Profile
Associate Professor.
Major transitions in evolution.
Avid fan of charismatic microfauna.
Publications
Berdahl, Andrew; Brelsford, Christa; Bacco, Caterina De; Dumas, Marion; Ferdinand, Vanessa; Grochow, Joshua A; Hébert-Dufresne, Laurent; Kallus, Yoav; Kempes, Christopher P; Kolchinsky, Artemy; Larremore, Daniel B; Libby, Eric; Power, Eleanor A; Stern, Caitlin A; Tracey, Brendan D
Dynamics of beneficial epidemics Journal Article
In: Scientific Reports, vol. 9, no. 1, pp. 15093, 2019, ISSN: 2045-2322.
@article{Berdahl2019,
title = {Dynamics of beneficial epidemics},
author = {Andrew Berdahl and Christa Brelsford and Caterina De Bacco and Marion Dumas and Vanessa Ferdinand and Joshua A Grochow and Laurent Hébert-Dufresne and Yoav Kallus and Christopher P Kempes and Artemy Kolchinsky and Daniel B Larremore and Eric Libby and Eleanor A Power and Caitlin A Stern and Brendan D Tracey},
url = {https://doi.org/10.1038/s41598-019-50039-w},
doi = {10.1038/s41598-019-50039-w},
issn = {2045-2322},
year = {2019},
date = {2019-10-22},
journal = {Scientific Reports},
volume = {9},
number = {1},
pages = {15093},
abstract = {Pathogens can spread epidemically through populations. Beneficial contagions, such as viruses that enhance host survival or technological innovations that improve quality of life, also have the potential to spread epidemically. How do the dynamics of beneficial biological and social epidemics differ from those of detrimental epidemics? We investigate this question using a breadth-first modeling approach involving three distinct theoretical models. First, in the context of population genetics, we show that a horizontally-transmissible element that increases fitness, such as viral DNA, spreads superexponentially through a population, more quickly than a beneficial mutation. Second, in the context of behavioral epidemiology, we show that infections that cause increased connectivity lead to superexponential fixation in the population. Third, in the context of dynamic social networks, we find that preferences for increased global infection accelerate spread and produce superexponential fixation, but preferences for local assortativity halt epidemics by disconnecting the infected from the susceptible. We conclude that the dynamics of beneficial biological and social epidemics are characterized by the rapid spread of beneficial elements, which is facilitated in biological systems by horizontal transmission and in social systems by active spreading behavior of infected individuals.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Libby, Eric
Modularity of the life cycle Journal Article
In: Nature Ecology & Evolution, vol. 3, no. 8, pp. 1142-1143, 2019, ISSN: 2397-334X.
@article{Libby2019b,
title = {Modularity of the life cycle},
author = {Eric Libby},
url = {https://doi.org/10.1038/s41559-019-0956-5},
doi = {10.1038/s41559-019-0956-5},
issn = {2397-334X},
year = {2019},
date = {2019-08-01},
journal = {Nature Ecology & Evolution},
volume = {3},
number = {8},
pages = {1142-1143},
abstract = {Life stages in Bacillus subtilis are controlled by regulatory blocks that can be kept or lost across species in response to selection in different environments.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Lind, Peter A; Libby, Eric; Herzog, Jenny; Rainey, Paul B
Predicting mutational routes to new adaptive phenotypes Journal Article
In: eLife, no. 38822, 2019.
@article{Lind2019,
title = {Predicting mutational routes to new adaptive phenotypes},
author = {Peter A Lind and Eric Libby and Jenny Herzog and Paul B Rainey},
url = {https://elifesciences.org/articles/38822},
doi = {10.7554/eLife.38822},
year = {2019},
date = {2019-01-08},
journal = {eLife},
number = {38822},
abstract = {Predicting evolutionary change poses numerous challenges. Here we take advantage of the model bacterium Pseudomonas fluorescens in which the genotype-to-phenotype map determining evolution of the adaptive ‘wrinkly spreader’ (WS) type is known. We present mathematical descriptions of three necessary regulatory pathways and use these to predict both the rate at which each mutational route is used and the expected mutational targets. To test predictions, mutation rates and targets were determined for each pathway. Unanticipated mutational hotspots caused experimental observations to depart from predictions but additional data led to refined models. A mismatch was observed between the spectra of WS-causing mutations obtained with and without selection due to low fitness of previously undetected WS-causing mutations. Our findings contribute toward the development of mechanistic models for forecasting evolution, highlight current limitations, and draw attention to challenges in predicting locus-specific mutational biases and fitness effects.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Libby, Eric; Hébert-Dufresne, Laurent; Hosseini, Sayed-Rzgar; Wagner, Andreas
Syntrophy emerges spontaneously in complex metabolic systems Journal Article
In: PLOS Computational Biology, vol. 15, no. 7, pp. 1-17, 2019.
@article{10.1371/journal.pcbi.1007169,
title = {Syntrophy emerges spontaneously in complex metabolic systems},
author = {Eric Libby and Laurent Hébert-Dufresne and Sayed-Rzgar Hosseini and Andreas Wagner},
url = {https://doi.org/10.1371/journal.pcbi.1007169},
doi = {10.1371/journal.pcbi.1007169},
year = {2019},
date = {2019-01-01},
journal = {PLOS Computational Biology},
volume = {15},
number = {7},
pages = {1-17},
publisher = {Public Library of Science},
abstract = {Author summary By exchanging resources, the members of a microbial community can survive in environments where individual species cannot. Despite the abundance of such syntrophy, little is known about its evolutionary origin. The predominant hypothesis is that syntrophy arises when originally independent organisms in the same community become interdependent by accumulating mutations. In this view, syntrophy arises when organisms co-evolve. In sharp contrast we find that different metabolism can interact syntrophically without a shared evolutionary history. We show that syntrophy is an inherent and emergent property of the complex chemical reaction networks that constitute metabolism.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Libby, Eric; Lind, Peter A
Probabilistic Models for Predicting Mutational Routes to New Adaptive Phenotypes Journal Article
In: Bio-protocol, vol. 9, no. 20, 2019.
@article{Libby1362757,
title = {Probabilistic Models for Predicting Mutational Routes to New Adaptive Phenotypes},
author = {Eric Libby and Peter A Lind},
doi = {10.21769/BioProtoc.3407},
year = {2019},
date = {2019-01-01},
journal = {Bio-protocol},
volume = {9},
number = {20},
institution = {IceLab},
abstract = {Understanding the translation of genetic variation to phenotypic variation is a fundamental problem in genetics and evolutionary biology. The introduction of new genetic variation through mutation can lead to new adaptive phenotypes, but the complexity of the genotype-to-phenotype map makes it challenging to predict the phenotypic effects of mutation. Metabolic models, in conjunction with flux balance analysis, have been used to predict evolutionary optimality. These methods however rely on large scale models of metabolism, describe a limited set of phenotypes, and assume that selection for growth rate is the prime evolutionary driver. Here we describe a method for computing the relative likelihood that mutational change will translate into a phenotypic change between two molecular pathways. The interactions of molecular components in the pathways are modeled with ordinary differential equations. Unknown parameters are offset by probability distributions that describe the concentrations of molecular components, the reaction rates for different molecular processes, and the effects of mutations. Finally, the likelihood that mutations in a pathway will yield phenotypic change is estimated with stochastic simulations. One advantage of this method is that only basic knowledge of the interaction network underlying a phenotype is required. However, it can also incorporate available information about concentrations and reaction rates as well as mutational biases and mutational robustness of molecular components. The method estimates the relative probabilities that different pathways produce phenotypic change, which can be combined with fitness models to predict evolutionary outcomes.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Libby, Eric; Ratcliff, William
Shortsighted Evolution Constrains the Efficacy of Long-Term Bet Hedging Journal Article
In: The American Naturalist, vol. 193, pp. 000-000, 2019.
@article{article,
title = {Shortsighted Evolution Constrains the Efficacy of Long-Term Bet Hedging},
author = {Eric Libby and William Ratcliff},
doi = {10.1086/701786},
year = {2019},
date = {2019-01-01},
journal = {The American Naturalist},
volume = {193},
pages = {000-000},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Libby, Eric; Driscoll, William W; Ratcliff, William C
Programmed cell death can increase the efficacy of microbial bet-hedging Journal Article
In: Scientific reports, vol. 8, no. 1, pp. 1120, 2018.
@article{libby2018programmed,
title = {Programmed cell death can increase the efficacy of microbial bet-hedging},
author = {Eric Libby and William W Driscoll and William C Ratcliff},
doi = {10.1038/s41598-017-18687-y
publisher=Nature Publishing Group},
year = {2018},
date = {2018-01-01},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {1120},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Lind, Peter A; Libby, Eric; Herzog, Jenny; Rainey, Paul B
Disentangling the effects of genetic architecture, mutational bias and selection on evolutionary forecasting Journal Article
In: bioRxiv, pp. 335711, 2018.
@article{lind2018disentangling,
title = {Disentangling the effects of genetic architecture, mutational bias and selection on evolutionary forecasting},
author = {Peter A Lind and Eric Libby and Jenny Herzog and Paul B Rainey},
doi = {10.1101/335711
publisher=Cold Spring Harbor Laboratory},
year = {2018},
date = {2018-01-01},
journal = {bioRxiv},
pages = {335711},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Estrela, Sylvie; Libby, Eric; Cleve, Jeremy Van; Débarre, Florence; Deforet, Maxime; Harcombe, William R; Peña, Jorge; Brown, Sam P; Hochberg, Michael E
Environmentally Mediated Social Dilemmas Journal Article
In: Trends in Ecology & Evolution, 2018, ISSN: 0169-5347.
@article{ESTRELA2018,
title = {Environmentally Mediated Social Dilemmas},
author = {Sylvie Estrela and Eric Libby and Jeremy Van Cleve and Florence Débarre and Maxime Deforet and William R Harcombe and Jorge Peña and Sam P Brown and Michael E Hochberg},
url = {http://www.sciencedirect.com/science/article/pii/S0169534718302490},
doi = {https://doi.org/10.1016/j.tree.2018.10.004},
issn = {0169-5347},
year = {2018},
date = {2018-01-01},
journal = {Trends in Ecology & Evolution},
abstract = {By consuming and producing environmental resources, organisms inevitably change their habitats. The consequences of such environmental modifications can be detrimental or beneficial not only to the focal organism but also to other organisms sharing the same environment. Social evolution theory has been very influential in studying how social interactions mediated by public ‘goods’ or ‘bads’ evolve by emphasizing the role of spatial structure. The environmental dimensions driving these interactions, however, are typically abstracted away. We propose here a new, environment-mediated taxonomy of social behaviors where organisms are categorized by their production or consumption of environmental factors that can help or harm others in the environment. We discuss microbial examples of our classification and highlight the importance of environmental intermediates more generally.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Tavera-Mendoza, Luz E; Westerling, Thomas; Libby, Eric; Marusyk, Andriy; Cato, Laura; Cassani, Raymundo; Cameron, Lisa A; Ficarro, Scott B; Marto, Jarrod A; Klawitter, Jelena; others,
Vitamin D receptor regulates autophagy in the normal mammary gland and in luminal breast cancer cells Journal Article
In: Proceedings of the National Academy of Sciences, pp. 201615015, 2017.
@article{tavera2017vitamin,
title = {Vitamin D receptor regulates autophagy in the normal mammary gland and in luminal breast cancer cells},
author = {Luz E Tavera-Mendoza and Thomas Westerling and Eric Libby and Andriy Marusyk and Laura Cato and Raymundo Cassani and Lisa A Cameron and Scott B Ficarro and Jarrod A Marto and Jelena Klawitter and others},
doi = {10.1073/pnas.1615015114
publisher=National Acad Sciences},
year = {2017},
date = {2017-01-01},
journal = {Proceedings of the National Academy of Sciences},
pages = {201615015},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Kempes, Christopher P; van Bodegom, Peter M; Wolpert, David; Libby, Eric; Amend, Jan; Hoehler, Tori
Drivers of bacterial maintenance and minimal energy requirements Journal Article
In: Frontiers in microbiology, vol. 8, pp. 31, 2017.
@article{kempes2017drivers,
title = {Drivers of bacterial maintenance and minimal energy requirements},
author = {Christopher P Kempes and Peter M van Bodegom and David Wolpert and Eric Libby and Jan Amend and Tori Hoehler},
doi = {10.3389/fmicb.2017.00031
publisher=Frontiers},
year = {2017},
date = {2017-01-01},
journal = {Frontiers in microbiology},
volume = {8},
pages = {31},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Ratcliff, William C; Herron, Matthew; Conlin, Peter L; Libby, Eric
Nascent life cycles and the emergence of higher-level individuality Journal Article
In: Phil. Trans. R. Soc. B, vol. 372, no. 1735, pp. 20160420, 2017.
@article{ratcliff2017nascent,
title = {Nascent life cycles and the emergence of higher-level individuality},
author = {William C Ratcliff and Matthew Herron and Peter L Conlin and Eric Libby},
doi = {10.1098/rstb.2016.0420
publisher=The Royal Society},
year = {2017},
date = {2017-01-01},
journal = {Phil. Trans. R. Soc. B},
volume = {372},
number = {1735},
pages = {20160420},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Kallus, Yoav; Miller, John H; Libby, Eric
Paradoxes in leaky microbial trade Journal Article
In: Nature Communications, vol. 8, no. 1, pp. 1361, 2017.
@article{kallus2017paradoxes,
title = {Paradoxes in leaky microbial trade},
author = {Yoav Kallus and John H Miller and Eric Libby},
doi = {10.1038/s41467-017-01628-8
publisher=Nature Publishing Group},
year = {2017},
date = {2017-01-01},
journal = {Nature Communications},
volume = {8},
number = {1},
pages = {1361},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Wolpert, David; Libby, Eric; Grochow, Joshua A; DeDeo, Simon
10 The Many Faces of State Space Compression Journal Article
In: From Matter to Life: Information and Causality, pp. 199, 2017.
@article{wolpert201710,
title = {10 The Many Faces of State Space Compression},
author = {David Wolpert and Eric Libby and Joshua A Grochow and Simon DeDeo},
doi = {10.1017/9781316584200.010
publisher=Cambridge University Press},
year = {2017},
date = {2017-01-01},
journal = {From Matter to Life: Information and Causality},
pages = {199},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Hébert-Dufresne, Laurent; Allard, Antoine; Noël, Pierre-André; Young, Jean-Gabriel; Libby, Eric
Strategic tradeoffs in competitor dynamics on adaptive networks Journal Article
In: Scientific reports, vol. 7, no. 1, pp. 7576, 2017.
@article{hebert2017strategic,
title = {Strategic tradeoffs in competitor dynamics on adaptive networks},
author = {Laurent Hébert-Dufresne and Antoine Allard and Pierre-André Noël and Jean-Gabriel Young and Eric Libby},
doi = {10.1038/s41598-017-07621-x publisher=Nature Publishing Group},
year = {2017},
date = {2017-01-01},
journal = {Scientific reports},
volume = {7},
number = {1},
pages = {7576},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Libby, Eric; Conlin, Peter L; Kerr, Ben; Ratcliff, William C
Stabilizing multicellularity through ratcheting Journal Article
In: Phil. Trans. R. Soc. B, vol. 371, no. 1701, pp. 20150444, 2016.
@article{libby2016stabilizing,
title = {Stabilizing multicellularity through ratcheting},
author = {Eric Libby and Peter L Conlin and Ben Kerr and William C Ratcliff},
doi = {10.1098/rstb.2015.0444
publisher=The Royal Society},
year = {2016},
date = {2016-01-01},
journal = {Phil. Trans. R. Soc. B},
volume = {371},
number = {1701},
pages = {20150444},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Lachmann, Michael; Libby, Eric
Epigenetic inheritance systems contribute to the evolution of a germline Journal Article
In: Phil. Trans. R. Soc. B, vol. 371, no. 1701, pp. 20150445, 2016.
@article{lachmann2016epigenetic,
title = {Epigenetic inheritance systems contribute to the evolution of a germline},
author = {Michael Lachmann and Eric Libby},
doi = {10.1098/rstb.2015.0445
publisher=The Royal Society},
year = {2016},
date = {2016-01-01},
journal = {Phil. Trans. R. Soc. B},
volume = {371},
number = {1701},
pages = {20150445},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Wolinsky, Emma; Libby, Eric
Evolution of regulated phenotypic expression during a transition to multicellularity Journal Article
In: Evolutionary ecology, vol. 30, no. 2, pp. 235–250, 2016.
@article{wolinsky2016evolution,
title = {Evolution of regulated phenotypic expression during a transition to multicellularity},
author = {Emma Wolinsky and Eric Libby},
doi = {10.1007/s10682-015-9814-3
publisher=Springer},
year = {2016},
date = {2016-01-01},
journal = {Evolutionary ecology},
volume = {30},
number = {2},
pages = {235--250},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Gallie, Jenna; Libby, Eric; Bertels, Frederic; Remigi, Philippe; Jendresen, Christian B; Ferguson, Gayle C; Desprat, Nicolas; Buffing, Marieke F; Sauer, Uwe; Beaumont, Hubertus JE; others,
Bistability in a metabolic network underpins the de novo evolution of colony switching in Pseudomonas fluorescens Journal Article
In: PLoS biology, vol. 13, no. 3, pp. e1002109, 2015.
@article{gallie2015bistability,
title = {Bistability in a metabolic network underpins the de novo evolution of colony switching in Pseudomonas fluorescens},
author = {Jenna Gallie and Eric Libby and Frederic Bertels and Philippe Remigi and Christian B Jendresen and Gayle C Ferguson and Nicolas Desprat and Marieke F Buffing and Uwe Sauer and Hubertus JE Beaumont and others},
doi = {10.1371/journal.pbio.1002109
publisher=Public Library of Science},
year = {2015},
date = {2015-01-01},
journal = {PLoS biology},
volume = {13},
number = {3},
pages = {e1002109},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Ratcliff, William C; Hawthorne, Peter; Libby, Eric
Courting disaster: How diversification rate affects fitness under risk Journal Article
In: Evolution, vol. 69, no. 1, pp. 126–135, 2015.
@article{ratcliff2015courting,
title = {Courting disaster: How diversification rate affects fitness under risk},
author = {William C Ratcliff and Peter Hawthorne and Eric Libby},
doi = {10.1111/evo.12568
publisher=Wiley Online Library},
year = {2015},
date = {2015-01-01},
journal = {Evolution},
volume = {69},
number = {1},
pages = {126--135},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Libby, Eric; Ratcliff, William; Travisano, Michael; Kerr, Ben
Geometry shapes evolution of early multicellularity Journal Article
In: PLoS computational biology, vol. 10, no. 9, pp. e1003803, 2014.
@article{libby2014geometry,
title = {Geometry shapes evolution of early multicellularity},
author = {Eric Libby and William Ratcliff and Michael Travisano and Ben Kerr},
doi = {10.1371/journal.pcbi.1003803
publisher=Public Library of Science},
year = {2014},
date = {2014-01-01},
journal = {PLoS computational biology},
volume = {10},
number = {9},
pages = {e1003803},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Libby, Eric; Ratcliff, William C
Ratcheting the evolution of multicellularity Journal Article
In: Science, vol. 346, no. 6208, pp. 426–427, 2014.
@article{libby2014ratcheting,
title = {Ratcheting the evolution of multicellularity},
author = {Eric Libby and William C Ratcliff},
doi = {10.1126/science.1262053
publisher=American Association for the Advancement of Science},
year = {2014},
date = {2014-01-01},
journal = {Science},
volume = {346},
number = {6208},
pages = {426--427},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Libby, Eric; Rainey, Paul B
A conceptual framework for the evolutionary origins of multicellularity Journal Article
In: Physical biology, vol. 10, no. 3, pp. 035001, 2013.
@article{libby2013conceptual,
title = {A conceptual framework for the evolutionary origins of multicellularity},
author = {Eric Libby and Paul B Rainey},
doi = {10.1088/1478-3975/10/3/035001
publisher=IOP Publishing},
year = {2013},
date = {2013-01-01},
journal = {Physical biology},
volume = {10},
number = {3},
pages = {035001},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Libby, Eric; Rainey, Paul B
Eco-evolutionary feedback and the tuning of proto-developmental life cycles Journal Article
In: PloS one, vol. 8, no. 12, pp. e82274, 2013.
@article{libby2013eco,
title = {Eco-evolutionary feedback and the tuning of proto-developmental life cycles},
author = {Eric Libby and Paul B Rainey},
doi = {10.1371/journal.pone.0082274
publisher=Public Library of Science},
year = {2013},
date = {2013-01-01},
journal = {PloS one},
volume = {8},
number = {12},
pages = {e82274},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Rainey, Paul B; Beaumont, Hubertus JE; Ferguson, Gayle C; Gallie, Jenna; Kost, Christian; Libby, Eric; Zhang, Xue-Xian
The evolutionary emergence of stochastic phenotype switching in bacteria Inproceedings
In: Microbial cell factories, pp. S14, 2011.
@inproceedings{rainey2011evolutionary,
title = {The evolutionary emergence of stochastic phenotype switching in bacteria},
author = {Paul B Rainey and Hubertus JE Beaumont and Gayle C Ferguson and Jenna Gallie and Christian Kost and Eric Libby and Xue-Xian Zhang},
doi = {10.1186/1475-2859-10-S1-S14
organization=BioMed Central},
year = {2011},
date = {2011-01-01},
booktitle = {Microbial cell factories},
volume = {10},
number = {1},
pages = {S14},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}
Libby, Eric; Rainey, Paul B
Exclusion rules, bottlenecks and the evolution of stochastic phenotype switching Journal Article
In: Proceedings of the Royal Society of London B: Biological Sciences, pp. rspb20110146, 2011.
@article{libby2011exclusion,
title = {Exclusion rules, bottlenecks and the evolution of stochastic phenotype switching},
author = {Eric Libby and Paul B Rainey},
doi = {10.1098/rspb.2011.0146
publisher=The Royal Society},
year = {2011},
date = {2011-01-01},
journal = {Proceedings of the Royal Society of London B: Biological Sciences},
pages = {rspb20110146},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Libby, Eric; Glass, Leon
The calculus of committee composition Journal Article
In: PloS one, vol. 5, no. 9, pp. e12642, 2010.
@article{libby2010calculus,
title = {The calculus of committee composition},
author = {Eric Libby and Leon Glass},
doi = {10.1371/journal.pone.0012642
publisher=Public Library of Science},
year = {2010},
date = {2010-01-01},
journal = {PloS one},
volume = {5},
number = {9},
pages = {e12642},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Wang, Tian-Tian; Tavera-Mendoza, Luz Elisa; Laperriere, David; Libby, Eric; MacLeod, Naomi Burton; Nagai, Yoshihiko; Bourdeau, Veronique; Konstorum, Anna; Lallemant, Benjamin; Zhang, Rui; others,
Large-scale in silico and microarray-based identification of direct 1, 25-dihydroxyvitamin D3 target genes Journal Article
In: Molecular endocrinology, vol. 19, no. 11, pp. 2685–2695, 2005.
@article{wang2005large,
title = {Large-scale in silico and microarray-based identification of direct 1, 25-dihydroxyvitamin D3 target genes},
author = {Tian-Tian Wang and Luz Elisa Tavera-Mendoza and David Laperriere and Eric Libby and Naomi Burton MacLeod and Yoshihiko Nagai and Veronique Bourdeau and Anna Konstorum and Benjamin Lallemant and Rui Zhang and others},
doi = {10.1210/me.2005-0106 publisher=Oxford University Press},
year = {2005},
date = {2005-01-01},
journal = {Molecular endocrinology},
volume = {19},
number = {11},
pages = {2685--2695},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Wolpert, David H; Grochow, Joshua A; Libby, Eric; DeDeo, Simon
Optimal high-level descriptions of dynamical systems Journal Article
In: arXiv preprint arXiv:1409.7403, 0000.
@article{wolpert2014optimal,
title = {Optimal high-level descriptions of dynamical systems},
author = {David H Wolpert and Joshua A Grochow and Eric Libby and Simon DeDeo},
journal = {arXiv preprint arXiv:1409.7403},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Libby, Eric; Ratcliff, William C.
Shortsighted Evolution Constrains the Efficacy of Long-Term Bet Hedging Journal Article Forthcoming
In: The American Naturalist, vol. 0, Forthcoming.
@article{Libby2019,
title = {Shortsighted Evolution Constrains the Efficacy of Long-Term Bet Hedging},
author = {Eric Libby and William C. Ratcliff},
url = {https://www.journals.uchicago.edu/doi/abs/10.1086/701786},
doi = {10.1086/701786},
journal = {The American Naturalist},
volume = {0},
abstract = {To survive unpredictable environmental change, many organisms adopt bet-hedging strategies that are initially costly but provide a long-term fitness benefit. The temporal extent of these deferred fitness benefits determines whether bet-hedging organisms can survive long enough to realize them. In this article, we examine a model of microbial bet hedging in which there are two paths to extinction: unpredictable environmental change and demographic stochasticity. In temporally correlated environments, these drivers of extinction select for different switching strategies. Rapid phenotype switching ensures survival in the face of unpredictable environmental change, while slower-switching organisms become extinct. However, when both switching strategies are present in the same population, then demographic stochasticity—enforced by a limited population size—leads to extinction of the faster-switching organism. As a result, we find a novel form of evolutionary suicide whereby selection in a fluctuating environment can favor bet-hedging strategies that ultimately increase the risk of extinction. Population structures with multiple subpopulations and dispersal can reduce the risk of extinction from unpredictable environmental change and shift the balance so as to facilitate the evolution of slower-switching organisms.},
keywords = {},
pubstate = {forthcoming},
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The evolution of life on earth has been shaped by a few pivotal events. One of the most significant of these events was the evolution of multicellularity. It is hard to imagine our world before the appearance of multicellular organisms—especially because almost everything we can see with the naked eye is multicellular. Eric Libby’s research explores the conditions that make it possible for multicellularity to evolve and the impact being multicellular has on the evolution of complex life. In essence, he is interested in how simple organisms evolve into complex ones.
Eric’s journey to IceLab was long and wandering. He graduated from Rice University in Houston, Texas with a degree in Computational and Applied Mathematics. He then drove to Montreal to do a PhD with Leon Glass at the Center for Nonlinear Dynamics at McGill University. There Eric modeled genetic networks, did some bioinformatics/systems biology, and taught mathematical biology to physiology students. Afterwards, Eric did a stint as a science journalist in Washington DC as part of a AAAS Mass Media Fellowship. He left North America for the South Pacific to do a postdoc with Paul Rainey in microbial evolution at the New Zealand Institute for Advanced Study. Missing snakes and uncuddly plants, his next position was as an Omidyar fellow at the Santa Fe Institute. After hiking in the arid, sunny Southwest he moved with his family to Umeå to see winter before it goes extinct from the world.
Current Projects
The evolution of complex multicellular traits
Eric Libby (IceLab), William Ratcliffe (Georgia Tech), Peter Yunker (Georgia Tech)
The origins of eukaryotes via endosymbiosis
Eric Libby (IceLab), Chris Kempes (Santa Fe Institute), Jordan Okie (Arizona State University)
The evolution and tuning of life cycles
Eric Libby (IceLab), Mimi Koehl (UC Berkeley), William Ratcliffe (Georgia Tech)
Microbial trade and the evolution of syntrophy
Eric Libby (IceLab), Andreas Wagner (University of Zurich), Laurent Hebert-Dufresne (University of Vermont)
Agnostic Biosignatures
Eric Libby (IceLab) and collaborators from the Laboratory for Agnostic Biosignatures (LAB). The LAB team includes planetary scientists, biologists, chemists, computer scientists, mathematicians, and veteran instrument scientists. The investigators hail from eight US universities and institutions as well as two foreign universities. Research is funded by the NASA Astrobiology Program. More information here: https://www.agnosticbiosignatures.org/
The Latest Posts
This IceLabber hasn’t posted yet, but there’s plenty of interesting material for you to read while you wait.
Secondary metabolite discovery and a plant wall biodesign opportunity
Secondary metabolite discovery and a plant wall biodesign opportunity May 25, 2023 Watch Lunch Pitch Video Pitch 1: Laura Carroll: Machine learning approaches for microbial [...]
Predicting gene expression, microproteins, and new tools
Predicting gene expression, microproteins, and new tools May 11, 2023 Watch Lunch Pitch Video Pitch 1: Jian-Feng Mao: Predicting allele-specific gene expression (ASE) in poplar [...]
Algal photosynthesis, statistical tools, becoming Bayesian, and modelling cell shape.
In search of collaborators to study algal photosynthesis, becoming Bayesian, cell shape and apply statistical tools. May 4, 2023 Five researchers pitched projects during the IceLab multidisciplinary postdoctoral project call information [...]
Conifers adapting to light and using autoencoders on zero-filled data
Conifers adapting to light and using autoencoders on zero-filled data April 27, 2023 Watch Lunch Pitch Video Pitch 1: Sonali Ranade: Adaptation in the Christmas [...]
Metabolism: not the limiting factor in prokaryotic endosymbiosis
Metabolism: not the limiting factor in prokaryotic endosymbiosis “One of the great mysteries of biology,” says Eric Libby, former SFI Postdoctoral Fellow, now an associate professor at the Integrated Science Lab (IceLab), Umeå University in [...]
In memory of Carl Kempe
In memory of Carl Kempe Permanent secretary, Kempe foundations We are deeply saddened by the passing of Carl Kempe. Carl was integral in shaping our creative culture for disseminating [...]