Jared T. Simpson

60.8k citations

35 papers · 7.5k · 5 hit papers · h-index 20

Impact in

Molecular Biology top 1%
- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- Gut microbiota and health
- Fungal and yeast genetics research
Ecology top 1%
- Microbial Community Ecology and Physiology
- Bacteriophages and microbial interactions

Papers in

Molecular Biology 25
- Genomics and Phylogenetic Studies 15
- RNA and protein synthesis mechanisms 9
- RNA modifications and cancer 8
- Genomics and Chromatin Dynamics 4
- Fungal and yeast genetics research 3
- Epigenetics and DNA Methylation 3
Infectious Diseases 5
- SARS-CoV-2 and COVID-19 Research 5

Co-authors: Nicholas J. Loman (2 shared papers)Shaun D. Jackman (2 shared papers)Steven J.M. Jones (1 shared paper)Kim Wong (1 shared paper)İnanç Birol (1 shared paper)Jacqueline E. Schein (1 shared paper)Richard Durbin (8 shared papers)Joshua Quick (1 shared paper)
Journals: Nature Methods (4 papers)Genome Research (4 papers)Bioinformatics (4 papers)Genome biology (2 papers)Journal of Computational Biology (1 paper)
Partner nations: Canada United Kingdom United States

In The Last Decade

Jared T. Simpson

33 papers receiving 7.4k citations

Jared T. Simpson's Hit Papers

5 papers align trajectories log scale

Detecting DNA cytosine methylation using nanopore sequencing 2017 · 668 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.

2017 Nature Methods
2017 Nature Biotechnology
2015 Nature Methods
2011 Genome Research
2009 Genome Research

Peers

Countries citing papers authored by Jared T. Simpson

Since Specialization

Citations

This map shows the geographic impact of Jared T. Simpson'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 Jared T. Simpson with the expected number of citations based on a country's size and research output (numbers larger than one mean the country cites Jared T. Simpson more than expected).

Fields of papers citing papers by Jared T. Simpson

Since Specialization

Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by Jared T. Simpson. 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 Jared T. Simpson. The network helps show where Jared T. Simpson may publish in the future.

Co-authors

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

All Works

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20 of 20 papers shown

Showing the 20 most-cited of 35 papers — load more, or switch the sort, to bring in the rest.

#	Work
1	ABySS: A parallel assembler for short read sequence data Genome Research ·Jared T. Simpson, Kim Wong, Shaun D. Jackman, Jacqueline E. Schein, Steven J.M. Jones, İnanç Birol Hit paper breakdown →	2009	2629
2	Shotgun metagenomics, from sampling to analysis Nature Biotechnology ·Christopher Quince, Alan W. Walker, Jared T. Simpson, Nicholas J. Loman, Nicola Segata Hit paper breakdown →	2017	1218
3	A complete bacterial genome assembled de novo using only nanopore sequencing data Nature Methods ·Nicholas J. Loman, Joshua Quick, Jared T. Simpson Hit paper breakdown →	2015	838
4	Detecting DNA cytosine methylation using nanopore sequencing Nature Methods ·Jared T. Simpson, Rachael E. Workman, Philip C. Zuzarte, Matei David, Lewis Jonathan Dursi, Winston Timp Hit paper breakdown →	2017	668
5	Efficient de novo assembly of large genomes using compressed data structures Genome Research ·Jared T. Simpson, Richard Durbin Hit paper breakdown →	2011	489
6	Trait Variation in Yeast Is Defined by Population History PLoS Genetics ·Jonas Warringer, Enikö Zörgö, Francisco A. Cubillos, Amin Zia, Arne B. Gjuvsland, Jared T. Simpson, Annabelle Forsmark, Richard Durbin, Stig W. Omholt, Edward J. Louis, Gianni Liti, Alan M Moses, Anders Blomberg	2011	263
7	A High-Definition View of Functional Genetic Variation from Natural Yeast Genomes Molecular Biology and Evolution ·Anders Bergström, Jared T. Simpson, F. Salinas, Benjamin Barré, Leopold Parts, Amin Zia, Alex N. Nguyen Ba, Alan M Moses, Edward J. Louis, Ville Mustonen, Jonas Warringer, Richard Durbin, Gianni Liti	2014	217
8	Revealing the genetic structure of a trait by sequencing a population under selection Genome Research ·Leopold Parts, Francisco A. Cubillos, Jonas Warringer, Kanika Jain, F. Salinas, Suzannah J. Bumpstead, Mikael Molin, Amin Zia, Jared T. Simpson, Michael A. Quail, Alan M Moses, Edward J. Louis, Richard Durbin, Gianni Liti	2011	191
9	Efficient construction of an assembly string graph using the FM-index Bioinformatics ·Jared T. Simpson, Richard Durbin	2010	150
10	Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing Nature Methods ·Isac Lee, Roham Razaghi, Timothy Gilpatrick, Michael M. Molnar, Ariel Gershman, Norah Sadowski, Fritz J. Sedlazeck, Kasper D. Hansen, Jared T. Simpson, Winston Timp	2020	126
11	New Twists in Detecting mRNA Modification Dynamics Trends in biotechnology ·Ina Anreiter, Quoseena Mir, Jared T. Simpson, Sarath Chandra Janga, Matthias Soller	2020	101
12	Exploring genome characteristics and sequence quality without a reference Bioinformatics ·Jared T. Simpson	2014	99
13	Nanocall: an open source basecaller for Oxford Nanopore sequencing data Bioinformatics ·Matei David, Lewis Jonathan Dursi, Delia Yao, Paul C. Boutros, Jared T. Simpson	2016	93
14	Capturing the dynamics of genome replication on individual ultra-long nanopore sequence reads Nature Methods ·Carolin A. Müller, Michael A. Boemo, Paolo Spingardi, Benedikt M. Kessler, Skirmantas Kriaučionis, Jared T. Simpson, Conrad A. Nieduszynski	2019	88
15	GPU accelerated adaptive banded event alignment for rapid comparative nanopore signal analysis BMC Bioinformatics ·Hasindu Gamaarachchi, Chun Wai Lam, Gihan Jayatilaka, Hiruna Samarakoon, Jared T. Simpson, Martin A. Smith, Sri Parameswaran	2020	76
16	The Theory and Practice of Genome Sequence Assembly Annual Review of Genomics and Human Genetics ·Jared T. Simpson, Mihai Pop	2015	66
17	Copy number variant detection in inbred strains from short read sequence data Bioinformatics ·Jared T. Simpson, Rebecca E. McIntyre, David J. Adams, Richard Durbin	2009	39
18	On the Representation of De Bruijn Graphs Journal of Computational Biology ·Rayan Chikhi, Antoine Limasset, Shaun D. Jackman, Jared T. Simpson, Paul Medvedev	2015	36
19	Revealing nascent RNA processing dynamics with nano-COP Nature Protocols ·Heather L. Drexler, Karine Choquet, Hope E. Merens, Paul S. Tang, Jared T. Simpson, L. Stirling Churchman	2021	31
20	Deep short-read sequencing of chromosome 17 from the mouse strains A/J and CAST/Ei identifies significant germline variation and candidate genes that regulate liver triglyceride levels Genome biology ·Ian Sudbery, Jim Stalker, Jared T. Simpson, Thomas Keane, Alistair G. Rust, Matthew E. Hurles, Klaudia Walter, Dee Lynch, Lydia Teboul, Steve D. M. Brown, Heng Li, Zemin Ning, Joseph H. Nadeau, Colleen M. Croniger, Richard Durbin, David J. Adams	2009	29

About Jared T. Simpson

Jared T. Simpson is a scholar working on Molecular Biology, Infectious Diseases, Genetics, Plant Science and Ecology, having authored 35 papers that have together received 7.5k indexed citations. Recurring topics across this work include Genomics and Phylogenetic Studies (15 papers), RNA and protein synthesis mechanisms (9 papers), RNA modifications and cancer (8 papers), SARS-CoV-2 and COVID-19 Research (5 papers), Genomics and Chromatin Dynamics (4 papers), Fungal and yeast genetics research (3 papers), Epigenetics and DNA Methylation (3 papers) and Chromosomal and Genetic Variations (3 papers). The work is most often cited by research in Molecular Biology (4.9k citations), Ecology (1.2k citations), Plant Science (1.5k citations), Genetics (1.0k citations) and Endocrinology (176 citations). Jared T. Simpson has collaborated with scholars based in Canada, United Kingdom and United States. Frequent co-authors include Nicholas J. Loman, Shaun D. Jackman, Steven J.M. Jones, Kim Wong, İnanç Birol, Jacqueline E. Schein, Richard Durbin, Joshua Quick, Alan W. Walker and Nicola Segata. Their work appears in journals such as Nature Methods, Genome Research, Bioinformatics, Genome biology and Journal of Computational 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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Jared T. Simpson

Jared T. Simpson's Hit Papers

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