Jonathan Crabtree

18.4k citations

38 papers · 4.0k indexed · 2 hit papers · h-index 24

Impact in

Endocrinology top 1%
- Escherichia coli research studies
Molecular Biology top 5%
- Gut microbiota and health
- Genomics and Phylogenetic Studies

Papers in ⓘ

Endocrinology 2
Infectious Diseases 7
- Antifungal resistance and susceptibility 3

Co-authors: Owen White (9 shared papers)Joshua Orvis (9 shared papers)Jacques Ravel (5 shared papers)Jennifer R. Wortman (9 shared papers)Anup Mahurkar (10 shared papers)Curtis Huttenhower (2 shared papers)Rob Knight (3 shared papers)Arthur Brady (2 shared papers)
Journals: Bioinformatics (4 papers)Nucleic Acids Research (4 papers)Nature Communications (2 papers)Nature Biotechnology (2 papers)BMC Genomics (2 papers)
Partner nations: United States United Kingdom Germany

In The Last Decade

Jonathan Crabtree

37 papers receiving 3.9k citations

Hit Papers

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Strains, functions and dynamics in the expanded Human Microbiome Project 2017 · 804 citations

Peers

Countries citing papers authored by Jonathan Crabtree

Since Specialization

Citations

This map shows the geographic impact of Jonathan Crabtree's research. It shows the number of citations coming from papers published by authors working in each country. You can also color the map by specialization and compare the number of citations received by Jonathan Crabtree with the expected number of citations based on a country's size and research output (numbers larger than one mean the country cites Jonathan Crabtree more than expected).

Fields of papers citing papers by Jonathan Crabtree

Since Specialization

Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by Jonathan Crabtree. Nodes represent research fields, and links connect fields that are likely to share authors. Colored nodes show fields that tend to cite the papers produced by Jonathan Crabtree. The network helps show where Jonathan Crabtree may publish in the future.

Co-authors

The 25 scholars most cited alongside Jonathan Crabtree, linked wherever they have co-authored with each other. Click a name or a connecting line to browse the papers they share.

Border = papers with Jonathan Crabtree Line = papers co-authored together Jonathan Crabtree links everyone, so they are left out of the graph.

All Works

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20 of 20 papers shown

Showing the 20 most-cited of 38 papers — load more, or switch the sort, to bring in the rest.

#	Work
1	Strains, functions and dynamics in the expanded Human Microbiome Project Nature ·Jason Lloyd‐Price, Anup Mahurkar, Ali Rahnavard, Jonathan Crabtree, Joshua Orvis, A. Brantley Hall, Arthur Brady, Heather H. Creasy, Carrie McCracken, Michelle Giglio, Daniel McDonald, Eric A. Franzosa, Rob Knight, Owen White, Curtis Huttenhower Hit paper breakdown →	2017	804
2	The Pangenome Structure ofEscherichia coli: Comparative Genomic Analysis ofE. coliCommensal and Pathogenic Isolates Journal of Bacteriology ·David A. Rasko, M. J. Rosovitz, Garry S. A. Myers, Emmanuel F. Mongodin, W. Florian Fricke, Pawel Gajer, Jonathan Crabtree, Mohammed Sebaihia, Nicholas R. Thomson, Roy R. Chaudhuri, Ian R. Henderson, Vanessa Sperandio, Jacques Ravel Hit paper breakdown →	2008	598
3	Draft genome sequence of the oilseed species Ricinus communis Nature Biotechnology ·Agnes P. Chan, Jonathan Crabtree, Qi Zhao, Hernán Lorenzi, Joshua Orvis, Daniela Puiu, Admasu Melake‐Berhan, Kristine Jones, Julia C. Redman, Grace Chen, Edgar B. Cahoon, Melaku Gedil, Mario Stanke, Brian J. Haas, Jennifer R. Wortman, Claire M. Fraser, Jacques Ravel, Pablo D. Rabinowicz	2010	366
4	Comparative Genomics of Brassica oleracea and Arabidopsis thaliana Reveal Gene Loss, Fragmentation, and Dispersal after Polyploidy The Plant Cell ·Christopher D. Town, Foo Cheung, Rama Maiti, Jonathan Crabtree, Brian J. Haas, Jennifer R. Wortman, Erin Hine, Ryan Althoff, Tamara S. Arbogast, Luke J. Tallon, Marielle Vigouroux, Martin Trick, Ian Bancroft	2006	319
5	Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium Nature Biotechnology ·Rashmi Sinha, Galeb Abu-Ali, Emily Vogtmann, Anthony A. Fodor, Boyu Ren, Amnon Amir, Emma Schwager, Jonathan Crabtree, Siyuan Ma, Christian C. Abnet, Rob Knight, Owen White, Curtis Huttenhower	2017	314
6	Sub-Telomere Directed Gene Expression during Initiation of Invasive Aspergillosis PLoS Pathogens ·Andrew McDonagh, Natalie D. Fedorova, Jonathan Crabtree, Yan Yu, Sun Kim, Dan Chen, Omar Loss, Timothy C. Cairns, Gustavo H. Goldman, Darius Armstrong‐James, Ken Haynes, Hubertus Haas, Markus Schrettl, Gregory S. May, William C. Nierman, Elaine Bignell	2008	202
7	The Aspergillus Genome Database (AspGD): recent developments in comprehensive multispecies curation, comparative genomics and community resources Nucleic Acids Research ·M. B. Arnaud, Gustavo C. Cerqueira, Diane O. Inglis, Marek S. Skrzypek, Jill Binkley, Marcus C. Chibucos, Jonathan Crabtree, Catherine Howarth, Joshua Orvis, Prachi Shah, F. Wymore, Gail Binkley, Stuart R. Miyasato, Matt Simison, Gavin Sherlock, Jennifer R. Wortman	2011	132
8	Functional Dynamics of the Gut Microbiome in Elderly People during Probiotic Consumption mBio ·Emiley A. Eloe‐Fadrosh, Arthur Brady, Jonathan Crabtree, Elliott F. Drábek, Bing Ma, Anup Mahurkar, Jacques Ravel, Miriam Haverkamp, Anne‐Maria Fiorino, Christine Botelho, Irina Andreyeva, Patricia L. Hibberd, Claire M. Fraser	2015	126
9	A comprehensive non-redundant gene catalog reveals extensive within-community intraspecies diversity in the human vagina Nature Communications ·Bing Ma, Michael France, Jonathan Crabtree, Johanna B. Holm, Michael S. Humphrys, Rebecca M. Brotman, Jacques Ravel	2020	103
10	The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community Nucleic Acids Research ·Martha B. Arnaud, Marcus C. Chibucos, Maria C. Costanzo, Jonathan Crabtree, Diane O. Inglis, Adil Lotia, Joshua Orvis, Prachi Shah, Marek S. Skrzypek, Gail Binkley, Stuart R. Miyasato, Jennifer R. Wortman, Gavin Sherlock	2009	99
11	An integrated genomic and transcriptomic survey of mucormycosis-causing fungi Nature Communications ·Marcus C. Chibucos, Sameh S. M. Soliman, Teclegiorgis Gebremariam, Hong-Kyu Lee, Sean C. Daugherty, Joshua Orvis, Amol C. Shetty, Jonathan Crabtree, Tracy H. Hazen, Kizee A. Etienne, Priti Kumari, Timothy D. O’Connor, David A. Rasko, Scott G. Filler, Claire M. Fraser, Shawn R. Lockhart, Christopher D. Skory, Ashraf S. Ibrahim, Vincent M. Bruno	2016	92
12	Comparative genomics of mutualistic viruses of Glyptapantelesparasitic wasps Genome biology ·Christopher A. Desjardins, Dawn E. Gundersen‐Rindal, Jessica B. Hostetler, Luke J. Tallon, Douglas Fadrosh, Roger W. Fuester, Monica J. Pedroni, Brian J. Haas, Michael C. Schatz, Kristine Jones, Jonathan Crabtree, Heather Forberger, Vishvanath Nene	2008	86
13	Continuing Evolution of Burkholderia mallei Through Genome Reduction and Large-Scale Rearrangements Genome Biology and Evolution ·Liliana Losada, Catherine M. Ronning, David DeShazer, Donald E. Woods, Natalie D. Fedorova, Sun Kim, Svetlana A. Shabalina, Talima Pearson, Lauren Brinkac, Patrick Tan, Tannistha Nandi, Jonathan Crabtree, Jonathan H. Badger, Steve M. Beckstrom-Sternberg, Muhammad Saqib, Steven E. Schutzer, Paul Keim, William C. Nierman	2010	83
14	Ergatis: a web interface and scalable software system for bioinformatics workflows Bioinformatics ·Joshua Orvis, Jonathan Crabtree, Kevin Galens, Aaron Gussman, Jason Inman, Eduardo Lee, Sreenath Nampally, David R. Riley, Jaideep P. Sundaram, Victor Felix, Brett R. Whitty, Anup Mahurkar, Jennifer R. Wortman, Owen White, Samuel V. Angiuoli	2010	79
15	Genomic Epidemiology of the Haitian Cholera Outbreak: a Single Introduction Followed by Rapid, Extensive, and Continued Spread Characterized the Onset of the Epidemic mBio ·Mark Eppinger, Talima Pearson, Sara S. K. Koenig, Ofori N. Pearson, Nathan Hicks, Sonia Agrawal, Fatemeh Sanjar, Kevin Galens, S. J. Daugherty, Jonathan Crabtree, René S. Hendriksen, Lance B. Price, Bishnu Prasad Upadhyay, Geeta Shakya, Claire M. Fraser, Jacques Ravel, Paul Keim	2014	67
16	Distinguishing potential bacteria-tumor associations from contamination in a secondary data analysis of public cancer genome sequence data Microbiome ·Kelly Robinson, Jonathan Crabtree, John S. Mattick, Kathleen E. Anderson, Julie C. Dunning Hotopp	2017	64
17	Sybil: Methods and Software for Multiple Genome Comparison and Visualization Methods in molecular biology ·Jonathan Crabtree, Samuel V. Angiuoli, Jennifer R. Wortman, Owen White	2007	49
18	Using Sybil for interactive comparative genomics of microbes on the web Bioinformatics ·David R. Riley, Samuel V. Angiuoli, Jonathan Crabtree, Julie C. Dunning Hotopp, Hervé Tettelin	2011	47
19	Whole genome comparison of theA. fumigatusfamily Medical Mycology ·Jennifer R. Wortman, Nadia Fedorova, Jonathan Crabtree, Vinita Joardar, Rama Maiti, Brian J. Haas, Paolo Amedeo, Elaine C Lee, Samuel V. Angiuoli, Bo Jiang, Michael J. Anderson, David W. Denning, Owen White, William C. Nierman	2006	37
20	Behavioral control for real-time simulated human agents John P. Granieri, Welton Becket, Barry D. Reich, Jonathan Crabtree, Norman I. Badler	1995	37

About Jonathan Crabtree

Jonathan Crabtree is a scholar working on Endocrinology, Infectious Diseases, Molecular Biology, Parasitology and Information Systems and Management, having authored 38 papers that have together received 4.0k indexed citations. Recurring topics across this work include Genomics and Phylogenetic Studies (15 papers), Gut microbiota and health (7 papers), Probiotics and Fermented Foods (3 papers), Plant Pathogens and Fungal Diseases (3 papers), Antifungal resistance and susceptibility (3 papers), Human Motion and Animation (3 papers), Chromosomal and Genetic Variations (3 papers) and Algorithms and Data Compression (3 papers). The work is most often cited by research in Endocrinology (422 citations), Molecular Biology (2.4k citations), Infectious Diseases (638 citations), Microbiology (185 citations) and Molecular Medicine (146 citations). Jonathan Crabtree has collaborated with scholars based in United States, United Kingdom and Germany. Frequent co-authors include Owen White, Joshua Orvis, Jacques Ravel, Jennifer R. Wortman, Anup Mahurkar, Curtis Huttenhower, Rob Knight, Arthur Brady, David A. Rasko and Heather H. Creasy. Their work appears in journals such as Bioinformatics, Nucleic Acids Research, Nature Communications, Nature Biotechnology and BMC Genomics.

Rankless uses publication and citation data sourced from OpenAlex, an open and comprehensive bibliographic database. While OpenAlex provides broad and valuable coverage of the global research landscape, it—like all bibliographic datasets—has inherent limitations. These include incomplete records, variations in author disambiguation, differences in journal indexing, and delays in data updates. As a result, some metrics and network relationships displayed in Rankless may not fully capture the entirety of a scholar's output or impact.

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