Search Results - computing algorithms and (((bioinformatics OR informatics) OR bioinformatika) OR informatika)

Porting of an Atmospheric Chemistry Solver to Parallel CPU-GPU Execution

Authors: Guzman Ruiz, Christian

Thesis Advisors: Acosta, Mario C. (Mario César), César Galobardes, Eduardo

Source: TDX (Tesis Doctorals en Xarxa)

Subject Terms: Informàtica d'alt rendiment, High-Performance Computing, Computación de alto rendimient, GPU, Models climàtics químics, Chemistry Climate models, Modelos climáticos químicos, Tecnologies

File Description: application/pdf

Access URL: http://hdl.handle.net/10803/693090

Massive cosmological data generation and distribution

Authors: Tallada Crespi, Pau

Thesis Advisors: Tonello , Nadia, Carretero Palacios, Jorge, César Galobardes, Eduardo

Source: TDX (Tesis Doctorals en Xarxa)

Subject Terms: Gestió de dades, Data management, Gestión de datos, Distribució de dades, Data distribution, Distribución de datos, Optimització d'algorismes, Algorithm optimization, Optimización de algoritmos, Tecnologies

File Description: application/pdf

Access URL: http://hdl.handle.net/10803/691707

Post-quantum cryptography acceleration for next generation computers

Authors: Kostalampros, Ioannis-Vatistas

Contributors: University/Department: Universitat Politècnica de Catalunya. Departament d'Arquitectura de Computadors

Thesis Advisors: Moretó Planas, Miquel, Hernández Luz, Carles

Source: TDX (Tesis Doctorals en Xarxa)

Subject Terms: Àrees temàtiques de la UPC::Informàtica, 004 - Informàtica

File Description: application/pdf

Access URL: http://hdl.handle.net/10803/695219
https://dx.doi.org/10.5821/dissertation-2117-441612

Derivation and Analysis of Distributed Computing Algorithms in Biological Systems

Authors: Chandrasekhar, Arjun

Subject Terms: Bioinformatics, Computer science, Ecology, Algorithms in Nature, Ant Biology, Distributed Computing, Neuroscience, Optimization

File Description: application/pdf

Access URL: https://escholarship.org/uc/item/03v7w5sf
https://escholarship.org/content/qt03v7w5sf/qt03v7w5sf.pdf

Replacing non-biomedical concepts improves embedding of biomedical concepts

Authors: Niyonkuru, Enock Gomez, Mauricio Soto Casarighi, Elena et al.

Source: PLOS ONE. 20(5)

Subject Terms: Information and Computing Sciences, Biological Sciences, Bioinformatics and Computational Biology, Algorithms, Machine Learning, Semantics, Medical Informatics Computing, General Science & Technology

File Description: application/pdf

Access URL: https://escholarship.org/uc/item/43k9s6k4
https://escholarship.org/content/qt43k9s6k4/qt43k9s6k4.pdf

Leveraging gene correlations in single cell transcriptomic data

Authors: Silkwood, Kai Dollinger, Emmanuel Gervin, Joshua et al.

Source: BMC Bioinformatics. 25(1)

Subject Terms: 31 Biological Sciences (for-2020), 3102 Bioinformatics and Computational Biology (for-2020), Human Genome (rcdc), Genetics (rcdc), Single-Cell Analysis (mesh), Humans (mesh), Sequence Analysis, RNA (mesh), Transcriptome (mesh), Algorithms (mesh), Gene Expression Profiling (mesh), Gene Regulatory Networks (mesh), Single cell RNA sequencing, Gene-gene correlation, Gene regulatory network, Gene co-expression network, Melanoma, Humans (mesh), Gene Expression Profiling (mesh), Sequence Analysis, RNA (mesh), Algorithms (mesh), Gene Regulatory Networks (mesh), Single-Cell Analysis (mesh), Transcriptome (mesh), Gene co-expression network, Gene regulatory network, Gene–gene correlation, Melanoma, Single cell RNA sequencing, Single-Cell Analysis (mesh), Humans (mesh), Sequence Analysis, RNA (mesh), Transcriptome (mesh), Algorithms (mesh), Gene Expression Profiling (mesh), Gene Regulatory Networks (mesh), 01 Mathematical Sciences (for), 06 Biological Sciences (for), 08 Information and Computing Sciences (for), Bioinformatics (science-metrix), 31 Biological sciences (for-2020), 46 Information and computing sciences (for-2020), 49 Mathematical sciences (for-2020)

Access URL: https://escholarship.org/uc/item/15k712w5

FluxRETAP: a REaction TArget Prioritization genome-scale modeling technique for selecting genetic targets

Authors: Czajka, Jeffrey J Kim, Joonhoon Tang, Yinjie J et al.

Source: Bioinformatics. 41(9)

Subject Terms: 31 Biological Sciences (for-2020), 3106 Industrial Biotechnology (for-2020), Genetics (rcdc), Biotechnology (rcdc), Bioengineering (rcdc), Escherichia coli (mesh), Metabolic Engineering (mesh), Software (mesh), Synthetic Biology (mesh), Pseudomonas putida (mesh), Machine Learning (mesh), Genome, Bacterial (mesh), Algorithms (mesh), Metabolic Networks and Pathways (mesh), Pseudomonas putida (mesh), Escherichia coli (mesh), Genome, Bacterial (mesh), Algorithms (mesh), Software (mesh), Metabolic Networks and Pathways (mesh), Synthetic Biology (mesh), Metabolic Engineering (mesh), Machine Learning (mesh), Escherichia coli (mesh), Metabolic Engineering (mesh), Software (mesh), Synthetic Biology (mesh), Pseudomonas putida (mesh), Machine Learning (mesh), Genome, Bacterial (mesh), Algorithms (mesh), Metabolic Networks and Pathways (mesh), 01 Mathematical Sciences (for), 06 Biological Sciences (for), 08 Information and Computing Sciences (for), Bioinformatics (science-metrix), 31 Biological sciences (for-2020), 46 Information and computing sciences (for-2020), 49 Mathematical sciences (for-2020)

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Access URL: https://escholarship.org/uc/item/1n5748bq
https://escholarship.org/content/qt1n5748bq/qt1n5748bq.pdf

DNABERT-S: pioneering species differentiation with species-aware DNA embeddings

Authors: Zhou, Zhihan Wu, Weimin Ho, Harrison et al.

Source: Bioinformatics. 41(Supplement_1)

Subject Terms: 31 Biological Sciences (for-2020), 3102 Bioinformatics and Computational Biology (for-2020), 3105 Genetics (for-2020), 46 Information and Computing Sciences (for-2020), 4611 Machine Learning (for-2020), Human Genome (rcdc), Genetics (rcdc), Generic health relevance (hrcs-hc), 3 Good Health and Well Being (sdg), Sequence Analysis, DNA (mesh), DNA (mesh), Genomics (mesh), Algorithms (mesh), Species Specificity (mesh), Genome (mesh), 46 Information and Computing Sciences (for-2020), 31 Biological Sciences (for-2020), 3105 Genetics (for-2020), 4611 Machine Learning (for-2020), Human Genome (rcdc), Genetics (rcdc), Generic health relevance (hrcs-hc), 3 Good Health and Well Being (sdg), DNA (mesh), Sequence Analysis, DNA (mesh), Genomics (mesh), Species Specificity (mesh), Genome (mesh), Algorithms (mesh), Sequence Analysis, DNA (mesh), DNA (mesh), Genomics (mesh), Algorithms (mesh), Species Specificity (mesh), Genome (mesh), 01 Mathematical Sciences (for), 06 Biological Sciences (for), 08 Information and Computing Sciences (for), Bioinformatics (science-metrix), 31 Biological sciences (for-2020), 46 Information and computing sciences (for-2020), 49 Mathematical sciences (for-2020)

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Access URL: https://escholarship.org/uc/item/9kf0s9g0
https://escholarship.org/content/qt9kf0s9g0/qt9kf0s9g0.pdf

NEMO: computational challenges in ocean simulation

Authors: Tintó Prims, Oriol

Contributors: University/Department: Universitat Autònoma de Barcelona. Departament d'Arquitectura de Computadors i Sistemes Operatius

Thesis Advisors: oriol.tinto@bsc.es, Cortés Fité, Ana, Acosta, Mario C. (Mario César), Doblas-Reyes, Francisco J.

Source: TDX (Tesis Doctorals en Xarxa)

Subject Terms: Model oceànic, Modelo oceánico, Oceanic model, Computació d'altes prestacions, Computación de altas prestaciones, High performance computing, Paral·lelisme, Paralelismo, Parallelism, Tecnologies

File Description: application/pdf

Access URL: http://hdl.handle.net/10803/669877

SetBERT: the deep learning platform for contextualized embeddings and explainable predictions from high-throughput sequencing

Authors: Ludwig, David W Guptil, Christopher Alexander, Nicholas R et al.

Source: Bioinformatics. 41(7)

Subject Terms: 46 Information and Computing Sciences (for-2020), 31 Biological Sciences (for-2020), 3102 Bioinformatics and Computational Biology (for-2020), Bioengineering (rcdc), Networking and Information Technology R&D (NITRD) (rcdc), Human Genome (rcdc), Genetics (rcdc), Machine Learning and Artificial Intelligence (rcdc), 3 Good Health and Well Being (sdg), Deep Learning (mesh), High-Throughput Nucleotide Sequencing (mesh), Sequence Analysis, DNA (mesh), Microbiota (mesh), Software (mesh), Computational Biology (mesh), Algorithms (mesh), Sequence Analysis, DNA (mesh), Computational Biology (mesh), Algorithms (mesh), Software (mesh), High-Throughput Nucleotide Sequencing (mesh), Microbiota (mesh), Deep Learning (mesh), Deep Learning (mesh), High-Throughput Nucleotide Sequencing (mesh), Sequence Analysis, DNA (mesh), Microbiota (mesh), Software (mesh), Computational Biology (mesh), Algorithms (mesh), 01 Mathematical Sciences (for), 06 Biological Sciences (for), 08 Information and Computing Sciences (for), Bioinformatics (science-metrix), 31 Biological sciences (for-2020), 46 Information and computing sciences (for-2020), 49 Mathematical sciences (for-2020)

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Access URL: https://escholarship.org/uc/item/7b07t0b7
https://escholarship.org/content/qt7b07t0b7/qt7b07t0b7.pdf

Aro: a machine learning approach to identifying single molecules and estimating classification error in fluorescence microscopy images

Authors: Wu, Allison Chia-Yi Rifkin, Scott A

Source: BMC Bioinformatics. 16(1)

Subject Terms: 46 Information and Computing Sciences (for-2020), 31 Biological Sciences (for-2020), 4603 Computer Vision and Multimedia Computation (for-2020), Networking and Information Technology R&D (NITRD) (rcdc), Bioengineering (rcdc), Algorithms (mesh), Animals (mesh), Artificial Intelligence (mesh), Caenorhabditis elegans (mesh), Computational Biology (mesh), Embryo, Nonmammalian (mesh), Fluorescence (mesh), Fluorescent Dyes (mesh), Image Processing, Computer-Assisted (mesh), In Situ Hybridization, Fluorescence (mesh), Microscopy, Fluorescence (mesh), Nanotechnology (mesh), RNA, Messenger (mesh), Software (mesh), Staining and Labeling (mesh), Single molecule imaging, smFISH, Random forest, Image informatics, RNA, Fluorescence microscopy, Machine learning, Image quality, Embryo, Nonmammalian (mesh), Animals (mesh), Caenorhabditis elegans (mesh), RNA, Messenger (mesh), Fluorescent Dyes (mesh), Microscopy, Fluorescence (mesh), Staining and Labeling (mesh), In Situ Hybridization, Fluorescence (mesh), Computational Biology (mesh), Algorithms (mesh), Nanotechnology (mesh), Fluorescence (mesh), Artificial Intelligence (mesh), Image Processing, Computer-Assisted (mesh), Software (mesh), Algorithms (mesh), Animals (mesh), Artificial Intelligence (mesh), Caenorhabditis elegans (mesh), Computational Biology (mesh), Embryo, Nonmammalian (mesh), Fluorescence (mesh), Fluorescent Dyes (mesh), Image Processing, Computer-Assisted (mesh), In Situ Hybridization, Fluorescence (mesh), Microscopy, Fluorescence (mesh), Nanotechnology (mesh), RNA, Messenger (mesh), Software (mesh), Staining and Labeling (mesh), 01 Mathematical Sciences (for), 06 Biological Sciences (for), 08 Information and Computing Sciences (for), Bioinformatics (science-metrix), 31 Biological sciences (for-2020), 46 Information and computing sciences (for-2020), 49 Mathematical sciences (for-2020)

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Access URL: https://escholarship.org/uc/item/21v4j6jw
https://escholarship.org/content/qt21v4j6jw/qt21v4j6jw.pdf

Kingdom-wide CRISPR guide design with ALLEGRO

Authors: Mohseni, Amirsadra Nia, Reyhane Ghorbani Tafrishi, Aida et al.

Source: Nucleic Acids Research. 53(15)

Subject Terms: Biological Sciences, Bioinformatics and Computational Biology, Biotechnology, Genetics, Human Genome, Generic health relevance, RNA, Guide, CRISPR-Cas Systems, CRISPR-Cas Systems, Genome, Fungal, Gene Editing, Algorithms, Kluyveromyces, Saccharomyces cerevisiae, Clustered Regularly Interspaced Short Palindromic Repeats, Yarrowia, Rhodotorula, Gene Library, Saccharomycetales, Environmental Sciences, Information and Computing Sciences, Developmental Biology, Biological sciences, Chemical sciences, Environmental sciences

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Access URL: https://escholarship.org/uc/item/9zm954ng
https://escholarship.org/content/qt9zm954ng/qt9zm954ng.pdf

A hierarchical parallel implementation model for algebra-based CFD simulations on hybrid supercomputers

Authors: Álvarez Farré, Xavier

Contributors: University/Department: Universitat Politècnica de Catalunya. Departament de Màquines i Motors Tèrmics

Thesis Advisors: Oliva Llena, Asensio, Gorobets, Andrei

Source: TDX (Tesis Doctorals en Xarxa)

Subject Terms: Àrees temàtiques de la UPC::Física

File Description: application/pdf

Access URL: http://hdl.handle.net/10803/687793
https://dx.doi.org/10.5821/dissertation-2117-384828

TRFill: synergistic use of HiFi and Hi-C sequencing enables accurate assembly of tandem repeats for population-level analysis.

Authors: Wen, Huaming Yang, Jinbao Zhao, Xianjia et al.

Source: Genome biology. 26(1)

Subject Terms: Centromere, Telomere, Humans, Sequence Analysis, DNA, Tandem Repeat Sequences, Algorithms, Software, Solanum lycopersicum, Gap filling, Genome assembly, Reference-guided genome assembly, Segmental duplications, Tandem repeats, Environmental Sciences, Biological Sciences, Information and Computing Sciences, Bioinformatics

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Access URL: https://escholarship.org/uc/item/1s4297xt
https://escholarship.org/content/qt1s4297xt/qt1s4297xt.pdf

Systematic benchmarking of computational methods to identify spatially variable genes

Authors: Li, Zhijian M.Patel, Zain Song, Dongyuan et al.

Source: Genome Biology. 26(1)

Subject Terms: 31 Biological Sciences (for-2020), 3102 Bioinformatics and Computational Biology (for-2020), Human Genome (rcdc), Genetics (rcdc), Networking and Information Technology R&D (NITRD) (rcdc), Benchmarking (mesh), Computational Biology (mesh), Algorithms (mesh), Gene Expression Profiling (mesh), Humans (mesh), Transcriptome (mesh), Benchmarking, Spatially variable genes, Simulation, Spatial omics, Visium, MERFISH, Humans (mesh), Gene Expression Profiling (mesh), Computational Biology (mesh), Algorithms (mesh), Benchmarking (mesh), Transcriptome (mesh), Benchmarking, MERFISH, Simulation, Spatial omics, Spatially variable genes, Visium, Benchmarking (mesh), Computational Biology (mesh), Algorithms (mesh), Gene Expression Profiling (mesh), Humans (mesh), Transcriptome (mesh), 05 Environmental Sciences (for), 06 Biological Sciences (for), 08 Information and Computing Sciences (for), Bioinformatics (science-metrix)

Access URL: https://escholarship.org/uc/item/16x872z6

High Throughput Computational Studies of Macromolecular Structure Flexibility

Authors: Hospital Gasch, Adam

Contributors: University/Department: Universitat de Barcelona. Departament de Bioquímica i Biologia Molecular (Farmàcia)

Thesis Advisors: Gelpí Buchaca, Josep Lluís, Orozco López, Modesto

Source: TDX (Tesis Doctorals en Xarxa)

Subject Terms: Dinàmica molecular, Dinámica molecular, Molecular dynamics, Bioinformàtica, Bioninformática, Bioinformatics, Càlcul intensiu (Informàtica), Computación de altas prestaciones, High performance computing, Ciències Experimentals i Matemàtiques

File Description: application/pdf

Access URL: http://hdl.handle.net/10803/284440

Functional protein mining with conformal guarantees

Authors: Boger, Ron S Chithrananda, Seyone Angelopoulos, Anastasios N et al.

Source: Nature Communications. 16(1)

Subject Terms: 46 Information and Computing Sciences (for-2020), 3101 Biochemistry and Cell Biology (for-2020), 3102 Bioinformatics and Computational Biology (for-2020), 31 Biological Sciences (for-2020), Proteins (mesh), Algorithms (mesh), Computational Biology (mesh), Protein Conformation (mesh), Data Mining (mesh), Databases, Protein (mesh), Reproducibility of Results (mesh), Proteins (mesh), Reproducibility of Results (mesh), Computational Biology (mesh), Protein Conformation (mesh), Algorithms (mesh), Databases, Protein (mesh), Data Mining (mesh), Proteins (mesh), Algorithms (mesh), Computational Biology (mesh), Protein Conformation (mesh), Data Mining (mesh), Databases, Protein (mesh), Reproducibility of Results (mesh)

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Access URL: https://escholarship.org/uc/item/3br9k1dr
https://escholarship.org/content/qt3br9k1dr/qt3br9k1dr.pdf

clusterMaker2: a major update to clusterMaker, a multi-algorithm clustering app for Cytoscape

Authors: Utriainen, Maija Morris, John H

Source: BMC Bioinformatics. 24(1)

Subject Terms: Biological Sciences, Bioinformatics and Computational Biology, Networking and Information Technology R&D (NITRD), Bioengineering, Generic health relevance, Mobile Applications, Saccharomyces cerevisiae, Algorithms, Protein Interaction Maps, Cluster Analysis, Clustering, Community detection, Network analysis, Visualization, Cytoscape, Mathematical Sciences, Information and Computing Sciences, Bioinformatics, Biological sciences, Information and computing sciences, Mathematical sciences

File Description: application/pdf

Access URL: https://escholarship.org/uc/item/4pt6q1c3
https://escholarship.org/content/qt4pt6q1c3/qt4pt6q1c3.pdf

A generalized covariate-adjusted top-scoring pair algorithm with applications to diabetic kidney disease stage classification in the Chronic Renal Insufficiency Cohort (CRIC) Study

Authors: Kwan, Brian Fuhrer, Tobias Montemayor, Daniel et al.

Source: BMC Bioinformatics. 24(1)

Subject Terms: Mathematical Sciences, Information and Computing Sciences, Statistics, Machine Learning, Kidney Disease, Diabetes, Clinical Research, Renal and urogenital, Humans, Diabetic Nephropathies, Betaine, Algorithms, Metabolomics, Renal Insufficiency, Chronic, Diabetes Mellitus, Biomarker, Classification, Feature selection, Kidney disease, Order statistics, Ranking algorithm, Biological Sciences, Bioinformatics, Biological sciences, Information and computing sciences, Mathematical sciences

File Description: application/pdf

Access URL: https://escholarship.org/uc/item/004995rm
https://escholarship.org/content/qt004995rm/qt004995rm.pdf

Particle-in-cell algorithms for plasma simulations on heterogeneous architectures

Authors: Sáez Pous, Xavier

Contributors: University/Department: Universitat Politècnica de Catalunya. Departament d'Arquitectura de Computadors

Thesis Advisors: Cela Espín, José M. (José María), Soba Pascual, Alejandro

Source: TDX (Tesis Doctorals en Xarxa)

File Description: application/pdf

Access URL: http://hdl.handle.net/10803/381258
https://dx.doi.org/10.5821/dissertation-2117-96109