Functional Genomics Group PICB |
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BRIESEMANN Marko, M.Sc. Bioinformatics Room: 316 Email: brie @ picb.ac.cn Date of Arrival: 2008-03-25 Homepage: http://www.picb.ac.cn/brie Research area:I am working on the reconstruction of the gene regulatory network underlying the circadian clock in the model organism drosophila melanogaster. To this end, I am combining publicly available micro array data sets to increase the validity of identified circadian oscillating genes. The core circadian network is regulated by transcription factors, which also control downstream targets through cis-regulatory elements. Comparative genomics data for drosophila is available and adds crucial informations for the identification of transcription factor binding site motifs. Therefore, I further combine a large scale promoter sequence search with comparative genomics information. For most of the programming tasks I am using R and perl .Recent work:In 2009/2010 I was doing a research internship at the Center for Developmental Biology RIKEN in the Systems Biology Laboratory in Kobe, Japan. I worked on a project closely related to my PhD.-thesis of gene regulatory network of circadian clocks using different computational methods. I was analyzing ChIP-on-Chip data for an important circadian transcription factor using Weeder. Furthermore, I learned basics of Ruby and the Ruby-based Model-Viewer-Controller framework implementation Ruby-on-Rails.Important tools:R stat - a Free Software environment for statistical computing. Together with bioconductor, an open source tool-box for the analysis of high-throughtput data, R is a quite powerful. perl Perl is powerful scripting language, especially appropriate for sequence analysis and text matching using regulatory expressions. BioPerl - A library for Perl, for DNA and Protein sequence analysis. Reading fastA-files and other formats is standardized, object-oriented and thus one can concentrate on the analysis part. Biology-related web-applications MEME Tool-collection site for finding overrepresented motifs in a given sequence set. Pscan - Tool for finding overrepresented transcription factor binding sites in a set of genes, which show similar expression patterns. TOMTOM- a positional matrix comparison tool. Looks up a given PWM in different repositories, such as Jaspar, Transfac and some drosophila studies. Tools on gene regulation A comprehensive collection of state-of-the-arte gene regulation tools. The cluster approach is included as well. STRING-DB Protein-Protein Interaction database for many species (mammals, flies etc.), as well as homology information. Weeder Tool to find overrepresented motifs in a given set of sequences in fastA-format. Literature related to genomics, bioinformatics and physiology The Statistics of Sequence Similarity Scores A nice overview of statistics to assess significance of sequence alignments for homology studies. A wikipedia glossary on gene expression terminology. Useful to get a quick overview on current definitions. drosophila related sites Flybase - Gene information database for drosophila. Interactive Fly - Information on genes and their role in development in drosophila. Drosophila regulator targets - Reliable prediction of regulator targets using 12 Drosophila genomes. Database for predicted Transcription factor targets. redFly - Database for conserved cis-regulatory modules. flyreg - Drosophila DNase I Footprint Database (v2.0). OregAnno - The Open REGulatory ANNOtation database (ORegAnno) is an open database for the curation of known regulatory elements from scientific literature. It provides a non-redundant set of high quality binding site information for 87 transcription factors and 101 target genes. Integrated into redfly by 2007. Circadian Clock genes were not included in the original version. modEncode - Derivate from the Encode project for the model organisms drosophila melanogaster and C. Elegans. Huge collection of experimental data for ChIP-on-Chip and Chip-Seq for histone modifier, transcription factors and in different tissues and developmental stages. Micro array repositories Genbank Various interesting texts on science and related subjects The Unreasonable Effectiveness of Mathematics by R. W. HAMMING - An essay on the foundations of mathematics and the relation between assumptions, postulates, theorems and real-world applications of math. The author presents examples to show that the order of the four changes with need and time, argueing furtermore that inconsistensies in the fundamentals of math will not shake the wide-spread use. Thomas Kuhn and The Structure of Scientific Revolutions A theory on the history of scientific revolution by Thomas Kuhn from the 60's. He addresses topics like normal science, revolutionary sciences and paradigm shifts. Later he established some ideas on the creation of theories which should be: accurate, consistent, have a broad scope, be simple and fruitful. A review on the book by Steven Weinberg you can find here . Occam's Razor A very interesting theory on the selection of competing theories. Publications:Haifang Wang, Yuting Liu, Marko Briesemann, and Jun Yan: "Computational Analysis of Gene Regulations in Animal Sleep Deprivation", Physiol. Genomics (May 25, 2010),hereMaster's Thesis: "Evaluation and extension of a community detection approach using linear programming" [pdf] Bachelor's Thesis: "Algorithmic Identification of labeled endothelial progenitor cells from MRI data in the murine stroke model " [pdf] Curriculum Vitae:
Links:My Pictures on Flickr,My Pictures on seenby, My account on LinkedIn | ||||||||||||||
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