Jonathan Allen

20.0k total citations · 2 hit papers
73 papers, 5.8k citations indexed

About

Jonathan Allen is a scholar working on Molecular Biology, Electrical and Electronic Engineering and Computational Theory and Mathematics. According to data from OpenAlex, Jonathan Allen has authored 73 papers receiving a total of 5.8k indexed citations (citations by other indexed papers that have themselves been cited), including 35 papers in Molecular Biology, 14 papers in Electrical and Electronic Engineering and 13 papers in Computational Theory and Mathematics. Recurrent topics in Jonathan Allen's work include Computational Drug Discovery Methods (13 papers), Genomics and Phylogenetic Studies (12 papers) and Nanowire Synthesis and Applications (9 papers). Jonathan Allen is often cited by papers focused on Computational Drug Discovery Methods (13 papers), Genomics and Phylogenetic Studies (12 papers) and Nanowire Synthesis and Applications (9 papers). Jonathan Allen collaborates with scholars based in United States, United Kingdom and Australia. Jonathan Allen's co-authors include Steven L. Salzberg, Mihaela Pertea, Joshua Orvis, Jennifer R. Wortman, Owen White, Brian J. Haas, C. Robin Buell, Wei Zhu, Lincoln J. Lauhon and Daniel E. Perea and has published in prestigious journals such as Advanced Materials, Nature Communications and Nature Materials.

In The Last Decade

Jonathan Allen

71 papers receiving 5.7k citations

Hit Papers

align trajectories sort by overperformance

What are hit papers?

Hit papers significantly outperform the citation benchmark for their cohort. A paper qualifies if it has ≥500 total citations, achieves ≥1.5× the top-1% citation threshold for papers in the same subfield and year (this is the minimum needed to enter the top 1%, not the average within it), or reaches the top citation threshold in at least one of its specific research topics.

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

2008 2.3k citations Brian J. Haas, Steven L. Salzberg et al. Genome biology profile →
High-resolution detection of Au catalyst atoms in Si nanowires

2008 515 citations Jonathan Allen, Daniel E. Perea et al. profile →

Author Peers

Peers are selected by citation overlap in the author's most active subfields. citations · hero ref

Author						Papers	Cites
Jonathan Allen	2.2k	1.3k	1.2k	1.1k	879	73	5.8k
Xi Wang	1.8k 0.8×	686 0.5×	593 0.5×	572 0.5×	980 1.1×	247	5.3k
David Sept	6.7k 3.0×	1.4k 1.1×	502 0.4×	434 0.4×	1.1k 1.3×	110	11.2k
Kazuyoshi Murata	3.5k 1.6×	817 0.7×	601 0.5×	194 0.2×	607 0.7×	136	5.9k
Margaret E. Johnson	2.7k 1.2×	386 0.3×	617 0.5×	235 0.2×	698 0.8×	100	5.5k
P. J. Simpson	2.2k 1.0×	1.1k 0.9×	738 0.6×	1.4k 1.3×	1.3k 1.5×	233	6.7k
Hans Söderlund	3.0k 1.3×	990 0.8×	699 0.6×	343 0.3×	719 0.8×	110	6.0k
Douglas B. Weibel	3.6k 1.6×	4.1k 3.2×	276 0.2×	1.2k 1.0×	943 1.1×	99	9.2k
David J. Meyer	4.9k 2.2×	623 0.5×	641 0.5×	1.2k 1.0×	800 0.9×	225	9.6k
José L. Carrascosa	4.9k 2.2×	774 0.6×	913 0.8×	286 0.3×	1.2k 1.4×	217	9.6k
Andriy Shevchenko	4.2k 1.9×	829 0.7×	576 0.5×	450 0.4×	456 0.5×	150	7.1k

Countries citing papers authored by Jonathan Allen

Since Specialization

Citations

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

Fields of papers citing papers by Jonathan Allen

Since Specialization

Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by Jonathan Allen. 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 Allen. The network helps show where Jonathan Allen may publish in the future.

Co-authorship network of co-authors of Jonathan Allen

This figure shows the co-authorship network connecting the top 25 collaborators of Jonathan Allen. A scholar is included among the top collaborators of Jonathan Allen based on the total number of citations received by their joint publications. Widths of edges represent the number of papers authors have co-authored together. Node borders signify the number of papers an author published with Jonathan Allen. Jonathan Allen is excluded from the visualization to improve readability, since they are connected to all nodes in the network.

All Works

Sort: Min cites: Since: Top N: Style:

20 of 20 papers shown

Kim, Hyo-Jin, et al.. (2025). Protein-ligand binding affinity prediction using multi-instance learning with docking structures. Frontiers in Pharmacology. 15. 1518875–1518875.

Martí, Jose Manuel, Car Reen Kok, James B. Thissen, et al.. (2025). Addressing the dynamic nature of reference data: a new nucleotide database for robust metagenomic classification. mSystems. 10(4). e0123924–e0123924. 1 indexed citations

Jones, Derek C., Brian J. Bennion, Weihong Xu, et al.. (2024). HDBind: encoding of molecular structure with hyperdimensional binary representations. Scientific Reports. 14(1). 29025–29025. 4 indexed citations

Allen, Jonathan, et al.. (2024). Enhancing Docking Accuracy with PECAN2, a 3D Atomic Neural Network Trained without Co-Complex Crystal Structures. SHILAP Revista de lepidopterología. 6(1). 642–657. 2 indexed citations

Allen, Jonathan, Kevin McLoughlin, Da Shi, et al.. (2023). Evaluating point-prediction uncertainties in neural networks for protein-ligand binding prediction. SHILAP Revista de lepidopterología. 1(1). 100004–100004. 3 indexed citations

Green, Stefan J., Tamás Török, Jonathan Allen, et al.. (2023). Metagenomic Methods for Addressing NASA's Planetary Protection Policy Requirements on Future Missions: A Workshop Report. Astrobiology. 23(8). 897–907. 2 indexed citations

Drocco, Jeffrey A., et al.. (2023). A Computational Pipeline to Identify and Characterize Binding Sites and Interacting Chemotypes in SARS-CoV-2. ACS Omega. 8(24). 21871–21884. 2 indexed citations

Kirshner, Daniel, Brian J. Bennion, Yue Yang, et al.. (2023). Clustering Protein Binding Pockets and Identifying Potential Drug Interactions: A Novel Ligand-Based Featurization Method. Journal of Chemical Information and Modeling. 63(21). 6655–6666. 3 indexed citations

Kimbrel, Jeffrey A., Aram Avila-Herrera, Jose Manuel Martí, et al.. (2022). Multiple Mutations Associated with Emergent Variants Can Be Detected as Low-Frequency Mutations in Early SARS-CoV-2 Pandemic Clinical Samples. Viruses. 14(12). 2775–2775. 5 indexed citations

10.

Blay, Vincent, Tijana Radivojević, Jonathan Allen, Corey Hudson, & Héctor García Martín. (2022). MACAW: An Accessible Tool for Molecular Embedding and Inverse Molecular Design. Journal of Chemical Information and Modeling. 62(15). 3551–3564. 5 indexed citations

11.

Sichtig, Heike, Timothy D. Minogue, Yi Yan, et al.. (2019). FDA-ARGOS is a database with public quality-controlled reference genomes for diagnostic use and regulatory science. Nature Communications. 10(1). 3313–3313. 261 indexed citations

12.

Ames, Sasha, Shea N. Gardner, Jose Manuel Martí, et al.. (2015). Using populations of human and microbial genomes for organism detection in metagenomes. Genome Research. 25(7). 1056–1067. 25 indexed citations

13.

Allen, Jonathan, Shea N. Gardner, Elizabeth Vitalis, & Tom Slezak. (2009). Conserved amino acid markers from past influenza pandemic strains. BMC Microbiology. 9(1). 77–77. 40 indexed citations

14.

Haas, Brian J., Steven L. Salzberg, Wei Zhu, et al.. (2008). Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome biology. 9(1). R7–R7. 2294 indexed citations breakdown →

15.

Lauhon, Lincoln J., Daniel E. Perea, Jonathan Allen, et al.. (2006). Three-dimensional nanoscale composition mapping of semiconductor nanowires.. APS March Meeting Abstracts. 163 indexed citations

16.

Fernandes, Maria Sofia, David Michalovich, Shirley Astle, et al.. (2005). Regulated expression of putative membrane progestin receptor homologues in human endometrium and gestational tissues. Journal of Endocrinology. 187(1). 89–101. 114 indexed citations

17.

Allen, Jonathan, Mihaela Pertea, & Steven L. Salzberg. (2004). Computational Gene Prediction Using Multiple Sources of Evidence. Genome Research. 14(1). 142–148. 84 indexed citations

18.

Allen, Jonathan. (1994). César Manrique y el futuro imposible. Americanae (AECID Library). 64–68.

19.

Kling, Rob, Isaac D. Scherson, & Jonathan Allen. (1993). Massively parallel computing and information capitalism. MIT Press eBooks. 191–241. 4 indexed citations

20.

Allen, Jonathan. (1983). Research Laboratory of Electronics. 51 indexed citations

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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