Wordprocessing GPU-Accelerated Sparse Matrix-Matrix Multiplication by Iterative Row Merging

Authors: Felix Gremse, Andreas Höfter, Lars Ole Schwen, Fabian Kiessling, Uwe Naumann

DOI: 10.1137/130948811

Date Published: 8th Jan 2015

Projects: D3: Inflammation and Regeneration: the whole organ

Journal: SIAM J. Sci. Comput.

Citation: SIAM J. Sci. Comput. 37(1) : C54

Scales: Organism

Abstract (Expand)

We present an algorithm for general sparse matrix-matrix multiplication (SpGEMM) on many-core architectures, such as GPUs. SpGEMM is implemented by iterative row merging, similar to merge sort, except ...

Created: 26th Jan 2015 at 16:56   Last updated: 26th Jan 2015 at 17:01


Wordprocessing Genetics, epigenetics and regulation of drug metabolizing cytochrome P450 enzymes

Authors: Ulrich M Zanger, Kathrin Klein, Maria Thomas, Jessica K Rieger, Roman Tremmel, Benjamin A Kandel, Marcus Klein, Tarek Magdy

PubMed ID: 24196843

Date Published: 8th Nov 2013

Scales: Not specified

Abstract (Expand)

Of 57 functional human cytochromes P450 (CYP) about a dozen liver-expressed, highly variable forms are responsible for the biotransformation of most drugs. Owing to numerous genetic and non-genetic ...

Created: 8th Jan 2014 at 13:58


Wordprocessing GRN2SBML: Automated encoding and annotation of inferred gene regulatory networks complying with SBML

Authors: S. Vlaic, B. Hoffmann, P. Kupfer, M. Weber, A. Drager

DOI: 10.1093/bioinformatics/btt370

Date Published: 26th Jun 2013

Projects: A3.4: Linking signalling to metabolic functions, A3.6: Transcription factor network and links to metabolism in NAFLD

Journal: Bioinformatics

Citation: Bioinformatics 29(17) : 2216

Scales: Cell

Abstract (Expand)

Summary: GRN2SBML automatically encodes gene regulatory networks derived from several inference tools in SBML. Providing a graphical user interface, the networks can be annotated via the SOAP-based ...

Created: 1st Jul 2013 at 23:57   Last updated: 24th Oct 2013 at 16:14


Wordprocessing Genetics is a major determinant of expression of the human hepatic uptake transporter OATP1B1, but not of OATP1B3 and OATP2B1

Authors: Anne T Nies, Mikko Niemi, Oliver Burk, Stefan Winter, Ulrich M Zanger, Bruno Stieger, Matthias Schwab, Elke Schaeffeler

PubMed ID: 23311897

Date Published: 11th Jan 2013

Scales: Not specified

Abstract (Expand)

ABSTRACT: BACKGROUND: Organic anion transporting polypeptide (OATP) 1B1, OATP1B3, and OATP2B1 (encoded by SLCO1B1, SLCO1B3, SLCO2B1) mediate the hepatic uptake of endogenous compounds like bile acids ...

Created: 16th Jan 2013 at 09:16   Last updated: 24th Oct 2013 at 16:15


Wordprocessing Genetic and functional identification of the likely causative variant for cholesterol gallstone disease at the ABCG5/8 lithogenic locus

Authors: Oliver von Kampen, Stephan Buch, Michael Nothnagel, Lorena Azocar, Hector Molina, Mario Brosch, Wiebke Erhart, Witigo von Schönfels, Jan Egberts, Marcus Seeger, Alexander Arlt, Tobias Balschun, Andre Franke, Markus M Lerch, Julia Mayerle, Wolfgang Kratzer, Bernhard O Boehm, Klaus Huse, Bodo Schniewind, Katharina Tiemann, Zhao-Yyan Jiang, Tian-Quan Han, Balraj Mittal, Anshika Srivastava, Mogens Fenger, Torben Jørgensen, Ramin Schirin-Sokhan, Anke Tönjes, Henning Wittenburg, Michael Stumvoll, Holger Kalthoff, Frank Lammert, Jürgen Tepel, Klaus Puschel, Thomas Becker, Stefan Schreiber, Matthias Platzer, Henry Völzke, Michael Krawczak, Juan Francisco Miquel, Clemens Schafmayer, Jochen Hampe

PubMed ID: 22898925

Date Published: 18th Aug 2012

Projects: G: Clinical translation

Journal: Hepatology

Citation: Hepatology 57(6): 2407-17

Scales: Organism

Abstract (Expand)

BACKGROUND & AIMS: The sterolin locus (ABCG5/ABCG8) has been solidly shown to confer susceptibility for cholesterol gallstone disease in humans. Both the responsible variant and the molecular ...

Created: 4th Oct 2012 at 19:37   Last updated: 24th Oct 2013 at 16:16


Wordprocessing Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting

Authors: Claudia Fritsch, Alexander Herrmann, Michael Nothnagel, Karol Szafranski, Klaus Huse, Frank Schumann, Stefan Schreiber, Matthias Platzer, Michael Krawczak, Jochen Hampe, Mario Brosch

PubMed ID: 22879431

Date Published: 9th Aug 2012

Projects: A1.2: Detoxification in hepatocytes challenged by steatotic conditions, G: Clinical translation

Journal: Genome Res.

Citation: Genome Res. 22(11): 2208-18

Scales: Cell

Abstract (Expand)

So far, the annotation of translation initiation sites (TISs) has been based mostly upon bioinformatics rather than experimental evidence. We adapted ribosomal footprinting to puromycin-treated cells ...

Created: 4th Oct 2012 at 19:40   Last updated: 24th Oct 2013 at 16:16


Wordprocessing Genomics of ADME gene expression: mapping expression quantitative trait loci relevant for absorption, distribution, metabolism and excretion of drugs in human liver

Authors: A Schröder, K Klein, S Winter, M Schwab, M Bonin, A Zell, U M Zanger

PubMed ID: 22006096

Date Published: 18th Oct 2011

Scales: Not specified

Abstract (Expand)

Expression quantitative trait loci (eQTL) analysis is a powerful approach toward identifying genetic loci associated with quantitative changes in gene expression. We applied genome-wide association ...

Created: 3rd Nov 2011 at 10:45   Last updated: 24th Oct 2013 at 16:17


Wordprocessing Glucocorticoids increase interleukin-6-dependent gene induction by interfering with the expression of the suppressor of cytokine signaling 3 feedback inhibitor

Authors: Anna Dittrich, Christina Khouri, Sara Dutton Sackett, Christian Ehlting, Oliver Böhmer, Ute Albrecht, Johannes G Bode, Christian Trautwein, Fred Schaper

PubMed ID: 21898505

Date Published: 8th Sep 2011

Scales: Cell

Abstract (Expand)

Glucocorticoids are known to be potent regulators of inflammation and have been used pharmacologically against inflammatory, immune, and lymphoproliferative diseases for more than 50 years. Due to their ...

Created: 31st Aug 2012 at 11:45   Last updated: 24th Oct 2013 at 16:17


Wordprocessing Germans cook up liver project

Author: Alison Abbott

PubMed ID: 21164453

Date Published: 18th Dec 2010

Projects: Virtual Liver

Journal: Nature

Citation: Nature 468(7326): 879

Scales: Not specified


Not specified

Created: 3rd Mar 2011 at 14:11   Last updated: 24th Oct 2013 at 16:19


Wordprocessing Genome-wide comparison between IL-17 and combined TNF-alpha/IL-17 induced genes in primary murine hepatocytes

Authors: Titus Sparna, Julia Rétey, Kathrin Schmich, Ute Albrecht, Katrin Naumann, Norbert Gretz, Hans-Peter Fischer, Johannes G Bode, Irmgard Merfort

PubMed ID: 20374638

Date Published: 7th Apr 2010

Scales: Cell

Abstract (Expand)

Cytokines such as TNF-alpha and IL-1 beta are known for their contribution to inflammatory processes in liver. In contrast, the cytokine IL-17 has not yet been assigned a role in liver diseases. IL-17 ...

Created: 30th Aug 2012 at 12:22   Last updated: 24th Oct 2013 at 16:20

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