Publications related to Bypass of the requirement for cdc16p GAP function in Schizosaccharomyces pombe by mutation of the septation initiation network genes

The role of LRRK2 in lung adenocarcinoma

Lung cancer is the leading cause of cancer-related deaths worldwide and the most common lung cancer subtype is lung adenocarcinoma (LUAD). Frequently mutated genes involve activating mutations in KRAS and loss of function mutations in TP53. LUADs primarily ...

EPFL2024

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

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

Toward universal cell embeddings: integrating single-cell RNA-seq datasets across species with SATURN

Maria Brbic, Ziang Li

Analysis of single-cell datasets generated from diverse organisms offers unprecedented opportunities to unravel fundamental evolutionary processes of conservation and diversification of cell types. However, interspecies genomic differences limit the joint ...

Nature Portfolio2024

Single-mitosis dissection of acute and chronic DNA mutagenesis and repair

Christina Ernst

How chronic mutational processes and punctuated bursts of DNA damage drive evolution of the cancer genome is poorly understood. Here, we demonstrate a strategy to disentangle and quantify distinct mechanisms underlying genome evolution in single cells, dur ...

Nature Portfolio2024

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

Variant-specific pathophysiological mechanisms of AFF3 differently influence transcriptome profiles

Christian Iseli, Nicolas Jean Philippe Guex, Giovanna Ambrosini

Background: We previously described the KINSSHIP syndrome, an autosomal dominant disorder associated with intellectual disability (ID), mesomelic dysplasia and horseshoe kidney,caused by de novo variants in the degron of AFF3. Mouse knock-ins and overexpre ...

BMC2024

A common NFKB1 variant detected through antibody analysis in UK Biobank predicts risk of infection and allergy

Jacques Fellay, Flavia Aurelia Shoko Hodel

Infectious agents contribute significantly to the global burden of diseases through both acute infection and their chronic sequelae. We leveraged the UK Biobank to identify genetic loci that influence humoral immune response to multiple infections. From 45 ...

2024

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

Mutation-Attention (MuAt): deep representation learning of somatic mutations for tumour typing and subtyping

Sebastian Martin Waszak

Background: Cancer genome sequencing enables accurate classification of tumours and tumour subtypes. However, prediction performance is still limited using exome-only sequencing and for tumour types with low somatic mutation burden such as many paediatri ...

2023

Cryo-EM structures and binding of mouse and human ACE2 to SARS-CoV-2 variants of concern indicate that mutations enabling immune escape could expand host range

Henning Paul-Julius Stahlberg, Didier Trono, Priscilla Turelli, Florence Pojer, Sergey Nazarov, Kelvin Ka Ching Lau, Dongchun Ni, Alexander Myasnikov, Emiko Uchikawa

nvestigation of potential hosts of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is crucial to understanding future risks of spillover and spillback. SARS-CoV-2 has been reported to be transmitted from humans to various animals after req ...

2023

Characterisation of conditional alleles of the Schizosaccharomyces pombe cytokinesis regulator byr4

Michael Grüner Vindfeldt

Regulation of cytokinesis is essential for the cell during its division cycle. Failure to do so can lead to aneuploidy, which can be fatal and lead to senescence or cancer. A useful model organism for studying cytokinesis in eukaryotes is Schizosaccharomyc ...

EPFL2023

Primary data for EPFL thesis "Characterisation of conditional alleles of the Schizosaccharomyces pombe cytokinesis regulator byr4"

Michael Grüner Vindfeldt

Regulation of cytokinesis is essential for the cell during its division cycle. Failure to do so can lead to aneuploidy, which can be fatal and lead to senescence or cancer. A useful model organism for studying cytokinesis in eukaryotes is Schizosaccharomyc ...

EPFL Infoscience2023

The role of the NF-kappaB pathway in Amyotrophic lateral sclerosis pathogenesis

Emma Charlotta Källstig

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative motor disorder, which results in death within a few years of diagnosis. While the cause of most cases of ALS is unknown, 10% of cases are familial (fALS), and associated with mutations in one of ov ...

EPFL2023

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

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

Reanalysis of mtDNA mutations of human primordial germ cells (PGCs) reveals NUMT contamination and suggests that selection in PGCs may be positive

Konstantin Popadin

The resilience of the mitochondrial genome (mtDNA) to a high mutational pressure depends, in part, on negative purifying selection in the germline. A paradigm in the field has been that such selection, at least in part, takes place in primordial germ cells ...

Elsevier Sci Ltd2023

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

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

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 ...

National Academy of Sciences2023

Optimization of elastic wave propagation in a reconfigurable medium by genetic algorithms with adaptive mutation probability

Romain Christophe Rémy Fleury, Janez Rus

We introduce a reconfigurable medium for the manipulation of elastic propagation properties of Lamb waves. It is based on a shape memory polymer (SMP) with temperature-dependent Young's modulus. Waves are excited by a laser pulse and detected by a laser vi ...

IOP Publishing Ltd2023

Computational Studies for the Design of Metalloenzyme Mimics

Guido Frisari

At present, there is no general standard automated method for engineering metalloenzymes, industrially-relevant systems able to catalyze environmentally friendly reactions. One of the most studied natural metalloenzymes is the second isoform of human carbo ...

EPFL2023