Rob Knight

50 papers A* 3B 3C 2Journal 31Unranked 10
YearRankTypeTitle / Venue / Authors
2024 C conf
Learning the Game: Decoding the Differences between Novice and Expert Players in a Citizen Science Game with Millions of Players.
FDG
Eddie Cai, Roman Sarrazin-Gendron, Renata Mutalova, Parham Ghasemloo Gheidari, Alexander Butyaev, Gabriel Richard, Sébastien Caisse, Rob Knight, Mathieu Blanchette, Attila Szantner, Jérôme Waldispühl
2024 B conf
Mitigating memory latency in FM Index search.
e-Science
Igor Sfiligoi, Daniel McDonald, Rob Knight
2024 J jnl
Scaling DEPP phylogenetic placement to ultra-large reference trees: a tree-aware ensemble approach.
Bioinform.
Yueyu Jiang, Daniel McDonald, Daniela Perry, Rob Knight, Siavash Mirarab
2023 — conf
GenoMiX: Accelerated Simultaneous Analysis of Human Genomics, Microbiome Metagenomics, and Viral Sequences.
BioCAS
Tianqi Zhang, Antonio González, Niema Moshiri, Rob Knight, Tajana Rosing
2023 J jnl
Host-Variable-Embedding Augmented Microbiome-Based Simultaneous Detection of Multiple Diseases by Deep Learning.
Adv. Intell. Syst.
Shunyao Wu, Zhiruo Li, Yuzhu Chen, Mingqian Zhang, Yangyang Sun, Jieqi Xing, Fengyang Zhao, Shi Huang, Rob Knight, Xiaoquan Su
2023 — conf
Player-Guided AI outperforms standard AI in Sequence Alignment Puzzles.
CI
Renata Mutalova, Roman Sarrazin-Gendron, Parham Ghasemloo Gheidari, Eddie Cai, Gabriel Richard, Sébastien Caisse, Rob Knight, Mathieu Blanchette, Attila Szantner, Jérôme Waldispühl
2023 A* conf
Playing the System: Can Puzzle Players Teach us How to Solve Hard Problems?
CHI
Renata Mutalova, Roman Sarrazin-Gendron, Eddie Cai, Gabriel Richard, Parham Ghasemloo Gheidari, Sébastien Caisse, Rob Knight, Mathieu Blanchette, Attila Szantner, Jérôme Waldispühl
2023 — conf
Testing GitHub projects on custom resources using unprivileged Kubernetes runners.
PEARC
Igor Sfiligoi, Daniel McDonald, Rob Knight, Frank Würthwein
2023 J jnl
Testing GitHub projects on custom resources using unprivileged Kubernetes runners.
CoRR
Igor Sfiligoi, Daniel McDonald, Rob Knight, Frank Würthwein
2022 J jnl
Applications and Comparison of Dimensionality Reduction Methods for Microbiome Data.
Frontiers Bioinform.
George Armstrong, Gibraan Rahman, Cameron Martino, Daniel McDonald, Antonio González, Gal Mishne, Rob Knight
2022 — conf
SALIENT: Ultra-Fast FPGA-based Short Read Alignment.
FPT
Behnam Khaleghi, Tianqi Zhang, Cameron Martino, George Armstrong, Ameen Akel, Ken Curewitz, Justin Eno, Sean Eilert, Rob Knight, Niema Moshiri, Tajana Rosing
2021 — conf
Accelerating Key Bioinformatics Tasks 100-fold by Improving Memory Access.
PEARC
Igor Sfiligoi, Daniel McDonald, Rob Knight
2021 J jnl
Accelerating key bioinformatics tasks 100-fold by improving memory access.
CoRR
Igor Sfiligoi, Daniel McDonald, Rob Knight
2021 B conf
Enabling microbiome research on personal devices.
e-Science
Igor Sfiligoi, Daniel McDonald, Rob Knight
2021 J jnl
Enabling microbiome research on personal devices.
CoRR
Igor Sfiligoi, Daniel McDonald, Rob Knight
2021 J jnl
Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops.
PLoS Comput. Biol.
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, Jamie T. Morton, Renato R. M. Oliveira, Andrew Sanchez, Anthony Simard, Yoshiki Vazquez-Baeza, Michal Ziemski, Hazuki E. Miwa, Terry A. Kerere, Carline Coote, Richard Bonneau, Rob Knight, Guilherme Oliveira, Piraveen Gopalasingam, Benjamin D. Kaehler, Emily K. Cope, Jessica L. Metcalf, Michael S. Robeson II, Nicholas A. Bokulich, J. Gregory Caporaso
2021 A* conf
Galileo: Citizen-led Experimentation Using a Social Computing System.
CHI
Vineet Pandey, Tushar Koul, Chen Yang, Daniel McDonald, Mad Price Ball, Bastian Greshake Tzovaras, Rob Knight, Scott R. Klemmer
2020 J jnl
Porting and optimizing UniFrac for GPUs.
CoRR
Igor Sfiligoi, Daniel McDonald, Rob Knight
2020 — conf
Porting and optimizing UniFrac for GPUs: Reducing microbiome analysis runtimes by orders of magnitude.
PEARC
Igor Sfiligoi, Daniel McDonald, Rob Knight
2020 J jnl
SHOGUN: a modular, accurate and scalable framework for microbiome quantification.
Bioinform.
Benjamin Hillmann, Gabriel A. Al-Ghalith, Robin R. Shields-Cutler, Qiyun Zhu, Rob Knight, Dan Knight
2020 J jnl
Utilizing stability criteria in choosing feature selection methods yields reproducible results in microbiome data.
CoRR
Lingjing Jiang, Niina Haiminen, Anna Paola Carrieri, Shi Huang, Yoshiki Vazquez-Baeza, Laxmi Parida, Ho-Cheol Kim, Austin D. Swafford, Rob Knight, Loki Natarajan
2019 J jnl
Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks.
PLoS Comput. Biol.
Adam Rule, Amanda Birmingham, Cristal Zuñiga, Ilkay Altintas, Shih-Cheng Huang, Rob Knight, Niema Moshiri, Mai H. Nguyen, Sara Brin Rosenthal, Fernando Pérez, Peter W. Rose
2019 J jnl
The genetic basis for adaptation of model-designed syntrophic co-cultures.
PLoS Comput. Biol.
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, Rob Knight, Adam M. Feist
2018 B conf
Docent: transforming personal intuitions to scientific hypotheses through content learning and process training.
L@S
Vineet Pandey, Justine W. Debelius, Embriette R. Hyde, Tomasz Kosciólek, Rob Knight, Scott R. Klemmer
2018 J jnl
Ten Simple Rules for Reproducible Research in Jupyter Notebooks.
CoRR
Adam Rule, Amanda Birmingham, Cristal Zuñiga, Ilkay Altintas, Shih-Cheng Huang, Rob Knight, Niema Moshiri, Mai H. Nguyen, Sara Brin Rosenthal, Fernando Pérez, Peter W. Rose
2017 A* conf
Gut Instinct: Creating Scientific Theories with Online Learners.
CHI
Vineet Pandey, Amnon Amir, Justine W. Debelius, Embriette R. Hyde, Tomasz Kosciólek, Rob Knight, Scott R. Klemmer
2016 J jnl
Integrating citizen science with online learning to ask better questions.
CoRR
Vineet Pandey, Scott R. Klemmer, Amnon Amir, Justine W. Debelius, Embriette R. Hyde, Tomasz Kosciólek, Rob Knight
2016 — conf
Using machine learning to identify major shifts in human gut microbiome protein family abundance in disease.
IEEE BigData
Mehrdad Yazdani, Bryn C. Taylor, Justine W. Debelius, Weizhong Li, Rob Knight, Larry Smarr
2015 J jnl
The unifrac significance test is sensitive to tree topology.
BMC Bioinform.
Catherine A. Lozupone, Rob Knight
2013 J jnl
A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets.
PLoS Comput. Biol.
Omry Koren, Dan Knight, Antonio González, Levi Waldron, Nicola Segata, Rob Knight, Curtis Huttenhower, Ruth E. Ley
2013 J jnl
Toward Anthropomimetic Robotics: Development, Simulation, and Control of a Musculoskeletal Torso.
Artif. Life
Steffen Wittmeier, Cristiano Alessandro, Nenad Bascarevic, Konstantinos Dalamagkidis, David Devereux, Alan Diamond, Michael Jäntsch, Kosta Jovanovic, Rob Knight, Hugo Gravato Marques, Predrag Milosavljevic, Bhargav Mitra, Bratislav Svetozarevic, Veljko Potkonjak, Rolf Pfeifer, Alois C. Knoll, Owen Holland
2012 J jnl
A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis.
Briefings Bioinform.
Yijun Sun, Yunpeng Cai, Susan M. Huse, Rob Knight, William G. Farmerie, Xiaoyu Wang, Volker Mai
2012 J jnl
SitePainter: a tool for exploring biogeographical patterns.
Bioinform.
Antonio González, Jesse Stombaugh, Christian L. Lauber, Noah Fierer, Rob Knight
2011 J jnl
Boulder ALignment Editor (ALE): a web-based RNA alignment tool.
Bioinform.
Jesse Stombaugh, Jeremy Widmann, Daniel McDonald, Rob Knight
2011 J jnl
PrimerProspector:
Bioinform.
William A. Walters, J. Gregory Caporaso, Christian L. Lauber, Donna Berg-Lyons, Noah Fierer, Rob Knight
2011 J jnl
The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data.
Appl. Ontology
Robert Hoehndorf, Colin R. Batchelor, Thomas Bittner, Michel Dumontier, Karen Eilbeck, Rob Knight, Chris Mungall, Jane S. Richardson, Jesse Stombaugh, Eric Westhof, Craig L. Zirbel, Neocles Leontis
2011 J jnl
TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata.
Bioinform.
Meg Pirrung, Ryan Kennedy, J. Gregory Caporaso, Jesse Stombaugh, Doug Wendel, Rob Knight
2011 J jnl
UCHIME improves sensitivity and speed of chimera detection.
Bioinform.
Robert C. Edgar, Brian J. Haas, José Carlos Clemente, Christopher Quince, Rob Knight
2010 — conf
ECCE1: The first of a series of anthropomimetic musculoskeletal upper torsos.
Humanoids
Hugo Gravato Marques, Michael Jäntsch, Steffen Wittmeier, Owen Holland, Cristiano Alessandro, Alan Diamond, Max Lungarella, Rob Knight
2010 J jnl
PyNAST: a flexible tool for aligning sequences to a template alignment.
Bioinform.
J. Gregory Caporaso, Kyle Bittinger, Frederic D. Bushman, Todd Z. DeSantis, Gary L. Andersen, Rob Knight
2009 J jnl
CodonExplorer: an online tool for analyzing codon usage and sequence composition, scaling from genes to genomes.
Bioinform.
Micah Hamady, Stephanie A. Wilson, Jesse Zaneveld, Noboru Sueoka, Rob Knight
2009 — conf
Ensemble dispatching on an IBM Blue Gene/L for a bioinformatics knowledge environment.
SC-MTAGS
Paul Marshall, Matthew Woitaszek, Henry M. Tufo, Rob Knight, Daniel McDonald, Julia Goodrich
2008 J jnl
Comparison of methods for estimating the nucleotide substitution matrix.
BMC Bioinform.
Maribeth Oscamou, Daniel McDonald, Von Bing Yap, Gavin A. Huttley, Manuel E. Lladser, Rob Knight
2008 J jnl
Pathological rate matrices: from primates to pathogens.
BMC Bioinform.
Harold W. Schranz, Von Bing Yap, Simon Easteal, Rob Knight, Gavin A. Huttley
2008 C conf
Towards mental life as it could be - a robot with imagination.
ALIFE
Hugo Gravato Marques, Owen Holland, Rob Knight, Richard A. Newcombe
2007 — ch.
Database-Driven Grid Computing and Distributed Web Applications: A Comparison.
Grid Computing for Bioinformatics and Computational Biology
Hans De Sterck, Aleks Papo, Chen Zhang, Micah Hamady, Rob Knight
2006 J jnl
Fast-Find: A novel computational approach to analyzing combinatorial motifs.
BMC Bioinform.
Micah Hamady, Erin Peden, Rob Knight, Ravinder Singh
2006 J jnl
UniFrac - An online tool for comparing microbial community diversity in a phylogenetic context.
BMC Bioinform.
Catherine A. Lozupone, Micah Hamady, Rob Knight
2006 J jnl
Using the nucleotide substitution rate matrix to detect horizontal gene transfer.
BMC Bioinform.
Micah Hamady, Meredith D. Betterton, Rob Knight
2005 — conf
A Lightweight, Scalable Grid Computing Framework for Parallel Bioinformatics Applications.
HPCS
Hans De Sterck, Rob S. Markel, Rob Knight