James J. Davis

16.1k citations

35 papers · 7.1k indexed · 4 hit papers · h-index 20

Impact in

Molecular Medicine top 0.2%
- Antibiotic Resistance in Bacteria
Endocrinology top 0.5%

Papers in

Molecular Medicine 8
- Antibiotic Resistance in Bacteria 8
Clinical Biochemistry 6
- Bacterial Identification and Susceptibility Testing 6

Co-authors: Robert Olson Rick Stevens Fangfang Xia Maulik Shukla Alice R. Wattam Ross Overbeek Veronika Vonstein Gordon D. Pusch
Journals: Scientific Reports (4 papers)American Journal Of Pathology (3 papers)mSystems (3 papers)Frontiers in Microbiology (3 papers)mBio (2 papers)
Partner nations: United States Denmark United Kingdom

In The Last Decade

James J. Davis

33 papers receiving 7.0k citations

Hit Papers

align trajectories log scale

Signals of Significantly Increased Vaccine Breakthrough, Decreased Hospitalization Rates, and Less Severe Disease in Patients with Coronavirus Disease 2019 Caused by the Omicron Variant of Severe Acute Respiratory Syndrome Coronavirus 2 in Houston, Texas 2022 · 127 citations

What are hit papers?

Hit papers significantly outperform the citation benchmark for their cohort. A paper qualifies if any of the following hold:

it has ≥500 total citations;
it reaches ≥1.5× the top-1% citation threshold for papers in the same subfield and year (the threshold is the minimum needed to enter the top 1%, not the average within it);
it reaches the top citation threshold in at least one of its specific research topics.

2022 American Journal Of Pathology
2022 Proceedings of the National Academy of Sciences
2015 Scientific Reports
2013 Nucleic Acids Research

Peers

Countries citing papers authored by James J. Davis

Since Specialization

Citations

This map shows the geographic impact of James J. Davis'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 James J. Davis with the expected number of citations based on a country's size and research output (numbers larger than one mean the country cites James J. Davis more than expected).

Fields of papers citing papers by James J. Davis

Since Specialization

Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by James J. Davis. 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 James J. Davis. The network helps show where James J. Davis may publish in the future.

Co-authors

The 25 scholars most cited alongside James J. Davis, 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 James J. Davis Line = papers co-authored together James J. Davis links everyone, so they are left out of the graph.

All Works

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20 of 20 papers shown

#	Work
1	Predicting variable gene content in Escherichia coli using conserved genes mSystems ·Marcus Nguyen, Zachary C. Elmore, Pascal Joanne, M.S. de Oliveira, Breanna S. Ireland, Neha Nawalkar, Bruce Parrello, Aaron A. Best, James J. Davis	2023	0
2	Multiple spillovers from humans and onward transmission of SARS-CoV-2 in white-tailed deer Proceedings of the National Academy of Sciences ·Suresh V. Kuchipudi, Meera Surendran Nair, Rachel M. Ruden, Michele Yon, Ruth H. Nissly, Kurt J. Vandegrift, Rahul K. Nelli, Lingling Li, Bhushan M. Jayarao, Costas D. Maranas, Laslo F. Nađ, Katriina Willgert, Andrew J. K. Conlan, Randall J. Olsen, James J. Davis, James M. Musser, Peter J. Hudson, Vivek Kapur Hit paper breakdown →	2022	124
3	Early detection of emerging SARS-CoV-2 variants of interest for experimental evaluation SHILAP Revista de lepidopterología ·Zachary S. Wallace, James J. Davis, Anna Maria Niewiadomska, Robert Olson, Maulik Shukla, Rick Stevens, Yun Zhang, Christian M. Zmasek, Richard H. Scheuermann	2022	2
4	PlasmidHostFinder: Prediction of Plasmid Hosts Using Random Forest mSystems ·Derya Aytan-Aktug, Philip T. L. C. Clausen, Aleksandr Sergeyevich Matveev, Patrick Munk, Saria Otani, Marcus Nguyen, James J. Davis, Ole Lund, Frank M. Aarestrup	2022	19
5	Transmission history of SARS-CoV-2 in humans and white-tailed deer Scientific Reports ·Katriina Willgert, Xavier Didelot, Fernanda Hellena de Lima Queiroz, Suresh V. Kuchipudi, Rachel M. Ruden, Michele Yon, Ruth H. Nissly, Kurt J. Vandegrift, Rahul K. Nelli, Lingling Li, Bhushan M. Jayarao, Laslo F. Nađ, Randall J. Olsen, James J. Davis, James M. Musser, Peter J. Hudson, Vivek Kapur, Andrew J. K. Conlan	2022	13
6	Signals of Significantly Increased Vaccine Breakthrough, Decreased Hospitalization Rates, and Less Severe Disease in Patients with Coronavirus Disease 2019 Caused by the Omicron Variant of Severe Acute Respiratory Syndrome Coronavirus 2 in Houston, Texas American Journal Of Pathology ·Paul Christensen, Randall J. Olsen, Sheng Long, Sun Li, James J. Davis, Matthew Ojeda Saavedra, Kristina Reppond, Madison Shyer, Jessica Cambric, Ryan Gadd, Rashi M. Thakur, Akanksha Batajoo, Mariane Gonçalves Martynychen Canan1, Phil Schloss, A. S. Pushkin, Jacob Kinskey, Guy Williams, Robert Olson, Jimmy Gollihar, James M. Musser Hit paper breakdown →	2022	127
7	Trajectory of Growth of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Variants in Houston, Texas, January through May 2021, Based on 12,476 Genome Sequences American Journal Of Pathology ·Randall J. Olsen, Paul Christensen, S. Wesley Long, Sishir Subedi, Parsa Hodjat, Robert Olson, Marcus Nguyen, James J. Davis, Prasanti Yerramilli, Matthew Ojeda Saavedra, Layne Pruitt, Kristina Reppond, Madison Shyer, Jessica Cambric, Ryan Gadd, Rashi M. Thakur, Akanksha Batajoo, Ilya J. Finkelstein, Jimmy Gollihar, James M. Musser	2021	10
8	A Genome-Based Model to Predict the Virulence of Pseudomonas aeruginosa Isolates mBio ·Nathan B. Pincus, Egon A. Ozer, Jonathan P. Allen, Marcus Nguyen, James J. Davis, Deborah R. Winter, 覚元葛谷, Cheng‐Hsun Chiu, Laura Zamorano, Antonio Oliver, Alan R. Hauser	2020	18
9	Carbapenems drive the collateral resistance to ceftaroline in cystic fibrosis patients with MRSA Communications Biology ·Alvaro Oliveira Magalhaes, Mélanie Roch, Agustina Taglialegna, S. Wesley Long, Matthew Ojeda Saavedra, Warren E. Rose, James J. Davis, Lucas R. Hoffman, Rafael E. Hernandez, Roberto R. Rosato, Adriana E. Rosato	2020	13
10	Using Machine Learning To Predict Antimicrobial MICs and Associated Genomic Features for Nontyphoidal Salmonella Journal of Clinical Microbiology ·Marcus Nguyen, S. Wesley Long, Patrick F. McDermott, Randall J. Olsen, Robert Olson, Rick Stevens, Gregory H. Tyson, Shaohua Zhao, James J. Davis	2018	182
11	Developing an in silico minimum inhibitory concentration panel test for Klebsiella pneumoniae Scientific Reports ·Marcus Nguyen, Thomas Brettin, S. Wesley Long, James M. Musser, Randall J. Olsen, Robert Olson, Maulik Shukla, Rick Stevens, Fangfang Xia, Hyunseung Yoo, James J. Davis	2018	123
12	Whole-Genome Sequencing of a Human Clinical Isolate of the Novel Species Klebsiella quasivariicola sp. nov Genome Announcements ·S. Wesley Long, Hyean-Wee Kim, Matthew Ojeda Saavedra, Concepcion Cantu, James J. Davis, Thomas Brettin, Randall J. Olsen	2017	41
13	Daptomycin Resistance in Clinical MRSA Strains Is Associated with a High Biological Fitness Cost Frontiers in Microbiology ·Mélanie Roch, Paula Gagetti, James J. Davis, Paola Ceriana, Е.Н. Граменицкий, Alejandra Corso, Adriana E. Rosato	2017	52
14	Computing and Applying Atomic Regulons to Understand Gene Expression and Regulation Frontiers in Microbiology ·José P. Faria, James J. Davis, Janaka N. Edirisinghe, Ronald C. Taylor, Pamela Weisenhorn, Robert Olson, Rick Stevens, Miguel Rocha, Isabel Rocha, Aaron A. Best, Matthew DeJongh, Nathan Tintle, Bruce Parrello, Ross Overbeek, Christopher S. Henry	2016	5
15	Space, Labor Markets, and History: An Exploration of American Indian Employment Hardship and Socioeconomic Inequality OhioLink ETD Center (Ohio Library and Information Network) ·James J. Davis	2015	1
16	RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes Scientific Reports ·Thomas Brettin, James J. Davis, Terry Disz, Robert A. Edwards, Svetlana Gerdes, Gary J. Olsen, Robert Olson, Ross Overbeek, Bruce Parrello, Gordon D. Pusch, Maulik Shukla, Yulia A. Krivolapova, Rick Stevens, Veronika Vonstein, Alice R. Wattam, Fangfang Xia Hit paper breakdown →	2015	1988
17	Enabling comparative modeling of closely related genomes: example genus Brucella 3 Biotech ·José P. Faria, Janaka N. Edirisinghe, James J. Davis, T. Disz, Anna Hausmann, Christopher S. Henry, Robert Olson, Ross Overbeek, Gordon D. Pusch, Maulik Shukla, Veronika Vonstein, Alice R. Wattam	2014	4
18	In search of genome annotation consistency: solid gene clusters and how to use them 3 Biotech ·James J. Davis, Gary J. Olsen, Ross Overbeek, Veronika Vonstein, Fangfang Xia	2013	4
19	The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST) Nucleic Acids Research ·Ross Overbeek, Robert Olson, Gordon D. Pusch, G J Olsen, James J. Davis, Terry Disz, Robert A. Edwards, Svetlana Gerdes, Bruce Parrello, Maulik Shukla, Veronika Vonstein, Alice R. Wattam, Fangfang Xia, Rick Stevens Hit paper breakdown →	2013	3521
20	Modal Codon Usage: Assessing the Typical Codon Usage of a Genome Molecular Biology and Evolution ·James J. Davis, G J Olsen	2009	30

About James J. Davis

James J. Davis is a scholar working on Molecular Medicine, Clinical Biochemistry, Infectious Diseases, Molecular Biology and Animal Science and Zoology, having authored 35 papers that have together received 7.1k indexed citations. Recurring topics across this work include Genomics and Phylogenetic Studies (20 papers), Antibiotic Resistance in Bacteria (8 papers), SARS-CoV-2 and COVID-19 Research (6 papers), Bacterial Identification and Susceptibility Testing (6 papers), Microbial Metabolic Engineering and Bioproduction (5 papers), RNA and protein synthesis mechanisms (5 papers), Viral gastroenteritis research and epidemiology (4 papers) and Bacteriophages and microbial interactions (4 papers). The work is most often cited by research in Molecular Medicine (1.2k citations), Endocrinology (848 citations), Ecology (2.4k citations), Microbiology (468 citations) and Clinical Biochemistry (496 citations). James J. Davis has collaborated with scholars based in United States, Denmark and United Kingdom. Frequent co-authors include Robert Olson, Rick Stevens, Fangfang Xia, Maulik Shukla, Alice R. Wattam, Ross Overbeek, Veronika Vonstein, Gordon D. Pusch, Svetlana Gerdes and Robert A. Edwards. Their work appears in journals such as Scientific Reports, American Journal Of Pathology, mSystems, Frontiers in Microbiology and mBio.

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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