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Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach

Related publications (30)

Identifying genetic and dietary modulators of metabolic disorders using systems genetics

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

Aging Fly Cell Atlas identifies exhaustive aging features at cellular resolution

Maria Brbic, Sandy Lee

Aging is characterized by a decline in tissue function, but the underlying changes at cellular resolution across the organism remain unclear. Here, we present the Aging Fly Cell Atlas, a single-nucleus transcriptomic map of the whole aging Drosophila. We c ...

American Association for the Advancement of Science2023

Efficient and sensitive profiling of RNA–protein interactions using TLC-CLIP

Didier Trono, Julien Léonard Duc, Christina Ernst

RNA-binding proteins are instrumental for post-transcriptional gene regulation, controlling all aspects throughout the lifecycle of RNA molecules. However, transcriptome-wide methods to profile RNA-protein interactions in vivo remain technically challengin ...

2023

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

Modeling, analysis, and design of complex biological networks

Mohammadomid Oftadeh

Automating experimental procedures has resulted in an unprecedented increase in the volume of generated data, which, in turn, has caused an accumulation of unprocessed data. As a result, the need to develop tools to analyze data systematically has been ris ...

EPFL2023

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

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

SARS-CoV-2 hijacks a cell damage response, which induces transcription of a more efficient Spike S-acyltransferase

Béatrice Kunz, Didier Trono, Françoise Gisou van der Goot Grunberg, Laurence Gouzi Abrami, Audrey Geneviève Chuat, Francisco De Magalhães Sarmento R De Mesquita, Lucie Josepha Marie Bracq, Joana Carlevaro Fita, Nattawadee Panyain

SARS-CoV-2 infection requires Spike protein-mediated fusion between the viral and cellular membranes. The fusogenic activity of Spike depends on its post-translational lipid modification by host S-acyltransferases, predominantly ZDHHC20. Previous observati ...

Nature Research2023

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

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

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

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