• Personal Bio

• Timeline

• Contact Me

I do research in biological computing (including experimental design), pattern recognition and querying in trees and graphs, pattern discovery in time series, cryptographic file systems, database tuning, and wireless. See Research Activity in brief. If you want a truly stimulating reading experience, try my resume in pdf.

• Books

  For excerpts of my book (with journalist Cathy Lazere) of biographies of great computer scientists, see Out of Their Minds: the lives and discoveries of 15 great computer scientists (book published by Copernicus/Springer Verlag).

• Natural Computing

  In 2010, we published Natural Computing a book about the ongoing synthesis between computing and biology. Here is a little video preview (you will have to poke around to find it)

• Puzzles

  I have also had the pleasure of writing a mathematical puzzle column for Dr. Dobb's Journal whose readers are very sharp and continue to write the Puzzling Adventures Column for Scientific American . The puzzle-writing has led to six books about a mathematical detective named Dr. Ecco. Try them if you dare. Starting in the fall of 2014, I have become the puzzle columnist of the Communications of the ACM (CACM). Much of my research work has a puzzle flavor.

• Database Tuning

  Professionally, I have written two books about database tuning. The second, co-authored with Philippe Bonnet, appeared in May, 2002 and is called Database Tuning: principles, experiments, and troubleshooting techniques (published by Morgan Kaufmann). We have been updating material on that topic ever since.

• Books with Students

  In 2004, I wrote a book with my excellent PhD student Yunyue Zhu entitled High Performance Discovery in Time Series: techniques and case studies published by Springer Verlag Publishers in June 2004. More recently, I have written two books with Masters students on computational biology/bioinformatics: Stored Clocked Programs Inside DNA: a simplifying framework for Nanocomputing with Jessie Chang published by Morgan Claypool in 2011 and Network Inference in Molecular Biology -- a hands-on framework with Jesse Lingeman published by Springer in 2012.

• Bioinformatics Edited Collections

  With the extremely energetic Jason Wang and other colleagues, I have helped co-edit two books in bioinformatics:
  1. Pattern Discovery in Biomolecular Data: Tools, Techniques, and Applications Jason Wang, Bruce Shapiro, and Dennis Shasha (Eds.) Oxford University Press, November, 1999.
  2. Data Mining in Bioinformatics J. T. L. Wang, M. J. Zaki, H. T. T. Toivonen and D. Shasha (eds.), 350 pages, Springer-Verlag, August 2004.

• Statistics is Easy

  In my work with biologists, I find myself needing statistics. Because I find that academic statistics books tend to make the subject overly complex and lay statistics books tend to gloss assumptions (e.g. about normality) Manda Wilson and I have written a short book entitled Statistics is Easy! that uses a resampling approach to statistics (thus avoiding distribution assumptions) and explains most of the concepts using counting. The book also contains a link to python code that implements the statistics we discuss in the book. Please take a look at an excerpt.

• Russian Immigrants

  Because I was so fascinated by the Russian students we've had at NYU, I have co-authored with Marina Shron (a playwright born in St. Petersburg), Red Blues: voices from the last wave of Russian immigrants Here is an excerpt from that book.

• Technical Reports by the Department

  Here is a link to the technical reports offered by the department. NYU Computer Science Tech Reports

  Designer of this Website

  This website was designed by my son Tyler and his company OmniNerds. He also designed the site of Grace & Sha , where you can find some music which I co-wrote with the beautiful singer Grace. Here you can find more of our music videos.

  A Mathematical Artist whose Work I Like

  Dan Jiji does work with thousands of straight lines. Very cool patterns emerge. See this work for example.