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Santiago Marco-Sola
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The GEM mapper: fast, accurate and versatile alignment by filtration
S Marco-Sola, M Sammeth, R Guigó, P Ribeca
Nature methods 9 (12), 1185-1188, 2012
6452012
Fast computation and applications of genome mappability
T Derrien, J Estellé, S Marco Sola, DG Knowles, E Raineri, R Guigó, ...
PloS one 7 (1), e30377, 2012
5692012
A draft human pangenome reference
WW Liao, M Asri, J Ebler, D Doerr, M Haukness, G Hickey, S Lu, JK Lucas, ...
Nature 617 (7960), 312-324, 2023
3302023
Fast gap-affine pairwise alignment using the wavefront algorithm
S Marco-Sola, JC Moure, M Moreto, A Espinosa
Bioinformatics 37 (4), 456-463, 2021
1292021
From wet‐lab to variations: concordance and speed of bioinformatics pipelines for whole genome and whole exome sequencing
S Laurie, M Fernandez‐Callejo, S Marco‐Sola, JR Trotta, J Camps, ...
Human mutation 37 (12), 1263-1271, 2016
632016
gemBS: high throughput processing for DNA methylation data from bisulfite sequencing
A Merkel, M Fernández-Callejo, E Casals, S Marco-Sola, R Schuyler, ...
Bioinformatics 35 (5), 737-742, 2019
522019
Thread-cooperative, bit-parallel computation of levenshtein distance on GPU
A Chacón, S Marco-Sola, A Espinosa, P Ribeca, JC Moure
Proceedings of the 28th ACM international conference on Supercomputing, 103-112, 2014
462014
ChimPipe: accurate detection of fusion genes and transcription-induced chimeras from RNA-seq data
B Rodríguez-Martín, E Palumbo, S Marco-Sola, T Griebel, P Ribeca, ...
BMC genomics 18, 1-17, 2017
422017
Building pangenome graphs
E Garrison, A Guarracino, S Heumos, F Villani, Z Bao, L Tattini, ...
bioRxiv, 2023.04. 05.535718, 2023
382023
Boosting the FM-index on the GPU: Effective techniques to mitigate random memory access
A Chacón, S Marco-Sola, A Espinosa, P Ribeca, JC Moure
IEEE/ACM transactions on computational biology and bioinformatics 12 (5 …, 2014
332014
Optimal gap-affine alignment in O(s) space
S Marco-Sola, JM Eizenga, A Guarracino, B Paten, E Garrison, M Moreto
Bioinformatics 39 (2), btad074, 2023
312023
AnchorWave: Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism, and whole-genome duplication
B Song, S Marco-Sola, M Moreto, L Johnson, ES Buckler, MC Stitzer
Proceedings of the National Academy of Sciences 119 (1), e2113075119, 2022
302022
An FPGA accelerator of the wavefront algorithm for genomics pairwise alignment
A Haghi, S Marco-Sola, L Alvarez, D Diamantopoulos, C Hagleitner, ...
2021 31st International Conference on Field-Programmable Logic and …, 2021
272021
The deephealth toolkit: a unified framework to boost biomedical applications
M Cancilla, L Canalini, F Bolelli, S Allegretti, S Carrión, R Paredes, ...
2020 25th International Conference on Pattern Recognition (ICPR), 9881-9888, 2021
212021
Gaps and complex structurally variant loci in phased genome assemblies
D Porubsky, MR Vollger, WT Harvey, AN Rozanski, P Ebert, G Hickey, ...
Genome research 33 (4), 496-510, 2023
182023
Efficient Alignment of Illumina‐Like High‐Throughput Sequencing Reads with the GEnomic Multi‐tool (GEM) Mapper
S Marco‐Sola, P Ribeca
Current Protocols in Bioinformatics 50 (1), 11.13. 1-11.13. 20, 2015
162015
Accelerating edit-distance sequence alignment on GPU using the wavefront algorithm
Q Aguado-Puig, S Marco-Sola, JC Moure, D Castells-Rufas, L Alvarez, ...
IEEE access 10, 63782-63796, 2022
142022
FM-index on GPU: A cooperative scheme to reduce memory footprint
A Chacón, SM Sola, A Espinosa, P Ribeca, JC Moure
2014 IEEE International Symposium on Parallel and Distributed Processing …, 2014
132014
WFA-GPU: Gap-affine pairwise alignment using GPUs
Q Aguado-Puig, S Marco-Sola, JC Moure, C Matzoros, D Castells-Rufas, ...
bioRxiv, 2022.04. 18.488374, 2022
122022
Sargantana: A 1 GHz+ in-order RISC-V processor with SIMD vector extensions in 22nm FD-SOI
V Soria-Pardos, M Doblas, G López–Paradís, G Candón, N Rodas, ...
2022 25th Euromicro Conference on Digital System Design (DSD), 254-261, 2022
92022
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