Integrating systems biology with clinical research (2008)
Pepperkok, Rainer, Wiemann, Stefan
A report on the conference 'Systems Genomics 2008', Heidelberg, Germany, 2-3 May 2008.
Maturation of the mammalian secretome (2007)
Simpson, Jeremy C, Mateos, Alvaro, Pepperkok, Rainer
Abstract A recent use of quantitative proteomics to determine the constituents of the endoplasmic reticulum and Golgi complex is discussed in the light of other available methodologies for cataloging...
The subcellular localization of the mammalian proteome comes a fraction closer (2006)
Simpson, Jeremy C, Pepperkok, Rainer
Abstract Another step along the road towards determining the subcellular localization of a complete mammalian proteome has been taken with a study using cellular fractionation and protein correlation...
The subcellular localization of the mammalian proteome comes a fraction closer (2006)
Simpson, Jeremy C, Pepperkok, Rainer
Abstract Another step along the road towards determining the subcellular localization of a complete mammalian proteome has been taken with a study using cellular fractionation and protein correlation...
The LIFEdb database in 2006 (2006)
Mehrle, Alexander, Rosenfelder, Heiko, Schupp, Ingo, Del Val, Coral, Arlt, Dorit, Hahne, Florian, ...
LIFEdb (http://www.LIFEdb.de) integrates data from large-scale functional genomics assays and manual cDNA annotation with bioinformatics gene expression and protein analysis. New features of LIFEdb...
Reynaud, Emmanuel G, Andrade, Miguel A, Bonneau, Fabien, Ly, Thi, Knop, Michael, Scheffzek, Klaus, ...
Abstract Background Compartmentalization is a key feature of eukaryotic cells, but its evolution remains poorly understood. GTPases are the oldest enzymes that use nucleotides as substrates and they...
gamma-BAR, a novel AP-1-interacting protein involved in post-Golgi trafficking (2005)
Neubrand,Veronika E., Will,Rainer D., Möbius,Wiebke, Poustka,Annemarie, Wiemann,Stefan, Schu,Peter, ...
Keese, Michael, Magdeburg, Richard J., Herzog, Torsten, Hasenberg, Till, Offterdinger, Martin, Pepperkok, Rainer, ...
gamma-BAR, a novel AP-1-interacting protein involved in post-Golgi trafficking (2005)
Neubrand, Veronika E., Will, Rainer D., Möbius, Wiebke, Poustka, Annemarie, Wiemann, Stefan, Schu, Peter, ...
siRNA cell arrays for high-content screening microscopy (2004)
Erfle, Holger, Simpson, Jeremy C., Bastiaens, Philippe I. H., Pepperkok, Rainer
Automatic Identification of Subcellular Phenotypes on Human Cell Arrays (2004)
Conrad, Christian, Erfle, Holger, Warnat, Patrick, Daigle, Nathalie, Lörch, Thomas, Ellenberg, Jan, ...
Light microscopic analysis of cell morphology provides a high-content readout of cell function and protein localization. Cell arrays and microwell transfection assays on cultured cells have made cell...
"Harvester" a fast meta search engine of human protein resources (2004)
Liebel, Urban, Kindler, Bjoern, Pepperkok, Rainer
Summary: We have developed a web-based tool termed "Harvester" that bulk-collects bioinformatic data on human proteins from various databases and prediction servers. The information on every single...
Starkuviene, Vytaute, Liebel, Urban, Simpson, Jeremy C., Erfle, Holger, Poustka, Annemarie, Wiemann, Stefan, ...
Here we describe the establishment of microscope-based functional screening assays in intact cells that allow us to systematically identify new proteins involved in secretory membrane traffic, and...
Bannasch, Detlev, Mehrle, Alexander, Glatting, Karl-Heinz, Pepperkok, Rainer, Poustka, Annemarie, Wiemann, Stefan
We have implemented LIFEdb (http://www.dkfz.de/LIFEdb) to link information regarding novel human full‐length cDNAs generated and sequenced by the German cDNA Consortium with functional...
'Harvester': a fast meta search engine of human protein resources (2004)
Liebel, Urban, Kindler, Bjoern, Pepperkok, Rainer
Summary: We have developed a Web-based tool named ‘Harvester’ that bulk-collects bioinformatic data on human proteins from various databases and prediction servers. The information on every...
From ORFeome to Biology: A Functional Genomics Pipeline (2004)
Wiemann, Stefan, Arlt, Dorit, Huber, Wolfgang, Wellenreuther, Ruth, Schleeger, Simone, Mehrle, Alexander, ...
As several model genomes have been sequenced, the elucidation of protein function is the next challenge toward the understanding of biological processes in health and disease. We have generated a...
"Harvester" a fast meta search engine of human protein resources (2004)
Liebel, Urban, Kindler, Bjoern, Pepperkok, Rainer
Summary: We have developed a web-based tool termed "Harvester" that bulk-collects bioinformatic data on human proteins from various databases and prediction servers. The information on every single...
Localizing the proteome (2003)
Simpson, Jeremy C, Pepperkok, Rainer
Abstract The subcellular localization of the entire proteome of an organism, the yeast Saccharomyces cerevisiae , has been revealed for the first time. Comparison with less comprehensive studies of...
Richards, Ayanthi A., Stang, Espen, Pepperkok, Rainer, Parton, Robert G.
Simian virus 40 (SV40) is a nonenveloped virus that has been shown to pass from surface caveolae to the endoplasmic reticulum in an apparently novel infectious entry pathway. We now show that the...
Richards, Ayanthi A., Stang, Espen, Pepperkok, Rainer, Parton, Robert G.
Simian virus 40 (SV40) is a nonenveloped virus that has been shown to pass from surface caveolae to the endoplasmic reticulum in an apparently novel infectious entry pathway. We now show that the...
Being in the right location at the right time (2001)
Pepperkok, Rainer, Simpson, Jeremy C, Wiemann, Stefan
Abstract Taking each coding sequence from the human genome in turn and identifying the subcellular localization of the corresponding protein would be a significant contribution to understanding the...
Kaiserslautern, Univ., Diss., 1992 (Nicht für den Austausch).
Schickedanz, Jörg, Philipson, Lennart, Ansorge, Wilhelm, Pepperkok, Rainer, Klein, Rüdiger, Koszinowski, Ulrich H.
The immediate-early (IE) genes of murine cytomegalovirus (MCMV) are expressed in the absence of prior viral protein synthesis and regulate the transcription of MCMV early genes. The effect of MCMV IE...
Biogenesis of Tubular ER-to-Golgi Transport IntermediatesV⃞
Simpson, Jeremy C., Nilsson, Tommy, Pepperkok, Rainer
Tubular transport intermediates (TTIs) have been described as one class of transport carriers in endoplasmic reticulum (ER)-to-Golgi transport. In contrast to vesicle budding and fusion, little is...
Inhibitors of COP-mediated Transport and Cholera Toxin Action Inhibit Simian Virus 40 Infection
Richards, Ayanthi A., Stang, Espen, Pepperkok, Rainer, Parton, Robert G.
Simian virus 40 (SV40) is a nonenveloped virus that has been shown to pass from surface caveolae to the endoplasmic reticulum in an apparently novel infectious entry pathway. We now show that the...
Being in the right location at the right time
Pepperkok, Rainer, Simpson, Jeremy C, Wiemann, Stefan
Taking each coding sequence from the human genome in turn and identifying the subcellular localization of the corresponding protein would be a significant contribution to understanding the function...
Bannasch, Detlev, Mehrle, Alexander, Glatting, Karl-Heinz, Pepperkok, Rainer, Poustka, Annemarie, Wiemann, Stefan
We have implemented LIFEdb (http://www.dkfz.de/LIFEdb) to link information regarding novel human full-length cDNAs generated and sequenced by the German cDNA Consortium with functional information on...
Simpson, Jeremy C, Pepperkok, Rainer
The subcellular localization of the entire proteome of the yeast Saccharomyces cerevisiae, and comparison with less comprehensive studies of mammalian cells, provides insights into the localization...
Automatic Identification of Subcellular Phenotypes on Human Cell Arrays
Conrad, Christian, Erfle, Holger, Warnat, Patrick, Daigle, Nathalie, Lörch, Thomas, Ellenberg, Jan, ...
Light microscopic analysis of cell morphology provides a high-content readout of cell function and protein localization. Cell arrays and microwell transfection assays on cultured cells have made cell...
Starkuviene, Vytaute, Liebel, Urban, Simpson, Jeremy C., Erfle, Holger, Poustka, Annemarie, Wiemann, Stefan, ...
Here we describe the establishment of microscope-based functional screening assays in intact cells that allow us to systematically identify new proteins involved in secretory membrane traffic, and...
From ORFeome to Biology: A Functional Genomics Pipeline
Wiemann, Stefan, Arlt, Dorit, Huber, Wolfgang, Wellenreuther, Ruth, Schleeger, Simone, Mehrle, Alexander, ...
As several model genomes have been sequenced, the elucidation of protein function is the next challenge toward the understanding of biological processes in health and disease. We have generated a...
Brunet, Stéphane, Sardon, Teresa, Zimmerman, Timo, Wittmann, Torsten, Pepperkok, Rainer, Karsenti, Eric, ...
TPX2 has multiple functions during mitosis, including microtubule nucleation around the chromosomes and the targeting of Xklp2 and Aurora A to the spindle. We have performed a detailed domain...
Regulation of Microtubule-dependent Recycling at the Trans-Golgi Network by Rab6A and Rab6A'D⃞
Young, Joanne, Stauber, Tobias, Del Nery, Elaine, Vernos, Isabelle, Pepperkok, Rainer, Nilsson, Tommy
The small GTPase rab6A but not the isoform rab6A' has previously been identified as a regulator of the COPI-independent recycling route that carries Golgi-resident proteins and certain toxins from...
γ-BAR, a novel AP-1-interacting protein involved in post-Golgi trafficking
Neubrand, Veronika E, Will, Rainer D, Möbius, Wiebke, Poustka, Annemarie, Wiemann, Stefan, Schu, Peter, ...
A novel peripheral membrane protein (2c18) that interacts directly with the gamma ‘ear' domain of the adaptor protein complex 1 (AP-1) in vitro and in vivo is described. Ultrastructural analysis...
Systematic subcellular localization of novel proteins identified by large-scale cDNA sequencing
Simpson, Jeremy C., Wellenreuther, Ruth, Poustka, Annemarie, Pepperkok, Rainer, Wiemann, Stefan
As a first step towards a more comprehensive functional characterization of cDNAs than bioinformatic analysis, which can only make functional predictions for about half of the cDNAs sequenced, we...
Reynaud, Emmanuel G, Andrade, Miguel A, Bonneau, Fabien, Ly, Thi Bach Nga, Knop, Michael, Scheffzek, Klaus, ...
Mehrle, Alexander, Rosenfelder, Heiko, Schupp, Ingo, Del Val, Coral, Arlt, Dorit, Hahne, Florian, ...
LIFEdb () integrates data from large-scale functional genomics assays and manual cDNA annotation with bioinformatics gene expression and protein analysis. New features of LIFEdb include (i) an...
Yang, Yao-dong, Elamawi, Rabab, Bubeck, Julia, Pepperkok, Rainer, Ritzenthaler, Christophe, Robinson, David G.
Despite the ubiquitous presence of the COPI, COPII, and clathrin vesicle budding machineries in all eukaryotes, the organization of the secretory pathway in plants differs significantly from that in...
Inhibitors of COP-mediated Transport and Cholera Toxin Action Inhibit Simian Virus 40 Infection
Richards, Ayanthi A., Stang, Espen, Pepperkok, Rainer, Parton, Robert G.
Simian virus 40 (SV40) is a nonenveloped virus that has been shown to pass from surface caveolae to the endoplasmic reticulum in an apparently novel infectious entry pathway. We now show that the...
Being in the right location at the right time
Pepperkok, Rainer, Simpson, Jeremy C, Wiemann, Stefan
Taking each coding sequence from the human genome in turn and identifying the subcellular localization of the corresponding protein would be a significant contribution to understanding the function...
Bannasch, Detlev, Mehrle, Alexander, Glatting, Karl-Heinz, Pepperkok, Rainer, Poustka, Annemarie, Wiemann, Stefan
We have implemented LIFEdb (http://www.dkfz.de/LIFEdb) to link information regarding novel human full-length cDNAs generated and sequenced by the German cDNA Consortium with functional information on...
Simpson, Jeremy C, Pepperkok, Rainer
The subcellular localization of the entire proteome of the yeast Saccharomyces cerevisiae, and comparison with less comprehensive studies of mammalian cells, provides insights into the localization...
Automatic Identification of Subcellular Phenotypes on Human Cell Arrays
Conrad, Christian, Erfle, Holger, Warnat, Patrick, Daigle, Nathalie, Lörch, Thomas, Ellenberg, Jan, ...
Light microscopic analysis of cell morphology provides a high-content readout of cell function and protein localization. Cell arrays and microwell transfection assays on cultured cells have made cell...
Starkuviene, Vytaute, Liebel, Urban, Simpson, Jeremy C., Erfle, Holger, Poustka, Annemarie, Wiemann, Stefan, ...
Here we describe the establishment of microscope-based functional screening assays in intact cells that allow us to systematically identify new proteins involved in secretory membrane traffic, and...
From ORFeome to Biology: A Functional Genomics Pipeline
Wiemann, Stefan, Arlt, Dorit, Huber, Wolfgang, Wellenreuther, Ruth, Schleeger, Simone, Mehrle, Alexander, ...
As several model genomes have been sequenced, the elucidation of protein function is the next challenge toward the understanding of biological processes in health and disease. We have generated a...
Brunet, Stéphane, Sardon, Teresa, Zimmerman, Timo, Wittmann, Torsten, Pepperkok, Rainer, Karsenti, Eric, ...
TPX2 has multiple functions during mitosis, including microtubule nucleation around the chromosomes and the targeting of Xklp2 and Aurora A to the spindle. We have performed a detailed domain...
Regulation of Microtubule-dependent Recycling at the Trans-Golgi Network by Rab6A and Rab6A'D⃞
Young, Joanne, Stauber, Tobias, Del Nery, Elaine, Vernos, Isabelle, Pepperkok, Rainer, Nilsson, Tommy
The small GTPase rab6A but not the isoform rab6A' has previously been identified as a regulator of the COPI-independent recycling route that carries Golgi-resident proteins and certain toxins from...
γ-BAR, a novel AP-1-interacting protein involved in post-Golgi trafficking
Neubrand, Veronika E, Will, Rainer D, Möbius, Wiebke, Poustka, Annemarie, Wiemann, Stefan, Schu, Peter, ...
A novel peripheral membrane protein (2c18) that interacts directly with the gamma ‘ear' domain of the adaptor protein complex 1 (AP-1) in vitro and in vivo is described. Ultrastructural analysis...
Systematic subcellular localization of novel proteins identified by large-scale cDNA sequencing
Simpson, Jeremy C., Wellenreuther, Ruth, Poustka, Annemarie, Pepperkok, Rainer, Wiemann, Stefan
As a first step towards a more comprehensive functional characterization of cDNAs than bioinformatic analysis, which can only make functional predictions for about half of the cDNAs sequenced, we...
Yang, Yao-dong, Elamawi, Rabab, Bubeck, Julia, Pepperkok, Rainer, Ritzenthaler, Christophe, Robinson, David G.
Despite the ubiquitous presence of the COPI, COPII, and clathrin vesicle budding machineries in all eukaryotes, the organization of the secretory pathway in plants differs significantly from that in...
Reynaud, Emmanuel G, Andrade, Miguel A, Bonneau, Fabien, Ly, Thi Bach Nga, Knop, Michael, Scheffzek, Klaus, ...
Mehrle, Alexander, Rosenfelder, Heiko, Schupp, Ingo, Del Val, Coral, Arlt, Dorit, Hahne, Florian, ...
LIFEdb () integrates data from large-scale functional genomics assays and manual cDNA annotation with bioinformatics gene expression and protein analysis. New features of LIFEdb include (i) an...
Biogenesis of Tubular ER-to-Golgi Transport IntermediatesV⃞
Simpson, Jeremy C., Nilsson, Tommy, Pepperkok, Rainer
Tubular transport intermediates (TTIs) have been described as one class of transport carriers in endoplasmic reticulum (ER)-to-Golgi transport. In contrast to vesicle budding and fusion, little is...
The subcellular localization of the mammalian proteome comes a fraction closer
Simpson, Jeremy C, Pepperkok, Rainer
A recent study shows the successful application of protein correlation profiling to the subcellular localization of organelle proteins in mammalian cells.
High-Content Microscopy Identifies New Neurite Outgrowth Regulators
Laketa, Vibor, Simpson, Jeremy C., Bechtel, Stephanie, Wiemann, Stefan, Pepperkok, Rainer
Neurons, with their long axons and elaborate dendritic arbour, establish the complex circuitry that is essential for the proper functioning of the nervous system. Whereas a catalogue of structural,...
Analysis of Intraviral Protein-Protein Interactions of the SARS Coronavirus ORFeome
Von Brunn, Albrecht, Teepe, Carola, Simpson, Jeremy C., Pepperkok, Rainer, Friedel, Caroline C., Zimmer, Ralf, ...
The severe acute respiratory syndrome coronavirus (SARS-CoV) genome is predicted to encode 14 functional open reading frames, leading to the expression of up to 30 structural and non-structural...
Maturation of the mammalian secretome
Simpson, Jeremy C, Mateos, Alvaro, Pepperkok, Rainer
What methodology will define the complete secretome?
Sterols regulate ER-export dynamics of secretory cargo protein ts-O45-G
Runz, Heiko, Miura, Kota, Weiss, Matthias, Pepperkok, Rainer
Alterations in endoplasmic reticulum (ER) cholesterol are fundamental for a variety of cellular processes such as the regulation of lipid homeostasis or efficient protein degradation. We show that...
Partitioning of the Golgi Apparatus during Mitosis in Living HeLa Cells
Shima, David T., Haldar, Kasturi, Pepperkok, Rainer, Watson, Rose, Warren, Graham
The Golgi apparatus of HeLa cells was fluorescently tagged with a green fluorescent protein (GFP), localized by attachment to the NH2-terminal retention signal of N-acetylglucosaminyltransferase I...
Shima, David T., Cabrera-Poch, Noemí, Pepperkok, Rainer, Warren, Graham
During mitosis, the ribbon of the Golgi apparatus is transformed into dispersed tubulo-vesicular membranes, proposed to facilitate stochastic inheritance of this low copy number organelle at...
Scheel, Jochen, Pepperkok, Rainer, Lowe, Martin, Griffiths, Gareth, Kreis, Thomas E.
Addition of brefeldin A (BFA) to mammalian cells rapidly results in the removal of coatomer from membranes and subsequent delivery of Golgi enzymes to the endoplasmic reticulum (ER). Microinjected...
Involvement of the Transmembrane Protein p23 in Biosynthetic Protein Transport
Rojo, Manuel, Pepperkok, Rainer, Emery, Gregory, Kellner, Roland, Stang, Espen, Parton, Robert G., ...
Here, we report the localization and characterization of BHKp23, a member of the p24 family of transmembrane proteins, in mammalian cells. We find that p23 is a major component of tubulovesicular...
Majoul, Irina, Sohn, Kai, Wieland, Felix Theodor, Pepperkok, Rainer, Pizza, Mariagrazia, Hillemann, Jörg, ...
A cholera toxin mutant (CTX–K63) unable to raise cAMP levels was used to study in Vero cells the retrograde transport of the toxin A subunit (CTX-A–K63), which possesses a COOH-terminal KDEL...
Gillham, Helen, Pepperkok, Rainer, Gullick, William J.
Phosphatidylinositol 3-kinase (PI 3-kinase) is a lipid kinase which has been implicated in mitogenesis, protein trafficking, inhibition of apoptosis, and integrin and actin functions. Here we show...
Pepperkok, Rainer, Hotz-Wagenblatt, Agnes, König, Norbert, Girod, Andreas, Bossemeyer, Dirk, Kinzel, Volker
The catalytic (C) subunit of protein kinase A functions both in the cytoplasm and the nucleus. A major charge variant representing about one third of the enzyme in striated muscle results from...
Integrating systems biology with clinical research
Pepperkok, Rainer, Wiemann, Stefan
A report on the conference 'Systems Genomics 2008', Heidelberg, Germany, 2-3 May 2008.