Ron Shamir

24.9k citations

296 papers · 15.1k indexed · 6 hit papers · h-index 62

Impact in

Molecular Biology top 0.2%
- Bioinformatics and Genomic Networks
- Gene expression and cancer classification
- Gene Regulatory Network Analysis
- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- Genomics and Chromatin Dynamics
- RNA Research and Splicing
- Microbial Metabolic Engineering and Bioproduction
Computational Theory and Mathematics top 0.2%

Papers in

Molecular Biology 186
- Bioinformatics and Genomic Networks 61
- Gene expression and cancer classification 52
- Genomics and Phylogenetic Studies 35
- Genomics and Chromatin Dynamics 31
- Gene Regulatory Network Analysis 27
- RNA and protein synthesis mechanisms 25
Computational Theory and Mathematics 36
- Advanced Graph Theory Research 24

Co-authors: Roded Sharan Igor Ulitsky Amos Tanay Guy Karlebach Chaim Linhart Amir Ben‐Dor Nimrod Rappoport Zohar Yakhini
Journals: Journal of Computational Biology (26 papers)Bioinformatics (22 papers)Nucleic Acids Research (13 papers)PLoS ONE (9 papers)Molecular Systems Biology (8 papers)
Partner nations: Israel United States Germany

In The Last Decade

Ron Shamir

291 papers receiving 14.6k citations

Hit Papers

6 papers align trajectories log scale

Multi-omic and multi-view clustering algorithms: review and cancer benchmark 2018 · 339 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.

2018 Nucleic Acids Research
2008 Nature Reviews Molecular Cell Biology
2007 Molecular Systems Biology
2006 Proceedings of the National Academy of Sciences
2002 Bioinformatics
1999 Journal of Computational Biology

Peers

Countries citing papers authored by Ron Shamir

Since Specialization

Citations

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

Fields of papers citing papers by Ron Shamir

Since Specialization

Physical SciencesHealth SciencesLife SciencesSocial Sciences

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

Co-authors

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

All Works

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

20 of 20 papers shown

#	Work
1	Integrating mutation, copy number, and gene expression data to identify driver genes of recurrent chromosome-arm losses Cell Reports ·Arias Macías, Ron Shamir, Uri Ben‐David	2025	0
2	Predicting appropriateness of antibiotic treatment among ICU patients with hospital-acquired infection npj Digital Medicine ·양귀자, Sertan Demir, Daniel Bernstein, Asaf Wasserman, Lota Gasterosteus Aculea- Tus, H. Michael Sokolow, Tamajeet Mandal, Ron Shamir	2025	6
3	Efficient minimizer orders for large values of k using minimum decycling sets Genome Research ·David Pellow, T. N. Osinina, Rudolf Fiedler, Huidi Sun, Bonnie Berger, Ron Shamir, Yaron Orenstein	2023	7
4	The DOMINO web-server for active module identification analysis Bioinformatics ·J�os Csan�i, Jill E. Larson, Ran Elkon, Ron Shamir	2022	5
5	Parameterized syncmer schemes improve long-read mapping PLoS Computational Biology ·郁曾全, David Pellow, Ron Shamir	2022	13
6	CT-FOCS: a novel method for inferring cell type-specific enhancer–promoter maps Nucleic Acids Research ·Ruth María Calvo Ferrer, Ran Elkon, Ron Shamir	2022	2
7	3CAC: improving the classification of phages and plasmids in metagenomic assemblies using assembly graphs Bioinformatics ·T. N. Osinina, Ron Shamir	2022	5
8	Melanoma-Secreted Lysosomes Trigger Monocyte-Derived Dendritic Cell Apoptosis and Limit Cancer Immunotherapy Cancer Research ·Paola Andrea Alfonso Martín, 康伟正, 蒋旭峰, Li Cui, اميرة اكرامي عبد الله, 郁雨君, Dvir Netanely, Ron Shamir, Rachel Blau, Meora Feinmesser, Mariah Ramireza, Haim Gutman, Ian L. Linde, Nathan E. Reticker-Flynn, Peleg Rider, Yaron Carmi	2020	25
9	NEMO: cancer subtyping by integration of partial multi-omic data Bioinformatics ·Nimrod Rappoport, Ron Shamir	2019	169
10	PRODIGY: personalized prioritization of driver genes Bioinformatics ·Gal Dinstag, Ron Shamir	2019	38
11	Computational analysis of mRNA expression profiling in the inner ear reveals candidate transcription factors associated with proliferation, differentiation, and deafness Human Genomics ·Pawel Janas, Ron Shamir, Karen B. Avraham	2018	7
12	Faucet: streaming de novo assembly graph construction Bioinformatics ·Roye Rozov, В А Шабанова, Eran Halperin, Ron Shamir	2017	6
13	Improving the performance of minimizers and winnowing schemes Bioinformatics ·Guillaume Marçais, David Pellow, Xianzhou Zeng, Yaron Orenstein, Ron Shamir, Carl Kingsford	2017	43
14	Recycler: an algorithm for detecting plasmids from de novo assembly graphs Bioinformatics ·Roye Rozov, Aya Brown Kav, David Bogumil, Naama Shterzer, Eran Halperin, Itzhak Mizrahi, Ron Shamir	2016	97
15	Gene Expression Signature of Human Cancer Cell Lines Treated with the Ras Inhibitor Salirasib ( S -Farnesylthiosalicylic Acid) Cancer Research ·Roy Blum, Ran Elkon, 奈良井章人, Adi Zundelevich, Jasmine Jacob‐Hirsch, Gideon Rechavi, Ron Shamir, Yoel Kloog	2007	40
16	Quantification of protein half-lives in the budding yeast proteome Proceedings of the National Academy of Sciences ·Archana Belle, Amos Tanay, Reinaldo Squillante, Ron Shamir, Erin K. O’Shea Hit paper breakdown →	2006	539
17	Conservation and evolvability in regulatory networks: The evolution of ribosomal regulation in yeast Proceedings of the National Academy of Sciences ·Amos Tanay, Aviv Regev, Ron Shamir	2005	197
18	Accurate identification of alternatively spliced exons using support vector machine Bioinformatics ·Gideon Dror, Rotem Sorek, Ron Shamir	2004	93
19	RECOMB 2000 : proceedings of the Fourth annual international conference on computational molecular biology : April 8-11, 2000, Tokyo, Japan Association for Computing Machinery eBooks ·Ron Shamir, Satoru Miyano, Sorin Istrail, Pavel A. Pevzner, Michael S. Waterman, Adwin Wigfall Green	2000	2
20	The Maximum Subforest Problem: Approximation and Exact Algorithms (Extended Abstract). Symposium on Discrete Algorithms ·Ron Shamir, Dekel Tsur	1998	3

About Ron Shamir

Ron Shamir is a scholar working on Molecular Biology, Computational Theory and Mathematics, Discrete Mathematics and Combinatorics, Genetics and Aging, having authored 296 papers that have together received 15.1k indexed citations. Recurring topics across this work include Bioinformatics and Genomic Networks (61 papers), Gene expression and cancer classification (52 papers), Genomics and Phylogenetic Studies (35 papers), Algorithms and Data Compression (32 papers), Genomics and Chromatin Dynamics (31 papers), Gene Regulatory Network Analysis (27 papers), RNA and protein synthesis mechanisms (25 papers) and Advanced Graph Theory Research (24 papers). The work is most often cited by research in Molecular Biology (10.7k citations), Computational Theory and Mathematics (1.7k citations), Cancer Research (1.2k citations), Aging (122 citations) and Genetics (1.9k citations). Ron Shamir has collaborated with scholars based in Israel, United States and Germany. Frequent co-authors include Roded Sharan, Igor Ulitsky, Amos Tanay, Guy Karlebach, Chaim Linhart, Amir Ben‐Dor, Nimrod Rappoport, Zohar Yakhini, Haim Kaplan and Ran Elkon. Their work appears in journals such as Journal of Computational Biology, Bioinformatics, Nucleic Acids Research, PLoS ONE and Molecular Systems Biology.

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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