BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btm497 Data and text mining (2008)
Chung-chih Lin, Yuh-show Tsai, Yu-shi Lin, Tai-yu Chiu, Chia-cheng Hsiung, May-i. Lee, ...
Boosting multiclass learning with repeating codes and weak detectors for protein subcellular localization
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...
Lin, Chung-Chih, Tsai, Yuh-Show, Lin, Yu-Shi, Chiu, Tai-Yu, Hsiung, Chia-Cheng, Lee, May-I., ...
Motivation: Determining locations of protein expression is essential to understand protein function. Advances in green fluorescence protein (GFP) fusion proteins and automated fluorescence microscopy...
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 systematic functional characterisation of Xq28 genes prioritises candidate disease genes (2006)
Kolb-Kokocinski, Anja, Mehrle, Alexander, Bechtel, Stephanie, Simpson, Jeremy C, Kioschis, Petra, Wiemann, Stefan, ...
Abstract Background Well known for its gene density and the large number of mapped diseases, the human sub-chromosomal region Xq28 has long been a focus of genome research. Over 40 of approximately...
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, ...
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, ...
A role for the small GTPase Rab21 in the early endocytic pathway (2004)
Simpson, Jeremy C., Griffiths, Gareth, Wessling-Resnick, Marianne, Fransen, Jack A. M., Bennett, Holly, Jones, Arwyn Tomos
Rab proteins comprise a family of monomeric GTPases that control cellular membrane traffic. Rab21 is a poorly characterised member with no known function. Human Rab21 cDNA from K562 cells was...
A role for the small GTPase Rab21 in the early endocytic pathway (2004)
Simpson, Jeremy C., Griffiths, Gareth, Wessling-Resnick, Marianne, Fransen, Jack A. M., Bennett, Holly, Jones, Arwyn Tomos
Rab proteins comprise a family of monomeric GTPases that control cellular membrane traffic. Rab21 is a poorly characterised member with no known function. Human Rab21 cDNA from K562 cells was...
siRNA cell arrays for high-content screening microscopy (2004)
Erfle, Holger, Simpson, Jeremy C., Bastiaens, Philippe I. H., Pepperkok, Rainer
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...
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...
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...
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...
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...
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...
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...
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...
Spatiotemporal dynamics of the COPI vesicle machinery
Elsner, Markus, Hashimoto, Hitoshi, Simpson, Jeremy C., Cassel, Dan, Nilsson, Tommy, Weiss, Matthias
Assembly of the coat protein I (COPI) vesicle coat is controlled by the small GTPase ADP ribosylation factor 1 (ARF1) and its GTPase-activating protein, ARFGAP1. Here, we investigate the diffusional...
The systematic functional characterisation of Xq28 genes prioritises candidate disease genes
Kolb-Kokocinski, Anja, Mehrle, Alexander, Bechtel, Stephanie, Simpson, Jeremy C, Kioschis, Petra, Wiemann, Stefan, ...
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...
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...
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...
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...
Spatiotemporal dynamics of the COPI vesicle machinery
Elsner, Markus, Hashimoto, Hitoshi, Simpson, Jeremy C., Cassel, Dan, Nilsson, Tommy, Weiss, Matthias
Assembly of the coat protein I (COPI) vesicle coat is controlled by the small GTPase ADP ribosylation factor 1 (ARF1) and its GTPase-activating protein, ARFGAP1. Here, we investigate the diffusional...
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 systematic functional characterisation of Xq28 genes prioritises candidate disease genes
Kolb-Kokocinski, Anja, Mehrle, Alexander, Bechtel, Stephanie, Simpson, Jeremy C, Kioschis, Petra, Wiemann, Stefan, ...
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?
Schallus, Thomas, Jaeckh, Christine, Fehér, Krisztina, Palma, Angelina S., Liu, Yan, Simpson, Jeremy C., ...
N-Glycosylation starts in the endoplasmic reticulum (ER) where a 14-sugar glycan composed of three glucoses, nine mannoses, and two N-acetylglucosamines (Glc3Man9GlcNAc2) is transferred to nascent...