Lars M Steinmetz

Summary

Affiliation: European Molecular Biology Laboratory
Country: Germany

Publications

  1. ncbi Maximizing the potential of functional genomics
    Lars M Steinmetz
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nat Rev Genet 5:190-201. 2004
  2. pmc Integrative analysis of the mitochondrial proteome in yeast
    Holger Prokisch
    Institute of Human Genetics, GSF National Research Center for Environment and Health, Neuherberg, Germany
    PLoS Biol 2:e160. 2004
  3. pmc Genome-wide allele- and strand-specific expression profiling
    Julien Gagneur
    Gene Expression Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Mol Syst Biol 5:274. 2009
  4. pmc Bidirectional promoters generate pervasive transcription in yeast
    Zhenyu Xu
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nature 457:1033-7. 2009
  5. pmc High-resolution transcription atlas of the mitotic cell cycle in budding yeast
    Marina V Granovskaia
    EMBL European Molecular Biology Laboratory, Department of Genome Biology, Meyerhofstr, Heidelberg, Germany
    Genome Biol 11:R24. 2010
  6. pmc Sequential elimination of major-effect contributors identifies additional quantitative trait loci conditioning high-temperature growth in yeast
    Himanshu Sinha
    European Molecular Biology Laboratory, Heidelberg, Germany
    Genetics 180:1661-70. 2008
  7. pmc An efficient method for genome-wide polyadenylation site mapping and RNA quantification
    Stefan Wilkening
    Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Nucleic Acids Res 41:e65. 2013
  8. pmc Antisense expression increases gene expression variability and locus interdependency
    Zhenyu Xu
    Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Mol Syst Biol 7:468. 2011
  9. pmc Dissecting the genetic basis of resistance to malaria parasites in Anopheles gambiae
    Stephanie A Blandin
    European Molecular Biology Laboratory EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Science 326:147-50. 2009
  10. pmc Role of histone modifications and early termination in pervasive transcription and antisense-mediated gene silencing in yeast
    Manuele Castelnuovo
    Department of Cell Biology and NCCR Frontiers in Genetics, iGE3, University of Geneva, 1211 Geneva, Switzerland, EBI EMBL Hinxton, Cambridge CB101SD, England, European Molecular Biology Laboratory, 69117 Heidelberg, Germany, Department of Genetics, Stanford University, Stanford, CA 94395 USA and Stanford Genome Technology Center, Palo Alto, CA 94303, USA
    Nucleic Acids Res 42:4348-62. 2014

Collaborators

Detail Information

Publications38

  1. ncbi Maximizing the potential of functional genomics
    Lars M Steinmetz
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nat Rev Genet 5:190-201. 2004
  2. pmc Integrative analysis of the mitochondrial proteome in yeast
    Holger 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...
  3. pmc Genome-wide allele- and strand-specific expression profiling
    Julien 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...
  4. pmc Bidirectional promoters generate pervasive transcription in yeast
    Zhenyu Xu
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nature 457:1033-7. 2009
    ....
  5. pmc High-resolution transcription atlas of the mitotic cell cycle in budding yeast
    Marina 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...
  6. pmc Sequential elimination of major-effect contributors identifies additional quantitative trait loci conditioning high-temperature growth in yeast
    Himanshu 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...
  7. pmc An efficient method for genome-wide polyadenylation site mapping and RNA quantification
    Stefan 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...
  8. pmc Antisense expression increases gene expression variability and locus interdependency
    Zhenyu 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...
  9. pmc Dissecting the genetic basis of resistance to malaria parasites in Anopheles gambiae
    Stephanie 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...
  10. pmc Role of histone modifications and early termination in pervasive transcription and antisense-mediated gene silencing in yeast
    Manuele Castelnuovo
    Department of Cell Biology and NCCR Frontiers in Genetics, iGE3, University of Geneva, 1211 Geneva, Switzerland, EBI EMBL Hinxton, Cambridge CB101SD, England, European Molecular Biology Laboratory, 69117 Heidelberg, Germany, Department of Genetics, Stanford University, Stanford, CA 94395 USA and Stanford Genome Technology Center, Palo Alto, CA 94303, USA
    Nucleic Acids Res 42:4348-62. 2014
    ..Finally, depending on the efficiency of Nrd1/Nab3/Sen1 early termination, asRNA levels are modulated and their capability of silencing is changed. ..
  11. pmc The genomic and transcriptomic landscape of a HeLa cell line
    Jonathan J M Landry
    European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
    G3 (Bethesda) 3:1213-24. 2013
    ..This study underscores the importance of accounting for the strikingly aberrant characteristics of HeLa cells when designing and interpreting experiments, and has implications for the use of HeLa as a model of human biology. ..
  12. ncbi System-wide identification of RNA-binding proteins by interactome capture
    Alfredo 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...
  13. pmc Genome-wide survey of post-meiotic segregation during yeast recombination
    Eugenio 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...
  14. pmc Assessing systems properties of yeast mitochondria through an interaction map of the organelle
    Fabiana 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...
  15. pmc An evaluation of high-throughput approaches to QTL mapping in Saccharomyces cerevisiae
    Stefan Wilkening
    European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
    Genetics 196:853-65. 2014
    ..We also reveal confounding factors like mutations and aneuploidy in pooled approaches, providing valuable lessons for future designs of complex trait mapping studies. ..
  16. pmc Genotyping 1000 yeast strains by next-generation sequencing
    Stefan Wilkening
    Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstr 1, 69117, Heidelberg, Germany
    BMC Genomics 14:90. 2013
    ....
  17. pmc Extensive transcriptional heterogeneity revealed by isoform profiling
    Vicent Pelechano
    Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nature 497:127-31. 2013
    ..These data also indicate that isoform diversity as well as RNA abundance should be considered when assessing the functional repertoire of genomes...
  18. doi Gene regulation by antisense transcription
    Vicent Pelechano
    Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Nat Rev Genet 14:880-93. 2013
    ..The genomic arrangement of antisense RNAs opposite sense genes indicates that they might be part of self-regulatory circuits that allow genes to regulate their own expression. ..
  19. pmc Drift and conservation of differential exon usage across tissues in primate species
    Alejandro Reyes
    Genome Biology Unit and Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
    Proc Natl Acad Sci U S A 110:15377-82. 2013
    ..Our findings support the theory that isoform regulation is an important target of evolution in primates, and our method provides a powerful tool for discovering potentially functional tissue-dependent isoforms. ..
  20. pmc High-resolution mapping of meiotic crossovers and non-crossovers in yeast
    Eugenio 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...
  21. ncbi Systematic screens for human disease genes, from yeast to human and back
    Fabiana 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...
  22. pmc Identification of mitochondrial disease genes through integrative analysis of multiple datasets
    Raeka 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...
  23. ncbi Genome-wide polyadenylation site mapping
    Vicent 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...
  24. ncbi Capturing cellular machines by systematic screens of protein complexes
    Julien 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...
  25. pmc Functional consequences of bidirectional promoters
    Wu 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...
  26. pmc Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D
    Fabiana 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...
  27. pmc easyRNASeq: a bioconductor package for processing RNA-Seq data
    Nicolas Delhomme
    Genome Biology Computational Support, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Bioinformatics 28:2532-3. 2012
    ..g. DESeq and edgeR. However, the processing tasks lying in between these require the precise interplay of many Bioconductor packages, e.g. Biostrings, IRanges or external solutions are to be sought...
  28. doi Insights into RNA biology from an atlas of mammalian mRNA-binding proteins
    Alfredo 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...
  29. ncbi Re-analysis of data and its integration
    Lars 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...
  30. pmc Genome-wide H4 K16 acetylation by SAS-I is deposited independently of transcription and histone exchange
    Franziska Heise
    Zentrum für Medizinische Biotechnologie, Abteilung Genetik, Universitat Duisburg Essen, Essen, Germany
    Nucleic Acids Res 40:65-74. 2012
    ....
  31. pmc Mosaic genome architecture of the Anopheles gambiae species complex
    Rui 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...
  32. pmc Complex genetic interactions in a quantitative trait locus
    Himanshu 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...
  33. ncbi Systematic screen for human disease genes in yeast
    Lars 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...
  34. ncbi Gene function on a genomic scale
    Lars 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...
  35. pmc Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789
    Wu 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...
  36. pmc A high-resolution map of transcription in the yeast genome
    Lior 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...
  37. ncbi Transcript mapping with high-density oligonucleotide tiling arrays
    Wolfgang Huber
    European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge CB10 1SD, UK
    Bioinformatics 22:1963-70. 2006
    ....
  38. ncbi Dissecting the architecture of a quantitative trait locus in yeast
    Lars 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...