Simon Kasif

37.7k citations

124 papers · 8.2k indexed · 5 hit papers · h-index 39

Impact in

Molecular Biology top 1%
- Bioinformatics and Genomic Networks
- Genomics and Phylogenetic Studies
- Gene expression and cancer classification
- Machine Learning in Bioinformatics
- RNA and protein synthesis mechanisms
- Gene Regulatory Network Analysis
- Epigenetics and DNA Methylation
- Genomics and Chromatin Dynamics
Periodontics top 1%

Papers in ⓘ

Molecular Biology 76
- Bioinformatics and Genomic Networks 29
- Genomics and Phylogenetic Studies 22
- Machine Learning in Bioinformatics 18
- RNA and protein synthesis mechanisms 18
- Gene expression and cancer classification 15
- Microbial Metabolic Engineering and Bioproduction 10
- Genomics and Chromatin Dynamics 9
Computational Theory and Mathematics 17

Co-authors: Steven L. Salzberg (12 shared papers)Arthur L. Delcher (13 shared papers)Owen White (2 shared papers)T. M. Murali (6 shared papers)Sreerama K. Murthy (2 shared papers)Stanley Letovsky (1 shared paper)Timothy S. Gardner (1 shared paper)Guillaume Cottarel (1 shared paper)
Journals: Bioinformatics (9 papers)Nucleic Acids Research (8 papers)PLoS ONE (7 papers)Proceedings of the National Academy of Sciences (6 papers)Journal of Biological Chemistry (4 papers)
Partner nations: United States Israel Singapore

In The Last Decade

Simon Kasif

121 papers receiving 7.9k citations

Hit Papers

5 papers align trajectories log scale

Deep Sequencing of the Oral Microbiome Reveals Signatures of Periodontal Disease 2012 · 319 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.

2012 PLoS ONE
2008 PLoS Genetics
2007 PLoS Biology
1999 Nucleic Acids Research
1998 Nucleic Acids Research

Peers

Countries citing papers authored by Simon Kasif

Since Specialization

Citations

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

Fields of papers citing papers by Simon Kasif

Since Specialization

Physical SciencesHealth SciencesLife SciencesSocial Sciences

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

Co-authors

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

All Works

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

20 of 20 papers shown

Showing the 20 most-cited of 124 papers — load more, or switch the sort, to bring in the rest.

#	Work
1	Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles PLoS Biology ·Jeremiah J. Faith, Boris Hayete, Joshua T. Thaden, Ilaria Mogno, Jamey Wierzbowski, Guillaume Cottarel, Simon Kasif, James J. Collins, Timothy S. Gardner Hit paper breakdown →	2007	1104
2	Genomewide Analysis of PRC1 and PRC2 Occupancy Identifies Two Classes of Bivalent Domains PLoS Genetics ·Manching Ku, Richard P. Koche, Esther Rheinbay, Eric M. Mendenhall, Mitsuhiro Endoh, Tarjei S. Mikkelsen, Aviva Presser, Chad Nusbaum, Xiaohui Xie, S. Andrew, Mazhar Adli, Simon Kasif, Leon M. Ptaszek, Chad A. Cowan, Eric S. Lander, Haruhiko Koseki, B Bernstein Hit paper breakdown →	2008	787
3	Microbial gene identification using interpolated Markov models Nucleic Acids Research ·Steven L. Salzberg, Arthur L. Delcher, Simon Kasif, Owen White Hit paper breakdown →	1998	709
4	Alignment of whole genomes Nucleic Acids Research ·Arthur L. Delcher, Simon Kasif, R. D. Fleischmann, J. Peterson, Owen White, Steven L. Salzberg Hit paper breakdown →	1999	575
5	A System for Induction of Oblique Decision Trees Journal of Artificial Intelligence Research ·Sreerama K. Murthy, Simon Kasif, Steven L. Salzberg	1994	358
6	Deep Sequencing of the Oral Microbiome Reveals Signatures of Periodontal Disease PLoS ONE ·Bo Liu, Lina L. Faller, Niels Klitgord, Varun Mazumdar, Mohammad Ghodsi, Doron D. Sommer, Theodore Gibbons, Todd J. Treangen, Yi-Chien Chang, Shan Li, O. Colin Stine, Hatice Hastürk, Simon Kasif, Daniel Segrè, Mihai Pop, Salomon Amar Hit paper breakdown →	2012	319
7	Predicting protein function from protein/proteininteraction data: a probabilistic approach Bioinformatics ·Stanley Letovsky, Simon Kasif	2003	261
8	EXTRACTING CONSERVED GENE EXPRESSION MOTIFS FROM GENE EXPRESSION DATA PubMed ·T. M. Murali, Simon Kasif	2002	248
9	Whole-genome annotation by using evidence integration in functional-linkage networks Proceedings of the National Academy of Sciences ·Ulaş Karaöz, T. M. Murali, Stan Letovsky, Yu Zheng, Chunming Ding, Charles R. Cantor, Simon Kasif	2004	209
10	An Aberrant Transcription Factor Network Essential for Wnt Signaling and Stem Cell Maintenance in Glioblastoma Cell Reports ·Esther Rheinbay, Mario L. Suvà, Shawn Gillespie, Hiroaki Wakimoto, Anoop P. Patel, Mohd Shahid, Ozgur Oksuz, Samuel D. Rabkin, Robert L. Martuza, Miguel N. Rivera, David N. Louis, Simon Kasif, S. Andrew, B Bernstein	2013	197
11	Immediate-Early and Delayed Primary Response Genes Are Distinct in Function and Genomic Architecture Journal of Biological Chemistry ·John W. Tullai, Michael Schäffer, Steven Mullenbrock, Gabriel Sholder, Simon Kasif, Geoffrey M. Cooper	2007	134
12	Network-Based Analysis of Affected Biological Processes in Type 2 Diabetes Models PLoS Genetics ·Manway Liu, Arthur Liberzon, Sek Won Kong, Weil Lai, Peter J. Park, Isaac S. Kohane, Simon Kasif	2007	132
13	RankGene: identification of diagnostic genesbased on expression data Bioinformatics ·Yang Su, T. M. Murali, Vladimir Pavlović, Michael Schäffer, Simon Kasif	2003	132
14	Computational methods in molecular biology Elsevier eBooks ·Steven L. Salzberg, David B. Searls, Simon Kasif	1998	128
15	Defects in muscle branched-chain amino acid oxidation contribute to impaired lipid metabolism Molecular Metabolism ·Carles Lerín, Allison B. Goldfine, Tanner Boes, Manway Liu, Simon Kasif, Jonathan M. Dreyfuss, Ana Luísa De Sousa‐Coelho, Grace Daher, Irini Manoli, Justin R. Sysol, Elvira Isganaitis, Niels Jessen, Laurie J. Goodyear, Kirk Beebe, Walt Gall, Charles P. Venditti, Mary‐Elizabeth Patti	2016	118
16	Identification of functional links between genes using phylogenetic profiles Bioinformatics ·Jie Wu, Simon Kasif, Charles DeLisi	2003	114
17	Towards the identification of essential genes using targeted genome sequencing and comparative analysis BMC Genomics ·Adam M Gustafson, Evan S. Snitkin, Stephen C.J. Parker, Charles DeLisi, Simon Kasif	2006	114
18	Computational Identification of Operons in Microbial Genomes Genome Research ·Yu Zheng, Joseph D. Szustakowski, Lance Fortnow, Richard J. Roberts, Simon Kasif	2001	104
19	Optimized Multiplex PCR: Efficiently Closing a Whole-Genome Shotgun Sequencing Project Genomics ·Hervé Tettelin, Diana Radune, Simon Kasif, Hoda Khouri, Steven L. Salzberg	1999	98
20	RimO, a MiaB-like enzyme, methylthiolates the universally conserved Asp88 residue of ribosomal protein S12 in Escherichia coli Proceedings of the National Academy of Sciences ·Brian P. Anton, Lana Saleh, Jack S. Benner, Elisabeth A. Raleigh, Simon Kasif, Richard J. Roberts	2008	96

About Simon Kasif

Simon Kasif is a scholar working on Molecular Biology, Computational Theory and Mathematics, Artificial Intelligence, Hardware and Architecture and Computer Networks and Communications, having authored 124 papers that have together received 8.2k indexed citations. Recurring topics across this work include Bioinformatics and Genomic Networks (29 papers), Genomics and Phylogenetic Studies (22 papers), Machine Learning in Bioinformatics (18 papers), RNA and protein synthesis mechanisms (18 papers), Gene expression and cancer classification (15 papers), Microbial Metabolic Engineering and Bioproduction (10 papers), Genomics and Chromatin Dynamics (9 papers) and Adipose Tissue and Metabolism (9 papers). The work is most often cited by research in Molecular Biology (5.9k citations), Periodontics (256 citations), Computational Theory and Mathematics (644 citations), Artificial Intelligence (1.1k citations) and Genetics (794 citations). Simon Kasif has collaborated with scholars based in United States, Israel and Singapore. Frequent co-authors include Steven L. Salzberg, Arthur L. Delcher, Owen White, T. M. Murali, Sreerama K. Murthy, Stanley Letovsky, Timothy S. Gardner, Guillaume Cottarel, Boris Hayete and Ilaria Mogno. Their work appears in journals such as Bioinformatics, Nucleic Acids Research, PLoS ONE, Proceedings of the National Academy of Sciences and Journal of Biological Chemistry.

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.

Explore authors with similar magnitude of impact