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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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16S rRNA sequence embeddings: Meaningful numeric feature representations of nucleotide sequences that are convenient for downstream analyses

PLoS computational biology, 2019-02, Vol.15 (2), p.e1006721

2019

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Comprehensive benchmarking and ensemble approaches for metagenomic classifiers

Genome Biology, 2017-09, Vol.18 (1), p.182-19, Article 182

2017

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Using the RDP classifier to predict taxonomic novelty and reduce the search space for finding novel organisms

PloS one, 2012-03, Vol.7 (3), p.e32491

2012

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Emerging Priorities for Microbiome Research

Frontiers in microbiology, 2020-02, Vol.11, p.136-136

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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Teaching Microbiome Analysis: From Design to Computation Through Inquiry

Frontiers in microbiology, 2020-10, Vol.11, p.528051

2020

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Exploring thematic structure and predicted functionality of 16S rRNA amplicon data

PloS one, 2019-12, Vol.14 (12), p.e0219235

2019

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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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Correction: Candidate variants in DNA replication and repair genes in early-onset renal cell carcinoma patients referred for germline testing

BMC genomics, 2023-07, Vol.24 (1), p.388-388, Article 388

2023

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Candidate variants in DNA replication and repair genes in early-onset renal cell carcinoma patients referred for germline testing

BMC genomics, 2023-04, Vol.24 (1), p.212-17, Article 212

2023

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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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Combining gene prediction methods to improve metagenomic gene annotation

BMC bioinformatics, 2011-01, Vol.12 (1), p.20-20, Article 20

2011

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MetaMutationalSigs: comparison of mutational signature refitting results made easy

Bioinformatics, 2022-04, Vol.38 (8), p.2344-2347

2022

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Healthcare Shift Workers' Temporal Habits for Eating, Sleeping, and Light Exposure: A Multi-Instrument Pilot Study

Journal of circadian rhythms, 2020-10, Vol.18 (1), p.6-6

2020

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Opportunities and obstacles for deep learning in biology and medicine

Journal of the Royal Society interface, 2018-04, Vol.15 (141), p.20170387

2018

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Environmental and ecological factors that shape the gut bacterial communities of fish: a meta-analysis

Molecular ecology, 2012-07, Vol.21 (13), p.3363-3378

2012

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Nanopore sequencing in microgravity

NPJ microgravity, 2016-10, Vol.2 (1), p.16035-16035, Article 16035

2016

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Correction to: Comprehensive benchmarking and ensemble approaches for metagenomic classifiers

Genome Biology, 2019-04, Vol.20 (1), p.72-72, Article 72

2019

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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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A toolkit for ARB to integrate custom databases and externally built phylogenies

PloS one, 2015-01, Vol.10 (1), p.e0109277

2015

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

16S rRNA sequence embeddings: Meaningful numeric feature representations of nucleotide sequences that are convenient for downstream analyses

Comprehensive benchmarking and ensemble approaches for metagenomic classifiers

Using the RDP classifier to predict taxonomic novelty and reduce the search space for finding novel organisms

Emerging Priorities for Microbiome Research

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

Teaching Microbiome Analysis: From Design to Computation Through Inquiry

Exploring thematic structure and predicted functionality of 16S rRNA amplicon data

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

Correction: Candidate variants in DNA replication and repair genes in early-onset renal cell carcinoma patients referred for germline testing

Candidate variants in DNA replication and repair genes in early-onset renal cell carcinoma patients referred for germline testing

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

Combining gene prediction methods to improve metagenomic gene annotation

MetaMutationalSigs: comparison of mutational signature refitting results made easy

Healthcare Shift Workers' Temporal Habits for Eating, Sleeping, and Light Exposure: A Multi-Instrument Pilot Study

Opportunities and obstacles for deep learning in biology and medicine

Environmental and ecological factors that shape the gut bacterial communities of fish: a meta-analysis

Nanopore sequencing in microgravity

Correction to: Comprehensive benchmarking and ensemble approaches for metagenomic classifiers

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

A toolkit for ARB to integrate custom databases and externally built phylogenies

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

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