Results 111 to 120 of about 1,232,205 (304)

Challenges in experimental data integration within genome-scale metabolic models

Algorithms for Molecular Biology, 2010
A report of the meeting "Challenges in experimental data integration within genome-scale metabolic models", Institut Henri Poincaré, Paris, October 10-11 2009, organized by the CNRS-MPG joint program in Systems Biology.
Képès François, Samal Areejit, Bourguignon Pierre-Yves, Jost Jürgen, Martin Olivier C   +4 more
doaj   +1 more source

Gut microbiome and aging—A dynamic interplay of microbes, metabolites, and the immune system

FEBS Letters, EarlyView.
Age‐dependent shifts in microbial communities engender shifts in microbial metabolite profiles. These in turn drive shifts in barrier surface permeability of the gut and brain and induce immune activation. When paired with preexisting age‐related chronic inflammation this increases the risk of neuroinflammation and neurodegenerative diseases.
Aaron Mehl, Eran Blacher
wiley   +1 more source

PyBioNetFit and the Biological Property Specification Language

iScience, 2019
Summary: In systems biology modeling, important steps include model parameterization, uncertainty quantification, and evaluation of agreement with experimental observations.
Eshan D. Mitra, Ryan Suderman, Joshua Colvin, Alexander Ionkov, Andrew Hu, Herbert M. Sauro, Richard G. Posner, William S. Hlavacek   +7 more
doaj   +1 more source

Physics of Transport and Traffic Phenomena in Biology: from molecular motors and cells to organisms

, 2005
Traffic-like collective movements are observed at almost all levels of biological systems. Molecular motor proteins like, for example, kinesin and dynein, which are the vehicles of almost all intra-cellular transport in eukayotic cells, sometimes ...
Aghababaie, Anderson, Anderson, Anderson, Anderson, Anderson, Andreas Schadschneider, Antal, Aridor, Aridor, Arndt, Arndt, Astumian, Bonabeau, Bonabeau, Bonabeau, Bonabeau, Bonabeau, Burd, Burd, Burstedde, Camazine, Chopard, Chopard, Chou, Chowdhury, Chowdhury, Chowdhury, Coffey, Couzin, de Gier, Debashish Chowdhury, Derenyi, Derenyi, Derrida, Derrida, Derrida, Dorigo, Ebneth, Edelstein-Keshet, Evans, Evans, Evans, Evans, Evans, Feynman, Fisher, Frey, Fukui, Gautrais, Gipps, Goldstein, Goldstein, Goldstein, Goldstein, Goldstein, Grimm, Gross, Gueron, Hackney, Harms, Helbing, Helbing, Helbing, Helbing, Helbing, Helbing, Henderson, Hiratsuka, Hirokawa, Howard, Huang, Hughes, Hughes, Hölldobler, Jackson, Janowsky, John, Juhasz, Juhasz, Jülicher, Kafri, Katsuhiro Nishinari, Kirchner, Kirchner, Kirchner, Klein, Klumpp, Klumpp, Klumpp, Klumpp, Klüpfel, Kolomeisky, Krieger, Krug, Krug, Kruse, Ktitarev, Lakatos, Leduc, Lee, Lipowsky, Lipowsky, MacDonald, MacDonald, Mahnke, Mai, Mandelkow, Marchesoni, Marconi, Marro, Mikhailov, Mogilner, Mukherji, Muramatsu, Nagase, Nakayama, Nedlec, Nedlec, Nieuwenhuizen, Nieuwenhuizen, Nishinari, Nishinari, Nitta, O'Loan, O'Loan, Odell, Okada, Okada, Okada, Parmeggiani, Parmeggiani, Popescu, Popkov, Popkov, Popkov, Railsback, Rajewsky, Rajewsky, Ratnieks, Ratnieks, Rauch, Reimann, Risken, Saffarian, Sankararaman, Schadschneider, Schmittmann, Schweitzer, Schütz, Schütz, Shaw, Shaw, Shaw, Smoluchowski, Stamer, Surrey, Theraulaz, Theraulaz, Thompson, Tripathi, Watmough, Weibel, Welte, Whittaker, Wilson, Wolfram, Wolfram, Ziebert   +168 more
core   +1 more source

A methionine‐lined active site governs carbocation stabilization and product specificity in a bacterial terpene synthase

FEBS Letters, EarlyView.
This study reveals a unique active site enriched in methionine residues and demonstrates that these residues play a critical role by stabilizing carbocation intermediates through novel sulfur–cation interactions. Structure‐guided mutagenesis further revealed variants with significantly altered product profiles, enhancing pseudopterosin formation. These
Marion Ringel, Carl P. O. Helmer, Shani Zev, Ronja Driller, Emily Buhr, Markus Reinbold, Renana Schwartz, Gabriel Foley, Mikael Boden, Daniel Garbe, Gerhard Schenk, Dan Thomas Major, Bernhard Loll, Thomas Brück   +13 more
wiley   +1 more source

The Body-wide Transcriptome Landscape of Disease Models

iScience, 2018
Summary: Virtually all diseases affect multiple organs. However, our knowledge of the body-wide effects remains limited. Here, we report the body-wide transcriptome landscape across 13–23 organs of mouse models of myocardial infarction, diabetes, kidney ...
Satoshi Kozawa, Ryosuke Ueda, Kyoji Urayama, Fumihiko Sagawa, Satsuki Endo, Kazuhiro Shiizaki, Hiroshi Kurosu, Glicia Maria de Almeida, Sharif M. Hasan, Kiyokazu Nakazato, Shinji Ozaki, Yoshinori Yamashita, Makoto Kuro-o, Thomas N. Sato   +13 more
doaj   +1 more source

Comparison of H. pylori in silico metabolic model predictions with experimental data [PDF]

, 2009
[Excerpt] The Systems Biology approach has been replacing the reductionist view that dominated biology research in the last decades. Present biochemical knowledge and genomic databases allowed the development of metabolic models for several organisms ...
Azevedo, N. F., Correia, Daniela M., Cunha, M. L. R., Rocha, I., Vieira, M. J.   +4 more
core  

Valosin‐containing protein counteracts ATP‐driven dissolution of FUS condensates through its ATPase activity in vitro

FEBS Letters, EarlyView.
Biomolecular condensates formed by fused in sarcoma (FUS) are dissolved by high ATP concentrations yet persist in cells. Using a reconstituted system, we demonstrate that valosin‐containing protein (VCP), an AAA+ ATPase, counteracts ATP‐driven dissolution of FUS condensates through its D2 ATPase activity.
Hitomi Kimura, Shin‐ichi Tate, Kyota Yasuda   +2 more
wiley   +1 more source

OME Remote Objects (OMERO): a flexible, model-driven data management system for experimental biology

, 2012
Data-intensive research depends on tools that manage multi-dimensional, heterogeneous data sets. We have built OME Remote Objects (OMERO), a software platform that enables access to and use of a wide range of biological data. OMERO uses a server-based middleware application to provide a unified interface for images, matrices, and tables. OMERO’s design
Allan, Chris, Burel, Jean-Marie, Moore, Josh, Blackburn, Colin, Linkert, Melissa, Loynton, Scott, MacDonald, Donald, Moore, William J., Neves, Carlos, Patterson, Andrew, Porter, Michael, Tarkowska, Aleksandra, Loranger, Brian, Avondo, Jerome, Lagerstedt, Ingvar, Lianas, Luca, Leo, Simone, Hands, Katherine, Hay, Ron T., Patwardhan, Ardan, Best, Christoph, Kleywegt, Gerard J., Zanetti, Gianluigi, Swedlow, Jason R.   +23 more
openaire   +1 more source

Diversity and complexity in neural organoids

FEBS Letters, EarlyView.
Neural organoid research aims to expand genetic diversity on one side and increase tissue complexity on the other. Chimeroids integrate multiple donor genomes within single organoids. Self‐organising multi‐identity organoids, exogenous cell seeding, or enforced assembly of region‐specific organoids contribute to tissue complexity.
Ilaria Chiaradia, Madeline A. Lancaster
wiley   +1 more source