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Simon R. Harris

Active 2005–2025

121
Papers
34,535
Citations
87
h-index
119
i10-index

Citations

Citations per year for Simon R. Harris1973: 1 citations1986: 1 citations1992: 2 citations1999: 1 citations2004: 3 citations2005: 1 citations2006: 4 citations2007: 4 citations2008: 8 citations2009: 25 citations2010: 46 citations2011: 72 citations2012: 201 citations2013: 347 citations2014: 586 citations2015: 573 citations2016: 537 citations2017: 498 citations2018: 492 citations2019: 1,455 citations2020: 1,541 citations2021: 1,369 citations2022: 985 citations2023: 661 citations2024: 1,180 citations2025: 490 citations2026: 15 citations1974–1985: no citations, so these years are not shown1987–1991: no citations, so these years are not shown1993–1998: no citations, so these years are not shown2000–2003: no citations, so these years are not shown

Citation sources

Countries

World map of the countries and regions citing this authorUnited States: 2,715 citing papers, 16.3% of this breakdownUnited Kingdom: 2,206 citing papers, 13.2% of this breakdownChina: 922 citing papers, 5.5% of this breakdownAustralia: 821 citing papers, 4.9% of this breakdownGermany: 752 citing papers, 4.5% of this breakdownFrance: 704 citing papers, 4.2% of this breakdownCanada: 489 citing papers, 2.9% of this breakdownSpain: 425 citing papers, 2.5% of this breakdownSwitzerland: 420 citing papers, 2.5% of this breakdownSweden: 384 citing papers, 2.3% of this breakdownNetherlands: 366 citing papers, 2.2% of this breakdownItaly: 347 citing papers, 2.1% of this breakdown
0%16.3%Other 36.9%

Institutions

Fields

  • Biochemistry, Genetics and Molecular Biology40.3%
  • Medicine33.1%
  • Agricultural and Biological Sciences10.2%
  • Immunology and Microbiology9.2%
  • Environmental Science4.5%
  • Computer Science0.5%
  • Other2.2%

Topics

  • Antibiotic Resistance in Bacteria6.8%
  • Genomics and Phylogenetic Studies6.2%
  • Mycobacterium research and diagnosis3.9%
  • Tuberculosis Research and Epidemiology3.5%
  • Salmonella and Campylobacter epidemiology3.3%
  • Antimicrobial Resistance in Staphylococcus3.2%
  • Other73.1%

Coauthors

All papers

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  1. Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

    Authors: Nicholas J. Croucher, Andrew J. Page, Thomas R. Connor, Aidan Delaney, Jacqueline A. Keane, Stephen D. Bentley, Julian Parkhill, Simon R. Harris - Nucleic Acids Research 2014 cited by 2,884

  2. Epidemic of carbapenem-resistant Klebsiella pneumoniae in Europe is driven by nosocomial spread

    Authors: Sophia David, Sandra Reuter, Simon R. Harris, Corinna Glasner, Theresa Feltwell, Silvia Argimón, Khalil Abudahab, Richard Goater, Tommaso Giani, Giulia Errico, Marianne Aspbury, Sara Sjunnebo, the EuSCAPE Working Group, Andi Koraqi, Denada Lacej, Petra Apfalter, Rainer Hartl, Y. Glupczynski, Te‐Din Huang, Tanya Strateva, Yuliya Marteva-Proevska, Arjana Tambić Andrašević, Iva Butić, Despo Pieridou-Bagatzouni, Panagiota Maikanti-Charalampous, Jaroslav Hrabák, Helena Žemličková, Anette M. Hammerum, Lotte Jakobsen, Marina Ivanova, Anastasia Pavelkovich, Jari Jalava, Monica Österblad, Laurent Dortet, Sophie Vaux, Martin Kaase, Sören Gatermann, Alkiviadis Vatopoulos, Kyriaki Tryfinopoulou, Ákos Tóth, Laura Jánvári, Teck Wee Boo, Elaine McGrath, Yehuda Carmeli, Amos Adler, Annalisa Pantosti, Monica Monaco, Lul Raka, Arsim Kurti, Arta Balode, Māra Saule, Jolanta Miciulevičienė, Aistė Mierauskaitė, Monique Perrin-Weniger, Paul Reichert, Nina Nestorova, Sonia Debattista, Gordana Mijović, Milena Lopičić, Ørjan Samuelsen, Bjørg Haldorsen, Dorota Żabicka, Elżbieta Literacka, Manuela Caniça, Vera Manageiro, Ana Kaftandzieva, Elena Trajkovska-Dokic, Maria Damian, Brânduşa Elena Lixandru, Zora Jelesić, Anika Trudić, M Nikś, Eva Schréterová, Mateja Pirš, Tjaša Cerar, Jesús Oteo, Belén Aracil, Christian G. Giske, Karin Sjöström, Deniz Gür, Aslı Çakar, Neil Woodford, Katie L. Hopkins, Camilla Wiuff, Derek Brown, the ESGEM Study Group, Edward J. Feil, Gian María Rossolini, David M. Aanensen, Hajo Grundmann - Nature Microbiology 2019 cited by 818

  3. Circlator: automated circularization of genome assemblies using long sequencing reads

    Authors: Martin Hunt, Nishadi De Silva, Thomas D. Otto, Julian Parkhill, Jacqueline A. Keane, Simon R. Harris - Genome biology 2015 cited by 1,237

  4. Fast and flexible bacterial genomic epidemiology with PopPUNK

    Authors: John A. Lees, Simon R. Harris, Gerry Tonkin‐Hill, Rebecca A. Gladstone, Stephanie W. Lo, Jeffrey N. Weiser, Jukka Corander, Stephen D. Bentley, Nicholas J. Croucher - Genome Research 2019 cited by 505

  5. Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data

    Authors: Tim Carver, Simon R. Harris, Matthew Berriman, Julian Parkhill, Jacqueline A. McQuillan - Bioinformatics, Bioinform. 2011 cited by 1,260

  6. SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments

    Authors: Andrew J. Page, Ben Taylor, Aidan Delaney, Jorge Soares, Torsten Seemann, Jacqueline A. Keane, Simon R. Harris - Microbial Genomics 2016 cited by 1,298

  7. A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers

    Authors: Michael A. Quail, Miriam Smith, Paul Coupland, Thomas D. Otto, Simon R. Harris, Thomas R. Connor, Anna Bertoni, Harold Swerdlow, Yong Gu - BMC Genomics 2012 cited by 2,052

  8. Bayesian inference of ancestral dates on bacterial phylogenetic trees

    Authors: Xavier Didelot, Nicholas J. Croucher, Stephen D. Bentley, Simon R. Harris, Daniel J. Wilson - Nucleic Acids Research 2018 cited by 342

  9. Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans

    Authors: Iñaki Comas, Mireia Coscollá, Tāo Luò, Sònia Borrell, Kathryn E. Holt, Midori Kato‐Maeda, Julian Parkhill, Bijaya Malla, Stefan Berg, Guy Thwaites, Dorothy Yeboah‐Manu, Graham Bothamley, Jian Mei, Lan‐Hai Wei, Stephen Bentley, Simon R. Harris, Stefan Niemann, Roland Diel, Abraham Aseffa, Qian Gao, Douglas B. Young, Sébastien Gagneux - Nature Genetics 2013 cited by 1,063

  10. Emergence and global spread of epidemic healthcare-associated Clostridium difficile

    Authors: Miao He, Fábio Miyajima, Paul Roberts, Louise Ellison, Derek Pickard, Melissa J. Martin, Thomas R. Connor, Simon R. Harris, Derek Fairley, Kathleen B. Bamford, Stephanie d’Arc, John Brazier, Derek Brown, John Coia, Gill Douce, Dale N. Gerding, Heejung Kim, Tse Hsien Koh, Haru Kato, Mitsutoshi Senoh, Tom Louie, Stephen Michell, Emma Butt, Sharon J. Peacock, Nick M Brown, Tom Riley, G. Songer, Mark H. Wilcox, Munir Pirmohamed, Ed J. Kuijper, Peter M. Hawkey, Brendan W. Wren, Gordon Dougan, Julian Parkhill, Trevor D. Lawley - Nature Genetics 2012 cited by 740

  11. Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events

    Authors: Vanessa Wong, Stephen Baker, Derek Pickard, Julian Parkhill, Andrew J. Page, Nicholas Feasey, Robert A. Kingsley, Nicholas R. Thomson, Jacqueline A. Keane, François‐Xavier Weill, David Edwards, Jane Hawkey, Simon R. Harris, Alison E. Mather, Amy K. Cain, James Hadfield, Peter Hart, Nga Tran Vu Thieu, Elizabeth J. Klemm, Dafni A. Glinos, Robert F. Breiman, Conall Watson, Samuel Kariuki, Melita A. Gordon, Robert S. Heyderman, Chinyere K. Okoro, Jan Jacobs, Octavie Lunguya, W. John Edmunds, Chisomo Msefula, José A. Chabalgoity, Mike Kama, Kylie Jenkins, Shanta Dutta, Florian Marks, Josefina Campos, Corinne N. Thompson, Stephen Obaro, Calman A. MacLennan, Christiane Dolecek, Karen H. Keddy, Anthony M. Smith, Christopher M. Parry, Abhilasha Karkey, Kim Mulholland, James Campbell, Sabina Dongol, Buddha Basnyat, Muriel Dufour, Don Bandaranayake, Take Naseri, Shalini Singh, Mochammad Hatta, Paul N. Newton, Robert Onsaŕe, Lupeoletalalei Isaia, David A. B. Dance, Viengmon Davong, Guy Thwaites, Lalith Wijedoru, John A. Crump, Elizabeth de Pinna, Satheesh Nair, Eric J. Nilles, Duy Pham Thanh, Paul Turner, Sona Soeng, Mary Valcanis, Joan Powling, Karolina Dimovski, Geoff Hogg, Jeremy Farrar, Kathryn E. Holt, Gordon Dougan - Nature Genetics 2015 cited by 489

  12. Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics

    Authors: Mark R. Davies, Liam McIntyre, Ankur Mutreja, Jake A. Lacey, John A. Lees, Rebecca J. Towers, Sebastián Duchêne, Pierre R. Smeesters, Hannah R. Frost, David J. Price, Matthew T. G. Holden, Sophia David, Philip M. Giffard, Kate A. Worthing, Anna C. Seale, James A. Berkley, Simon R. Harris, Tania Rivera-Hernández, Olga Berking, Amanda J. Cork, Rosângela S. L. A. Torres, Trevor Lithgow, Richard A. Strugnell, René Bergmann, Patric Nitsche-Schmitz, G. S. Chhatwal, Stephen D. Bentley, John D. Fraser, Nicole J. Moreland, Jonathan R. Carapetis, Andrew C. Steer, Julian Parkhill, Allan Saul, Deborah A. Williamson, Bart J. Currie, Steven Y. C. Tong, Gordon Dougan, Mark J. Walker - Nature Genetics 2019 cited by 211

  13. SKA: Split Kmer Analysis Toolkit for Bacterial Genomic Epidemiology

    Authors: Simon R. Harris - 2018 cited by 142

  14. ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads

    Authors: Martin Hunt, Alison E. Mather, Leonor Sánchez-Busó, Andrew J. Page, Julian Parkhill, Jacqueline A. Keane, Simon R. Harris - Microbial Genomics 2017 cited by 634

  15. Systematic longitudinal survey of invasive Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131

    Authors: Teemu Kallonen, Hayley J. Brodrick, Simon R. Harris, Jukka Corander, Nicholas M. Brown, Véronique Martin, Sharon J. Peacock, Julian Parkhill - Genome Research 2017 cited by 293

  16. Evidence for several waves of global transmission in the seventh cholera pandemic

    Authors: Ankur Mutreja, Dong Wook Kim, Nicholas R. Thomson, Thomas R. Connor, Jehee Lee, Samuel Kariuki, Nicholas J. Croucher, Seon Young Choi, Simon R. Harris, Michael Lebens, Swapan Kumar Niyogi, Eun Jin Kim, Thandavarayan Ramamurthy, Jongsik Chun, James L. N. Wood, John D. Clemens, Cécil Czerkinsky, G. Balakrish Nair, Jan Holmgren, Julian Parkhill, Gordon Dougan - Nature 2011 cited by 799

  17. Emergence and spread of a human-transmissible multidrug-resistant nontuberculous mycobacterium

    Authors: Josephine M. Bryant, Dorothy Grogono, Daniela Rodriguez-Rincon, Isobel Everall, Karen Brown, Pablo Moreno, Deepshikha Verma, Emily Hill, Judith Drijkoningen, Peter H. Gilligan, Charles R. Esther, Peadar G. Noone, Olivia Giddings, Scott C. Bell, Rachel Thomson, Claire Wainwright, Chris Coulter, Sushil Pandey, Michelle Wood, Rebecca E. Stockwell, Kay A. Ramsay, Laura J. Sherrard, Timothy J. Kidd, Nassib Jabbour, Graham Johnson, Luke D. Knibbs, Lídia Morawska, Peter D. Sly, Andrew Jones, Diana Bilton, Ian F. Laurenson, Michael Ruddy, Stephen Bourke, I.C.J.W. Bowler, S. Jonathan Chapman, Andrew Clayton, M. Cullen, Owen Dempsey, Miles Denton, Maya Desai, Richard J. Drew, F. Edenborough, J. C. Evans, Jonathan Folb, T. Daniels, Helen Humphrey, B. Isalska, Søren Jensen‐Fangel, Bodil Jönsson, Andrew Jones, Terese L. Katzenstein, Troels Lillebæk, Gordon MacGregor, Sarah Mayell, Michael Millar, Deborah Modha, E.F. Nash, Christopher J. O’Brien, Deirdre O’Brien, Chandra Ohri, C. Pao, D. Peckham, Felicity Perrin, Audrey Perry, T. Pressler, Laura Prtak, Tavs Qvist, A. Robb, Helen Rodgers, Kirsten Schaffer, Nadia Shafi, Jakko van Ingen, Martin Walshaw, Danie Watson, N. West, J.L. Whitehouse, Charles Haworth, Simon R. Harris, Diane Ordway, Julian Parkhill, R. Andrés Floto - Science 2016 cited by 596

  18. Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis

    Authors: Kirsten I. Bos, Kelly M. Harkins, Alexander Herbig, Mireia Coscollá, Nico Weber, Iñaki Comas, Stephen A Forrest, Josephine M. Bryant, Simon R. Harris, Verena J. Schuenemann, Tessa J. Campbell, Kerttu Majander, Alicia K. Wilbur, Ricardo Aníbal Guichón, Dawnie Wolfe Steadman, Della Collins Cook, Stefan Niemann, Marcel A. Behr, Martín José Zumárraga, Ricardo Bastida, Daniel H. Huson, Kay Nieselt, Douglas B. Young, Julian Parkhill, Jane E. Buikstra, Sébastien Gagneux, Anne C. Stone, Johannes Krause - Nature 2014 cited by 630

  19. Phylogenomics of Mycobacterium africanum reveals a new lineage and a complex evolutionary history

    Authors: Mireia Coscollá, Sébastien Gagneux, Fabrizio Menardo, Chloé Loiseau, Paula Ruiz-Rodríguez, Sònia Borrell, Isaac Darko Otchere, Adwoa Asante-Poku, Prince Asare, Leonor Sánchez-Busó, Florian Gehre, C. N’Dira Sanoussi, Martín Antonio, Dissou Affolabi, Janet Fyfe, Patrick Beckert, Stefan Niemann, Abraham Alabi, Martin P. Grobusch, Robin Kobbe, Julian Parkhill, Christian Beisel, Lukas Fenner, Erik C. Böttger, Conor J. Meehan, Simon R. Harris, Bouke C. de Jong, Dorothy Yeboah‐Manu, Daniela Brites - Microbial Genomics 2021 cited by 205

  20. A community-driven resource for genomic epidemiology and antimicrobial resistance prediction of Neisseria gonorrhoeae at Pathogenwatch

    Authors: Leonor Sánchez-Busó, Corin Yeats, Benjamin Taylor, Richard Goater, Anthony Underwood, Khalil Abudahab, Silvia Argimón, C. Kevin, Tatum D. Mortimer, Daniel Golparian, Michelle Cole, Yonatan H. Grad, Irene Martín, Brian H. Raphael, William M. Shafer, Katy Town, Teodora Wi, Simon R. Harris, Magnus Unemo, David M. Aanensen - Genome Medicine 2021 cited by 125

  21. Evolution of MRSA During Hospital Transmission and Intercontinental Spread

    Authors: Simon R. Harris, Edward J. Feil, Matthew T. G. Holden, Michael A. Quail, Emma K. Nickerson, Narisara Chantratita, Susana Gardete, Ana Tavares, Nick Day, Jodi A. Lindsay, Jonathan D. Edgeworth, Hermı́nia de Lencastre, Julian Parkhill, Sharon J. Peacock, Stephen D. Bentley - Science 2010 cited by 1,123

  22. Rapid Pneumococcal Evolution in Response to Clinical Interventions

    Authors: Nicholas J. Croucher, Simon R. Harris, Christophe Fraser, Michael A. Quail, John H. Burton, Mark van der Linden, Lesley McGee, Anne von Gottberg, Jae Hoon Song, Kwan Soo Ko, Bruno Pichon, Stephen Baker, Christopher M. Parry, Lotte Lambertsen, Dea Shahinas, Dylan R. Pillai, Timothy J. Mitchell, Gordon Dougan, Alexander Tomasz, Keith P. Klugman, Julian Parkhill, William P. Hanage, Stephen D. Bentley - Science 2011 cited by 921

  23. Evolution and transmission of drug-resistant tuberculosis in a Russian population

    Authors: Nicola Casali, Vladyslav Nikolayevskyy, Yanina Balabanova, Simon R. Harris, Olga Ignatyeva, Irina Kontsevaya, Jukka Corander, Josephine M. Bryant, Julian Parkhill, Sergey Nejentsev, Rolf D. Horstmann, Timothy J. Brown, Francis Drobniewski - Nature Genetics 2014 cited by 498

  24. Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa

    Authors: Chinyere K. Okoro, Robert A. Kingsley, Thomas R. Connor, Simon R. Harris, Christopher M. Parry, Manar Najim Al‐Mashhadani, Samuel Kariuki, Chisomo Msefula, Melita A. Gordon, Elizabeth de Pinna, John Wain, Robert S. Heyderman, Stephen Obaro, Pedro L. Alonso, Inácio Mandomando, Calman A. MacLennan, Milagritos D. Tapia, Myron M. Levine, Sharon M. Tennant, Julian Parkhill, Gordon Dougan - Nature Genetics 2012 cited by 413