Improving inference of transcriptional regulatory networks based on network evolutionary models

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Text-to-image models, such as Stable Diffusion, can generate high-quality images from simple textual prompts. With methods such as Textual Inversion, it is possible to expand the vocabulary of these models with additional concepts, by learning the vocabula ...

Temporal activation of Hox genes in mouse pseudo-embryos in vitro initiates at the anterior part of the cluster and is accompanied by asymmetric loading of cohesin. Posterior CTCF sites then successively act as transient insulators, regulating the timed tr ...

In this work, we present, analyze, and implement a class of multilevel Markov chain Monte Carlo(ML-MCMC) algorithms based on independent Metropolis--Hastings proposals for Bayesian inverse problems. In this context, the likelihood function involves solving ...

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 ...

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 ...

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 ...

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 ...

The design of an oil free turbocharger supported on herringbone grooved gas bearing was formulated as a multi-objective problem, which was solved by coupling a reduced order parametric model for gas bearing supported rotors with an evolutionary algorithm. ...

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 ...

Modern machine learning (ML) models are capable of impressive performances. However, their prowess is not due only to the improvements in their architecture and training algorithms but also to a drastic increase in computational power used to train them.|S ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

Improving inference of transcriptional regulatory networks based on network evolutionary models

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VETIM: Expanding the Vocabulary of Text-to-Image Models only with Text

Sequential and directional insulation by conserved CTCF sites underlies the Hox timer in stembryos

Analysis of a Class of Multilevel Markov Chain Monte Carlo Algorithms Based on Independent Metropolis–Hastings

Spatiotemporal wildfire modeling through point processes with moderate and extreme marks

Deciphering the molecular events leading to the global restoration of the chromatin landscape during mitotic exit

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

Cellularization across eukaryotes: Conserved mechanisms and novel strategies

Design and experimental investigation of a herringbone grooved gas bearing supported turbocharger

Development of a Robotic Microsurgeon for Embryonic Research

Byzantine-Resilient Learning Beyond Gradients: Distributing Evolutionary Search

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

PSGL-1 is an evolutionarily conserved antiviral restriction factor

Transcriptomic data meta-analysis reveals common and injury model specific gene expression changes in the regenerating zebrafish heart

Identifying genetic and dietary modulators of metabolic disorders using systems genetics

Transposon-activated POU5F1B promotes colorectal cancer growth and metastasis

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

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