John Ingraham

4.5k total citations · 1 hit paper
20 papers, 2.0k citations indexed

About

John Ingraham is a scholar working on Molecular Biology, Genetics and Cell Biology. According to data from OpenAlex, John Ingraham has authored 20 papers receiving a total of 2.0k indexed citations (citations by other indexed papers that have themselves been cited), including 16 papers in Molecular Biology, 4 papers in Genetics and 2 papers in Cell Biology. Recurrent topics in John Ingraham's work include RNA and protein synthesis mechanisms (9 papers), Protein Structure and Dynamics (5 papers) and Genomics and Phylogenetic Studies (5 papers). John Ingraham is often cited by papers focused on RNA and protein synthesis mechanisms (9 papers), Protein Structure and Dynamics (5 papers) and Genomics and Phylogenetic Studies (5 papers). John Ingraham collaborates with scholars based in United States, Germany and Austria. John Ingraham's co-authors include Debora S. Marks, Adam J. Riesselman, Chris Sander, Thomas A. Hopf, Michael Springer, Charlotta Schärfe, Frank J. Poelwijk, Jan Neuhard, R T Vinopal and J. Preiss and has published in prestigious journals such as Cell, Proceedings of the National Academy of Sciences and Nucleic Acids Research.

In The Last Decade

John Ingraham

20 papers receiving 1.9k citations

Hit Papers

Mutation effects predicted from sequence co-variation 2017 2026 2020 2023 2017 100 200 300 400
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.

  1. Mutation effects predicted from sequence co-variation
    2017 447 citations Thomas A. Hopf, John Ingraham et al. Nature Biotechnology profile →

Peers — A (Enhanced Table)

Peers by citation overlap · career bar shows stage (early→late) cites · hero ref

Name h Career Trend Papers Cites
John Ingraham United States 17 1.6k 436 247 150 111 20 2.0k
Jean-François Gibrat France 13 1.9k 1.2× 220 0.5× 391 1.6× 144 1.0× 170 1.5× 34 2.4k
William P. Russ United States 16 2.3k 1.4× 320 0.7× 226 0.9× 108 0.7× 88 0.8× 19 2.9k
Hetunandan Kamisetty United States 10 2.0k 1.2× 332 0.8× 500 2.0× 200 1.3× 113 1.0× 23 2.3k
Thomas A. Hopf United States 17 3.2k 1.9× 685 1.6× 564 2.3× 235 1.6× 120 1.1× 21 3.8k
Lucy J. Colwell United Kingdom 24 2.5k 1.5× 312 0.7× 527 2.1× 318 2.1× 96 0.9× 44 3.1k
P. Douglas Renfrew United States 17 2.0k 1.2× 140 0.3× 362 1.5× 272 1.8× 92 0.8× 39 2.6k
Kensaku Sakamoto Japan 36 3.8k 2.3× 655 1.5× 209 0.8× 55 0.4× 201 1.8× 101 4.2k
Bryan S. Der United States 18 1.6k 1.0× 233 0.5× 246 1.0× 47 0.3× 91 0.8× 22 1.9k
Shandar Ahmad Japan 29 2.3k 1.4× 165 0.4× 392 1.6× 402 2.7× 75 0.7× 96 2.9k
Christian Barrett United States 24 2.2k 1.3× 534 1.2× 214 0.9× 38 0.3× 194 1.7× 36 2.5k

Countries citing papers authored by John Ingraham

Since Specialization
Citations

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

Fields of papers citing papers by John Ingraham

Since Specialization
Physical SciencesHealth SciencesLife SciencesSocial Sciences

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

Co-authorship network of co-authors of John Ingraham

This figure shows the co-authorship network connecting the top 25 collaborators of John Ingraham. A scholar is included among the top collaborators of John Ingraham 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 John Ingraham. John Ingraham is excluded from the visualization to improve readability, since they are connected to all nodes in the network.

All Works

20 of 20 papers shown
1.
Fram, Benjamin, Yang Su, Adam J. Riesselman, et al.. (2024). Simultaneous enhancement of multiple functional properties using evolution-informed protein design. Nature Communications. 15(1). 5141–5141. 13 indexed citations
2.
Ingraham, John, et al.. (2022). The state of remote learning in plastic surgery: A systematic review of modalities. SHILAP Revista de lepidopterología. 10. 100102–100102. 1 indexed citations
3.
Yuan, Bo, Ciyue Shen, Augustin Luna, et al.. (2020). CellBox: Interpretable Machine Learning for Perturbation Biology with Application to the Design of Cancer Combination Therapy. Cell Systems. 12(2). 128–140.e4. 69 indexed citations
4.
Pattanaik, Lagnajit, John Ingraham, Colin A. Grambow, & William H. Green. (2020). Generating transition states of isomerization reactions with deep learning. Physical Chemistry Chemical Physics. 22(41). 23618–23626. 55 indexed citations
5.
Shen, Judy Hanwen, Bo Yuan, Augustin Luna, et al.. (2020). Abstract 2102: Interpretable machine learning for perturbation biology. Cancer Research. 80(16_Supplement). 2102–2102. 1 indexed citations
6.
Ingraham, John, Vikas Garg, Regina Barzilay, & Tommi Jaakkola. (2019). Generative models for graph-based protein design. DSpace@MIT (Massachusetts Institute of Technology). 32. 15794–15805. 98 indexed citations
7.
Hopf, Thomas A., Anna G. Green, Benjamin Schubert, et al.. (2018). The EVcouplings Python framework for coevolutionary sequence analysis. Bioinformatics. 35(9). 1582–1584. 172 indexed citations
8.
Ingraham, John, Adam J. Riesselman, Chris Sander, & Debora S. Marks. (2018). Learning Protein Structure with a Differentiable Simulator. International Conference on Learning Representations. 44 indexed citations
9.
Riesselman, Adam J., John Ingraham, & Debora S. Marks. (2018). Deep generative models of genetic variation capture the effects of mutations. Nature Methods. 15(10). 816–822. 334 indexed citations
10.
Hopf, Thomas A., John Ingraham, Frank J. Poelwijk, et al.. (2017). Mutation effects predicted from sequence co-variation. Nature Biotechnology. 35(2). 128–135. 447 indexed citations breakdown →
11.
Weinreb, Caleb, Adam J. Riesselman, John Ingraham, et al.. (2016). 3D RNA and Functional Interactions from Evolutionary Couplings. Cell. 165(4). 963–975. 110 indexed citations
12.
Tóth-Petróczy, Ágnes, John Ingraham, Thomas A. Hopf, et al.. (2016). Structured States of Disordered Proteins from Genomic Sequences. Cell. 167(1). 158–170.e12. 91 indexed citations
13.
Savir, Yonatan, Sean M. Carroll, John Ingraham, et al.. (2015). Galactose metabolic genes in yeast respond to a ratio of galactose and glucose. Proceedings of the National Academy of Sciences. 112(5). 1636–1641. 92 indexed citations
14.
Lee, Tak Yeon, et al.. (2012). CTArcade. 2309–2314. 17 indexed citations
15.
Karp, Peter D., Ingrid M. Keseler, Alexander G. Shearer, et al.. (2007). Multidimensional annotation of the Escherichia coli K-12 genome. Nucleic Acids Research. 35(22). 7577–7590. 136 indexed citations
16.
Hsu, David S., et al.. (1992). Diversity of cleavage patterns of Salmonella 23S rRNA. Journal of General Microbiology. 138(1). 199–203. 31 indexed citations
17.
Beck, Christoph F., John Ingraham, O. Maaløe, & Jan Neuhard. (1973). Relationship between the concentration of nucleoside triphosphates and the rate of synthesis of RNA. Journal of Molecular Biology. 78(1). 117–121. 31 indexed citations
18.
Vinopal, R T, et al.. (1969). Isolation of mutants of Escherichia coli B altered in their ability to synthesize glycogen. Journal of Bacteriology. 97(2). 970–972. 103 indexed citations
19.
Ingraham, John, et al.. (1969). Cold-sensitive Mutations in Salmonella typhimurium Which Affect Ribosome Synthesis. Journal of Bacteriology. 97(3). 1298–1304. 98 indexed citations
20.
Neuhard, Jan & John Ingraham. (1968). Mutants of Salmonella typhimurium requiring cytidine for growth. Journal of Bacteriology. 95(6). 2431–2433. 47 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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