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Contact details +6492136273

Prof Thomas Pfeiffer PhD

Professor in Computational Biology/Biochemistry

New Zealand Institute for Advanced Study

Professional

Qualifications

  • Doctor of Philosophy - Swiss Federal Institute of Technology Zurich (2004)

Research Expertise

Research Interests

Game theory; Decision making; Meta-science; Metabolic Biochemistry; Computational Biology

Area of Expertise

Field of research codes
Biochemistry and Cell Biology (060100): Biological Adaptation (060303): Biological Sciences (060000): Cell Metabolism (060104): Evolutionary Biology (060300): Life Histories (060308): Synthetic Biology (060113): Systems Biology (060114)

Research Projects

Summary of Research Projects

Position Current Completed
Project Leader 1 4

Completed Projects

Project Title: Predict to decide: Investigating decision markets in theory, experiments and practical applications

Date Range: 2018 - 2022

Funding Body: Royal Society of New Zealand

Project Team:

Research Outputs

Journal

Schaerer, M., Plessis, CD., Nguyen, MHB., Aert, RCMV., Tiokhin, L., Lakens, D., . . . Lemay, EP. (2023). On the trajectory of discrimination: A meta-analysis and forecasting survey capturing 44 years of field experiments on gender and hiring decisions. Organizational Behavior and Human Decision Processes. 179
[Journal article]Authored by: Pfeiffer, T.
Gordon, M., Bishop, M., Chen, Y., Dreber, A., Goldfedder, B., Holzmeister, F., . . . Pfeiffer, T. (2022). Forecasting the publication and citation outcomes of COVID-19 preprints. Royal Society Open Science. 9(9)
[Journal article]Authored by: Pfeiffer, T.
Delios, A., Clemente, EG., Wu, T., Tan, H., Wang, Y., Gordon, M., . . . Idzikowska, K. (2022). Examining the generalizability of research findings from archival data. Proceedings of the National Academy of Sciences of the United States of America. 119(30)
[Journal article]Authored by: Pfeiffer, T.
Gordon, M., & Pfeiffer, T. (2021). Can scientists change their minds?. Nature Human Behaviour. 5(12), 1598-1599
[Journal article]Authored by: Pfeiffer, T.
Viganola, D., Buckles, G., Chen, Y., Diego-Rosell, P., Johannesson, M., Nosek, BA., . . . Dreber, A. (2021). Using prediction markets to predict the outcomes in the Defense Advanced Research Projects Agency's next-generation social science programme. Royal Society Open Science. 8(7)
[Journal article]Authored by: Pfeiffer, T.
Gordon, M., Viganola, D., Dreber, A., Johannesson, M., & Pfeiffer, T. (2021). Predicting replicability-Analysis of survey and prediction market data from large-scale forecasting projects. PLoS ONE. 16(4 April)
[Journal article]Authored by: Pfeiffer, T.
Tierney, W., Hardy, J., Ebersole, CR., Viganola, D., Clemente, EG., Gordon, M., . . . Hammersley, JJ. (2021). A creative destruction approach to replication: Implicit work and sex morality across cultures. Journal of Experimental Social Psychology. 93
[Journal article]Authored by: Pfeiffer, T.
Ebersole, CR., Mathur, MB., Baranski, E., Bart-Plange, DJ., Buttrick, NR., Chartier, CR., . . . Montealegre, A. (2020). Many Labs 5: Testing Pre-Data-Collection Peer Review as an Intervention to Increase Replicability. Advances in Methods and Practices in Psychological Science. 3(3), 309-331
[Journal article]Authored by: Pfeiffer, T.
Tierney, W., Hardy, JH., Ebersole, CR., Leavitt, K., Viganola, D., Clemente, EG., . . . Marsh, MS. (2020). Creative destruction in science. Organizational Behavior and Human Decision Processes. 161, 291-309
[Journal article]Authored by: Pfeiffer, T.
Gordon, M., Viganola, D., Bishop, M., Chen, Y., Dreber, A., Goldfedder, B., . . . Pfeiffer, T. (2020). Are replication rates the same across academic fields? Community forecasts from the DARPA SCORE programme. Royal Society Open Science. 7(7), Retrieved from https://royalsocietypublishing.org/doi/10.1098/rsos.200566
[Journal article]Authored by: Pfeiffer, T.
Landy, JF., Liam, M., Ding, IL., Viganola, D., Tierney, W., Dreber, A., . . . Hilgard, J. (2020). Crowdsourcing Hypothesis Tests: Making transparent how design choices shape research results. Psychological Bulletin. 146(5), 451-479
[Journal article]Authored by: Pfeiffer, T.
Forsell, E., Viganola, D., Pfeiffer, T., Almenberg, J., Wilson, B., Chen, Y., . . . Dreber, A. (2019). Predicting replication outcomes in the Many Labs 2 study. Journal of Economic Psychology. 75
[Journal article]Authored by: Pfeiffer, T.
Viganola, D., Eitan, O., Inbar, Y., Dreber, A., Johannesson, M., Pfeiffer, T., . . . Uhlmann, EL. (2018). Datasets from a research project examining the role of politics in social psychological research. Scientific Data. 5
[Journal article]Authored by: Pfeiffer, T.
Camerer, CF., Dreber, A., Holzmeister, F., Ho, TH., Huber, J., Johannesson, M., . . . Wu, H. (2018). Evaluating the replicability of social science experiments in Nature and Science between 2010 and 2015. Nature Human Behaviour. 2(9), 637-644
[Journal article]Authored by: Pfeiffer, T.
Eitan, O., Viganola, D., Inbar, Y., Dreber, A., Johannesson, M., Pfeiffer, T., . . . Uhlmann, EL. (2018). Is research in social psychology politically biased? Systematic empirical tests and a forecasting survey to address the controversy. Journal of Experimental Social Psychology. 79, 188-199
[Journal article]Authored by: Pfeiffer, T.
Camerer, CF., Dreber, A., Forsell, E., Ho, TH., Huber, J., Johannesson, M., . . . Wu, H. (2016). Evaluating replicability of laboratory experiments in economics. Science. 351(6280), 1433-1436 Retrieved from http://science.sciencemag.org/content/351/6280
[Journal article]Authored by: Pfeiffer, T.
Widder, S., Allen, RJ., Pfeiffer, T., Curtis, TP., Wiuf, C., Sloan, WT., . . . Wilmes, P. (2016). Challenges in microbial ecology: Building predictive understanding of community function and dynamics. ISME Journal. 10(11), 2557-2568
[Journal article]Authored by: Pfeiffer, T.
Dreber, A., Pfeiffer, T., Almenberg, J., Isaksson, S., Wilson, B., Chen, Y., . . . Wachter, KW. (2015). Using prediction markets to estimate the reproducibility of scientific research. Proceedings of the National Academy of Sciences of the United States of America. 112(50), 15343-15347
[Journal article]Authored by: Pfeiffer, T.
Munafo, MR., Pfeiffer, T., Altmejd, A., Heikensten, E., Almenberg, J., Bird, A., . . . Dreber, A. (2015). Using prediction markets to forecast research evaluations. Royal Society Open Science. 2(10)
[Journal article]Authored by: Pfeiffer, T.
Pfeiffer, T., & Morley, A. (2014). An evolutionary perspective on the Crabtree effect. Frontiers in Molecular Biosciences. 1(OCT)
[Journal article]Authored by: Pfeiffer, T.
Okeke, IN., Manning, RS., & Pfeiffer, T. (2014). Diagnostic schemes for reducing epidemic size of african viral hemorrhagic fever outbreaks. Journal of Infection in Developing Countries. 8(9), 1148-1159
[Journal article]Authored by: Pfeiffer, T.
Pfeiffer, T., Gao, XA., Mao, A., Chen, Y., & Rand, DG. (2012). Adaptive polling for information aggregation. Proceedings of the National Conference on Artificial Intelligence. 1, 122-128
[Journal article]Authored by: Pfeiffer, T.
Evangelou, E., Siontis, KC., Pfeiffer, T., & Ioannidis, JPA. (2012). Perceived information gain from randomized trials correlates with publication in high-impact factor journals. Journal of Clinical Epidemiology. 65(12), 1274-1281
[Journal article]Authored by: Pfeiffer, T.
Evangelou, E., Siontis, KC., Pfeiffer, T., & Ioannidis, JPA. (2012). Perceived information gain from randomized trials correlates with publication in high-impact factor journals. Journal of Clinical Epidemiology.
[Journal article]Authored by: Pfeiffer, T.
Pfeiffer, T., Tran, L., Krumme, C., & Rand, DG. (2012). The value of reputation. Journal of the Royal Society Interface. 9(76), 2791-2797
[Journal article]Authored by: Pfeiffer, T.
Pfeiffer, T., Bertram, L., & Ioannidis, JPA. (2011). Quantifying selective reporting and the Proteus phenomenon for multiple datasets with similar bias. PLoS ONE. 6(3)
[Journal article]Authored by: Pfeiffer, T.
Soyer, OS., & Pfeiffer, T. (2010). Evolution under fluctuating environments explains observed robustness in metabolic networks. PLoS Computational Biology. 6(8)
[Journal article]Authored by: Pfeiffer, T.
Pfeiffer, T., & Almenberg, J. (2010). Prediction markets and their potential role in biomedical research - A review. BioSystems. 102(2-3), 71-76
[Journal article]Authored by: Pfeiffer, T.
Novak, M., Pfeiffer, T., Ackermann, M., & Bonhoeffer, S. (2009). Bacterial growth properties at low optical densities. Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology. 96(3), 267-274
[Journal article]Authored by: Pfeiffer, T.
Rutte, C., & Pfeiffer, T. (2009). Evolution of reciprocal altruism by copying observed behaviour. Current Science. 97(11), 1573-1578
[Journal article]Authored by: Pfeiffer, T.
Almenberg, J., Kittlitz, K., & Pfeiffer, T. (2009). An experiment on prediction markets in science. PLoS ONE. 4(12)
[Journal article]Authored by: Pfeiffer, T.
Rand, DG., & Pfeiffer, T. (2009). Systematic differences in impact across publication tracks at PNAS. PLoS ONE. 4(12)
[Journal article]Authored by: Pfeiffer, T.
Pfeiffer, T., & Hoffmann, R. (2009). Large-scale assessment of the effect of popularity on the reliability of research. PLoS ONE. 4(6)
[Journal article]Authored by: Pfeiffer, T.
Rand, DG., Pfeiffer, T., Dreber, A., Sheketoff, RW., Wernerfelt, NC., & Benkler, Y. (2009). Dynamic remodeling of in-group bias during the 2008 residential election. Proceedings of the National Academy of Sciences of the United States of America. 106(15), 6187-6191
[Journal article]Authored by: Pfeiffer, T.
Pfeiffer, T., Rand, DG., & Dreber, A. (2009). Decision-making in research tasks with sequential testing. PLoS ONE. 4(2)
[Journal article]Authored by: Pfeiffer, T.
Schuster, S., Kreft, JU., Schroeter, A., & Pfeiffer, T. (2008). Use of game-theoretical methods in biochemistry and biophysics. Journal of Biological Physics. 34(1-2 SPEC. ISS.), 1-17
[Journal article]Authored by: Pfeiffer, T.
Schuster, S., Pfeiffer, T., & Fell, DA. (2008). Is maximization of molar yield in metabolic networks favoured by evolution?. Journal of Theoretical Biology. 252(3), 497-504
[Journal article]Authored by: Pfeiffer, T.
Steiner, UK., & Pfeiffer, T. (2007). Optimizing time and resource allocation trade-offs for investment into morphological and behavioral defense. American Naturalist. 169(1), 118-129
[Journal article]Authored by: Pfeiffer, T.
Pfeiffer, T., & Hoffmann, R. (2007). Temporal patterns of genes in scientific publications. Proceedings of the National Academy of Sciences of the United States of America. 104(29), 12052-12056
[Journal article]Authored by: Pfeiffer, T.
Soyer, OS., Pfeiffer, T., & Bonhoeffer, S. (2006). Simulating the evolution of signal transduction pathways. JOURNAL OF THEORETICAL BIOLOGY. 241(2), 223-232
[Journal article]Authored by: Pfeiffer, T.
Pfeiffer, T., & Nowak, MA. (2006). Climate change: All in the game. Nature. 441(7093), 583-584
[Journal article]Authored by: Pfeiffer, T.
Novak, M., Pfeiffer, T., Lenski, RE., Sauer, U., & Bonhoeffer, S. (2006). Experimental tests for an evolutionary trade-off between growth rate and yield in E. coli. American Naturalist. 168(2), 242-251
[Journal article]Authored by: Pfeiffer, T.
Pfeiffer, T., & Nowak, MA. (2006). Digital cows grazing on digital grounds. CURRENT BIOLOGY. 16(22), R946-R949
[Journal article]Authored by: Pfeiffer, T.
Pfeiffer, T., & Schuster, S. (2005). Game-theoretical approaches to studying the evolution of biochemical systems. TRENDS IN BIOCHEMICAL SCIENCES. 30(1), 20-25
[Journal article]Authored by: Pfeiffer, T.
Pfeiffer, T., Rutte, C., Killingback, T., Taborsky, M., & Bonhoeffer, S. (2005). Evolution of cooperation by generalized reciprocity. PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES. 272(1568), 1115-1120
[Journal article]Authored by: Pfeiffer, T.
Pfeiffer, T., Soyer, OS., & Bonhoeffer, S. (2005). The evolution of connectivity in metabolic networks. PLOS BIOLOGY. 3(7), 1269-1275
[Journal article]Authored by: Pfeiffer, T.
Pfeiffer, T., & Bonhoeffer, S. (2004). Evolution of cross-feeding in microbial populations. AMERICAN NATURALIST. 163(6), E126-E135
[Journal article]Authored by: Pfeiffer, T.
Pfeiffer, T., & Bonhoeffer, S. (2003). An evolutionary scenario for the transition to undifferentiated multicellularity. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 100(3), 1095-1098
[Journal article]Authored by: Pfeiffer, T.
Pfeiffer, T., & Bonhoeffer, S. (2002). Evolutionary consequences of tradeoffs between yield and rate of ATP production. ZEITSCHRIFT FUR PHYSIKALISCHE CHEMIE-INTERNATIONAL JOURNAL OF RESEARCH IN PHYSICAL CHEMISTRY & CHEMICAL PHYSICS. 216, 51-63
[Journal article]Authored by: Pfeiffer, T.
Schuster, S., Klamt, S., Weckwerth, W., Moldenhauer, F., & Pfeiffer, T. (2002). Use of network analysis of metabolic systems in bioengineering. BIOPROCESS AND BIOSYSTEMS ENGINEERING. 24(6), 363-372
[Journal article]Authored by: Pfeiffer, T.
Pfeiffer, T., Schuster, S., & Bonhoeffer, S. (2001). Cooperation and competition in the evolution of ATP-producing pathways. SCIENCE. 292(5516), 504-507
[Journal article]Authored by: Pfeiffer, T.

Book

Pfeiffer, T., & Bonhoeffer, S. (2009). Evolutionary origin and consequences of design properties of metabolic networks. In Statistical and Evolutionary Analysis of Biological Networks. (pp. 113 - 126).
[Chapter]Authored by: Pfeiffer, T.

Conference

Wang, W., & Pfeiffer, T.Securities Based Decision Markets. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). (pp. 79 - 92). 0302-9743.
[Conference]Authored by: Pfeiffer, T.
Lai, H., Morley, A., & Pfeiffer, T. (2017). Experimental evolution uncovers the role of phenotype switching in a newly identified CTG-clade yeast. Poster session presented at the meeting of NZMS Annual Conference 2017
[Conference Poster]Authored by: Pfeiffer, T.
Cunnington, E., & Pfeiffer, T. (2017, November). Investigation of Saccharomyces cerevisiae adaptations during an evolution in emulsion culture. Presented at NZMS Annual Conference 2017. Auckland, New Zealand.
[Conference Oral Presentation]Authored by: Pfeiffer, T.
Pfeiffer, T. (2015, June). Investigating the fitness effects of aerobic fermentation in yeast. Presented at Metabolic Pathway Analysis 2015. Braga, Portugal.
[Conference Oral Presentation]Authored by: Pfeiffer, T.
Pfeiffer, T., Tran, L., Krumme, C., & Rand, DG. (2013). The value of reputation. Poster session presented at the meeting of The European Society for Evolutionary Biology. Lisbon, Portugal
[Conference Poster]Authored by: Pfeiffer, T.
Pfeiffer, T. (2013, November). Game theory and the origin of the Crabtree effect. Presented at YPD Conference 2013. Auckland, New Zealand.
[Conference Oral Presentation]Authored by: Pfeiffer, T.
Pfeiffer, T., Gao, XA., Mao, A., Chen, Y., & Rand, DG.Adaptive Polling for Information Aggregation. Proceedings of the 26th AAAI Conference on Artificial Intelligence, AAAI 2012. (pp. 122 - 128).
[Conference]Authored by: Pfeiffer, T.
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 (2)(pp. 351 - 361). 1367-4803.
[Conference]Authored by: Pfeiffer, T.
Pfeiffer, T., Sanchez-Valdenebro, I., Nuno, JC., Montero, F., & Schuster, S.METATOOL: for studying metabolic networks. BIOINFORMATICS. 15 (3)(pp. 251 - 257). 1367-4803.
[Conference]Authored by: Pfeiffer, T.

Uncategorised

Eitan, O., Viganola, D., Inbar, Y., Dreber, A., Johannesson, M., Pfeiffer, T., . . . Uhlmann, EL.JulyNovemberEitan, O., Viganola, D., Inbar, Y., Dreber, A., Johannesson, M., Pfeiffer, T., . . . Uhlmann, EL.MayEitan, O., Viganola, D., Inbar, Y., Dreber, A., Johannesson, M., Pfeiffer, T., . . . Uhlmann, EL.JulyNovemberNovember
[Preprint]Authored by: Pfeiffer, T.

Teaching and Supervision

Summary of Doctoral Supervision

Position Current Completed
Main Supervisor 0 4
Co-supervisor 0 2

Completed Doctoral Supervision

Main Supervisor of:

  • 2023 - Wenlong Wang - Doctor of Philosophy
    Decision Markets Implementations for Human Forecasters and Multi-agent Learning Systems
  • 2023 - Pansye Elkashef - Doctor of Philosophy
    An Experimental Analysis of Information Aggregation in Decision Markets
  • 2021 - Michael Gordon - Doctor of Philosophy
    Estimating credibility of science claims – Analysis of forecasting data from metascience projects
  • 2018 - Annabel Morley - Doctor of Philosophy
    Investigating the Evolutionary Changes in Crabtree-negative Yeasts During a Long-term Evolution Experiment

Co-supervisor of:

  • 2016 - Siwen Pan - Doctor of Philosophy
    Frontiers in Decision Theory
  • 2016 - Yuriy Pichugin - Doctor of Philosophy
    Theoretical investigation into the origins of multicellularity