bluuebunny/crossref_metadata_2025_split huggingface dataset:
Kinetic Analysis of Secretory Protein Traffic and Characterization of Golgi to Plasma Membrane Transport Intermediates in Living Cells
Authors: Hirschberg Koret , Miller Chad M. , Ellenberg Jan , Presley John F. , Siggia Eric D. , Phair Robert D. , Lippincott-Schwartz Jennifer 
Published: July 2002

Quantitative time-lapse imaging data of single cells expressing the transmembrane protein, vesicular stomatitis virus ts045 G protein fused to green fluorescent protein (VSVG–GFP), were used for kinetic modeling of protein traffic through the various compartments of the secretory pathway. A series of first order rate laws was sufficient to accurately describe VSVG–GFP transport, and provided compartment residence times and rate constants for transport into and out of the Golgi complex and delivery to the plasma membrane. For ER to Golgi transport the mean rate constant (i.e., the fraction of VSVG–GFP moved per unit of time) was 2.8% per min, for Golgi to plasma membrane transport it was 3.0% per min, and for transport from the plasma membrane to a degradative site it was 0.25% per min. Because these rate constants did not change as the concentration of VSVG–GFP in different compartments went from high (early in the experiment) to low (late in the experiment), secretory transport machinery was never saturated during the experiments.
The processes of budding, translocation, and fusion of post-Golgi transport intermediates carrying VSVG– GFP to the plasma membrane were also analyzed using quantitative imaging techniques. Large pleiomorphic tubular structures, rather than small vesicles, were found to be the primary vehicles for Golgi to plasma membrane transport of VSVG–GFP. These structures budded as entire domains from the Golgi complex and underwent dynamic shape changes as they moved along microtubule tracks to the cell periphery. They carried up to 10,000 VSVG–GFP molecules and had a mean life time in COS cells of 3.8 min. In addition, they fused with the plasma membrane without intersecting other membrane transport pathways in the cell. These properties suggest that the post-Golgi intermediates represent a unique transport organelle for conveying large quantities of protein cargo from the Golgi complex directly to the plasma membrane.
Asymptotic properties of Banach spaces under renormings
Authors: Odell E. , Schlumprecht Th. 
Published: July 2002

It is shown that a separable Banach space

X
X

can be given an equivalent norm

|

|

|

⋅

|

|

|

|||\, \cdot |||\,

with the following properties: If

(

x

n

)
⊆
X

(x_{n})\subseteq X

is relatively weakly compact and

lim

m
→
∞

lim

n
→
∞

|

|

|

x

m

+

x

n

|

|

|

=
2

lim

m
→
∞

|

|

|

x

m

|

|

|

\lim _{m\to \infty } \lim _{n\to \infty } |||\, x_{m}+x_{n}|||\, = 2\lim _{m\to \infty } |||\, x_{m}|||\,

, then

(

x

n

)

(x_{n})

converges in norm. This yields a characterization of reflexivity once proposed by V.D. Milman. In addition it is shown that some spreading model of a sequence in

(
X
,

|

|

|

⋅

|

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)

(X,|||\, \cdot |||\, )

is 1-equivalent to the unit vector basis of

ℓ

1

\ell _{1}

(respectively,

c

0

c_{0}

) implies that

X
X

contains an isomorph of

ℓ

1

\ell _{1}

(respectively,

c

0

c_{0}

).
Towards detection of orthologues in sequence databases.
Authors: Yuan Y P , Eulenstein O , Vingron M , Bork P 
Published: July 2002

Abstract
MOTIVATION: Numerous homologous sequences from diverse species can be retrieved from databases using programs such as BLAST. However, due to multigene families, evolutionary relationship often cannot be easily determined and proper functional assignment becomes difficult. Thus, discrimination between orthologues and paralogues within BLAST output lists of homologous sequences becomes more and more important. RESULT: We therefore developed a method that attempts to construct a reconciled tree from a gene tree of selected sequences and its corresponding phylogenetic tree of the species involved (species tree). An interface on the Web is developed to enable users to analyse the BLAST result. BLAST outputs are parsed and, for the selected sequences, multiple alignments are constructed either globally or for local regions. Bootstrapped trees are returned and compared with the expected species tree. In cases of discrepancies, gene duplications are assumed and a reconciled tree is computed. The reconciled tree shows probable orthologues and paralogues as predicted.
W2H: WWW interface to the GCG sequence analysis package.
Authors: Senger M , Flores T , Glatting K , Ernst P , Hotz-Wagenblatt A , Suhai S 
Published: July 2002

Abstract
MOTIVATION: The user-friendly, graphical X-windows interface (WPI) to the GCG sequence analysis package can often not be used due to the lack of an X-server on PC or Macintosh computers. Because Web browsers like Netscape are much more common on those platforms, we decided to develop W2H, a WWW interface to the GCG Sequence Analysis Software Package with nearly the same functionality as the X-windows interface WPI. RESULTS: The new WWW interface (W2H) to the GCG Sequence Analysis Software Package (Wisconsin Package) supports modern Web technologies, like client-pull method, or embedded scripting language, and provides a reasonable platform independence. The interface is quite comprehensive with advanced features like sequence selector, search set builder, enzyme chooser, access to sequence databases, uploading client files to the GCG server or displaying and manipulating graphical outputs in addition to GCG analysis programs. W2H also manages secure access to both GCG server and user data. For special environments, like workshops, conferences and company intranets, there is a special mode (Intranet mode) with less security constraints. The behaviour of W2H is mostly controlled by meta-data files describing the applications and giving a base for dynamic creation of HTML documents. This paper presents mainly the development approaches used, and architectural design aspects of W2H. AVAILABILITY: W2H is available by ftp://ftp.ebi.ac. uk/pub/software/unix/w2h or ftp://genome.dkfz-heidelberg.de/pub/w2h CONTACT: m.senger@ebi.ac.uk
Graphical interface to the genetic network database GeNet.
Authors: Serov V N , Spirov A V , Samsonova M G 
Published: July 2002

Abstract
SUMMARY: We designed a Java applet which enables the visualization of genetic networks and can be used as a Web publishing tool by molecular biologists studying the mechanisms of gene interactions. AVAILABILITY: http://www. csa.ru/Inst/gorb_dep/inbios/ genet/Graph/Genes_Graph.html CONTACT: samson@fn.csa.ru
DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis.
Authors: Rozas J , Rozas R 
Published: July 2002

Abstract
SUMMARY: DnaSP is a Windows integrated software package for the analysis of the DNA polymorphism from nucleotide sequence data. DnaSP version 3 incorporates several methods for estimating the amount and pattern of DNA polymorphism and divergence, and for conducting neutrality tests. AVAILABILITY: For academic uses, DnaSP is available free of charge from: http://www.bio.ub.es/julio/DnaSP.html CONTACT: julio@porthos.bio.ub.es
REPuter: fast computation of maximal repeats in complete genomes.
Authors: Kurtz S , Schleiermacher C 
Published: July 2002

Abstract
SUMMARY: A software tool was implemented that computes exact repeats and palindromes in entire genomes very efficiently. AVAILABILITY: Via the Bielefeld Bioinformatics Server (http://bibiserv.techfak.uni-bielefeld.de/rep uter/).
Saturated BLAST: an automated multiple intermediate sequence

search used to detect distant homology
Authors: Li Weizhong , Pio Frederic , Pawłowski Krzysztof , Godzik Adam 
Published: July 2002

Abstract
Motivation: Two proteins can have a similar 3-dimensional structure and biological function, but have sequences sufficiently different that traditional protein sequence comparison algorithms do not identify their relationship. The desire to identify such relations has led to the development of more sensitive sequence alignment strategies. One such strategy is the Intermediate Sequence Search (ISS), which connects two proteins through one or more intermediate sequences. In its brute-force implementation, ISS is a strategy that repetitively uses the results of the previous query as new search seeds, making it time-consuming and difficult to analyze.
Results: Saturated BLAST is a package that performs ISS in an efficient and automated manner. It was developed using Perl and Perl/Tk and implemented on the LINUX operating system. Starting with a protein sequence, Saturated BLAST runs a BLAST search and identifies representative sequences for the next generation of searches. The procedure is run until convergence or until some predefined criteria are met. Saturated BLAST has a friendly graphic user interface, a built-in BLAST result parser, several multiple alignment tools, clustering algorithms and various filters for the elimination of false positives, thereby providing an easy way to edit, visualize, analyze, monitor and control the search. Besides detecting remote homologies, Saturated BLAST can be used to maintain protein family databases and to search for new genes in genomic databases.
Availability: Free from http://bioinformatics.burnham-inst.org/xblast
Contact: liwz@sdsc.eduor adam@burnham-inst.org
* To whom correspondence should be addressed.
JESAM: CORBA software components to create and publish EST
alignments and clusters
Authors: Parsons J. D. , Rodriguez-Tomé P. 
Published: July 2002

Abstract
Motivation: Expressed Sequence Tags (ESTs) are cheap, easy and quick to obtain relative to full genomic sequencing and currently sample more eukaryotic genes than any other data source. They are particularly useful for developing Sequence Tag Sites (STSs for mapping), polymorphism discovery, disease gene hunting, mass spectrometer proteomics, and most ironically for finding genes and predicting gene structure after the great effort of genomic sequencing. However, ESTs have many problems and the public EST databases contain all the errors and high redundancy intrinsic to the submitted data so it is often found that derived database views, which reduce both errors and redundancy, are more effective starting points for research than the original raw submissions. Existing derived views such as EST cluster databases and consensus databases have never published supporting evidence or intermediary results leading to difficulties trusting, correcting, and customizing the final published database. These difficulties have lead many groups to wastefully repeat the complex intermediary work of others in order to offer slightly different final views. A better approach might be to discover the most expensive common calculations used by all the approaches and then publish all intermediary results. Given a globally accessible database with a suitable component interface, like the JESAM software described in this paper, the creation of customized EST-derived databases could be achieved with minimum effort.
Results: Databases of EST and full-length mRNA sequences for four model organisms have been self-compared by searching for overlaps consistent with contiguity. The sequence comparisons are performed in parallel using a PVM process farm and previous results are stored to allow incremental updates with minimal effort. The overlap databases have been published with CORBA interfaces to enable flexible global access as demonstrated by example Java applet browsers. Simple cDNA supercluster databases built as alignment database clients are themselves published via CORBA interfaces browsable with prototypical applets. A comparison with UniGene Mouse and Rat databases revealed undesirable features in both and the advantages of contrasting perspectives on complex data.
Availability: The software is packaged as two Jar files available from: URL: http://corba.ebi.ac.uk/EST/jesam/jesam.html. One jar contains all the Java source code, and the other contains all the C, C++ and IDL code. Links to working examples of the alignment and cluster viewers (if remote firewall permits) can be found at http://corba.ebi.ac.uk/EST. All the Washington University mouse EST traces are available for browsing at the same URL.
Contact: jparsons@ebi.ac.uk
Secondary structure alone is generally not statistically
significant for the detection of noncoding RNAs
Authors: Rivas Elena , Eddy Sean R. 
Published: July 2002

Abstract
Motivation: Several results in the literature suggest that biologically interesting RNAs have secondary structures that are more stable than expected by chance. Based on these observations, we developed a scanning algorithm for detecting noncoding RNA genes in genome sequences, using a fully probabilistic version of the Zuker minimum-energy folding algorithm.
Results: Preliminary results were encouraging, but certain anomalies led us to do a carefully controlled investigation of this class of methods. Ultimately, our results argue that for the probabilistic model there is indeed a statistical effect, but it comes mostly from local base-composition bias and not from RNA secondary structure. For the thermodynamic implementation (which evaluates statistical significance by doing Monte Carlo shuffling in fixed-length sequence windows, thus eliminating the base-composition effect) the signals for noncoding RNAs are still usually indistinguishable from noise, especially when certain statistical artifacts resulting from local base-composition inhomogeneity are taken into account. We conclude that although a distinct, stable secondary structure is undoubtedly important in most noncoding RNAs, the stability of most noncoding RNA secondary structures is not sufficiently different from the predicted stability of a random sequence to be useful as a general genefinding approach.
Contact: eddy@genetics.wustl.edu
* To whom correspondence should be addressed.
Generation of patterns from gene expression data by assigning

confidence to differentially expressed genes
Authors: Manduchi Elisabetta , Grant Gregory R. , McKenzie Steven E. , Overton G. Christian , Surrey Saul , Stoeckert Jr. Christian J. 
Published: July 2002

Abstract
Motivation: A protocol is described to attach expression patterns to genes represented in a collection of hybridization array experiments. Discrete values are used to provide an easily interpretable description of differential expression. Binning cutoffs for each sample type are chosen automatically, depending on the desired false-positive rate for the predictions of differential expression. Confidence levels are derived for the statement that changes in observed levels represent true changes in expression. We have a novel method for calculating this confidence, which gives better results than the standard methods. Our method reflects the broader change of focus in the field from studying a few genes with many replicates to studying many (possibly thousands) of genes simultaneously, but with relatively few replicates. Our approach differs from standard methods in that it exploits the fact that there are many genes on the arrays. These are used to estimate for each sample type an appropriate distribution that is employed to control the false-positive rate of the predictions made. Satisfactory results can be obtained using this method with as few as two replicates.
Results: The method is illustrated through applications to macroarray and microarray datasets. The first is an erythroid development dataset that we have generated using nylon filter arrays. Clones for genes whose expression is known in these cells were assigned expression patterns which are in accordance with what was expected and which are not picked up by the standards methods. Moreover, genes differentially expressed between normal and leukemic cells were identified. These included genes whose expression was altered upon induction of the leukemic cells to differentiate. The second application is to the microarray data by Alizadeh et al. (2000). Our results are in accordance with their major findings and offer confidence measures for the predictions made. They also provide new insights for further analysis.
Availability: Software is available on request from the authors.
Contact: manduchi@pcbi.upenn.edu
To whom correspondence should be addressed.
Pro-Frame: similarity-based gene recognition in eukaryotic DNA

sequences with errors
Authors: Mironov Andrey A. , Novichkov Pavel S. , Gelfand Mikhail S. 
Published: July 2002

Abstract
Summary: Performance of existing algorithms for similarity-based gene recognition in eukaryotes drops when the genomic DNA has been sequenced with errors. A modification of the spliced alignment algorithm allows for gene recognition in sequences with errors, in particular frameshifts. It tolerates up to 5% of sequencing errors without considerable drop of prediction reliability when a sufficiently close homologous protein is available (normalized evolutionary distance similarity score 50% or higher).
Availability: The program is free for academic users and available upon request at http://www.anchorgen.com
Contact: mgelfand@anchorgen.com
Database-driven Multi Locus Sequence Typing (MLST) of bacterial
pathogens
Authors: Chan Man-Suen , Maiden Martin C. J. , Spratt Brian G. 
Published: July 2002

Abstract
Motivation: Multi Locus Sequence Typing (MLST) is a newly developed typing method for bacteria based on the sequence determination of internal fragments of seven house-keeping genes. It has proved useful in characterizing and monitoring disease-causing and antibiotic resistant lineages of bacteria. The strength of this approach is that unlike data obtained using most other typing methods, sequence data are unambiguous, can be held on a central database and be queried through a web server.
Results: A database-driven software system (mlstdb) has been developed, which is used by public health laboratories and researchers globally to query their nucleotide sequence data against centrally held databases over the internet. The mlstdb system consists of a set of perl scripts for defining the database tables and generating the database management interface and dynamic web pages for querying the databases.
Availability: http://www.mlst.net.
Contact: mchan@molbiol.ox.ac.uk
* To whom correspondence should be addressed.
2 Present address: Department of Paediatrics, The Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DS, UK.
3 Present address: Department of Infectious Disease Epidemiology, Imperial College School of Medicine, University of London, St Mary’s Campus, Norfolk Place, London W2 1PG, UK.
A Java applet for visualizing protein–protein interaction
Authors: Mrowka Ralf 
Published: July 2002

Abstract
Summary: A web applet for browsing protein–protein interactions was implemented. It enables the display of interaction relationships, based upon neighboring distance and biological function.
Availability: The Java applet is available at http://www.charite.de/bioinformatics
Contact: Mrowka@rz.hu-berlin.de
TreeWiz: interactive exploration of huge trees
Authors: Rost Ursula , Bornberg-Bauer Erich 
Published: July 2002

Abstract
Motivation: The rapidly increasing amount and disparity of biological data requires interpretation at many levels of description. Human judgement and intuition are important because not all data can be automatically and comprehensively analyzed. Visualization of trees and substructures corresponding to certain features are often used to analyze phylogenies or taxonomies. Unfortunately, most existing tools do not cope with the size of current datasets, the required functionality, or both.
Results: We introduce a program for visualization of huge trees and also for the interactive exploration of their content. We have developed a range of new schemes which are tailored for biological problems. Users can get an overview, zoom in, filter out data and retrieve details from standard databases such as SWISS-PROT. Furthermore, it is possible to analyze the relationship between chosen leaf sets that are specified by common features on a second level of representation. On a PC (with ≈ 512 MB RAM), trees of up to several tens of thousands of leaves can be loaded and both rapidly and interactively explored. We demonstrate the use of this program for the analysis of the SYSTERS data set (which contains hierarchically clustered protein sequences) to which PFAM domains were added as features.
Availability: TreeWiz is written in JAVA and is free for academic use. The full application as well as a restricted applet version can be found on the web-page http://www.eml.org/english/staff/homes/ulla/rost.html.
Contact: Ursula.Rost@eml.villa-bosch.de
* To whom correspondence should be addressed.
A Bayesian framework for combining gene
predictions
Authors: Pavlović Vladimir , Garg Ashutosh , Kasif Simon 
Published: July 2002

Abstract
Motivation: Gene identification and gene discovery in new genomic sequences is one of the most timely computational questions addressed by bioinformatics scientists. This computational research has resulted in several systems that have been used successfully in many whole-genome analysis projects. As the number of such systems grows the need for a rigorous way to combine the predictions becomes more essential.
Results: In this paper we provide a Bayesian network framework for combining gene predictions from multiple systems. The framework allows us to treat the problem as combining the advice of multiple experts. Previous work in the area used relatively simple ideas such as majority voting. We introduce, for the first time, the use of hidden input/output Markov models for combining gene predictions. We apply the framework to the analysis of the Adh region in Drosophila that has been carefully studied in the context of gene finding and used as a basis for the GASP competition. The main challenge in combination of gene prediction programs is the fact that the systems are relying on similar features such as cod on usage and as a result the predictions are often correlated. We show that our approach is promising to improve the prediction accuracy and provides a systematic and flexible framework for incorporating multiple sources of evidence into gene prediction systems.
Availability: Software can be made available on request from the authors.
Contact: vladimir@bu.edu
* Part of this research was presented at Computational Genomics 2000, Baltimore, MD, November 2000. Portions of this research were conducted at Compaq Computer Corporation, Cambridge Research Laboratory, Cambridge, MA.
OligoArray: genome-scale oligonucleotide design for microarrays
Authors: Rouillard Jean-Marie , Herbert Christopher J. , Zuker Michael 
Published: July 2002

Abstract
Summary: OligoArray is a program that computes gene specific and secondary structure free oligonucleotides for genome-scale oligonucleotide microarray construction or other applications.
Availability: The program code is distributed under the GNU General Public License and is freely available for non-profit use via request from the authors.
Contact: jean-marie.rouillard@cgm.cnrs-gif.fr
Supplementary information: http://berry.engin.umich.edu/oligoarray