[CV] [Research] [Publications] [Software] [Media] [Collaborations]
Thomas Pfeiffer Program for Evolutionary Dynamics Harvard University One Brattle Square Cambridge MA 02138, USA pfeiffer @ fas.harvard.edu
[iHOP] [PubMed] [KEGG] [GoogleScholar] [ISCB] [EvolDir] [SMB]

CV

• 1994-1999  Studies of biophysics at the Humboldt-Universität zu Berlin, and at the Universidad Complutense de Madrid 
• 1999  Diploma thesis at the Humboldt-Universität zu Berlin, group of Theoretical Biophysics, supervised by  Stefan Schuster 
• 2000-2001  PhD position at the Friedrich-Miescher-Institut, Basel, group of Theoretical and Computational Biology, supervised by Sebastian Bonhoeffer 
• 2001-2003  PhD position at the group for Experimental Ecology and Theoretical Biology, ETH Zurich, supervised by Sebastian Bonhoeffer 
• 2003-2005  Research fellow at the ETH Computational Laboratory
• 2005-2010  Researcher at the Program of Evolutionary Dynamics at Harvard University, funded by Society in Science
• Since 2010 FQEB Prize Fellow at the Program of Evolutionary Dynamics at Harvard University, affiliated with Tufts Medical School and Harvard SEAS Computer Science
  

• Evolution of scientific knowledge. Publications in scientific journals contain a large fraction of scientific knowledge of mankind. The question of how this knowledge is obtained and how it evolves over time has fascinated philosophers - and a number of evolutionary biologists - for a long time. Using information from publication databases I aim to understand how scientific information is transferred from publication to publication and from researcher to researcher; how researchers choose their research topics; and what factors determine their success. Long-term perspective of my research project is to test theories for the evolution of knowledge such as Richard Dawkins concept of memes.
• Reciprocal altruism and the use of social information. Reciprocal altruism is a major explanation for the emergence of cooperation among unrelated individuals. Cooperation may be beneficial if it is reciprocated by other individuals in future interactions. In direct reciprocity, individuals reciprocate previous cooperative interactions with the present partner. In indirect reciprocity, cooperation may be reciprocated by individuals other than the present partner. Using computer simulations, I am studying which type of information (observed vs. experienced; individual-specific vs. unspecific) can be used by strategies of reciprocal altruism.
  
• Evolution of complex biochemical networks. Processes in living organisms are the result of interactions of biochemical compounds in highly complex networks. It is a major challenge in biology to understand the design and functioning of these networks. Since biochemical networks emerge as a result of Darwinian evolution it is a promising approach to study the impact of evolutionary processes on network design and functioning. In my research projects I am studying the consequences of tradeoffs between rate and yield of ATP-producing pathways, the emergence of crossfeeding in microbial populations, and the origin of "hub metabolites" in metabolic networks.
  

Publications

1. Pfeiffer T, Bertram L, Ioannnidis JPA. Quantifying Selective Reporting and the Proteus Phenomenon for Multiple Datasets with Similar Bias. PLoS ONE 6 (2010) e18362 [PLoS ONE] [Accompanying R code]
   
2. Pfeiffer T, Almenberg J. Prediction markets and their potential role in biomedical research - a review. Biosystems 102 (2010) 71-6. [Biosystems][PubMed]
   
3. Soyer OS, Pfeiffer T. Evolution under fluctuating environments  explaines observed robustness in metabolic networks. PLoS Comp Biol 6 (2010) e1000907. [PLoS][PubMed]
   
4. Almenberg J, Kittlitz K, Pfeiffer T. An experiment on prediction markets in science. Pl.oS ONE 4 (2009) e8500 [PLoS] [PubMed]
5. Rutte C, Pfeiffer T. Evolution of reciprocal altruism by copying of observed behavior. Current Science 97 (2009) 1573-8 [CurrSci] [PubMed]
6. Rand DG, Pfeiffer T. Systematic differences in citation count across publiction tracks at PNAS. PLoS ONE 4 (2009) e8092 [PLoS] [PubMed]
7. Novak M, Pfeiffer T, Ackermann M, Bonhoeffer S. Bacterial growth properties at low optical densities. Antonie Van Leeuwenhoek 96 (2009) 267-75 [PubMed]
8. Pfeiffer T, Hoffmann R. On the reliability of published research: An evaluation of protein interactions. PLoS ONE 4 (2009) e5996 [PubMed] [PLoS]
   
9. Rand DG, Pfeiffer T, Dreber A, Sheketoff R, Wernerfelt N, Benkler Y. From foe to friend: Tracing democratic in-group bias. PNAS  106 (2009) [PNAS] [PubMed]
10. Pfeiffer T, Rand DG, Dreber A. Decision-making in research tasks with sequential testing. PLoS ONE 4 (2009) e4607 [PubMed] [PLoS]
    
11. Schuster S, Kreft JU, Schroeter A, Pfeiffer T. Use of game-theoretical methods in biochemistry and biophysics. J Biol Phys 34 (2008) 1-17 [JBiolPhys] [PubMed]
    
12. Schuster S, Pfeiffer T, Fell DA. Is maximization of molar yield in metabolic networks a universal principle? JTB 252 (2008) 497-504 [PubMed]
    
13. Pfeiffer T, Hoffmann R. Temporal patterns of genes in scientific publications. PNAS 104 (2007) 12052-6 [PubMed] [PNAS]
    
14. Steiner UK, Pfeiffer T. Optimizing time and resource allocation trade-offs for investment in morphological and behavioral defense. Am Nat. 169 (2007) 118-29 [PubMed]
15. Pfeiffer T, Nowak MA. Digital cows grazing on digital grounds Current Biology (Essay) 22 (2006) R946-9 [PubMed]
16. Pfeiffer T, Nowak MA. All in the game. Nature (News & Views)  441(2006) 583-4. [Nature] [PubMed]
17. Novak M, Pfeiffer T, Lenski RE, Sauer U, Bonhoeffer S. Experimental evidence for an evolutionary trade-off between growth rate and yield in E. coli. Am Nat. 168 (2006) 242-51 [PubMed]
18. Soyer OS, Pfeiffer T, Bonhoeffer S. Simulating the evolution of signal transduction networks. JTB 241 (2006) 223-32. [PubMed]
19. Pfeiffer T, Soyer OS, Bonhoeffer S. Evolution of connectivity in metabolic networks. PLoS B 3 (2005) e228. [PLoS] [PubMed]
20. Pfeiffer T, Rutte C, Killingback T, Taborsky M, Bonhoeffer S. Evolution of cooperation by generalized reciprocity. Proceedings B 272 (2005) 1115-20. [ProcB] [PubMed]
21. Pfeiffer T, Schuster S. Game-theoretical approaches to studying the evolution of biochemical systems. TiBS 30 (2005) 20-5. [TiBS] [PubMed]
22. Pfeiffer T, Bonhoeffer S. Evolution of crossfeeding in microbial populations. Am Nat. 163 (2004) E126-35. [PubMed]
23. Pfeiffer T, Bonhoeffer S. An evolutionary scenario for the transition to undifferentiated multicellularity. PNAS 100 (2003) 1095-1098. [PNAS] [PubMed]
24. Schuster S, Klamt S, Weckwerth W, Moldenhauer F, Pfeiffer T. Use of network analysis of metabolic systems in bioengineering. Bioprocess Biosyst Eng. 24 (2002) 363-72
25. Pfeiffer T, Bonhoeffer S. Evolutionary consequences of tradeoffs between yield and rate of ATP production. Z Phys Chem. 216 (2002) 51-63
26. Schuster S, Pfeiffer T, Moldenhauer F, Koch I, Dandekar T. Exploring the pathway structure of metabolism: decomposition into subnetworks and application to Mycoplasma pneumoniae. Bioinformatics 18 (2002) 351-361. [Bioinformatics] [PubMed]
27. Pfeiffer T, Schuster S, Bonhoeffer S, Cooperation and competition in the evolution of ATP-producing pathways. Science 292 (2001) 504-7. [Science] [PubMed]
28. Pfeiffer T, Sanchez-Valdenebro I, Nuno JC, Montero F, Schuster S. METATOOL: for studying metabolic networks. Bioinformatics 15 (1999) 251-7. [PubMed]

[Publications on ResearcherID]

Software

METATOOL - for topological analysis of metabolic networks (elementary modes, kernel,enzyme subsets, ...)

MultiWeightFunction - R code for field-wide estimates of publication bias (see Pfeiffer et al. PLoS ONE 2011)

Media

• www.newsweek.com
  

• www.overcomingbias.com

• neuroskeptic.blogspot.com
  

• scienceblogs.com

• Deep Thoughts and Silliness (blog)
  

On the growth of literary yeast genes (17.07.2007, by Bob O'Hara)


• Science Life: ETH Life - das tägliche Webjournal

• Tagesberichte: ETH Life - das tägliche Webjournal
  

Collaborations

• Stefan Schuster (Bioinformatics, University of Jena), see also METATOOL
  
• Sebastian Bonhoeffer and Maja Novak (Theoretical Biology, ETH Zurich)
• Claudia Rutte (University of Lausanne)
  
• Robert Hoffmann (MSKCC/MIT), see also iHOP - Information Hyperlinked over Proteins
  
• Anna Dreber and Johan Almenberg (Stockholm School of Economics)
• Consensus Point