Design of Specific Mammalian Promoters by in silico Prediction (2009)
Heinemann, Tim, Kramer, Stephen, Velten, Lars, Kranz, Anna-Lena, Bauer, Tobias, Faura, Marti Bernardo, ...
The purpose of this RFC is to provide a) a method for the design of rational synthetic promoter sequences based on a statistical analysis about the spatial preference of transcription factor binding...
Units for Promoter Measurement in Mammalian Cells (2009)
Velten, Lars, Iwamoto, Nao, Hiller, Corinna, Uckelmann, Hannah, Zhu, Chenchen, Zhao, Bingqing, ...
The purpose of this RFC is to provide units for the characterization of promoter strength for use in mammalian cells. RMPU is mRNA based and directly proportional to PoPS, whereas REU is protein...
RA-PCR, a method for the generation of randomized promoter libraries (2009)
Velten, Lars, Haas, Simon, Rademacher, Anne, Meyer, Hannah, Eils, Roland
The purpose of this RFC is to provide instructions for the synthesis of promoters in mammalian cells that are active at a desired cellular condition (where a cellular condition is specified by the...
Cloning Standard for Mammalian BioBrick Parts and Devices (2009)
Bartoschek, Michael, Mugahid, Douaa, Rademacher, Anne, Meyer, Hannah, Velten, Lars, Reis, Yara, ...
To introduce a common cloning standard for BioBrick parts that find application in mammalian cells.
Harder, Nathalie, Mora-Bermúdez, Felipe, Godinez, William J., Wünsche, Annelie, Eils, Roland, Ellenberg, Jan, ...
Live-cell imaging allows detailed dynamic cellular phenotyping for cell biology and, in combination with small molecule or drug libraries, for high-content screening. Fully automated analysis of live...
Markus Ulrich, Joel Beaudouin, Stefan Hezel, Jochen Ulrich, Roland Eils
microscopy images
Plaimas, Kitiporn, Mallm, Jan-Phillip, Oswald, Marcus, Svara, Fabian, Sourjik, Victor, Eils, Roland, ...
Abstract Background Computational identification of new drug targets is a major goal of pharmaceutical bioinformatics. Results This paper presents a machine learning strategy to study and validate...
An ultrasensitive sorting mechanism for EGF Receptor Endocytosis (2008)
Schmidt-Glenewinkel, Hannah, Vacheva, Ivayla, Hoeller, Daniela, Dikic, Ivan, Eils, Roland
Abstract Background The Epidermal Growth Factor (EGF) receptor has been shown to internalize via clathrin-independent endocytosis (CIE) in a ligand concentration dependent manner. From a modeling...
Die Mühen der vergangenen Monate haben sich gelohnt: Bei der Vergabe der Preise beim international renommierten iGEM-Wettbewerb des Massachusetts Institute of Technology (MIT) in Boston konnte das...
Kim, Il-Han, Nagel, Jens, Otten, Simone, Knerr, Boris, Eils, Roland, Rohr, Karl, ...
Abstract Background GFP-fusion proteins and immunostaining are methods broadly applied to investigate the three-dimensional organization of cells and cell nuclei, the latter often studied in addition...
Warnat, Patrick, Oberthuer, André, Fischer, Matthias, Westermann, Frank, Eils, Roland, Brors, Benedikt
Abstract Background Neuroblastoma patients show heterogeneous clinical courses ranging from life-threatening progression to spontaneous regression. Recently, gene expression profiles of neuroblastoma...
Schramm, Gunnar, Zapatka, Marc, Eils, Roland, König, Rainer
Abstract Background Biochemical investigations over the last decades have elucidated an increasingly complete image of the cellular metabolism. To derive a systems view for the regulation of the...
Svetlana Bulashevska, Ezekiel Adebiyi, Benedikt Brors, Roland Eils
The most fatal and prevalent form of malaria is caused by the bloodborne pathogen Plasmodium falciparum (henceforth P.f). Annually, approximately three million people died of malaria. Despite P.f...
Bulashevska, Alla, Eils, Roland
Abstract Background The subcellular location of a protein is closely related to its function. It would be worthwhile to develop a method to predict the subcellular location for a given protein when...
GOPET: A tool for automated predictions of Gene Ontology terms (2006)
Vinayagam, Arunachalam, Del Val, Coral, Schubert, Falk, Eils, Roland, Glatting, Karl-Heinz, Suhai, Sándor, ...
Abstract Background Vast progress in sequencing projects has called for annotation on a large scale. A Number of methods have been developed to address this challenging task. These methods, however,...
König, Rainer, Schramm, Gunnar, Oswald, Marcus, Seitz, Hanna, Sager, Sebastian, Zapatka, Marc, ...
Abstract Background Microarray technology produces gene expression data on a genomic scale for an endless variety of organisms and conditions. However, this vast amount of information needs to be...
Oberthuer, André, Berthold, Frank, Warnat, Patrick, Hero, Barbara, Kahlert, Yvonne, Spitz, Rüdiger, ...
PURPOSE: To develop a gene expression–based classifier for neuroblastoma patients that reliably predicts courses of the disease. PATIENTS AND METHODS: Two hundred fifty-one neuroblastoma specimens...
Group testing for pathway analysis improves comparability of different microarray datasets (2006)
Manoli, Theodora, Gretz, Norbert, Gröne, Hermann-Josef, Kenzelmann, Marc, Eils, Roland, Brors, Benedikt
Motivation: The wide use of DNA microarrays for the investigation of the cell transcriptome triggered the invention of numerous methods for the processing of microarray data and lead to a growing...
Ulrich, Markus, Kappel, Constantin, Beaudouin, Joel, Hezel, Stefan, Ulrich, Jochen, Eils, Roland
Summary: Tropical is a software for simulation and parameter estimation of reaction–diffusion models. Based on spatio-temporal microscopy images, Tropical estimates reaction and diffusion...
Argonaute--a database for gene regulation by mammalian microRNAs (2006)
Shahi, Priyanka, Loukianiouk, Serguei, Bohne-Lang, Andreas, Kenzelmann, Marc, Küffer, Stefan, Maertens, Sabine, ...
MicroRNAs (miRNAs) constitute a recently discovered class of small non-coding RNAs that regulate expression of target genes either by decreasing the stability of the target mRNA or by translational...
Warnat, Patrick, Eils, Roland, Brors, Benedikt
Abstract Background The extensive use of DNA microarray technology in the characterization of the cell transcriptome is leading to an ever increasing amount of microarray data from cancer studies....
CGH-Profiler: Data mining based on genomic aberration profiles (2005)
Schubert, Falk, Tausch, Bernhard, Joos, Stefan, Eils, Roland
Abstract Background CGH-Profiler is a program that supports the analysis of genomic aberrations measured by Comparative Genomic Hybridisation (CGH). Comparative genomic hybridisation (CGH) is a...
Andreas Bolzer, Gregor Kreth, Irina Solovei, Daniela Koehler, Kaan Saracoglu, Christine Fauth, ...
Through advanced microscopy and labeling techniques these authors can visualize and identify all of the chromosomes in a human nucleus--a key landmark towards understanding how our genome is...
Andreas Bolzer, Gregor Kreth, Irina Solovei, Daniela Koehler, Kaan Saracoglu, Christine Fauth, ...
Studies of higher-order chromatin arrangements are an essential part of ongoing attempts to explore changes in epigenome structure and their functional implications during development and cell...
Inferring genetic regulatory logic from expression data (2005)
Bulashevska, Svetlana, Eils, Roland
Motivation: High-throughput molecular genetics methods allow the collection of data about the expression of genes at different time points and under different conditions. The challenge is to infer...
Inferring genetic regulatory logic from expression data (2005)
Bulashevska, Svetlana, Eils, Roland
Motivation: High throughput molecular genetics methods allow to collect data about expression of genes at different time points and under different conditions. The challenge is to infer gene...
Bacher, Christian P, Reichenzeller, Michaela, Athale, Chaitanya, Herrmann, Harald, Eils, Roland
Abstract Background The dynamics of nuclear organization, nuclear bodies and RNPs in particular has been the focus of many studies. To understand their function, knowledge of their spatial nuclear...
Applying Support Vector Machines for Gene ontology based gene function prediction (2004)
Vinayagam, Arunachalam, König, Rainer, Moormann, Jutta, Schubert, Falk, Eils, Roland, Glatting, Karl-Heinz, ...
Abstract Background The current progress in sequencing projects calls for rapid, reliable and accurate function assignments of gene products. A variety of methods has been designed to annotate...
Rainer Koè Nig, Danila Baldessari, Nicolas Pollet, Christof Niehrs, Roland Eils
Reliability of gene expression ratios for cDNA
Gene expression analysis on biochemical networks using the Potts spin model (2004)
Motivation: Microarray technology allows us to profile the expression of a large subset or all genes of a cell. Biochemical research over the last three decades has elucidated an increasingly...
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...
König, Rainer, Baldessari, Danila, Pollet, Nicolas, Niehrs, Christof, Eils, Roland
In a typical gene expression profiling experiment with multiple conditions, a common reference sample is used for co‐hybridization with the samples to yield expression ratios. Differential...
Zugl.: Heidelberg, Univ., Diss., 1995.
Heidelberg, Universiẗat, Diss., 1995.
Quantitative Imaging of Pre-mRNA Splicing Factors in Living CellsV⃞
Eils, Roland, Gerlich, Daniel, Tvaruskó, Wolfgang, Spector, David L., Misteli, Tom
Schoch, Claudia, Kohlmann, Alexander, Schnittger, Susanne, Brors, Benedikt, Dugas, Martin, Mergenthaler, Susanne, ...
Acute myeloid leukemia (AML) is a heterogeneous group of genetically defined diseases. Their classification is important with regard to prognosis and treatment. We performed microarray analyses for...
Schmidt-Kittler, Oleg, Ragg, Thomas, Daskalakis, Angela, Granzow, Martin, Ahr, Andre, Blankenstein, Thomas J. F., ...
According to the present view, metastasis marks the end in a sequence of genomic changes underlying the progression of an epithelial cell to a lethal cancer. Here, we aimed to find out at what stage...
Visualizing telomere dynamics in living mammalian cells using PNA probes
Molenaar, Chris, Wiesmeijer, Karien, Verwoerd, Nico P., Khazen, Shadi, Eils, Roland, Tanke, Hans J., ...
Chromosome ends are protected from degradation by the presence of the highly repetitive hexanucleotide sequence of TTAGGG and associated proteins. These so-called telomeric complexes are suggested to...
König, Rainer, Baldessari, Danila, Pollet, Nicolas, Niehrs, Christof, Eils, Roland
In a typical gene expression profiling experiment with multiple conditions, a common reference sample is used for co-hybridization with the samples to yield expression ratios. Differential expression...
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...
Applying Support Vector Machines for Gene ontology based gene function prediction
Vinayagam, Arunachalam, König, Rainer, Moormann, Jutta, Schubert, Falk, Eils, Roland, Glatting, Karl-Heinz, ...
Three-Dimensional Maps of All Chromosomes in Human Male Fibroblast Nuclei and Prometaphase Rosettes
Bolzer, Andreas, Kreth, Gregor, Solovei, Irina, Koehler, Daniela, Saracoglu, Kaan, Fauth, Christine, ...
Studies of higher-order chromatin arrangements are an essential part of ongoing attempts to explore changes in epigenome structure and their functional implications during development and cell...
CGH-Profiler: Data mining based on genomic aberration profiles
Schubert, Falk, Tausch, Bernhard, Joos, Stefan, Eils, Roland
Argonaute—a database for gene regulation by mammalian microRNAs
Shahi, Priyanka, Loukianiouk, Serguei, Bohne-Lang, Andreas, Kenzelmann, Marc, Küffer, Stefan, Maertens, Sabine, ...
MicroRNAs (miRNAs) constitute a recently discovered class of small non-coding RNAs that regulate expression of target genes either by decreasing the stability of the target mRNA or by translational...
GOPET: A tool for automated predictions of Gene Ontology terms
Vinayagam, Arunachalam, Del Val, Coral, Schubert, Falk, Eils, Roland, Glatting, Karl-Heinz, Suhai, Sándor, ...
Quantitative Imaging of Pre-mRNA Splicing Factors in Living CellsV⃞
Eils, Roland, Gerlich, Daniel, Tvaruskó, Wolfgang, Spector, David L., Misteli, Tom
Schoch, Claudia, Kohlmann, Alexander, Schnittger, Susanne, Brors, Benedikt, Dugas, Martin, Mergenthaler, Susanne, ...
Acute myeloid leukemia (AML) is a heterogeneous group of genetically defined diseases. Their classification is important with regard to prognosis and treatment. We performed microarray analyses for...
Schmidt-Kittler, Oleg, Ragg, Thomas, Daskalakis, Angela, Granzow, Martin, Ahr, Andre, Blankenstein, Thomas J. F., ...
According to the present view, metastasis marks the end in a sequence of genomic changes underlying the progression of an epithelial cell to a lethal cancer. Here, we aimed to find out at what stage...
Visualizing telomere dynamics in living mammalian cells using PNA probes
Molenaar, Chris, Wiesmeijer, Karien, Verwoerd, Nico P., Khazen, Shadi, Eils, Roland, Tanke, Hans J., ...
Chromosome ends are protected from degradation by the presence of the highly repetitive hexanucleotide sequence of TTAGGG and associated proteins. These so-called telomeric complexes are suggested to...
König, Rainer, Baldessari, Danila, Pollet, Nicolas, Niehrs, Christof, Eils, Roland
In a typical gene expression profiling experiment with multiple conditions, a common reference sample is used for co-hybridization with the samples to yield expression ratios. Differential expression...
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...
Applying Support Vector Machines for Gene ontology based gene function prediction
Vinayagam, Arunachalam, König, Rainer, Moormann, Jutta, Schubert, Falk, Eils, Roland, Glatting, Karl-Heinz, ...
Three-Dimensional Maps of All Chromosomes in Human Male Fibroblast Nuclei and Prometaphase Rosettes
Bolzer, Andreas, Kreth, Gregor, Solovei, Irina, Koehler, Daniela, Saracoglu, Kaan, Fauth, Christine, ...
Studies of higher-order chromatin arrangements are an essential part of ongoing attempts to explore changes in epigenome structure and their functional implications during development and cell...
CGH-Profiler: Data mining based on genomic aberration profiles
Schubert, Falk, Tausch, Bernhard, Joos, Stefan, Eils, Roland
Argonaute—a database for gene regulation by mammalian microRNAs
Shahi, Priyanka, Loukianiouk, Serguei, Bohne-Lang, Andreas, Kenzelmann, Marc, Küffer, Stefan, Maertens, Sabine, ...
MicroRNAs (miRNAs) constitute a recently discovered class of small non-coding RNAs that regulate expression of target genes either by decreasing the stability of the target mRNA or by translational...
GOPET: A tool for automated predictions of Gene Ontology terms
Vinayagam, Arunachalam, Del Val, Coral, Schubert, Falk, Eils, Roland, Glatting, Karl-Heinz, Suhai, Sándor, ...
Warnat, Patrick, Oberthuer, André, Fischer, Matthias, Westermann, Frank, Eils, Roland, Brors, Benedikt
Computational imaging in cell biology
Eils, Roland, Athale, Chaitanya
Microscopy of cells has changed dramatically since its early days in the mid-seventeenth century. Image analysis has concurrently evolved from measurements of hand drawings and still photographs to...
An ultrasensitive sorting mechanism for EGF Receptor Endocytosis
Schmidt-Glenewinkel, Hannah, Vacheva, Ivayla, Hoeller, Daniela, Dikic, Ivan, Eils, Roland
Bar-Joseph, Ziv, Siegfried, Zahava, Brandeis, Michael, Brors, Benedikt, Lu, Yong, Eils, Roland, ...
Characterization of the transcriptional regulatory network of the normal cell cycle is essential for understanding the perturbations that lead to cancer. However, the complete set of cycling genes in...
Gene network dynamics controlling keratinocyte migration
Busch, Hauke, Camacho-Trullio, David, Rogon, Zbigniew, Breuhahn, Kai, Angel, Peter, Eils, Roland, ...
Translation of large-scale data into a coherent model that allows one to simulate, predict and control cellular behavior is far from being resolved. Assuming that long-term cellular behavior is...
Live Cell Dynamics of Promyelocytic Leukemia Nuclear Bodies upon Entry into and Exit from Mitosis
Chen, Yi-Chun M., Kappel, Constantin, Beaudouin, Joel, Eils, Roland, Spector, David L.
Promyelocytic leukemia nuclear bodies (PML NBs) have been proposed to be involved in tumor suppression, viral defense, DNA repair, and/or transcriptional regulation. To study the dynamics of PML NBs...
Machine learning based analyses on metabolic networks supports high-throughput knockout screens
Plaimas, Kitiporn, Mallm, Jan-Phillip, Oswald, Marcus, Svara, Fabian, Sourjik, Victor, Eils, Roland, ...
Dynamics of HIV-1 Assembly and Release
Ivanchenko, Sergey, Godinez, William J., Lampe, Marko, Kräusslich, Hans-Georg, Eils, Roland, Rohr, Karl, ...
Assembly and release of human immunodeficiency virus (HIV) occur at the plasma membrane of infected cells and are driven by the Gag polyprotein. Previous studies analyzed viral morphogenesis using...
Optimal Experimental Design for Parameter Estimation of a Cell Signaling Model
Bandara, Samuel, Schlöder, Johannes P., Eils, Roland, Bock, Hans Georg, Meyer, Tobias
Differential equation models that describe the dynamic changes of biochemical signaling states are important tools to understand cellular behavior. An essential task in building such representations...