Daniel A Dalquen

University College London | UCL · Department of Genetics, Evolution and Environment (GEE)

Genomes and transcriptomes are now typically sequenced by individual laboratories but analyzing them often remains challenging. One essential step in many analyses lies in identifying orthologs-corresponding genes across multiple species-but this is far from trivial. The Orthologous MAtrix (OMA) database is a leading resource for identifying orthol...

Genomes and transcriptomes are now typically sequenced by individual labs, but analysing them often remains challenging. One essential step in many analyses lies in identifying orthologs — corresponding genes across multiple species — but this is far from trivial. The OMA (Orthologous MAtrix) database is a leading resource for identifying orthologs...

Deep coalescence and introgression make it challenging to infer phylogenetic relationships among closely related species that arose through radiative speciation events. Despite numerous phylogenetic analyses and the availability of whole genomes, the phylogeny in the Anopheles gambiae species complex has not been confidently resolved. Here we extra...

We discuss a few principles to guide the design of efficient Metropolis–Hastings proposals for well-behaved target distributions without deeply divided modes. We illustrate them by developing and evaluating novel proposal kernels using a variety of target distributions. Here, efficiency is measured by the variance ratio relative to the independent...

We develop a maximum likelihood (ML) method for estimating migration rates between species using genomic sequence data. A species tree is used to accommodate the phylogenetic relationships among three species, allowing for migration between the two sister species, while the third species is used as an outgroup. A Markov chain characterization of th...

Achieving high accuracy in orthology inference is essential for many comparative, evolutionary and functional genomic analyses, yet the true evolutionary history of genes is generally unknown and orthologs are used for very different applications across phyla, requiring different precision-recall trade-offs. As a result, it is difficult to assess t...

Bidirectional best hits (BBH), which entails identifying the pairs of genes in two di.erent genomes that are more similar to each other than either is to any other gene in the other genome, is a simple and widely used method to infer orthology. A recent study has analysed the link between BBH and orthology in bacteria and archaea and concluded that...

The identification of orthologous genes, a prerequisite for numerous analyses in comparative and functional genomics, is commonly performed computationally from protein sequences. Several previous studies have compared the accuracy of orthology inference methods, but simulated data has not typically been considered in cross-method assessment studie...

PDF containing Figures S1-S8. (PDF)

Background In eukaryotes, variation in gene copy numbers is often associated with deleterious effects, but may also have positive effects. For prokaryotes, studies on gene copy number variation are rare. Previous studies have suggested that high numbers of rRNA gene copies can be advantageous in environments with changing resource availability, but...

Distance matrix of cyanobacterial ITS-region. Distance matrix of the internal transcribed spacer sequence region in cyanobacteria. Genetic distances have been estimated according to the K80 substitution model. White lines separate sequence copies of different species. Distances ≥5.7 are displayed by the same blue color.

Distribution of 16S rRNA copy numbers using additional data from rrndb3. Boxplot representations of the 16S rRNA gene copy number distribution across the previously defined morphological groups. Additional data on 16S rRNA copy numbers were received from the rrndb-database [45]. Spearman’s rank correlation coefficient (ρ) and Pearson’s correlation...

Distance matrix of Bacteroidetes. Genetic distances have been estimated according to the K80 substitution model. White lines separate sequence copies of different species.

In computational evolutionary biology, verification and benchmarking is a challenging task because the evolutionary history of studied biological entities is usually not known. Computer programs for simulating sequence evolution in silico have shown to be viable test beds for the verification of newly developed methods and to compare different algo...

In computational evolutionary biology, verification and benchmarking is a challenging task because the evolutionary history of studied biological entities is usually not known. Computer programs for simulating sequence evolution in silico have shown to be viable test beds for the verification of newly developed methods and to compare different algo...

This paper evaluates hybrid hardware-software structures for acceleration and power savings in audio coding algorithms. Using the well known MPEG I/II layer 3 (mp3) decoder as example, we demonstrate the general principles and trade-offs. The results, obtained for mp3, are valid for (but not limited to) the full family of MPEG codecs, due to algori...