Trans-acting antisense RNAs mediate transcriptional gene cosuppression in S. cerevisiae (2009)
Camblong, Jurgi, Beyrouthy, Nissrine, Guffanti, Elisa, Schlaepfer, Guillaume, Steinmetz, Lars M., Stutz, Françoise
Homology-dependent gene silencing, a phenomenon described as cosuppression in plants, depends on siRNAs. We provide evidence that in Saccharomyces cerevisiae, which is missing the RNAi machinery,...
Array-based genotyping in S.cerevisiae using semi-supervised clustering (2009)
Bourgon, Richard, Mancera, Eugenio, Brozzi, Alessandro, Steinmetz, Lars M., Huber, Wolfgang
Motivation: Microarrays provide an accurate and cost-effective method for genotyping large numbers of individuals at high resolution. The resulting data permit the identification of loci at which...
Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D (2007)
Perocchi, Fabiana, Xu, Zhenyu, Clauder-Münster, Sandra, Steinmetz, Lars M.
Recent transcription profiling studies have revealed an unanticipatedly large proportion of antisense transcription across eukaryotic and bacterial genomes. However, the extent and significance of...
Fabiana Perocchi, Lars J. Jensen, Julien Gagneur, Uwe Ahting, Christian Von Mering, Peer Bork, ...
Mitochondria carry out specialized functions; compartmentalized, yet integrated into the metabolic and signaling processes of the cell. Although many mitochondrial proteins have been identified,...
Complex Genetic Interactions in a Quantitative Trait Locus (2006)
Himanshu Sinha, Bradly P. Nicholson, Lars M. Steinmetz, John H. McCusker
Whether in natural populations or between two unrelated members of a species, most phenotypic variation is quantitative. To analyze such quantitative traits, one must first map the underlying...
BIOINFORMATICS ORIGINAL PAPER (2006)
Gene Expression, Wolfgang Huber, Joern Toedling, Lars M. Steinmetz
Transcript mapping with high-density oligonucleotide tiling arrays Vol. 22 no. 16 2006, pages 1963–1970 doi:10.1093/bioinformatics/btl289
Transcript mapping with high-density oligonucleotide tiling arrays (2006)
Huber, Wolfgang, Toedling, Joern, Steinmetz, Lars M.
Motivation: High-density DNA tiling microarrays are a powerful tool for the characterization of complete transcriptomes. The two major analytical challenges are the segmentation of the hybridization...
Integrative Analysis of the Mitochondrial Proteome in Yeast (2004)
Holger Prokisch, Curt Scharfe, David G. Camp, Wenzhong Xiao, Lior David, Christophe Andreoli, ...
Although individual approaches fall short, integrating multiple common genetic and biochemical approaches yields a description of mitochondrial proteins that is more than the sum of its parts.
Integrative Analysis of the Mitochondrial Proteome in Yeast (2004)
Holger Prokisch, Curt Scharfe, Wenzhong Xiao, Lior David, Christophe Andreoli, ...
In this study yeast mitochondria were used as a model system to apply, evaluate, and integrate different genomic approaches to define the proteins of an organelle. Liquid chromatography mass...
Integrative Analysis of the Mitochondrial Proteome in Yeast
Prokisch, Holger, Scharfe, Curt, Camp, David G, Xiao, Wenzhong, David, Lior, Andreoli, Christophe, ...
In this study yeast mitochondria were used as a model system to apply, evaluate, and integrate different genomic approaches to define the proteins of an organelle. Liquid chromatography mass...
Elevated evolutionary rates in the laboratory strain of Saccharomyces cerevisiae
Gu, Zhenglong, David, Lior, Petrov, Dmitri, Jones, Ted, Davis, Ronald W., Steinmetz, Lars M.
By using the maximum likelihood method, we made a genome-wide comparison of the evolutionary rates in the lineages leading to the laboratory strain (S288c) and a wild strain (YJM789) of Saccharomyces...
Complex Genetic Interactions in a Quantitative Trait Locus
Sinha, Himanshu, Nicholson, Bradly P, Steinmetz, Lars M, McCusker, John H
Whether in natural populations or between two unrelated members of a species, most phenotypic variation is quantitative. To analyze such quantitative traits, one must first map the underlying...
A high-resolution map of transcription in the yeast genome
David, Lior, Huber, Wolfgang, Granovskaia, Marina, Toedling, Joern, Palm, Curtis J., Bofkin, Lee, ...
There is abundant transcription from eukaryotic genomes unaccounted for by protein coding genes. A high-resolution genome-wide survey of transcription in a well annotated genome will help relate...
Assessing Systems Properties of Yeast Mitochondria through an Interaction Map of the Organelle
Perocchi, Fabiana, Jensen, Lars J, Gagneur, Julien, Ahting, Uwe, Von Mering, Christian, Bork, Peer, ...
Mitochondria carry out specialized functions; compartmentalized, yet integrated into the metabolic and signaling processes of the cell. Although many mitochondrial proteins have been identified,...
Integrative Analysis of the Mitochondrial Proteome in Yeast
Prokisch, Holger, Scharfe, Curt, Camp, David G, Xiao, Wenzhong, David, Lior, Andreoli, Christophe, ...
In this study yeast mitochondria were used as a model system to apply, evaluate, and integrate different genomic approaches to define the proteins of an organelle. Liquid chromatography mass...
Elevated evolutionary rates in the laboratory strain of Saccharomyces cerevisiae
Gu, Zhenglong, David, Lior, Petrov, Dmitri, Jones, Ted, Davis, Ronald W., Steinmetz, Lars M.
By using the maximum likelihood method, we made a genome-wide comparison of the evolutionary rates in the lineages leading to the laboratory strain (S288c) and a wild strain (YJM789) of Saccharomyces...
Complex Genetic Interactions in a Quantitative Trait Locus
Sinha, Himanshu, Nicholson, Bradly P, Steinmetz, Lars M, McCusker, John H
Whether in natural populations or between two unrelated members of a species, most phenotypic variation is quantitative. To analyze such quantitative traits, one must first map the underlying...
A high-resolution map of transcription in the yeast genome
David, Lior, Huber, Wolfgang, Granovskaia, Marina, Toedling, Joern, Palm, Curtis J., Bofkin, Lee, ...
There is abundant transcription from eukaryotic genomes unaccounted for by protein coding genes. A high-resolution genome-wide survey of transcription in a well annotated genome will help relate...
Assessing Systems Properties of Yeast Mitochondria through an Interaction Map of the Organelle
Perocchi, Fabiana, Jensen, Lars J, Gagneur, Julien, Ahting, Uwe, Von Mering, Christian, Bork, Peer, ...
Mitochondria carry out specialized functions; compartmentalized, yet integrated into the metabolic and signaling processes of the cell. Although many mitochondrial proteins have been identified,...
Mosaic Genome Architecture of the Anopheles gambiae Species Complex
Wang-Sattler, Rui, Blandin, Stephanie, Ning, Ye, Blass, Claudia, Dolo, Guimogo, Touré, Yeya T., ...
Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D
Perocchi, Fabiana, Xu, Zhenyu, Clauder-Münster, Sandra, Steinmetz, Lars M.
Recent transcription profiling studies have revealed an unanticipatedly large proportion of antisense transcription across eukaryotic and bacterial genomes. However, the extent and significance of...
Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789
Wei, Wu, McCusker, John H., Hyman, Richard W., Jones, Ted, Ning, Ye, Cao, Zhiwei, ...
We sequenced the genome of Saccharomyces cerevisiae strain YJM789, which was derived from a yeast isolated from the lung of an AIDS patient with pneumonia. The strain is used for studies of fungal...
Sinha, Himanshu, David, Lior, Pascon, Renata C., Clauder-Münster, Sandra, Krishnakumar, Sujatha, Nguyen, Michelle, ...
Several quantitative trait loci (QTL) mapping strategies can successfully identify major-effect loci, but often have poor success detecting loci with minor effects, potentially due to the confounding...
Array-based genotyping in S.cerevisiae using semi-supervised clustering
Bourgon, Richard, Mancera, Eugenio, Brozzi, Alessandro, Steinmetz, Lars M., Huber, Wolfgang
Motivation: Microarrays provide an accurate and cost-effective method for genotyping large numbers of individuals at high resolution. The resulting data permit the identification of loci at which...
Genome-wide allele- and strand-specific expression profiling
Gagneur, Julien, Sinha, Himanshu, Perocchi, Fabiana, Bourgon, Richard, Huber, Wolfgang, Steinmetz, Lars M
Recent reports have shown that most of the genome is transcribed and that transcription frequently occurs concurrently on both DNA strands. In diploid genomes, the expression level of each allele...