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Symbolic kinetic models in python (SKiMpy): intuitive modeling of large-scale biological kinetic models
Publications associées (33)
Aging Fly Cell Atlas identifies exhaustive aging features at cellular resolution
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 ...
AMER ASSOC ADVANCEMENT SCIENCE2023Current challenges in understanding the role of enhancers in disease
Enhancers play a central role in the spatiotemporal control of gene expression and tend to work in a cell-type-specific manner. In addition, they are suggested to be major contributors to phenotypic variation, evolution and disease. There is growing eviden ...
NATURE PORTFOLIO2022Transposable elements contribute to the spatiotemporal microRNA landscape in human brain development
Didier Trono, Evaristo Jose Planet Letschert, Shaoline Sheppard, Christopher James Playfoot
Transposable elements (TEs) contribute to the evolution of gene regulatory networks and are dynamically expressed throughout human brain development and disease. One gene regulatory mechanism influenced by TEs is the miRNA system of post-transcriptional co ...
2022New and improved methods for integrated models of metabolism and gene expression
The beginning of the 21st century was marked by the advent of disruptive technologies, which ushered an era of groundbreaking advances in fundamental sciences, carried by the great pace at which computational capabilities spread and evolved. But the new ce ...
EPFL2021The emergence and promise of single-cell temporal-omics approaches
Gioele La Manno, Alex Russell Lederer
Single-cell transcriptomics enables the measurement of gene expression in complex biological systems at the resolution of individual cells. Multivariate analysis of single-cell data helps describe the variation in expression accompanying cellular processes ...
CURRENT BIOLOGY LTD2020The Ovulatory Signal Precipitates LRH-1 Transcriptional Switching Mediated by Differential Chromatin Accessibility
In the ovary, follicular growth and maturation are complicated processes that involve a series of morphological and physiological changes in oocytes and somatic cells leading to ovulation and luteinization, essential processes for fertility. Given the comp ...
CELL PRESS2019Enhanced flux prediction by integrating relative expression and relative metabolite abundance into thermodynamically consistent metabolic models
Vassily Hatzimanikatis, Noushin Hadadi, Vikash Kumar Pandey
The ever-increasing availability of transcriptomic and metabolomic data can be used to deeply analyze and make ever-expanding predictions about biological processes, as changes in the reaction fluxes through genome-wide pathways can now be tracked. Current ...
2019Circadian clock- and feeding-dependent regulation of translation initiation and elongation in the liver
Circadian rhythms allow organisms to anticipate and adapt to periodic environmental changes related to the day-night cycle. These rhythms originate from a genetic network ticking in almost every cell of our body and the coordination between different organ ...
EPFL2018Assessment of early response biomarkers in relation to long-term survival in patients with HER2-negative breast cancer receiving neoadjuvant chemotherapy plus bevacizumab: Results from the Phase II PROMIX trial
Pathologic complete response (pCR) is a predictor for favorable outcome after neoadjuvant treatment in early breast cancer. Modulation of gene expression may also provide early readouts of biological activity and prognosis, offering the possibility for tim ...
Wiley2018The evolution of gene expression and binding specificity of the largest transcription factor family in primates
Didier Trono, Jeffrey David Jensen, Adamantia Kapopoulou, Lisha Mathew
The KRAB-containing zinc finger (KRAB-ZF) proteins represent the largest family of transcription factors (TFs) in humans, yet for the great majority, their function and specific genomic target remain unknown. However, it has been shown that a large fractio ...
Wiley-Blackwell2016