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Genetic grouping of SARS-CoV-2 coronavirus sequences using informative subtype markers for pandemic spread visualization

PLoS computational biology, 2020-09, Vol.16 (9), p.e1008269

2020

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Learning, visualizing and exploring 16S rRNA structure using an attention-based deep neural network

PLoS computational biology, 2021-09, Vol.17 (9), p.e1009345-e1009345

2021

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Amino Acid k-mer Feature Extraction for Quantitative Antimicrobial Resistance (AMR) Prediction by Machine Learning and Model Interpretation for Biological Insights

Biology (Basel, Switzerland), 2020-11, Vol.9 (11), p.365

2020

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Interpretable and Predictive Deep Neural Network Modeling of the SARS-CoV-2 Spike Protein Sequence to Predict COVID-19 Disease Severity

Biology (Basel, Switzerland), 2022-12, Vol.11 (12), p.1786

2022

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Complet+: a computationally scalable method to improve completeness of large-scale protein sequence clustering

PeerJ (San Francisco, CA), 2023-02, Vol.11, p.e14779-e14779, Article e14779

2023

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Predicting Institution Outcomes for Inter Partes Review (IPR) Proceedings at the United States Patent Trial & Appeal Board by Deep Learning of Patent Owner Preliminary Response Briefs

Applied sciences, 2022-04, Vol.12 (7), p.3656

2022

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Mapping Data to Deep Understanding: Making the Most of the Deluge of SARS-CoV-2 Genome Sequences

mSystems, 2022-04, Vol.7 (2), p.e0003522-e0003522

2022

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Streamlining Computational Fragment-Based Drug Discovery through Evolutionary Optimization Informed by Ligand-Based Virtual Prescreening

Journal of chemical information and modeling, 2024-05, Vol.64 (9), p.3826-3840

2024

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Predicting COVID-19 disease severity from SARS-CoV-2 spike protein sequence by mixed effects machine learning

Computers in biology and medicine, 2022-10, Vol.149, p.105969-105969, Article 105969

2022

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Temporal Global Changes in Gene Expression during Temperature Transition in Yersinia pestis

Journal of Bacteriology, 2004-09, Vol.186 (18), p.6298-6305

2004

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Fragment databases from screened ligands for drug discovery (FDSL-DD)

Journal of molecular graphics & modelling, 2024-03, Vol.127, p.108669-108669, Article 108669

2024

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Accelerated search for biomolecular network models to interpret high-throughput experimental data

BMC bioinformatics, 2007-07, Vol.8 (1), p.258-258, Article 258

2007

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Estimating the Effect of Human Base Excision Repair Protein Variants on the Repair of Oxidative DNA Base Damage

Cancer epidemiology, biomarkers & prevention, 2006-05, Vol.15 (5), p.1000-1008

2006

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Genetic Variability of Yersinia pestis Isolates as Predicted by PCR-Based IS100 Genotyping and Analysis of Structural Genes Encoding Glycerol-3-Phosphate Dehydrogenase (glpD)

Journal of Bacteriology, 2002-02, Vol.184 (4), p.1019-1027

2002

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Discovering the unknown: improving detection of novel species and genera from short reads

BioMed research international, 2011-01, Vol.2011 (1), p.495849

2011

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Systems approaches to the networks of aging

Ageing research reviews, 2006-11, Vol.5 (4), p.434-448

2006

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Signal Processing for Metagenomics: Extracting Information from the Soup

Current genomics, 2009-11, Vol.10 (7), p.493-510

2009

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Semi-Supervised and Incremental Sequence Analysis for Taxonomic Classification

2023 IEEE Symposium Series on Computational Intelligence (SSCI), 2023, p.1132-1138

2023

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Integrated modeling methodology for microtubule dynamics and Taxol kinetics with experimentally identifiable parameters

Computer methods and programs in biomedicine, 2007-10, Vol.88 (1), p.18-25

2007

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A quantitative model of human DNA base excision repair. I. Mechanistic insights

Nucleic acids research, 2002-04, Vol.30 (8), p.1817-1825

2002

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Mining, Modeling, and Evaluation of Subnetworks From Large Biomolecular Networks and Its Comparison Study

IEEE journal of biomedical and health informatics, 2009-03, Vol.13 (2), p.184-194

2009

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Multi-platform investigation of the metabolome in a leptin receptor defective murine model of type 2 diabetes

Molecular bioSystems, 2008-10, Vol.4 (10), p.1015-1023

2008

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Assignment of MS-based metabolomic datasets via compound interaction pair mapping

Metabolomics, 2008-03, Vol.4 (1), p.94-103

2008

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Oxidative DNA damage background estimated by a system model of base excision repair

Free radical biology & medicine, 2004-08, Vol.37 (3), p.422-427

2004

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Linear fuzzy gene network models obtained from microarray data by exhaustive search

BMC bioinformatics, 2004-08, Vol.5 (1), p.108-108, Article 108

2004

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Genetic grouping of SARS-CoV-2 coronavirus sequences using informative subtype markers for pandemic spread visualization

Learning, visualizing and exploring 16S rRNA structure using an attention-based deep neural network

Amino Acid k-mer Feature Extraction for Quantitative Antimicrobial Resistance (AMR) Prediction by Machine Learning and Model Interpretation for Biological Insights

Interpretable and Predictive Deep Neural Network Modeling of the SARS-CoV-2 Spike Protein Sequence to Predict COVID-19 Disease Severity

Complet+: a computationally scalable method to improve completeness of large-scale protein sequence clustering

Predicting Institution Outcomes for Inter Partes Review (IPR) Proceedings at the United States Patent Trial & Appeal Board by Deep Learning of Patent Owner Preliminary Response Briefs

Mapping Data to Deep Understanding: Making the Most of the Deluge of SARS-CoV-2 Genome Sequences

Streamlining Computational Fragment-Based Drug Discovery through Evolutionary Optimization Informed by Ligand-Based Virtual Prescreening

Predicting COVID-19 disease severity from SARS-CoV-2 spike protein sequence by mixed effects machine learning

Temporal Global Changes in Gene Expression during Temperature Transition in Yersinia pestis

Fragment databases from screened ligands for drug discovery (FDSL-DD)

Accelerated search for biomolecular network models to interpret high-throughput experimental data

Estimating the Effect of Human Base Excision Repair Protein Variants on the Repair of Oxidative DNA Base Damage

Genetic Variability of Yersinia pestis Isolates as Predicted by PCR-Based IS100 Genotyping and Analysis of Structural Genes Encoding Glycerol-3-Phosphate Dehydrogenase (glpD)

Discovering the unknown: improving detection of novel species and genera from short reads

Systems approaches to the networks of aging

Signal Processing for Metagenomics: Extracting Information from the Soup

Semi-Supervised and Incremental Sequence Analysis for Taxonomic Classification

Integrated modeling methodology for microtubule dynamics and Taxol kinetics with experimentally identifiable parameters

A quantitative model of human DNA base excision repair. I. Mechanistic insights

Mining, Modeling, and Evaluation of Subnetworks From Large Biomolecular Networks and Its Comparison Study

Multi-platform investigation of the metabolome in a leptin receptor defective murine model of type 2 diabetes

Assignment of MS-based metabolomic datasets via compound interaction pair mapping

Oxidative DNA damage background estimated by a system model of base excision repair

Linear fuzzy gene network models obtained from microarray data by exhaustive search

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