Rob Knight

Publication Activity (10 Years)

Years Active: 2005-2023
Publications (10 Years): 22

Top Topics

Orders Of Magnitude Speedup

Dimensionality Reduction Methods

Top Venues

PLoS Comput. Biol.

Publications

Igor Sfiligoi, Daniel McDonald, Rob Knight, Frank Würthwein
Testing GitHub projects on custom resources using unprivileged Kubernetes runners. CoRR (2023)
Renata Mutalova, Roman Sarrazin-Gendron, Eddie Cai, Gabriel Richard, Parham Ghasemloo Gheidari, Sébastien Caisse, Rob Knight, Mathieu Blanchette, Attila Szantner, Jérôme Waldispühl
Playing the System: Can Puzzle Players Teach us How to Solve Hard Problems? CHI (2023)
George Armstrong, Gibraan Rahman, Cameron Martino, Daniel McDonald, Antonio Gonzalez, Gal Mishne, Rob Knight
Applications and Comparison of Dimensionality Reduction Methods for Microbiome Data. Frontiers Bioinform. 2 (2022)
Behnam Khaleghi, Tianqi Zhang, Cameron Martino, George Armstrong, Ameen Akel, Ken Curewitz, Justin Eno, Sean Eilert, Rob Knight, Niema Moshiri, Tajana Rosing
SALIENT: Ultra-Fast FPGA-based Short Read Alignment. FPT (2022)
Igor Sfiligoi, Daniel McDonald, Rob Knight
Accelerating Key Bioinformatics Tasks 100-fold by Improving Memory Access. PEARC (2021)
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
Experiences and lessons learned from two virtual, hands-on microbiome bioinformatics workshops. PLoS Comput. Biol. 17 (6) (2021)
Igor Sfiligoi, Daniel McDonald, Rob Knight
Enabling microbiome research on personal devices. e-Science (2021)
Igor Sfiligoi, Daniel McDonald, Rob Knight
Accelerating key bioinformatics tasks 100-fold by improving memory access. CoRR (2021)
Igor Sfiligoi, Daniel McDonald, Rob Knight
Enabling microbiome research on personal devices. CoRR (2021)
Vineet Pandey, Tushar Koul, Chen Yang, Daniel McDonald, Mad Price Ball, Bastian Greshake Tzovaras, Rob Knight, Scott R. Klemmer
Galileo: Citizen-led Experimentation Using a Social Computing System. CHI (2021)
Lingjing Jiang, Niina Haiminen, Anna Paola Carrieri, Shi Huang, Yoshiki Vazquez-Baeza, Laxmi Parida, Ho-Cheol Kim, Austin D. Swafford, Rob Knight, Loki Natarajan
Utilizing stability criteria in choosing feature selection methods yields reproducible results in microbiome data. CoRR (2020)
Benjamin Hillmann, Gabriel A. Al-Ghalith, Robin R. Shields-Cutler, Qiyun Zhu, Rob Knight, Dan Knights
SHOGUN: a modular, accurate and scalable framework for microbiome quantification. Bioinform. 36 (13) (2020)
Igor Sfiligoi, Daniel McDonald, Rob Knight
Porting and optimizing UniFrac for GPUs. CoRR (2020)
Gregory D. Poore, Evguenia Kopylova, Qiyun Zhu, Carolina Carpenter, Serena Fraraccio, Stephen Wandro, Tomasz Kosciólek, Stefan Janssen, Jessica Metcalf, Se Jin Song, Jad Kanbar, Sandrine Miller-Montgomery, Robert Heaton, Rana Mckay, Sandip Pravin Patel, Austin D. Swafford, Rob Knight
Microbiome analyses of blood and tissues suggest cancer diagnostic approach. Nat. 579 (7800) (2020)
Igor Sfiligoi, Daniel McDonald, Rob Knight
Porting and optimizing UniFrac for GPUs: Reducing microbiome analysis runtimes by orders of magnitude. PEARC (2020)
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
The genetic basis for adaptation of model-designed syntrophic co-cultures. PLoS Comput. Biol. 15 (3) (2019)
Adam Rule, Amanda Birmingham, Cristal Zuniga, Ilkay Altintas, Shih-Cheng Huang, Rob Knight, Niema Moshiri, Mai H. Nguyen, Sara Brin Rosenthal, Fernando Pérez, Peter W. Rose
Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks. PLoS Comput. Biol. 15 (7) (2019)
Adam Rule, Amanda Birmingham, Cristal Zuniga, Ilkay Altintas, Shih-Cheng Huang, Rob Knight, Niema Moshiri, Mai H. Nguyen, Sara Brin Rosenthal, Fernando Pérez, Peter W. Rose
Ten Simple Rules for Reproducible Research in Jupyter Notebooks. CoRR (2018)
Vineet Pandey, Justine W. Debelius, Embriette R. Hyde, Tomasz Kosciólek, Rob Knight, Scott R. Klemmer
Docent: transforming personal intuitions to scientific hypotheses through content learning and process training. L@S (2018)
Vineet Pandey, Amnon Amir, Justine W. Debelius, Embriette R. Hyde, Tomasz Kosciólek, Rob Knight, Scott R. Klemmer
Gut Instinct: Creating Scientific Theories with Online Learners. CHI (2017)
Mehrdad Yazdani, Bryn C. Taylor, Justine W. Debelius, Weizhong Li, Rob Knight, Larry Smarr
Using machine learning to identify major shifts in human gut microbiome protein family abundance in disease. IEEE BigData (2016)
Vineet Pandey, Scott R. Klemmer, Amnon Amir, Justine W. Debelius, Embriette R. Hyde, Tomasz Kosciólek, Rob Knight
Integrating citizen science with online learning to ask better questions. CoRR (2016)
Catherine A. Lozupone, Rob Knight
The unifrac significance test is sensitive to tree topology. BMC Bioinform. 16 (2015)
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
Toward Anthropomimetic Robotics: Development, Simulation, and Control of a Musculoskeletal Torso. Artif. Life 19 (1) (2013)
Omry Koren, Dan Knights, Antonio Gonzalez, Levi Waldron, Nicola Segata, Rob Knight, Curtis Huttenhower, Ruth E. Ley
A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets. PLoS Comput. Biol. 9 (1) (2013)
Antonio Gonzalez, Jesse Stombaugh, Christian L. Lauber, Noah Fierer, Rob Knight
SitePainter: a tool for exploring biogeographical patterns. Bioinform. 28 (3) (2012)
Yijun Sun, Yunpeng Cai, Susan M. Huse, Rob Knight, William G. Farmerie, Xiaoyu Wang, Volker Mai
A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis. Briefings Bioinform. 13 (1) (2012)
Jesse Stombaugh, Jeremy Widmann, Daniel McDonald, Rob Knight
Boulder ALignment Editor (ALE): a web-based RNA alignment tool. Bioinform. 27 (12) (2011)
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
The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data. Appl. Ontology 6 (1) (2011)
Robert C. Edgar, Brian J. Haas, José Carlos Clemente, Christopher Quince, Rob Knight
UCHIME improves sensitivity and speed of chimera detection. Bioinform. 27 (16) (2011)
Meg Pirrung, Ryan Kennedy, J. Gregory Caporaso, Jesse Stombaugh, Doug Wendel, Rob Knight
TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata. Bioinform. 27 (21) (2011)
William A. Walters, J. Gregory Caporaso, Christian L. Lauber, Donna Berg-Lyons, Noah Fierer, Rob Knight
design and taxonomic analysis of barcoded polymerase chain reaction primers. Bioinform. 27 (8) (2011)
J. Gregory Caporaso, Kyle Bittinger, Frederic D. Bushman, Todd Z. DeSantis, Gary L. Andersen, Rob Knight
PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinform. 26 (2) (2010)
Hugo Gravato Marques, Michael Jäntsch, Steffen Wittmeier, Owen Holland, Cristiano Alessandro, Alan Diamond, Max Lungarella, Rob Knight
ECCE1: The first of a series of anthropomimetic musculoskeletal upper torsos. Humanoids (2010)
Micah Hamady, Stephanie A. Wilson, Jesse Zaneveld, Noboru Sueoka, Rob Knight
CodonExplorer: an online tool for analyzing codon usage and sequence composition, scaling from genes to genomes. Bioinform. 25 (10) (2009)
Paul Marshall, Matthew Woitaszek, Henry M. Tufo, Rob Knight, Daniel McDonald, Julia Goodrich
Ensemble dispatching on an IBM Blue Gene/L for a bioinformatics knowledge environment. SC-MTAGS (2009)
Harold W. Schranz, Von Bing Yap, Simon Easteal, Rob Knight, Gavin A. Huttley
Pathological rate matrices: from primates to pathogens. BMC Bioinform. 9 (2008)
Hugo Gravato Marques, Owen Holland, Rob Knight, Richard A. Newcombe
Towards mental life as it could be - a robot with imagination. ALIFE (2008)
Maribeth Oscamou, Daniel McDonald, Von Bing Yap, Gavin A. Huttley, Manuel E. Lladser, Rob Knight
Comparison of methods for estimating the nucleotide substitution matrix. BMC Bioinform. 9 (2008)
Micah Hamady, Erin Peden, Rob Knight, Ravinder Singh
Fast-Find: A novel computational approach to analyzing combinatorial motifs. BMC Bioinform. 7 (2006)
Catherine A. Lozupone, Micah Hamady, Rob Knight
UniFrac - An online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinform. 7 (2006)
Micah Hamady, M. D. Betterton, Rob Knight
Using the nucleotide substitution rate matrix to detect horizontal gene transfer. BMC Bioinform. 7 (2006)
Hans De Sterck, Rob S. Markel, Rob Knight
A Lightweight, Scalable Grid Computing Framework for Parallel Bioinformatics Applications. HPCS (2005)