Replaying the Evolutionary Tape: Biomimetic Reverse Engineering of Gene Networks

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

Jan Sickmann Hesthaven, Cecilia Pagliantini, 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

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

Substrates and Cyclic Peptide Inhibitors of the Oligonucleotide-Activated Sirtuin 7

Alexander Lund Nielsen

The sirtuins are NAD+-dependent lysine deacylases, comprising seven isoforms (SIRT1-7) in humans, which are involved in the regulation of a plethora of biological processes, including gene expression and metabolism. The sirtuins share a common hydrolytic m ...

Wiley-VCH Verlag GmbH2023

Cellularization across eukaryotes: Conserved mechanisms and novel strategies

Omaya Pierre Dudin

Many eukaryotes form multinucleated cells during their devel-opment. Some cells persist as such during their lifetime, others choose to cleave each nucleus individually using a specialized cytokinetic process known as cellularization. What is cellula-rizat ...

CURRENT BIOLOGY LTD2023

Network Alignment With Holistic Embeddings

Quoc Viet Hung Nguyen, Thành Tâm Nguyên, Chi Thang Duong, Thanh Trung Huynh

Network alignment is the task of identifying topologically and semantically similar nodes across (two) different networks. It plays an important role in various applications ranging from social network analysis to bioinformatic network interactions. Howeve ...

IEEE COMPUTER SOC2023

Statistical learning quantifies transposable element-mediated cis-regulation

Didier Trono, Julien Léonard Duc, Evaristo Jose Planet Letschert, Alexandre Coudray, Cyril David Son-Tuyên Pulver, Raphaël Gérard Théodore Michel Marie de Deloÿe et Fourcade de Fondeville, Julien Paul André Pontis, Delphine Yvette L Grun, Shaoline Sheppard

Background: Transposable elements (TEs) have colonized the genomes of most metazoans, and many TE-embedded sequences function as cis-regulatory elements (CREs) for genes involved in a wide range of biological processes from early embryo- genesis to innate ...

2023

Upper part-load instability in a reduced-scale Francis turbine: an experimental study

François Avellan, Elena Vagnoni, Andres Müller, Ali Amini

Francis turbines with medium or high specific speeds may experience a particular type of instability in the upper part load in which the precessing vortex has an elliptical shape. The occurrence of the upper part-load instability (UPLI) is accompanied by l ...

SPRINGER2023

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

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

Towards a pattern language for complex-mode mission concept generation

Jean-Paul Richard Kneib, Jeffrey Huang, Anne-Marlene Rüede

New space mission profiles arise from the convergence of reduced launch prices, miniaturization of electronics and the maturation of on-orbit servicing technologies. Additionally, a shift towards challenging Lunar objectives pushes for interconnected and c ...

PERGAMON-ELSEVIER SCIENCE LTD2023

Integrative transcriptome analyses of Transposable Elements (TEs) and genes contribute to a better understanding of colorectal cancer

Eunji Shin

Cancer is the second leading cause of death worldwide. Cancer develops through multiple hallmark functions including apoptosis evasion, unlimited replicative potential, metastasis, and immune avoidance. Over the past few decades, researchers have reported ...

EPFL2022

Quantization for Decentralized Learning Under Subspace Constraints

Ali H. Sayed, Stefan Vlaski, Roula Nassif

In this article, we consider decentralized optimization problems where agents have individual cost functions to minimize subject to subspace constraints that require the minimizers across the network to lie in low-dimensional subspaces. This constrained fo ...

IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC2023