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Dominic Schmidt

Dominic Schmidt Doctoral Student Darwin College, Department of Oncology, University of Cambridge Cancer Research UK, Cambridge Research Institute Li Ka Shing Centre Robinson Way, Cambridge, CB2 0RE phone: +44-1223404248 email: Dominic.Schmidt 'at' cancer 'dot' org 'dot' uk

Research

Research Interests I received my german diplom degree in Biochemistry at the Max Planck Institute for Molecular Genetics in the department for Vertebrate Genomics of Hans Lehrach in the laboratory of Marie-Laure Yaspo. The focus of my research was the analysis of gene regulatory networks, especially for human chromosome 21 encoded transcription factors. For this purpose I worked with ChIP-chip using high density oligonucleotide microarrays and developed ChIP-seq using next generation sequencing technology. We published ChIP-seq for RNA-polymerase II in human cells together with RNA-seq: Sultan M, Schulz MH, Richard H, Magen A, Klingenhoff A, Scherf M, Seifert M, Borodina T, Soldatov A, Parkhomchuk D, Schmidt D, O'Keeffe S, Haas S, Vingron M, Lehrach H, and Yaspo ML. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 2008 Aug 15; 321(5891) 956-60. doi:10.1126/science.1160342 pmid:18599741. Myriad points of control influence gene expression; however, it has also been an unresolved question as to which of these mechanisms has the most influence globally. We recently showed that each layer of transcriptional regulation within the adult hepatocyte, from the binding of liver master regulators and chromatin remodelling complexes to the output of the transcriptional machinery, is directed primarily by DNA sequence. Although conservation of motifs alone cannot predict transcription factor binding, we show that within the genetic sequence there must be embedded adequate instructions to direct species-specific transcription: Wilson MD, Barbosa-Morais NL, Schmidt D, Conboy CM, Vanes L, Tybulewicz VL, Fisher EM, Tavare S, and Odom DT. Species-Specific Transcription in Mice Carrying Human Chromosome 21. Science 2008 Sep 11. doi:10.1126/science.1160930 pmid:18787134. We recently published a detailed protocol for ChIP-seq for whole tissues and cell lines. Further more we compared the influence of sequencing depth on peak calling using matched ChIP-chip data from the identical sequencing libraries: Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, and Odom DT. ChIP-seq: Using high-throughput sequencing to discover protein-DNA interactions. Methods 2009 Mar 9. doi:10.1016/j.ymeth.2009.03.001 pmid:19275939. Schmidt D, Stark R, Wilson MD, Brown GD, and Odom DT. Genome-scale validation of deep-sequencing libraries. PLoS ONE 2008; 3(11) e3713. doi:10.1371/journal.pone.0003713 pmid:19002256. My recent research uses ChIP-seq and RNA-seq to understand the rules behind species-specific gene regulation. Coming soon...

Publications

Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, and Odom DT. ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Methods. 2009 Jul;48(3):240-8. DOI:10.1016/j.ymeth.2009.03.001 | Schmidt D, Stark R, Wilson MD, Brown GD, and Odom DT. Genome-scale validation of deep-sequencing libraries. PLoS One. 2008;3(11):e3713. DOI:10.1371/journal.pone.0003713 | Wilson MD, Barbosa-Morais NL, Schmidt D, Conboy CM, Vanes L, Tybulewicz VL, Fisher EM, Tavaré S, and Odom DT. Species-specific transcription in mice carrying human chromosome 21. Science. 2008 Oct 17;322(5900):434-8. DOI:10.1126/science.1160930 | Sultan M, Schulz MH, Richard H, Magen A, Klingenhoff A, Scherf M, Seifert M, Borodina T, Soldatov A, Parkhomchuk D, Schmidt D, O'Keeffe S, Haas S, Vingron M, Lehrach H, and Yaspo ML. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science. 2008 Aug 15;321(5891):956-60. DOI:10.1126/science.1160342 |

Miscellaneous

Picture Gallerie ChIP-seq Carroll-lab Odom-lab Cambridge punting NYC Rainbow Room '08 St.Patrick's Day 2008 Odom_Lab_Jan2009