default search action
Google
Google Scholar
Semantic Scholar
Internet Archive Scholar
CiteSeerX
ORCIDRob Knight 0001
Person information
- affiliation: UC San Diego, USA
Refine list
refinements active!
zoomed in on ?? of ?? records
view refined list in
export refined list as
2020 – today
- 2024
[j24]Yueyu Jiang
, Daniel McDonald, Daniela Perry, Rob Knight, Siavash Mirarab:
Scaling DEPP phylogenetic placement to ultra-large reference trees: a tree-aware ensemble approach. Bioinform. 40(6) (2024)- [c18]Igor Sfiligoi, Daniel McDonald, Rob Knight:
Mitigating memory latency in FM Index search. e-Science 2024: 1-2 - [c17]Eddie Cai, Roman Sarrazin-Gendron, Renata Mutalova, Parham Ghasemloo Gheidari, Alexander Butyaev, Gabriel Richard, Sébastien Caisse, Rob Knight, Mathieu Blanchette, Attila Szantner, Jérôme Waldispühl:
Learning the Game: Decoding the Differences between Novice and Expert Players in a Citizen Science Game with Millions of Players. FDG 2024: 31 - 2023
- [j23]Shunyao Wu, Zhiruo Li, Yuzhu Chen, Mingqian Zhang, Yangyang Sun, Jieqi Xing, Fengyang Zhao, Shi Huang, Rob Knight, Xiaoquan Su:
Host-Variable-Embedding Augmented Microbiome-Based Simultaneous Detection of Multiple Diseases by Deep Learning. Adv. Intell. Syst. 5(12) (2023) - [c16]Tianqi Zhang, Antonio González, Niema Moshiri, Rob Knight, Tajana Rosing:
GenoMiX: Accelerated Simultaneous Analysis of Human Genomics, Microbiome Metagenomics, and Viral Sequences. BioCAS 2023: 1-5 - [c15]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: 679:1-679:15 - [c14]Renata Mutalova, Roman Sarrazin-Gendron, Parham Ghasemloo Gheidari, Eddie Cai, Gabriel Richard, Sébastien Caisse, Rob Knight, Mathieu Blanchette, Attila Szantner, Jérôme Waldispühl:
Player-Guided AI outperforms standard AI in Sequence Alignment Puzzles. CI 2023: 53-62 - [c13]Igor Sfiligoi, Daniel McDonald, Rob Knight, Frank Würthwein:
Testing GitHub projects on custom resources using unprivileged Kubernetes runners. PEARC 2023: 332-335 - [i7]Igor Sfiligoi, Daniel McDonald, Rob Knight, Frank Würthwein:
Testing GitHub projects on custom resources using unprivileged Kubernetes runners. CoRR abs/2305.10346 (2023) - 2022
- [j22]George Armstrong, Gibraan Rahman, Cameron Martino, Daniel McDonald, Antonio González, Gal Mishne, Rob Knight:
Applications and Comparison of Dimensionality Reduction Methods for Microbiome Data. Frontiers Bioinform. 2: 821861 (2022) - [c12]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: 1-10 - 2021
- [j21]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) - [c11]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: 565:1-565:14 - [c10]Igor Sfiligoi, Daniel McDonald, Rob Knight:
Enabling microbiome research on personal devices. e-Science 2021: 229-230 - [c9]Igor Sfiligoi, Daniel McDonald, Rob Knight:
Accelerating Key Bioinformatics Tasks 100-fold by Improving Memory Access. PEARC 2021: 7:1-7:5 - [i6]Igor Sfiligoi, Daniel McDonald, Rob Knight:
Accelerating key bioinformatics tasks 100-fold by improving memory access. CoRR abs/2104.09565 (2021) - [i5]Igor Sfiligoi, Daniel McDonald, Rob Knight:
Enabling microbiome research on personal devices. CoRR abs/2107.05397 (2021) - 2020
- [j20]Benjamin Hillmann, Gabriel A. Al-Ghalith, Robin R. Shields-Cutler, Qiyun Zhu, Rob Knight, Dan Knight:
SHOGUN: a modular, accurate and scalable framework for microbiome quantification. Bioinform. 36(13): 4088-4090 (2020) - [c8]Igor Sfiligoi, Daniel McDonald, Rob Knight:
Porting and optimizing UniFrac for GPUs: Reducing microbiome analysis runtimes by orders of magnitude. PEARC 2020: 500-504 - [i4]Igor Sfiligoi, Daniel McDonald, Rob Knight:
Porting and optimizing UniFrac for GPUs. CoRR abs/2005.05826 (2020) - [i3]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 abs/2012.00001 (2020)
2010 – 2019
- 2019
- [j19]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) - [j18]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:
Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks. PLoS Comput. Biol. 15(7) (2019) - 2018
- [c7]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: 9:1-9:10 - [i2]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:
Ten Simple Rules for Reproducible Research in Jupyter Notebooks. CoRR abs/1810.08055 (2018) - 2017
- [c6]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: 6825-6836 - 2016
- [c5]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: 1272-1280 - [i1]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 abs/1609.05763 (2016) - 2015
- [j17]Catherine A. Lozupone, Rob Knight:
The unifrac significance test is sensitive to tree topology. BMC Bioinform. 16: 211:1-211:3 (2015) - 2013
- [j16]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): 171-193 (2013) - [j15]Omry Koren, Dan Knight, Antonio González, 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) - 2012
- [j14]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): 107-121 (2012) - [j13]Antonio González, Jesse Stombaugh, Christian L. Lauber, Noah Fierer, Rob Knight:
SitePainter: a tool for exploring biogeographical patterns. Bioinform. 28(3): 436-438 (2012) - 2011
- [j12]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): 53-89 (2011) - [j11]William A. Walters, J. Gregory Caporaso, Christian L. Lauber, Donna Berg-Lyons, Noah Fierer, Rob Knight:
PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers. Bioinform. 27(8): 1159-1161 (2011) - [j10]Jesse Stombaugh, Jeremy Widmann, Daniel McDonald, Rob Knight:
Boulder ALignment Editor (ALE): a web-based RNA alignment tool. Bioinform. 27(12): 1706-1707 (2011) - [j9]Robert C. Edgar, Brian J. Haas, José Carlos Clemente, Christopher Quince, Rob Knight:
UCHIME improves sensitivity and speed of chimera detection. Bioinform. 27(16): 2194-2200 (2011) - [j8]Meg Pirrung, Ryan Kennedy, J. Gregory Caporaso, Jesse Stombaugh, Doug Wendel, Rob Knight:
TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata. Bioinform. 27(21): 3067-3069 (2011) - 2010
- [j7]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): 266-267 (2010) - [c4]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: 391-396
2000 – 2009
- 2009
- [j6]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): 1331-1332 (2009) - [c3]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 - 2008
- [j5]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) - [j4]Harold W. Schranz, Von Bing Yap, Simon Easteal, Rob Knight, Gavin A. Huttley:
Pathological rate matrices: from primates to pathogens. BMC Bioinform. 9 (2008) - [c2]Hugo Gravato Marques, Owen Holland, Rob Knight, Richard A. Newcombe:
Towards mental life as it could be - a robot with imagination. ALIFE 2008: 782 - 2007
- [p1]Hans De Sterck, Aleks Papo, Chen Zhang, Micah Hamady, Rob Knight:
Database-Driven Grid Computing and Distributed Web Applications: A Comparison. Grid Computing for Bioinformatics and Computational Biology 2007: 247-266 - 2006
- [j3]Micah Hamady, Erin Peden, Rob Knight, Ravinder Singh:
Fast-Find: A novel computational approach to analyzing combinatorial motifs. BMC Bioinform. 7: 1 (2006) - [j2]Catherine A. Lozupone, Micah Hamady, Rob Knight:
UniFrac - An online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinform. 7: 371 (2006) - [j1]Micah Hamady, Meredith D. Betterton, Rob Knight:
Using the nucleotide substitution rate matrix to detect horizontal gene transfer. BMC Bioinform. 7: 476 (2006) - 2005
- [c1]Hans De Sterck, Rob S. Markel, Rob Knight:
A Lightweight, Scalable Grid Computing Framework for Parallel Bioinformatics Applications. HPCS 2005: 251-257
Coauthor Index
manage site settings
To protect your privacy, all features that rely on external API calls from your browser are turned off by default. You need to opt-in for them to become active. All settings here will be stored as cookies with your web browser. For more information see our F.A.Q.
Unpaywalled article links
Add open access links from 
to the list of external document links (if available).
Privacy notice: By enabling the option above, your browser will contact the API of unpaywall.org to load hyperlinks to open access articles. Although we do not have any reason to believe that your call will be tracked, we do not have any control over how the remote server uses your data. So please proceed with care and consider checking the Unpaywall privacy policy.
Archived links via Wayback Machine
For web page which are no longer available, try to retrieve content from the 
of the Internet Archive (if available).
Privacy notice: By enabling the option above, your browser will contact the API of archive.org to check for archived content of web pages that are no longer available. Although we do not have any reason to believe that your call will be tracked, we do not have any control over how the remote server uses your data. So please proceed with care and consider checking the Internet Archive privacy policy.
Reference lists
Add a list of references from 
, 
, and 
to record detail pages.
load references from crossref.org and opencitations.net
Privacy notice: By enabling the option above, your browser will contact the APIs of crossref.org, opencitations.net, and semanticscholar.org to load article reference information. Although we do not have any reason to believe that your call will be tracked, we do not have any control over how the remote server uses your data. So please proceed with care and consider checking the Crossref privacy policy and the OpenCitations privacy policy, as well as the AI2 Privacy Policy covering Semantic Scholar.
Citation data
Add a list of citing articles from and to record detail pages.
load citations from opencitations.net
Privacy notice: By enabling the option above, your browser will contact the API of opencitations.net and semanticscholar.org to load citation information. Although we do not have any reason to believe that your call will be tracked, we do not have any control over how the remote server uses your data. So please proceed with care and consider checking the OpenCitations privacy policy as well as the AI2 Privacy Policy covering Semantic Scholar.
OpenAlex data
Load additional information about publications from 
.
Privacy notice: By enabling the option above, your browser will contact the API of openalex.org to load additional information. Although we do not have any reason to believe that your call will be tracked, we do not have any control over how the remote server uses your data. So please proceed with care and consider checking the information given by OpenAlex.
last updated on 2024-10-07 22:19 CEST by the dblp team
all metadata released as open data under CC0 1.0 license
see also: Terms of Use | Privacy Policy | Imprint
dblp was originally created in 1993 at:
since 2018, dblp has been operated and maintained by:
the dblp computer science bibliography is funded and supported by:
