User:Jesse Bloom

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Contact Info

Jesse Bloom
Jesse Bloom
  • Jesse Bloom
  • Division of Biology
  • California Institute of Technology
  • MC 147-75
  • 1200 E California Blvd
  • Pasadena, CA 91125
  • jesse.bloom@gmail.com

I am currently a Beckman Institute Postdoctoral Scholar working with Dr. David Baltimore at Caltech.

Education

  • 2007, PhD in Chemistry from the California Institute of Technology. Primary research with Dr. Frances Arnold in the Department of Chemical Engineering. Also performed work with Dr. Christoph Adami and Dr. Claus Willke.
  • 2002, MPhil in Theoretical Chemistry from Cambridge University. Performed research with Dr. David Wales.
  • 2001, BS in Biological Chemistry from the University of Chicago. Performed research with Dr. Susan Lindquist.

Here is a PDF copy of my CV: Media:Bloom_CV_2.pdf

Research interests

I am interested in the molecular evolution and engineering of proteins and viruses. My research employs both experimental and computational techniques.

Publications

  1. Bloom JD and Glassman MJ. Inferring stabilizing mutations from protein phylogenies: application to influenza hemagglutinin. PLoS Comput Biol 2009 Apr; 5(4) e1000349. doi:10.1371/journal.pcbi.1000349 pmid:19381264. PubMed HubMed PubGet [PLoSCompBio2009]
  2. Bloom JD and Arnold FH. In the light of directed evolution: pathways of adaptive protein evolution. Proc Natl Acad Sci U S A 2009 Jun 16; 106 Suppl 1 9995-10000. doi:10.1073/pnas.0901522106 pmid:19528653. PubMed HubMed PubGet [PNAS2009]
  3. Dong J, Bloom JD, Goncharov V, Chattopadhyay M, Millhauser GL, Lynn DG, Scheibel T, and Lindquist S. Probing the role of PrP repeats in conformational conversion and amyloid assembly of chimeric yeast prions. J Biol Chem 2007 Nov 23; 282(47) 34204-12. doi:10.1074/jbc.M704952200 pmid:17893150. PubMed HubMed PubGet [JBC2007]
  4. Li Y, Drummond DA, Sawayama AM, Snow CD, Bloom JD, and Arnold FH. A diverse family of thermostable cytochrome P450s created by recombination of stabilizing fragments. Nat Biotechnol 2007 Sep; 25(9) 1051-6. doi:10.1038/nbt1333 pmid:17721510. PubMed HubMed PubGet [NatBiotech2007]
  5. Bloom JD, Lu Z, Chen D, Raval A, Venturelli OS, and Arnold FH. Evolution favors protein mutational robustness in sufficiently large populations. BMC Biol 2007 Jul 17; 5 29. doi:10.1186/1741-7007-5-29 pmid:17640347. PubMed HubMed PubGet [BMCBiol2007]
  6. Bloom JD, Romero PA, Lu Z, and Arnold FH. Neutral genetic drift can alter promiscuous protein functions, potentially aiding functional evolution. Biol Direct 2007 Jun 28; 2 17. doi:10.1186/1745-6150-2-17 pmid:17598905. PubMed HubMed PubGet [BiolDirect2007]
  7. Bloom JD, Arnold FH, and Wilke CO. Breaking proteins with mutations: threads and thresholds in evolution. Mol Syst Biol 2007; 3 76. doi:10.1038/msb4100119 pmid:17262035. PubMed HubMed PubGet [MolSystBiol2007]
  8. Bloom JD, Raval A, and Wilke CO. Thermodynamics of neutral protein evolution. Genetics 2007 Jan; 175(1) 255-66. doi:10.1534/genetics.106.061754 pmid:17110496. PubMed HubMed PubGet [Genetics2007]
  9. Bloom JD, Drummond DA, Arnold FH, and Wilke CO. Structural determinants of the rate of protein evolution in yeast. Mol Biol Evol 2006 Sep; 23(9) 1751-61. doi:10.1093/molbev/msl040 pmid:16782762. PubMed HubMed PubGet [MBE2006]
  10. Otey CR, Landwehr M, Endelman JB, Hiraga K, Bloom JD, and Arnold FH. Structure-guided recombination creates an artificial family of cytochromes P450. PLoS Biol 2006 May; 4(5) e112. doi:10.1371/journal.pbio.0040112 pmid:16594730. PubMed HubMed PubGet [PLoSBiol2006]
  11. Bloom JD, Labthavikul ST, Otey CR, and Arnold FH. Protein stability promotes evolvability. Proc Natl Acad Sci U S A 2006 Apr 11; 103(15) 5869-74. doi:10.1073/pnas.0510098103 pmid:16581913. PubMed HubMed PubGet [PNAS2006]
  12. Drummond DA, Bloom JD, Adami C, Wilke CO, and Arnold FH. Why highly expressed proteins evolve slowly. Proc Natl Acad Sci U S A 2005 Oct 4; 102(40) 14338-43. doi:10.1073/pnas.0504070102 pmid:16176987. PubMed HubMed PubGet [PNAS2005b]
  13. Scheibel T, Bloom J, and Lindquist SL. The elongation of yeast prion fibers involves separable steps of association and conversion. Proc Natl Acad Sci U S A 2004 Feb 24; 101(8) 2287-92. pmid:14983002. PubMed HubMed PubGet [PNAS2004]
  14. Wilke CO, Bloom JD, Drummond DA, and Raval A. Predicting the tolerance of proteins to random amino acid substitution. Biophys J 2005 Dec; 89(6) 3714-20. doi:10.1529/biophysj.105.062125 pmid:16150971. PubMed HubMed PubGet [BiophysJ2005]
  15. Bloom JD, Meyer MM, Meinhold P, Otey CR, MacMillan D, and Arnold FH. Evolving strategies for enzyme engineering. Curr Opin Struct Biol 2005 Aug; 15(4) 447-52. doi:10.1016/j.sbi.2005.06.004 pmid:16006119. PubMed HubMed PubGet [CurrOpinStructBiol2005]
  16. Bloom JD, Silberg JJ, Wilke CO, Drummond DA, Adami C, and Arnold FH. Thermodynamic prediction of protein neutrality. Proc Natl Acad Sci U S A 2005 Jan 18; 102(3) 606-11. doi:10.1073/pnas.0406744102 pmid:15644440. PubMed HubMed PubGet [PNAS2005]
  17. Bloom JD and Adami C. Evolutionary rate depends on number of protein-protein interactions independently of gene expression level: response. BMC Evol Biol 2004 Jun 1; 4 14. doi:10.1186/1471-2148-4-14 pmid:15171796. PubMed HubMed PubGet [BMCEvolBiol2004]
  18. Bloom JD, Wilke CO, Arnold FH, and Adami C. Stability and the evolvability of function in a model protein. Biophys J 2004 May; 86(5) 2758-64. doi:10.1016/S0006-3495(04)74329-5 pmid:15111394. PubMed HubMed PubGet [BiophysJ2004]
  19. Bloom JD and Adami C. Apparent dependence of protein evolutionary rate on number of interactions is linked to biases in protein-protein interactions data sets. BMC Evol Biol 2003 Oct 2; 3 21. doi:10.1186/1471-2148-3-21 pmid:14525624. PubMed HubMed PubGet [BMCEvolBiol2003]
  20. Scheibel T, Kowal AS, Bloom JD, and Lindquist SL. Bidirectional amyloid fiber growth for a yeast prion determinant. Curr Biol 2001 Mar 6; 11(5) 366-9. pmid:11267875. PubMed HubMed PubGet [CurrBiol2001]
All Medline abstracts: PubMed HubMed

Software

The PIPS (Phylogenetic Inference of Protein Stability) package infers the effects of mutations on protein stability using sequences of known phylogeny. To download the source code for this package, click here. While the source code is heavily documented, unfortunately this version does not come with any user manual or installation guide, so you'll have to figure it out on your own. An improved and more user-friendly version is currently under development.

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