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View article: Evolution of gene order in prokaryotes is driven primarily by gene gain and loss
Evolution of gene order in prokaryotes is driven primarily by gene gain and loss Open
Evolution of bacterial and archaeal genomes is highly dynamic, including extensive gene gain via horizontal gene transfer (HGT) and gene loss as well as different types of genome rearrangements, such as inversions and translocations, so th…
View article: Evolution of gene order in prokaryotes is driven primarily by gene gain and loss
Evolution of gene order in prokaryotes is driven primarily by gene gain and loss Open
Evolution of bacterial and archaeal genomes is highly dynamic including extensive gene gain via horizontal gene transfer and gene loss as well as different types of genome rearrangements, such as inversions and translocations, so that gene…
View article: Untying Rates of Gene Gain and Loss Leads to a New Phylogenetic Approach
Untying Rates of Gene Gain and Loss Leads to a New Phylogenetic Approach Open
The advent of the genomic era has produced an incredible wealth and resolution of molecular data, posing an unprecedented challenge for molecular systematics, necessitating novel techniques and paradigms. Consequently, whole genome approac…
View article: The Multi-State Epigenetic Pacemaker enables the identification of combinations of factors that influence DNA methylation
The Multi-State Epigenetic Pacemaker enables the identification of combinations of factors that influence DNA methylation Open
Epigenetic clocks, DNA methylation-based predictive models of chronological age, are often utilized to study aging associated biology. Despite their widespread use, these methods do not account for other factors that also contribute to the…
View article: Outbreaks, Metastases and Homomorphisms: Phylogenetic Inference of Migration Histories of Heterogeneous Populations under Evolutionary and Structural Constraints
Outbreaks, Metastases and Homomorphisms: Phylogenetic Inference of Migration Histories of Heterogeneous Populations under Evolutionary and Structural Constraints Open
Many human diseases, including viral infections and cancers, are driven by the evolutionary dynamics of heterogeneous populations of genomic variants. A major type of evolutionary behavior of these populations is migration including viral …
View article: Privacy-preserving biological age prediction over federated human methylation data using fully homomorphic encryption
Privacy-preserving biological age prediction over federated human methylation data using fully homomorphic encryption Open
DNA methylation data play a crucial role in estimating chronological age in mammals, offering real-time insights into an individual's aging process. The epigenetic pacemaker (EPM) model allows inference of the biological age as deviations …
View article: Privacy Preserving Epigenetic PaceMaker Stronger Privacy and Improved Efficiency
Privacy Preserving Epigenetic PaceMaker Stronger Privacy and Improved Efficiency Open
DNA methylation data plays a crucial role in estimating chronological age in mammals, offering real-time insights into an individual’s aging process. The Epigenetic Pacemaker (EPM) model allows inference of the biological age as deviations…
View article: Identifying epigenetic aging moderators using the epigenetic pacemaker
Identifying epigenetic aging moderators using the epigenetic pacemaker Open
Epigenetic clocks are DNA methylation-based chronological age prediction models that are commonly employed to study age-related biology. The difference between the predicted and observed age is often interpreted as a form of biological age…
View article: The Multi-State Epigenetic Pacemaker enables the identification of combinations of factors that influence DNA methylation
The Multi-State Epigenetic Pacemaker enables the identification of combinations of factors that influence DNA methylation Open
Epigenetic clocks, DNA methylation based predictive models of chronological age, are often utilized to study aging associated biology. Despite their widespread use, these methods do not account for other factors that also contribute to the…
View article: The effects of age, sex, weight, and breed on canid methylomes
The effects of age, sex, weight, and breed on canid methylomes Open
Unlike genomes, which are static throughout the lifespan of an organism, DNA methylomes are dynamic. To study these dynamics, we developed quantitative models that measure the effect of multiple factors on DNA methylomes including, age, se…
View article: Gene Transfer-based Phylogenetics: Analytical Expressions and Additivity via Birth–Death Theory
Gene Transfer-based Phylogenetics: Analytical Expressions and Additivity via Birth–Death Theory Open
The genomic era has opened up vast opportunities in molecular systematics, one of which is deciphering the evolutionary history in fine detail. Under this mass of data, analysing the point mutations of standard markers is too crude and slo…
View article: The effects of age, sex, weight, and breed on canid methylomes
The effects of age, sex, weight, and breed on canid methylomes Open
Unlike genomes, which are static throughout the lifespan of an organism, DNA methylomes are dynamic. To study these dynamics, we developed quantitative models that measure the effect of multiple factors on DNA methylomes including, age, se…
View article: On the quartet distance given partial information
On the quartet distance given partial information Open
Let $T$ be an arbitrary phylogenetic tree with $n$ leaves. It is well-known that the average quartet distance between two assignments of taxa to the leaves of $T$ is $\frac 23 \binom{n}{4}$. However, a longstanding conjecture of Bandelt an…
View article: The Epigenetic Pacemaker is a more sensitive tool than penalized regression for identifying moderators of epigenetic aging
The Epigenetic Pacemaker is a more sensitive tool than penalized regression for identifying moderators of epigenetic aging Open
Epigenetic clocks, DNA methylation based chronological age prediction models, are commonly employed to study age related biology. The error between the predicted and observed age is often interpreted as a form of biological age acceleratio…
View article: Hibernation slows epigenetic aging in yellow-bellied marmots
Hibernation slows epigenetic aging in yellow-bellied marmots Open
Species that hibernate live longer than would be expected based solely on their body size. Hibernation is characterized by long periods of metabolic suppression (torpor) interspersed by short periods of increased metabolism (arousal). The …
View article: Hibernation slows epigenetic aging in yellow-bellied marmots
Hibernation slows epigenetic aging in yellow-bellied marmots Open
Species that hibernate live longer than would be expected based solely on their body size. Hibernation is characterized by long periods of metabolic suppression (torpor) interspersed by short periods of increased metabolism (arousal). The …
View article: Inference of mutability landscapes of tumors from single cell sequencing data
Inference of mutability landscapes of tumors from single cell sequencing data Open
One of the hallmarks of cancer is the extremely high mutability and genetic instability of tumor cells. Inherent heterogeneity of intra-tumor populations manifests itself in high variability of clone instability rates. Analogously to fitne…
View article: A New Phylogenomic Approach For Quantifying Horizontal Gene Transfer Trends in Prokaryotes
A New Phylogenomic Approach For Quantifying Horizontal Gene Transfer Trends in Prokaryotes Open
It is well established nowadays that among prokaryotes, various families of orthologous genes exhibit conflicting evolutionary history. A prime factor for this conflict is horizontal gene transfer (HGT) - the transfer of genetic material n…
View article: The Epigenetic Pacemaker: modeling epigenetic states under an evolutionary framework
The Epigenetic Pacemaker: modeling epigenetic states under an evolutionary framework Open
Summary Epigenetic rates of change, much as evolutionary mutation rate along a lineage, vary during lifetime. Accurate estimation of the epigenetic state has vast medical and biological implications. To account for these non-linear epigene…
View article: Detecting horizontal gene transfer: a probabilistic approach
Detecting horizontal gene transfer: a probabilistic approach Open
Background Horizontal gene transfer (HGT) is the event of a DNA sequence being transferred between species not by inheritance. HGT is a crucial factor in prokaryotic evolution and is a significant source for genomic novelty resulting in an…
View article: Horizontal Gene Transfer Phylogenetics: A Random Walk Approach
Horizontal Gene Transfer Phylogenetics: A Random Walk Approach Open
The dramatic decrease in time and cost for generating genetic sequence data has opened up vast opportunities in molecular systematics, one of which is the ability to decipher the evolutionary history of strains of a species. Under this fin…
View article: ‘Multi-SpaM’: a maximum-likelihood approach to phylogeny reconstruction using multiple spaced-word matches and quartet trees
‘Multi-SpaM’: a maximum-likelihood approach to phylogeny reconstruction using multiple spaced-word matches and quartet trees Open
Word-based or ‘alignment-free’ methods for phylogeny inference have become popular in recent years. These methods are much faster than traditional, alignment-based approaches, but they are generally less accurate. Most alignment-free metho…
View article: Human epigenetic ageing is logarithmic with time across the entire lifespan
Human epigenetic ageing is logarithmic with time across the entire lifespan Open
Epigenetic changes during ageing have been characterized by multiple epigenetic clocks that allow the prediction of chronological age based on methylation status. Despite their accuracy and utility, epigenetic age biomarkers leave many que…
View article: Human epigenetic ageing is logarithmic with time across the entire lifespan
Human epigenetic ageing is logarithmic with time across the entire lifespan Open
Epigenetic changes during ageing have been characterized by multiple epigenetic clocks that allow the prediction of chronological age based on methylation status. Despite their accuracy and utility, epigenetic age biomarkers leave many que…
View article: Human Epigenetic Aging is Logarithmic with Time across the Entire LifeSpan
Human Epigenetic Aging is Logarithmic with Time across the Entire LifeSpan Open
Epigenetic changes during aging have been characterized by multiple epigenetic clocks, that allow the prediction of chronological age based on methylation status. Despite their accuracy and utility, epigenetic age biomarkers leave many que…