bluuebunny/crossref_metadata_2025_split huggingface dataset:
Compressed suffix tree—a basis for genome-scale sequence analysis
Authors: Välimäki Niko , Gerlach Wolfgang , Dixit Kashyap , Mäkinen Veli 
Published: January 2007

Abstract
Summary: Suffix tree is one of the most fundamental data structures in string algorithms and biological sequence analysis. Unfortunately, when it comes to implementing those algorithms and applying them to real genomic sequences, often the main memory size becomes the bottleneck. This is easily explained by the fact that while a DNA sequence of length n from alphabet Σ = {A, C, G, T } can be stored in n log |Σ|= 2n bits, its suffix tree occupies O(n log n) bits. In practice, the size difference easily reaches factor 50.
We provide an implementation of the compressed suffix tree very recently proposed by Sadakane (Theory of Computing Systems, in press). The compressed suffix tree occupies space proportional to the text size, i.e. O(n log} | Σ |) bits, and supports all typical suffix tree operations with at most log n factor slowdown. Our experiments show that, e.g. on a 10 MB DNA sequence, the compressed suffix tree takes 10% of the space of normal suffix tree. Typical operations are slowed down by factor 60.
Availability: The C++ implementation under GNU license is available at http://www.cs.helsinki.fi/group/suds/cst/. An example program implementing a typical pattern discovery task is included. Experimental results in this note correspond to version 0.95.
Contact: vmakinen@cs.helsinki.fi
AphidBase: a database for aphid genomic resources
Authors: Gauthier Jean-Pierre , Legeai Fabrice , Zasadzinski Alain , Rispe Claude , Tagu Denis 
Published: January 2007

AbstractAphidBase aims to (i) store recently acquired genomic resources on aphids and (ii) compare them to other insect resources as functional annotation tools. For that, the Drosophila melanogaster genome has been loaded in the database using the GMOD open source software for a comparison with the 17 069 pea aphid unique transcripts (contigs) and the 13 639 gene transcripts of the Anopheles gambiae. Links to FlyBase and A.gambiae Entrez databases allow a rapid characterization of the putative functions of the aphid sequences. Text mining of the D.melanogaster literature was performed to construct a network of co-cited gene or protein names, which should facilitate functional annotation of aphid homolog sequences. AphidBase represents one of the first genomic databases for a hemipteran insect.Availability: http://w3.rennes.inra.fr/AphidBaseContact: denis.tagu@rennes.inra.fr, jean-pierre.gauthier@rennes.infra.fr
Comparison of human protein–protein interaction maps
Authors: Futschik Matthias E. , Chaurasia Gautam , Herzel Hanspeter 
Published: January 2007

AbstractMotivation: Large-scale mappings of protein–protein interactions have started to give us new views of the complex molecular mechanisms inside a cell. After initial projects to systematically map protein interactions in model organisms such as yeast, worm and fly, researchers have begun to focus on the mapping of the human interactome. To tackle this enormous challenge, different approaches have been proposed and pursued. While several large-scale human protein interaction maps have recently been published, their quality remains to be critically assessed.Results: We present here a first comparative analysis of eight currently available large-scale maps with a total of over 10 000 unique proteins and 57 000 interactions included. They are based either on literature search, orthology or by yeast-two-hybrid assays. Comparison reveals only a small, but statistically significant overlap. More importantly, our analysis gives clear indications that all interaction maps imply considerable selection and detection biases. These results have to be taken into account for future assembly of the human interactome.Availability: An integrated human interaction network called Unified Human Interactome (UniHI) is made publicly accessible at http://www.mdc-berlin.de/unihi.Contact: m.futschik@biologie.hu-berlin.deSupplementary information: Supplementary data are available at Bioinformatics online.
APOPTO-CELL—a simulation tool and interactive database for analyzing cellular susceptibility to apoptosis
Authors: Huber Heinrich J. , Rehm Markus , Plchut Martin , Düssmann Heiko , Prehn Jochen H. M. 
Published: January 2007

AbstractWe have developed a web service that provides a comprehensive analysis of the susceptibility of cells to undergo apoptosis in response to an activation of the mitochondrial apoptotic pathway. Based on ordinary differential equations, (pre-determined) protein concentrations and release kinetics of mitochondrial pro-apoptotic factors, a network of 52 reactions and 19 reaction partners can be employed as a tool to display temporal protein profiles, to identify key regulatory proteins and to determine critical threshold concentrations required for the execution of apoptosis in HeLa cancer cells or other cell types. The web service also provides an interactive database function for the deposition of cell-type-specific quantitative data. In addition, the web service provides an output that can be compared directly to experimental results obtained from real-time single-cell experiments, making this a widely applicable systems biology tool for apoptosis and cancer researchers.Availability: http://systemsbiology.rcsi.ie/apopto-cell.htmlContact: mrehm@rcsi.ieSupplementary information: Supplementary data are available at Bioinformatics online.
LFM-Pro: a tool for detecting significant local structural sites in proteins
Authors: Sacan Ahmet , Ozturk Ozgur , Ferhatosmanoglu Hakan , Wang Yusu 
Published: January 2007

AbstractMotivation: The rapidly growing protein structure repositories have opened up new opportunities for discovery and analysis of functional and evolutionary relationships among proteins. Detecting conserved structural sites that are unique to a protein family is of great value in identification of functionally important atoms and residues. Currently available methods are computationally expensive and fail to detect biologically significant local features.Results: We propose Local Feature Mining in Proteins (LFM-Pro) as a framework for automatically discovering family-specific local sites and the features associated with these sites. Our method uses the distance field to backbone atoms to detect geometrically significant structural centers of the protein. A feature vector is generated from the geometrical and biochemical environment around these centers. These features are then scored using a statistical measure, for their ability to distinguish a family of proteins from a background set of unrelated proteins, and successful features are combined into a representative set for the protein family. The utility and success of LFM-Pro are demonstrated on trypsin-like serine proteases family of proteins and on a challenging classification dataset via comparison with DALI. The results verify that our method is successful both in identifying the distinctive sites of a given family of proteins, and in classifying proteins using the extracted features.Availability: The software and the datasets are freely available for academic research use at http://bioinfo.ceng.metu.edu.tr/Pub/LFMProContact: ahmet@ceng.metu.edu.tr, ozturk@cse.ohiostate.edu,hakan@cse.ohiostate.edu,yusu@cse.ohiostate.edu
A computational system to select candidate genes for complex human traits
Authors: Gaulton Kyle J. , Mohlke Karen L. , Vision Todd J. 
Published: January 2007

AbstractMotivation: Identification of the genetic variation underlying complex traits is challenging. The wealth of information publicly available about the biology of complex traits and the function of individual genes permits the development of informatics-assisted methods for the selection of candidate genes for these traits.Results: We have developed a computational system named CAESAR that ranks all annotated human genes as candidates for a complex trait by using ontologies to semantically map natural language descriptions of the trait with a variety of gene-centric information sources. In a test of its effectiveness, CAESAR successfully selected 7 out of 18 (39%) complex human trait susceptibility genes within the top 2% of ranked candidates genome-wide, a subset that represents roughly 1% of genes in the human genome and provides sufficient enrichment for an association study of several hundred human genes. This approach can be applied to any well-documented mono- or multi-factorial trait in any organism for which an annotated gene set exists.Availability: CAESAR scripts and test data can be downloaded from http://visionlab.bio.unc.edu/caesar/Contact: kgaulton@email.unc.edu
Modeling nonlinearity in dilution design microarray data
Authors: Zheng Xiuwen , Huang Hung-Chung , Li Wenyuan , Liu Peng , Li Quan-Zhen , Liu Ying 
Published: January 2007

AbstractMotivation: Dilution design (Mixed tissue RNA) has been utilized by some researchers to evaluate and assess the performance of multiple microarray platforms. Current microarray data analysis approaches assume that the quantified signal intensities are linearly related to the expression of the corresponding genes in the sample. However, there are sources of nonlinearity in microarray expression measurements. Such nonlinearity study in the expressions of the RNA mixtures provides a new way to analyze gene expression data, and we argue that the nonlinearity can reveal novel information for microarray data analysis. Therefore, we proposed a statistical model, called proportion model, which is based on the linear regression analysis. To approximately quantify the nonlinearity in the dilution design, a new calibration, beta ratio (BR) was derived from the proportion model. Furthermore, a new adjusted fold change (adj-FC) was proposed to predict the true FC without nonlinearity, in particular for large FC.Results: We applied our method to one microarray dilution dataset. The experimental results indicated that, to some extent, there are global biases comparing with the linear assumption for the significant genes. Further analysis of those highly expressed genes with significant nonlinearity revealed some promising results, e.g. ‘poison’ effect was discovered for some genes in RNA mixtures. The adj-FCs of those genes with ‘poison’ effect, indicate that the nonlinearity can be also caused by the inherent feature of the genes besides signal noise and technical variation. Moreover, when percentage of overlapping genes (POG) was used as a cross-platform consistency measure, adj-FC outperformed simple fold change to show that Affymetrix and Illumina platforms are consistent.Availability: The R codes which implements all described methods, and some Supplementary material, are freely available from http://www.utdallas.edu/~ying.liu/BetaRatio.htmContact: ying.liu@utdallas.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Identifying bacterial genes and endosymbiont DNA with Glimmer
Authors: Delcher Arthur L. , Bratke Kirsten A. , Powers Edwin C. , Salzberg Steven L. 
Published: January 2007

AbstractMotivation: The Glimmer gene-finding software has been successfully used for finding genes in bacteria, archæa and viruses representing hundreds of species. We describe several major changes to the Glimmer system, including improved methods for identifying both coding regions and start codons. We also describe a new module of Glimmer that can distinguish host and endosymbiont DNA. This module was developed in response to the discovery that eukaryotic genome sequencing projects sometimes inadvertently capture the DNA of intracellular bacteria living in the host.Results: The new methods dramatically reduce the rate of false-positive predictions, while maintaining Glimmer's 99% sensitivity rate at detecting genes in most species, and they find substantially more correct start sites, as measured by comparisons to known and well-curated genes. We show that our interpolated Markov model (IMM) DNA discriminator correctly separated 99% of the sequences in a recent genome project that produced a mixture of sequences from the bacterium Prochloron didemni and its sea squirt host, Lissoclinum patella.Availability: Glimmer is OSI Certified Open Source and available at http://cbcb.umd.edu/software/glimmerContact: adelcher@umiacs.umd.edu
R/qtlbim: QTL with Bayesian Interval Mapping in experimental crosses
Authors: Yandell Brian S. , Mehta Tapan , Banerjee Samprit , Shriner Daniel , Venkataraman Ramprasad , Moon Jee Young , Neely W. Whipple , Wu Hao , von Smith Randy , Yi Nengjun 
Published: January 2007

AbstractSummary: R/qtlbim is an extensible, interactive environment for the Bayesian Interval Mapping of QTL, built on top of R/qtl (Broman et al., 2003), providing Bayesian analysis of multiple interacting quantitative trait loci (QTL) models for continuous, binary and ordinal traits in experimental crosses. It includes several efficient Markov chain Monte Carlo (MCMC) algorithms for evaluating the posterior of genetic architectures, i.e. the number and locations of QTL, their main and epistatic effects and gene–environment interactions. R/qtlbim provides extensive informative graphical and numerical summaries, and model selection and convergence diagnostics of the MCMC output, illustrated through the vignette, example and demo capabilities of R (R Development Core Team 2006).Availability: The package is freely available from cran.r-project.org.Contact: byandell@wisc.edu or nyi@ms.soph.uab.edu
A new versatile database created for geneticists and breeders to link molecular and phenotypic data in perennial crops: theAppleBreed DataBase
Authors: Antofie A. , Lateur M. , Oger R. , Patocchi A. , Durel C. E. , Van de Weg W. E. 
Published: January 2007

AbstractObjective: AppleBreed DataBase (DB) aims to store genotypic and phenotypic data from multiple pedigree verified plant populations (crosses, breeding selections and commercial cultivars) so that they are easily accessible for geneticists and breeders. It will help in elucidating the genetics of economically important traits, in identifying molecular markers associated with agronomic traits, in allele mining and in choosing the best parental cultivars for breeding. It also provides high traceability of data over generations, years and localities. AppleBreed DB could serve as a generic database design for other perennial crops with long economic lifespans, long juvenile periods and clonal propagation.Results: AppleBreed DB is organized as a relational database. The core element is the GENOTYPE entity, which has two sub-classes at the physical level: TREE and DNA-SAMPLE. This approach facilitates all links between plant material, phenotypic and molecular data. The entities TREE, DNA-SAMPLE, PHENOTYPE and MOLECULAR DATA allow multi-annual observations to be stored as individual samples of individual trees, even if the nature of these observations differs greatly (e.g. molecular data on parts of the apple genome, physico-chemical measurements of fruit quality traits, and evaluation of disease resistance). AppleBreed DB also includes synonyms for cultivars and pedigrees. Finally, it can be loaded and explored through the web, and comes with tools to present basic statistical overviews and with validation procedures for phenotypic and marker data to certify data quality.AppleBreed DB was developed initially as a tool for scientists involved in apple genetics within the framework of the European project, ‘High-quality Disease Resistance in Apples for Sustainable Agriculture’ (HiDRAS), but it is also applicable to many other perennial crops.Contact: oger@cra.wallonie.be
Assessment of phylogenomic and orthology approaches for phylogenetic inference
Authors: Dutilh B. E. , van Noort V. , van der Heijden R. T. J. M. , Boekhout T. , Snel B. , Huynen M. A. 
Published: January 2007

AbstractMotivation: Phylogenomics integrates the vast amount of phylogenetic information contained in complete genome sequences, and is rapidly becoming the standard for reliably inferring species phylogenies. There are, however, fundamental differences between the ways in which phylogenomic approaches like gene content, superalignment, superdistance and supertree integrate the phylogenetic information from separate orthologous groups. Furthermore, they all depend on the method by which the orthologous groups are initially determined. Here, we systematically compare these four phylogenomic approaches, in parallel with three approaches for large-scale orthology determination: pairwise orthology, cluster orthology and tree-based orthology.Results: Including various phylogenetic methods, we apply a total of 54 fully automated phylogenomic procedures to the fungi, the eukaryotic clade with the largest number of sequenced genomes, for which we retrieved a golden standard phylogeny from the literature. Phylogenomic trees based on gene content show, relative to the other methods, a bias in the tree topology that parallels convergence in lifestyle among the species compared, indicating convergence in gene content.Conclusions: Complete genomes are no guarantee for good or even consistent phylogenies. However, the large amounts of data in genomes enable us to carefully select the data most suitable for phylogenomic inference. In terms of performance, the superalignment approach, combined with restrictive orthology, is the most successful in recovering a fungal phylogeny that agrees with current taxonomic views, and allows us to obtain a high-resolution phylogeny. We provide solid support for what has grown to be a common practice in phylogenomics during its advance in recent years.Contact: dutilh@cmbi.ru.nlSupplementary information: Supplementary data are available at Bioinformatics online.
Inositol Polyphosphate 5-Phosphatases 1 and 2 Are Required for Regulating Seedling Growth
Authors: Gunesekera Bhadra , Torabinejad Javad , Robinson Jamille , Gillaspy Glenda E. 
Published: January 2007

Abstract
Signals can be perceived and amplified at the cell membrane by receptors coupled to the production of a variety of second messengers, including myoinositol 1,4,5-trisphosphate [Ins(1,4,5)P3]. The myoinositol polyphosphate 5-phosphatases (5PTases; EC 3.1.3.56) comprise a large protein family that hydrolyzes 5-phosphates from a variety of myoinositol phosphate (InsP) and phosphoinositide phosphate (PtdInsP) substrates. Arabidopsis thaliana has 15 genes encoding 5PTases. Biochemical analyses of a subgroup of 5PTase enzymes suggest that these enzymes have both overlapping and unique substrate preferences. Ectopic expression of these genes in transgenic plants can reduce Ins(1,4,5)P3 levels and alter abscisic acid (ABA) signaling. To further explore the function of 5PTases in signaling, we have identified and characterized T-DNA insertional mutants for 5PTase1 and 5PTase2 and produced a double mutant. When grown in the dark, the seeds from these mutants germinate faster than wild-type seeds and the mutant seedlings have longer hypocotyls than wild-type seedlings. Seeds from these mutant lines also demonstrate an increase in sensitivity to ABA. These changes in early seedling growth are accompanied by mass increases in Ins(1,4,5)P3, but not by changes in endogenous ABA content. By labeling the endogenous myoinositol pool in 5ptase1 and 5ptase2 mutants, we detected increases in Ins(1,4,5)P3 and a decrease in PtdIns, PtdIns(4)P, and phosphatidylinositol (4,5) bisphosphate. Taken together, these data indicate that the At5PTase1 and At5PTase2 genes have nonredundant roles in hydrolyzing inositol second-messenger substrates and that regulation of Ins(1,4,5)P3 levels is important during germination and early seedling development.
Developmental Analysis of Maize Endosperm Proteome Suggests a Pivotal Role for Pyruvate Orthophosphate Dikinase
Authors: Méchin Valérie , Thévenot Claudine , Le Guilloux Martine , Prioul Jean-Louis , Damerval Catherine 
Published: January 2007

AbstractAlthough the morphological steps of maize (Zea mays) endosperm development are well described, very little is known concerning the coordinated accumulation of the numerous proteins involved. Here, we present a proteomic study of maize endosperm development. The accumulation pattern of 409 proteins at seven developmental stages was examined. Hierarchical clustering analysis allowed four main developmental profiles to be recognized. Comprehensive investigation of the functions associated with clusters resulted in a consistent picture of the developmental coordination of cellular processes. Early stages, devoted to cellularization, cell division, and cell wall deposition, corresponded to maximal expression of actin, tubulins, and cell organization proteins, of respiration metabolism (glycolysis and tricarboxylic acid cycle), and of protection against reactive oxygen species. An important protein turnover, which is likely associated with the switch from growth and differentiation to storage, was also suggested from the high amount of proteases. A relative increase of abundance of the glycolytic enzymes compared to tricarboxylic acid enzymes is consistent with the recent demonstration of anoxic conditions during starch accumulation in the endosperm. The specific late-stage accumulation of the pyruvate orthophosphate dikinase may suggest a critical role of this enzyme in the starch-protein balance through inorganic pyrophosphate-dependent restriction of ADP-glucose synthesis in addition to its usually reported influence on the alanine-aromatic amino acid synthesis balance.
An IRE-Like AGC Kinase Gene, MtIRE, Has Unique Expression in the Invasion Zone of Developing Root Nodules in Medicago truncatula
Authors: Pislariu Catalina I. , Dickstein Rebecca 
Published: January 2007

Abstract
The AGC protein kinase family (cAMP-dependent protein kinases A, cGMP-dependent protein kinases G, and phospholipid-dependent protein kinases C) have important roles regulating growth and development in animals and fungi. They are activated via lipid second messengers by 3-phosphoinositide-dependent protein kinase coupling lipid signals to phosphorylation of the AGC kinases. These phosphorylate downstream signal transduction protein targets. AGC kinases are becoming better studied in plants, especially in Arabidopsis (Arabidopsis thaliana), where specific AGC kinases have been shown to have key roles in regulating growth signal pathways. We report here the isolation and characterization of the first AGC kinase gene identified in Medicago truncatula, MtIRE. It was cloned by homology with the Arabidopsis INCOMPLETE ROOT HAIR ELONGATION (IRE) gene. Semiquantitative reverse transcription-polymerase chain reaction analysis shows that, unlike its Arabidopsis counterpart, MtIRE is not expressed in uninoculated roots, but is expressed in root systems that have been inoculated with Sinorhizobium meliloti and are developing root nodules. MtIRE expression is also found in flowers. Expression analysis of a time course of nodule development and of nodulating root systems of many Medicago nodulation mutants shows MtIRE expression correlates with infected cell maturation during nodule development. During the course of these experiments, nine Medicago nodulation mutants, including sli and dnf1 to 7 mutants, were evaluated for the first time for their microscopic nodule phenotype using S. meliloti constitutively expressing lacZ. Spatial localization of a pMtIRE-gusA transgene in transformed roots of composite plants showed that MtIRE expression is confined to the proximal part of the invasion zone, zone II, found in indeterminate nodules. This suggests MtIRE is useful as an expression marker for this region of the invasion zone.