Search Results - computing algorithms and (bioinformatics OR informatika)

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

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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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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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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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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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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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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

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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

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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

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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)

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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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Bipartite tight spectral clustering (BiTSC) algorithm for identifying conserved gene co-clusters in two species

Authors: Sun, Yidan Eden Zhou, Heather J Li, Jingyi Jessica

Source: Bioinformatics. 37(9)

Subject Terms: 31 Biological Sciences (for-2020), 3102 Bioinformatics and Computational Biology (for-2020), Networking and Information Technology R&D (NITRD) (rcdc), Genetics (rcdc), Bioengineering (rcdc), Generic health relevance (hrcs-hc), Algorithms (mesh), Animals (mesh), Cluster Analysis (mesh), Drosophila melanogaster (mesh), Gene Expression (mesh), Gene Expression Profiling (mesh), Animals (mesh), Drosophila melanogaster (mesh), Cluster Analysis (mesh), Gene Expression Profiling (mesh), Gene Expression (mesh), Algorithms (mesh), Algorithms (mesh), Animals (mesh), Cluster Analysis (mesh), Drosophila melanogaster (mesh), Gene Expression (mesh), Gene Expression Profiling (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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ChromaFactor: Deconvolution of single-molecule chromatin organization with non-negative matrix factorization

Authors: Gunsalus, Laura M Keiser, Michael J Pollard, Katherine S

Source: PLOS Computational Biology. 21(2)

Subject Terms: Biochemistry and Cell Biology, Biological Sciences, Human Genome, Genetics, Biotechnology, 1.1 Normal biological development and functioning, 2.1 Biological and endogenous factors, Generic health relevance, Chromatin, Computational Biology, Humans, Single Molecule Imaging, Algorithms, Single-Cell Analysis, Mathematical Sciences, Information and Computing Sciences, Bioinformatics

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Tree polynomials identify a link between co-transcriptional R-loops and nascent RNA folding

Authors: Liu, Pengyu Lusk, Jacob Jonoska, Nataša et al.

Source: PLOS Computational Biology. 20(12)

Subject Terms: Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, 1.1 Normal biological development and functioning, RNA, Computational Biology, Transcription, Genetic, Nucleic Acid Conformation, Algorithms, Software, RNA Folding, R-Loop Structures, Mathematical Sciences, Information and Computing Sciences, Bioinformatics

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Automatic wound detection and size estimation using deep learning algorithms

Authors: Carrión, Héctor Jafari, Mohammad Bagood, Michelle Dawn et al.

Source: PLOS Computational Biology. 18(3)

Subject Terms: Data Management and Data Science, Information and Computing Sciences, Bioengineering, Machine Learning and Artificial Intelligence, Networking and Information Technology R&D (NITRD), Algorithms, Animals, Deep Learning, Image Processing, Computer-Assisted, Mice, Wound Healing, Mathematical Sciences, Biological Sciences, Bioinformatics

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NFTest: automated testing of Nextflow pipelines

Authors: Patel, Yash Zhu, Chenghao Yamaguchi, Takafumi N et al.

Source: Bioinformatics. 40(2)

Subject Terms: 46 Information and Computing Sciences (for-2020), 31 Biological Sciences (for-2020), 3102 Bioinformatics and Computational Biology (for-2020), 4612 Software Engineering (for-2020), Bioengineering (rcdc), Networking and Information Technology R&D (NITRD) (rcdc), 3 Good Health and Well Being (sdg), Computational Biology (mesh), Software (mesh), Algorithms (mesh), Language (mesh), Workflow (mesh), Language (mesh), Computational Biology (mesh), Algorithms (mesh), Software (mesh), Workflow (mesh), Computational Biology (mesh), Software (mesh), Algorithms (mesh), Language (mesh), Workflow (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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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)

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Denoising Autoencoder, A Deep Learning Algorithm, Aids the Identification of A Novel Molecular Signature of Lung Adenocarcinoma

Authors: Wang, Jun Xie, Xueying Shi, Junchao et al.

Source: Genomics Proteomics & Bioinformatics. 18(4)

Subject Terms: Information and Computing Sciences, Machine Learning, Clinical Research, Cancer, Lung Cancer, Lung, Rare Diseases, Genetics, 4.1 Discovery and preclinical testing of markers and technologies, Detection, screening and diagnosis, Good Health and Well Being, Adenocarcinoma of Lung, Algorithms, Deep Learning, Humans, Lung Neoplasms, Transcriptome, Denoising autoencoder, Unsupervised learning, Lung cancer, Prognosis, Molecular signature, Mathematical Sciences, Biological Sciences, Bioinformatics, Biological sciences, Information and computing sciences, Mathematical sciences

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Deep distributed computing to reconstruct extremely large lineage trees

Authors: Konno, Naoki Kijima, Yusuke Watano, Keito et al.

Source: Nature Biotechnology. 40(4)

Subject Terms: Biological Sciences, Bioinformatics and Computational Biology, Evolutionary Biology, Genetics, Algorithms, Cell Lineage, Mutation, Phylogeny, Software

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GSearch: ultra-fast and scalable genome search by combining K-mer hashing with hierarchical navigable small world graphs

Authors: Zhao, Jianshu Both, Jean Pierre Rodriguez-R, Luis M et al.

Source: Nucleic Acids Research. 52(16)

Subject Terms: Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Networking and Information Technology R&D (NITRD), Algorithms, Genomics, Software, Genome, Viral, Databases, Genetic, Environmental Sciences, Information and Computing Sciences, Developmental Biology, Biological sciences, Chemical sciences, Environmental sciences

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