the Theory of Molecular Machines
Bits measure biological conservation!
|Brief overview: Tom Schneider is best known for inventing sequence logos, a computer graphic depicting patterns in DNA, RNA or protein that is now widely used by molecular biologists. Logos are only the beginning, however, as the information theory measure used to compute them gives results in bits. But why would a binding site have some number of bits? This led to a simple theory: the number of bits in the DNA binding site of a protein is the number needed to find the sites in the genome. Click on the dinosaur to see how these evolve! Next Tom asked how are bits related to binding energy? He solved this problem by using a version of the second law of thermodynamics to convert the bits to the energy needed to select them. Dividing the bits used to define a binding site by the bits that could have been selected for the given energy, he then discovered that the efficiency of DNA binding site selections is near 70% and he constructed a theory to explain this result. Schneider has a number of nanotechnology patents derived in part from this theory.|
--- Richard Dawkins, The Blind Watchmaker, 1986, Norton, p. 112.
|Note: These pages use two addional windows, a glossary and references. You can use frames in the bar to the left or launch them separately by clicking on these links. Once you have launched the windows, you can instantly look up papers or get glossary definitions. You can try this with the icons to the right in the green bar.|
were invented here!
were invented here!
how DNA gets information!
Sphere packing -
Molecular efficiency -
a measure of biological states
|Recommendations for Making Sequence Logos|
Publications using this server (PDF)
Publications using this server (text)
This server is recommended by the American College of Medical Genetics.
osmotic: Density of σ70 promoter-like sites in the intergenic regions dictates the redistribution of RNA polymerase during osmotic stress in Escherichia coli
Zhe Sun, Cedric Cagliero, Jerome Izard, Yixiong Chen, Yan Ning Zhou, William F Heinz, Thomas D Schneider and Ding Jun Jin
|Presentation: Evolution in a Nutshell at Science UNRESTRICTED 2019 May 07. as of 20l9 Mar 15.|
What is a Preprint? as of 2019 Feb 15
Restriction enzymes use a 24 dimensional coding space to recognize 6 base long DNA sequences.
Thomas D. Schneider and Vishnu Jejjala
|Presentation: Evolution in a Nutshell at Science UNRESTRICTED 2018 May 03. as of 20l8 May 01.|
|Video and slides for my 2016 "Information Theory in Biology" talk in Kanpur India are now available on the Videos page as of 2017 Dec 27.|
|Glossary: Reviews of the book: A Mind at Play by Jimmy Soni and Rob Goodman, 2017 as of 2017 Sep 11.|
Mac OS X Binary versions
of the Delila system programs were released in a single zip directory:
|Presentation: Evolution in a Nutshell at Science UNRESTRICTED 2017 May 11. as of 2017 May 10.|
|talk: "Three Principles of Biological States: Ecology and Cancer" at the University of Missouri Life Sciences Week, 1:15 p.m. April 11 in the Monsanto Auditorium at Bond Life Sciences Center.|
|paper: Qian.Adhya2016 Z. Qian, A. Trostel, D. E. A. Lewis, S. Jun Lee, X. He, A. M. Stringer, J. T. Wade, T. D. Schneider, T. Durfee, and S. Adhya. Genome-Wide Transcriptional Regulation and Chromosome Structural Arrangement by GalR in E. coli Front Mol Biosci, 3:74, 2016. http://dx.doi.org/10.3389/fmolb.2016.00074 as of 2016 Nov 21|
|program upgrade: The lister program has been upgraded so that multi-part sequence walkers are now completely connected using vertical lines along with the rainbow horizontal connections: as of 2016 Oct 15|
"Information Theory in Biology"
at the meeting
Department of Electrical Engineering
Indian Institute of Technology, Kanpur, India,
Wednesday, October 19th, 2016.
Speaker: Thomas Schneider, National Institute of Health, USA
In this talk I will sweep across the major ideas I have developed using information theory to understand biology (see https://alum.mit.edu/www/toms/). We will begin with measuring the information of protein or RNA binding sites on DNA or RNA (Rsequence, bits per site) using Claude Shannon's information theory. The resulting information curve can be displayed by the now-popular graphical method of sequence logos which we invented. The total information of binding sites (area under a logo) is predicted by the genome size and number of sites (Rfrequency, bits per site), and this leads to a model for the evolution of binding sites which you can run (https://alum.mit.edu/www/toms/papers/ev/). I will then introduce how to apply the same theory to individual binding sites, sequence walkers. An important question is the relationship between binding site information and the binding energy. This lead to my discovery that many molecular systems are 70% efficient. Surprisingly, the mathematics that explains 70% efficiency applies to all biological systems that have distinct states.as of 2016 Oct 05.
|Presentation: Evolution in a Nutshell at Science UNRESTRICTED 2015 Apr 09. as of 2015 Apr 06.|
|talk: Three Principles of Biological States: Ecology and Cancer by Tom Schneider 2014 Oct 29 Wednesday 09:04-10:13 at the meeting Biological and Bio-Inspired Information Theory (14w5170) at the Banff International Research Station (BIRS), Banff, Canada.|
Escherichia coli sigma38 promoters use two UP elements
instead of a -35
NIH Research Festival 2014. Wednesday, September 24, 2014 - Poster Session IV as of 2014 Sep 20.
Three Universal Principles of Biological States
Bibliography: suggested reading
Frederick Faculty Seminar Series, Campus: NCI at Frederick, Location: Building 549 Auditorium 2014 June 11 12:00 PM to 1:30 PM. as of 2014 May 14.
|Patent: Nanoprobe, US Patent No. 8,703,734 Issued April 22, 2014, Ilya Lyakhov, Thomas D. Schneider, and Danielle Needle. as of 2014 Apr 28.|
|Paper: An important paper was published confirming for the first time my 70% efficiency discovery: Analysis of DevR regulated genes in Mycobacterium tuberculosis. Bandyopadhyay A, Biswas S, Maity AK, Banik SK. Syst Synth Biol. 2014 Mar;8(1):3-20. (PubMed link, preprint at arxiv.) They observed that the DevR protein has 66% isothermal efficiency. as of 2014 Mar 11|
|talk: Why is the Genetic Code Degenerate? at Bits <-> Biology 2014 May 1, Building E14, 6th floor, MIT My presentation is available as a PDF created by PowerDot. VIDEO LINK as of 2014 Feb 28|
|paper: Average of Fractions a trivial but surprising result. as of 2014 Jan 19|
|talk: Why is the Genetic Code Degenerate? at the meeting Mathematical and Statistical Models for Genetic Coding September 26th to 28th 2013, Mannheim, Germany as of 2013 Sep 18.|
|paper: Confirmation of Base Flipping in Transcriptional Initiation Predicted by Information Theory in our flexprom paper! as of 2012 Nov 28.|
|talk: Sequence Logos and the Helix of DNA (PDF) as of 2012 nov 09.|
|Patent: Nanoprobe, by Ilya Lyakhov, Thomas D. Schneider, and Danielle Needle. Allowed 2012 Sep 24 as of 2012 Oct 05.|
|video: TechAlliance presents National Biotechnology Week - Cytognomix Inc. as of 2012 Sep 19. The technology Pete Rogan is talking about is the individual information method developed in my lab.|
|paper: Promoter variants in the MSMB gene associated with prostate cancer regulate MSMB/NCOA4 fusion transcripts as of 2012 Jun 05.|
|Presentation: Evolution in a Nutshell at Science UNRESTRICTED 2012 Apr 24. as of 2012 Apr 23.|
|paper: An unusual feature associated with LEE1 P1 promoters in enteropathogenic Escherichia coli (EPEC) as of 2012 Mar 23.|
Evolution of Binding Sites
by Tom Schneider.
PDF version of the talk is available.
This talk emphasizes the Shannon uncertainty formula.
See Information Theory Primer
to learn more.
as of 2012 Mar 15
|Patent: Molecular motor, United States Patent: 8,086,432 by Thomas D. Schneider and Ilya Gennadiyevich Lyakhov. Issued 2011 Dec 27. Freepatentsonline for 8086432. as of 2012 Jan 09.|
Why Do Restriction Enzymes Prefer 4 and 6 Base DNA Sequences?
Bibliography: suggested reading
Frederick Faculty Seminar Series, Campus: NCI at Frederick, Location: Building 549 Auditorium 2012 Jan 11 12:00 PM to 1:30 PM. as of 2011 Dec 07.
|paper: A Brief Review of Molecular Information Theory is now available at PubMed, PubMedCentral as of 2011 Dec 02.|
|New pages: Mathematical Terms of Biological Information Theory. as of 2011 Nov 12.|
Peter K. Rogan.
Rapid and comprehensive identification of prokaryotic organisms.
In this patent Pete Rogan made a clever use of sequence logos.
See figure 2: this is a logo of 16S rRNAs. Pete
used the logo to
chose well conserved parts (into which to put PCR primers)
surrounding less conserved parts (which are different for
Thus the sequence of the fragment obtained can rapidly
identify a bacterial species.
The patent will issue on December 13th as US Pat 8,076,104.
as of 2011 Sep 17.
|Article: Gaining Skills That Last a Lifetime (PDF) an article about Elaine (Bucheimer) Cagnina, former Werner H. Kirsten student intern working with Tom Schneider at NCI at Frederick in 1995-1996 in the March 2011 NCI at Frederick Poster, page 13 (whole issue, PDF) as of 2011 May 24.|
|Program upgrade: MakeLogo now has Form Control. The forms are: normal logo, varlogo, equallogo, rarelogo and rareequallogo. as of 2011 Mar 09.|
|Review of James Gleick's interview with NPR as of 2011 Mar 09.|
|Presentation: Evolution in a Nutshell at Science UNRESTRICTED 2011 May 4. as of 2011 Feb 21.|
|Talk: by Tom Schneider. 70% efficiency of bistate molecular machines explained by information theory, high dimensional geometry and evolutionary convergence, at the Electrical & Computer Engineering Colloquium Series Rutgers Department of Electrical and Computer Engineering, February 23, 2011. Host: Dr. Athina Petropulu and Dr. Christopher Rose. Slides from Tom's talk. as of 2011 Feb 11.|
|Review of Tillman.Russel1961 as of 2011 Feb 09.|
|US Patent 7,871,777 Issues: MedusaTM Sequencing by Thomas D. Schneider, Ilya Lyakhov and Danielle Needle. as of 2011 Jan 11.|
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