Santiago Marco‐Sola
A5052502603- Genomics and Phylogenetic Studies
- Algorithms and Data Compression
- Chromosomal and Genetic Variations
- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- Advanced Data Storage Technologies
- Medical Imaging and Pathology Studies
- Parallel Computing and Optimization Techniques
- Protist diversity and phylogeny
- Genomics and Rare Diseases
- Genomic variations and chromosomal abnormalities
- Plant Virus Research Studies
- RNA Research and Splicing
- Evolutionary Algorithms and Applications
- Machine Learning in Bioinformatics
- Enzyme Structure and Function
- Plant Disease Resistance and Genetics
- Epigenetics and DNA Methylation
- Genetic Syndromes and Imprinting
- Protein Structure and Dynamics
- Biomedical Text Mining and Ontologies
- Genetic Mapping and Diversity in Plants and Animals
- Network Packet Processing and Optimization
- COVID-19 diagnosis using AI
- Molecular Biology Techniques and Applications
Universitat Politècnica de Catalunya
2017-2025
Barcelona Supercomputing Center
2020-2025
Universitat Autònoma de Barcelona
2018-2023
Centro Nacional de Análisis Genómico
2012-2016
Centre for Genomic Regulation
2016
Universitat Pompeu Fabra
2016
Abstract Here the Human Pangenome Reference Consortium presents a first draft of human pangenome reference. The contains 47 phased, diploid assemblies from cohort genetically diverse individuals 1 . These cover more than 99% expected sequence in each genome and are accurate at structural base pair levels. Based on alignments assemblies, we generate that captures known variants haplotypes reveals new alleles structurally complex loci. We also add 119 million pairs euchromatic polymorphic...
Abstract The short arms of the human acrocentric chromosomes 13, 14, 15, 21 and 22 (SAACs) share large homologous regions, including ribosomal DNA repeats extended segmental duplications 1,2 . Although resolution these regions in first complete assembly a genome—the Telomere-to-Telomere Consortium’s CHM13 (T2T-CHM13)—provided model their homology 3 , it remained unclear whether patterns were ancestral or maintained by ongoing recombination exchange. Here we show that contain...
Abstract Pangenome graphs can represent all variation between multiple reference genomes, but current approaches to build them exclude complex sequences or are based upon a single reference. In response, we developed the PanGenome Graph Builder (PGGB), pipeline for constructing pangenome without bias exclusion. PGGB uses all-to-all alignments graph in which identify variation, measure conservation, detect recombination events, and infer phylogenetic relationships.
Abstract Single-nucleotide variants (SNVs) in segmental duplications (SDs) have not been systematically assessed because of the limitations mapping short-read sequencing data 1,2 . Here we constructed 1:1 unambiguous alignments spanning high-identity SDs across 102 human haplotypes and compared pattern SNVs between unique duplicated regions 3,4 We find that are elevated 60% to estimate at least 23% this increase is due interlocus gene conversion (IGC) with up 4.3 megabase pairs SD sequence...
Abstract Motivation Pairwise alignment of sequences is a fundamental method in modern molecular biology, implemented within multiple bioinformatics tools and libraries. Current advances sequencing technologies press for the development faster pairwise algorithms that can scale with increasing read lengths production yields. Results In this article, we present wavefront algorithm (WFA), an exact gap-affine takes advantage homologous regions between to accelerate process. As opposed...
Significance One fundamental analysis needed to interpret genome assemblies is alignment. Yet, accurately aligning regulatory and transposon regions outside of genes remains challenging. We introduce Anchored Wavefront alignment (AnchorWave), which implements a duplication informed longest path algorithm identify collinear performs base pair–resolved, end-to-end for blocks using an efficient two-piece affine gap cost strategy. AnchorWave improves the under number scenarios: genomes with high...
Abstract Motivation Pairwise sequence alignment remains a fundamental problem in computational biology and bioinformatics. Recent advances genomics sequencing technologies demand faster scalable algorithms that can cope with the ever-increasing lengths. Classical pairwise based on dynamic programming are strongly limited by quadratic requirements time memory. The recently proposed wavefront algorithm (WFA) introduced an efficient to perform exact gap-affine O(ns) time, where s is optimal...
DNA methylation is essential for normal embryogenesis and development in mammals can be captured at single base pair resolution by whole genome bisulfite sequencing (WGBS). Current available analysis tools are becoming rapidly outdated as they lack sensible functionality efficiency to handle large amounts of data now commonly created.We developed gemBS, a fast high-throughput bioinformatics pipeline specifically designed scale BS-Seq that combines high performance BS-mapper (GEM3) variant...
As whole genome sequencing becomes cheaper and faster, it will progressively substitute targeted next-generation as standard practice in research diagnostics. However, computing cost-performance ratio is not advancing at an equivalent rate. Therefore, essential to evaluate the robustness of variant detection process taking into account resources required. We have benchmarked six combinations state-of-the-art read aligners (BWA-MEM GEM3) callers (FreeBayes, GATK HaplotypeCaller, SAMtools) on...
Advances in genomics and sequencing technologies demand faster more scalable analysis methods that can process longer sequences with higher accuracy. However, classical pairwise alignment methods, based on dynamic programming (DP), impose impractical computational requirements to align long noisy like those produced by PacBio Nanopore technologies. The recently proposed wavefront (WFA) algorithm paves the way for efficient tools, improving time memory complexity over previous methods....
Approximate string matching is a very important problem in computational biology; it requires the fast computation of distance as one its essential components. Myers' bit-parallel algorithm improves classical dynamic programming approach to Levenshtein computation, and offers competitive performance on CPUs. The main challenge when designing an efficient GPU implementation expose enough SIMD parallelism while at same time keeping relatively small working set for each thread.
Abstract Motivation Pairwise sequence alignment is a core component of multiple sequencing-data analysis tools. Recent advancements in sequencing technologies have enabled the generation longer sequences at much lower price. Thus, long-read become increasingly popular sequencing-based studies. However, classical algorithms face significant scalability challenges when aligning long sequences. As result, several heuristic methods been developed to improve performance expense accuracy, as they...
Chimeric transcripts are commonly defined as linking two or more different genes in the genome, and can be explained by various biological mechanisms such genomic rearrangement, read-through trans-splicing, but also technical artefacts. Several studies have shown their importance cancer, cell pluripotency motility. Many programs recently been developed to identify chimeras from Illumina RNA-seq data (mostly fusion cancer). However outputs of on same dataset widely inconsistent, tend include...
The recent advent of high-throughput sequencing machines producing big amounts short reads has boosted the interest in efficient string searching techniques. As today, many mainstream sequence alignment software tools rely on a special data structure, called FM-index, which allows for fast exact searches large genomic references. However, such translate into pseudo-random memory access pattern, thus making limiting factor all computation-efficient implementations, both CPUs and GPUs. Here,...
Given the overwhelming impact of machine learning on last decade, several libraries and frameworks have been developed in recent years to simplify design training neural networks, providing array-based programming, automatic differentiation user-friendly access hardware accelerators. None those tools, however, was designed with native transparent support for Cloud Computing or heterogeneous High-Performance (HPC). The DeepHealth Toolkit is an open source Deep Learning toolkit aimed at...
Sequence alignment remains a fundamental problem with practical applications ranging from pattern recognition to computational biology. Traditional algorithms based on dynamic programming are hard parallelize, require significant amounts of memory, and fail scale for large inputs. This work presents eWFA-GPU, GPU (graphics processing unit)-accelerated tool compute the exact edit-distance sequence wavefront algorithm (WFA). approach exploits similarities between input sequences accelerate...
In the last years, advances in next-generation sequencing technologies have enabled proliferation of genomic applications that guide personalized medicine. These an enormous computational cost due to large amount data they process. The first step many these consists aligning reads against a reference genome. Very recently, wavefront alignment algorithm has been introduced, significantly reducing execution time read This paper presents FPGA-based hardware/software co-designed accelerator such...
The human pangenome, a new reference sequence, addresses many limitations of the current GRCh38 reference. first release is based on 94 high-quality haploid assemblies from individuals with diverse backgrounds. We employed k-mer indexing strategy for comparative analysis across multiple assemblies, including pangenome reference, GRCh38, and CHM13, telomere-to-telomere assembly. Our approach enabled us to identify valuable collection universally conserved sequences all referred as...
Arm usage has substantially grown in the High-Performance Computing (HPC) community. Japanese supercomputer Fugaku, powered by Arm-based A64FX processors, held top position on Top500 list between June 2020 and 2022, currently sitting fourth position. The recently released 7th generation of Amazon EC2 instances for compute-intensive workloads (C7 g) is also Graviton3 processors. Projects like European Mont-Blanc U.S. DOE/NNSA Astra are further examples irruption HPC. In parallel, over last...
Abstract Motivation Advances in genomics and sequencing technologies demand faster more scalable analysis methods that can process longer sequences with higher accuracy. However, classical pairwise alignment methods, based on dynamic programming (DP), impose impractical computational requirements to align long noisy like those produced by PacBio, Nanopore technologies. The recently proposed WFA algorithm paves the way for efficient tools, improving time memory complexity over previous...
Modern Illumina-like high-throughput sequencing machines allow the cheap decoding of great amounts DNA. The GEnomic Multi-tool (GEM) mapper is one fastest and most sensitive methods known to date align such data a genomic reference. This unit explains how use it effectively.