A Lightweight, Scalable Grid Computing Framework for Parallel Bioinformatics Applications. - Hans De Sterck; Rob S. Markel; Rob Knight 001 (HPCS, 2005)

Using the nucleotide substitution rate matrix to detect horizontal gene transfer. - Micah Hamady; Meredith D. Betterton; Rob Knight 001 (BMC Bioinform., 2006)

Fast-Find: A novel computational approach to analyzing combinatorial motifs. - Micah Hamady; Erin Peden; Rob Knight 001; Ravinder Singh (BMC Bioinform., 2006)

UniFrac - An online tool for comparing microbial community diversity in a phylogenetic context. - Catherine A. Lozupone; Micah Hamady; Rob Knight 001 (BMC Bioinform., 2006)

Database-Driven Grid Computing and Distributed Web Applications: A Comparison. - Hans De Sterck; Aleks Papo; Chen Zhang 010; Micah Hamady; Rob Knight 001 (Grid Computing for Bioinformatics and Computational Biology, 2007)

Towards mental life as it could be - a robot with imagination. - Hugo Gravato Marques; Owen Holland; Rob Knight 001; Richard A. Newcombe (ALIFE, 2008)

Comparison of methods for estimating the nucleotide substitution matrix. - Maribeth Oscamou; Daniel McDonald; Von Bing Yap; Gavin A. Huttley; Manuel E. Lladser; Rob Knight 001 (BMC Bioinform., 2008)

Pathological rate matrices: from primates to pathogens. - Harold W. Schranz; Von Bing Yap; Simon Easteal; Rob Knight 001; Gavin A. Huttley (BMC Bioinform., 2008)

Ensemble dispatching on an IBM Blue Gene/L for a bioinformatics knowledge environment. - Paul Marshall; Matthew Woitaszek; Henry M. Tufo; Rob Knight 001; Daniel McDonald; Julia Goodrich (SC-MTAGS, 2009)

CodonExplorer: an online tool for analyzing codon usage and sequence composition, scaling from genes to genomes. - Micah Hamady; Stephanie A. Wilson; Jesse Zaneveld; Noboru Sueoka; Rob Knight 001 (Bioinform., 2009)

ECCE1: The first of a series of anthropomimetic musculoskeletal upper torsos. - Hugo Gravato Marques; Michael Jäntsch; Steffen Wittmeier; Owen Holland; Cristiano Alessandro; Alan Diamond; Max Lungarella; Rob Knight 001 (Humanoids, 2010)

PyNAST: a flexible tool for aligning sequences to a template alignment. - J. Gregory Caporaso; Kyle Bittinger; Frederic D. Bushman; Todd Z. DeSantis; Gary L. Andersen; Rob Knight 001 (Bioinform., 2010)

The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data. - Robert Hoehndorf; Colin R. Batchelor; Thomas Bittner; Michel Dumontier; Karen Eilbeck; Rob Knight 001; Chris Mungall; Jane S. Richardson; Jesse Stombaugh; Eric Westhof; Craig L. Zirbel; Neocles Leontis (Appl. Ontology, 2011)

UCHIME improves sensitivity and speed of chimera detection. - Robert C. Edgar; Brian J. Haas; José Carlos Clemente; Christopher Quince; Rob Knight 001 (Bioinform., 2011)

TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata. - Meg Pirrung; Ryan Kennedy; J. Gregory Caporaso; Jesse Stombaugh; Doug Wendel; Rob Knight 001 (Bioinform., 2011)

Boulder ALignment Editor (ALE): a web-based RNA alignment tool. - Jesse Stombaugh; Jeremy Widmann; Daniel McDonald; Rob Knight 001 (Bioinform., 2011)

PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers. - William A. Walters; J. Gregory Caporaso; Christian L. Lauber; Donna Berg-Lyons; Noah Fierer; Rob Knight 001 (Bioinform., 2011)

A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis. - Yijun Sun; Yunpeng Cai; Susan M. Huse; Rob Knight 001; William G. Farmerie; Xiaoyu Wang; Volker Mai (Briefings Bioinform., 2012)

SitePainter: a tool for exploring biogeographical patterns. - Antonio González; Jesse Stombaugh; Christian L. Lauber; Noah Fierer; Rob Knight 001 (Bioinform., 2012)

Toward Anthropomimetic Robotics: Development, Simulation, and Control of a Musculoskeletal Torso. - Steffen Wittmeier; Cristiano Alessandro; Nenad Bascarevic; Konstantinos Dalamagkidis; David Devereux; Alan Diamond; Michael Jäntsch; Kosta Jovanovic; Rob Knight 001; Hugo Gravato Marques; Predrag Milosavljevic; Bhargav Mitra; et al. (Artif. Life, 2013)

A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets. - Omry Koren; Dan Knight; Antonio González; Levi Waldron; Nicola Segata; Rob Knight 001; Curtis Huttenhower; Ruth E. Ley (PLoS Comput. Biol., 2013)

The unifrac significance test is sensitive to tree topology. - Catherine A. Lozupone; Rob Knight 001 (BMC Bioinform., 2015)

Using machine learning to identify major shifts in human gut microbiome protein family abundance in disease. - Mehrdad Yazdani; Bryn C. Taylor; Justine W. Debelius; Weizhong Li; Rob Knight 001; Larry Smarr (IEEE BigData, 2016)

Integrating citizen science with online learning to ask better questions. - Vineet Pandey; Scott R. Klemmer; Amnon Amir; Justine W. Debelius; Embriette R. Hyde; Tomasz Kosciólek; Rob Knight 001 (CoRR, 2016)

Gut Instinct: Creating Scientific Theories with Online Learners. - Vineet Pandey; Amnon Amir; Justine W. Debelius; Embriette R. Hyde; Tomasz Kosciólek; Rob Knight 001; Scott R. Klemmer (CHI, 2017)

Docent: transforming personal intuitions to scientific hypotheses through content learning and process training. - Vineet Pandey; Justine W. Debelius; Embriette R. Hyde; Tomasz Kosciólek; Rob Knight 001; Scott R. Klemmer (L@S, 2018)

Ten Simple Rules for Reproducible Research in Jupyter Notebooks. - Adam Rule; Amanda Birmingham; Cristal Zuñiga; Ilkay Altintas; Shih-Cheng Huang; Rob Knight 001; Niema Moshiri; Mai H. Nguyen; Sara Brin Rosenthal; Fernando Pérez; Peter W. Rose (CoRR, 2018)

The genetic basis for adaptation of model-designed syntrophic co-cultures. - Colton J. Lloyd; Zachary A. King; Troy E. Sandberg; Ying Hefner; Connor A. Olson; Patrick V. Phaneuf; Edward J. O'Brien; Jon G. Sanders; Rodolfo A. Salido; Karenina Sanders; Caitriona Brennan; Gregory Humphrey; et al. (PLoS Comput. Biol., 2019)

Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks. - Adam Rule; Amanda Birmingham; Cristal Zuñiga; Ilkay Altintas; Shih-Cheng Huang; Rob Knight 001; Niema Moshiri; Mai H. Nguyen; Sara Brin Rosenthal; Fernando Pérez; Peter W. Rose (PLoS Comput. Biol., 2019)

Porting and optimizing UniFrac for GPUs: Reducing microbiome analysis runtimes by orders of magnitude. - Igor Sfiligoi; Daniel McDonald; Rob Knight 001 (PEARC, 2020)

SHOGUN: a modular, accurate and scalable framework for microbiome quantification. - Benjamin Hillmann; Gabriel A. Al-Ghalith; Robin R. Shields-Cutler; Qiyun Zhu; Rob Knight 001; Dan Knight (Bioinform., 2020)

Porting and optimizing UniFrac for GPUs. - Igor Sfiligoi; Daniel McDonald; Rob Knight 001 (CoRR, 2020)

Utilizing stability criteria in choosing feature selection methods yields reproducible results in microbiome data. - Lingjing Jiang; Niina Haiminen; Anna Paola Carrieri; Shi Huang; Yoshiki Vazquez-Baeza; Laxmi Parida; Ho-Cheol Kim; Austin D. Swafford; Rob Knight 001; Loki Natarajan (CoRR, 2020)

Galileo: Citizen-led Experimentation Using a Social Computing System. - Vineet Pandey; Tushar Koul; Chen Yang; Daniel McDonald; Mad Price Ball; Bastian Greshake Tzovaras; Rob Knight 001; Scott R. Klemmer (CHI, 2021)

Enabling microbiome research on personal devices. - Igor Sfiligoi; Daniel McDonald; Rob Knight 001 (e-Science, 2021)

Accelerating Key Bioinformatics Tasks 100-fold by Improving Memory Access. - Igor Sfiligoi; Daniel McDonald; Rob Knight 001 (PEARC, 2021)

Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops. - Matthew R. Dillon; Evan Bolyen; Anja Adamov; Aeriel Belk; Emily Borsom; Zachary Burcham; Justine W. Debelius; Heather Deel; Alex Emmons; Mehrbod Estaki; Chloe Herman; Christopher R. Keefe; et al. (PLoS Comput. Biol., 2021)

SALIENT: Ultra-Fast FPGA-based Short Read Alignment. - Behnam Khaleghi; Tianqi Zhang; Cameron Martino; George Armstrong; Ameen Akel; Ken Curewitz; Justin Eno; Sean Eilert; Rob Knight 001; Niema Moshiri; Tajana Rosing (FPT, 2022)

Applications and Comparison of Dimensionality Reduction Methods for Microbiome Data. - George Armstrong; Gibraan Rahman; Cameron Martino; Daniel McDonald; Antonio González; Gal Mishne; Rob Knight 001 (Frontiers Bioinform., 2022)

GenoMiX: Accelerated Simultaneous Analysis of Human Genomics, Microbiome Metagenomics, and Viral Sequences. - Tianqi Zhang; Antonio González; Niema Moshiri; Rob Knight 001; Tajana Rosing (BioCAS, 2023)

Playing the System: Can Puzzle Players Teach us How to Solve Hard Problems? - Renata Mutalova; Roman Sarrazin-Gendron; Eddie Cai; Gabriel Richard; Parham Ghasemloo Gheidari; Sébastien Caisse; Rob Knight 001; Mathieu Blanchette; Attila Szantner; Jérôme Waldispühl (CHI, 2023)

Player-Guided AI outperforms standard AI in Sequence Alignment Puzzles. - Renata Mutalova; Roman Sarrazin-Gendron; Parham Ghasemloo Gheidari; Eddie Cai; Gabriel Richard; Sébastien Caisse; Rob Knight 001; Mathieu Blanchette; Attila Szantner; Jérôme Waldispühl (CI, 2023)

Testing GitHub projects on custom resources using unprivileged Kubernetes runners. - Igor Sfiligoi; Daniel McDonald; Rob Knight 001; Frank Würthwein (PEARC, 2023)

Host-Variable-Embedding Augmented Microbiome-Based Simultaneous Detection of Multiple Diseases by Deep Learning. - Shunyao Wu; Zhiruo Li; Yuzhu Chen; Mingqian Zhang; Yangyang Sun; Jieqi Xing; Fengyang Zhao; Shi Huang; Rob Knight 001; Xiaoquan Su (Adv. Intell. Syst., 2023)

Mitigating memory latency in FM Index search. - Igor Sfiligoi; Daniel McDonald; Rob Knight 001 (e-Science, 2024)

Learning the Game: Decoding the Differences between Novice and Expert Players in a Citizen Science Game with Millions of Players. - Eddie Cai; Roman Sarrazin-Gendron; Renata Mutalova; Parham Ghasemloo Gheidari; Alexander Butyaev; Gabriel Richard; Sébastien Caisse; Rob Knight 001; Mathieu Blanchette; Attila Szantner; Jérôme Waldispühl (FDG, 2024)

Scaling DEPP phylogenetic placement to ultra-large reference trees: a tree-aware ensemble approach. - Yueyu Jiang; Daniel McDonald; Daniela Perry; Rob Knight 001; Siavash Mirarab (Bioinform., 2024)