Publications related to Evolution of biological complexity

Industrial Biotechnology Conservation Processes: Similarities with Natural Long-Term Preservation of Biological Organisms

Philippe Abdel Sayed, Corinne Scaletta, Lee Ann Laurent-Applegate, Nathalie Hirt-Burri, Laurent Alexis Clément Vannay, Alexis Laurent

Cryopreservation and lyophilization processes are widely used for conservation purposes in the pharmaceutical, biotechnological, and food industries or in medical transplantation. Such processes deal with extremely low temperatures (e.g., -196 degrees C) a ...

MDPI2023

A Wasserstein-based measure of conditional dependence

Negar Kiyavash, Seyed Jalal Etesami, Kun Zhang

Measuring conditional dependencies among the variables of a network is of great interest to many disciplines. This paper studies some shortcomings of the existing dependency measures in detecting direct causal influences or their lack of ability for group ...

2022

Intrinsically High Capacity of Animal Cells From a Symbiotic Cnidarian to Deal With Pro-Oxidative Conditions

Gaëlle Delphine Toullec

The cnidarian-dinoflagellate symbiosis is a mutualistic intracellular association based on the photosynthetic activity of the endosymbiont. This relationship involves significant constraints and requires co-evolution processes, such as an extensive capacit ...

FRONTIERS MEDIA SA2022

Applicability of the landscape evolution model in the absence of rills

David Andrew Barry, Andrea Rinaldo, Paolo Perona, Seifeddine Jomaa, Mohsen Cheraghi, Andrea Cimatoribus

Despite numerous applications of physically-based models for incised landscapes, their applicability for overland flow on unchanneled surfaces is not known. This work challenges a widely used landscape evolution model for the case of non-uniform rainfall a ...

2022

Exploiting Marginal Stability in Slow-Fast Quasilinear Dynamical Systems

Alessia Ferraro

The accurate investigation of many geophysical phenomena via direct numerical simulations is computationally not possible nowadays due to the huge range of spatial and temporal scales to be resolved. Therefore advances in this field rely on the development ...

EPFL2022

Gene expression across mammalian organ development

Maria del Carmen Sandi Perez, Ioannis Xenarios

The evolution of gene expression in mammalian organ development remains largely uncharacterized. Here we report the transcriptomes of seven organs (cerebrum, cerebellum, heart, kidney, liver, ovary and testis) across developmental time points from early or ...

2019

Statistical and physical characterization of rainfall-driven overland flow morphologies

Mohsen Cheraghi

Environmental transport processes are highly coupled with the shape of landscapes. Modern catchment analysis with high-resolution data and huge computational powers demand more detailed within-cell metrics for surface evolution modeling. This dissertation ...

EPFL2019

Robust Adaptive Decision Making: Bayesian Optimization and Beyond

Ilija Bogunovic

The central task in many interactive machine learning systems can be formalized as the sequential optimization of a black-box function. Bayesian optimization (BO) is a powerful model-based framework for \emph{adaptive} experimentation, where the primary go ...

EPFL2019

Thermal Diffusion in Binary Mixtures: Transient Behavior and Transport Coefficients from Equilibrium and Nonequilibrium Molecular Dynamics

Sara Bonella, Mauro Ferrario

Equilibrium and nonequilibrium molecular dynamics simulations are combined to compute the full set of coefficients that appear in the phenomenological equations describing thermal transport in a binary mixture subject to a constant thermal, gradient The Dy ...

Amer Chemical Soc2017

KRAB zinc-finger proteins contribute to the evolution of gene regulatory networks

Didier Trono, Michaël Imbeault, Pierre-Yves Joseph Laurent Helleboid

The human genome encodes some 350 Kruppel-associated box (KRAB) domain-containing zinc-finger proteins (KZFPs), the products of a rapidly evolving gene family that has been traced back to early tetrapods(1,2). The function of most KZFPs is unknown, but a f ...

Nature Publishing Group2017

Influence of load history on the force-displacement response of in-plane loaded unreinforced masonry walls

Katrin Beyer, Bastian Valentin Wilding, Kiarash Mohtasham Dolatshahi

Empirical drift capacity models for in-plane loaded unreinforced masonry (URM) walls are derived from results of quasi-static cyclic shear-compression tests. The experimentally determined drift capacities are, however, dependent on the applied demand, i.e. ...

2017

Time-Varying Gaussian Process Bandit Optimization

Volkan Cevher, Jonathan Mark Scarlett, Ilija Bogunovic

We consider the sequential Bayesian optimization problem with bandit feedback, adopting a formulation that allows for the reward function to vary with time. We model the reward function using a Gaussian process whose evolution obeys a simple Markov model. ...

2016

The Seamless Peer and Cloud Evolution Framework

Dario Floreano, Joshua Evan Auerbach, Giovanni Iacca, Guillaume Paul Olivier Leclerc

Evolutionary algorithms are increasingly being applied to problems that are too computationally expensive to run on a single personal computer due to costly fitness function evaluations and/or large numbers of fitness evaluations. Here, we introduce the Se ...

ACM Press2016

On the relative roles of background selection and genetic hitchhiking in shaping human cytomegalovirus genetic diversity

Jeffrey David Jensen

A central focus of population genetics has been examining the contribution of selective and neutral processes in shaping patterns of intraspecies diversity. In terms of selection specifically, surveys of higher organisms have shown considerable variation i ...

Wiley-Blackwell2016

Assessing Recent Selection and Functionality at Long Noncoding RNA Loci in the Mouse Genome

Anamaria Necsulea

Long noncoding RNAs (lncRNAs) are one of the most intensively studied groups of noncoding elements. Debate continues over what proportion of lncRNAs are functional or merely represent transcriptional noise. Although characterization of individual lncRNAs h ...

Oxford Univ Press2015

Viability Principles for Constrained Optimization Using a (1+1)-CMA-ES

Dario Floreano, Andrea Maesani

Viability Evolution is an abstraction of artificial evolution which operates by eliminating candidate solutions that do not satisfy viability criteria. Viability criteria are defined as boundaries on the values of objectives and constraints of the problem ...

Springer International Publishing2014

Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data

Bart Deplancke, Sebastian Martin Waszak, Sunil Kumar Raghav, Nouria Hernandez, Alisa Yurovsky

Motivation: High-throughput sequencing technologies enable the genome-wide analysis of the impact of genetic variation on molecular phenotypes at unprecedented resolution. However, although powerful, these technologies can also introduce unexpected artifac ...

Oxford University Press2014

The Minimal Complexity of Adapting Agents Increases with Fitness

What is the relationship between the complexity and the fitness of evolved organisms, whether natural or artificial? It has been asserted, primarily based on empirical data, that the complexity of plants and animals increases as their fitness within a part ...

Public Library Science2013

The alignment between institutions and technology in network industries

Matthias Finger, Nicolas Crettenand

Network industries, such as electricity, railways and air transport, are very complex technical, economic, and political systems in which the alignment between technology and institutions has a significant impact on performance. This alignment has been stu ...

2013

Robust Demographic Inference from Genomic and SNP Data

Matthieu Foll

We introduce a flexible and robust simulation-based framework to infer demographic parameters from the site frequency spectrum (SFS) computed on large genomic datasets. We show that our composite-likelihood approach allows one to study evolutionary models ...

Public Library of Science2013