User:Tsbayer: Difference between revisions

From OpenWetWare
Jump to navigationJump to search
No edit summary
Line 1: Line 1:
=Travis Bayer=
=Travis Bayer=
I work on synthetic biology in the [[ Smolke]] Lab at [http://caltech.edu Caltech].  I used to work for the [[Ellington Lab]] doing directed evolution.


*I received a BS in Biology at the [http://www.utexas.edu/ University of Texas] working for [http://ellingtonlab.org  Andy Ellington].
*I am currently a grad student in [[Smolke|Christina Smolke's]] lab at [http://www.caltech.edu  Caltech].




===Interests===
==Research interests==


*Robustness and evolvability in biology
Biological systems are robust to change from a number of sources including fluctuating environments, stochastic cellular functions, and mutations in cellular components.  My current research explores how evolution has organized biological networks  to provide robustness to change (both in an organism's environment and over evolutionary timescales), and how we can rewire existing networks to be more or less robust to perturbation.  Future goals include understanding how network architecture constrains or promotes future adaptation, understanding robustness in disease and development, and using these "design principles" plus synthetic tools to engineer systems-level behavior in complex systems. 
*Engineering life with functional nucleic acids


==Publications==


===Publications===
Tabor JJ, Bayer TS, Simpson ZB , Levy M, Ellington AD. Operons are genetic noise insulators. Submitted. 2006.
<biblio>
#bayer5 pmid=16314457
#bayer4 pmid=15723047
#bayer3 pmid=15253644
#bayer2 pmid=12384610
#bayer1 pmid=12052180
</biblio>


*Tabor JJ, Bayer TS, Simpson ZB , Levy M, Ellington AD. Operons are genetic noise insulators. Submitted. 2006.


*Bayer TS, Smolke CD.  Programmable ligand-controlled riboregulators of eukaryotic gene expression.  ''Nature Biotechnology''. 2005 Mar;23(3):337-43.
==Etcetera==


*Bayer TS, Booth LN, Knudsen SM, Ellington AD.  Arginine-rich motifs present multiple interfaces for specific binding by RNA.  ''RNA''. 2005 Dec;11(12):1848-57.
*Tech talks: [[Smolke:Tech_21Aug06|21 August 2006]]


*Kirby R, Cho EJ, Gehrke B, Bayer T, Park YS, Neikirk DP, McDevitt JT, Ellington AD. Aptamer-based sensor arrays for the detection and      quantitation of proteins. ''Analytical Chemistry''. 2004 Jul 15;76(14):4066-75.  
*Social engineering:  Here in the Smolke lab, we also enjoy designing [[Smolke:Lab drinks|cocktails]]...


*Cox JC, Hayhurst A, Hesselberth J, Bayer TS, Georgiou G, Ellington AD.  Automated selection of aptamers against protein targets translated in vitro: from gene to aptamer. ''Nucleic Acids Research''. 2002 Oct 15;30(20):e108.
*[[LightCannon|Take pictures with coli]]


*Cox JC, Rajendran M, Riedel T, Davidson EA, Sooter LJ, Bayer TS, Schmitz-Brown M, Ellington AD. Automated acquisition of aptamer sequences.  ''Combinatorial Chemistry and High Throughput Screening''. 2002 Jun;5(4):289-99.
*[[Bi23_Syllabus|Syllabus]] for a class I taught about engineering biology with nucleic acids.


*[[Smolke:Happy_hours|Happy hour]] in and around Pasadena


===Bi23: Nucleic acids from origins to bioengineering===


Last term I got to teach a class that I made up.  It was mostly about synthetic biology, although I tried to talk about origins some.  How biological function emerges, whether by human design or natural evolution, is a highly entertaining topic that draws on all kinds of science and engineering fields (and philosophy too!).  Then the class evolved into a discussion of coming up with clever 'biohacks', or ways to reprogram functions of natural and synthetic genetic systems.  Mostly for devious ends.  I'll put up the slides and notes for it, and some of our hacks...
==Contact==


[[Bi23 Syllabus]]
*email:  tsbayer AT caltech.edu


[[Some Bi23 projects]]
*phone:  626.395.2680


*mail:  MC 210-41  Pasadena, CA  91125


===Nucleic acid design===


Much of my work could be termed 'nucleic acid design'.  The basic idea is to engineer molecules with specified functions - functions like binding, catalysis, gene regulation, or fluorescent signaling.  I would like to use this space to put up some of the "design principles" that I have found helpful (hopefully this will augment what can be found in publications).  There is an entire community doing this kind of work:  the Ellington, Breaker, Liu, Smolke, Pierce, labs, among many others.  Check out [[Jeff Tabor]]'s stuff to start with.
[[Controlling gene expression]]: Riboregulators, riboswitches, RNAi...
[[The Wide World of Aptamers]] - and the people who love them...
[[Building Better Biosensors]]
===Contact===
*Email
user: tsbayer
server: caltech.edu
*Phone
626.395.2680
*Mail
MC 210-41
Pasadena, CA  91125
==Life imitates art, literally==
[[Image:cannon.jpg|thumb|left|300px|Bacterial photograph by [[User:Justinhlo | Justin Lo]], Course 20 major at MIT]]
<br style="clear:both" />
[http://www.mitcannon.com MIT steals our cannon]
[http://www.flemingcannon.com  Caltech gets it back]
[[LightCannon]] - take your own bacterial photographs!
==Protocols and Recipes==
Protocols
Recipes and other stuff
*[[Smolke:Coffee|Lab coffee]]
*[[Smolke:Lab drinks|Lab drinks]]


==Fun with geography==
==Fun with geography==

Revision as of 16:38, 24 August 2006

Travis Bayer


Research interests

Biological systems are robust to change from a number of sources including fluctuating environments, stochastic cellular functions, and mutations in cellular components. My current research explores how evolution has organized biological networks to provide robustness to change (both in an organism's environment and over evolutionary timescales), and how we can rewire existing networks to be more or less robust to perturbation. Future goals include understanding how network architecture constrains or promotes future adaptation, understanding robustness in disease and development, and using these "design principles" plus synthetic tools to engineer systems-level behavior in complex systems.


Publications

Tabor JJ, Bayer TS, Simpson ZB , Levy M, Ellington AD. Operons are genetic noise insulators. Submitted. 2006.

  1. Bayer TS, Booth LN, Knudsen SM, and Ellington AD. Arginine-rich motifs present multiple interfaces for specific binding by RNA. RNA. 2005 Dec;11(12):1848-57. DOI:10.1261/rna.2167605 | PubMed ID:16314457 | HubMed [bayer5]
  2. Bayer TS and Smolke CD. Programmable ligand-controlled riboregulators of eukaryotic gene expression. Nat Biotechnol. 2005 Mar;23(3):337-43. DOI:10.1038/nbt1069 | PubMed ID:15723047 | HubMed [bayer4]
  3. Kirby R, Cho EJ, Gehrke B, Bayer T, Park YS, Neikirk DP, McDevitt JT, and Ellington AD. Aptamer-based sensor arrays for the detection and quantitation of proteins. Anal Chem. 2004 Jul 15;76(14):4066-75. DOI:10.1021/ac049858n | PubMed ID:15253644 | HubMed [bayer3]
  4. Cox JC, Hayhurst A, Hesselberth J, Bayer TS, Georgiou G, and Ellington AD. Automated selection of aptamers against protein targets translated in vitro: from gene to aptamer. Nucleic Acids Res. 2002 Oct 15;30(20):e108. DOI:10.1093/nar/gnf107 | PubMed ID:12384610 | HubMed [bayer2]
  5. Cox JC, Rajendran M, Riedel T, Davidson EA, Sooter LJ, Bayer TS, Schmitz-Brown M, and Ellington AD. Automated acquisition of aptamer sequences. Comb Chem High Throughput Screen. 2002 Jun;5(4):289-99. DOI:10.2174/1386207023330291 | PubMed ID:12052180 | HubMed [bayer1]

All Medline abstracts: PubMed | HubMed


Etcetera

  • Social engineering: Here in the Smolke lab, we also enjoy designing cocktails...
  • Syllabus for a class I taught about engineering biology with nucleic acids.


Contact

  • email: tsbayer AT caltech.edu
  • phone: 626.395.2680
  • mail: MC 210-41 Pasadena, CA 91125


Fun with geography

<html> <a href="http://clustrmaps.com/counter/maps.php?url=http://openwetware.org/wiki/User:Tsbayer" id="clustrMapsLink"><img src="http://clustrmaps.com/counter/index2.php?url=http://openwetware.org/wiki/User:Tsbayer" border=1 alt="Locations of visitors to this page"onError="this.onError=null; this.src='http://www.meetomatic.com/images/clustrmaps-back-soon.jpg'; document.getElementById('clustrMapsLink').href='http://clustrmaps.com/'"> </a> </html>

Retrieved from "https://openwetware.org/mediawiki/index.php?title=User:Tsbayer&oldid=64505"