Balwierz, Piotr J, Carninci, Piero, Daub, Carsten O, Kawai, Jun, Hayashizaki, Yoshihide, Van Belle, Werner, ...
Abstract With the advent of ultra high-throughput sequencing technologies, increasingly researchers are turning to deep sequencing for gene expression studies. Here we present a set of rigorous...
Kawaji, Hideya, Hayashizaki, Yoshihide, Daub, Carsten O
Abstract Background As larger datasets are produced with the development of genome-scale experimental techniques, it has become essential to explicitly describe the meta-data (information describing...
Severin, Jessica, Waterhouse, Andrew M, Kawaji, Hideya, Lassmann, Timo, Van Nimwegen, Erik, Balwierz, Piotr J, ...
Abstract EdgeExpressDB is a novel database and set of interfaces for interpreting biological networks and comparing large high-throughput expression datasets that requires minimal development for new...
Transcriptional features of genomic regulatory blocks (2009)
Akalin, Altuna, Fredman, David, Arner, Erik, Dong, Xianjun, Bryne, Jan, Suzuki, Harukazu, ...
Abstract Background Genomic regulatory blocks (GRBs) are chromosomal regions spanned by highly conserved non-coding elements (HCNEs), most of which serve as regulatory inputs of one target gene in...
The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation (2009)
Kawaji, Hideya, Severin, Jessica, Lizio, Marina, Waterhouse, Andrew, Katayama, Shintaro, Irvine, Katharine M, ...
Abstract In FANTOM4, an international collaborative research project, we collected a wide range of genome-scale data, including 24 million mRNA 5'-reads (CAGE tags) and microarray expression profiles...
The regulated retrotransposon transcriptome of mammalian cells (2009)
Faulkner, Geoffrey J., Kimura, Yasumasa, Daub, Carsten O., Wani, Shivangi, Plessy, Charles, Irvine, Katharine M., ...
Although repetitive elements pervade mammalian genomes, their overall contribution to transcriptional activity is poorly defined. Here, as part of the FANTOM4 project, we report that 6–30% of...
Hashimoto, Takehiro, Grimmond, Sean M., Daub, Carsten O., Hayashizaki, Yoshihide, Faulkner, Geoffrey J.
Summary: Multi-mapping sequence tags are a significant impediment to short-read sequencing platforms. These tags are routinely omitted from further analysis, leading to experimental bias and reduced...
TagDust--a program to eliminate artifacts from next generation sequencing data (2009)
Lassmann, Timo, Hayashizaki, Yoshihide, Daub, Carsten O.
Motivation: Next-generation parallel sequencing technologies produce large quantities of short sequence reads. Due to experimental procedures various types of artifacts are commonly sequenced...
der Mathematisch-Naturwissenschaftlichen Fakultät (2008)
Carsten O. Daub, Dekan Prof, Dr. Robert Seckler, Gutachter Prof, Dr. Hanspeter Herzel, Prof Dr, ...
Analysis of integrated transcriptomics and metabolomics data — a systems biology approach
Employing conservation of co-expression to improve functional inference (2008)
Daub, Carsten O, Sonnhammer, Erik LL
Abstract Background Observing co-expression between genes suggests that they are functionally coupled. Co-expression of orthologous gene pairs across species may improve function prediction beyond...
Hidden layers of human small RNAs (2008)
Kawaji, Hideya, Nakamura, Mari, Takahashi, Yukari, Sandelin, Albin, Katayama, Shintaro, Fukuda, Shiro, ...
Abstract Background Small RNA attracts increasing interest based on the discovery of RNA silencing and the rapid progress of our understanding of these phenomena. Although recent studies suggest the...
Abhiman, Saraswathi, Daub, Carsten O., Sonnhammer, Erik L. L.
Protein families typically embody a range of related functions and may thus be decomposed into subfamilies with, for example, distinct substrate specificities. Detection of functionally divergent...
Abhiman, Saraswathi, Daub, Carsten O., Sonnhammer, Erik L.L.
Protein families typically embody a range of related functions and may thus be decomposed into subfamilies with e.g. distinct substrate specificities. Detection of functionally divergent subfamilies...
Nikiforova, Victoria J., Daub, Carsten O., Hesse, Holger, Willmitzer, Lothar, Hoefgen, Rainer
The systematic accumulation of gene expression data, although revolutionary, is insufficient in itself for an understanding of system-level physiology. In the post-genomic era, the next cognitive...
Nikiforova, Victoria J., Daub, Carsten O., Hesse, Holger, Willmitzer, Lothar, Hoefgen, Rainer
The systematic accumulation of gene expression data, although revolutionary, is insufficient in itself for an understanding of system-level physiology. In the post-genomic era, the next cognitive...
Nikiforova, Victoria J., Daub, Carsten O., Hesse, Holger, Willmitzer, Lothar, Hoefgen, Rainer
The systematic accumulation of gene expression data, although revolutionary, is insufficient in itself for an understanding of system-level physiology. In the post-genomic era, the next cognitive...
Daub, Carsten O, Steuer, Ralf, Selbig, Joachim, Kloska, Sebastian
Abstract Background The information theoretic concept of mutual information provides a general framework to evaluate dependencies between variables. In the context of the clustering of genes with...
Analysis of integrated transcriptomics and metabolomics data : a systems biology approach / (2004)
Potsdam, University, Diss., 2004 (Nicht für den Austausch).
Potsdam, University, Diss., 2004.
improved similarity measure for analysing gene expression data (2003)
Bmc Bioinformatics, Carsten O Daub, Ralf Steuer, Joachim Selbig, Sebastian Kloska, Biomed Central
Estimating mutual information using B-spline functions – an
MetaGeneAlyse: analysis of integrated transcriptional and metabolite data (2003)
Daub, Carsten O., Kloska, Sebastian, Selbig, Joachim
Summary: New techniques in sample preparation allow high throughput analysis of samples on the transcriptional as well as on the metabolic level. We present a service accessible via the web that...
Hidden layers of human small RNAs
Kawaji, Hideya, Nakamura, Mari, Takahashi, Yukari, Sandelin, Albin, Katayama, Shintaro, Fukuda, Shiro, ...
Transcriptional features of genomic regulatory blocks
Akalin, Altuna, Fredman, David, Arner, Erik, Dong, Xianjun, Bryne, Jan Christian, Suzuki, Harukazu, ...
CAGE tag mapping of transcription start sites across different human tissues shows that genomic regulatory blocks have unique features that are the likely cause of their ability to respond to...
Severin, Jessica, Waterhouse, Andrew M, Kawaji, Hideya, Lassmann, Timo, Van Nimwegen, Erik, Balwierz, Piotr J, ...
EdgeExpressDB is a novel database and set of interfaces for interpreting biological networks and comparing large high-throughput expression datasets.
The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation
Kawaji, Hideya, Severin, Jessica, Lizio, Marina, Waterhouse, Andrew, Katayama, Shintaro, Irvine, Katharine M, ...
The genome-scale data collected by the FANTOM4 collaborative research project are presented as an integrated web resource.
MiR-107 and MiR-185 Can Induce Cell Cycle Arrest in Human Non Small Cell Lung Cancer Cell Lines
Takahashi, Yukari, Forrest, Alistair R. R., Maeno, Emi, Hashimoto, Takehiro, Daub, Carsten O., Yasuda, Jun
Balwierz, Piotr J, Carninci, Piero, Daub, Carsten O, Kawai, Jun, Hayashizaki, Yoshihide, Van Belle, Werner, ...
A set of methods is presented for normalization, quantification of noise and co-expression analysis for gene expression studies using deep sequencing.