Host genomics of SARS-CoV-2 infection

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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 ...

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 ...

Benchmarking of scATAC-seq protocols demonstrates the effects of data quality on downstream analyses. ...

Digital contact tracing substantially improves the identification of high-risk contacts during pandemics. Despite several attempts to encourage people to use digital contact-tracing applications by developing and rolling out decentralized privacy-preservin ...

Two anaerobic, tetrachloroethene- (PCE-) respiring bacterial isolates, designated strain ACSDCE T and strain ACSTCE, were characterized using a polyphasic approach. Cells were Gram-stain-negative, motile, non-spore-forming and shared a vibrioid- to spirill ...

Vibrio cholerae has caused seven cholera pandemics in the past two centuries. The seventh and ongoing pandemic has been particularly severe on the African continent. Here, we report long read-based genome sequences of six V. cholerae strains isolated in th ...

In the context of SARS-CoV-2 pandemic, mathematical modelling has played a funda-mental role for making forecasts, simulating scenarios and evaluating the impact of pre-ventive political, social and pharmaceutical measures. Optimal control theory represent ...

5-Methylcytosine (5mC) is a widespread silencing mechanism that controls genomic parasites. In eukaryotes, 5mC has gained complex roles in gene regulation beyond parasite control, yet 5mC has also been lost in many lineages. The causes for 5mC retention an ...

Background Immersive virtual reality (iVR)-based digital therapeutics are gaining clinical attention in the field of pain management. Based on known analogies between pain and dyspnoea, we investigated the effects of visual respiratory feedback on persiste ...

DNA-binding proteins physically interact with the DNA and directly affect genomic functions. The eukaryotic genome is compacted into chromatin, limiting the DNA access to nuclear factors. In this Ph.D. thesis, I explored the dynamic mechanisms, that allow ...

How chronic mutational processes and punctuated bursts of DNA damage drive evolution of the cancer genome is poorly understood. Here, we demonstrate a strategy to disentangle and quantify distinct mechanisms underlying genome evolution in single cells, dur ...

Regulation of gene expression is a complex but highly guided process. While genomic technologies and computational approaches have allowed high-throughput mapping of cis-regulatory elements (CREs) and their interactions in 3D, their precise role in regulat ...

During the COVID-19 pandemic, forecasting COVID-19 trends to support planning and response was a priority for scientists and decision makers alike. In the United States, COVID-19 forecasting was coordinated by a large group of universities, companies, and ...

Coronary heart disease (CHD) is one of the most pressing health problems of our time and a major cause of preventable death. CHD results from complex interactions between genetic and environmental factors. Using multiplex serological testing for persistent ...

Global change exposes ecosystems to changes in the frequency, magnitude, and concomitancy of disturbances, which impact the composition and functioning of these systems. Here, we experimentally evaluate the effects of salinity disturbances and eutrophicati ...

Background: Transposable elements (TEs) have colonized the genomes of most metazoans, and many TE-embedded sequences function as cis-regulatory elements (CREs) for genes involved in a wide range of biological processes from early embryo- genesis to innate ...

Aerobic granular sludge (AGS) consists of a microbial consortium that has an important role in wastewater treatment. This study investigates AGS microorganisms cultivated in a laboratory-scale sequencing batch reactor. Metagenomic sequencing was conducted ...

Understanding the ecological impacts of viruses on natural and engineered ecosystems relies on the accurate identification of viral sequences from community sequencing data. To maximize viral recovery from metagenomes, researchers frequently combine viral ...

Genetic and cellular drivers of the cellular uptake of SARS-CoV-2 can be screened at high throughput via droplet microfluidics and size-exclusion methods for the analysis of the formation of fusions between cells expressing the virus's spike protein and ce ...

Host genomics of SARS-CoV-2 infection

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Modeling, analysis, and design of complex biological networks

Meeting our Makers: Uncovering the cis-regulatory activity of transposable elements using statistical learning

Systematic benchmarking of single-cell ATAC-sequencing protocols

DP-ACT: Decentralized Privacy-Preserving Asymmetric Digital Contact Tracing

Sulfurospirillum diekertiae sp. nov., a tetrachloroethene-respiring bacterium isolated from contaminated soil

Genome sequences of Vibrio cholerae strains isolated in the DRC between 2009 and 2012

Optimized numerical solutions of SIRDVW multiage model controlling SARS-CoV-2 vaccine roll out: An application to the Italian scenario

DNA methylation enables recurrent endogenization of giant viruses in an animal relative

Virtual reality intervention alleviates dyspnoea in patients recovering from COVID-19 pneumonia

Development of multiplexed single-molecule imaging techniques to study chromatin invasion dynamics of chromatin effector proteins

Single-mitosis dissection of acute and chronic DNA mutagenesis and repair

Chromatin modules and their implication in genomic organization and gene regulation

Challenges of COVID-19 Case Forecasting in the US, 2020-2021

Associations of genetic and infectious risk factors with coronary heart disease

The cost of adaptability: resource availability constrains functional stability under pulsed disturbances

Statistical learning quantifies transposable element-mediated cis-regulation

Microbial genome collection of aerobic granular sludge cultivated in sequencing batch reactors using different carbon source mixtures

Benchmarking informatics approaches for virus discovery: caution is needed when combining in silico identification methods

Screening for drivers of SARS-CoV-2 uptake