Approximating the edit distance for genomes with duplicate genes under DCJ, insertion and deletion

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Chromatin modules and their implication in genomic organization and gene regulation

Judith Franziska Kribelbauer, Bart Deplancke, Guido Van Mierlo

Regulation of gene expression is a complex but highly guided process. While genomic technologies and computational approaches have allowed high-throughput mapping of cis-regulatory elements (CREs) and their interactions in 3D, their precise role in regulat ...

ELSEVIER SCIENCE LONDON2023

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

Christof Holliger, Julien Maillard

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 ...

Society for General Microbiology2023

Modeling, analysis, and design of complex biological networks

Mohammadomid Oftadeh

Automating experimental procedures has resulted in an unprecedented increase in the volume of generated data, which, in turn, has caused an accumulation of unprocessed data. As a result, the need to develop tools to analyze data systematically has been ris ...

EPFL2023

Whole-genome doubling drives oncogenic loss of chromatin segregation

Juan Diaz Miyar, Elisa Oricchio, Natalya Katanayeva, Daniele Tavernari, Ruxandra-Andreea Lambuta

Whole-genome doubling (WGD) is a recurrent event in human cancers and it promotes chromosomal instability and acquisition of aneuploidies(1-8). However, the three-dimensional organization of chromatin in WGD cells and its contribution to oncogenic phenotyp ...

NATURE PORTFOLIO2023

Space-Efficient Representations of Graphs

Jakab Tardos

With the increasing prevalence of massive datasets, it becomes important to design algorithmic techniques for dealing with scenarios where the input to be processed does not fit in the memory of a single machine. Many highly successful approaches have emer ...

EPFL2022

Nature vs. Nurture: Feature vs. Structure for Graph Neural Networks

Karl Aberer, Quoc Viet Hung Nguyen, Thành Tâm Nguyên, Chi Thang Duong

Graph neural networks take node features and graph structure as input to build representations for nodes and graphs. While there are a lot of focus on GNN models, understanding the impact of node features and graph structure to GNN performance has received ...

ELSEVIER2022

KRAB zinc-finger proteins and their transposable element targets: between antagonism and cooperation

Jonas Caspar De Tribolet-Hardy

There are 377 Krüppel-associated box (KRAB) domain-containing zinc finger proteins (KZFPs) in the human genome, making them the largest family of transcription factors. KZFPs are defined by a N-terminal KRAB domain and several zinc-finger domains arranged ...

EPFL2022

Random walks and forbidden minors III: poly(d epsilon(-1))-time partition oracles for minor-free graph classes

Akash Kumar

Consider the family of bounded degree graphs in any minor-closed family (such as planar graphs). Let d be the degree bound and n be the number of vertices of such a graph. Graphs in these classes have hyperfinite decompositions, where, one removes a small ...

IEEE COMPUTER SOC2022

Deterministic particle approximation of aggregation-diffusion equations on unbounded domains

Emanuela Radici

We consider a one-dimensional aggregation-diffusion equation, which is the gradient flow in the Wasserstein space of a functional with competing attractive-repulsive interactions. We prove that the fully deterministic particle approximations with piecewise ...

2022

Graph Representation Learning with Optimal Transport: Analysis and Applications

Effrosyni Simou

In several machine learning settings, the data of interest are well described by graphs. Examples include data pertaining to transportation networks or social networks. Further, biological data, such as proteins or molecules, lend themselves well to graph- ...

EPFL2022

Distributed Graph Learning With Smooth Data Priors

Pascal Frossard, Mireille El Gheche, Isabela Cunha Maia Nobre

Graph learning is often a necessary step in processing or representing structured data, when the underlying graph is not given explicitly. Graph learning is generally performed centrally with a full knowledge of the graph signals, namely the data that live ...

IEEE2022

A systematic CRISPR approach to understanding the role of Drosophila antimicrobial peptides in immunity in vivo

Mark Austin Hanson

Antimicrobial peptides (AMPs) are host-encoded antibiotics that combat invading microbes. These short immune effectors are conserved in plants, animals, and fungi. Early work showed that AMPs killed bacteria in generalist fashions in vitro: i.e. AMPs that ...

EPFL2022