Links Related to DNA/Molecular Computation
Very much "under construction", these are collected for myself; hopefully useful to some others as well
http://barzilai.org/dna/links.html
New Updates
Preamble
  • There's Plenty of Room at the Bottom Feynman's visionary talk (1959).
    Surveys & Overviews
  • History of DNA computing ('94-'96)
  • Ogihara, Ray and Smith, 1997, Biomolecular computing--a shape of computing to come. SIGACT News on Complexity Theory 28(3):2-11.
  • Future Perspectives on Molecular Computing (from Hagiya's project, MCP).
    Adleman's Seminal Paper
  • Adleman's original paper (without pictures)
  • For original paper, see November 11, 1994 Science, (Vol. 266, pp. 1021-1024).
    Expositions
  • Summary by students in a Computational Biology course, of Adleman's paper.
  • The view from 30,000 feet of Adleman's paper.

  • For somewhat more technical/accurate expositions of Adleman's paper, see:
  • On the Path to Computation with DNA by David Gifford in Science Vol 266, 11/11/94, pp. 993-994.
  • A Partially transcribed online version of Gifford's exposition.

  • Computing with DNA by Adleman himself, Scientific American, August 1998.
  • Test Tube Computing with DNA by Keith Devlin in Math horizons April 1995
    Expositions in the Popular Press
  • Gene Genie (Originally appeared in Wired)
  • Nice Quotes by Adleman about Mathematics, from Gene Genie.
  • "A Vat of DNA may be computer of the future" NY Times article by Gina Kolada.
    First Followups to Adleman's Seminal Paper
  • Lipton's Speeding up Computation via Molecular Biology (postscript)   (Lipton's FTP dir)
  • Adleman's: On Constructing a Molecular Computer (postscript)
  • Summary/exposition as of early '97 of both '94 paper and "On Constructing..." by Adleman.
    Resources
  • HUGE bibliography of molecular computation
  • DNA Computers Page (AOL)
  • JUL 99 conference
  • Erik Winfree's References -- "where to start".
    Selected Background from Biochemistrcy/Genetics
  • A Gorgeous diagram: the human genome at four levels of detail.
  • Erik Winfree's References -- "where to start".
  • Basic molecular biology notions and Laboratory techniques with potential use for computation (Lila Kari)
  • Implementing models of DNA computing: Concerns from the laboratory
  • Microbiology 101 lab manual from Hurlbert
  • Agarose Gel Electrophoresis and PCR explained w/cartoons & animation.
  • PCR in a nutshell (click "animation")
  • Agarose gel electrophoresis
  • The Gene Machine
  • Microbiology textbook online
    Groups, Centers
  • USC Computational Biology
  • USC Molecular Science Lab with Adleman and Rothemund (includes Adleman's homepage)
  • European Molecular Computing Consortium
  • Molecular Computer Project (MCP) in Japan. With Java applet. (More info at UW site)
  • Leiden Center for Natural Computation
  • DNA Computing on surfaces Wisc. Chem.
  • Liverpool Biocomputation Group

    People
  • Eric Winfree and his Molecular Computation Page
  • David Harlan Wood who taught S98 course on DNA computing... incl  links to Abstracts from Summer '98 conference.
  • Sam Roweis
  • Paul Wilhelm Karl Rothemund's links and Touring Machine paper
  • Lila Kari with many links. See also her the arival of biological mathematics (postscript), another rexposition of Adleman '94.
  • Animesh Ray (ray@ar.biology.rochester.edu )
  • Irv Rabinovitz's links.
    Misc. Related Items

  • DNA, Computers, and Killer Apps (I Peterson at MAA's MathLAnd) (Lipton)
  • Federal storage dilemma looms (1/26/99, CNN).
  • Abstract on converting algorithms to operations on molecules.
  • DNA Based Computers II
  • RNA, computing for (chess) Knight Problem
  • implementing addition w/DNA computation (long, HTML)
  • Computing the Uncomputable (short)
  • On the Scalability...
    Nanotechnology
  • DNA makes tiny tweezers (8/10/00 BBC)
  • The Advantages of Nanotechnology   from   Nanotechnology page (Xerox).
  • Ned Seeman DNA for nano-tech (e.g. Truncated Octahedron) 
    "A major effort in our laboratory is devoted to DNA
Nanotechnology.The attachment of specific sticky ends to a branched
junction enables the construction of stick figures, whose edges are
double-stranded DNA. This approach has already been used to assemble a
cube and a truncated octahedron from DNA. Ultimate goals for this
approach include the assembly of a biochip computer and the rational
synthesis of periodic matter. It may also be possible to use this
methodology to do DNA Based Computing."
    Computer Science (Just a few links thrown together, not meant as reference)
  • Introduction to Cryptography
  • Lecture on SAT and NP-completeness
  • HPP via WWW
  • Marvin Minsky
    More Distant Relatives

    Using Computers to Analyze Genome
  • Click "a postscript copy" (motifs.ps) for "An algorithm for finding novel gaped motifs in DNA seqs"; also G Benson abstract.

    Quantum Computing
  • AMC97: Quantum, DNA, Optical computers
  • Quantum Computing
  • Quantum Computing another
  • Quantum Computing, Part III
  • Adleman on HIV search for "Adleman" on this page to find.
  • Combinatorial Chemistry

  • Brief History of Quantum computing is not so brief...
  • A short introduction to quantum computing
  • Intro to NMR