Rob Knight

Orcid: 0000-0002-0975-9019

Affiliations:
  • UC San Diego, USA


According to our database1, Rob Knight authored at least 47 papers between 2005 and 2024.

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Timeline

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Bibliography

2024
Scaling DEPP phylogenetic placement to ultra-large reference trees: a tree-aware ensemble approach.
Bioinform., 2024

Learning the Game: Decoding the Differences between Novice and Expert Players in a Citizen Science Game with Millions of Players.
Proceedings of the 19th International Conference on the Foundations of Digital Games, 2024

Mitigating memory latency in FM Index search.
Proceedings of the 20th IEEE International Conference on e-Science, 2024

2023
Host-Variable-Embedding Augmented Microbiome-Based Simultaneous Detection of Multiple Diseases by Deep Learning.
Adv. Intell. Syst., December, 2023

Testing GitHub projects on custom resources using unprivileged Kubernetes runners.
Proceedings of the Practice and Experience in Advanced Research Computing, 2023

Player-Guided AI outperforms standard AI in Sequence Alignment Puzzles.
Proceedings of The ACM Collective Intelligence Conference, 2023

Playing the System: Can Puzzle Players Teach us How to Solve Hard Problems?
Proceedings of the 2023 CHI Conference on Human Factors in Computing Systems, 2023

GenoMiX: Accelerated Simultaneous Analysis of Human Genomics, Microbiome Metagenomics, and Viral Sequences.
Proceedings of the IEEE Biomedical Circuits and Systems Conference, 2023

2022
Applications and Comparison of Dimensionality Reduction Methods for Microbiome Data.
Frontiers Bioinform., 2022

SALIENT: Ultra-Fast FPGA-based Short Read Alignment.
Proceedings of the International Conference on Field-Programmable Technology, 2022

2021
Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops.
PLoS Comput. Biol., 2021

Accelerating Key Bioinformatics Tasks 100-fold by Improving Memory Access.
Proceedings of the PEARC '21: Practice and Experience in Advanced Research Computing, 2021

Enabling microbiome research on personal devices.
Proceedings of the 17th IEEE International Conference on eScience, 2021

Galileo: Citizen-led Experimentation Using a Social Computing System.
Proceedings of the CHI '21: CHI Conference on Human Factors in Computing Systems, 2021

2020
Utilizing stability criteria in choosing feature selection methods yields reproducible results in microbiome data.
CoRR, 2020

Porting and optimizing UniFrac for GPUs.
CoRR, 2020

SHOGUN: a modular, accurate and scalable framework for microbiome quantification.
Bioinform., 2020

Porting and optimizing UniFrac for GPUs: Reducing microbiome analysis runtimes by orders of magnitude.
Proceedings of the PEARC '20: Practice and Experience in Advanced Research Computing, 2020

2019
Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks.
PLoS Comput. Biol., 2019

The genetic basis for adaptation of model-designed syntrophic co-cultures.
PLoS Comput. Biol., 2019

2018
Ten Simple Rules for Reproducible Research in Jupyter Notebooks.
CoRR, 2018

Docent: transforming personal intuitions to scientific hypotheses through content learning and process training.
Proceedings of the Fifth Annual ACM Conference on Learning at Scale, 2018

2017
Gut Instinct: Creating Scientific Theories with Online Learners.
Proceedings of the 2017 CHI Conference on Human Factors in Computing Systems, 2017

2016
Integrating citizen science with online learning to ask better questions.
CoRR, 2016

Using machine learning to identify major shifts in human gut microbiome protein family abundance in disease.
Proceedings of the 2016 IEEE International Conference on Big Data (IEEE BigData 2016), 2016

2015
The unifrac significance test is sensitive to tree topology.
BMC Bioinform., 2015

2013
A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets.
PLoS Comput. Biol., 2013

Toward Anthropomimetic Robotics: Development, Simulation, and Control of a Musculoskeletal Torso.
Artif. Life, 2013

2012
SitePainter: a tool for exploring biogeographical patterns.
Bioinform., 2012

A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis.
Briefings Bioinform., 2012

2011
PrimerProspector: <i>de novo</i> design and taxonomic analysis of barcoded polymerase chain reaction primers.
Bioinform., 2011

Boulder ALignment Editor (ALE): a web-based RNA alignment tool.
Bioinform., 2011

TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata.
Bioinform., 2011

UCHIME improves sensitivity and speed of chimera detection.
Bioinform., 2011

The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data.
Appl. Ontology, 2011

2010
PyNAST: a flexible tool for aligning sequences to a template alignment.
Bioinform., 2010

ECCE1: The first of a series of anthropomimetic musculoskeletal upper torsos.
Proceedings of the 10th IEEE-RAS International Conference on Humanoid Robots, 2010

2009
CodonExplorer: an online tool for analyzing codon usage and sequence composition, scaling from genes to genomes.
Bioinform., 2009

Ensemble dispatching on an IBM Blue Gene/L for a bioinformatics knowledge environment.
Proceedings of the 2nd Workshop on Many-Task Computing on Grids and Supercomputers, 2009

2008
Pathological rate matrices: from primates to pathogens.
BMC Bioinform., 2008

Comparison of methods for estimating the nucleotide substitution matrix.
BMC Bioinform., 2008

Towards mental life as it could be - a robot with imagination.
Proceedings of the Eleventh International Conference on the Synthesis and Simulation of Living Systems, 2008

2007
Database-Driven Grid Computing and Distributed Web Applications: A Comparison.
Proceedings of the Grid Computing for Bioinformatics and Computational Biology, 2007

2006
UniFrac - An online tool for comparing microbial community diversity in a phylogenetic context.
BMC Bioinform., 2006

Fast-Find: A novel computational approach to analyzing combinatorial motifs.
BMC Bioinform., 2006

Using the nucleotide substitution rate matrix to detect horizontal gene transfer.
BMC Bioinform., 2006

2005
A Lightweight, Scalable Grid Computing Framework for Parallel Bioinformatics Applications.
Proceedings of the 19th Annual International Symposium on High Performance Computing Systems and Applications (HPCS 2005), 2005


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