Computational and Statistical analyses of Molecular Evolution and Demography using Large-scale Sequencing Data

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Background: Reproductive isolation can result from adaptive processes (e.g., ecological speciation and mutation-order speciation) or stochastic processes such as "system drift" model. Ecological speciation predicts barriers to gene flow between populations ...

Growing evidence indicates that transposable elements (TEs) play important roles in evolution by providing genomes with coding and non-coding sequences. Identification of TE-derived functional elements, however, has relied on TE annotations in individual s ...

Viral metagenomics is a useful tool for detecting multiple human viruses in urban sewage. However, more refined protocols are required for its effective use in disease surveillance. In this study, we investigated the performance of three different preampli ...

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 ...

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 ...

Mammalian tail length is controlled by several genetic determinants, among which are Hox13 genes, whose function is to terminate the body axis. Accordingly, the precise timing in the transcriptional activation of these genes may impact upon body length. Un ...

High-throughput transcriptomics is of increasing fundamental biological and clinical interest. The generation of molecular data from large collections of samples, such as biobanks and drug libraries, is boosting the development of new biomarkers and treatm ...

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 ...

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 ...

Microorganisms are a key component in the chain of life. They are essential for agriculture, produce a large proportion of oxygen, and play a central role in the cycle of elements. Microorganisms are widely used in the production of food and alcoholic beve ...

Glacier-fed streams are the cold, ultra-oligotrophic, and unstable streams that are fed by glacial meltwater. Despite these extreme conditions, they harbour a diverse and abundant microbial diversity that develops into biofilms, covering the boulders and s ...

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 ...

Cell fate progression of pluripotent progenitors is strictly regulated, resulting in high human cell diversity. Epigenetic modifications also orchestrate cell fate restriction. Unveiling the epigenetic mechanisms underlying human cell diversity has been di ...

Cis-genetic effects are key determinants of transcriptional divergence in discrete tissues and cell types. However, how cis- and trans-effects act across continuous trajectories of cellular differentiation in vivo is poorly understood. Here, we quantify al ...

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 ...

Owing to stochastic fluctuations arising from finite population size, known as genetic drift, the ability of a population to explore a rugged fitness landscape depends on its size. In the weak mutation regime, while the mean steady-state fitness increases ...

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 ...

Previous studies have identified topologically associating domains (TADs) as basic units of genome organization. We present evidence of a previously unreported level of genome folding, where distant TAD pairs, megabases apart, interact to form meta-domains ...

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 ...

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 ...

Computational and Statistical analyses of Molecular Evolution and Demography using Large-scale Sequencing Data

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Reproductive isolation arises during laboratory adaptation to a novel hot environment

Ancestral genome reconstruction enhances transposable element annotation by identifying degenerate integrants

Comparison of Three Viral Nucleic Acid Preamplification Pipelines for Sewage Viral Metagenomics

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

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

CTCF-dependent insulation of Hoxb13 and the heterochronic control of tail length

Multi-well plate lid for single-step pooling of 96 samples for high-throughput barcode-based sequencing

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

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

Reconstruction and analysis of genome-scale metabolic networks in single organisms and microbial communities

The microbial genomics of glacier-fed streams: adaptations to an extreme ecosystem

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

Single-cell epigenomic reconstruction of developmental trajectories from pluripotency in human neural organoid systems

The dynamic genetic determinants of increased transcriptional divergence in spermatids

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

Impact of population size on early adaptation in rugged fitness landscapes

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

Chromosome-level organization of the regulatory genome in the Drosophila nervous system

Identifying genetic and dietary modulators of metabolic disorders using systems genetics

Modeling, analysis, and design of complex biological networks