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Phylogeography of Influenza A(H3N2) Virus in Peru, 2010-2012.
Published in:
2015
By:
- Pollett, Simon;
- Nelson, Martha I;
- Kasper, Matthew;
- Tinoco, Yeny;
- Simons, Mark;
- Romero, Candice;
- Silva, Marita;
- Lin, Xudong;
- Halpin, Rebecca A;
- Fedorova, Nadia;
- Stockwell, Timothy B;
- Wentworth, David;
- Holmes, Edward C;
- Bausch, Daniel G
Publication type:
journal article
Phylogeography of Influenza A(H3N2) Virus in Peru, 2010-2012.
Published in:
Emerging Infectious Diseases, 2015, v. 21, n. 8, p. 1330, doi. 10.3201/eid2108.150084
By:
- Pollett, Simon;
- Nelson, Martha I.;
- Kasper, Matthew;
- Tinoco, Yeny;
- Simons, Mark;
- Romero, Candice;
- Silva, Marita;
- Lin, Xudong;
- Halpin, Rebecca A.;
- Fedorova, Nadia;
- Stockwell, Timothy B.;
- Wentworth, David;
- Holmes, Edward C.;
- Bausch, Daniel G.
Publication type:
Article
Whole genome analyses of G1P[8] rotavirus strains from vaccinated and non-vaccinated South African children presenting with diarrhea.
Published in:
Journal of Medical Virology, 2015, v. 87, n. 1, p. 79, doi. 10.1002/jmv.23971
By:
- Magagula, Nonkululeko B.;
- Esona, Mathew D.;
- Nyaga, Martin M.;
- Stucker, Karla M.;
- Halpin, Rebecca A.;
- Stockwell, Timothy B.;
- Seheri, Mapaseka L.;
- Steele, A. Duncan;
- Wentworth, David E.;
- Mphahlele, M. Jeffrey
Publication type:
Article
The contrasting phylodynamics of human influenza B viruses.
Published in:
eLife, 2015, p. 1, doi. 10.7554/eLife.05055.001
By:
- Vijaykrishna, Dhanasekaran;
- Holmes, Edward C.;
- Joseph, Udayan;
- Fourment, Mathieu;
- Su, Yvonne CF;
- Halpin, Rebecca;
- Lee, Raphael TC;
- Yi-Mo Deng;
- Gunalan, Vithiagaran;
- Xudong Lin;
- Stockwell, Timothy B.;
- Fedorova, Nadia B.;
- Bin Zhou;
- Spirason, Natalie;
- Kühnert, Denise;
- Bošková, Veronika;
- Stadler, Tanja;
- Costa, Anna-Maria;
- Dwyer, Dominic E.;
- Q. Sue Huang
Publication type:
Article
VIGOR extended to annotate genomes for additional 12 different viruses.
Published in:
Nucleic Acids Research, 2012, v. 40, p. W186, doi. 10.1093/nar/gks528
By:
- Shiliang Wang;
- Sundaram, Jaideep P.;
- Stockwell, Timothy B.
Publication type:
Article
The HuRef Browser: a web resource for individual human genomics.
Published in:
Nucleic Acids Research, 2009, v. 37, n. suppl_1, p. D1018, doi. 10.1093/nar/gkn939
By:
- Axelrod, Nelson;
- Lin, Yuan;
- Ng, Pauline C.;
- Stockwell, Timothy B.;
- Crabtree, Jonathan;
- Huang, Jiaqi;
- Kirkness, Ewen;
- Strausberg, Robert L.;
- Frazier, Marvin E.;
- Venter, J. Craig;
- Kravitz, Saul;
- Levy, Samuel
Publication type:
Article
Respiratory Syncytial Virus whole-genome sequencing identifies convergent evolution of sequence duplication in the C-terminus of the G gene.
Published in:
Scientific Reports, 2016, p. 26311, doi. 10.1038/srep26311
By:
- Schobel, Seth A.;
- Stucker, Karla M.;
- Moore, Martin L.;
- Anderson, Larry J.;
- Larkin, Emma K.;
- Shankar, Jyoti;
- Bera, Jayati;
- Puri, Vinita;
- Shilts, Meghan H.;
- Rosas-Salazar, Christian;
- Halpin, Rebecca A.;
- Fedorova, Nadia;
- Shrivastava, Susmita;
- Stockwell, Timothy B.;
- Peebles, R. Stokes;
- Hartert, Tina V.;
- Das, Suman R.
Publication type:
Article
Evolution and spread of Venezuelan equine encephalitis complex alphavirus in the Americas.
Published in:
PLoS Neglected Tropical Diseases, 2017, v. 11, n. 8, p. 1, doi. 10.1371/journal.pntd.0005693
By:
- Forrester, Naomi L.;
- Wertheim, Joel O.;
- Dugan, Vivian G.;
- Auguste, Albert J.;
- Lin, David;
- Adams, A. Paige;
- Chen, Rubing;
- Gorchakov, Rodion;
- Leal, Grace;
- Estrada-Franco, Jose G.;
- Pandya, Jyotsna;
- Halpin, Rebecca A.;
- Hari, Kumar;
- Jain, Ravi;
- Stockwell, Timothy B.;
- Das, Suman R.;
- Wentworth, David E.;
- Smith, Martin D.;
- Kosakovsky Pond, Sergei L.;
- Weaver, Scott C.
Publication type:
Article
Standardized Metadata for Human Pathogen/Vector Genomic Sequences.
Published in:
PLoS ONE, 2014, v. 9, n. 6, p. 1, doi. 10.1371/journal.pone.0099979
By:
- Dugan, Vivien G.;
- Emrich, Scott J.;
- Giraldo-Calderón, Gloria I.;
- Harb, Omar S.;
- Newman, Ruchi M.;
- Pickett, Brett E.;
- Schriml, Lynn M.;
- Stockwell, Timothy B.;
- Stoeckert Jr, Christian J.;
- Sullivan, Dan E.;
- Singh, Indresh;
- Ward, Doyle V.;
- Yao, Alison;
- Zheng, Jie;
- Barrett, Tanya;
- Birren, Bruce;
- Brinkac, Lauren;
- Bruno, Vincent M.;
- Caler, Elizabet;
- Chapman, Sinéad
Publication type:
Article
North Atlantic Migratory Bird Flyways Provide Routes for Intercontinental Movement of Avian Influenza Viruses.
Published in:
PLoS ONE, 2014, v. 9, n. 3, p. 1, doi. 10.1371/journal.pone.0092075
By:
- Dusek, Robert J.;
- Hallgrimsson, Gunnar T.;
- Ip, Hon S.;
- Jónsson, Jón E.;
- Sreevatsan, Srinand;
- Nashold, Sean W.;
- TeSlaa, Joshua L.;
- Enomoto, Shinichiro;
- Halpin, Rebecca A.;
- Lin, Xudong;
- Fedorova, Nadia;
- Stockwell, Timothy B.;
- Dugan, Vivien G.;
- Wentworth, David E.;
- Hall, Jeffrey S.
Publication type:
Article
Deep Sequencing Reveals Mixed Infection with 2009 Pandemic Influenza A (H1N1) Virus Strains and the Emergence of Oseltamivir Resistance.
Published in:
Journal of Infectious Diseases, 2011, v. 203, n. 2, p. 168, doi. 10.1093/infdis/jiq040
By:
- Ghedin, Elodie;
- Laplante3, Jennifer;
- DePasse, Jay;
- Wentworth, David E.;
- Santos, Roberto P.;
- Lepow, Martha L.;
- Porter, Joanne;
- Stellrecht, Kathleen;
- Xudong Lin;
- Operario, Darwin;
- Griesemer, Sara;
- Fitch, Adam;
- Halpin, Rebecca A.;
- Stockwell, Timothy B.;
- Spiro, David J.;
- Holmes, Edward C.;
- George, Kirsten St.
Publication type:
Article
Response to Constant and Interval Exercise Protocols in the Elderly.
Published in:
Journal of Exercise Physiology Online, 2012, v. 15, n. 2, p. 30
By:
- Stockwell, Timothy B.;
- McKean, Mark R.;
- Burkett, Brendan J.
Publication type:
Article
Novel computational methods for increasing PCR primer design effectiveness in directed sequencing.
Published in:
BMC Bioinformatics, 2008, v. 9, p. 1, doi. 10.1186/1471-2105-9-191
By:
- Li, Kelvin;
- Brownley, Anushka;
- Stockwell, Timothy B.;
- Beeson, Karen;
- McIntosh, Tina C.;
- Busam, Dana;
- Ferriera, Steve;
- Murphy, Sean;
- Levy, Samuel
Publication type:
Article
Migratory flyway and geographical distance are barriers to the gene flow of influenza virus among North American birds.
Published in:
Ecology Letters, 2012, v. 15, n. 1, p. 24, doi. 10.1111/j.1461-0248.2011.01703.x
By:
- Lam, Tommy Tsan-Yuk;
- Ip, Hon S.;
- Ghedin, Elodie;
- Wentworth, David E.;
- Halpin, Rebecca A.;
- Stockwell, Timothy B.;
- Spiro, David J.;
- Dusek, Robert J.;
- Bortner, James B.;
- Hoskins, Jenny;
- Bales, Bradley D.;
- Yparraguirre, Dan R.;
- Holmes, Edward C.
Publication type:
Article
ANDES: Statistical tools for the ANalyses of DEep Sequencing.
Published in:
BMC Research Notes, 2010, v. 3, p. 199, doi. 10.1186/1756-0500-3-199
By:
- Li, Kelvin;
- Venter, Eli;
- Yooseph, Shibu;
- Stockwell, Timothy B.;
- Eckerle, Lance D.;
- Denison, Mark R.;
- Spiro, David J.;
- Methé, Barbara A.
Publication type:
Article
VariantClassifier: A hierarchical variant classifier forannotated genomes.
Published in:
BMC Research Notes, 2010, v. 3, p. 191, doi. 10.1186/1756-0500-3-191
By:
- Li, Kelvin;
- Stockwell, Timothy B.
Publication type:
Article
Poor Immunogenicity, Not Vaccine Strain Egg Adaptation, May Explain the Low H3N2 Influenza Vaccine Effectiveness in 2012–2013.
Published in:
Clinical Infectious Diseases, 2018, v. 67, n. 3, p. 327, doi. 10.1093/cid/ciy097
By:
- Cobey, Sarah;
- Gouma, Sigrid;
- Parkhouse, Kaela;
- Chambers, Benjamin S;
- Ertl, Hildegund C;
- Schmader, Kenneth E;
- Halpin, Rebecca A;
- Lin, Xudong;
- Stockwell, Timothy B;
- Das, Suman R
Publication type:
Article
Ecosystem Interactions Underlie the Spread of Avian Influenza A Viruses with Pandemic Potential.
Published in:
PLoS Pathogens, 2016, v. 12, n. 5, p. 1, doi. 10.1371/journal.ppat.1005620
By:
- Bahl, Justin;
- Pham, Truc T.;
- Hill, Nichola J.;
- Hussein, Islam T. M.;
- Ma, Eric J.;
- Easterday, Bernard C.;
- Halpin, Rebecca A.;
- Stockwell, Timothy B.;
- Wentworth, David E.;
- Kayali, Ghazi;
- Krauss, Scott;
- Schultz-Cherry, Stacey;
- Webster, Robert G.;
- Webby, Richard J.;
- Swartz, Michael D.;
- Smith, Gavin J. D.;
- Runstadler, Jonathan A.
Publication type:
Article
Characterization of Uncultivable Bat Influenza Virus Using a Replicative Synthetic Virus.
Published in:
PLoS Pathogens, 2014, v. 10, n. 10, p. 1, doi. 10.1371/journal.ppat.1004420
By:
- Zhou, Bin;
- Ma, Jingjiao;
- Liu, Qinfang;
- Bawa, Bhupinder;
- Wang, Wei;
- Shabman, Reed S.;
- Duff, Michael;
- Lee, Jinhwa;
- Lang, Yuekun;
- Cao, Nan;
- Nagy, Abdou;
- Lin, Xudong;
- Stockwell, Timothy B.;
- Richt, Juergen A.;
- Wentworth, David E.;
- Ma, Wenjun
Publication type:
Article
Influenza A Virus Migration and Persistence in North American Wild Birds.
Published in:
PLoS Pathogens, 2013, v. 9, n. 8, p. 1, doi. 10.1371/journal.ppat.1003570
By:
- Bahl, Justin;
- Krauss, Scott;
- Kühnert, Denise;
- Fourment, Mathieu;
- Raven, Garnet;
- Pryor, S. Paul;
- Niles, Lawrence J.;
- Danner, Angela;
- Walker, David;
- Mendenhall, Ian H.;
- Su, Yvonne C. F.;
- Dugan, Vivien G.;
- Halpin, Rebecca A.;
- Stockwell, Timothy B.;
- Webby, Richard J.;
- Wentworth, David E.;
- Drummond, Alexei J.;
- Smith, Gavin J. D.;
- Webster, Robert G.
Publication type:
Article
Infidelity of SARS-CoV Nsp14-Exonuclease Mutant Virus Replication Is Revealed by Complete Genome Sequencing.
Published in:
PLoS Pathogens, 2010, v. 6, n. 5, p. 1, doi. 10.1371/journal.ppat.1000896
By:
- Eckerle, Lance D.;
- Becker, Michelle M.;
- Halpin, Rebecca A.;
- Kelvin Li;
- Eli Venter;
- Xiaotao Lu;
- Scherbakova, Sana;
- Graham, Rachel L.;
- Baric, Ralph S.;
- Stockwell, Timothy B.;
- Spiro, David J.;
- Denison, Mark R.
Publication type:
Article
The effective rate of influenza reassortment is limited during human infection.
Published in:
PLoS Pathogens, 2017, v. 13, n. 2, p. 1, doi. 10.1371/journal.ppat.1006203
By:
- Sobel Leonard, Ashley;
- McClain, Micah T.;
- Smith, Gavin J. D.;
- Wentworth, David E.;
- Halpin, Rebecca A.;
- Lin, Xudong;
- Ransier, Amy;
- Stockwell, Timothy B.;
- Das, Suman R.;
- Gilbert, Anthony S.;
- Lambkin-Williams, Rob;
- Ginsburg, Geoffrey S.;
- Woods, Christopher W.;
- Koelle, Katia;
- Illingworth, Christopher J. R.
Publication type:
Article
The Diploid Genome Sequence of an Individual Human.
Published in:
PLoS Biology, 2007, v. 5, n. 10, p. e254, doi. 10.1371/journal.pbio.0050254
By:
- Levy, Samuel;
- Sutton, Granger;
- Ng, Pauline C.;
- Feuk, Lars;
- Halpern, Aaron L.;
- Walenz, Brian P.;
- Axelrod, Nelson;
- Jiaqi Huang;
- Kirkness, Ewen F.;
- Denisov, Gennady;
- Yuan Lin;
- MacDonald, Jeffrey R.;
- Andy Wing Chun Pang;
- Shago, Mary;
- Stockwell, Timothy B.;
- Tsiamouri, Alexia;
- Bafna, Vineet;
- Bansal, Vikas;
- Kravitz, Saul A.;
- Busam, Dana A.
Publication type:
Article
The soft palate is an important site of adaptation for transmissible influenza viruses.
Published in:
Nature, 2015, v. 526, n. 7571, p. 122, doi. 10.1038/nature15379
By:
- Lakdawala, Seema S.;
- Jayaraman, Akila;
- Halpin, Rebecca A.;
- Lamirande, Elaine W.;
- Shih, Angela R.;
- Stockwell, Timothy B.;
- Lin, Xudong;
- Simenauer, Ari;
- Hanson, Christopher T.;
- Vogel, Leatrice;
- Paskel, Myeisha;
- Minai, Mahnaz;
- Moore, Ian;
- Orandle, Marlene;
- Das, Suman R.;
- Wentworth, David E.;
- Sasisekharan, Ram;
- Subbarao, Kanta
Publication type:
Article
Mechanism of chimera formation during the Multiple Displacement Amplification reaction.
Published in:
BMC Biotechnology, 2007, v. 7, p. 19, doi. 10.1186/1472-6750-7-19
By:
- Lasken, Roger S;
- Stockwell, Timothy B
Publication type:
Article
Genetic Variation in an Individual Human Exome.
Published in:
PLoS Genetics, 2008, v. 4, n. 8, p. 1, doi. 10.1371/journal.pgen.1000160
By:
- Ng, Pauline C.;
- Levy, Samuel;
- Jiaqi Huang;
- Stockwell, Timothy B.;
- Walenz, Brian P.;
- Kelvin Li;
- Axelrod, Nelson;
- Busam, Dana A.;
- Strausberg, Robert L.;
- Venter, J. Craig
Publication type:
Article
Nanoliter Reactors Improve Multiple Displacement Amplification of Genomes from Single Cells.
Published in:
PLoS Genetics, 2007, v. 3, n. 9, p. 1702, doi. 10.1371/journal.pgen.0030155
By:
- Marcy, Yann;
- Ishoey, Thomas;
- Lasken, Roger S.;
- Stockwell, Timothy B.;
- Walenz, Brian P.;
- Halpern, Aaron L.;
- Beeson, Karen Y.;
- Goldberg, Susanne M. D.;
- Quake, Stephen R.
Publication type:
Article
Biological Sexing of a 4000-Year-Old Egyptian Mummy Head to Assess the Potential of Nuclear DNA Recovery from the Most Damaged and Limited Forensic Specimens.
Published in:
Genes, 2018, v. 9, n. 3, p. 135, doi. 10.3390/genes9030135
By:
- Loreille, Odile;
- Ratnayake, Shashikala;
- Bazinet, Adam L.;
- Stockwell, Timothy B.;
- Sommer, Daniel D.;
- Rohland, Nadin;
- Mallick, Swapan;
- Johnson, Philip L.F.;
- Skoglund, Pontus;
- Onorato, Anthony J.;
- Bergman, Nicholas H.;
- Reich, David;
- Irwin, Jodi A.
Publication type:
Article
Automated degenerate PCR primer design for high-throughput sequencing improves efficiency of viral sequencing.
Published in:
Virology Journal, 2012, v. 9, n. 1, p. 261, doi. 10.1186/1743-422X-9-261
By:
- Li, Kelvin;
- Shrivastava, Susmita;
- Brownley, Anushka;
- Katzel, Dan;
- Bera, Jayati;
- Nguyen, Anh Thu;
- Thovarai, Vishal;
- Halpin, Rebecca;
- Stockwell, Timothy B.
Publication type:
Article
Genetic stability of foot-and-mouth disease virus during long-term infections in natural hosts.
Published in:
PLoS ONE, 2018, v. 13, n. 2, p. 1, doi. 10.1371/journal.pone.0190977
By:
- Ramirez-Carvajal, Lisbeth;
- Pauszek, Steven J.;
- Ahmed, Zaheer;
- Farooq, Umer;
- Naeem, Khalid;
- Shabman, Reed S.;
- Stockwell, Timothy B.;
- Rodriguez, Luis L.
Publication type:
Article
The Ebola virus VP35 protein binds viral immunostimulatory and host RNAs identified through deep sequencing.
Published in:
PLoS ONE, 2017, v. 12, n. 6, p. 1, doi. 10.1371/journal.pone.0178717
By:
- Dilley, Kari A.;
- Puri, Vinita;
- Stockwell, Timothy B.;
- Shabman, Reed S.;
- Voorhies, Alexander A.;
- Lorenzi, Hernan;
- Luthra, Priya;
- Basler, Christopher F.
Publication type:
Article

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