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Coordinating Role of RXRα in Downregulating Hepatic Detoxification during Inflammation Revealed by Fuzzy-Logic Modeling

Authors: Roland Keller, Marcus Klein, Maria Thomas, Andreas Dräger, Ute Metzger, Markus F. Templin, Thomas O. Joos, Wolfgang E. Thasler, Andreas Zell, Ulrich M. Zanger

DOI: 10.1371/journal.pcbi.1004431

Date Published: 4th Jan 2016

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

Journal: PLoS Comput Biol

Citation: PLoS Comput Biol 12(1) : e1004431

Scales: Cell

Abstract (Expand)

During various inflammatory processes circulating cytokines including IL-6, IL-1β, and TNFα elicit a broad and clinically relevant impairment of hepatic detoxification that is based on the downregulation ...

Created: 7th Jan 2016 at 15:20 Last updated: 7th Jan 2016 at 15:24

Causes of upregulation of glycolysis in lymphocytes upon stimulation. A comparison with other cell types

Authors: H. Stark, M. Fichtner, R. Konig, S. Lorkowski, S. Schuster

PubMed ID: 26382968

Date Published: 14th Sep 2015

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

Journal: Biochimie

Citation: Biochimie. 2015 Nov;118:185-94. doi: 10.1016/j.biochi.2015.09.017. Epub 2015 Sep 14.

Scales: Cell

Abstract (Expand)

In this review, we revisit the metabolic shift from respiration to glycolysis in lymphocytes upon activation, which is known as the Warburg effect in tumour cells. We compare the situation in lymphocytes ...

Created: 11th Dec 2015 at 16:06

Comparative Analysis and Functional Characterization of HC-AFW1 Hepatocarcinoma Cells: CYP Expression and Induction by Nuclear Receptor Agonists

Authors: A. Braeuning, M. Thomas, U. Hofmann, S. Vetter, E. Zeller, B. Petzuch, J. Johanning, W. Schroth, T. S. Weiss, U. M. Zanger, M. Schwarz

PubMed ID: 26310804

Date Published: 28th Aug 2015

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

Journal: Drug Metab Dispos

Citation: Drug Metab Dispos. 2015 Aug 26. pii: dmd.115.064667.

Scales: Cell

Abstract (Expand)

Enzymatic conversion of most xenobiotic compounds is accomplished by hepatocytes in the liver, which are also an important target for the manifestation of the toxic effects of foreign compounds. Most ...

Created: 17th Sep 2015 at 10:17

Crucial HSP70 co-chaperone complex unlocks metazoan protein disaggregation

Authors: Nadinath B. Nillegoda, Janine Kirstein, Anna Szlachcic, Mykhaylo Berynskyy, Antonia Stank, Florian Stengel, Kristin Arnsburg, Xuechao Gao, Annika Scior, Ruedi Aebersold, D. Lys Guilbride, Rebecca C. Wade, Richard I. Morimoto, Matthias P. Mayer, Bernd Bukau

DOI: 10.1038/nature14884

Date Published: 5th Aug 2015

Projects: A3.2: Cross-talk of signaling pathways and endocytic machinery in hepato...

Journal: Nature

Citation: Nature 524(7564) : 247

Scales: Organism

Abstract (Expand)

Protein aggregates are the hallmark of stressed and ageing cells, and characterize several pathophysiological states. Healthy metazoan cells effectively eliminate intracellular protein aggregates, ...

Created: 18th Sep 2015 at 13:35 Last updated: 18th Sep 2015 at 13:41

Computational Approaches for Studying Drug Binding Kinetics

Authors: Julia Romanowska, Daria B. Kokh, Jonathan C. Fuller, Rebecca C. Wade

DOI: 10.1002/9783527673025.ch11

Date Published: 11th May 2015

Projects: F3: Kinetic data handling

Book: Thermodynamics and Kinetics of Drug Binding

Citation: Methods and Principles in Medicinal Chemistry : 211

Scales: Cell

Abstract (Expand)

The binding kinetics of a drug to its macromolecular receptor can be of key importance for its overall efficacy. Thus, there is a need for methods to compute and predict kinetic parameters for drug-receptor ...

Created: 18th Sep 2015 at 13:23 Last updated: 18th Sep 2015 at 13:26

Computational prediction of molecular pathogen-host interactions based on dual transcriptome data

Authors: Sylvie Schulze, Sebastian G. Henkel, Dominik Driesch, Reinhard Guthke, JÃ¶rg Linde

DOI: 10.3389/fmicb.2015.00065

Date Published: 6th Feb 2015

Projects: Virtual Liver

Journal: Front. Microbiol.

Citation: Front. Microbiol. 6

Scales: Cell and Intercellular

Abstract:

Not specified

Created: 11th Feb 2015 at 08:18 Last updated: 11th Feb 2015 at 08:24

COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project

Authors: Frank T Bergmann, Richard Adams, Stuart Moodie, Jonathan Cooper, Mihai Glont, Martin Golebiewski, Michael Hucka, Camille Laibe, Andrew K Miller, David P Nickerson, Brett G Olivier, Nicolas Rodriguez, Herbert M Sauro, Martin Scharm, Stian Soiland-Reyes, Dagmar Waltemath, Florent Yvon, Nicolas Le Novère

PubMed ID: 25494900

Date Published: 14th Dec 2014

Projects: F1: The data management system

Journal: BMC Bioinformatics

Citation: BMC Bioinformatics 15(1): 369

Scales: Not specified

Abstract (Expand)

BackgroundWith the ever increasing use of computational models in the biosciences, the need to share models and reproduce the results of published studies efficiently and easily is becoming more ...

Created: 9th Jan 2015 at 15:06

Cause and cure of sloppiness in ordinary differential equation models

Authors: Christian Tönsing, Jens Timmer, Clemens Kreutz

PubMed ID: 25215847

Date Published: 11th Aug 2014

Projects: A2.5: Integration of insulin and Wnt signalling in hepatocytes, A3.2: Cross-talk of signaling pathways and endocytic machinery in hepato..., B2.1: Hepatic stellate cells as source and target for hepatocellular gro...

Journal: Phys Rev E Stat Nonlin Soft Matter Phys

Citation: Phys Rev E Stat Nonlin Soft Matter Phys 90(2): 023303

Scales: Cell

Abstract (Expand)

Data-based mathematical modeling of biochemical reaction networks, e.g., by nonlinear ordinary differential equation (ODE) models, has been successfully applied. In this context, parameter estimation ...

Created: 30th Jan 2015 at 15:58

Clinical Translation in the Virtual Liver Network

Authors: L Kuepfer, R Kerb, A M Henney

DOI: 10.1038/psp.2014.25

Date Published: 30th Jul 2014

Projects: G: Clinical translation

Journal: CPT: pharmacomet. syst. pharmacol.

Citation: CPT: pharmacomet. syst. pharmacol. 3(7) : e127

Scales: Organism

Abstract:

Not specified

Created: 13th Aug 2014 at 19:07 Last updated: 13th Aug 2014 at 19:12

Concomitant use of tamoxifen and endoxifen in postmenopausal early breast cancer: prediction of plasma levels by physiologically-based pharmacokinetic modeling

Authors: Kristin Dickschen, Thomas Eissing, Thomas Mürdter, Matthias Schwab, Stefan Willmann, Georg Hempel

PubMed ID: 24936398

Date Published: 5th Jun 2014

Projects: G3: Clinical Translation to Pharmaceutical Drug Development

Journal: Springerplus

Citation: Springerplus 3: 285

Scales: Not specified

Abstract (Expand)

To overcome cytochrome P450 2D6 (CYP2D6) mediated tamoxifen resistance in postmenopausal early breast cancer, CYP2D6 phenotype-adjusted tamoxifen dosing in patients with impaired CYP2D6 metabolism ...

Created: 7th Apr 2015 at 14:48

Challenges for an enzymatic reaction kinetics database

Authors: Ulrike Wittig, Maja Rey, Renate Kania, Meik Bittkowski, Lei Shi, Martin Golebiewski, Andreas Weidemann, Wolfgang Müller, Isabel Rojas

PubMed ID: 24165050

Date Published: 30th Oct 2013

Projects: F3: Kinetic data handling, F: Data management

Journal: FEBS J.

Citation: FEBS J. :

Scales: Not specified

Abstract (Expand)

The scientific literature contains a tremendous amount of kinetic data describing the dynamic behaviour of biochemical reactions over time. These data are needed for computational modelling to create ...

Created: 27th Nov 2013 at 13:21

Comparative analysis of TGF-beta/Smad signaling dependent cytostasis in human hepatocellular carcinoma cell lines

Authors: J. Dzieran, J. Fabian, T. Feng, C. Coulouarn, I. Ilkavets, A. Kyselova, K. Breuhahn, S. Dooley, N. M. Meindl-Beinker

PubMed ID: 23991075

Date Published: 22nd Aug 2013

Projects: A3.2: Cross-talk of signaling pathways and endocytic machinery in hepato...

Journal: PLoS One

Citation: PLoS One. 2013 Aug 22;8(8):e72252. doi: 10.1371/journal.pone.0072252. eCollection 2013.

Scales: Not specified

Abstract (Expand)

Hepatocellular carcinoma (HCC) is a major public health problem due to increased incidence, late diagnosis and limited treatment options. TGF-beta is known to provide cytostatic signals during early ...

Created: 27th Jul 2015 at 07:19

Chemerin is highly expressed in hepatocytes and is induced in non-alcoholic steatohepatitis liver

Authors: Sabrina Krautbauer, Josef Wanninger, Kristina Eisinger, Yvonne Hader, Michael Beck, Andrea Kopp, Andreas Schmid, Thomas S Weiss, Christoph Dorn, Christa Buechler

PubMed ID: 23906870

Date Published: 29th Jul 2013

Projects: A1.1: Central liver metabolism and its regulation under nutritional chal..., A3.6: Transcription factor network and links to metabolism in NAFLD, CTU SOP Human Hepatocytes, Show cases

Journal: Exp. Mol. Pathol.

Citation: Exp. Mol. Pathol. 95(2): 199-205

Scales: Cell and Liver

Abstract (Expand)

Chemerin is a recently described adipokine whose adipose tissue and serum levels are increased in obesity. Chemerin is expressed in the liver, and here, expression of chemerin has been studied in liver ...

Created: 30th Jan 2014 at 17:11

Caveolin-1 abrogates TGF-β mediated hepatocyte apoptosis

Authors: C Meyer, Y Liu, A Kaul, I Peipe, S Dooley

PubMed ID: 23328673

Date Published: 19th Jan 2013

Projects: A3.2: Cross-talk of signaling pathways and endocytic machinery in hepato..., A3.3: Hepatocyte polarity

Journal: Cell Death Dis

Citation: Cell Death Dis 4: e466

Scales: Cell

Abstract (Expand)

Transforming growth factor (TGF)-β has a dual role in liver, providing cytostatic effects during liver damage and regeneration, as well as carcinogenic functions in malignant transformation and ...

Created: 23rd Jan 2013 at 17:53 Last updated: 24th Oct 2013 at 16:15

Cytochrome P450 enzymes in drug metabolism: regulation of gene expression, enzyme activities, and impact of genetic variation

Authors: Ulrich M Zanger, Matthias Schwab

PubMed ID: 23333322

Date Published: 16th Jan 2013

Projects: A1.2: Detoxification in hepatocytes challenged by steatotic conditions, A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes, G1: Clinical Translation to Invasively Characterized Patients, G2: Clinical Translation to Non-Invasive Volunteer Setting, G3: Clinical Translation to Pharmaceutical Drug Development, G4: Whole-Body Detoxification in Mouse Models

Journal: Pharmacol. Ther.

Citation: Pharmacol. Ther. 138(1): 103-41

Scales: Not specified

Abstract (Expand)

Cytochromes P450 (CYP) are a major source of variability in drug pharmacokinetics and response. Of 57 putatively functional human CYPs only about a dozen enzymes, belonging to the CYP1, 2, and 3 families, ...

Created: 8th Jan 2014 at 14:40

Cellular ERK Phospho-form Profiles with Conserved Preference for a Switch-like Pattern

Authors: Bettina Hahn, Lorenza Alice D Alessandro, Sofia Depner, Katharina Waldow, Martin Erich Boehm, Julie Bachmann, Marcel Schilling, Ursula Klingmüller, Wolf Dieter Lehmann

PubMed ID: 23210697

Date Published: 6th Dec 2012

Projects: No Projects

Journal: J. Proteome Res.

Citation: J. Proteome Res. 12(2): 637-46

Scales: Not specified

Abstract (Expand)

ERK is a member of the MAPK pathway with essential functions in cell proliferation, differentiation and survival. Complete ERK activation by the kinase MEK requires dual phosphorylation at T and Y ...

Created: 10th Jan 2013 at 14:19 Last updated: 24th Oct 2013 at 16:15

Comprehensive estimation of input signals and dynamics in biochemical reaction networks

Authors: M Schelker, A Raue, J Timmer, C Kreutz

PubMed ID: 22962477

Date Published: 11th Sep 2012

Projects: A2: Integration of Signalling Pathways in Hepatocellular Response

Journal: Bioinformatics

Citation: Bioinformatics 28(18): i529-i534

Scales: Cell

Abstract (Expand)

Cellular information processing can be described mathematically using differential equations. Often, external stimulation of cells by compounds such as drugs or hormones leading to activation has to ...

Created: 29th Oct 2012 at 10:19 Last updated: 24th Oct 2013 at 16:15

CardioNet: A human metabolic network suited for the study of cardiomyocyte metabolism

Authors: Anja Karlstaedt, Daniela Fliegner, Georgios Kararigas, Hugo S Ruderisch, Vera Regitz-Zagrosek, Hermann G Holzhütter

PubMed ID: 22929619

Date Published: 29th Aug 2012

Projects: No Projects

Journal: BMC Syst Biol

Citation: BMC Syst Biol 6: 114

Scales: Not specified

Abstract (Expand)

ABSTRACT: BACKGROUND: Availability of oxygen and nutrients in the coronary circulation is a crucial determinant of cardiac performance. Nutrient composition of coronary blood may significantly vary in ...

Created: 4th Jan 2013 at 12:48 Last updated: 24th Oct 2013 at 16:16

Central energy metabolism remains robust in acute steatotic hepatocytes challenged by a high free fatty acid load

Authors: Jens Niklas, Anne Bonin, Stefanie Mangin, Joachim Bucher, Stephanie Kopacz, Madlen Matz-Soja, Carlo Thiel, Rolf Gebhardt, Ute Hofmann, Klaus Mauch

PubMed ID: 22831974

Date Published: 27th Jul 2012

Projects: A1: Cellular metabolism, A: Cellular level

Journal: BMB Rep

Citation: BMB Rep 45(7): 396-401

Scales: Not specified

Abstract (Expand)

Overnutrition is one of the major causes of non-alcoholic fatty liver disease (NAFLD). NAFLD is characterized by an accumulation of lipids (triglycerides) in hepatocytes and is often accompanied by ...

Created: 14th Aug 2012 at 14:54 Last updated: 24th Oct 2013 at 16:16

CySBML: a Cytoscape plugin for SBML

Authors: Matthias König, Andreas Dräger, Hermann-Georg Holzhütter

PubMed ID: 22772946

Date Published: 10th Jul 2012

Projects: A1: Cellular metabolism, A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes, F: Data management

Journal: Bioinformatics (Oxford, England)

Citation: Bioinformatics 28(18): 2402-3

Scales: Not specified

Abstract (Expand)

SUMMARY: CySBML is a plugin designed to work with SBML in Cytoscape having the following features: SBML import, support of the SBML Layout and Qualitative Model packages, navigation in network layouts ...

Created: 12th Jul 2012 at 08:37 Last updated: 24th Oct 2013 at 16:16

Concurrent epigenetic silencing of wnt/β-catenin pathway inhibitor genes in B cell chronic lymphocytic leukaemia

Authors: Evgeny A Moskalev, Katrin Luckert, Ivan A Vorobjev, Sergey E Mastitsky, Aleena A Gladkikh, Achim Stephan, Marita Schrenk, Kamil D Kaplanov, Olga B Kalashnikova, Oliver Pötz, Thomas O Joos, Jörg D Hoheisel

PubMed ID: 22672427

Date Published: 6th Jun 2012

Projects: No Projects

Journal: BMC Cancer

Citation: BMC Cancer 12: 213

Scales: Not specified

Abstract:

ABSTRACT:

Created: 27th Nov 2012 at 13:25 Last updated: 24th Oct 2013 at 16:16

Choline-releasing glycerophosphodiesterase EDI3 drives tumor cell migration and metastasis

Authors: J. D. Stewart, R. Marchan, M. S. Lesjak, J. Lambert, R. Hergenroeder, J. K. Ellis, C.-H. Lau, H. C. Keun, G. Schmitz, J. Schiller, M. Eibisch, C. Hedberg, H. Waldmann, E. Lausch, B. Tanner, J. Sehouli, J. Sagemueller, H. Staude, E. Steiner, J. G. Hengstler

DOI: 10.1073/pnas.1117654109

Date Published: 22nd May 2012

Projects: C2: Organization of the sinusoidal system and the liver lobule - referen..., C6: Organization and function of the sinusoidal system and the liver lob...

Journal: Proceedings of the National Academy of Sciences

Citation: Proceedings of the National Academy of Sciences 109(21) : 8155

Scales: Not specified

Abstract:

Not specified

Created: 29th Oct 2012 at 12:28 Last updated: 24th Oct 2013 at 16:16

Comparison of various approaches to calculating the optimal hematocrit in vertebrates

Authors: Heiko Stark, Stefan Schuster

PubMed ID: 22604890

Date Published: 19th May 2012

Projects: D1: Regulation of Blood Flow and Perfusion in the Liver

Journal: Journal of applied physiology (Bethesda, Md. : 1985)

Citation: J. Appl. Physiol. 113(3): 355-67

Scales: Liver

Abstract (Expand)

An interesting problem in hemorheology is to calculate that volume fraction of erythrocytes (hematocrit) that is optimal for transporting a maximum amount of oxygen. If the hematocrit is too low, too ...

Created: 1st Aug 2012 at 11:57 Last updated: 24th Oct 2013 at 16:16

ChemSpot: a hybrid system for chemical named entity recognition

Authors: Tim Rocktäschel, Michael Weidlich, Ulf Leser

PubMed ID: 22500000

Date Published: 12th Apr 2012

Projects: F2: The Liver Knowledge Base (LKB), F: Data management

Journal: Bioinformatics

Citation: Bioinformatics 28(12): 1633-40

Scales: Not specified

Abstract (Expand)

The accurate identification of chemicals in text is important for many applications, including computer-assisted reconstruction of metabolic networks or retrieval of information about substances in ...

Created: 11th Jul 2012 at 08:21 Last updated: 24th Oct 2013 at 16:16

Caspase-3 feeds back on caspase-8, Bid and XIAP in type I Fas signaling in primary mouse hepatocytes

Authors: Karine Sá Ferreira, Clemens Kreutz, Sabine Macnelly, Karin Neubert, Angelika Haber, Matthew Bogyo, Jens Timmer, Christoph Borner

PubMed ID: 22246639

Date Published: 17th Jan 2012

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

Journal: Apoptosis : an international journal on programmed cell death

Citation: Apoptosis 17(5): 503-15

Scales: Not specified

Abstract (Expand)

The TNF-R1 like receptor Fas is highly expressed on the plasma membrane of hepatocytes and plays an essential role in liver homeostasis. We recently showed that in collagen-cultured primary mouse ...

Created: 20th Mar 2012 at 21:32 Last updated: 24th Oct 2013 at 16:17

Controlled vocabularies and semantics in systems biology

Authors: Mélanie Courtot, Nick Juty, Christian Knüpfer, Dagmar Waltemath, Anna Zhukova, Andreas Dräger, Michel Dumontier, Andrew Finney, Martin Golebiewski, Janna Hastings, Stefan Hoops, Sarah Keating, Douglas B Kell, Samuel Kerrien, James Lawson, Allyson Lister, James Lu, Rainer Machne, Pedro Mendes, Matthew Pocock, Nicolas Rodriguez, Alice Villeger, Darren J Wilkinson, Sarala Wimalaratne, Camille Laibe, Michael Hucka, Nicolas Le Novère

PubMed ID: 22027554

Date Published: 27th Oct 2011

Projects: A3.4: Linking signalling to metabolic functions, B5: Cell-cell communication influences detoxifying functions in hepatocytes, F1: The data management system, F3: Kinetic data handling, Showcase Steatosis

Journal: Mol. Syst. Biol.

Citation: Mol. Syst. Biol. 7: 543

Scales: Cell, Intercellular, Liver lobule, Liver and Organism

Abstract (Expand)

The use of computational modeling to describe and analyze biological systems is at the heart of systems biology. Model structures, simulation descriptions and numerical results can be encoded in ...

Created: 27th Oct 2011 at 15:09 Last updated: 24th Oct 2013 at 16:17

Caspase-8 activity has an essential role in CD95/Fas-mediated MAPK activation

Authors: A M M Kober, S Legewie, C Pforr, N Fricker, R Eils, P H Krammer, I N Lavrik

PubMed ID: 21975294

Date Published: 7th Oct 2011

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

Journal: Cell Death Dis

Citation: Cell Death Dis 2: e212

Scales: Cell

Abstract (Expand)

Stimulation of CD95/Fas/APO-1 results in the induction of both apoptotic and non-apoptotic signaling pathways. The processes regulating these two opposing pathways have not been thoroughly elucidated ...

Created: 3rd Sep 2012 at 11:25 Last updated: 24th Oct 2013 at 16:17

Combined serum and tissue proteomic study applied to a c-Myc transgenic mouse model of hepatocellular carcinoma identified novel disease regulated proteins suitable for diagnosis and therapeutic intervention strategies

Authors: Maria Stella Ritorto, Jürgen Borlak

PubMed ID: 21644509

Date Published: 6th Jun 2011

Projects: CTU Proteomics

Journal: J. Proteome Res.

Citation: J. Proteome Res. 10(7): 3012-30

Scales: Liver

Abstract (Expand)

Hepatocellular carcinoma (HCC) is the third leading cause of cancer death in the U.S. Notably, most HCCs display c-Myc hyperactivity but this transcription factor participates in the regulation of as ...

Created: 19th Jan 2014 at 17:53

Cell therapeutic options in liver diseases: cell types, medical devices and regulatory issues

Authors: Andreas K Nussler, Katrin Zeilinger, Lilianna Schyschka, Sabrina Ehnert, Jörg C Gerlach, Xueying Yan, Serene M L Lee, Maren Ilowski, Wolfgang E Thasler, Thomas S Weiss

PubMed ID: 21461918

Date Published: 3rd Apr 2011

Projects: CTU SOP Human Hepatocytes, HepatoSys

Journal: J Mater Sci Mater Med

Citation: J Mater Sci Mater Med 22(5): 1087-99

Scales: Cell

Abstract (Expand)

Although significant progress has been made in the field of orthotopic liver transplantation, cell-based therapies seem to be a promising alternative to whole-organ transplantation. The reasons are ...

Created: 30th Jan 2014 at 17:20

Computing combinatorial intervention strategies and failure modes in signaling networks

Authors: Regina Samaga, Axel Von Kamp, Steffen Klamt

PubMed ID: 20078396

Date Published: 19th Jan 2010

Projects: No Projects

Journal: J. Comput. Biol.

Citation: J. Comput. Biol. 17(1): 39-53

Scales: Not specified

Abstract (Expand)

The identification of combinatorial intervention strategies and the elucidation of failure modes that may cause aberrant behavior of cellular signaling networks are highly relevant topics in cell ...

Created: 14th Aug 2012 at 10:31 Last updated: 24th Oct 2013 at 16:20

Cross-species analysis of the glycolytic pathway by comparison of molecular interaction fields

Authors: Matthias Stein, Razif R Gabdoulline, Rebecca C Wade

PubMed ID: 20024078

Date Published: 16th Dec 2009

Projects: F3: Kinetic data handling, HepatoSys

Journal: Mol Biosyst

Citation: Mol Biosyst 6(1): 152-64

Scales: Not specified

Abstract (Expand)

The electrostatic potential of an enzyme is a key determinant of its substrate interactions and catalytic turnover. Here we invoke comparative analysis of protein electrostatic potentials, along with ...

Created: 31st Oct 2012 at 14:08 Last updated: 24th Oct 2013 at 16:21

Computational lipidology: predicting lipoprotein density profiles in human blood plasma

Authors: Katrin Hübner, Thomas Schwager, Karl Winkler, Jens-Georg Reich, Hermann-Georg Holzhütter

PubMed ID: 18497853

Date Published: 24th May 2008

Projects: A1.1: Central liver metabolism and its regulation under nutritional chal...

Journal: PLoS Comput. Biol.

Citation: PLoS Comput. Biol. 4(5): e1000079

Scales: Not specified

Abstract (Expand)

Monitoring cholesterol levels is strongly recommended to identify patients at risk for myocardial infarction. However, clinical markers beyond "bad" and "good" cholesterol are needed ...

Created: 4th Jan 2013 at 12:57 Last updated: 24th Oct 2013 at 16:22

Characterizing the N-terminal processing motif of MHC class I ligands

Authors: Mark M Schatz, Björn Peters, Nadja Akkad, Nina Ullrich, Alejandra Nacarino Martinez, Oliver Carroll, Sascha Bulik, Hans-Georg Rammensee, Peter van Endert, Hermann-Georg Holzhütter, Stefan Tenzer, Hansjörg Schild

PubMed ID: 18292545

Date Published: 23rd Feb 2008

Projects: No Projects

Journal: J. Immunol.

Citation: J. Immunol. 180(5): 3210-7

Scales: Not specified

Abstract (Expand)

Most peptide ligands presented by MHC class I molecules are the product of an intracellular pathway comprising protein breakdown in the cytosol, transport into the endoplasmic reticulum, and successive ...

Created: 4th Jan 2013 at 11:07 Last updated: 24th Oct 2013 at 16:22

Calculating enzyme kinetic parameters from protein structures

Authors: Matthias Stein, Razif R Gabdoulline, Rebecca C Wade

PubMed ID: 18208384

Date Published: 23rd Jan 2008

Projects: HepatoSys

Journal: Biochem. Soc. Trans.

Citation: Biochem. Soc. Trans. 36(Pt 1): 51-4

Scales: Cell

Abstract (Expand)

Enzyme kinetic parameters can differ between different species and isoenzymes for the same catalysed reaction. Computational approaches to calculate enzymatic kinetic parameters from the three-dimensional ...

Created: 31st Oct 2012 at 14:12 Last updated: 24th Oct 2013 at 16:23

Computer aided optimization of carbon atom labeling for tracer experiments

Authors: Benjamin Sefa Menküc, Christoph Gille, Hermann-Georg Holzhütter

PubMed ID: 19425141

Date Published: 2008

Projects: No Projects

Journal: Genome Inform

Citation: Genome Inform 20: 270-6

Scales: Not specified

Abstract (Expand)

Isotopomer tracer experiments are indispensable for the determination of flux rates in already known pathways as well as for the identification of new pathways. The information gained from such experiments ...

Created: 4th Jan 2013 at 13:01 Last updated: 24th Oct 2013 at 16:23

Competing docking interactions can bring about bistability in the MAPK cascade

Authors: Stefan Legewie, Birgit Schoeberl, Nils Blüthgen, Hanspeter Herzel

PubMed ID: 17526574

Date Published: 25th May 2007

Projects: HepatoSys

Journal: Biophys. J.

Citation: Biophys. J. 93(7): 2279-88

Scales: Not specified

Abstract (Expand)

Mitogen-activated protein kinases are crucial regulators of various cell fate decisions including proliferation, differentiation, and apoptosis. Depending on the cellular context, the Raf-Mek-Erk ...

Created: 11th Sep 2012 at 13:07 Last updated: 24th Oct 2013 at 16:23

COMBINE analysis of the specificity of binding of Ras proteins to their effectors

Authors: Sanja Tomić, Branimir Bertosa, Ting Wang, Rebecca C Wade

PubMed ID: 17295314

Date Published: 14th Feb 2007

Projects: HepatoSys

Journal: Proteins

Citation: Proteins 67(2): 435-47

Scales: Not specified

Abstract (Expand)

The small guanosine triphosphate (GTP)-binding proteins of the Ras family are involved in many cellular pathways leading to cell growth, differentiation, and apoptosis. Understanding the interaction ...

Created: 31st Oct 2012 at 14:17 Last updated: 24th Oct 2013 at 16:23

COPASI--a COmplex PAthway SImulator

Authors: Stefan Hoops, Sven Sahle, Ralph Gauges, Christine Lee, Jürgen Pahle, Natalia Simus, Mudita Singhal, Liang Xu, Pedro Mendes, Ursula Kummer

PubMed ID: 17032683

Date Published: 10th Oct 2006

Projects: HepatoSys

Journal: Bioinformatics

Citation: Bioinformatics 22(24): 3067-74

Scales: Not specified

Abstract (Expand)

Simulation and modeling is becoming a standard approach to understand complex biochemical processes. Therefore, there is a big need for software tools that allow access to diverse simulation and modeling ...

Created: 11th Sep 2012 at 13:26 Last updated: 24th Oct 2013 at 16:24

Computational processing and error reduction strategies for standardized quantitative data in biological networks

Authors: Marcel Schilling, Thomas Maiwald, Sebastian Bohl, Markus Kollmann, Clemens Kreutz, Jens Timmer, Ursula Klingmüller

PubMed ID: 16336276

Date Published: 13th Dec 2005

Projects: HepatoSys

Journal: FEBS J.

Citation: FEBS J. 272(24): 6400-11

Scales: Not specified

Abstract (Expand)

High-quality quantitative data generated under standardized conditions is critical for understanding dynamic cellular processes. We report strategies for error reduction, and algorithms for automated ...

Created: 23rd Aug 2012 at 13:22 Last updated: 24th Oct 2013 at 16:24