A5079496228- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- Evolution and Genetic Dynamics
- Algorithms and Data Compression
- Chromosomal and Genetic Variations
- Genetic diversity and population structure
- Bioinformatics and Genomic Networks
- Cystic Fibrosis Research Advances
- Protein Structure and Dynamics
- Microbial Metabolic Engineering and Bioproduction
- Machine Learning in Bioinformatics
- Origins and Evolution of Life
- RNA modifications and cancer
- Genome Rearrangement Algorithms
- RNA Research and Splicing
- Bayesian Methods and Mixture Models
- Genomics and Chromatin Dynamics
- Genetic Associations and Epidemiology
- HIV Research and Treatment
- Genetics, Bioinformatics, and Biomedical Research
- Genetic Mapping and Diversity in Plants and Animals
- CRISPR and Genetic Engineering
- Gene expression and cancer classification
- Photosynthetic Processes and Mechanisms
- Ecosystem dynamics and resilience
Universitätsklinik Balgrist
2025
University of Zurich
2025
University of Oxford
2015-2024
Turing Institute
2019-2023
The Alan Turing Institute
2019-2023
British Library
2019-2023
Tel Aviv University
2018
Reykjavík University
2013
University of North Carolina at Chapel Hill
2013
University of Cape Town
2013
Abstract We investigate the shape of a phylogenetic tree reconstructed from sequences evolving under coalescent with recombination. The motivation is that evolutionary inferences are often made trees population data even though recombination may well occur (mtDNA or viral sequences) does (nuclear sequences). size and direction biases when single ignoring Standard software (PHYLIP) was used to construct best simulated With present, length terminal branches total branch larger, time most...
RNA secondary structures are important in many biological processes and efficient structure prediction can give vital directions for experimental investigations. Many available programs only use a single sequence at time. This may be sufficient some applications, but often it is possible to obtain related sequences with conserved structure. These should included structural analyses improved results. work presents practical way of predicting that especially useful when obtained. The method...
Abstract MOTIVATION: Many computerized methods for RNA secondary structure prediction have been developed. Few of these methods, however, employ an evolutionary model, thus relevant information is often left out from the determination. This paper introduces a method which incorporates history into prediction. The reported here based on stochastic context-free grammars (SCFGs) to give prior probability distribution structures. RESULTS: phylogenetic tree relating sequences can be found by...
Abstract Background Two central problems in computational biology are the determination of alignment and phylogeny a set biological sequences. The traditional approach to this problem is first build multiple these sequences, followed by phylogenetic reconstruction step based on alignment. However, inference fundamentally interdependent, ignoring fact leads biased overconfident estimations. Whether main interest be sequence or phylogeny, major goal co-estimation both. Results We developed...
Among the fundamental problems in molecular evolution and analysis of homologous sequences are alignment, phylogeny reconstruction, reconstruction ancestral sequences. This paper presents a fast, combined solution to these problems. The new algorithm gives an approximation minimal history terms distance function on is weighted path length constructed from substitutions insertions-deletions segments any length. Substitutions with arbitrary metric set nucleotides or amino acids, indels gap...
It has become clear that a large proportion of functional DNA in the human genome does not code for protein. Identification this non-coding sequence using comparative approaches is proving difficult and previously been thought to require deep sequencing multiple vertebrates. Here we introduce new model method that, instead nucleotide substitutions, uses evolutionary imprint insertions deletions (indels) infer past consequences selection. The predicts distribution indels under neutrality,...
The origin of life is one the most fundamental, but also difficult problems in science. Despite differences between various proposed scenarios, common element seems to be emergence an autocatalytic set or cycle at some stage. However, there still disagreement as how likely it that such self-sustaining sets could arise “spontaneously”. This largely caused by lack formal models. Here, we briefly review criticism against and evidence favor sets, then make a case for their plausibility based on...
Sequence alignment underpins all of comparative genomics, yet it remains an incompletely solved problem. In particular, the statistical uncertainty within inferred alignments is often disregarded, while parametric or phylogenetic inferences are considered meaningless without confidence estimates. Here, we report on a theoretical and simulation study pairwise genomic DNA at human-mouse divergence. We find that >15% aligned bases incorrect in existing whole-genome alignments, identify three...
Abstract Finding causal relationships between genotypic and phenotypic variation is a key focus of evolutionary biology, human genetics plant breeding. To identify genome-wide patterns underlying trait diversity, we assembled high-quality reference genome Cardamine hirsuta , close relative the model Arabidopsis thaliana . We combined comparative transcriptome analyses with experimental tools available in C. to investigate gene function diversification. Our findings highlight prevalent role...
The evolutionary process of genetic recombination has the potential to rapidly change properties a viral pathogen, and its presence is crucial factor consider in development treatments vaccines. It can also significantly affect results phylogenetic analyses inference rates. detection from samples sequencing data very challenging problem further complicated for SARS-CoV-2 by relatively slow accumulation diversity. extent which ongoing not yet resolved. To address this, we use parsimony-based...
By viewing the ancestral recombination graph as defining a sequence of trees, we show how possible evolutionary histories consistent with given data can be constructed using minimum number events. In contrast to previously known methods, which yield only estimated lower bounds, our method detecting always gives events if right kind rooted trees are used in algorithm. A new bound defined fewer constraints used. As well studying often it actually is equal minimum, test this performs comparison...
Abstract In this article we develop a coalescent model with intralocus gene conversion. The distribution of the tract length is geometric in concordance results published literature. We derive simulation scheme and deduce number analytical for compare patterns variability samples simulated according to recombination similar conversion alone. Further, an expression expected topology shifts sample present-day sequences caused by events derived.
Abstract Motivation: Bayesian analysis is one of the most popular methods in phylogenetic inference. The commonly used fix a single multiple alignment and consider only substitutions as phylogenetically informative mutations, though alignments phylogenies should be inferred jointly insertions deletions also carry signals. Methods addressing these issues have been developed recently there has not so far user-friendly program with graphical interface that implements methods. Results: We an...
Abstract Background RNA secondary structure prediction, or folding, is a classic problem in bioinformatics: given sequence of nucleotides, the aim to predict base pairs formed its three dimensional conformation. The inverse designing folding into particular target has only more recently received notable interest. With growing appreciation and understanding functional structural properties motifs, interest utilising biomolecules nano-scale designs, bound increase. However, whereas from an...