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Jared T. Simpson

Active 2009–2025

45
Papers
22,672
Citations
37
h-index
44
i10-index

Citations

Citations per year for Jared T. Simpson1983: 2 citations1994: 3 citations2003: 1 citations2005: 1 citations2006: 1 citations2009: 17 citations2010: 97 citations2011: 168 citations2012: 254 citations2013: 270 citations2014: 328 citations2015: 312 citations2016: 415 citations2017: 478 citations2018: 450 citations2019: 1,025 citations2020: 1,077 citations2021: 1,062 citations2022: 765 citations2023: 600 citations2024: 854 citations2025: 425 citations2026: 24 citations1984–1993: no citations, so these years are not shown1995–2002: no citations, so these years are not shown2004: no citations, so this year is not shown2007–2008: no citations, so these years are not shown

Citation sources

Countries

World map of the countries and regions citing this authorUnited States: 3,145 citing papers, 23.4% of this breakdownUnited Kingdom: 1,235 citing papers, 9.2% of this breakdownChina: 1,023 citing papers, 7.6% of this breakdownGermany: 755 citing papers, 5.6% of this breakdownFrance: 552 citing papers, 4.1% of this breakdownCanada: 551 citing papers, 4.1% of this breakdownAustralia: 499 citing papers, 3.7% of this breakdownItaly: 394 citing papers, 2.9% of this breakdownSpain: 355 citing papers, 2.7% of this breakdownNetherlands: 300 citing papers, 2.2% of this breakdownSwitzerland: 275 citing papers, 2.1% of this breakdownSweden: 272 citing papers, 2% of this breakdown
0%23.4%Other 30.4%

Institutions

Fields

  • Biochemistry, Genetics and Molecular Biology60.8%
  • Medicine16.4%
  • Agricultural and Biological Sciences7.4%
  • Environmental Science4.6%
  • Computer Science3.3%
  • Immunology and Microbiology2.6%
  • Other4.9%

Topics

  • Genomics and Phylogenetic Studies12.3%
  • RNA and protein synthesis mechanisms3.3%
  • Cancer Genomics and Diagnostics3.1%
  • RNA modifications and cancer3.1%
  • Chromosomal and Genetic Variations3%
  • Gut microbiota and health2.5%
  • Other72.7%

Coauthors

All papers

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  1. Shotgun metagenomics, from sampling to analysis

    Authors: Christopher Quince, Alan W. Walker, Jared T. Simpson, Nicholas J. Loman, Nicola Segata - Nature Biotechnology 2017 cited by 2,155

  2. Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

    Authors: Valérie Schneider, Tina A. Graves-Lindsay, Kerstin Howe, Nathan Bouk, Hsiu-Chuan Chen, Paul Kitts, Terence D. Murphy, Kim D. Pruitt, Françoise Thibaud‐Nissen, Derek Albracht, Robert S. Fulton, Milinn Kremitzki, Vincent Magrini, Chris Markovic, Sean McGrath, Karyn Meltz Steinberg, Kate Auger, William Chow, Joanna Collins, Glenn Harden, Tim Hubbard, Sarah Pelan, Jared T. Simpson, Glen Threadgold, James Torrance, Jonathan Wood, Laura Clarke, Sergey Koren, Matthew Boitano, Paul Peluso, Heng Li, Chen-Shan Chin, Adam M. Phillippy, Richard Durbin, Richard K. Wilson, Paul Flicek, Evan E. Eichler, Deanna M. Church - Genome Research 2017 cited by 1,294

  3. Detecting DNA cytosine methylation using nanopore sequencing

    Authors: Jared T. Simpson, Rachael E. Workman, Philip C. Zuzarte, Matei David, Lewis Jonathan Dursi, Winston Timp - Nature Methods 2017 cited by 1,257

  4. Nanopore native RNA sequencing of a human poly(A) transcriptome

    Authors: Rachael E. Workman, Alison D. Tang, Paul S. Tang, Miten Jain, John R. Tyson, Roham Razaghi, Philip C. Zuzarte, Timothy Gilpatrick, Alexander Payne, Joshua Quick, Norah Sadowski, Nadine Holmes, Jaqueline Góes de Jesus, Karen L. Jones, Cameron M. Soulette, Terrance P. Snutch, Nicholas J. Loman, Benedict Paten, Matthew Loose, Jared T. Simpson, Hugh E. Olsen, Angela N. Brooks, Mark Akeson, Winston Timp - Nature Methods 2019 cited by 750

  5. Real-time, portable genome sequencing for Ebola surveillance

    Authors: Joshua Quick, Nicholas J. Loman, Sophie Duraffour, Jared T. Simpson, Ettore Severi, Lauren A. Cowley, Joseph Akoi Boré, Raymond Koundouno, Gytis Dudas, Amy Mikhail, Nobila Ouédraogo, Babak Afrough, Amadou Bah, Jonathan H. J. Baum, Beate Becker‐Ziaja, Jan Peter Boettcher, Mar Cabeza-Cabrerizo, Álvaro Camino-Sánchez, Lisa L. Carter, Juliane Doerrbecker, Theresa Enkirch, Isabel García-Dorival, Nicole Hetzelt, Julia Hinzmann, Tobias Holm, Liana E. Kafetzopoulou, Michel Koropogui, Abigael Kosgey, Eeva Kuisma, Christopher H. Logue, Antonio Mazzarelli, Sarah Meisel, Marc Mertens, Janine Michel, Didier Ngabo, Katja Nitzsche, Elisa Pallasch, Livia Victoria Patrono, Jasmine Portmann, Johanna Repits, Natasha Y. Rickett, Andreas Sachse, Katrin Singethan, Inês Vitoriano, Rahel L. Yemanaberhan, Elsa Gayle Zekeng, Trina Racine, Alexander Bello, Amadou Alpha Sall, Ousmane Faye, Oumar Faye, N’Faly Magassouba, C.V. Williams, Victoria Amburgey, Linda Winona, Emily Davis, Jon Gerlach, F Clarke -Washington, Vanessa Monteil, Marine Jourdain, Marion Bererd, Alimou Camara, Hermann Somlaré, Abdoulaye Camara, Marianne Gérard, Guillaume Bado, Bernard Baillet, Déborah Delaune, Koumpingnin Nebié, Abdoulaye Diarra, Yacouba Savane, Raymond Pallawo, Giovanna Jaramillo Gutierrez, Natacha Milhano, Isabelle Roger, Christopher J. Williams, Facinet Yattara, Kuiama Lewandowski, James G. Taylor, Phillip A. Rachwal, Daniel J. Turner, Georgios Pollakis, Julian A. Hiscox, David A. Matthews, Matthew K. O’ Shea, Andrew Johnston, Duncan Wilson, Emma Hutley, Erasmus Smit, Antonino Di, Roman Wölfel, Kilian Stoecker, Erna Fleischmann, Martin Gabriel, Simon A. Weller, Lamine Koivogui, Boubacar Diallo, Sakoba Keïta, Andrew Rambaut, Pierre Formenty and 2 more - Nature 2016 cited by 1,584

  6. Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples

    Authors: Joshua Quick, Nathan D. Grubaugh, Steven T. Pullan, Ingra Morales Claro, Andrew D. Smith, Karthik Gangavarapu, Glenn Oliveira, Refugio Robles‐Sikisaka, Thomas F. Rogers, Nathan Beutler, Dennis R. Burton, Lia Laura Lewis‐Ximenez, Jaqueline Góes de Jesus, Marta Giovanetti, Sarah C. Hill, Allison Black, Trevor Bedford, Miles W. Carroll, Márcio Roberto Teixeira Nunes, Luíz Carlos Júnior Alcântara, Éster Cerdeira Sabino, Sally A. Baylis, Nuno R. Faria, Matthew Loose, Jared T. Simpson, Oliver G. Pybus, Kristian G. Andersen, Nicholas J. Loman - Nature Protocols 2017 cited by 1,309

  7. A complete bacterial genome assembled de novo using only nanopore sequencing data

    Authors: Nicholas J. Loman, Joshua Quick, Jared T. Simpson - Nature Methods 2015 cited by 1,513

  8. ABySS: A parallel assembler for short read sequence data

    Authors: Jared T. Simpson, Kim Wong, Shaun D. Jackman, Jacqueline E. Schein, Steven J.M. Jones, İnanç Birol - Genome Research 2009 cited by 3,765

  9. A renewed model of pancreatic cancer evolution based on genomic rearrangement patterns

    Authors: Faiyaz Notta, Michelle Chan‐Seng‐Yue, Mathieu Lemire, Yilong Li, Gavin W. Wilson, Ashton A. Connor, Robert E. Denroche, Sheng-Ben Liang, Andrew Brown, Jaeseung Kim, Tao Wang, Jared T. Simpson, Timothy Beck, Ayelet Borgida, Nicholas Buchner, Dianne Chadwick, Sara Hafezi‐Bakhtiari, John E. Dick, Lawrence E. Heisler, Michael A. Hollingsworth, Emin Ibrahimov, Gun Ho Jang, Jeremy Johns, Lars Jorgensen, Calvin Law, Olga Ludkovski, Ilinca M. Lungu, Karen Ng, Danielle Pasternack, Gloria M. Petersen, Liran I. Shlush, Lee E. Timms, Ming‐Sound Tsao, Julie M. Wilson, Christina K. Yung, George Zogopoulos, John M.S. Bartlett, Ludmil B. Alexandrov, Francisco X. Real, Sean P. Cleary, Michael H. A. Roehrl, John D. McPherson, Lincoln Stein, Thomas J. Hudson, Peter J. Campbell, Steven Gallinger - Nature 2016 cited by 547

  10. Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing

    Authors: Isac Lee, Roham Razaghi, Timothy Gilpatrick, Michael M. Molnar, Ariel Gershman, Norah Sadowski, Fritz J. Sedlazeck, Kasper D. Hansen, Jared T. Simpson, Winston Timp - Nature Methods 2020 cited by 245

  11. Establishment and cryptic transmission of Zika virus in Brazil and the Americas

    Authors: Nuno R. Faria, Josh Quick, Ingra Morales Claro, Julien Thézé, Jhennifer Guimarães Lourenço de Jesus, Marta Giovanetti, Moritz U. G. Kraemer, Sarah C. Hill, Allison Black, Antônio Charlys da Costa, L.C. Junqueira Franco, Serena Pocas Moreno Silva, Chieh‐Hsi Wu, Jayna Raghwani, Simon Cauchemez, Louis du Plessis, Mariana Pastorello Verotti, W. K. de Oliveira, Eduardo Hage Carmo, Giovanini Evelim Coelho, A. C. F. S. Santelli, Livia Vinhal, Cláudio Maierovitch Pessanha Henriques, Jared T. Simpson, Matthew Loose, Kristian G. Andersen, Nathan D. Grubaugh, Sneha Somasekar, Charles Y. Chiu, José Esteban Muñoz‐Medina, César González-Bonilla, Carlos F. Arias, Lia Laura Lewis‐Ximenez, Sally A. Baylis, Alexandre Chieppe, Shirlei Ferreira de Aguiar, Carlos Augusto Fernandes, P. S. Lemos, Bruna Laís Sena do Nascimento, H. A. O Monteiro, Isadora Cristina de Siqueira, Maria Gabriela de Queiroz, Themis Rocha de Souza, João Felipe Bezerra, Marisa Lemos, G. F. Pereira, D. Loudal, Lúcia Cristina Corrêa Moura, Rafael Dhália, R. F. França, Tereza Magalhães, Ernesto T. A. Marques, Thomas Jaenisch, Gabriel Luz Wallau, Magliones Carneiro de Lima, Valdinete Alves do Nascimento, Erenilde Marques de Cerqueira, Maricélia Maia de Lima, D. L. Mascarenhas, José Pereira de Moura Neto, Anna S. Levin, Tânia Regina Tozetto‐Mendoza, Sílvia Nunes Szente Fonseca, Maria Cássia Mendes-Corrêa, Flavio Augusto de Pádua Milagres, Aluísio Augusto Cotrim Segurado, Edward C. Holmes, Andrew Rambaut, Trevor Bedford, Márcio Roberto Teixeira Nunes, Éster Cerdeira Sabino, L. C. J. Alcantara, Nicholas J. Loman, Oliver G. Pybus - Nature, Nat. 2017 cited by 674

  12. New Twists in Detecting mRNA Modification Dynamics

    Authors: Ina Anreiter, Quoseena Mir, Jared T. Simpson, Sarath Chandra Janga, Matthias Soller - Trends in biotechnology 2020 cited by 158

  13. Capturing the dynamics of genome replication on individual ultra-long nanopore sequence reads

    Authors: Carolin A. Müller, Michael A. Boemo, Paolo Spingardi, Benedikt M. Kessler, Skirmantas Kriaučionis, Jared T. Simpson, Conrad A. Nieduszynski - Nature Methods 2019 cited by 152

  14. Efficient de novo assembly of large genomes using compressed data structures

    Authors: Jared T. Simpson, Richard Durbin - Genome Research 2011 cited by 817

  15. MinION Analysis and Reference Consortium: Phase 1 data release and analysis

    Authors: Camilla L. C. Ip, Matthew Loose, John R. Tyson, Mariateresa de Cesare, Bonnie L. Brown, Miten Jain, Richard M. Leggett, David A. Eccles, Vadim Zalunin, John M. Urban, Paolo Piazza, Rory J. Bowden, Benedict Paten, Solomon Mwaigwisya, Elizabeth M. Batty, Jared T. Simpson, Terrance P. Snutch, Ewan Birney, David Buck, Sara Goodwin, Hans J. Jansen, Justin O'Grady, Hugh E. Olsen, MinION Analysis, Reference Consortium - F1000Research 2015 cited by 341

  16. Nanopore native RNA sequencing of a human poly(A) transcriptome

    Authors: Rachael E. Workman, Alison D. Tang, Paul S. Tang, Miten Jain, John R. Tyson, Philip C. Zuzarte, Timothy Gilpatrick, Roham Razaghi, Joshua Quick, Norah Sadowski, Nadine Holmes, Jaqueline Góes de Jesus, Karen L. Jones, Terrance P. Snutch, Nicholas J. Loman, Benedict Paten, Matthew Loose, Jared T. Simpson, Hugh E. Olsen, Angela N. Brooks, Mark Akeson, Winston Timp - 2018 cited by 142

  17. Insights into hominid evolution from the gorilla genome sequence

    Authors: Aylwyn Scally, Julien Y. Dutheil, LaDeana W. Hillier, Gregory E. Jordan, Ian Goodhead, Javier Herrero, Asger Hobolth, Tuuli Lappalainen, Thomas Mailund, Tomàs Marquès‐Bonet, Shane McCarthy, Stephen H. Montgomery, Petra Schwalie, Amy Tang, Michelle C. Ward, Yali Xue, Bryndís Yngvadóttir, Can Alkan, Lars Nørvang Andersen, Qasim Ayub, Edward V. Ball, Kathryn Beal, Brenda J. Bradley, Yuan Chen, Chris M. Clee, Stephen Fitzgerald, Tina Graves, Yong Gu, P. D. Heath, Andreas Heger, Emre Karakoç, Anja Kolb‐Kokocinski, Gavin K. Laird, Gerton Lunter, Stephen Meader, Matthew Mort, James C. Mullikin, Kasper Munch, Timothy D. O’Connor, Andrew D. Phillips, Javier Prado-Martinez, Anthony S. Rogers, Saba Sajjadian, Dominic Schmidt, Katy Shaw, Jared T. Simpson, Peter D. Stenson, Daniel J. Turner, Linda Vigilant, Albert J. Vilella, Weldon Whitener, Baoli Zhu, D.N. Cooper, Pieter de Jong, Emmanouil T. Dermitzakis, Evan E. Eichler, Paul Flicek, Nick Goldman, Nicholas I. Mundy, Zemin Ning, Duncan T. Odom, Chris P. Ponting, Michael A. Quail, Oliver A. Ryder, Stephen M. J. Searle, Wesley C. Warren, Richard K. Wilson, Mikkel Heide Schierup, Jane Rogers, Chris Tyler‐Smith, Richard Durbin - Nature 2012 cited by 814

  18. Efficient construction of an assembly string graph using the FM-index

    Authors: Jared T. Simpson, Richard Durbin - Bioinformatics, Bioinform. 2010 cited by 259

  19. Revealing nascent RNA processing dynamics with nano-COP

    Authors: Heather L. Drexler, Karine Choquet, Hope E. Merens, Paul S. Tang, Jared T. Simpson, L. Stirling Churchman - Nature Protocols 2021 cited by 49

  20. Trait Variation in Yeast Is Defined by Population History

    Authors: 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 - PLoS Genetics 2011 cited by 384

  21. Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

    Authors: Valérie Schneider, Tina Graves-Lindsay, Kerstin Howe, Nathan Bouk, Hsiu-Chuan Chen, Paul Kitts, Terence D. Murphy, Kim D. Pruitt, Françoise Thibaud‐Nissen, Derek Albracht, Robert S. Fulton, Milinn Kremitzki, Vincent Magrini, Chris Markovic, Sean McGrath, Karyn Meltz Steinberg, Kate Auger, William Chow, Joanna Collins, Glenn Harden, Tim Hubbard, Sarah Pelan, Jared T. Simpson, Glen Threadgold, James Torrance, Jonathan Wood, Laura Clarke, Sergey Koren, Matthew Boitano, Heng Li, Chen-Shan Chin, Adam M. Phillippy, Richard Durbin, Richard K. Wilson, Paul Flicek, Deanna M. Church - 2016 cited by 116

  22. Candidate Cancer Driver Mutations in Distal Regulatory Elements and Long-Range Chromatin Interaction Networks

    Authors: Helen Zhu, Liis Uusküla-Reimand, Keren Isaev, Lina Wadi, Azad Alizada, Shimin Shuai, Vincent Huang, Dike Aduluso-Nwaobasi, Marta Paczkowska, Diala Abd-Rabbo, Oliver Ocsenas, Minggao Liang, John Thompson, Yao Li, Luyao Ruan, Michał Krassowski, Irakli Dzneladze, Jared T. Simpson, Mathieu Lupien, Lincoln Stein, Paul C. Boutros, Michael D. Wilson, Jüri Reimand - Molecular Cell 2020 cited by 108

  23. A community effort to create standards for evaluating tumor subclonal reconstruction

    Authors: DREAM SMC-Het Participants, Adriana Salcedo, Maxime Tarabichi, Shadrielle M. G. Espiritu, Amit G. Deshwar, Matei David, Nathan M. Wilson, Stefan C. Dentro, Jeff Wintersinger, Lydia Liu, Minjeong Ko, Srinivasan Sivanandan, Hongjiu Zhang, Kaiyi Zhu, Tai-Hsien Ou Yang, John Chilton, Alex Buchanan, Christopher M. Lalansingh, Christine P’ng, Catalina Anghel, Imaad Umar, Bernard Lo, William Y. Zou, Jared T. Simpson, Joshua M. Stuart, Dimitris Anastassiou, Yuanfang Guan, Adam D. Ewing, Kyle Ellrott, David C. Wedge, Quaid Morris, Peter Van Loo, Paul C. Boutros - Nature Biotechnology 2020 cited by 99

  24. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

    Authors: Keith Bradnam, Joseph Fass, Anton Alexandrov, Paul Baranay, Michael Bechner, İnanç Birol, Sébastien Boisvert, Jarrod Chapman, Guillaume Chapuis, Rayan Chikhi, Hamidreza Chitsaz, Wen‐Chi Chou, Jacques Corbeil, Cristian Del Fabbro, Roderick Docking, Richard Durbin, Dent Earl, Scott Emrich, Pavel Fedotov, Nuno A. Fonseca, Ganeshkumar Ganapathy, Richard A. Gibbs, Sante Gnerre, Élénie Godzaridis, Steve Goldstein, Matthias Haimel, Giles Hall, David Haussler, Joseph Hiatt, Isaac Ho, Jason T. Howard, Martin Hunt, Shaun D. Jackman, David B. Jaffe, Erich D. Jarvis, Huaiyang Jiang, С. В. Казаков, Paul Kersey, Jacob O. Kitzman, James Knight, Sergey Koren, Tak‐Wah Lam, Dominique Lavenier, François Laviolette, Yingrui Li, Zhenyu Li, Binghang Liu, Yue Liu, Ruibang Luo, Iain MacCallum, Matthew D. MacManes, Nicolas Maillet, Sergey Melnikov, Delphine Naquin, Zemin Ning, Thomas D. Otto, Benedict Paten, Octávio S. Paulo, Adam M. Phillippy, Francisco Pina‐Martins, Michael Place, Dariusz Przybylski, Xiang Qin, Carson Qu, Filipe J. Ribeiro, Stephen Richards, Daniel S. Rokhsar, J. Graham Ruby, Simone Scalabrin, Michael C. Schatz, David C. Schwartz, Alexey Sergushichev, Ted Sharpe, Timothy I. Shaw, Jay Shendure, Yujian Shi, Jared T. Simpson, Henry Song, Fedor Tsarev, Francesco Vezzi, Riccardo Vicedomini, Bruno Vieira, Jun Wang, Kim C. Worley, Shuangye Yin, Siu Ming Yiu, Jianying Yuan, Guojie Zhang, Hao Zhang, Shiguo Zhou, Ian Korf - GigaScience 2013 cited by 735