Peter Schattner

Peter Schattner
Hello. This page is outdated, is no longer being maintained and will probably be removed. To find out more about me and my new book Sex, Love, and DNA: What Molecular Biology Teaches Us About Being Human please visit my new website at peterschattner.com. Thanks.

My research interests are in the application of computers and technology to the medical and biological sciences.  For the last several years, my principal research focus has been in bioinformatics, in particular the computational detection and characterization of non-coding RNAs and mRNA cis-regulatory motifs. I have worked in bioinformatics both as an independent researcher and as a post-doc and research associate in the computational-biology research group at the University of California, Santa Cruz.

I have also been involved in the development of "open source" software as well as in teaching courses and seminars related to bioinformatics. I developed a tutorial on genome browsers and databases, which I presented at 2006 and 2007 ISMB Conferences and which I turned into a book, Genomes, Browsers and Databases.  I have also been a member of  the "Bioperl" group for whom I wrote numerous software modules as well as the package tutorial and have taught the use of Perl and Bioperl in bioinformatics in venues such as the O'Reilly Bioinformatics Conference, the ISMB and IEEE Bioinformatics Conferences, the California State University in Hayward CA and the University of California, Santa Cruz.

 Sex, Love and DNA Book Cover Previously I worked in the commercial sector, mostly in medical instrumentation.  At the Medical Technology Laboratory of SRI (Stanford Research Institute) I led or participated in research programs investigating novel ultrasound-imaging modalities.  I was also involved in technical and market assessments of emerging medical technologies.  At Diasonics I worked in both the ultrasound and magnetic resonance imaging (MRI) divisions (subsequently acquired by GE Medical Systems and Toshiba Medical Systems, respectively).  For the ultrasound group I designed circuitry for ultrasound imagers and Doppler systems.  For the MRI division,  I was involved in pulse sequence development and system integration.

I received my BA in physics with high honors from Swarthmore College. I received my Ph.D. in theoretical physics under Steven Weinberg at MIT. I have been a postdoctoral fellow at the Lawrence Berkeley Laboratory of the University of California and at the University of California, Santa Cruz.  I was elected to Phi Beta Kappa and to Sigma Xi, as well as chosen a Woodrow Wilson Fellow. I led the team that received the 1990 Matzuk Award for technical innovation of the American Institute of Ultrasound in Medicine.  I have published over twenty peer-reviewed papers in the scientific literature.

If you are interested in my non-scientific interests, you might want to look at the personal pages of my website.


Selected Publications:

  1. Schattner P. 2009  “Genomics Made Easier: An Introductory Tutorial to Genome Datamining”, Genomics 93(3):187-195 (preprint pdf)
  2. Xiao M.,Yang, C.X., Schattner P. and Y.T. Yu 2009 “Functionality and Substrate Specificity of human box H/ACA guide RNA”, RNA 15(1):176-86
  3. Schattner P. 2008 Genomes, Browsers and Databases, Cambridge University Press, 344pp.
  4. Schattner P. 2007 “Automated Querying of Genome Databases”, PLoS Computational Biology,  3(1):e1
  5. Hüttenhofer A. and P. Schattner 2006 “The principles of guiding by RNA: chimeric RNA-protein enzymes”, Nat. Rev. Genetics 7(6): 475-82 (pdf)   
  6. Schattner P. and M. Diekhans 2006 “Regions of Extreme Synonymous-Codon Selection in Mammalian Genes”, Nucleic Acids Res. 34(6):1700-10
  7. Schattner P., Barberan S. and T.M. Lowe 2006 “A Computational Screen for Pseudouridylation Guide H/ACA RNAs in Mammalian Genomes”, RNA. 2006 Jan;12(1):15-25   
  8. Schattner P., Brooks, A. and T.M. Lowe 2005 “The tRNAscan-SE, snoscan and snoGPS webservers for the detection of tRNAs and snoRNAs”, Nucleic Acids Res. 33(Web Server issue):W686-9
  9. Hüttenhofer A., Schattner P. and N. Polacek 2005 “Non-coding RNAs: hope or hype?”, Trends in Genetics 21(5): 289-97 (pdf)
  10. Schattner P., Decatur W., Davis, C. et al. 2004 “Genome-wide Searching for Pseudouridylation Guide snoRNAs: Analysis of the Saccharomyces cerevisiae genome”, Nucleic Acids Res. 32(14):4281-4296
  11. Schattner P.  2003 "Computational gene-finding for non-coding RNAs" in Non-coding RNAs editor: J Barcisewski (Landes Bioscience): 33-48 (abstract) (pdf)
  12. Stajich J.,  Block D., Boulez K. et al.,  2002, "The Bioperl Toolkit: Perl Modules for the Life Sciences". Genome Res. 12(10): 1611-1618.
  13. Schattner P.  2002 "Searching for RNA genes using base-composition statistics" Nucleic Acids Res. 30(9):2076-82. 
  14. Schattner P.  2002 "BPtutorial 1.0: The official tutorial of the Bioperl Project"

Contact information:

schattnerATsoeDOTucscDOTedu