Publications

 

Wordprocessing Model-Based Characterization of Inflammatory Gene Expression Patterns of Activated Macrophages


Authors: Julia Rex, Ute Albrecht, Christian Ehlting, Maria Thomas, Ulrich M. Zanger, Oliver Sawodny, Dieter Häussinger, Michael Ederer, Ronny Feuer, Johannes G. Bode

DOI: 10.1371/journal.pcbi.1005018

Date Published: 27th Jul 2016

Projects: B1: Intercellular communication of hepatocytes and macrophages

Journal: PLoS Comput Biol

Citation: PLoS Comput Biol 12(7) : e1005018

Scales: Cell and Intercellular

Abstract (Expand)

Macrophages are cells with remarkable plasticity. They integrate signals from their microenvironment leading to context-dependent polarization into classically (M1) or alternatively (M2) activated ...

Created: 23rd Nov 2016 at 13:29   Last updated: 23rd Nov 2016 at 13:32


 

Wordprocessing Mechanistically linked serum miRNAs distinguish between drug induced and fatty liver disease of different grades


Authors: Z. Liu, Y. Wang, J. Borlak, W. Tong

PubMed ID: 27045805

Date Published: 6th Apr 2016

Projects: A3.6: Transcription factor network and links to metabolism in NAFLD

Journal: Sci Rep

Citation: Sci Rep. 2016 Apr 5;6:23709. doi: 10.1038/srep23709.

Scales: Liver

Abstract (Expand)

Hepatic steatosis is characterised by excessive triglyceride accumulation in the form of lipid droplets (LD); however, mechanisms differ in drug induced (DIS) and/or non-alcoholic fatty liver disease ...

Created: 18th May 2016 at 10:50


 

Wordprocessing Mouse white adipose tissue-derived mesenchymal stem cells gain pericentral and periportal hepatocyte features after differentiation in vitro, which are preserved in vivo after hepatic transplantation


Authors: S. Winkler, M. Hempel, S. Bruckner, F. Mallek, A. Weise, T. Liehr, H. M. Tautenhahn, M. Bartels, B. Christ

PubMed ID: 26235702

Date Published: 19th Aug 2015

Projects: C6: Organization and function of the sinusoidal system and the liver lob...

Journal: Acta Physiol (Oxf)

Citation: Acta Physiol (Oxf). 2015 Oct;215(2):89-104. doi: 10.1111/apha.12560. Epub 2015 Aug 19.

Scales: Liver lobule

Abstract (Expand)

AIM: Mesenchymal stem cells may differentiate into hepatocyte-like cells in vitro and in vivo. Therefore, they are considered a novel cell resource for the treatment of various liver diseases. Here, ...

Created: 11th Nov 2015 at 11:22


 

Wordprocessing Mathematical modelling of fluid transport and its regulation at multiple scales


Authors: Osvaldo Chara, Lutz Brusch

DOI: 10.1016/j.biosystems.2015.02.004

Date Published: 1st Apr 2015

Scales: Cell and Liver lobule

Abstract (Expand)

Living matter equals water, to a first approximation, and water transport across barriers such as membranes and epithelia is vital. Water serves two competing functions. On the one hand, it is the ...

Created: 30th Apr 2015 at 15:04   Last updated: 30th Apr 2015 at 15:08


 

Wordprocessing Mathematical Modelling suggests Differential Impact of β-TrCP Paralogues on Wnt/β-catenin Signalling Dynamics


Authors: Uwe Benary, Bente Kofahl, Andreas Hecht, Jana Wolf

DOI: 10.1111/febs.13204

Date Published: 2015

Scales: Cell

Abstract (Expand)

The Wnt/β-catenin signalling pathway is involved in the regulation of a multitude of cellular processes by controlling the concentration of the transcriptional regulator β-catenin. Proteasomal degradation ...

Created: 20th Jan 2015 at 07:51   Last updated: 20th Jan 2015 at 07:52


 

Wordprocessing Multi-bio and multi-scale systems biology


Authors: Adriano Henney, Peter Hunter, Andrew McCulloch, Denis Noble

DOI: 10.1016/j.pbiomolbio.2015.03.001

Date Published: 2015

Projects: No Projects

Journal: Progress in Biophysics and Molecular Biology

Citation: Progress in Biophysics and Molecular Biology 117(1) : 1

Scales: Not specified

Abstract:

Not specified

Created: 6th Apr 2015 at 12:20   Last updated: 6th Apr 2015 at 12:21


 

Wordprocessing Modeling function-perfusion behavior in liver lobules including tissue, blood, glucose, lactate and glycogen by use of a coupled two-scale PDE-ODE approach


Authors: T Ricken, D Werner, H G Holzhütter, M König, U Dahmen, O Dirsch

PubMed ID: 25236798

Date Published: 19th Sep 2014

Projects: A1: Cellular metabolism, C: Liver lobule level, E: Model integration

Journal: Biomech Model Mechanobiol

Citation: Biomech Model Mechanobiol 14(3): 515-36

Scales: Cell and Liver lobule

Abstract (Expand)

This study focuses on a two-scale, continuum multicomponent model for the description of blood perfusion and cell metabolism in the liver. The model accounts for a spatial and time depending ...

Created: 30th Jun 2015 at 07:09


 

Wordprocessing morFeus: a web-based program to detect remotely conserved orthologs using symmetrical best hits and orthology network scoring


Authors: Ines Wagner, Michael Volkmer, Malvika Sharan, Jose M Villaveces, Felix Oswald, Vineeth Surendranath, Bianca H Habermann

PubMed ID: 25096057

Date Published: 6th Aug 2014

Scales: Not specified

Abstract (Expand)

Searching the orthologs of a given protein or DNA sequence is one of the most important and most commonly used Bioinformatics methods in Biology. Programs like BLAST or the orthology search engine ...

Created: 11th Aug 2014 at 16:33


 

Wordprocessing Modelling proteasome and proteasome regulator activities


Authors: Juliane Liepe, Herman-Georg Holzhütter, Peter M Kloetzel, Michael P H Stumpf, Michele Mishto

PubMed ID: 24970232

Date Published: 28th Jun 2014

Projects: No Projects

Journal: Biomolecules

Citation: Biomolecules 4(2): 585-99

Scales: Not specified

Abstract (Expand)

Proteasomes are key proteases involved in a variety of processes ranging from the clearance of damaged proteins to the presentation of antigens to CD8+ T-lymphocytes. Which cleavage sites are used ...

Created: 6th Jan 2015 at 09:32


 

Wordprocessing Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)


Authors: Dagmar Waltemath, Frank T. Bergmann, Claudine Chaouiya, Tobias Czauderna, Padraig Gleeson, Carole Goble, Martin Golebiewski, Michael Hucka, Nick Juty, Olga Krebs, Nicolas Le Novère, Huaiyu Mi, Ion I. Moraru, Chris J. Myers, David Nickerson, Brett G. Olivier, Nicolas Rodriguez, Falk Schreiber, Lucian Smith, Fengkai Zhang, Eric Bonnet

DOI: 10.4056/sigs.5279417

Date Published: 15th Mar 2014

Projects: F1: The data management system

Journal: Stand. Genomic Sci.

Citation: Stand. Genomic Sci. 9(3) : 1285

Scales: Not specified

Abstract (Expand)

The Computational Modeling in Biology Network (COMBINE) is an initiative to coordinate the development of community standards and formats in computational systems biology and related fields. This report ...

Created: 3rd Feb 2015 at 11:07   Last updated: 3rd Feb 2015 at 11:12


 

Wordprocessing Morpheus: a user-friendly modeling environment for multiscale and multicellular systems biology


Authors: J. Starruss, W. d. Back, L. Brusch, A. Deutsch

DOI: 10.1093/bioinformatics/btt772

Date Published: 17th Jan 2014

Scales: Cell, Intercellular and Liver lobule

Abstract (Expand)

Summary: Morpheus is a modeling environment for the simulation and integration of cell-based models with ordinary differential equations and reaction-diffusion systems. It allows rapid development of ...

Created: 20th Jan 2014 at 15:49   Last updated: 20th Jan 2014 at 16:16


 

Wordprocessing Mathematical Modeling of Regenerative Processes


Authors: Osvaldo Chara, Elly M. Tanaka, Lutz Brusch

DOI: 10.1016/B978-0-12-391498-9.00011-5

Date Published: 2014

Scales: Not specified

Abstract:

Not specified

Created: 22nd Jan 2015 at 16:09   Last updated: 22nd Jan 2015 at 16:11


 

Wordprocessing Manganese superoxide dismutase is reduced in the liver of male but not female humans and rodents with non-alcoholic fatty liver disease


Authors: Sabrina Krautbauer, Kristina Eisinger, Madeleine Lupke, Josef Wanninger, Petra Ruemmele, Yvonne Hader, Thomas S Weiss, Christa Buechler

PubMed ID: 24161595

Date Published: 22nd Oct 2013

Scales: Cell, Liver and Organism

Abstract (Expand)

Non-alcoholic fatty liver disease (NAFLD) is among the most common liver diseases. Oxidative stress is one of the pathogenic mechanisms contributing to the progression of simple fatty liver to non-alcoholic ...

Created: 30th Jan 2014 at 16:27


 

Wordprocessing Modeling approaches for qualitative and semi-quantitative analysis of cellular signaling networks


Authors: Regina Samaga, Steffen Klamt

PubMed ID: 23803171

Date Published: 26th Jun 2013

Projects: A2.3: Cross-talk and distinct properties of growth factor signalling reg...

Journal: Cell Commun. Signal

Citation: Cell Commun. Signal 11(1): 43

Scales: Cell

Abstract (Expand)

A central goal of systems biology is the construction of predictive models of bio-molecular networks. Cellular networks of moderate size have been modeled successfully in a quantitative way based on ...

Created: 13th Dec 2013 at 17:23


 

Wordprocessing Metabolic Gradients as Key Regulators in Zonation of Tumor Energy Metabolism: A Tissue-scale Model Based Study


Authors: Matthias König, Hermann-Georg Holzhütter, Nikolaus Berndt

PubMed ID: 23589477

Date Published: 17th Apr 2013

Projects: C3: Zonation of metabolism and its regulation

Journal: Biotechnol J

Citation: Biotechnol J 8(9): 1058-69

Scales: Not specified

Abstract (Expand)

Characteristics of many tumor types are the reprogramming of metabolism and the occurrence of regional hypoxia. In this work we investigated the hypothesis that metabolic reprogramming in combination ...

Created: 6th May 2013 at 09:31   Last updated: 24th Oct 2013 at 16:14


 

Wordprocessing Molecular Interactions between NAFLD and Xenobiotic Metabolism


Authors: Adviti Naik, Aleš Belič, Ulrich M Zanger, Damjana Rozman

PubMed ID: 23346097

Date Published: 22nd Jan 2013

Scales: Not specified

Abstract (Expand)

Non-alcoholic fatty liver disease (NAFLD), the hepatic manifestation of the metabolic syndrome, is a complex multifactorial disease characterized by metabolic deregulations that include accumulation ...

Created: 8th Jan 2014 at 14:35


 

Wordprocessing Metformin and cancer: from the old medicine cabinet to pharmacological pitfalls and prospects


Authors: Arian Emami Riedmaier, Pascale Fisel, Anne T Nies, Elke Schaeffeler, Matthias Schwab

PubMed ID: 23277337

Date Published: 2nd Jan 2013

Scales: Not specified

Abstract (Expand)

Metformin is a biguanide derivative used in the treatment of type II diabetes (T2D) and one of the world's most widely prescribed drugs. Owing to its safety profile, it has been recently promoted ...

Created: 8th Jan 2013 at 10:08   Last updated: 24th Oct 2013 at 16:15


 

Wordprocessing Modeling Wnt/β-Catenin Target Gene Expression in APC and Wnt Gradients Under Wild Type and Mutant Conditions


Authors: Uwe Benary, Bente Kofahl, Andreas Hecht, Jana Wolf

DOI: 10.3389/fphys.2013.00021

Date Published: 2013

Scales: Cell

Abstract (Expand)

The Wnt/β-catenin pathway is involved in the regulation of a multitude of physiological processes by controlling the differential expression of target genes. In certain tissues such as the adult liver, ...

Created: 27th Feb 2013 at 10:06   Last updated: 24th Oct 2013 at 16:15


 

Wordprocessing Metabolic Networks


Authors: Andreas Dräger, Hannes Planatscher

DOI: 10.1007/978-1-4419-9863-7_1277

Date Published: 2013

Projects: A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes

Book: Encyclopedia of Systems Biology

Citation: Encyclopedia of Systems Biology : 1249

Scales: Cell

Abstract (Expand)

Metabolic networks are interconnected pathways of biochemical reactions within living cells through which building blocks or compounds necessary for cellular functioning are assembled (anabolism) or ...

Created: 15th Aug 2013 at 23:34   Last updated: 23rd Jul 2015 at 13:38


 

Wordprocessing Metabolic Consequences of TGFb Stimulation in CulturedPrimary Mouse Hepatocytes Screened from Transcript Data with ModeScore�


Authors: Andreas Hoppe, Iryna Ilkavets, Steven Dooley, Hermann-Georg Holzhütter

DOI: 10.3390/metabo2040983

Date Published: 1st Dec 2012

Scales: Cell

Abstract (Expand)

Abstract: TGFβ signaling plays a major role in the reorganization of liver tissue upon injury and is an important driver of chronic liver disease. This is achieved by a deep impact on a cohort of ...

Created: 28th Nov 2012 at 12:21   Last updated: 24th Oct 2013 at 16:15


 

Wordprocessing Multidrug and toxin extrusion proteins as transporters of antimicrobial drugs


Authors: Anne T Nies, Katja Damme, Elke Schaeffeler, Matthias Schwab

PubMed ID: 22970772

Date Published: 13th Sep 2012

Projects: G2: Clinical Translation to Non-Invasive Volunteer Setting, G3: Clinical Translation to Pharmaceutical Drug Development

Journal: Expert Opin Drug Metab Toxicol

Citation: Expert Opin Drug Metab Toxicol 8(12): 1565-77

Scales: Not specified

Abstract (Expand)

INTRODUCTION: Antimicrobial drugs are essential in the treatment of infectious diseases. A better understanding of transport processes involved in drug disposition will improve the predictability of ...

Created: 10th Jan 2013 at 10:39   Last updated: 24th Oct 2013 at 16:15


 

Wordprocessing Multi-Scale Modeling in Morphogenesis: A Critical Analysis of the Cellular Potts Model


Author: Anja Voss-Böhme

DOI: 10.1371/journal.pone.0042852

Date Published: 11th Sep 2012

Scales: Cell

Abstract (Expand)

Cellular Potts models (CPMs) are used as a modeling framework to elucidate mechanisms of biological development. They allow a spatial resolution below the cellular scale and are applied particularly ...

Created: 21st Sep 2012 at 14:45   Last updated: 24th Oct 2013 at 16:15


 

Wordprocessing Multi-Target Regulation by Small RNAs Synchronizes Gene Expression Thresholds and May Enhance Ultrasensitive Behavior


Authors: Jörn Matthias Schmiedel, Ilka Maria Axmann, Stefan Legewie

PubMed ID: 22927924

Date Published: 21st Aug 2012

Scales: Cell

Abstract (Expand)

Cells respond to external cues by precisely coordinating multiple molecular events. Co-regulation may be established by the so-called single-input module (SIM), where a common regulator controls multiple ...

Created: 3rd Sep 2012 at 11:02   Last updated: 24th Oct 2013 at 16:16


 

Wordprocessing Modulation of glutamine metabolism by the PI(3)K-PKB-FOXO network regulates autophagy


Authors: Kristan E van der Vos, Pernilla Eliasson, Tassula Proikas-Cezanne, Stephin J Vervoort, Ruben van Boxtel, Marrit Putker, Iris J van Zutphen, Mario Mauthe, Sebastian Zellmer, Cornelieke Pals, Liesbeth P Verhagen, Marian J A Groot Koerkamp, A Koen Braat, Tobias B Dansen, Frank C Holstege, Rolf Gebhardt, Boudewijn M Burgering, Paul J Coffer

PubMed ID: 22820375

Date Published: 22nd Jul 2012

Projects: A1: Cellular metabolism, A: Cellular level

Journal: Nat. Cell Biol.

Citation: Nat. Cell Biol. 14(8): 829-37

Scales: Cell

Abstract (Expand)

The PI(3)K-PKB-FOXO signalling network provides a major intracellular hub for the regulation of cell proliferation, survival and stress resistance. Here we report an unexpected role for FOXO transcription ...

Created: 14th Aug 2012 at 14:52   Last updated: 24th Oct 2013 at 16:16


 

Wordprocessing Mesenchymal stem cell-derived hepatocytes for functional liver replacement


Authors: Bruno Christ, Peggy Stock

PubMed ID: 22737154

Date Published: 22nd Jun 2012

Scales: Cell and Liver

Abstract (Expand)

Mesenchymal stem cells represent an alternate cell source to substitute for primary hepatocytes in hepatocyte transplantation because of their multiple differentiation potential and nearly unlimited ...

Created: 19th Nov 2013 at 11:55


 

Wordprocessing MYC-regulated genes involved in liver cell dysplasia identified in a transgenic model of liver cancer


Authors: Danele Hunecke, Reinhard Spanel, Florian Länger, Suk Woo Nam, Juergen Borlak

PubMed ID: 22653869

Date Published: 2nd Jun 2012

Projects: A3.6: Transcription factor network and links to metabolism in NAFLD

Journal: J. Pathol.

Citation: J. Pathol. :

Scales: Cell

Abstract (Expand)

Foci of liver cell dysplasia (LCD) are distinct morphological entities and may evolve into hepatocellular carcinomas (HCCs). While most HCCs overexpress c-Myc, its role in LCD remains uncertain. ...

Created: 14th Dec 2012 at 19:25   Last updated: 24th Oct 2013 at 16:16


 

Wordprocessing Modeling the impact of granular embedding media, and pulling versus pushing cells on growing cell clones


Authors: Dirk Drasdo, Stefan Hoehme

DOI: 10.1088/1367-2630/14/5/055025

Date Published: 1st May 2012

Projects: No Projects

Journal: New J. Phys.

Citation: New J. Phys. 14(5) : 055025

Scales: Not specified

Abstract (Expand)

In this paper, we explore how potential biomechanical influences on cell cycle entrance and cell migration affect the growth dynamics of cell populations. We consider cell populations growing in free, ...

Created: 10th Sep 2012 at 17:48   Last updated: 24th Oct 2013 at 16:16


 

Wordprocessing Multiparametric image analysis reveals role of Caveolin1 in endosomal progression rather than internalization of EGFR


Authors: Hannah Schmidt-Glenewinkel, Eileen Reinz, Svetlana Bulashevska, Joel Beaudouin, Stefan Legewie, Angel Alonso, Roland Eils

PubMed ID: 22575653

Date Published: 1st Mar 2012

Scales: Cell

Abstract (Expand)

Endosomes constitute a central layer in the regulation of growth factor signaling. We applied flow cytometry, confocal microscopy and automated image quantification to define the role of Caveolin1 ...

Created: 11th Sep 2012 at 11:34   Last updated: 24th Oct 2013 at 16:16


 

Wordprocessing Multi-locus stepwise regression: a haplotype-based algorithm for finding genetic associations applied to atopic dermatitis


Authors: Sven Knüppel, Jorge Esparza-Gordillo, Ingo Marenholz, Hermann-Georg Holzhütter, Anja Bauerfeind, Andreas Ruether, Stephan Weidinger, Young-Ae Lee, Klaus Rohde

PubMed ID: 22284537

Date Published: 27th Jan 2012

Projects: No Projects

Journal: BMC Med. Genet.

Citation: BMC Med. Genet. 13: 8

Scales: Not specified

Abstract (Expand)

Genome-wide association studies (GWAS) provide an increasing number of single nucleotide polymorphisms (SNPs) associated with diseases. Our aim is to exploit those closely spaced SNPs in candidate ...

Created: 4th Jan 2013 at 13:03   Last updated: 24th Oct 2013 at 16:17


 

Wordprocessing Multiscale mechanistic modeling in pharmaceutical research and development


Authors: Lars Kuepfer, Jörg Lippert, Thomas Eissing

PubMed ID: 22161351

Date Published: 14th Dec 2011

Projects: E4: Vertical integration across biological scales, G: Clinical translation

Journal: Adv. Exp. Med. Biol.

Citation: Adv. Exp. Med. Biol. 736: 543-61

Scales: Organism

Abstract (Expand)

Discontinuation of drug development projects due to lack of efficacy or adverse events is one of the main cost drivers in pharmaceutical research and development (R&D). Investments have to be ...

Created: 1st Mar 2012 at 16:42   Last updated: 24th Oct 2013 at 16:17


 

Wordprocessing Mammalian MATE (SLC47A) transport proteins: impact on efflux of endogenous substrates and xenobiotics


Authors: Katja Damme, Anne T Nies, Elke Schaeffeler, Matthias Schwab

PubMed ID: 21923552

Date Published: 17th Sep 2011

Projects: G2: Clinical Translation to Non-Invasive Volunteer Setting, G4: Whole-Body Detoxification in Mouse Models

Journal: Drug Metab. Rev.

Citation: Drug Metab. Rev. 43(4): 499-523

Scales: Not specified

Abstract (Expand)

Multidrug and toxin extrusion proteins (MATEs; SLC47A) are mammalian transporters being predominately expressed in the brush-border membrane of proximal tubule epithelial cells in the kidney and the ...

Created: 18th Jul 2012 at 13:10   Last updated: 24th Oct 2013 at 16:17


 

Wordprocessing Metannogen: annotation of biological reaction networks


Authors: Christoph Gille, Katrin Hübner, Andreas Hoppe, Hermann-Georg Holzhütter

PubMed ID: 21824972

Date Published: 8th Aug 2011

Projects: A1.1: Central liver metabolism and its regulation under nutritional chal..., F2: The Liver Knowledge Base (LKB)

Journal: Bioinformatics

Citation: Bioinformatics 27(19): 2763-4

Scales: Not specified

Abstract (Expand)

Semantic annotations of the biochemical entities constituting a biological reaction network are indispensable to create biologically meaningful networks. They further heighten efficient exchange, reuse ...

Created: 4th Jan 2013 at 10:45   Last updated: 24th Oct 2013 at 16:18


 

Wordprocessing MIRNA-DISTILLER: A Stand-Alone Application to Compile microRNA Data from Databases


Authors: Jessica K Rieger, Denis A Bodan, Ulrich M Zanger

PubMed ID: 22303335

Date Published: 8th Jul 2011

Projects: A3.4: Linking signalling to metabolic functions

Journal: Front Genet

Citation: Front Genet 2: 39

Scales: Not specified

Abstract (Expand)

MicroRNAs (miRNA) are small non-coding RNA molecules of ∼22 nucleotides which regulate large numbers of genes by binding to seed sequences at the 3'-untranslated region of target gene transcripts. ...

Created: 14th May 2012 at 09:52   Last updated: 24th Oct 2013 at 16:18


 

Wordprocessing Murine hepatic stellate cells veto CD8 T cell activation by a CD54-dependent mechanism


Authors: Frank A. Schildberg, Alexandra Wojtalla, Sören V. Siegmund, Elmar Endl, Linda Diehl, Zeinab Abdullah, Christian Kurts, Percy A. Knolle

DOI: 10.1002/hep.24352

Date Published: 1st Jul 2011

Projects: B4: Regulation of pro-inflammatory stimuli through communication of live...

Journal: Hepatology

Citation: Hepatology 54(1) : 262

Scales: Not specified

Abstract (Expand)

The liver has a role in T cell tolerance induction, which is mainly achieved through the functions of tolerogenic hepatic antigen-presenting cells (APCs) and regulatory T cells. Hepatic stellate cells ...

Created: 18th Jul 2012 at 17:12   Last updated: 24th Oct 2013 at 16:18


 

Wordprocessing Mouse granzyme K has pro-inflammatory potential


Authors: L T Joeckel, R Wallich, P Martin, D Sanchez-Martinez, F C Weber, S F Martin, C Borner, J Pardo, C Froelich, M M Simon

PubMed ID: 21311565

Date Published: 11th Feb 2011

Projects: No Projects

Journal: Cell Death Differ.

Citation: Cell Death Differ. 18(7): 1112-9

Scales: Not specified

Abstract (Expand)

Granzymes (gzms) are key components of T-killer (Tc) cells believed to mediate pro-apoptotic activities. Recent evidence suggests that gzms also possess non-cytotoxic activities that contribute to host ...

Created: 22nd Jan 2014 at 15:28


 

Wordprocessing Modeling the TNFα-Induced Apoptosis Pathway in Hepatocytes


Authors: Rebekka Schlatter, Kathrin Schmich, Anna Lutz, Judith Trefzger, Oliver Sawodny, Michael Ederer, Irmgard Merfort

PubMed ID: 21533085

Date Published: 7th Oct 2010

Projects: A2.2: Regulation of pro-apoptotic and anti-apoptotic responses in hepato...

Journal: PLoS ONE

Citation: PLoS ONE 6(4): e18646

Scales: Cell

Abstract (Expand)

The proinflammatory cytokine TNFα fails to provoke cell death in isolated hepatocytes but has been implicated in hepatocyte apoptosis during liver diseases associated with chronic inflammation. Recently, ...

Created: 12th May 2011 at 15:13   Last updated: 24th Oct 2013 at 16:19


 

Wordprocessing ModuleMaster: A new tool to decipher transcriptional regulatory networks


Authors: Clemens Wrzodek, Adrian Schröder, Andreas Dräger, Dierk Wanke, Kenneth W. Berendzen, Marcel Kronfeld, Klaus Harter, Andreas Zell

DOI: 10.1016/j.biosystems.2009.09.005

Date Published: 2010

Scales: Not specified

Abstract (Expand)

In this article we present ModuleMaster, a novel application for finding cis-regulatory modules (CRMs) in sets of co-expressed genes. The application comes with a newly developed method which not only ...

Created: 27th Jan 2011 at 14:58   Last updated: 24th Oct 2013 at 16:20


 

Wordprocessing Modeling system states in liver cells: survival, apoptosis and their modifications in response to viral infection


Authors: Nicole Philippi, Dorothee Walter, Rebekka Schlatter, Karine Ferreira, Michael Ederer, Oliver Sawodny, Jens Timmer, Christoph Borner, Thomas Dandekar

PubMed ID: 19772631

Date Published: 12th May 2009

Projects: No Projects

Journal: BMC Syst Biol

Citation: BMC Syst Biol 3: 97

Scales: Not specified

Abstract (Expand)

BACKGROUND: The decision pro- or contra apoptosis is complex, involves a number of different inputs, and is central for the homeostasis of an individual cell as well as for the maintenance and regeneration ...

Created: 3rd Dec 2010 at 10:01   Last updated: 24th Oct 2013 at 16:21


 

Wordprocessing Membrane identity and GTPase cascades regulated by toggle and cut-out switches


Authors: Perla Del Conte-Zerial, Lutz Brusch, Jochen C Rink, Claudio Collinet, Yannis Kalaidzidis, Marino Zerial, Andreas Deutsch

PubMed ID: 18628746

Date Published: 15th Jul 2008

Projects: HepatoSys

Journal: Mol. Syst. Biol.

Citation: Mol. Syst. Biol. 4: 206

Scales: Not specified

Abstract (Expand)

Key cellular functions and developmental processes rely on cascades of GTPases. GTPases of the Rab family provide a molecular ID code to the generation, maintenance and transport of intracellular ...

Created: 29th Jul 2011 at 16:14   Last updated: 24th Oct 2013 at 16:22


 

Wordprocessing Modeling the in vitro 20S proteasome activity: the effect of PA28-alphabeta and of the sequence and length of polypeptides on the degradation kinetics


Authors: Michele Mishto, Fabio Luciani, Hermann-Georg Holzhütter, Elena Bellavista, Aurelia Santoro, Kathrin Textoris-Taube, Claudio Franceschi, Peter M Kloetzel, Alexey Zaikin

PubMed ID: 18336834

Date Published: 8th Feb 2008

Projects: No Projects

Journal: J. Mol. Biol.

Citation: J. Mol. Biol. 377(5): 1607-17

Scales: Not specified

Abstract (Expand)

Proteasomes are fundamental for the degradation of intracellular proteins, having a key role in several important metabolic and signaling pathways, in the cell cycle and in antigen presentation. In ...

Created: 4th Jan 2013 at 13:01   Last updated: 24th Oct 2013 at 16:22


 

Wordprocessing Mathematical modeling identifies inhibitors of apoptosis as mediators of positive feedback and bistability


Authors: Stefan Legewie, Nils Blüthgen, Hanspeter Herzel

PubMed ID: 16978046

Date Published: 28th Jul 2006

Projects: HepatoSys

Journal: PLoS Comput. Biol.

Citation: PLoS Comput. Biol. 2(9): e120

Scales: Not specified

Abstract (Expand)

The intrinsic, or mitochondrial, pathway of caspase activation is essential for apoptosis induction by various stimuli including cytotoxic stress. It depends on the cellular context, whether cytochrome ...

Created: 11th Sep 2012 at 13:08   Last updated: 24th Oct 2013 at 16:24


 

Wordprocessing Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study


Authors: J. M. Villaveces, R. C. Jimenez, P. Porras, N. Del-Toro, M. Duesbury, M. Dumousseau, S. Orchard, H. Choi, P. Ping, N. C. Zong, M. Askenazi, B. H. Habermann, H. Hermjakob

PubMed ID: 25652942

Date Published: No date defined

Scales: Not specified

Abstract (Expand)

The evidence that two molecules interact in a living cell is often inferred from multiple different experiments. Experimental data is captured in multiple repositories, but there is no simple way to ...

Created: 18th Dec 2015 at 12:58



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