Staff at EMBL

Dr. Lars Steinmetz

Joint Head of Unit and Senior Scientist
Genome Biology Steinmetz Group

EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

Biography

PhD 1997-2001, Stanford University.
Postdoctoral research at Stanford Genome Technology Center. Visiting group leader since 2003.
Group leader at EMBL since 2003.
Joint Head of Genome Biology Unit and Senior Scientist since 2009.
ERC Advanced Investigator since 2012.
Acting Professor of Genetics, Stanford University since 2013.

Publications

PubMed

An efficient method for genome-wide polyadenylation site mapping and RNA quantification. Wilkening, S., Pelechano, V., Jarvelin, A.I., Tekkedil, M.M., Anders, S., Benes, V. & Steinmetz, L.M. Nucleic Acids Res. 2013 Mar 1;41(5):e65. doi: 10.1093/nar/gks1249. Epub 2013 Jan7. PubMed

Genotyping 1000 yeast strains by next-generation sequencing. Wilkening, S., Tekkedil, M.M., Lin, G., Fritsch, E.S., Wei, W., Gagneur, J., Lazinski, D.W., Camilli, A. & Steinmetz, L.M. BMC Genomics. 2013 Feb 9;14(1):90. PubMed

The Genomic and Transcriptomic Landscape of a HeLa Cell Line. Landry, J.J., Pyl, P.T., Rausch, T., Zichner, T., Tekkedil, M.M., Stutz, A.M., Jauch, A., Aiyar, R.S., Pau, G., Delhomme, N., Gagneur, J., Korbel, J.O., Huber, W. & Steinmetz, L.M. G3 (Bethesda). 2013 Mar 26. pii: g3.113.005777v6. doi: 10.1534/g3.113.005777. PubMed

System-wide identification of RNA-binding proteins by interactome capture. Castello, A., Horos, R., Strein, C., Fischer, B., Eichelbaum, K., Steinmetz, L.M., Krijgsveld, J. & Hentze, M.W. Nat Protoc. 2013 Feb 14;8(3):491-500. doi: 10.1038/nprot.2013.020. Epub 2013 Feb14. PubMed

Multiple genomic changes associated with reorganization of gene regulation and adaptation in yeast. David, L., Ben-Harosh, Y., Stolovicki, E., Moore, L.S., Nguyen, M., Tamse, R., Dean, J., Mancera, E., Steinmetz, L.M. & Braun, E. Mol Biol Evol. 2013 Apr 14. PubMed

Silencing of Genes and Alleles by RNAi in Anopheles gambiae. Lamacchia, M., Clayton, J.R., Wang-Sattler, R., Steinmetz, L.M., Levashina, E.A. & Blandin, S.A. Methods Mol Biol. 2013;923:161-76. PubMed

Gene loops enhance transcriptional directionality. Tan-Wong, S.M., Zaugg, J.B., Camblong, J., Xu, Z., Zhang, D.W., Mischo, H.E., Ansari, A.Z., Luscombe, N.M., Steinmetz, L.M. & Proudfoot, N.J. Science. 2012 Nov 2;338(6107):671-5. doi: 10.1126/science.1224350. Epub 2012 Sep27. PubMed

RNA Polymerase II Collision Interrupts Convergent Transcription. Hobson, D.J., Wei, W., Steinmetz, L.M. & Svejstrup, J.Q. Mol Cell. 2012 Oct 2. pii: S1097-2765(12)00770-8. doi:10.1016/j.molcel.2012.08.027. PubMed

Set3 HDAC Mediates Effects of Overlapping Noncoding Transcription on Gene Induction Kinetics. Kim, T., Xu, Z., Clauder-Munster, S., Steinmetz, L.M. & Buratowski, S. Cell. 2012 Sep 5. PubMed

Extensive Degradation of RNA Precursors by the Exosome in Wild-Type Cells. Gudipati, R.K., Xu, Z., Lebreton, A., Seraphin, B., Steinmetz, L.M., Jacquier, A. & Libri, D. Mol Cell. 2012 Sep 19. pii: S1097-2765(12)00736-8. doi:10.1016/j.molcel.2012.08.018. PubMed

Genetic modifiers of chromatin acetylation antagonize the reprogramming of epi-polymorphisms. Abraham, A.L., Nagarajan, M., Veyrieras, J.B., Bottin, H., Steinmetz, L.M. & Yvert, G. PLoS Genet. 2012 Sep;8(9):e1002958. doi: 10.1371/journal.pgen.1002958. Epub 2012Sep 20. PubMed

Experimental Relocation of the Mitochondrial ATP9 Gene to the Nucleus Reveals Forces Underlying Mitochondrial Genome Evolution. Bietenhader, M.*, Martos, A.*, Tetaud, E.*, Aiyar, R.S.*, Sellem, C.H., Kucharczyk, R., Clauder-Munster, S., Giraud, M.F., Godard, F., Salin, B., Sagot, I., Gagneur, J., Dequard-Chablat, M., Contamine, V., Denmat, S.H., Sainsard-Chanet, A., Steinmetz, L.M. & di Rago, J.P. PLoS Genet. 2012 Aug;8(8):e1002876. Epub 2012 Aug 16.
*equal contributors PubMed

easyRNASeq: a bioconductor package for processing RNA-Seq data. Delhomme, N., Padioleau, I., Furlong, E.E. & Steinmetz, L.M. Bioinformatics. 2012 Jul 30. PubMed

Insights into RNA Biology from an Atlas of Mammalian mRNA-Binding Proteins. Castello, A., Fischer, B., Eichelbaum, K., Horos, R., Beckmann, B.M., Strein, C., Davey, N.E., Humphreys, D.T., Preiss, T., Steinmetz, L.M., Krijgsveld, J. & Hentze, M.W. Cell. 2012 Jun 8;149(6):1393-406. Epub 2012 May 31. PubMed

Rrp6p Controls mRNA Poly(A) Tail Length and Its Decoration with Poly(A) Binding Proteins. Schmid, M., Poulsen, M.B., Olszewski, P., Pelechano, V., Saguez, C., Gupta, I., Steinmetz, L.M., Moore, C. & Jensen, T.H. Mol Cell. 2012 Jun 7. PubMed

Genome-wide polyadenylation site mapping. Pelechano, V., Wilkening, S., Jarvelin, A.I., Tekkedil, M.M. & Steinmetz, L.M. Methods Enzymol. 2012;513:271-96. PubMed

Genome-wide H4 K16 acetylation by SAS-I is deposited independently of transcription and histone exchange. Heise, F., Chung, H.R., Weber, J.M., Xu, Z., Klein-Hitpass, L., Steinmetz, L.M., Vingron, M. & Ehrenhofer-Murray, A.E. Nucleic Acids Res. 2011 Sep 9. PubMed

A yeast-based assay identifies drugs active against human mitochondrial disorders. Couplan, E.*, Aiyar, R.S.*, Kucharczyk, R., Kabala, A., Ezkurdia, N., Gagneur, J., St Onge, R.P., Salin, B., Soubigou, F., Le Cann, M., Steinmetz, L.M., di Rago, J.P. & Blondel, M. Proc Natl Acad Sci U S A. 2011 Jun 29.
*equal contributors PubMed

Accumulation of noncoding RNA due to an RNase P defect in Saccharomyces cerevisiae. Marvin, M.C., Clauder-Munster, S., Walker, S.C., Sarkeshik, A., Yates JR, 3rd, Steinmetz, L.M. & Engelke, D.R. RNA. 2011 Jun 10. PubMed

Functional consequences of bidirectional promoters. Wei, W., Pelechano, V., Jarvelin, A.I. & Steinmetz, L.M. Trends Genet. 2011 May 20. PubMed

Genome-wide survey of post-meiotic segregation during yeast recombination. Mancera, E., Bourgon, R., Huber, W. & Steinmetz, L.M. Genome Biol. 2011 Apr 11;12(4):R36. PubMed

Antisense expression increases gene expression variability and locus interdependency. Xu, Z., Wei, W., Gagneur, J., Clauder-Munster, S., Smolik, M., Huber, W. & Steinmetz, L.M. Mol Syst Biol. 2011 Feb 15;7:468. PubMed

Yeast Sen1 helicase protects the genome from transcription-associated instability. Mischo, H.E., Gomez-Gonzalez, B., Grzechnik, P., Rondon, A.G., Wei, W., Steinmetz, L.M., Aguilera, A. & Proudfoot, N.J. Mol Cell. 2011 Jan 7;41(1):21-32. PubMed

Genome-wide transcriptome analysis in yeast using high-density tiling arrays. David, L., Clauder-Munster, S. & Steinmetz, L.M. Methods Mol Biol. 2011;759:107-23. PubMed

Execution of the meiotic noncoding RNA expression program and the onset of gametogenesis in yeast require the conserved exosome subunit Rrp6. Lardenois, A., Liu, Y., Walther, T., Chalmel, F., Evrard, B., Granovskaia, M., Chu, A., Davis, R.W., Steinmetz, L.M. & Primig, M. Proc Natl Acad Sci U S A. 2010 Dec 13. PubMed

The baker's yeast diploid genome is remarkably stable in vegetative growth and meiosis. Nishant, K.T., Wei, W., Mancera, E., Argueso, J.L., Schlattl, A., Delhomme, N., Ma, X., Bustamante, C.D., Korbel, J.O., Gu, Z., Steinmetz, L.M. & Alani, E. PLoS Genet. 2010 Sep 9;6(9). pii: e1001109. PubMed

Antagonistic changes in sensitivity to antifungal drugs by mutations of an important ABC transporter gene in a fungal pathogen. Guan, W., Jiang, H., Guo, X., Mancera, E., Xu, L., Li, Y., Steinmetz, L.M., Li, Y. & Gu, Z. PLoS One. 2010 Jun 25;5(6):e11309. PubMed

Natural single-nucleosome epi-polymorphisms in yeast. Nagarajan, M., Veyrieras, J.B., de Dieuleveult, M., Bottin, H., Fehrmann, S., Abraham, A.L., Croze, S., Steinmetz, L.M., Gidrol, X. & Yvert, G. PLoS Genet. 2010 Apr 22;6(4):e1000913. PubMed

Genetic analysis of variation in transcription factor binding in yeast. Zheng, W., Zhao, H., Mancera, E., Steinmetz, L.M. & Snyder, M. Nature. 2010 Mar 17. PubMed

High-resolution transcription atlas of the mitotic cell cycle in budding yeast. Granovskaia, M.V., Jensen, L.J., Ritchie, M.E., Toedling, J., Ning, Y., Bork, P., Huber, W. & Steinmetz, L.M. Genome Biol. 2010 Mar 1;11(3):R24. PubMed

Dissecting the genetic basis of resistance to malaria parasites in Anopheles gambiae. Blandin, S.A., Wang-Sattler, R., Lamacchia, M., Gagneur, J., Lycett, G., Ning, Y., Levashina, E.A. & Steinmetz, L.M. Science. 2009 Oct 2;326(5949):147-50. PubMed

Trans-acting antisense RNAs mediate transcriptional gene cosuppression in S. cerevisiae. Camblong, J., Beyrouthy, N., Guffanti, E., Schlaepfer, G., Steinmetz, L.M. & Stutz, F. Genes Dev. 2009 Jul 1;23(13):1534-45. PubMed

Genome-wide allele- and strand-specific expression profiling. Gagneur, J., Sinha, H., Perocchi, F., Bourgon, R., Huber, W. & Steinmetz, L.M. Mol Syst Biol. 2009;5:274. Epub 2009 Jun 16. PubMed

Array-based genotyping in S. cerevisiae using semi-supervised clustering. Bourgon, R., Mancera, E., Brozzi, A., Steinmetz, L.M. & Huber, W. Bioinformatics. 2009 Feb 23. PubMed

Bidirectional promoters generate pervasive transcription in yeast. Xu, Z., Wei, W., Gagneur, J., Perocchi, F., Clauder-Munster, S., Camblong, J., Guffanti, E., Stutz, F., Huber, W. & Steinmetz, L.M. Nature. 2009 Feb 19;457(7232):1033-7. Epub 2009 Jan 25. PubMed

Widespread bidirectional promoters are the major source of cryptic transcripts in yeast. Neil, H., Malabat, C., d'Aubenton-Carafa, Y., Xu, Z., Steinmetz, L.M. & Jacquier, A. Nature. 2009 Feb 19;457(7232):1038-42. Epub 2009 Jan 25. PubMed

Identification of mitochondrial disease genes through integrative analysis of multiple datasets. Aiyar, R.S., Gagneur, J. & Steinmetz, L.M. Methods. 2008 Dec;46(4):248-55. Epub 2008 Oct 16. PubMed

Sequential elimination of major-effect contributors identifies additional quantitative trait loci conditioning high-temperature growth in yeast. Sinha, H., David, L., Pascon, R.C., Clauder-Munster, S., Krishnakumar, S., Nguyen, M., Shi, G., Dean, J., Davis, R.W., Oefner, P.J., McCusker, J.H. & Steinmetz, L.M. Genetics. 2008 Nov;180(3):1661-70. Epub 2008 Sep 9. PubMed

High-resolution mapping of meiotic crossovers and non-crossovers in yeast. Mancera, E., Bourgon, R., Brozzi, A., Huber, W. & Steinmetz, L.M. Nature. 2008 Jul 24;454(7203):479-85. Epub 2008 Jul 9. PubMed

Systematic screens for human disease genes, from yeast to human and back. Perocchi, F., Mancera, E. & Steinmetz, L.M. Mol Biosyst. 2008 Jan;4(1):18-29. Epub 2007 Sep 25. PubMed

Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D. Perocchi, F., Xu, Z., Clauder-Munster, S. & Steinmetz, L.M. Nucleic Acids Res. 2007 Sep 26;. PubMed

Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789. Wei, W., McCusker, J.H., Hyman, R.W., Jones, T., Ning, Y., Cao, Z., Gu, Z., Bruno, D., Miranda, M., Nguyen, M., Wilhelmy, J., Komp, C., Tamse, R., Wang, X., Jia, P., Luedi, P., Oefner, P.J., David, L., Dietrich, F.S., Li, Y., Davis, R.W. & Steinmetz, L.M. Proc Natl Acad Sci U S A. 2007 Jul 31;104(31):12825-30. Epub 2007 Jul 25. PubMed

Mosaic Genome Architecture of the Anopheles gambiae Species Complex. Wang-Sattler, R., Blandin, S., Ning, Y., Blass, C., Dolo, G., Toure, Y.T., Torre, A.D., Lanzaro, G.C., Steinmetz, L.M., Kafatos, F.C. & Zheng, L. PLoS ONE. 2007 Nov 28;2(11):e1249. PubMed

Assessing systems properties of yeast mitochondria through an interaction map of the organelle. Perocchi, F., Jensen, L.J., Gagneur, J., Ahting, U., von Mering, C., Bork, P., Prokisch, H. & Steinmetz, L.M. PLoS Genet. 2006 Oct 20;2(10):e170. PubMed

Transcript mapping with high-density oligonucleotide tiling arrays. Huber, W., Toedling, J. & Steinmetz, L.M. Bioinformatics. 2006 Aug 15;22(16):1963-70. Epub 2006 Jun 20. PubMed

Capturing cellular machines by systematic screens of protein complexes. Gagneur, J., David, L. & Steinmetz, L.M. Trends Microbiol. 2006 Aug;14(8):336-9. Epub 2006 Jun 16. PubMed

Complex genetic interactions in a quantitative trait locus. Sinha, H., Nicholson, B.P., Steinmetz, L.M. & McCusker, J.H. PLoS Genet. 2006 Feb 3;2(2):e13. PubMed

A high-resolution map of transcription in the yeast genome. David, L., Huber, W., Granovskaia, M., Toedling, J., Palm, C.J., Bofkin, L., Jones, T., Davis, R.W. & Steinmetz, L.M. Proc Natl Acad Sci U S A. 2006 Apr 4;103(14):5320-5. Epub 2006 Mar 28. PubMed

Re-analysis of data and its integration. Jensen, L.J. & Steinmetz, L.M. FEBS Lett 2005 Mar 21;579(8):1802-7. PubMed

Elevated evolutionary rates in the laboratory strain of Saccharomyces cerevisiae. Gu, Z., David, L., Petrov, D., Jones, T., Davis, R.W. & Steinmetz, L.M. Proc Natl Acad Sci U S A 2005 Jan 25;102(4):1092-7. Epub 2005 Jan 12. PubMed

Integrative analysis of the mitochondrial proteome in yeast. Prokisch, H., Scharfe, C., Camp DG, 2nd, Xiao, W., David, L., Andreoli, C., Monroe, M.E., Moore, R.J., Gritsenko, M.A., Kozany, C., Hixson, K.K., Mottaz, H.M., Zischka, H., Ueffing, M., Herman, Z.S., Davis, R.W., Meitinger, T., Oefner, P.J., Smith, R.D. & Steinmetz, L.M. PLoS Biol 2004 Jun;2(6):e160. Epub 2004 Jun 15. PubMed

Maximizing the potential of functional genomics. Steinmetz, L.M. & Davis, R.W. Nat Rev Genet. 2004 Mar;5(3):190-201. PubMed

Role of duplicate genes in genetic robustness against null mutations. Gu, Z., Steinmetz, L.M., Gu, X., Scharfe, C., Davis, R.W. & Li, W.H. Nature 2003 Jan 2;421(6918):63-6. PubMed

Gene function on a genomic scale. Steinmetz, L.M. & Deutschbauer, A.M. J Chromatogr B Analyt Technol Biomed Life Sci 2002 Dec 25;782(1-2):151-63. PubMed

Systematic screen for human disease genes in yeast. Steinmetz, L.M., Scharfe, C., Deutschbauer, A.M., Mokranjac, D., Herman, Z.S., Jones, T., Chu, A.M., Giaever, G., Prokisch, H., Oefner, P.J. & Davis, R.W. Nat Genet 2002 Aug;31(4):400-4. PubMed

Evolutionary rate in the protein interaction network. Fraser, H.B., Hirsh, A.E., Steinmetz, L.M., Scharfe, C. & Feldman, M.W. Science 2002 Apr 26;296(5568):750-2. PubMed

Dissecting the architecture of a quantitative trait locus in yeast. Steinmetz, L.M., Sinha, H., Richards, D.R., Spiegelman, J.I., Oefner, P.J., McCusker, J.H. & Davis, R.W. Nature 2002 Mar 21;416(6878):326-30. PubMed

Transcriptional regulation and function during the human cell cycle. Cho, R.J., Huang, M., Campbell, M.J., Dong, H., Steinmetz, L., Sapinoso, L., Hampton, G., Elledge, S.J., Davis, R.W. & Lockhart, D.J. Nat Genet. 2001 Jan;27(1):48-54. PubMed

Combining genome sequences and new technologies for dissecting the genetics of complex phenotypes. Steinmetz, L.M., Mindrinos, M. & Oefner, P.J. Trends Plant Sci 2000 Sep;5(9):397-401. PubMed

High-density arrays and insights into genome function. Steinmetz, L.M. & Davis, R.W. Biotechnol Genet Eng Rev 2000;17:109-46. PubMed

A genome-wide transcriptional analysis of the mitotic cell cycle. Cho, R.J., Campbell, M.J., Winzeler, E.A., Steinmetz, L., Conway, A., Wodicka, L., Wolfsberg, T.G., Gabrielian, A.E., Landsman, D., Lockhart, D.J. & Davis, R.W. Mol Cell. 1998 Jul;2(1):65-73. PubMed