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Publications associées (76)

Optimality principles for the analysis of biological processes across scales: From enzyme kinetics to microbiome dynamics

Microorganisms are essential for life on Earth, performing key roles in numerous biological processes. Their influence extends across a wide spectrum, from human health and ecological balance to advancements in biotechnology and industrial applications. Th ...

EPFL2024

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 ...

Weinheim2023

Network Alignment With Holistic Embeddings

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

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

Perfect adaptation achieved by transport limitations governs the inorganic phosphate response in S. cerevisiae

Sebastian Maerkl, Shiyu Cheng, Hon Ming Andrew Yip, Evan James Olson, Michael Andrew Crone

Cells cope with and adapt to ever-changing environmental conditions. Sophisticated regulatory networks allow cells to adjust to these fluctuating environments. One such archetypal system is the Saccharomyces cerevisiae Pho regulon. When external inorganic ...

Washington2023

Bringing Functional Context to Emerging Proximity-mapping Proteomics Tools

Yimon Aye

If one considers chemical-biology toolsets that have had the greatest impact on numerous fields of life sciences over the most recent years, proximity-labeling tools, such as APEX, and Bio-ID arguably lead the way. This article reflects upon the current st ...

SWISS CHEMICAL SOC2022

Spearheading future omics analyses using dyngen, a multi-modal simulator of single cells

Wouter Saelens

We present dyngen, a multi-modal simulation engine for studying dynamic cellular processes at single-cell resolution. dyngen is more flexible than current single-cell simulation engines, and allows better method development and benchmarking, thereby stimul ...

NATURE RESEARCH2021

The influence of human genetic variation on Epstein–Barr virus sequence diversity

Jacques Fellay, Dylan Lawless, Olivier Noël Marie Naret, Christian Hammer, Sina Rüeger

Epstein–Barr virus (EBV) is one of the most common viruses latently infecting humans. Little is known about the impact of human genetic variation on the large inter-individual differences observed in response to EBV infection. To search for a potential imp ...

2021

HP agents and biochemical interactions

Hikari Ananda Infinity Yoshihara

The intense but transient increase in nuclear magnetic resonance signal provided by dynamic nuclear polarization (DNP) has enabled a range of new applications, including rapid, minimally-invasive metabolic imaging at the second timescale. This chapter prov ...

Academic Press2021

The more the merrier: how homo-oligomerization alters the interactome and function of ribonucleotide reductase

Yimon Aye

Stereotyped as a nexus of dNTP synthesis, the dual-subunit enzyme - ribonucleotide reductase (RNR) - is coming into view as a paradigm of oligomerization and moonlighting behavior. In the present issue of `omics', we discuss what makes the larger subunit o ...

ELSEVIER SCI LTD2020

Functional and Computational Genomics Reveal Unprecedented Flexibility in Stage-Specific Toxoplasma Metabolism

Vassily Hatzimanikatis, Matteo Lunghi, Damien Lionel Nicolas, Anush Chiappino-Pepe, Aarti Krishnan, Dominique Soldati-Favre

To survive and proliferate in diverse host environments with varying nutrient availability, the obligate intracellular parasite Toxoplasma gondii reprograms its metabolism. We have generated and curated a genome-scale metabolic model (iTgo) for the fast-re ...

CELL PRESS2020

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