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Items where contributor is "Neher, Richard A"

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2018

Sagulenko, Pavel and Puller, Vadim and Neher, Richard A.. (2018) TreeTime: Maximum-likelihood phylodynamic analysis. Virus Evolution, 4 (1, vex042). pp. 1-9.

Jackson, Laurelle and Hunter, Jessica and Cele, Sandile and Ferreira, Isabella Markham and Young, Andrew C. and Karim, Farina and Madansein, Rajhmun and Dullabh, Kaylesh J. and Chen, Chih-Yuan and Buckels, Noel J. and Ganga, Yashica and Khan, Khadija and Boulle, Mikael and Lustig, Gila and Neher, Richard A. and Sigal, Alex. (2018) Incomplete inhibition of HIV infection results in more HIV infected lymph node cells by reducing cell death. eLife, 7 (e30134). pp. 1-24.

Hadfield, James and Megill, Colin and Bell, Sidney M. and Huddleston, John and Potter, Barney and Callender, Charlton and Sagulenko, Pavel and Bedford, Trevor and Neher, Richard A.. (2018) Nextstrain: real-time tracking of pathogen evolution. Bioinformatics, 34 (23). pp. 4121-4123.

Karasov, Talia L. and Almario, Juliana and Friedemann, Claudia and Ding, Wei and Giolai, Michael and Heavens, Darren and Kersten, Sonja and Lundberg, Derek S. and Neumann, Manuela and Regalado, Julian and Neher, Richard A. and Kemen, Eric and Weigel, Detlef. (2018) Arabidopsis thaliana and Pseudomonas Pathogens Exhibit Stable Associations over Evolutionary Timescales. Cell Host & Microbe, 24 (1). 168-179.e4.

Neher, Richard A. and Bedford, Trevor. (2018) Real-time analysis and visualization of pathogen sequence data. Journal of clinical microbiology, 56 (11, e00480-18). pp. 1-9.

Javed, Mumina and Ueltzhoeffer, Viola and Heinrich, Maximilian and Siegrist, Hans Justus and Wildermuth, Ronja and Lorenz, Freia-Raphaella and Neher, Richard A. and Willmann, Matthias. (2018) Colistin susceptibility test evaluation of multiple-resistance-level Pseudomonas aeruginosa isolates generated in a morbidostat device. The journal of antimicrobial chemotherapy, 73 (12). pp. 3368-3374.

2017

Zanini, Fabio and Puller, Vadim and Brodin, Johanna and Albert, Jan and Neher, Richard A.. (2017) In vivo mutation rates and the landscape of fitness costs of HIV-1. Virus Evolution, 3 (1). vex003.

You, Yuan and Sawikowska, Aneta and Neumann, Manuela and Posé, David and Capovilla, Giovanna and Langenecker, Tobias and Neher, Richard A. and Krajewski, Pawel and Schmid, Markus. (2017) Temporal dynamics of gene expression and histone marks at the Arabidopsis shoot meristem during flowering. Nature Communications, 8. p. 15120.

Regenbogen, Bianca and Willmann, Matthias and Steglich, Matthias and Bunk, Boyke and Nübel, Ulrich and Peter, Silke and Neher, Richard A.. (2017) Rapid and consistent evolution of colistin resistance in XDR Pseudomonas aeruginosa during morbidostat culture. Antimicrobial agents and chemotherapy, 61 (9). e00043-17.

Puller, Vadim and Neher, Richard and Albert, Jan. (2017) Estimating time of HIV-1 infection from next-generation sequence diversity. PLoS Computational Biology, 13 (10). e1005775.

Ding, Wei and Baumdicker, Franz and Neher, Richard A.. (2017) panX: pan-genome analysis and exploration. Nucleic acids research. p. 12.

Morris, Dylan H. and Gostic, Katelyn M. and Pompei, Simone and Bedford, Trevor and Łuksza, Marta and Neher, Richard A. and Grenfell, Bryan T. and Lässig, Michael and McCauley, John W.. (2017) Predictive Modeling of Influenza Shows the Promise of Applied Evolutionary Biology. Trends in Microbiology, 26 (2). p. 17.