Publication

Refining transcriptional regulatory networks using network evolutionary models and gene histories

Publications associées (30)

Spatiotemporal wildfire modeling through point processes with moderate and extreme marks

Accurate spatiotemporal modeling of conditions leading to moderate and large wildfires provides better understanding of mechanisms driving fire-prone ecosystems and improves risk management. Here, we develop a joint model for the occurrence intensity and t ...

2023

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

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

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

Development of a Robotic Microsurgeon for Embryonic Research

Ece Özelçi

Understanding how biological matter takes its shape is instrumental to biology, bioengineering, medicine, and bioinspired engineering. Gaining information on the principles of morphogenesis could enable clinicians to correct developmental abnormalities, ev ...

EPFL2023

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

Giovanni Ciriello, 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

PSGL-1 is an evolutionarily conserved antiviral restriction factor

Chao Jiang, Ying Liu

The arms race between viruses and their hosts shaped the evolutionary history and the genome composition of both parties. Restriction factors are the first-line antiviral effectors encoded by the host genomes and are often conserved through evolution to pr ...

AMER SOC MICROBIOLOGY2023

Transposon-activated POU5F1B promotes colorectal cancer growth and metastasis

Didier Trono, Laurence Gouzi Abrami, Julien Léonard Duc, Sandra Eloise Kjeldsen, Alexandre Coudray, Sagane Dind, Evaristo Jose Planet Letschert, Laia Simo Riudalbas

The treatment of colorectal cancer (CRC) is an unmet medical need in absence of early diagnosis. Here, upon characterizing cancer-specific transposable element-driven transpochimeric gene transcripts (TcGTs) produced by this tumor in the SYSCOL cohort, we ...

Nature Research2022

Phylogenetic estimation of the viral fitness landscape of HIV-1 set-point viral load

Jacques Fellay, Luca Ferretti

Set-point viral load (SPVL), a common measure of human immunodeficiency virus (HIV)-1 virulence, is partially determined by viral genotype. Epidemiological evidence suggests that this viral property has been under stabilising selection, with a typical opti ...

OXFORD UNIV PRESS2022

From Trees to Barcodes and Back Again: A Combinatorial, Probabilistic and Geometric Study of a Topological Inverse Problem

Adélie Eliane Garin

In this thesis, we investigate the inverse problem of trees and barcodes from a combinatorial, geometric, probabilistic and statistical point of view. Computing the persistent homology of a merge tree yields a barcode B. Reconstructing a tree from B invol ...

EPFL2022