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Sorting genomes with rearrangements and segmental duplications through trajectory graphs

Related publications (31)

PSGL-1 is an evolutionarily conserved antiviral restriction factor

The arms race between viruses and their hosts shaped the evolutionary history and the genome composition of both parties. Restriction factors are the first-line antiviral effectors encoded by the host genomes and are often conserved through evolution to pr ...

AMER SOC MICROBIOLOGY2023

Development of multiplexed single-molecule imaging techniques to study chromatin invasion dynamics of chromatin effector proteins

Kristina Makasheva

DNA-binding proteins physically interact with the DNA and directly affect genomic functions. The eukaryotic genome is compacted into chromatin, limiting the DNA access to nuclear factors. In this Ph.D. thesis, I explored the dynamic mechanisms, that allow ...

EPFL2023

Multi-robot task allocation for safe planning against stochastic hazard dynamics

Orcun Karaca, Maryam Kamgarpour

We address multi-robot safe mission planning in uncertain dynamic environments. This problem arises in several applications including safety-critical exploration, surveillance, and emergency rescue missions. Computation of a multi-robot optimal control pol ...

IEEE2023

Distributionally Robust Linear Quadratic Control

Daniel Kuhn, Cagil Kocyigit, Bahar Taskesen

Linear-Quadratic-Gaussian (LQG) control is a fundamental control paradigm that is studied in various fields such as engineering, computer science, economics, and neuroscience. It involves controlling a system with linear dynamics and imperfect observations ...

2023

Sulfurospirillum diekertiae sp. nov., a tetrachloroethene-respiring bacterium isolated from contaminated soil

Christof Holliger, Julien Maillard, Junxiong Wang

Two anaerobic, tetrachloroethene- (PCE-) respiring bacterial isolates, designated strain ACSDCE T and strain ACSTCE, were characterized using a polyphasic approach. Cells were Gram-stain-negative, motile, non-spore-forming and shared a vibrioid- to spirill ...

2023

Bayesian reconstruction of memories stored in neural networks from their connectivity

Florent Gérard Krzakala, Lenka Zdeborová

The advent of comprehensive synaptic wiring diagrams of large neural circuits has created the field of connectomics and given rise to a number of open research questions. One such question is whether it is possible to reconstruct the information stored in ...

2023

A multigrid method for PDE-constrained optimization with uncertain inputs

Fabio Nobile, Tommaso Vanzan

In this manuscript, we present a collective multigrid algorithm to solve efficiently the large saddle-point systems of equations that typically arise in PDE-constrained optimization under uncertainty, and develop a novel convergence analysis of collective ...

Springer Science and Business Media LLC2024

Adaptive Symplectic Model Order Reduction Of Parametric Particle-Based Vlasov-Poisson Equation

Cecilia Pagliantini, Jan Sickmann Hesthaven, Nicolò Ripamonti

. High-resolution simulations of particle-based kinetic plasma models typically require a high number of particles and thus often become computationally intractable. This is exacerbated in multi-query simulations, where the problem depends on a set of para ...

AMER MATHEMATICAL SOC2023

Fairness and Explainability in Clustering Problems

Xinrui Jia

In this thesis we present and analyze approximation algorithms for three different clustering problems. The formulations of these problems are motivated by fairness and explainability considerations, two issues that have recently received attention in the ...

EPFL2023

Inborn errors of type I interferon immunity in patients with symptomatic acute hepatitis E

Jacques Fellay

Background and Aims:The clinical spectrum of human infection by HEV ranges from asymptomatic to severe acute hepatitis. Furthermore, HEV can cause diverse neurological manifestations, especially Parsonage-Turner syndrome. Here, we used a large-scale human ...

Lippincott Williams & Wilkins2023

Cis-regulatory effect of HPV integration is constrained by host chromatin architecture in cervical cancers

Giovanni Ciriello, Daniele Tavernari

Human papillomavirus (HPV) infections are the primary drivers of cervical cancers, and often HPV DNA gets integrated into the host genome. Although the oncogenic impact of HPV encoded genes is relatively well known, the cis-regulatory effect of integrated ...

Wiley2023