Publications

@article{fernandezmodeling,

title = {Modeling Protein Conformational Stability Using Amino Acid Sequence Autocorrelation Vectors and RBF Neural Networks},

author = {Michael Fernández and Julio Caballero and Leyden Fernández and Pedro Sánchez},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{fernandezamino,

title = {Amino Acid Sequence Autocorrelation vectors and ensembles of Bayesian-Regularized Genetic Neural Networks for prediction of conformational stability of protein mutants},

author = {Michael Fernández and Julio Caballero and Leyden Fernández and José Ignacio Abreu},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{arumugamsource,

title = {Source: Nature.},

author = {Manimozhiyan Arumugam and Jeroen Raes and Eric Pelletier and Denis Le Paslier and Takuji Yamada and Daniel R Mende and Gabriel R Fernandes and Julien Tap and Thomas Bruls and Jean-Michel Batto and others},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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}

}

@article{bota2011dynamic,

title = {Dynamic communities and their detection},

author = {András Bóta and Miklós Krész and András Pluhár},

journal = {Acta Cybernetica},

volume = {20},

number = {1},

pages = {35--52},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{doi:10.1111/een.12679,

title = {Ecological stoichiometry and nutrient partitioning in two insect herbivores responsible for large-scale forest disturbance in the Fennoscandian subarctic},

author = {Daniel B Metcalfe and Mehdi Cherif and Jane U Jepsen and Ole Petter L Vindstad and Jeppe Å Kristensen and Ulrika Belsing},

url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/een.12679},

doi = {10.1111/een.12679},

journal = {Ecological Entomology},

volume = {0},

number = {0},

abstract = {1. Outbreaks of herbivorous insects can have large impacts on regional soil carbon (C) storage and nutrient cycling. In northernmost Europe, population outbreaks of several geometrid moth species regularly cause large-scale defoliation in subarctic birch forests. An improved understanding is required of how leaf C and nutrients are processed after ingestion by herbivores and what this means for the quantity and quality of different materials produced (frass, bodies). 2. In this study, larvae of two geometrid species responsible for major outbreaks (Epirrita autumnata and Operophtera brumata) were raised on exclusive diets of Betula pubescens var. czerepanovii (N. I. Orlova) Hämet Ahti and two other abundant understorey species (Betula nana, Vaccinium myrtillus). The quantities of C, nitrogen (N) and phosphorus (P) ingested and allocated to frass, bodies and (in the case of C) respired were recorded. 3. Overall, 23%, 70% and 48% of ingested C, N and P were allocated to bodies, respectively, rather than frass and (in the case of C) respiration. Operophtera brumata consistently maintained more constant body stoichiometric ratios of C, N and P than did E. autumnata, across the wide variation in physico-chemical properties of plant diet supplied. 4. These observed differences and similarities on C and nutrient processing may improve researchers' ability to predict the amount and stoichiometry of frass and bodies generated after geometrid outbreaks.},

keywords = {Consumer-driven nutrient recycling, ecological stoichiometry, geometrid moth, homeostasis, stable isotope, subarctic birch forest},

pubstate = {published},

tppubtype = {article}

}

@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 = {evolution, extinction, Libby},

pubstate = {forthcoming},

tppubtype = {article}

}

@article{PPR:PPR57281,

title = {Reconstructing the human first trimester fetal-maternal interface using single cell transcriptomics},

author = {Vento-Tormo R and Efremova M and Botting RA and Turco MY and Vento-Tormo M and Meyer KB and Park J and Stephenson E and Polański K and Payne RP and Goncalves A and Zou A and Teichmann SA},

doi = {10.1101/429589},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Jonsson2019,

title = {Modelling of zero-inflation improves inference of metagenomic gene count data},

author = {Viktor Jonsson and Tobias Österlund and Olle Nerman and Erik Kristiansson},

doi = {https://doi.org/10.1177/0962280218811354},

journal = { Statistical Methods in Medical Research},

volume = {28},

number = {12},

pages = {3712–3728},

keywords = {Jonsson},

pubstate = {published},

tppubtype = {article}

}

@article{PPR:PPR21261,

title = {The IRE1a-XBP1 pathway promotes T helper cell differentiation by resolving secretory stress and accelerating proliferation},

author = {Pramanik J and Chen X and Kar G and Gomes T and Henriksson J and Miao Z and Natarajan K and McKenzie ANJ and Mahata B and Teichmann SA},

doi = {10.1101/235010},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{PPR:PPR21048,

title = {Unbiased classification of mosquito blood cells by single-cell genomics and high-content imaging},

author = {Severo MS and Landry JJ and Lindquist RL and Goosmann C and Brinkmann V and Collier P and Hauser AE and Benes V and Henriksson J and Teichmann SA and Levashina EA},

doi = {10.1101/234492},

keywords = {},

pubstate = {published},

tppubtype = {article}

}