Bioinformatics (Oxford, England)

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Relational patterns of gene expression via non-metric multidimensional scaling analysis
Bioinformatics (Oxford, England) - Tập 21 Số 6 - Trang 730-740 - 2005
Y‐h. Taguchi, Y. Oono
Abstract Motivation: Microarray experiments result in large-scale data sets that require extensive mining and refining to extract useful information. We demonstrate the usefulness of (non-metric) multidimensional scaling (MDS) method in analyzing a large number of genes. Applying MDS to the microarray data is certainly not new, but the existing works...... hiện toàn bộ
PySCeSToolbox: a collection of metabolic pathway analysis tools
Bioinformatics (Oxford, England) - Tập 34 Số 1 - Trang 124-125 - 2018
Carl D. Christensen, Jan‐Hendrik S. Hofmeyr, Johann M. Rohwer
Abstract Summary PySCeSToolbox is an extension to the Python Simulator for Cellular Systems (PySCeS) that includes tools for performing generalized supply–demand analysis, symbolic metabolic control analysis, and a framework for investigating the kinetic and thermodynamic aspects...... hiện toàn bộ
Causal analysis approaches in Ingenuity Pathway Analysis
Bioinformatics (Oxford, England) - Tập 30 Số 4 - Trang 523-530 - 2014
A. Krämer, Jeff Green, Jack Pollard, Stuart Tugendreich
Abstract Motivation: Prior biological knowledge greatly facilitates the meaningful interpretation of gene-expression data. Causal networks constructed from individual relationships curated from the literature are particularly suited for this task, since they create mechanistic hypotheses that explain the expression changes observed in datasets.... hiện toàn bộ
pyDockWEB: a web server for rigid-body protein–protein docking using electrostatics and desolvation scoring
Bioinformatics (Oxford, England) - Tập 29 Số 13 - Trang 1698-1699 - 2013
Brian Jiménez‐García, Carles Pons, Juan Fernández‐Recio
Abstract Summary: pyDockWEB is a web server for the rigid-body docking prediction of protein–protein complex structures using a new version of the pyDock scoring algorithm. We use here a new custom parallel FTDock implementation, with adjusted grid size for optimal FFT calculations, and a new version of pyDock, which dramatically speeds up calculatio...... hiện toàn bộ
InterProSurf: a web server for predicting interacting sites on protein surfaces
Bioinformatics (Oxford, England) - Tập 23 Số 24 - Trang 3397-3399 - 2007
Surendra S. Negi, Catherine H. Schein, Numan Oezguen, Trevor D. Power, Werner Braun
AbstractSummary: A new web server, InterProSurf, predicts interacting amino acid residues in proteins that are most likely to interact with other proteins, given the 3D structures of subunits of a protein complex. The prediction method is based on solvent accessible surface area of residues in the isolated subunits, a propensity scale for interface residues and a c...... hiện toàn bộ
A multi-algorithm, multi-timescale method for cell simulation
Bioinformatics (Oxford, England) - Tập 20 Số 4 - Trang 538-546 - 2004
Kouichi Takahashi, Kazunari Kaizu, Bin Hu, Masaru Tomita
Abstract Motivation: Many important problems in cell biology require the dense nonlinear interactions between functional modules to be considered. The importance of computer simulation in understanding cellular processes is now widely accepted, and a variety of simulation algorithms useful for studying certain subsystems have been designed. Many of t...... hiện toàn bộ
E-CELL: software environment for whole-cell simulation.
Bioinformatics (Oxford, England) - Tập 15 Số 1 - Trang 72-84 - 1999
Masaru Tomita, Kazuaki Hashimoto, Kazutoshi Takahashi, Toshio Shimizu, Yumi Matsuzaki, Fumito Miyoshi, Kanako Saito, Sakura Tanida, Katsuyuki Yugi, J. Craig Venter, Clyde A. Hutchison
Abstract MOTIVATION: Genome sequencing projects and further systematic functional analyses of complete gene sets are producing an unprecedented mass of molecular information for a wide range of model organisms. This provides us with a detailed account of the cell with which we may begin to build models for simulating intracellular molecular processes...... hiện toàn bộ
Integrating metabolic, transcriptional regulatory and signal transduction models inEscherichia coli
Bioinformatics (Oxford, England) - Tập 24 Số 18 - Trang 2044-2050 - 2008
Markus W. Covert, Nan Xiao, Tiffany J. Chen, Jonathan R. Karr
AbstractMotivation: The effort to build a whole-cell model requires the development of new modeling approaches, and in particular, the integration of models for different types of processes, each of which may be best described using different representation. Flux-balance analysis (FBA) has been useful for large-scale analysis of metabolic networks, and methods have...... hiện toàn bộ
E-Cell 2: Multi-platform E-Cell simulation system
Bioinformatics (Oxford, England) - Tập 19 Số 13 - Trang 1727-1729 - 2003
Kyôko Takahashi, Naota Ishikawa, Yasuhiro Sadamoto, Hiroyuki Sasamoto, Seiji Ohta, Akira Shiozawa, Fumito Miyoshi, Yoshiro Naito, Yoichi Nakayama, Masaru Tomita
Abstract Summary: A new version of the E-Cell simulation system, which runs on Windows as well as Linux, has been released as free software under the terms of the GNU General Public License. Availability: Downloadable from http://www.E-Cell.org
W2H: WWW interface to the GCG sequence analysis package.
Bioinformatics (Oxford, England) - Tập 14 Số 5 - Trang 452-457 - 1998
Martin Senger, Terán Flores, Karl-Heinz Glatting, Peter B. Ernst, Agnes Hotz‐Wagenblatt, Sándor Suhai
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...... hiện toàn bộ
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