TIBA: a tool for phylogeny inference from rearrangement data with bootstrap analysis

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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 ...

The Mycobacterium tuberculosis complex (MTBC) comprises nine human-adapted lineages that differ in their geographical distribution. Local adaptation of specific MTBC genotypes to the respective human host population has been invoked in this context. We aim ...

Local and global inference methods have been developed to infer structural contacts from multiple sequence alignments of homologous proteins. They rely on correlations in amino acid usage at contacting sites. Because homologous proteins share a common ance ...

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 ...

Outliers in discrete choice response data may result from misclassification and misreporting of the response variable and from choice behaviour that is inconsistent with modelling assumptions (e.g. random utility maximisation). In the presence of outliers, ...

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 ...

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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 ...

Despite the structural and functional information contained in the statistical coupling between pairs of residues in a protein, coevolution associated with function is often obscured by artifactual signals such as genetic drift, which shapes a protein's ph ...

In this thesis, we investigate the inverse problem of trees and barcodes from a combinatorial, geometric, probabilistic and statistical point of view. Computing the persistent homology of a merge tree yields a barcode B. Reconstructing a tree from B invol ...

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Background As trans women are disproportionately affected by the HIV epidemic, and are still understudied, we aimed to identify and characterize the trans women in the Swiss HIV Cohort Study (SHCS). Methods A combination of criteria from pre-existing cohor ...

Since its emergence in December 2019, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has spread globally and become a major public health burden. Despite its close phylogenetic relationship to SARS-CoV, SARS-CoV-2 exhibits increased human-to- ...

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Spiroplasma is a genus of Mollicutes whose members include plant pathogens, insect pathogens and endosymbionts of animals. Spiroplasma phenotypes have been repeatedly observed to be spontaneously lost in Drosophila cultures, and several studies have docume ...

The presence of the oligochaete species Quistadrilus multisetosus (Smith, 1900) originating from North America has been mentioned for several decades in Europe, the Middle East and Russia. Its distribution and abundance in Europe is still unknown but it ca ...

One of the most conserved traits in the evolution of biomineralizing organisms is the taxon-specific selection of skeletal minerals. All modern scleractinian corals are thought to produce skeletons exclusively of the calcium-carbonate polymorph aragonite. ...

TIBA: a tool for phylogeny inference from rearrangement data with bootstrap analysis

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

Bacterial diversity dominates variable macrophage responses of tuberculosis patients in Tanzania

Impact of phylogeny on structural contact inference from protein sequence data

Spatiotemporal wildfire modeling through point processes with moderate and extreme marks

Robust discrete choice models with t-distributed kernel errors

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

Regularization for distributionally robust state estimation and prediction

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

Extracting phylogenetic dimensions of coevolution reveals hidden functional signals

From Trees to Barcodes and Back Again: A Combinatorial, Probabilistic and Geometric Study of a Topological Inverse Problem

Transposon-activated POU5F1B promotes colorectal cancer growth and metastasis

The microbiome of cryospheric ecosystems

Filtered data and eigenfunction estimators for statistical inference of multiscale and interacting diffusion processes

HIERARCHICAL MARKOV CHAIN MONTE CARLO METHODS FOR BAYESIAN INVERSE PROBLEMS

Identifying and Characterizing Trans Women in the Swiss HIV Cohort Study as an Epidemiologically Distinct Risk Group

Disparate temperature-dependent virus-host dynamics for SARS-CoV-2 and SARS-CoV in the human respiratory epithelium

Sequential Domain Adaptation by Synthesizing Distributionally Robust Experts

Rapid molecular evolution of Spiroplasma symbionts of Drosophila

The foreign oligochaete species Quistadrilus multisetosus (Smith, 1900) in Lake Geneva: morphological and molecular characterization and environmental influences on its distribution

A modern scleractinian coral with a two-component calcite–aragonite skeleton