Institution
Helsinki Institute for Information Technology
Facility•Espoo, Finland•
About: Helsinki Institute for Information Technology is a facility organization based out in Espoo, Finland. It is known for research contribution in the topics: Population & Bayesian network. The organization has 630 authors who have published 1962 publications receiving 63426 citations.
Papers published on a yearly basis
Papers
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TL;DR: Approximate Bayesian computation refers to a family of algorithms for approximate inference that makes a minimal set of assumptions by only requiring that sampling from a model is possible.
Abstract: Bayesian inference plays an important role in phylogenetics, evolutionary biology, and in many other branches of science. It provides a principled framework for dealing with uncertainty and quantifying how it changes in the light of new evidence. For many complex models and inference problems, however, only approximate quantitative answers are obtainable. Approximate Bayesian computation (ABC) refers to a family of algorithms for approximate inference that makes a minimal set of assumptions by only requiring that sampling from a model is possible. We explain here the fundamentals of ABC, review the classical algorithms, and highlight recent developments. [ABC; approximate Bayesian computation; Bayesian inference; likelihood-free inference; phylogenetics; simulator-based models; stochastic simulation models; tree-based models.]
221 citations
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Max Planck Society1, Karlsruhe Institute of Technology2, Broad Institute3, Federal University of Rio de Janeiro4, Saarland University5, European Bioinformatics Institute6, Helsinki Institute for Information Technology7, Howard Hughes Medical Institute8, Centre national de la recherche scientifique9, University of Washington10, Wellcome Trust Sanger Institute11, Leiden University12, University of Pennsylvania13, China Agricultural University14, University of Groningen15, Wageningen University and Research Centre16, Catholic University of Leuven17, Illumina18, Regeneron19, Shaanxi University of Science and Technology20, Netherlands Cancer Institute21, University of Padua22
TL;DR: Already available approaches to construct and use pan-genomes are examined, the potential benefits of future technologies and methodologies are discussed, and open challenges from the vantage point of the above-mentioned biological disciplines are reviewed.
Abstract: Many disciplines, from human genetics and oncology to plant breeding, microbiology and virology, commonly face the challenge of analyzing rapidly increasing numbers of genomes. In case of Homo sapiens, the number of sequenced genomes will approach hundreds of thousands in the next few years. Simply scaling up established bioinformatics pipelines will not be sufficient for leveraging the full potential of such rich genomic data sets. Instead, novel, qualitatively different computational methods and paradigms are needed. We will witness the rapid extension of computational pan-genomics, a new sub-area of research in computational biology. In this article, we generalize existing definitions and understand a pan-genome as any collection of genomic sequences to be analyzed jointly or to be used as a reference. We examine already available approaches to construct and use pan-genomes, discuss the potential benefits of future technologies and methodologies and review open challenges from the vantage point of the above-mentioned biological disciplines. As a prominent example for a computational paradigm shift, we particularly highlight the transition from the representation of reference genomes as strings to representations as graphs. We outline how this and other challenges from different application domains translate into common computational problems, point out relevant bioinformatics techniques and identify open problems in computer science. With this review, we aim to increase awareness that a joint approach to computational pan-genomics can help address many of the problems currently faced in various domains.
220 citations
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University of Helsinki1, Helsinki Institute for Information Technology2, University of Turku3, Pennsylvania State University4, University of Cambridge5, University of Oxford6, Peking University7, University of Bristol8, Max Planck Society9, Stanford University10, University of Tampere11, Information Technology University12, Stockholm University13, European Bioinformatics Institute14, Human Genome Sequencing Center15, Massachusetts Institute of Technology16, Broad Institute17, Swiss Institute of Bioinformatics18, Science for Life Laboratory19, University of Rhode Island20
TL;DR: The genome of the Glanville fritillary butterfly, a widely recognized model species in metapopulation biology and eco-evolutionary research, is reported, which shows that fusion chromosomes have retained the ancestral chromosome segments and very few rearrangements have occurred across the fusion sites.
Abstract: Previous studies have reported that chromosome synteny in Lepidoptera has been well conserved, yet the number of haploid chromosomes varies widely from 5 to 223. Here we report the genome (393 Mb) ...
216 citations
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TL;DR: A genome-wide association study to identify single nucleotide polymorphisms (SNPs) and indels that could confer beta-lactam non-susceptibility using 3,085 Thai and 616 USA pneumococcal isolates as independent datasets for the variant discovery.
Abstract: Traditional genetic association studies are very difficult in bacteria, as the generally limited recombination leads to large linked haplotype blocks, confounding the identification of causative variants. Beta-lactam antibiotic resistance in Streptococcus pneumoniae arises readily as the bacteria can quickly incorporate DNA fragments encompassing variants that make the transformed strains resistant. However, the causative mutations themselves are embedded within larger recombined blocks, and previous studies have only analysed a limited number of isolates, leading to the description of “mosaic genes” as being responsible for resistance. By comparing a large number of genomes of beta-lactam susceptible and non-susceptible strains, the high frequency of recombination should break up these haplotype blocks and allow the use of genetic association approaches to identify individual causative variants. Here, we performed a genome-wide association study to identify single nucleotide polymorphisms (SNPs) and indels that could confer beta-lactam non-susceptibility using 3,085 Thai and 616 USA pneumococcal isolates as independent datasets for the variant discovery. The large sample sizes allowed us to narrow the source of beta-lactam non-susceptibility from long recombinant fragments down to much smaller loci comprised of discrete or linked SNPs. While some loci appear to be universal resistance determinants, contributing equally to non-susceptibility for at least two classes of beta-lactam antibiotics, some play a larger role in resistance to particular antibiotics. All of the identified loci have a highly non-uniform distribution in the populations. They are enriched not only in vaccine-targeted, but also non-vaccine-targeted lineages, which may raise clinical concerns. Identification of single nucleotide polymorphisms underlying resistance will be essential for future use of genome sequencing to predict antibiotic sensitivity in clinical microbiology.
212 citations
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TL;DR: The study demonstrates that the model selection can greatly benefit from using cross-validation outside the searching process both for guiding the model size selection and assessing the predictive performance of the finally selected model.
Abstract: The goal of this paper is to compare several widely used Bayesian model selection methods in practical model selection problems, highlight their differences and give recommendations about the preferred approaches. We focus on the variable subset selection for regression and classification and perform several numerical experiments using both simulated and real world data. The results show that the optimization of a utility estimate such as the cross-validation (CV) score is liable to finding overfitted models due to relatively high variance in the utility estimates when the data is scarce. This can also lead to substantial selection induced bias and optimism in the performance evaluation for the selected model. From a predictive viewpoint, best results are obtained by accounting for model uncertainty by forming the full encompassing model, such as the Bayesian model averaging solution over the candidate models. If the encompassing model is too complex, it can be robustly simplified by the projection method, in which the information of the full model is projected onto the submodels. This approach is substantially less prone to overfitting than selection based on CV-score. Overall, the projection method appears to outperform also the maximum a posteriori model and the selection of the most probable variables. The study also demonstrates that the model selection can greatly benefit from using cross-validation outside the searching process both for guiding the model size selection and assessing the predictive performance of the finally selected model.
207 citations
Authors
Showing all 632 results
Name | H-index | Papers | Citations |
---|---|---|---|
Dimitri P. Bertsekas | 94 | 332 | 85939 |
Olli Kallioniemi | 90 | 353 | 42021 |
Heikki Mannila | 72 | 295 | 26500 |
Jukka Corander | 66 | 411 | 17220 |
Jaakko Kangasjärvi | 62 | 146 | 17096 |
Aapo Hyvärinen | 61 | 301 | 44146 |
Samuel Kaski | 58 | 522 | 14180 |
Nadarajah Asokan | 58 | 327 | 11947 |
Aristides Gionis | 58 | 292 | 19300 |
Hannu Toivonen | 56 | 192 | 19316 |
Nicola Zamboni | 53 | 128 | 11397 |
Jorma Rissanen | 52 | 151 | 22720 |
Tero Aittokallio | 52 | 271 | 8689 |
Juha Veijola | 52 | 261 | 19588 |
Juho Hamari | 51 | 176 | 16631 |