bluuebunny/crossref_metadata_2025_split huggingface dataset:
Short interrupted palindromes on the extragenic DNA of

Escherichia coli K-12, Haemophilus influenzae and

Neisseria meningitidis
Authors: Vasconcelos Ana T. , Maia Marco A. Grivet Mattoso , de Almeida Darcy F. 
Published: July 2002

Abstract
Motivation: The importance of the various kinds of repetitive nucleotide sequences for the workings of bacterial DNA has been widely recognized. This work is concerned with the distribution of a particular group of repetitive sequences, the short-sequenced interrupted extragenic palindromes, on the genetic maps of Escherichia coli K-12, Haemophilus influenzae Rd and Neisseria meningitidis Z2491 and MC58. A tool has been developed based upon a statistical hypothesis test taking into account the markovian structure of random sequences in order to determine the non-random character of extragenic palindromes.
Results: Totals of 7631, 12904, 4722 and 5477 non-random short interrupted palindromes have been found on the E.coli, H.influenzae, and N.meningitidis serogroup A and serogroup B genomes, respectively. Their distribution patterns on the respective genomes vary according to the bacterial species considered. Based on their position on the genome, palindromes could be distinguished as those which integrate longer, repetitive sequences; those which stand in isolation, and still others are associated to specific genome sites.
Availability: The complete list of the observed palindromes is available at the site http://www/lncc.br/~atrv.
Contact: atrv@lncc.br
**** To whom correspondence should be addressed at Laboratório Nacional de Computação Cientı́fica, Rua Getúlio Vargas 333, Quitandinha, Petrópolis.
IE-Kb: intron exon knowledge base
Authors: Sakharkar Meena K. , Kangueane Pandjassarame , Woon Tong W. , Tan Tin W. , Kolatkar Prasanna R. , Long Manyuan , de Souza Sandro J 
Published: July 2002

Abstract
Summary: IE-Kb (Intron Exon-Knowledge base) illustrates the intron–exon dynamics in eukaryotic genes. We have developed three different knowledge sets, namely ‘Non-redundant ExInt’, ‘Non-redundant Pfam-ExInt complement’ and ‘Non-redundant GenBank eukaryotic subdivisional sets’ to understand this phenomenon. Statistical analysis is performed on each knowledge set and the results are made available online. The entries in knowledge sets are ranked based on their intron length, exon length and protein length with relational hyper-links to the corresponding intron phase, intron position, intron sequence, gene definition and parent GenBank entry.
Availability: http://intron.bic.nus.edu.sg/iekb/iekb.html
Contact: meena@bic.nus.edu.sg
* To whom correspondence should be addressed.
PANAL: an integrated resource for Protein sequence ANALysis
Authors: Silverstein Kevin A. T. , Kilian Alan , Freeman John L. , Johnson James E. , Awad Ihab A. , Retzel Ernest F. 
Published: July 2002

Abstract
Summary: We present PANAL, an integrated resource for protein sequence analysis. The tool allows the user to simultaneously search a protein sequence for motifs from several databases, and to view the result as an intuitive graphical summary.
Availability: PANAL can be freely accessed on our World Wide Web server: http://mgd.ahc.umn.edu/panal/. Source code is available upon request to non-profit organizations.
Contact: panal@ahc.umn.edu
* Authors to whom correspondence should be addressed.
ComboScreen facilitates the multiplex hybridization-based

screening of high-density clone arrays
Authors: Jamison D. Curtis , Thomas James W. , Green Eric D. 
Published: July 2002

Abstract
Motivation: The construction of physical maps based on bacterial clones [e.g. bacterial artificial chromosomes (BACs)] is valuable for a number of molecular genetics applications, including the high-resolution mapping of genomic regions of interest and the identification of clones suitable for systematic sequencing. A common approach for large-scale screening of bacterial clone libraries involves the hybridization of high-density arrays of immobilized, lysed colonies with collections of DNA probes. The use of a multiplex hybridization screening strategy, whereby pooled probes are analysed en masse, simplifies the effort by reducing the total number of parallel experiments required. However, this approach generates large amounts of hybridization-based data that must be carefully analysed, assimilated, and disambiguated in a careful but efficient manner.
Results: To facilitate the screening of high-density clone arrays by a multiplex hybridization approach, we have written a program called ComboScreen. This program provides an organizational framework and analytical tools required for the high-throughput hybridization screening of clone arrays with pools of probes. We have used this program extensively for constructing mouse sequence-ready BAC contig maps.
Availability: ComboScreen is freely available at http://genome.nhgri.nih.gov/comboscreen
Contact: cjamison@informaxinc.com, egreen@nhgri.nih.gov
To whom correspondence should be addressed.
Automatic analysis of agarose gel images
Authors: Umesh Adiga P. S. , Bhomra A. , Turri M. G. , Nicod A. , Datta S. R. , Jeavons P. , Mott R. , Flint J. 
Published: July 2002

Abstract
Motivation: Automatic tools to speed up routine biological processes are very much sought after in bio-medical research. Much repetitive work in molecular biology, such as allele calling in genetic analysis, can be made semi-automatic or task specific automatic by using existing techniques from computer science and signal processing. Computerized analysis is reproducible and avoids various forms of human error. Semi-automatic techniques with an interactive check on the results speed up the analysis and reduce the error.
Results: We have successfully implemented an image processing software package to automatically analyze agarose gel images of polymorphic DNA markers. We have obtained up to 90% accuracy for the classification of alleles in good quality images and up to 70% accuracy in average quality images. These results are obtained within a few seconds. Even after subsequent interactive checking to increase the accuracy of allele classification to 100%, the overall speed with which the data can be processed is greatly increased, compared to manual allele classification.
Availability: The IDL source code of the software is available on request from jonathan.flint@well.ox.ac.uk
* To whom all correspondence should be addressed.
Minimum conflict: a divide-and-conquer approach to phylogeny
estimation
Authors: Fuellen Georg , Wägele Johann-Wolfgang , Giegerich Robert 
Published: July 2002

Abstract
Motivation: Fast and reliable phylogeny estimation is rapidly gaining importance as more and more genomic sequence information is becoming available, and the study of the evolution of genes and genomes accelerates our understanding in biology and medicine alike. Branch attraction phenomena due to unequal amounts of evolutionary change in different parts of the phylogeny are one major problem for current methods, placing the species that evolved fast in one part of the phylogenetic tree, and the species that evolved slowly in the other.
Results: We describe a way to avoid the artifactual attraction of species that evolved slowly, by detecting shared old character states using a calibrated comparison with an outgroup. The corresponding focus on shared novel character states yields a fast and transparent phylogeny estimation algorithm, by application of the divide-and-conquer principle, and heuristic search: shared novelties give evidence of the exclusive common heritage (monophyly) of a subset of the species. They indicate conflict in a split of all species considered, if the split tears them apart. Only the split at the root of the phylogenetic tree cannot have such conflict. Therefore, we can work top-down, from the root to the leaves, by heuristically searching for a minimum-conflict split, and tackling the resulting two subsets in the same way. The algorithm, called ‘minimum conflict phylogeny estimation’ (mcope), has been validated successfully using both natural and artificial data. In particular, we reanalyze published trees, yielding more plausible phylogenies, and we analyze small ‘undisputed’ trees on the basis of alignments considering structural homology.
Availability: mcopeis available via http://bibiserv.techfak.uni-bielefeld.de/mcope/.
Contact: fuellen@alum.mit.edu
* To whom correspondence should be addressed.
SPiD: a subtilis protein interaction database
Authors: Hoebeke Mark , Chiapello Hélène , Noirot Philippe , Bessières Philippe 
Published: July 2002

Abstract
Motivation: Protein–protein interactions are a potential source of valuable clues in determining the functional role of as yet uncharacterized gene products in metabolic pathways. Graph-like structures emerging from the accumulation of interaction data make it difficult to maintain a consistent and global overview by hand. Bioinformatics tools are needed to perform this graph visualization while maintaining a link to the experimental data.
Results: ‘SPiD’ is an online database for exploring networks of interacting proteins in Bacillus subtilis characterized by the two-hybrid system. Graphical displays of interaction networks are created dynamically as users interactively navigate through these networks. Third party applications can interface the database through a Common Object Request Broker Architecture (CORBA) tier.
Availability: SPiD is available through its web site at http://www-mig.versailles.inra.fr/bdsi/SPiD, and through an Interoperable Object Reference (IOR) and its associated Interface Definition Language (IDL).
Contact: hoebeke@versailles.inra.fr
* To whom correspondence should be addressed.
mmsearch: a motif arrangement language and search
program
Authors: Junier Thomas , Pagni Marco , Bucher Philipp 
Published: July 2002

Abstract
Summary: This paper presents a language for describing arrangements of motifs in biological sequences, and a program that uses the language to find the arrangements in motif match databases. The program does not by itself search for the constituent motifs, and is thus independent of how they are detected, which allows it to use motif match data of various origins.
Availability: The program can be tested online at http://hits.isb-sib.ch and the distribution is available from ftp://ftp.isrec.isb-sib.ch/pub/software/unix/mmsearch-1.0.tar.gz
Contact: Thomas.Junier@isrec.unil.ch
Supplementary information: The full documentation about mmsearchis available from http://hits.isb-sib.ch/~tjunier/mmsearch/doc.
Basic Gene Grammars and DNA-ChartParser for language processing

of Escherichia coli promoter DNA sequences
Authors: Leung Siu-wai , Mellish Chris , Robertson Dave 
Published: July 2002

Abstract
Motivation: The field of ‘DNA linguistics’ has emerged from pioneering work in computational linguistics and molecular biology. Most formal grammars in this field are expressed using Definite Clause Grammars but these have computational limitations which must be overcome. The present study provides a new DNA parsing system, comprising a logic grammar formalism called Basic Gene Grammars and a bidirectional chart parser DNA-ChartParser.
Results: The use of Basic Gene Grammars is demonstrated in representing many formulations of the knowledge of Escherichia coli promoters, including knowledge acquired from human experts, consensus sequences, statistics (weight matrices), symbolic learning, and neural network learning. The DNA-ChartParser provides bidirectional parsing facilities for BGGs in handling overlapping categories, gap categories, approximate pattern matching, and constraints. Basic Gene Grammars and the DNA-ChartParser allowed different sources of knowledge for recognizing E.coli promoters to be combined to achieve better accuracy as assessed by parsing these DNA sequences in real-world data sets.
Availability: DNA-ChartParser runs under SICStus Prolog. It and a few examples of Basic Gene Grammars are available at the URL: http://www.dai.ed.ac.uk/~siu/DNA
Contact: {siu,chrism,dr}@dai.ed.ac.uk
Semi-automated update and cleanup of structural RNA alignment

databases
Authors: Gorodkin J. , Zwieb C. , Knudsen B. 
Published: July 2002

Abstract
Summary: We have developed a series of programs which assist in maintenance of structural RNA databases. A main program BLASTs the RNA database against GenBank and automatically extends and realigns the sequences to include the entire range of the RNA query sequences. After manual update of the database, other programs can examine base pair consistency and phylogenetic support. The output can be applied iteratively to refine the structural alignment of the RNA database. Using these tools, the number of potential misannotations per sequence was reduced from 20 to 3 in the Signal Recognition Particle RNA database.
Availability: A quick-server and programs are available at http://www.bioinf.au.dk/rnadbtool/
Contact: gorodkin@bioinf.au.dk
* These authors contributed equally to this work.
† To whom correspondence should be addressed.
Integrated gene and species phylogenies from unaligned whole
genome protein sequences
Authors: Stuart Gary W. , Moffett Karen , Baker Steve 
Published: July 2002

Abstract
Motivation: Most molecular phylogenies are based on sequence alignments. Consequently, they fail to account for modes of sequence evolution that involve frequent insertions or deletions. Here we present a method for generating accurate gene and species phylogenies from whole genome sequence that makes use of short character string matches not placed within explicit alignments. In this work, the singular value decomposition of a sparse tetrapeptide frequency matrix is used to represent the proteins of organisms uniquely and precisely as vectors in a high-dimensional space. Vectors of this kind can be used to calculate pairwise distance values based on the angle separating the vectors, and the resulting distance values can be used to generate phylogenetic trees. Protein trees so derived can be examined directly for homologous sequences. Alternatively, vectors defining each of the proteins within an organism can be summed to provide a vector representation of the organism, which is then used to generate species trees.
Results: Using a large mitochondrial genome dataset, we have produced species trees that are largely in agreement with previously published trees based on the analysis of identical datasets using different methods. These trees also agree well with currently accepted phylogenetic theory. In principle, our method could be used to compare much larger bacterial or nuclear genomes in full molecular detail, ultimately allowing accurate gene and species relationships to be derived from a comprehensive comparison of complete genomes. In contrast to phylogenetic methods based on alignments, sequences that evolve by relative insertion or deletion would tend to remain recognizably similar.
Availability: Both the program used to convert properly formatted sequence files into sparse n-gram matrices (aacode3) and the program used to generate PHYLIP compatible pairwise distance matrices from the Singular Value Decomposition (SVD) output (cosdist) are available at http://mama.indstate.edu/user/stuart. The SVD package is available at http://www.netlib.org/svdpack/index.html, and the PHYLIP package is available at http://evolution.genetics.washington.edu/phylip.html.
Contact: G-Stuart@indstate.edu
* To whom correspondence should be addressed.
A Bayesian approach to discriminate between alternative DNA
sequence segmentations
Authors: Husmeier Dirk , Wright Frank 
Published: July 2002

Abstract
Motivation: As a result of recombination or rate variation, a DNA sequence alignment may have a mosaic structure, where different segments correspond to different evolutionary histories. While several methods have been developed to predict DNA mosaic structures, they do not properly address the question of whether the predicted segmentation itself is statistically significant, or whether it is significantly better than an alternative mosaic structure predicted with another method. The objective of the present article is to devise an approximate Bayesian hypothesis test to discriminate between alternative candidate mosaic structures.
Results: We have applied the proposed discrimination scheme to various synthetic and real-world DNA sequence alignments. On the synthetic data, the algorithm identified the true mosaic structure in nine out of ten cases. On the real-world sequence alignments, it selected the same mosaic structures as predicted in the literature.
Availability: Software written in MATLAB as well as the data sets used in our study are available from http://www.bioss.sari.ac.uk/~dirk/software/ABBESS/INFO.html.
Contact: dirk@bioss.ac.uk; frank@bioss.ac.uk
Tclass: tumor classification system based on gene expression
profile
Authors: Wuju Li , Momiao Xiong 
Published: July 2002

Abstract
Summary: A method that incorporates feature selection into Fisher’s linear discriminant analysis for gene expression based tumor classification and a corresponding program Tclass were developed. The proposed method was applied to a public gene expression data set for colon cancer that consists of 22 normal and 40 tumor colon tissue samples to evaluate its performance for classification. Preliminary results demonstrated that using only a subset of genes ranging from 3 to 10 can achieve high classification accuracy.
Availability: The program is written in Matlab and is being rewritten in the Java language. The source code is available upon request.
Contact: wujuli@china.com; mxiong@sph.uth.tmc.edu.
CGO: utilizing and integrating gene expression microarray data
in clinical research and data management
Authors: Bumm Klaus , Zheng Mingzhong , Bailey Clyde , Zhan Fenghuang , Chiriva-Internati M. , Eddlemon Paul , Terry Julian , Barlogie Bart , Shaughnessy, Jr John D. 
Published: July 2002

Abstract
Summary: Clinical GeneOrganizer (CGO) is a novel windows-based archiving, organization and data mining software for the integration of gene expression profiling in clinical medicine. The program implements various user-friendly tools and extracts data for further statistical analysis. This software was written for Affymetrix GeneChip©*.txt files, but can also be used for any other microarray-derived data. The MS-SQL server version acts as a data mart and links microarray data with clinical parameters of any other existing database and therefore represents a valuable tool for combining gene expression analysis and clinical disease characteristics.
Availability: The software is available free of charge at http://lambertlab.uams.edu
Contact: ShaughnessyJohn@uams.edu
Supplementary information: A snapshot of detailed program-specific table relationships and information on other programs including various cancer gene expression profiles are available on above mentioned web site.
* To whom correspondence should be addressed.
Assessing the significance of consistently mis-regulated genes
in cancer associated gene expression matrices
Authors: Wahde Mattias , Klus Gregory T. , Bittner Michael L. , Chen Yidong , Szallasi Zoltan 
Published: July 2002

Abstract
Motivation: The simplest level of statistical analysis of cancer associated gene expression matrices is aimed at finding consistently up- or down-regulated genes within a given set of tumor samples. Considering the high level of gene expression diversity detected in cancer, one needs to assess the probability that the consistent mis-regulation of a given gene is due to chance. Furthermore, it is important to determine the required sample number that will ensure the meaningful statistical analysis of massively parallel gene expression measurements.
Results: The probability of consistent mis-regulation is calculated in this paper for binarized gene expression data, using combinatorial considerations. For practical purposes, we also provide a set of accurate approximate formulas for determining the same probability in a computationally less intensive way. When the pool of mis-regulatable genes is restricted, the probability of consistent mis-regulation can be overestimated. We show, however, that this effect has little practical consequences for cancer associated gene expression measurements published in the literature. Finally, in order to aid experimental design, we have provided estimates on the required sample number that will ensure that the detected consistent mis-regulation is not due to chance. Our results suggest that less than 20 sufficiently diverse tumor samples may be enough to identify consistently mis-regulated genes in a statistically significant manner.
Availability: An implementation using Mathematica tm of the main equation of the paper, (4), is available at www.me.chalmers.se/~mwahde/bioinfo.html.
Contact: mwahde@me.chalmers.se, zszallasi@chip.org
* To whom correspondence should be addressed.
CASA: a server for the critical assessment of protein sequence
alignment accuracy
Authors: Kahsay Robel Y. , Wang Guoli , Dongre Nataraj , Gao Guang , Dunbrack, Jr Roland L. 
Published: July 2002

Abstract
Summary: A public server for evaluating the accuracy of protein sequence alignment methods is presented. CASA is an implementation of the alignment accuracy benchmark presented by Sauder et al. (Proteins, 40, 6–22, 2000). The benchmark currently contains 39321 pairwise protein structure alignments produced with the CE program from SCOP domain definitions. The server produces graphical and tabular comparisons of the accuracy of a user’s input sequence alignments with other commonly used programs, such as BLAST, PSI-BLAST, Clustal W, and SAM-T99.
Availability: The server is located at http://capb.dbi.udel.edu/casa.
Contact: RL_ Dunbrack@fccc.edu
* To whom correspondence should be addressed.
Desktop prediction/analysis of mass spectrometric data in
proteomic projects by using massXpert
Authors: Rusconi Filippo , Belghazi Maya 
Published: July 2002

Abstract
Summary: With the ever-increasing demand for biopolymer mass spectrometry, specialized software is needed to both predict and process mass spectrometric data. With massXpert, we present a proteomics-oriented program mainly concerned with protein physico-chemistry and protein/peptide mass spectra simulations.
Availability: The massXpert program is free for academic and commercial use at http://frl.lptc.u-bordeaux.fr.
Contact: frusconi@lptc.u-bordeaux.fr
Supplementary information: The http://frl.lptc.u-bordeaux.frsite contains a tutorial for online perusal or download.
2 To whom correspondence should be addressed at: LPTC UMR CNRS 5472, UniversitéBordeaux I, F-33405 Talence Cedex, France.
24.64%‐Efficiency MA‐Free Perovskite Solar Cell with Voc of 1.19 V Enabled by a Hinge‐Type Fluorine‐Rich Complex
Authors: Li Zhijun , Wu Meizi , Yang Lu , Guo Kunpeng , Duan Yuwei , Li Yong , He Kun , Xing Yifan , Zhang Zheng , Zhou Hui , Xu Dongfang , Wang Jungang , Zou Hong , Li Da , Liu Zhike 
Published: January 2023

AbstractHigh density of defects at interface severely affects the performance of perovskite solar cells (PSCs). Herein, cobalt (II) hexafluoro‐2,4‐pentanedionat (CoFAc), a hinge‐type fluorine‐rich complex, is introduced onto the surface of formamidinium cesium lead iodide (FACsPbI3) film to address the issues of perovskite/Spiro‐OMeTAD interface. The existence of CoFAc passivates both organic cation and halide anion vacancies by establishing powerful hydrogen bonds with HC(NH2)2+ (FA+) and strong ionic bonds with Pb2+ in perovskite films. In addition, CoFAc serves as a connecting link to enhance interfacial hole‐transport kinetics via interacting with Spiro‐OMeTAD. Consequently, FACsPbI3 PSCs with CoFAc modification display a champion power conversion efficiency (PCE) of 24.64% with a charming open‐circuit voltage (VOC) of 1.191 V, which is the record VOC among all the reported organic‐inorganic hybrid PSCs with TiO2 as electron transport layer. Furthermore, CoFAc‐modified devices exhibit an outstanding long‐term stability, which can maintain 95% of their initial PCEs after exposure to ambient atmosphere for 1500 h without any encapsulation.