A citation-based method for searching scientific literature

Peter R Wilker, Jorge M Dinis, Gabriel Starrett, Masaki Imai, Masato Hatta, Chase W Nelson, David H O'Connor, Austin L Hughes, Gabriele Neumann, Yoshihiro Kawaoka, Thomas C Friedrich. Nat Commun 2013
Times Cited: 55







List of co-cited articles
500 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


Experimental adaptation of an influenza H5 HA confers respiratory droplet transmission to a reassortant H5 HA/H1N1 virus in ferrets.
Masaki Imai, Tokiko Watanabe, Masato Hatta, Subash C Das, Makoto Ozawa, Kyoko Shinya, Gongxun Zhong, Anthony Hanson, Hiroaki Katsura, Shinji Watanabe,[...]. Nature 2012
946
36

Influenza A virus transmission bottlenecks are defined by infection route and recipient host.
Andrew Varble, Randy A Albrecht, Simone Backes, Marshall Crumiller, Nicole M Bouvier, David Sachs, Adolfo García-Sastre, Benjamin R tenOever. Cell Host Microbe 2014
121
36

Airborne transmission of influenza A/H5N1 virus between ferrets.
Sander Herfst, Eefje J A Schrauwen, Martin Linster, Salin Chutinimitkul, Emmie de Wit, Vincent J Munster, Erin M Sorrell, Theo M Bestebroer, David F Burke, Derek J Smith,[...]. Science 2012
32

Quantifying influenza virus diversity and transmission in humans.
Leo L M Poon, Timothy Song, Roni Rosenfeld, Xudong Lin, Matthew B Rogers, Bin Zhou, Robert Sebra, Rebecca A Halpin, Yi Guan, Alan Twaddle,[...]. Nat Genet 2016
103
29

Selective Bottlenecks Shape Evolutionary Pathways Taken during Mammalian Adaptation of a 1918-like Avian Influenza Virus.
Louise H Moncla, Gongxun Zhong, Chase W Nelson, Jorge M Dinis, James Mutschler, Austin L Hughes, Tokiko Watanabe, Yoshihiro Kawaoka, Thomas C Friedrich. Cell Host Microbe 2016
38
36

Identification, characterization, and natural selection of mutations driving airborne transmission of A/H5N1 virus.
Martin Linster, Sander van Boheemen, Miranda de Graaf, Eefje J A Schrauwen, Pascal Lexmond, Benjamin Mänz, Theo M Bestebroer, Jan Baumann, Debby van Riel, Guus F Rimmelzwaan,[...]. Cell 2014
166
23

Mammalian adaptation of influenza A(H7N9) virus is limited by a narrow genetic bottleneck.
Hassan Zaraket, Tatiana Baranovich, Bryan S Kaplan, Robert Carter, Min-Suk Song, James C Paulson, Jerold E Rehg, Justin Bahl, Jeri C Crumpton, Jon Seiler,[...]. Nat Commun 2015
61
23

The potential for respiratory droplet-transmissible A/H5N1 influenza virus to evolve in a mammalian host.
Colin A Russell, Judith M Fonville, André E X Brown, David F Burke, David L Smith, Sarah L James, Sander Herfst, Sander van Boheemen, Martin Linster, Eefje J Schrauwen,[...]. Science 2012
212
21

Single-reaction genomic amplification accelerates sequencing and vaccine production for classical and Swine origin human influenza a viruses.
Bin Zhou, Matthew E Donnelly, Derek T Scholes, Kirsten St George, Masato Hatta, Yoshihiro Kawaoka, David E Wentworth. J Virol 2009
324
18

Quasispecies diversity determines pathogenesis through cooperative interactions in a viral population.
Marco Vignuzzi, Jeffrey K Stone, Jamie J Arnold, Craig E Cameron, Raul Andino. Nature 2006
690
16


Deep Sequencing Reveals Potential Antigenic Variants at Low Frequencies in Influenza A Virus-Infected Humans.
Jorge M Dinis, Nicholas W Florek, Omolayo O Fatola, Louise H Moncla, James P Mutschler, Olivia K Charlier, Jennifer K Meece, Edward A Belongia, Thomas C Friedrich. J Virol 2016
59
16

Deep Sequencing of Influenza A Virus from a Human Challenge Study Reveals a Selective Bottleneck and Only Limited Intrahost Genetic Diversification.
Ashley Sobel Leonard, Micah T McClain, Gavin J D Smith, David E Wentworth, Rebecca A Halpin, Xudong Lin, Amy Ransier, Timothy B Stockwell, Suman R Das, Anthony S Gilbert,[...]. J Virol 2016
59
16

Identifying selection in the within-host evolution of influenza using viral sequence data.
Christopher J R Illingworth, Andrej Fischer, Ville Mustonen. PLoS Comput Biol 2014
23
34

Haemagglutinin mutations responsible for the binding of H5N1 influenza A viruses to human-type receptors.
Shinya Yamada, Yasuo Suzuki, Takashi Suzuki, Mai Q Le, Chairul A Nidom, Yuko Sakai-Tagawa, Yukiko Muramoto, Mutsumi Ito, Maki Kiso, Taisuke Horimoto,[...]. Nature 2006
444
14

Inferring the inter-host transmission of influenza A virus using patterns of intra-host genetic variation.
J Conrad Stack, Pablo R Murcia, Bryan T Grenfell, James L N Wood, Edward C Holmes. Proc Biol Sci 2013
31
25

Viral mutation rates.
Rafael Sanjuán, Miguel R Nebot, Nicola Chirico, Louis M Mansky, Robert Belshaw. J Virol 2010
620
14

Intra- and interhost evolutionary dynamics of equine influenza virus.
Pablo R Murcia, Gregory J Baillie, Janet Daly, Debra Elton, Carley Jervis, Jennifer A Mumford, Richard Newton, Colin R Parrish, Karin Hoelzer, Gordon Dougan,[...]. J Virol 2010
74
14

Stochastic processes constrain the within and between host evolution of influenza virus.
John T McCrone, Robert J Woods, Emily T Martin, Ryan E Malosh, Arnold S Monto, Adam S Lauring. Elife 2018
77
14

Viral population analysis and minority-variant detection using short read next-generation sequencing.
Simon J Watson, Matthijs R A Welkers, Daniel P Depledge, Eve Coulter, Judith M Breuer, Menno D de Jong, Paul Kellam. Philos Trans R Soc Lond B Biol Sci 2013
125
12

H5N1 Virus Attachment to Lower Respiratory Tract.
Debby van Riel, Vincent J Munster, Emmie de Wit, Guus F Rimmelzwaan, Ron A M Fouchier, Ab D M E Osterhaus, Thijs Kuiken. Science 2006
467
12

Influenza virus drug resistance: a time-sampled population genetics perspective.
Matthieu Foll, Yu-Ping Poh, Nicholas Renzette, Anna Ferrer-Admetlla, Claudia Bank, Hyunjin Shim, Anna-Sapfo Malaspinas, Gregory Ewing, Ping Liu, Daniel Wegmann,[...]. PLoS Genet 2014
79
12

Kinetics of influenza A virus infection in humans.
Prasith Baccam, Catherine Beauchemin, Catherine A Macken, Frederick G Hayden, Alan S Perelson. J Virol 2006
382
12


Evolution of an Eurasian avian-like influenza virus in naïve and vaccinated pigs.
Pablo R Murcia, Joseph Hughes, Patrizia Battista, Lucy Lloyd, Gregory J Baillie, Ricardo H Ramirez-Gonzalez, Doug Ormond, Karen Oliver, Debra Elton, Jennifer A Mumford,[...]. PLoS Pathog 2012
60
12

Measurement of the mutation rates of animal viruses: influenza A virus and poliovirus type 1.
J D Parvin, A Moscona, W T Pan, J M Leider, P Palese. J Virol 1986
208
10


In vitro evolution of H5N1 avian influenza virus toward human-type receptor specificity.
Li-Mei Chen, Ola Blixt, James Stevens, Aleksandr S Lipatov, Charles T Davis, Brian E Collins, Nancy J Cox, James C Paulson, Ruben O Donis. Virology 2012
146
10

Evolution and ecology of influenza A viruses.
R G Webster, W J Bean, O T Gorman, T M Chambers, Y Kawaoka. Microbiol Rev 1992
10


Molecular basis for high virulence of Hong Kong H5N1 influenza A viruses.
M Hatta, P Gao, P Halfmann, Y Kawaoka. Science 2001
10

Quasispecies theory and the behavior of RNA viruses.
Adam S Lauring, Raul Andino. PLoS Pathog 2010
461
10

Avian flu: influenza virus receptors in the human airway.
Kyoko Shinya, Masahito Ebina, Shinya Yamada, Masao Ono, Noriyuki Kasai, Yoshihiro Kawaoka. Nature 2006
900
10

Hemagglutinin receptor binding avidity drives influenza A virus antigenic drift.
Scott E Hensley, Suman R Das, Adam L Bailey, Loren M Schmidt, Heather D Hickman, Akila Jayaraman, Karthik Viswanathan, Rahul Raman, Ram Sasisekharan, Jack R Bennink,[...]. Science 2009
321
10

Early alterations of the receptor-binding properties of H1, H2, and H3 avian influenza virus hemagglutinins after their introduction into mammals.
M Matrosovich, A Tuzikov, N Bovin, A Gambaryan, A Klimov, M R Castrucci, I Donatelli, Y Kawaoka. J Virol 2000
602
10

Mapping influenza transmission in the ferret model to transmission in humans.
Michael G Buhnerkempe, Katelyn Gostic, Miran Park, Prianna Ahsan, Jessica A Belser, James O Lloyd-Smith. Elife 2015
23
26

The Sequence Alignment/Map format and SAMtools.
Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin. Bioinformatics 2009
10

Transmission of equine influenza virus during an outbreak is characterized by frequent mixed infections and loose transmission bottlenecks.
Joseph Hughes, Richard C Allen, Marc Baguelin, Katie Hampson, Gregory J Baillie, Debra Elton, J Richard Newton, Paul Kellam, James L N Wood, Edward C Holmes,[...]. PLoS Pathog 2012
37
16



Contact transmission of influenza virus between ferrets imposes a looser bottleneck than respiratory droplet transmission allowing propagation of antiviral resistance.
Rebecca Frise, Konrad Bradley, Neeltje van Doremalen, Monica Galiano, Ruth A Elderfield, Peter Stilwell, Jonathan W Ashcroft, Mirian Fernandez-Alonso, Shahjahan Miah, Angie Lackenby,[...]. Sci Rep 2016
27
22


Transmission Bottleneck Size Estimation from Pathogen Deep-Sequencing Data, with an Application to Human Influenza A Virus.
Ashley Sobel Leonard, Daniel B Weissman, Benjamin Greenbaum, Elodie Ghedin, Katia Koelle. J Virol 2017
55
10

Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance.
Chunlin Wang, Yumi Mitsuya, Baback Gharizadeh, Mostafa Ronaghi, Robert W Shafer. Genome Res 2007
307
9

Sequential bottlenecks drive viral evolution in early acute hepatitis C virus infection.
Rowena A Bull, Fabio Luciani, Kerensa McElroy, Silvana Gaudieri, Son T Pham, Abha Chopra, Barbara Cameron, Lisa Maher, Gregory J Dore, Peter A White,[...]. PLoS Pathog 2011
171
9

Field monitoring of avian influenza viruses: whole-genome sequencing and tracking of neuraminidase evolution using 454 pyrosequencing.
Guillaume Croville, Sébastien Mathieu Soubies, Johanna Barbieri, Christophe Klopp, Jérôme Mariette, Olivier Bouchez, Christelle Camus-Bouclainville, Jean-Luc Guérin. J Clin Microbiol 2012
18
27

A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers.
Michael A Quail, Miriam Smith, Paul Coupland, Thomas D Otto, Simon R Harris, Thomas R Connor, Anna Bertoni, Harold P Swerdlow, Yong Gu. BMC Genomics 2012
9

Presence of oseltamivir-resistant pandemic A/H1N1 minor variants before drug therapy with subsequent selection and transmission.
Elodie Ghedin, Edward C Holmes, Jay V DePasse, Lady Tatiana Pinilla, Adam Fitch, Marie-Eve Hamelin, Jesse Papenburg, Guy Boivin. J Infect Dis 2012
49
10

Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic.
Gavin J D Smith, Dhanasekaran Vijaykrishna, Justin Bahl, Samantha J Lycett, Michael Worobey, Oliver G Pybus, Siu Kit Ma, Chung Lam Cheung, Jayna Raghwani, Samir Bhatt,[...]. Nature 2009
9

Hemagglutinin-neuraminidase balance confers respiratory-droplet transmissibility of the pandemic H1N1 influenza virus in ferrets.
Hui-Ling Yen, Chi-Hui Liang, Chung-Yi Wu, Heather L Forrest, Angela Ferguson, Ka-Tim Choy, Jeremy Jones, Diana Dik-Yan Wong, Peter Pak-Hang Cheung, Che-Hsiung Hsu,[...]. Proc Natl Acad Sci U S A 2011
151
9


Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.