Publications related to Topology and dynamics of the zebrafish segmentation clock core circuit

Emulating Multimemristive Behavior of Silicon Nanowire-Based Biosensors by Using CMOS-Based Implementations

Sandro Carrara, Junrui Chen, Kapil Bhardwaj

The research presented in this article draws inspiration from previous efforts aimed at replicating the functions of various solid-state memristors using a variety of materials. The memristor circuit emulator serves as a cost-effective tool for circuit des ...

Ieee-Inst Electrical Electronics Engineers Inc2024

Meeting our Makers: Uncovering the cis-regulatory activity of transposable elements using statistical learning

Cyril David Son-Tuyên Pulver

The adaptation of organisms to their environment depends on the innovative potential inherent to genetic variation. In complex organisms such as mammals, processes like development and immunity require tight gene regulation. Complex forms emerge more often ...

EPFL2024

Single-cell epigenomic reconstruction of developmental trajectories from pluripotency in human neural organoid systems

Fides Zenk

Cell fate progression of pluripotent progenitors is strictly regulated, resulting in high human cell diversity. Epigenetic modifications also orchestrate cell fate restriction. Unveiling the epigenetic mechanisms underlying human cell diversity has been di ...

Nature Portfolio2024

Unified Harmonic Power-Flow and Stability Analysis of Power Grids with Converter-Interfaced Distributed Energy Resources

Johanna Kristin Maria Becker

Modern power distribution systems are experiencing a large-scale integration of Converter-Interfaced Distributed Energy Resources (CIDERs). Their presence complicates the analysis and mitigation of harmonics, whose creation and propagation may be amplified ...

EPFL2024

Ancestral genome reconstruction enhances transposable element annotation by identifying degenerate integrants

Didier Trono, Evaristo Jose Planet Letschert, Wayo Matsushima

Growing evidence indicates that transposable elements (TEs) play important roles in evolution by providing genomes with coding and non-coding sequences. Identification of TE-derived functional elements, however, has relied on TE annotations in individual s ...

2024

Quantitative characterization of the inorganic phosphate gene regulatory networks in S. cerevisiae and bottom up engineering an orthogonal gene network

Shiyu Cheng

Gene regulatory networks (GRNs) play a crucial role in an organism's response to changing environmental conditions. Cellular behaviors typically result from the integration of multiple gene outputs, and their regulation often demands precise control of num ...

EPFL2024

Technology-Aware Logic Synthesis for Superconducting Electronics

Giovanni De Micheli, Dewmini Sudara Marakkalage, Siang-Yun Lee, Alessandro Tempia Calvino, Mingfei Yu, Rassul Bairamkulov

Superconducting electronics provide us with cryogenic digital circuits that can rival established technologies in performance and energy consumption. Today, the lack of tools for the design of large-scale integrated superconducting circuits is a major obst ...

2024

Decoding Chromatin Ubiquitylation: A Chemical Biology Perspective

Beat Fierz, Pauline Franz

Since Strahl and Allis proposed the "language of covalent histone modifications", a host of experimental studies have shed light on the different facets of chromatin regulation by epigenetic mechanisms. Initially proposed as a concept for controlling gene ...

Academic Press Ltd- Elsevier Science Ltd2024

Graph generative deep learning models with an application to circuit topologies

Igor Krawczuk

Modern integrated circuits are tiny yet incredibly complex technological artifacts, composed of millions and billions of individual structures working in unison. Managing their complexity and facilitating their design drove part of the co-evolution of mode ...

EPFL2024

Altruism, reciprocity, and tokens to reward forwarding data: Is that fair?

Verónica del Carmen Estrada Galiñanes, Arman Babaei

Decentralized storage networks offer services with intriguing possibilities to reduce inequalities in an extremely centralized market. Fair distribution of rewards, however, is still a persistent problem in the current generation of decentralized applicati ...

2024

The dynamic genetic determinants of increased transcriptional divergence in spermatids

Christina Ernst

Cis-genetic effects are key determinants of transcriptional divergence in discrete tissues and cell types. However, how cis- and trans-effects act across continuous trajectories of cellular differentiation in vivo is poorly understood. Here, we quantify al ...

Nature Portfolio2024

Highly Parallel RTL Simulation

Verification and testing of hardware heavily relies on cycle-accurate simulation of RTL. As single-processor performance is growing only slowly, conventional, single-threaded RTL simulation is becoming impractical for increasingly complex chip designs and ...

EPFL2024

Inheritance of H3K9 methylation regulates genome architecture in Drosophila early embryos

Fides Zenk

Constitutive heterochromatin is essential for transcriptional silencing and genome integrity. The establishment of constitutive heterochromatin in early embryos and its role in early fruitfly development are unknown. Lysine 9 trimethylation of histone H3 ( ...

Springernature2024

Statistical learning quantifies transposable element-mediated cis-regulation

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

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

Chromatin modules and their implication in genomic organization and gene regulation

Bart Deplancke, Judith Franziska Kribelbauer, 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

Design and manufacture of edible microfluidic logic gates

Dario Floreano, Shuhang Zhang, Bokeon Kwak

Edible robotics is an emerging research field with potential use in environmental, food, and medical scenarios. In this context, the design of edible control circuits could increase the behavioral complexity of edible robots and reduce their dependence on ...

IEEE2023

Environment-dependent epistasis increases phenotypic diversity in gene regulatory networks

Florence Gauye, Florian Baier

Mutations to gene regulatory networks can be maladaptive or a source of evolutionary novelty. Epistasis con-founds our understanding of how mutations affect the expression patterns of gene regulatory networks, a chal-lenge exacerbated by the dependence of ...

AMER ASSOC ADVANCEMENT SCIENCE2023

Deciphering the molecular events leading to the global restoration of the chromatin landscape during mitotic exit

Silja Michelle Placzek

Two fundamental properties of embryonic stem cells (ESCs) are their ability to self-renew and differentiate into all somatic cell types. Maintenance of their identity faces major challenges when transitioning through mitosis, as most DNA-binding proteins a ...

EPFL2023

Transcriptomic data meta-analysis reveals common and injury model specific gene expression changes in the regenerating zebrafish heart

Marius Alexandru Botos Rogozsan

Zebrafish have the capacity to fully regenerate the heart after an injury, which lies in sharp contrast to the irreversible loss of cardiomyocytes after a myocardial infarction in humans. Transcriptomics analysis has contributed to dissect underlying signa ...

Nature Portfolio2023

Instruction-Level Power Side-Channel Leakage Evaluation of Soft-Core CPUs on Shared FPGAs

Mirjana Stojilovic, Ognjen Glamocanin, Mathias Josef Payer, Shashwat Shrivastava, Jinwei Yao, Nour Ardo

Side-channel disassembly attacks recover CPU instructions from power or electromagnetic side-channel traces measured during code execution. These attacks typically rely on physical access, proximity to the victim device, and high sampling rate measuring in ...

2023