Research Topics
Genomes and Genes | Lars M SteinmetzSummaryAffiliation: European Molecular Biology Laboratory Country: Germany Publications
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Detail Information
Publications
Genotyping 1000 yeast strains by next-generation sequencingStefan Wilkening
Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstr 1, 69117, Heidelberg, Germany
BMC Genomics 14:90. 2013....
Maximizing the potential of functional genomicsLars M Steinmetz
European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
Nat Rev Genet 5:190-201. 2004- Integrative analysis of the mitochondrial proteome in yeastHolger Prokisch
Institute of Human Genetics, GSF National Research Center for Environment and Health, Neuherberg, Germany
PLoS Biol 2:e160. 2004..Furthermore, our systematic identification of genes involved in mitochondrial function and biogenesis in yeast expands the candidate genes available for mapping Mendelian and complex mitochondrial disorders in humans... - High-resolution transcription atlas of the mitotic cell cycle in budding yeastMarina V Granovskaia
EMBL European Molecular Biology Laboratory, Department of Genome Biology, Meyerhofstr, Heidelberg, Germany
Genome Biol 11:R24. 2010..To explore the complex transcriptome architecture underlying the budding yeast cell cycle, we used 8 bp tiling arrays to generate a 5 minute-resolution, strand-specific expression atlas of the whole genome... - Sequential elimination of major-effect contributors identifies additional quantitative trait loci conditioning high-temperature growth in yeastHimanshu Sinha
European Molecular Biology Laboratory, Heidelberg, Germany
Genetics 180:1661-70. 2008..The targeted backcrossing approach overcomes the difficulties posed by sample size, genetic linkage, and epistatic effects and facilitates identification of additional alleles with smaller contributions to complex traits... - Genome-wide allele- and strand-specific expression profilingJulien Gagneur
Gene Expression Unit, European Molecular Biology Laboratory, Heidelberg, Germany
Mol Syst Biol 5:274. 2009..Our results provide the first high-resolution analysis of differential expression on all four strands of an eukaryotic genome... - Bidirectional promoters generate pervasive transcription in yeastZhenyu Xu
European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
Nature 457:1033-7. 2009.... - Dissecting the genetic basis of resistance to malaria parasites in Anopheles gambiaeStephanie A Blandin
European Molecular Biology Laboratory EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
Science 326:147-50. 2009..The successful application of rasRNAi in Anopheles suggests that it could also be applied to other organisms where RNAi is feasible to dissect complex phenotypes to the level of individual quantitative trait alleles... - Antisense expression increases gene expression variability and locus interdependencyZhenyu Xu
Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
Mol Syst Biol 7:468. 2011..These results indicate a general regulatory effect of antisense expression on sense genes and emphasize the importance of antisense-initiating regions downstream of genes in models of gene regulation... - Identification of mitochondrial disease genes through integrative analysis of multiple datasetsRaeka S Aiyar
European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
Methods 46:248-55. 2008..Relevant public data resources are indicated. This report highlights the success and potential of data integration as well as its applicability to the search for mitochondrial disease genes... - Genome-wide survey of post-meiotic segregation during yeast recombinationEugenio Mancera
European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
Genome Biol 12:R36. 2011..This gives rise to somatic mosaicism in multicellular organisms and leads to unexpected allelic combinations among progeny. Despite its implications for inheritance, post-meiotic segregation has been studied at only a few loci... - Assessing systems properties of yeast mitochondria through an interaction map of the organelleFabiana Perocchi
European Molecular Biology Laboratory, Heidelberg, Germany
PLoS Genet 2:e170. 2006..Our network thus advances the understanding of the mitochondrial system in yeast and identifies properties of genes underlying human mitochondrial disorders... - High-resolution mapping of meiotic crossovers and non-crossovers in yeastEugenio Mancera
European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
Nature 454:479-85. 2008..In addition, because non-crossover hotspots create holes of reduced linkage within haplotype blocks, our results stress the need to incorporate non-crossovers into genetic linkage analysis... 
Genome-wide polyadenylation site mappingVicent Pelechano
Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
Methods Enzymol 513:271-96. 2012..This method is illustrated here for budding yeast. However, this method can be applied to any natural or artificially polyadenylated RNA...- System-wide identification of RNA-binding proteins by interactome captureAlfredo Castello
European Molecular Biology Laboratory EMBL, Heidelberg, Germany
Nat Protoc 8:491-500. 2013..Interactome capture can also be broadly used to compare different biological states, including metabolic stress, cell cycle, differentiation, development or the response to drugs... - Systematic screens for human disease genes, from yeast to human and backFabiana Perocchi
European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, Germany
Mol Biosyst 4:18-29. 2008..In an iterative fashion, the link between predicted human candidate genes and their disease phenotypes can be experimentally tested back in yeast... - Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin DFabiana Perocchi
European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
Nucleic Acids Res 35:e128. 2007..Our findings thus facilitate a more accurate assessment of the extent and position of antisense transcription, towards a better understanding of its role in cells... - An efficient method for genome-wide polyadenylation site mapping and RNA quantificationStefan Wilkening
Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
Nucleic Acids Res 41:e65. 2013..Finally, we observe that overlap of convergent 3'-UTRs is frequent but sharply limited by coding regions, suggesting factors that restrict compression of the yeast genome... - Capturing cellular machines by systematic screens of protein complexesJulien Gagneur
European Molecular Biology Laboratory, Heidelberg 69117, Germany
Trends Microbiol 14:336-9. 2006..These data will prove useful in defining principles and trends that arise when combining large-scale datasets of different natures, and in deriving properties of protein machines in cellular systems... - Functional consequences of bidirectional promotersWu Wei
Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
Trends Genet 27:267-76. 2011..Moreover, the bidirectional activity of a promoter is regulated at multiple points during transcription, giving rise to diverse types of transcripts... - Insights into RNA biology from an atlas of mammalian mRNA-binding proteinsAlfredo Castello
European Molecular Biology Laboratory, Heidelberg, Germany
Cell 149:1393-406. 2012..Interactome capture is broadly applicable to study mRNA interactome composition and dynamics in varied biological settings... - Genome-wide H4 K16 acetylation by SAS-I is deposited independently of transcription and histone exchangeFranziska Heise
Zentrum für Medizinische Biotechnologie, Abteilung Genetik, Universitat Duisburg Essen, Essen, Germany
Nucleic Acids Res 40:65-74. 2012.... - Re-analysis of data and its integrationLars Juhl Jensen
European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
FEBS Lett 579:1802-7. 2005..Here, we demonstrate the power of data re-analysis and integration by applying it in a case study to data from deletion phenotype screens and mRNA expression profiling... - Mosaic genome architecture of the Anopheles gambiae species complexRui Wang Sattler
European Molecular Biology Laboratory, Heidelberg, Germany
PLoS ONE 2:e1249. 2007..Attempts over the last three decades to reconstruct the phylogenetic history of the Anopheles gambiae species complex have been important for developing better strategies to control malaria transmission... - Complex genetic interactions in a quantitative trait locusHimanshu Sinha
Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
PLoS Genet 2:e13. 2006..Our findings demonstrate the variety and complexity of QTG contributions to phenotype, the impact of genetic background, and the value of quantitative genetic studies in S. cerevisiae... - A high-resolution map of transcription in the yeast genomeLior David
Stanford Genome Technology Center and Department of Biochemistry, Stanford University, Palo Alto, CA 94304, USA
Proc Natl Acad Sci U S A 103:5320-5. 2006..These findings may suggest a regulatory role of antisense transcription in S. cerevisiae. Moreover, the data show that even this well studied genome has transcriptional complexity far beyond current annotation... - Transcript mapping with high-density oligonucleotide tiling arraysWolfgang Huber
European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge CB10 1SD, UK
Bioinformatics 22:1963-70. 2006.... - Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789Wu Wei
Bioinformatics Center, Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Graduate School of the Chinese Academy of Sciences, Shanghai 200031, People s Republic of China
Proc Natl Acad Sci U S A 104:12825-30. 2007..The sequence of YJM789 contains clues to pathogenicity and spurs the development of more powerful approaches to dissecting the genetic basis of complex hereditary traits... - Gene function on a genomic scaleLars M Steinmetz
Department of Biochemistry, Stanford University School of Medicine, CA 94305, USA
J Chromatogr B Analyt Technol Biomed Life Sci 782:151-63. 2002..The promise of integrating these datasets has made it attractive to test whether genomic approaches can determine gene function with accuracy comparable to single gene approaches... - Systematic screen for human disease genes in yeastLars M Steinmetz
Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
Nat Genet 31:400-4. 2002..To apply these advantages to human disorders involving mitochondria, human orthologs were identified and linked to heritable diseases using genomic map positions... - Dissecting the architecture of a quantitative trait locus in yeastLars M Steinmetz
Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
Nature 416:326-30. 2002..It also demonstrates a deficiency in current approaches to QTL dissection with implications extending to traits in other organisms, including human genetic diseases...