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Fernando Izquierdo-Carrasco
Heidelberg Institute for Theoretical Studies
16Publications
7H-index
1,512Citations
Publications 16
Newest
#1Laura T Phillips (St George's, University of London)H-Index: 2
#2Adam A. Witney (St George's, University of London)H-Index: 28
Last.Syed Tariq Sadiq (St George's, University of London)H-Index: 17
view all 13 authors...
Introduction Next generation sequencing can accurately predict antibiotic susceptibility in Neisseria gonorrhoeae (NG) allowing preservation of first-line treatments in the face of widespread antimicrobial resistance (AMR). The rapid nature of novel hand-held nanopore sequencing (NPS) gives promise for utility at the point of care. We evaluated time to result post DNA extraction, and accuracy of MinION (Oxford Nanopore Technologies) NPS to predict phenotypic antimicrobial susceptibility (PAMS) o...
2 CitationsSource
#1Tomáš Flouri (Heidelberg Institute for Theoretical Studies)H-Index: 10
#2Fernando Izquierdo-Carrasco (Heidelberg Institute for Theoretical Studies)H-Index: 7
Last.Alexandros Stamatakis (Heidelberg Institute for Theoretical Studies)H-Index: 50
view all 8 authors...
We introduce the Phylogenetic Likelihood Library (PLL), a highly optimized application programming interface for developing likelihood-based phylogenetic inference and postanalysis software. The PLL implements appropriate data structures and functions that allow users to quickly implement common, error-prone, and labor-intensive tasks, such as likelihood calculations, model parameter as well as branch length optimization, and tree space exploration. The highly optimized and parallelized implemen...
50 CitationsSource
#1Bernhard MisofH-Index: 40
#2Shanlin LiuH-Index: 12
Last.Xin ZhouH-Index: 30
view all 101 authors...
Insects are the most speciose group of animals, but the phylogenetic relationships of many major lineages remain unresolved. We inferred the phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses of nucleotide and amino acid sequences, with site-specific nucleotide or domain-specific amino acid substitution models, produced statistically robust and congruent results resolving previously controversial phylogenetic relations hips. We dated the origin of insects to the Early Ord...
1,039 CitationsSource
#1Fernando Izquierdo-Carrasco (Heidelberg Institute for Theoretical Studies)H-Index: 7
#2John Cazes (Heidelberg Institute for Theoretical Studies)H-Index: 1
Last.Alexandros Stamatakis (Heidelberg Institute for Theoretical Studies)H-Index: 50
view all 4 authors...
Summary: New sequence data useful for phylogenetic and evolutionary analyses continues to be added to public databases. The construction of multiple sequence alignments and inference of huge phylogenies comprising large taxonomic groups are expensive tasks, both in terms of man hours and computational resources. Therefore, maintaining comprehensive phylogenies, based on representative and up-to-date molecular sequences, is challenging. PUmPER is a framework that can perpetually construct multi-g...
11 CitationsSource
#1Bernhard MisofH-Index: 40
#2Shanlin LiuH-Index: 12
Last.Xin ZhouH-Index: 30
view all 101 authors...
#1Bernhard MisofH-Index: 40
#2Shanlin LiuH-Index: 12
Last.Xin ZhouH-Index: 30
view all 101 authors...
2 Citations
#1Shinichi SunagawaH-Index: 45
#2Daniel R. MendeH-Index: 21
Last.Peer Bork (MDC: Max Delbrück Center for Molecular Medicine)H-Index: 178
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To quantify known and unknown microorganisms at species-level resolution using shotgun sequencing data, we developed a method that establishes metagenomic operational taxonomic units (mOTUs) based on single-copy phylogenetic marker genes. Applied to 252 human fecal samples, the method revealed that on average 43% of the species abundance and 58% of the richness cannot be captured by current reference genome-based methods. An implementation of the method is available at http://www.bork.embl.de/so...
247 CitationsSource
May 20, 2013 in ISBRA (International Symposium on Bioinformatics Research and Applications)
#1Jörg Hauser (Heidelberg Institute for Theoretical Studies)H-Index: 1
#2Kassian Kobert (Heidelberg Institute for Theoretical Studies)H-Index: 7
Last.Alexandros Stamatakis (Heidelberg Institute for Theoretical Studies)H-Index: 50
view all 7 authors...
Assigning an optimal combination of empirical amino acid substitution models (e.g., WAG, LG, MTART) to partitioned multi-gene datasets when branch lengths across partitions are linked, is suspected to be an NP-hard problem. Given p partitions and the approximately 20 empirical protein models that are available, one needs to compute the log likelihood score of 20 p possible model-to-partition assignments for obtaining the optimal assignment.
1 CitationsSource
#1Fernando Izquierdo-Carrasco (Exelixis)H-Index: 7
#2Nikolaos Alachiotis (Exelixis)H-Index: 12
Last.Alexandros Stamatakis (Exelixis)H-Index: 7
view all 6 authors...
Highly optimized library implementations for important scientific kernels can improve scientific productivity. To this end, we are currently developing the Phylogenetic Likelihood Library (PLL) that implements functions to compute and optimize the phylogenetic likelihood score on evolutionary trees. Here, we focus on novel techniques to orchestrate likelihood computations on large vector-like processors such as GPUs. We present a novel scheme for vectorizing computations and organizing condition...
7 CitationsSource
#1Diego Darriba (University of Vigo)H-Index: 9
#2Andre J. AbererH-Index: 15
Last.Alexandros StamatakisH-Index: 50
view all 6 authors...
We present a substantially improved and parallelized version of DPPDiv, a software tool for estimating species divergence times and lineage-specific substitution rates on a fixed tree topology. The improvement is achieved by integrating the DPPDiv code with the Phylogenetic Likelihood Library (PLL), a fast, optimized, and parallelized collection of functions for conducting likelihood computations on phylogenetic trees. We show that, integrating the PLL into a likelihoodbased application is strai...
8 CitationsSource
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