Concept

Ancestral sequence reconstruction

Related publications (13)

Molecular reconstruction and simulation of the Neuron-Glia-Vasculature system

The outstanding information processing capacity of the brain relies on numerous molecular mechanisms. It is an extremely energy-expensive function, which involves specialization and collaboration of different cell types. A common framework to study the com ...

EPFL2023

Mitochondrial Pseudogenes Suggest Repeated Inter-Species Hybridization among Direct Human Ancestors

Konstantin Popadin

The hypothesis that the evolution of humans involves hybridization between diverged species has been actively debated in recent years. We present the following novel evidence in support of this hypothesis: the analysis of nuclear pseudogenes of mtDNA ("NUM ...

MDPI2022

Subspace clustering in high-dimensions: Phase transitions & Statistical-to-Computational gap

Florent Gérard Krzakala, Lenka Zdeborová, Luca Pesce, Bruno Loureiro

A simple model to study subspace clustering is the high-dimensional k -Gaussian mixture model where the cluster means are sparse vectors. Here we provide an exact asymptotic characterization of the statistically optimal reconstruction error in this model i ...

2022

Exponentially long orbits in Hopfield neural networks

Wulfram Gerstner, Johanni Michael Brea, Samuel Pavio Muscinelli

We show that Hopfield neural networks with synchronous dynamics and asymmetric weights admit stable orbits that form sequences of maximal length. For N units, these sequences have length T = 2^N; that is, they cover the full state space. We present a mathe ...

Massachusetts Institute of Technology Press2017

Understanding and Engineering Thermostability in DNA Ligase from Thermococcus sp 1519

Matteo Dal Peraro, Hasan Pezeshgi Modarres

The physical chemical principles underlying,enzymatic thermostability are keys to understand the way evolution has shaped proteins,to adapt to a broad range of temperatures. Understanding the molecular determinants at the basis of protein thermostability i ...

Amer Chemical Soc2015

Modeling and Engineering Proteins Thermostability

Hasan Pezeshgi Modarres

Enzymes have evolved during millions of years to become efficient catalysts for specific biochemical reactions within a specific range of working conditions in the cellular environment. The activity of an enzyme is directly related to its folded structure ...

EPFL2015

A Systematic Survey of an Intragenic Epistatic Landscape

Jeffrey David Jensen, Claudia Bank

Mutations are the source of evolutionary variation. The interactions of multiple mutations can have important effects on fitness and evolutionary trajectories. We have recently described the distribution of fitness effects of all single mutations for a nin ...

Oxford Univ Press2015

Transcriptomic characterization of the enzymatic antioxidants FeSOD, MnSOD, APX and KatG in the dinoflagellate genus Symbiodinium

Thomas Krüger

Background The diversity of the symbiotic dinoflagellate Symbiodinium sp., as assessed by genetic markers, is well established. To what extent this diversity is reflected on the amino acid level of functional genes such as enzymatic antioxidants that play ...

BioMed Central2015

Reconstruction of Large-Scale Phylogenies

Vaibhav Rajan

The evolutionary relationships between organisms or phylogenies are fundamental to biology. They are invaluable as guiding tools to mine, organize and exploit the enormous amounts of biological data in the post-genomic era. The advent of high-throughput se ...

EPFL2012

Calibration in Circular Ultrasound Tomography Devices

Martin Vetterli, Amin Karbasi, Reza Parhizkar

We consider the position calibration problem in circular tomography devices, where sensors deviate from a perfect circle. We introduce a new method of calibration based on the time-of-flight measurements between sensors when the enclosed medium is homogene ...

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