A5019540563- Algorithms and Data Compression
- Genomics and Phylogenetic Studies
- Advanced Image and Video Retrieval Techniques
- Amyotrophic Lateral Sclerosis Research
- RNA and protein synthesis mechanisms
- semigroups and automata theory
- Chromosomal and Genetic Variations
- DNA and Biological Computing
- Natural Language Processing Techniques
- Network Packet Processing and Optimization
- Neurogenetic and Muscular Disorders Research
- Advanced Data Compression Techniques
- Genome Rearrangement Algorithms
- Genomics and Rare Diseases
- Cellular Automata and Applications
- Optimization and Search Problems
- Coding theory and cryptography
- Cerebrovascular and Carotid Artery Diseases
- Paleopathology and ancient diseases
- Plant nutrient uptake and metabolism
- Alzheimer's disease research and treatments
- Machine Learning in Bioinformatics
- Neurological disorders and treatments
- Moyamoya disease diagnosis and treatment
- Gene expression and cancer classification
University of Chile
2003-2024
Complejo Asistencial Sótero del Río
2015-2024
Hospital Clínico de la Universidad de Chile
2022
University of Helsinki
2013-2021
Helsinki Institute for Information Technology
2014-2018
Helsinki Art Museum
2017
Regeneron (United States)
2016
Abstract Many disciplines, from human genetics and oncology to plant breeding, microbiology virology, commonly face the challenge of analyzing rapidly increasing numbers genomes. In case Homo sapiens , number sequenced genomes will approach hundreds thousands in next few years. Simply scaling up established bioinformatics pipelines not be sufficient for leveraging full potential such rich genomic datasets. Instead, novel, qualitatively different computational methods paradigms are needed. We...
Typical human genome differs from the reference at 4-5 million sites. This diversity is increasingly catalogued in repositories such as ExAC/gnomAD, consisting of >15,000 whole-genomes and >126,000 exome sequences different individuals. Despite this enormous diversity, resequencing data workflows are still based on a single genome. Identification genotyping genetic variants typically carried out short-read aligned to reference, disregarding underlying variation. We propose new unified...
Our objective was to describe amyotrophic lateral sclerosis (ALS) mortality rates in the Chilean population over a 17-year period. death records (1994-2010) were reviewed for ICD-10 diagnosis G.12.2 (including motor neuron disease and similar conditions), weighted with data. Crude standardized by ALS calculated at nationwide level geographic zone. A risk analysis performed successive cohorts from 1910-1919 1960-1969, comparing slopes. One thousand six hundred seventy-one deaths recorded...
Given a collection of documents and query pattern, document retrieval is the problem obtaining that are relevant to query. The available beforehand so data structure, called an index, can be built on it speed up queries. While initially restricted natural language text collections, problems arise nowadays in applications like bioinformatics, multimedia databases, web mining. This requires more general setup where pattern sequences symbols, classical inverted indexes developed for words...
Abstract Recently the topic of computational pan-genomics has gained increasing attention, and particularly problem moving from a single-reference paradigm to pan-genomic one. Perhaps simplest way represent pan-genome is it as set sequences. While indexing highly repetitive collections been intensively studied in computer science community, research focused on efficient exact pattern patching, making most solutions not yet suitable be used bioinformatic analysis pipelines. Results: We...
Background: There is evolving evidence of non-uniform distribution ALS worldwide, with apparently lower incident and prevalent rates outside populations European origin. However, the phenotype, survival environmental risk in mixed ancestral origin have not been well established. Large scale population based studies incidence, prevalence, phenotype factors admixed are necessary to determine true demography ALS, test hypothesis differential ancestry. Methods: The Latin American Epidemiological...
To compare social cognition performance between patients with amyotrophic lateral sclerosis (ALS) and those behavioural variant frontotemporal dementia (bvFTD).We included 21 participants ALS, 20 bvFTD healthy controls who underwent a comprehensive cognitive battery, including the short version of Social Cognition Emotional Assessment (Mini-SEA), which comprises faux pas test Facial Emotion Recognition Test (FERT); Mini-Mental State Examination; Frontal Battery; lexical fluency (F-A-S),...
Traditionally biological similarity search has been studied under the abstraction of a single string to represent each genome. The more realistic representation diploid genomes, with two strings defining genome, so far largely omitted in this context. With development sequencing techniques and better phasing routines through haplotype assembly algorithms, we are not from situation when individual genomes could be represented their full complexity pair-wise alignment We propose generalization...
Variant calling workflows that utilize a single reference sequence are the de facto standard elementary genomic analysis routine for resequencing projects. Various ways to enhance with pangenomic information have been proposed, but scalability combined seamless integration existing remains challenge.We present PanVC founder sequences, scalable and accurate variant workflow based on multiple alignment of sequences. Scalability is achieved by removing duplicate parts up limit into alignment,...
ABSTRACT Detection of genomic variants is commonly conducted by aligning a set reads sequenced from an individual to the reference genome species and analyzing resulting read pileup . Typically, this process finds subset already reported in databases additional novel characteristic individual. Most effort literature has been put alignment problem on single sequence, although our gathered knowledge such as human pan-genomic : We know most common variation addition sequence. There have some...
Covering alignment problems arise from recent developments in genomics; so called pan-genome graphs are replacing reference genomes, and advances haplotyping enable full content of diploid genomes to be used as basis sequence analysis. In this paper, we show that the computational complexity will change for natural extensions alignments representations genomes. More broadly, our approach can also seen a minimal extension labelled directed acyclic (labeled DAGs). Namely, finding covering two...
Objective This study aimed to estimate amyotrophic lateral sclerosis (ALS) incidence and survival rates in the Metropolitan region of Chile.