Publications associées à Analysis of Polycerate Mutants Reveals the Evolutionary Co-option of HOXD1 for Horn Patterning in Bovidae

Publications associées (37)

The dynamic genetic determinants of increased transcriptional divergence in spermatids

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

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

Climbing into their Skin to Understand Contextual Protein-Protein Associations and Localizations: Functional Investigations in Transgenic Live Model Organisms

Yimon Aye

Borrowing some quotes from Harper Lee's novel "To Kill A Mockingbird" to help frame our manuscript, we discuss methods to profile local proteomes. We initially focus on chemical biology regimens that function in live organisms and use reactive biotin speci ...

Wiley-V C H Verlag Gmbh2024

The autism susceptibility kinase, TAOK2, phosphorylates eEF2 and modulates translation

Nagammal Neelagandan

Genes implicated in translation control have been associated with autism spectrum disorders (ASDs). However, some important genetic causes of autism, including the 16p11.2 microdeletion, bear no obvious connection to translation. Here, we use proteomics, g ...

Amer Assoc Advancement Science2024

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

Identifying genetic and dietary modulators of metabolic disorders using systems genetics

Xiaoxu Li

Long-term consumption of lipid-rich foods can contribute to common metabolic diseases and systemic low-grade inflammation. However, dietary responses and the development of non-communicable diseases are shaped by genetic factors and gene-by-environment int ...

EPFL2023

Cis-regulatory effect of HPV integration is constrained by host chromatin architecture in cervical cancers

Daniele Tavernari

Human papillomavirus (HPV) infections are the primary drivers of cervical cancers, and often HPV DNA gets integrated into the host genome. Although the oncogenic impact of HPV encoded genes is relatively well known, the cis-regulatory effect of integrated ...

Wiley2023

Genetic features and genomic targets of human KRAB-zinc finger proteins

Jacques Fellay, Didier Trono, Priscilla Turelli, Christian Axel Wandall Thorball, Julien Léonard Duc, Sandra Eloise Kjeldsen, Evaristo Jose Planet Letschert, Alexandre Coudray, Michaël Imbeault, Cyril David Son-Tuyên Pulver, Romain Forey, Jonas Caspar De Tribolet-Hardy

Krüppel-associated box (KRAB) domain-containing zinc finger proteins (KZFPs) are one of the largest groups of transcription factors encoded by tetrapods, with 378 members in human alone. KZFP genes are often grouped in clusters reflecting amplification by ...

2023

Wide-scale identification of novel/eliminated genes responsible for evolutionary transformations

Daria Korotkova

BackgroundIt is generally accepted that most evolutionary transformations at the phenotype level are associated either with rearrangements of genomic regulatory elements, which control the activity of gene networks, or with changes in the amino acid conten ...

2023

DNA modifications impact natural transformation of Acinetobacter baumannii

Melanie Blokesch, Nicolas Jean Philippe Guex, Christian Iseli, Alexandre Lemopoulos, Nina Vesel

Acinetobacter baumannii is a dangerous nosocomial pathogen, especially due to its ability to rapidly acquire new genetic traits, including antibiotic resistance genes (ARG). In A. baumannii, natural competence for transformation, one of the primary modes o ...

2023

Disruption of stem cell niche-confined R-spondin 3 expression leads to impaired hematopoiesis

Freddy Radtke, Ute Koch

Self-renewal and differentiation of stem and progenitor cells are tightly regulated to ensure tissue homeostasis. This regulation is enabled both remotely by systemic circulating cues, such as cytokines and hormones, and locally by various niche-confined f ...

ELSEVIER2023

Association of a Polygenic Risk Score With Osteoporosis in People Living With HIV: The Swiss HIV Cohort Study

Jacques Fellay, Christian Axel Wandall Thorball

An individual polygenic risk score was associated with osteoporosis in people living with HIV. The genetic effect was robust, as it persisted after multivariable adjustment for established traditional and HIV-related osteoporosis risk factors, including te ...

OXFORD UNIV PRESS INC2023

Predicting type 2 diabetes risk before and after solid organ transplantation using polygenic scores in a Danish cohort

Jacques Fellay, Christian Axel Wandall Thorball

Type 2 diabetes mellitus (T2DM) can be multifactorial where both genetics and environmental factors play a role. We aimed to investigate the use of polygenic risk scores (PRS) in the prediction of pre-transplant T2DM and post-transplant diabetes mellitus ( ...

Frontiers Media Sa2023

Stable parameterization of continuous and piecewise-linear functions

Michaël Unser, Alexis Marie Frederic Goujon, Joaquim Gonçalves Garcia Barreto Campos

Rectified-linear-unit (ReLU) neural networks, which play a prominent role in deep learning, generate continuous and piecewise-linear (CPWL) functions. While they provide a powerful parametric representation, the mapping between the parameter and function s ...

2023

Neural ADMIXTURE for rapid genomic clustering

Albert Dominguez Mantes

Characterizing the genetic structure of large cohorts has become increasingly important as genetic studies extend to massive, increasingly diverse biobanks. Popular methods decompose individual genomes into fractional cluster assignments with each cluster ...

SPRINGERNATURE2023

Extracting phylogenetic dimensions of coevolution reveals hidden functional signals

Anne-Florence Raphaëlle Bitbol

Despite the structural and functional information contained in the statistical coupling between pairs of residues in a protein, coevolution associated with function is often obscured by artifactual signals such as genetic drift, which shapes a protein's ph ...

Nature Portfolio2022

Towards mouse genetic-specific RNA-sequencing read mapping

Maxime Jan

Genetic variations affect behavior and cause disease but understanding how these variants drive complex traits is still an open question. A common approach is to link the genetic variants to intermediate molecular phenotypes such as the transcriptome using ...

2022

Generation of a Gal4-dependent gene recombination and illuminating mouse

Freddy Radtke

Cell labeling technologies, including the Cre/loxP system, are powerful tools in developmental biology. Although the conventional Cre/loxP system has been extensively used to label the expression of specific genes, it is less frequently used for labeling p ...

INT PRESS EDITING CENTRE INC2022

Natural competence of the pathogen Acinetobacter baumannii: an elusive phenomenon

Nina Vesel

Natural competence for transformation is an important driver of horizontal DNA exchange between different organisms. This can result in accumulation of dangerous genetic features, such as antibiotic resistance genes, in a single organism. One example of an ...

EPFL2022

Derivative voltammetry: a simple tool to probe reaction selectivity in photoelectrochemical cells

Kevin Sivula, Florent Alexandre Boudoire, Nukorn Plainpan

We demonstrate the use of the derivative voltammogram method to predict the selectivity of the photo-driven oxidation of 5-hydroxymethylfurfural (HMF) on a WO3 photoanode as a function of applied potential using only information obtained from the linear sw ...

2022