrics, such as scores produced by the Smith–Waterman algorithm, and methods based solely in L-tuple composition, such as Euclidean distance and Information content.
Results: The comparative study reported here used the SCOP/ASTRAL protein structure hierarchical database and accessed the discriminant value of alternative sequence dissimilarity measures by calculating areas under the Receiver Operating Characteristic curves. Although alignment methods resulted in very good classification accuracy at family and superfamily levels, alignment-free distances, in particular Standard Euclidean Distance, are as good as alignment algorithms when sequence similarity is smaller, such as for recognition of fold or class relationships. This observation justifies its advantageous use to pre-filter homologous proteins since word statistics techniques are computed much faster than the alignment methods.
Availability: All MATLAB code used to generate the data is available upon request to the authors. Additional material available at http://bioinformatics.musc.edu/wmetric
GAPSCORE: finding gene and protein names one word at a time
Authors: Chang Jeffrey T. , Schütze Hinrich , Altman Russ B. 
Published: January 2004

Abstract
Motivation: New high-throughput technologies have accelerated the accumulation of knowledge about genes and proteins. However, much knowledge is still stored as written natural language text. Therefore, we have developed a new method, GAPSCORE, to identify gene and protein names in text. GAPSCORE scores words based on a statistical model of gene names that quantifies their appearance, morphology and context.
Results: We evaluated GAPSCORE against the Yapex data set and achieved an F-score of 82.5% (83.3% recall, 81.5% precision) for partial matches and 57.6% (58.5% recall, 56.7% precision) for exact matches. Since the method is statistical, users can choose score cutoffs that adjust the performance according to their needs.
Availability: GAPSCORE is available at http://bionlp.stanford.edu/gapscore/
An empirical bayes adjustment to increase the sensitivity of detecting differentially expressed genes in microarray experiments
Authors: Datta Susmita , Satten Glen A. , Benos Dale J. , Xia Jiazeng , Heslin Martin J. , Datta Somnath 
Published: January 2004

Abstract
Motivation: Detection of differentially expressed genes is one of the major goals of microarray experiments. Pairwise comparison for each gene is not appropriate without controlling the overall (experimentwise) type 1 error rate. Dudoit et al. have advocated use of permutation-based step-down P-value adjustments to correct the observed significance levels for the individual (i.e. for each gene) two sample t-tests.
Results: In this paper, we consider an ANOVA formulation of the gene expression levels corresponding to multiple tissue types. We provide resampling-based step-down adjustments to correct the observed significance levels for the individual ANOVA t-tests for each gene and for each pair of tissue type comparisons. More importantly, we introduce a novel empirical Bayes adjustment to the t-test statistics that can be incorporated into the step-down procedure. Using simulated data, we show that the empirical Bayes adjustment improved the sensitivity of detecting differentially expressed genes up to 16%, while maintaining a high level of specificity. This adjustment also reduces the false non-discovery rate to some degree at the cost of a modest increase in the false discovery rate. We illustrate our approach using a human colon cancer dataset consisting of oligonucleotide arrays of normal, adenoma and carcinoma cells. The number of genes with differential expression level declared statistically significant was about 50 when comparing normal to adenoma cells and about five when comparing adenoma to carcinoma cells. This list includes genes previously known to be associated with colon cancer as well as some novel genes.
Availability: R code for the empirical Bayes adjustment and step-down P-value calculation via resampling are available from the supplementary web-site.
Supplementary information: http://www.mathstat.gsu.edu/~matsnd/EB/supp.htm
The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources
Authors: Crass T. , Antes I. , Basekow R. , Bork P. , Buning C. , Christensen M. , Claußen H. , Ebeling C. , Ernst P. , Gailus-Durner V. , Glatting K.-H. , Gohla R. , Gößling F. , Grote K. , Heidtke K. , Herrmann A. , O'Keeffe S. , Kießlich O. , Kolibal S. , Korbel J. O. , Lengauer T. , Liebich I. , van der Linden M. , Luz H. , Meissner K. , von Mering C. , Mevissen H.-T. , Mewes H.-W. , Michael H. , Mokrejs M. , Müller T. , Pospisil H. , Rarey M. , Reich J. G. , Schneider R. , Schomburg D. , Schulze-Kremer S. , Schwarzer K. , Sommer I. , Springstubbe S. , Suhai S. , Thoppae G. , Vingron M. , Warfsmann J. , Werner T. , Wetzler D. , Wingender E. , Zimmer R. 
Published: January 2004

Abstract
Summary: The Helmholtz Network for Bioinformatics (HNB) is a joint venture of eleven German bioinformatics research groups that offers convenient access to numerous bioinformatics resources through a single web portal. The ‘Guided Solution Finder’ which is available through the HNB portal helps users to locate the appropriate resources to answer their queries by employing a detailed, tree-like questionnaire. Furthermore, automated complex tool cascades (‘tasks’), involving resources located on different servers, have been implemented, allowing users to perform comprehensive data analyses without the requirement of further manual intervention for data transfer and re-formatting. Currently, automated cascades for the analysis of regulatory DNA segments as well as for the prediction of protein functional properties are provided.
Availability: The HNB portal is available at http://www.hnbioinfo.de
Is cross-validation better than resubstitution for ranking genes?
Authors: Braga-Neto Ulisses , Hashimoto Ronaldo , Dougherty Edward R. , Nguyen Danh V. , Carroll Raymond J. 
Published: January 2004

Abstract
Motivation: Ranking gene feature sets is a key issue for both phenotype classification, for instance, tumor classification in a DNA microarray experiment, and prediction in the context of genetic regulatory networks. Two broad methods are available to estimate the error (misclassification rate) of a classifier. Resubstitution fits a single classifier to the data, and applies this classifier in turn to each data observation. Cross-validation (in leave-one-out form) removes each observation in turn, constructs the classifier, and then computes whether this leave-one-out classifier correctly classifies the deleted observation. Resubstitution typically underestimates classifier error, severely so in many cases. Cross-validation has the advantage of producing an effectively unbiased error estimate, but the estimate is highly variable. In many applications it is not the misclassification rate per se that is of interest, but rather the construction of gene sets that have the potential to classify or predict. Hence, one needs to rank feature sets based on their performance.
Results: A model-based approach is used to compare the ranking performances of resubstitution and cross-validation for classification based on real-valued feature sets and for prediction in the context of probabilistic Boolean networks (PBNs). For classification, a Gaussian model is considered, along with classification via linear discriminant analysis and the 3-nearest-neighbor classification rule. Prediction is examined in the steady-distribution of a PBN. Three metrics are proposed to compare feature-set ranking based on error estimation with ranking based on the true error, which is known owing to the model-based approach. In all cases, resubstitution is competitive with cross-validation relative to ranking accuracy. This is in addition to the enormous savings in computation time afforded by resubstitution.
Formalization of mouse embryo anatomy
Authors: Burger Albert , Davidson Duncan , Baldock Richard 
Published: January 2004

Abstract
Motivation: The Edinburgh Mouse Atlas and Gene Expression Database project has developed a digital atlas of mouse development to provide a spatio-temporal framework for spatially mapped data such as in situ gene expression and cell lineage. As part of this database, a mouse embryo anatomy ontology has been created. A formalization of this anatomy is required to document its precise semantics and how it is used in the context of the Mouse Atlas.
Results: The paper describes the existing anatomy ontology and formalizes aspects of it using a predicate logic based approach. It therefore provides a guide for users of the current version of the ontology, as well as the basis for a description of the anatomy using an ontology language, such as OWL, thus enabling future work on reasoning about the Mouse Atlas in the context of an intelligent gene expression bioinformatics workflow system. The logic has been implemented in a Prolog prototype.
Availability: The Mouse Atlas is available on-line at http://genex.hgu.mrc.ac.uk
ROSO: optimizing oligonucleotide probes for microarrays
Authors: Reymond Nancie , Charles Hubert , Duret Laurent , Calevro Federica , Beslon Guillaume , Fayard Jean-Michel 
Published: January 2004

Abstract
Summary: ROSO is software to design optimal oligonucleotide probe sets for microarrays. Selected probes show no significant cross-hybridization, no stable secondary structures and their Tm are chosen to minimize the Tm variability of the probe set.
Availability: The program is available on the internet. Sources are freely available, for non-profit use, on request to the authors.
Supplementary information: http://pbil.univ-lyon1.fr/roso
LVB: parsimony and simulated annealing in the search for phylogenetic trees
Authors: Barker D. 
Published: January 2004

Abstract
Summary: The program LVB seeks parsimonious phylogenies from nucleotide alignments, using the simulated annealing heuristic. LVB runs fast and gives high quality results.
Availability: The software is available at http://www.rubic.reading.ac.uk/lvb/
Supplementary information: Supplementary information may be downloaded from http://www.rubic.reading.ac.uk/~daniel/
JDotter: a Java interface to multiple dotplots generated by dotter
Authors: Brodie Ryan , Roper Rachel L. , Upton Chris 
Published: January 2004

Abstract
Summary: Java-Dotter (JDotter) is a platform-independent Java interactive interface for the Linux version of Dotter, a widely used program for generating dotplots of large DNA or protein sequences. JDotter runs as a client–server application and can send new sequences to the Dotter program for alignment as well as rapidly access a repository of preprocessed dotplots. JDotter also interfaces with a sequence database or file system to display supplementary feature data. Thus, JDotter greatly simplifies access to dotplot data in laboratories that deal with large numbers of genomes and have a multi-platform organization.
Availability: Currently, JDotter is used via Java Web Start by the Poxvirus Bioinformatics Resource for examining dotplots of complete poxvirus genomes; http://athena.bioc.uvic.ca/pbr/jdotter/. The software is available for download from the same location.
Supplementary information: Installation instructions, the User's Manual, screenshots and examples are available at the JDotter home page http://athena.bioc.uvic.ca/pbr/jdotter/. The software and source code is free for non-commercial applications.
EST-PAGE—managing and analyzing EST data
Authors: Matukumalli Lakshmi K. , Grefenstette John J. , Sonstegard Tad S. , Van Tassell Curtis P. 
Published: January 2004

Abstract
Summary: EST-PAGE provides a bioinformatics solution for expressed sequence tags (EST) data entry, database management, GenBank submission, process control and data retrieval from a unified web interface that can be easily customized and adapted by groups working on diverse EST sequencing projects.
Availability: The system and source code are available upon request from the authors.
Supplementary information: http://EST-PAGE.binf.gmu.edu
APE: Analyses of Phylogenetics and Evolution in R language
Authors: Paradis Emmanuel , Claude Julien , Strimmer Korbinian 
Published: January 2004

Abstract
Summary: Analysis of Phylogenetics and Evolution (APE) is a package written in the R language for use in molecular evolution and phylogenetics. APE provides both utility functions for reading and writing data and manipulating phylogenetic trees, as well as several advanced methods for phylogenetic and evolutionary analysis (e.g. comparative and population genetic methods). APE takes advantage of the many R functions for statistics and graphics, and also provides a flexible framework for developing and implementing further statistical methods for the analysis of evolutionary processes.
Availability: The program is free and available from the official R package archive at http://cran.r-project.org/src/contrib/PACKAGES.html#ape. APE is licensed under the GNU General Public License.
AnaGram: protein function assignment
Authors: Pérez A. J. , Thode G. , Trelles O. 
Published: January 2004

Abstract
Summary: AnaGram is a web service for protein function assignment based on identity detection of small significant fragments (protomotifs) that can act as modular pieces in peptide construction. The system is able to assign function by finding correlations between protomotifs and functional annotations contained in SWISS-PROT and Medline databases. In addition, function ontologies are used for hierarchical organization of the predicted functions. Extensive tests have been carried out to evaluate the accuracy and performance of the system.
Availability: http://jaguar.genetica.uma.es/anagram.htm
Transposable element annotation of the rice genome
Authors: Juretic Nikoleta , Bureau Thomas E. , Bruskiewich Richard M. 
Published: January 2004

Abstract
Motivation: The high content of repetitive sequences in the genomes of many higher eukaryotes renders the task of annotating them computationally intensive. Presently, the only widely accepted method of searching and annotating transposable elements (TEs) in large genomic sequences is the use of the RepeatMasker program, which identifies new copies of TEs by pairwise sequence comparisons with a library of known TEs. Profile hidden Markov models (HMMs) have been used successfully in discovering distant homologs of known proteins in large protein databases, but this approach has only rarely been applied to known model TE families in genomic DNA.
Results: We used a combination of computational approaches to annotate the TEs in the finished genome of Oryza sativa ssp. japonica. In this paper, we discuss the strengths and the weaknesses of the annotation methods used. These approaches included: the default configuration of RepeatMasker using cross_match, an implementation of the Smith–Waterman–Gotoh algorithm; RepeatMasker using WU-BLAST for similarity searching; and the HMMER package, used to search for TEs with profile HMMs. All the results were converted into GFF format and post-processed using a set of Perl scripts.
RepeatMasker was used in the case of most TE families. The WU-BLAST implementation of RepeatMasker was found to be manifold faster than cross_match with only a slight loss in sensitivity and was thus used to obtain the final set of data. HMMER was used in the annotation of the Mutator-like element (MULE) superfamily and the miniature inverted-repeat transposable element (MITE) polyphyletic group of families, for which large libraries of elements were available and which could be divided into well-defined families. The HMMER search algorithm was extremely slow for models over 1000 bp in length, so MULE families with members over 1000 bp long were processed with RepeatMasker instead. The main disadvantage of HMMER in this application is that, since it was developed with protein sequences in mind, it does not search the negative DNA strand. With the exception of TE families with essentially palindromic sequences, reverse complement models had to be created and run to compensate for this shortcoming. We conclude that a modification of RepeatMasker to incorporate libraries of profile HMMs in searches could improve the ability to detect degenerated copies of TEs.
Availability: The Perl scripts and TE sequences used in construction of the RepeatMasker library and the profile HMMs are available upon request.