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, Australia and United Kingdom. Jonathan Allen's co-authors include Steven L. Salzberg, Mihaela Pertea, C. Robin Buell, Joshua Orvis, Wei Zhu, Brian J. Haas, Owen White, Jennifer R. Wortman, 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

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 Steven L. Salzberg, Jonathan Allen et al. profile →
High-resolution detection of Au catalyst atoms in Si nanowires

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

Peers

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

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20 of 20 papers shown

#	Work	Indexed citations
1	Protein-ligand binding affinity prediction using multi-instance learning with docking structures 2025 ·Frontiers in Pharmacology ·Hyo-Jin Kim, (unknown), (unknown), (unknown), (unknown), Jonathan Allen	0
2	Addressing the dynamic nature of reference data: a new nucleotide database for robust metagenomic classification 2025 ·mSystems ·Jose Manuel Martí, Car Reen Kok, James B. Thissen, (unknown), Aram Avila-Herrera, Crystal Jaing, Jonathan Allen, Nicholas A. Be	1
3	Enhancing Docking Accuracy with PECAN2, a 3D Atomic Neural Network Trained without Co-Complex Crystal Structures 2024 ·SHILAP Revista de lepidopterología ·(unknown), Jonathan Allen, William F. Bennett	2
4	Evaluating point-prediction uncertainties in neural networks for protein-ligand binding prediction 2023 ·SHILAP Revista de lepidopterología ·(unknown), Jonathan Allen, Kevin McLoughlin, Da Shi, Brian J. Bennion, Xiaohua Zhang, Felice C. Lightstone	3
5	Metagenomic Methods for Addressing NASA's Planetary Protection Policy Requirements on Future Missions: A Workshop Report 2023 ·Astrobiology ·Stefan J. Green, Tamás Török, Jonathan Allen, Emiley A. Eloe‐Fadrosh, Scott A. Jackson, Sunny C. Jiang, Stuart S. Levine, Shawn Levy, Lynn M. Schriml, W. Kelley Thomas, Jason M. Wood, Scott Tighe	2
6	Clustering Protein Binding Pockets and Identifying Potential Drug Interactions: A Novel Ligand-Based Featurization Method 2023 ·Journal of Chemical Information and Modeling ·(unknown), Daniel Kirshner, Brian J. Bennion, Yue Yang, Xiaohua Zhang, Adam Zemła, (unknown), (unknown), Derek Jones, Hyojin Kim, William F. Bennett, Sergio Wong, Jonathan Allen, Felice C. Lightstone	3
7	MACAW: An Accessible Tool for Molecular Embedding and Inverse Molecular Design 2022 ·Journal of Chemical Information and Modeling ·Vincent Blay, Tijana Radivojević, Jonathan Allen, Corey Hudson, Héctor García Martín	5
8	Multiple Mutations Associated with Emergent Variants Can Be Detected as Low-Frequency Mutations in Early SARS-CoV-2 Pandemic Clinical Samples 2022 ·Viruses ·Jeffrey A. Kimbrel, (unknown), Aram Avila-Herrera, Jose Manuel Martí, James B. Thissen, (unknown), (unknown), (unknown), Chris Daum, Sara Hall, Brent W. Segelke, Kathryn T. Arrildt, Sharon Messenger, Debra A. Wadford, Crystal Jaing, Jonathan Allen, Monica K. Borucki	5
9	FDA-ARGOS is a database with public quality-controlled reference genomes for diagnostic use and regulatory science 2019 ·Nature Communications ·Heike Sichtig, Timothy D. Minogue, Yi Yan, Christopher P. Stefan, Adrienne T. Hall, Luke J. Tallon, Lisa Sadzewicz, Suvarna Nadendla, William Klimke, Eneida Hatcher, Martin Shumway, (unknown), Jonathan Allen, Jeffrey W. Koehler, Tom Slezak, (unknown), Randal J. Schoepp, Uwe Scherf	261
10	A novel variant of torque teno virus 7 identified in patients with Kawasaki disease 2018 ·PLoS ONE ·James B. Thissen, Mariko Isshiki, Crystal Jaing, Yoshiro Nagao, (unknown), Jonathan Allen, (unknown), Thomas R. Slezak, Takafumi Ishida, Tetsuya Sano	20
11	Using populations of human and microbial genomes for organism detection in metagenomes 2015 ·Genome Research ·Sasha Ames, Shea N. Gardner, Jose Manuel Martí, Tom Slezak, Maya Gokhale, Jonathan Allen	25
12	Ultra-deep mutant spectrum profiling: improving sequencing accuracy using overlapping read pairs 2013 ·BMC Genomics ·Haiyin Chen‐Harris, Monica K. Borucki, (unknown), Tom Slezak, Jonathan Allen	37
13	Conserved amino acid markers from past influenza pandemic strains 2009 ·BMC Microbiology ·Jonathan Allen, Shea N. Gardner, Elizabeth Vitalis, Tom Slezak	40
14	A synergistic assembly of nanoscale lamellar photoconductor hybrids 2008 ·Nature Materials ·(unknown), Joshua E. Goldberger, David Stone, Jonathan Allen, Qing Ma, David J. Herman, (unknown), Lincoln J. Lauhon, Samuel I. Stupp	166
15	Three-dimensional nanoscale composition mapping of semiconductor nanowires. 2006 ·APS March Meeting Abstracts ·Lincoln J. Lauhon, Daniel E. Perea, Jonathan Allen, Steven J. May, Bruce W. Wessels, David N. Seidman	163
16	A phylogenetic generalized hidden Markov model for predicting alternatively spliced exons 2006 ·Algorithms for Molecular Biology ·Jonathan Allen, Steven L. Salzberg	9
17	Regulated expression of putative membrane progestin receptor homologues in human endometrium and gestational tissues 2005 ·Journal of Endocrinology ·Maria Sofia Fernandes, (unknown), David Michalovich, Shirley Astle, Steven Thornton, Hellevi Peltoketo, Eric W.‐F. Lam, Birgit Gellersen, Ilpo Huhtaniemi, Jonathan Allen, Jan J. Brosens	114
18	César Manrique y el futuro imposible 1994 ·Americanae (AECID Library) ·Jonathan Allen	0
19	Massively parallel computing and information capitalism 1993 ·MIT Press eBooks ·Rob Kling, Isaac D. Scherson, Jonathan Allen	4
20	Research Laboratory of Electronics 1983 ·Jonathan Allen	51

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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