-
1
-
-
33748455338
-
Type I interferons in host defense
-
Stetson DB, Medzhitov R. 2006. Type I interferons in host defense. Immunity 25:373–381. https://doi.org/10.1016/j.immuni.2006.08.007.
-
(2006)
Immunity
, vol.25
, pp. 373-381
-
-
Stetson, DB1
Medzhitov, R.2
-
2
-
-
33748475531
-
Type I interferon gene induction by the interferon regulatory factor family of transcription factors
-
Honda K, Takaoka A, Taniguchi T. 2006. Type I interferon gene induction by the interferon regulatory factor family of transcription factors. Immunity 25:349–360. https://doi.org/10.1016/j.immuni.2006.08.009.
-
(2006)
Immunity
, vol.25
, pp. 349-360
-
-
Honda, K1
Takaoka, A2
Taniguchi, T.3
-
3
-
-
0014653595
-
The results of controlled observations on the prophylaxis of influenza with interferon
-
Solov’ev V. 1969. The results of controlled observations on the prophylaxis of influenza with interferon. Bull World Health Organ 41:683–688.
-
(1969)
Bull World Health Organ
, vol.41
, pp. 683-688
-
-
Solov’ev, V.1
-
4
-
-
0023270494
-
Intranasally administered interferon as prophylaxis against experimentally induced influenza A virus infection in humans
-
Treanor JJ, Betts RF, Erb SM, Roth FK, Dolin R. 1987. Intranasally administered interferon as prophylaxis against experimentally induced influenza A virus infection in humans. J Infect Dis 156:379–383. https://doi.org/10.1093/infdis/156.2.379.
-
(1987)
J Infect Dis
, vol.156
, pp. 379-383
-
-
Treanor, JJ1
Betts, RF2
Erb, SM3
Roth, FK4
Dolin, R.5
-
5
-
-
33847292819
-
Protection from lethal influenza virus challenge by oral type 1 interferon
-
Beilharz MW, Cummins JM, Bennett AL. 2007. Protection from lethal influenza virus challenge by oral type 1 interferon. Biochem Biophys Res Commun 355:740–744. https://doi.org/10.1016/j.bbrc.2007.02.019.
-
(2007)
Biochem Biophys Res Commun
, vol.355
, pp. 740-744
-
-
Beilharz, MW1
Cummins, JM2
Bennett, AL.3
-
6
-
-
64049119567
-
Intranasal administration of alpha interferon reduces seasonal influenza A virus morbidity in ferrets
-
Kugel D, Kochs G, Obojes K, Roth J, Kobinger GP, Kobasa D, Haller O, Staeheli P, Von Messling V. 2009. Intranasal administration of alpha interferon reduces seasonal influenza A virus morbidity in ferrets. J Virol 83:3843–3851. https://doi.org/10.1128/JVI.02453-08.
-
(2009)
J Virol
, vol.83
, pp. 3843-3851
-
-
Kugel, D1
Kochs, G2
Obojes, K3
Roth, J4
Kobinger, GP5
Kobasa, D6
Haller, O7
Staeheli, P8
Von Messling, V.9
-
7
-
-
72849138377
-
Transmission of pandemic H1N1 influenza virus and impact of prior exposure to seasonal strains or interferon treatment
-
Steel J, Staeheli P, Mubareka S, Garcia-Sastre A, Palese P, Lowen AC. 2010. Transmission of pandemic H1N1 influenza virus and impact of prior exposure to seasonal strains or interferon treatment. J Virol 84: 21–26. https://doi.org/10.1128/JVI.01732-09.
-
(2010)
J Virol
, vol.84
, pp. 21-26
-
-
Steel, J1
Staeheli, P2
Mubareka, S3
Garcia-Sastre, A4
Palese, P5
Lowen, AC.6
-
8
-
-
33947108477
-
A question of self-preservation: immunopathology in influenza virus infection
-
La Gruta NL, Kedzierska K, Stambas J, Doherty PC. 2007. A question of self-preservation: immunopathology in influenza virus infection. Immunol Cell Biol 85:85–92. https://doi.org/10.1038/sj.icb.7100026.
-
(2007)
Immunol Cell Biol
, vol.85
, pp. 85-92
-
-
La Gruta, NL1
Kedzierska, K2
Stambas, J3
Doherty, PC.4
-
9
-
-
84899503850
-
Innate immunity to influenza virus infection
-
Iwasaki A, Pillai PS. 2014. Innate immunity to influenza virus infection. Nat Rev Immunol 14:315. https://doi.org/10.1038/nri3665.
-
(2014)
Nat Rev Immunol
, vol.14
, pp. 315
-
-
Iwasaki, A1
Pillai, PS.2
-
10
-
-
84878567290
-
Visualizing the beta interferon response in mice during infection with influenza A viruses expressing or lacking nonstructural protein 1
-
Kallfass C, Lienenklaus S, Weiss S, Staeheli P. 2013. Visualizing the beta interferon response in mice during infection with influenza A viruses expressing or lacking nonstructural protein 1. J Virol 87:6925–6930. https://doi.org/10.1128/JVI.00283-13.
-
(2013)
J Virol
, vol.87
, pp. 6925-6930
-
-
Kallfass, C1
Lienenklaus, S2
Weiss, S3
Staeheli, P.4
-
11
-
-
85016959780
-
Single-cell studies of IFN-β promoter activation by wild-type and NS1-defective influenza A viruses
-
Killip MJ, Jackson D, Perez-Cidoncha M, Fodor E, Randall RE. 2017. Single-cell studies of IFN-β promoter activation by wild-type and NS1-defective influenza A viruses. J Gen Virol 98:357–363. https://doi.org/10.1099/jgv.0.000687.
-
(2017)
J Gen Virol
, vol.98
, pp. 357-363
-
-
Killip, MJ1
Jackson, D2
Perez-Cidoncha, M3
Fodor, E4
Randall, RE.5
-
12
-
-
85043531075
-
Extreme heterogeneity of influenza virus infection in single cells
-
Russell AB, Trapnell C, Bloom JD. 2018. Extreme heterogeneity of influenza virus infection in single cells. Elife 7:e32303. https://doi.org/10.7554/eLife.32303.
-
(2018)
Elife
, vol.7
, pp. e32303
-
-
Russell, AB1
Trapnell, C2
Bloom, JD.3
-
13
-
-
85047800158
-
Dissection of influenza infection in vivo by single-cell RNA sequencing
-
679
-
Steuerman Y, Cohen M, Peshes-Yaloz N, Valadarsky L, Cohn O, David E, Frishberg A, Mayo L, Bacharach E, Amit I, Gat-Viks I. 2018. Dissection of influenza infection in vivo by single-cell RNA sequencing. Cell Syst 6:679.e4–691.e4. https://doi.org/10.1016/j.cels.2018.05.008.
-
(2018)
Cell Syst
, vol.6
, pp. e4-691e4
-
-
Steuerman, Y1
Cohen, M2
Peshes-Yaloz, N3
Valadarsky, L4
Cohn, O5
David, E6
Frishberg, A7
Mayo, L8
Bacharach, E9
Amit, I10
Gat-Viks, I.11
-
14
-
-
85053456878
-
Distinct antiviral signatures revealed by the magnitude and round of influenza virus replication in vivo
-
Sjaastad LE, Fay EJ, Fiege JK, Macchietto MG, Stone IA, Markman MW, Shen S, Langlois RA. 2018. Distinct antiviral signatures revealed by the magnitude and round of influenza virus replication in vivo. Proc Natl Acad Sci U S A 115:9610–9615. https://doi.org/10.1073/pnas .1807516115.
-
(2018)
Proc Natl Acad Sci U S A
, vol.115
, pp. 9610-9615
-
-
Sjaastad, LE1
Fay, EJ2
Fiege, JK3
Macchietto, MG4
Stone, IA5
Markman, MW6
Shen, S7
Langlois, RA.8
-
15
-
-
84947782751
-
Single-cell analysis and stochastic modelling unveil large cell-to-cell variability in influenza A virus infection
-
Heldt FS, Kupke SY, Dorl S, Reichl U, Frensing T. 2015. Single-cell analysis and stochastic modelling unveil large cell-to-cell variability in influenza A virus infection. Nat Commun 6:8938. https://doi.org/10.1038/ncomms9938.
-
(2015)
Nat Commun
, vol.6
, pp. 8938
-
-
Heldt, FS1
Kupke, SY2
Dorl, S3
Reichl, U4
Frensing, T.5
-
16
-
-
85078561383
-
Cell-to-cell variation in defective virus expression and effects on host responses during influenza virus infection
-
Wang C, Forst CV, Chou T, Geber A, Wang M, Hamou W, Smith M, Sebra R, Zhang B, Zhou B, Ghedin E. 2018. Cell-to-cell variation in defective virus expression and effects on host responses during influenza virus infection. bioRxiv https://doi.org/10.1101/487785.
-
(2018)
bioRxiv
-
-
Wang, C1
Forst, CV2
Chou, T3
Geber, A4
Wang, M5
Hamou, W6
Smith, M7
Sebra, R8
Zhang, B9
Zhou, B10
Ghedin, E.11
-
17
-
-
85051323990
-
Stochastic processes constrain the within and between host evolution of influenza virus
-
McCrone JT, Woods RJ, Martin ET, Malosh RE, Monto AS, Lauring AS. 2018. Stochastic processes constrain the within and between host evolution of influenza virus. Elife 7:e35962. https://doi.org/10.7554/eLife.35962.
-
(2018)
Elife
, vol.7
, pp. e35962
-
-
McCrone, JT1
Woods, RJ2
Martin, ET3
Malosh, RE4
Monto, AS5
Lauring, AS.6
-
18
-
-
85062095417
-
Reconciling disparate estimates of viral genetic diversity during human influenza infections
-
25 February
-
Xue KS, Bloom JD. 25 February 2019. Reconciling disparate estimates of viral genetic diversity during human influenza infections. Nat Genet https://doi.org/10.1038/s41588-019-0349-3.
-
(2019)
Nat Genet
-
-
Xue, KS1
Bloom, JD.2
-
19
-
-
84910682671
-
Influenza A virus transmission bottlenecks are defined by infection route and recipient host
-
Varble A, Albrecht RA, Backes S, Crumiller M, Bouvier NM, Sachs D, Garcia-Sastre A, tenOever BR. 2014. Influenza A virus transmission bottlenecks are defined by infection route and recipient host. Cell Host Microbe 16:691–700. https://doi.org/10.1016/j.chom.2014.09.020.
-
(2014)
Cell Host Microbe
, vol.16
, pp. 691-700
-
-
Varble, A1
Albrecht, RA2
Backes, S3
Crumiller, M4
Bouvier, NM5
Sachs, D6
Garcia-Sastre, A7
tenOever, BR.8
-
20
-
-
84878997106
-
Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells
-
236 –241
-
Shalek AK, Satija R, Adiconis X, Gertner RS, Gaublomme JT, Raychowdhury R, Schwartz S, Yosef N, Malboeuf C, Lu D, Trombetta JJ, Gennert D, Gnirke A, Goren A, Hacohen N, Levin JZ, Park H, Regev A. 2013. Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells. Nature 498:236 –241. https://doi.org/10.1038/ nature12172.
-
(2013)
Nature
, vol.498
-
-
Shalek, AK1
Satija, R2
Adiconis, X3
Gertner, RS4
Gaublomme, JT5
Raychowdhury, R6
Schwartz, S7
Yosef, N8
Malboeuf, C9
Lu, D10
Trombetta, JJ11
Gennert, D12
Gnirke, A13
Goren, A14
Hacohen, N15
Levin, JZ16
Park, H17
Regev, A.18
-
21
-
-
84903185013
-
Single cell RNA Seq reveals dynamic paracrine control of cellular variation
-
Shalek AK, Satija R, Shuga J, Trombetta JJ, Gennert D, Lu D, Chen P, Gertner RS, Gaublomme JT, Yosef N, Schwartz S, Fowler B, Weaver S, Wang J, Wang X, Ding R, Raychowdhury R, Friedman N, Hacohen N, Park H, May AP, Regev A. 2014. Single cell RNA Seq reveals dynamic paracrine control of cellular variation. Nature 510:363. https://doi.org/10.1038/ nature13437.
-
(2014)
Nature
, vol.510
, pp. 363
-
-
Shalek, AK1
Satija, R2
Shuga, J3
Trombetta, JJ4
Gennert, D5
Lu, D6
Chen, P7
Gertner, RS8
Gaublomme, JT9
Yosef, N10
Schwartz, S11
Fowler, B12
Weaver, S13
Wang, J14
Wang, X15
Ding, R16
Raychowdhury, R17
Friedman, N18
Hacohen, N19
Park, H20
May, AP21
Regev, A.22
more..
-
22
-
-
85052140965
-
Single-cell analysis reveals that stochasticity and paracrine signaling control interferon-alpha production by plasmacytoid dendritic cells
-
Wimmers F, Subedi N, van Buuringen N, Heister D, Vivie J, Beeren-Reinieren I, Woestenenk R, Dolstra H, Piruska A, Jacobs JF, van Oudenaarden A, Figdor CG, Huck WTS, de Vries JM, Tel J. 2018. Single-cell analysis reveals that stochasticity and paracrine signaling control interferon-alpha production by plasmacytoid dendritic cells. Nat Commun 9:3317. https://doi.org/10.1038/s41467-018-05784-3.
-
(2018)
Nat Commun
, vol.9
, pp. 3317
-
-
Wimmers, F1
Subedi, N2
van Buuringen, N3
Heister, D4
Vivie, J5
Beeren-Reinieren, I6
Woestenenk, R7
Dolstra, H8
Piruska, A9
Jacobs, JF10
van Oudenaarden, A11
Figdor, CG12
Huck, WTS13
de Vries, JM14
Tel, J.15
-
23
-
-
85020380942
-
Cell polarization and epigenetic status shape the heterogeneous response to type III interferons in intestinal epithelial cells
-
Bhushal S, Wolfsmuller M, Selvakumar T, Kemper L, Wirth D, Hornef M, Hauser H, Koster M. 2017. Cell polarization and epigenetic status shape the heterogeneous response to type III interferons in intestinal epithelial cells. Front Immunol 8:671– 671. https://doi.org/10.3389/fimmu.2017 .00671.
-
(2017)
Front Immunol
, vol.8
, pp. 671-671
-
-
Bhushal, S1
Wolfsmuller, M2
Selvakumar, T3
Kemper, L4
Wirth, D5
Hornef, M6
Hauser, H7
Koster, M.8
-
24
-
-
0345004816
-
Influenza A virus lacking the NS1 gene replicates in interferon-deficient systems
-
Garcia-Sastre A, Egorov A, Matassov D, Brandt S, Levy DE, Durbin JE, Palese P, Muster T. 1998. Influenza A virus lacking the NS1 gene replicates in interferon-deficient systems. Virology 252:324–330. https://doi.org/10.1006/viro.1998.9508.
-
(1998)
Virology
, vol.252
, pp. 324-330
-
-
Garcia-Sastre, A1
Egorov, A2
Matassov, D3
Brandt, S4
Levy, DE5
Durbin, JE6
Palese, P7
Muster, T.8
-
25
-
-
54449099369
-
The multifunctional NS1 protein of influenza A viruses
-
Hale BG, Randall RE, Ortin J, Jackson D. 2008. The multifunctional NS1 protein of influenza A viruses. J Gen Virol 89:2359–2376. https://doi.org/10.1099/vir.0.2008/004606-0.
-
(2008)
J Gen Virol
, vol.89
, pp. 2359-2376
-
-
Hale, BG1
Randall, RE2
Ortin, J3
Jackson, D.4
-
26
-
-
84929576523
-
Influenza A virus protein PA-X contributes to viral growth and suppression of the host antiviral and immune responses
-
Hayashi T, MacDonald LA, Takimoto T. 2015. Influenza A virus protein PA-X contributes to viral growth and suppression of the host antiviral and immune responses. J Virol 89:6442–6452. https://doi.org/10.1128/JVI.00319-15.
-
(2015)
J Virol
, vol.89
, pp. 6442-6452
-
-
Hayashi, T1
MacDonald, LA2
Takimoto, T.3
-
27
-
-
70649087924
-
Mechanisms and functional implications of the degradation of host RNA polymerase II in influenza virus infected cells
-
Vreede FT, Chan AY, Sharps J, Fodor E. 2010. Mechanisms and functional implications of the degradation of host RNA polymerase II in influenza virus infected cells. Virology 396:125–134. https://doi.org/10.1016/j.virol.2009.10.003.
-
(2010)
Virology
, vol.396
, pp. 125-134
-
-
Vreede, FT1
Chan, AY2
Sharps, J3
Fodor, E.4
-
28
-
-
80755169631
-
The influenza virus PB1-F2 protein has interferon antagonistic activity
-
Dudek SE, Wixler L, Nordhoff C, Nordmann A, Anhlan D, Wixler V, Ludwig S. 2011. The influenza virus PB1-F2 protein has interferon antagonistic activity. Biol Chem 392:1135–1144. https://doi.org/10.1515/BC.2011.174.
-
(2011)
Biol Chem
, vol.392
, pp. 1135-1144
-
-
Dudek, SE1
Wixler, L2
Nordhoff, C3
Nordmann, A4
Anhlan, D5
Wixler, V6
Ludwig, S.7
-
29
-
-
84959511733
-
Influenza virus activation of the interferon system
-
Killip MJ, Fodor E, Randall RE. 2015. Influenza virus activation of the interferon system. Virus Res 209:11–22. https://doi.org/10.1016/j.virusres.2015.02.003.
-
(2015)
Virus Res
, vol.209
, pp. 11-22
-
-
Killip, MJ1
Fodor, E2
Randall, RE.3
-
30
-
-
0022477122
-
Measurement of the mutation rates of animal viruses: influenza A virus and poliovirus type
-
Parvin JD, Moscona A, Pan W, Leider J, Palese P. 1986. Measurement of the mutation rates of animal viruses: influenza A virus and poliovirus type. J Virol 59:377–383.
-
(1986)
J Virol
, vol.59
, pp. 377-383
-
-
Parvin, JD1
Moscona, A2
Pan, W3
Leider, J4
Palese, P.5
-
31
-
-
0026561520
-
Heterogeneity of the mutation rates of influenza A viruses: isolation of mutator mutants
-
Suarez P, Valcarcel J, Ortin J. 1992. Heterogeneity of the mutation rates of influenza A viruses: isolation of mutator mutants. J Virol 66: 2491–2494.
-
(1992)
J Virol
, vol.66
, pp. 2491-2494
-
-
Suarez, P1
Valcarcel, J2
Ortin, J.3
-
32
-
-
0028009540
-
An estimation of the nucleotide substitution rate at defined positions in the influenza virus haemagglutinin gene
-
Suarez-Lopez P, Ortin J. 1994. An estimation of the nucleotide substitution rate at defined positions in the influenza virus haemagglutinin gene. J Gen Virol 75:389–393. https://doi.org/10.1099/0022-1317-75-2 -389.
-
(1994)
J Gen Virol
, vol.75
, pp. 389-393
-
-
Suarez-Lopez, P1
Ortin, J.2
-
33
-
-
84905001681
-
An experimentally determined evolutionary model dramatically improves phylogenetic fit
-
Bloom JD. 2014. An experimentally determined evolutionary model dramatically improves phylogenetic fit. Mol Biol Evol 31:1956–1978. https://doi.org/10.1093/molbev/msu173.
-
(2014)
Mol Biol Evol
, vol.31
, pp. 1956-1978
-
-
Bloom, JD.1
-
34
-
-
85026749797
-
A novel twelve class fluctuation test reveals higher than expected mutation rates for influenza A viruses
-
Pauly MD, Procario MC, Lauring AS. 2017. A novel twelve class fluctuation test reveals higher than expected mutation rates for influenza A viruses. Elife 6:e26437. https://doi.org/10.7554/eLife.26437.
-
(2017)
Elife
, vol.6
, pp. e26437
-
-
Pauly, MD1
Procario, MC2
Lauring, AS.3
-
35
-
-
85053552716
-
Mini viral RNAs act as innate immune agonists during influenza virus infection
-
te Velthuis A, Long J, Bauer DL, Fan R, Yen HL, Sharps J, Siegers J, Killip M, French H, Oliva-Martin MJ, Randall R, de Wit E, van Riel D, Poon L, Fodor E. 2018. Mini viral RNAs act as innate immune agonists during influenza virus infection. Nat Microbiol 3:1234–1242. https://doi.org/10.1038/s41564-018-0240-5.
-
(2018)
Nat Microbiol
, vol.3
, pp. 1234-1242
-
-
te Velthuis, A1
Long, J2
Bauer, DL3
Fan, R4
Yen, HL5
Sharps, J6
Siegers, J7
Killip, M8
French, H9
Oliva-Martin, MJ10
Randall, R11
de Wit, E12
van Riel, D13
Poon, L14
Fodor, E.15
-
36
-
-
85040570901
-
Genome-wide identification of interferon-sensitive mutations enables influenza vaccine design
-
Du Y, Xin L, Shi Y, Zhang TH, Wu NC, Dai L, Gong D, Brar G, Shu S, Luo J, Reiley W, Tseng YW, Bai H, Wu TT, Wang J, Shu Y, Sun R. 2018. Genome-wide identification of interferon-sensitive mutations enables influenza vaccine design. Science 359:290–296. https://doi.org/10.1126/science.aan8806.
-
(2018)
Science
, vol.359
, pp. 290-296
-
-
Du, Y1
Xin, L2
Shi, Y3
Zhang, TH4
Wu, NC5
Dai, L6
Gong, D7
Brar, G8
Shu, S9
Luo, J10
Reiley, W11
Tseng, YW12
Bai, H13
Wu, TT14
Wang, J15
Shu, Y16
Sun, R.17
-
37
-
-
84897515363
-
An unbiased genetic screen reveals the polygenic nature of the influenza virus anti-interferon response
-
Pérez-Cidoncha M, Killip MJ, Oliveros JC, Asensio VJ, Fernández Y, Bengoechea JA, Randall RE, Ortín J. 2014. An unbiased genetic screen reveals the polygenic nature of the influenza virus anti-interferon response. J Virol 88:4632–4646. https://doi.org/10.1128/JVI.00014-14.
-
(2014)
J Virol
, vol.88
, pp. 4632-4646
-
-
Pérez-Cidoncha, M1
Killip, MJ2
Oliveros, JC3
Asensio, VJ4
Fernández, Y5
Bengoechea, JA6
Randall, RE7
Ortín, J.8
-
38
-
-
77957997708
-
Preference of RIG-I for short viral RNA molecules in infected cells revealed by next-generation sequencing
-
Baum A, Sachidanandam R, Garcia-Sastre A. 2010. Preference of RIG-I for short viral RNA molecules in infected cells revealed by next-generation sequencing. Proc Natl Acad Sci U S A 107:16303–16308. https://doi.org/10.1073/pnas.1005077107.
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, pp. 16303-16308
-
-
Baum, A1
Sachidanandam, R2
Garcia-Sastre, A.3
-
39
-
-
84887308873
-
Defective viral genomes arising in vivo provide critical danger signals for the triggering of lung antiviral immunity
-
Tapia K, Kim W-K, Sun Y, Mercado-López X, Dunay E, Wise M, Adu M, López CB. 2013. Defective viral genomes arising in vivo provide critical danger signals for the triggering of lung antiviral immunity. PLoS Pathog 9:e1003703. https://doi.org/10.1371/journal.ppat.1003703.
-
(2013)
PLoS Pathog
, vol.9
, pp. e1003703
-
-
Tapia, K1
Kim, W-K2
Sun, Y3
Mercado-López, X4
Dunay, E5
Wise, M6
Adu, M7
López, CB.8
-
40
-
-
84930321672
-
Evidence for a novel mechanism of influenza virus-induced type I interferon expression by a defective RNA-encoded protein
-
Boergeling Y, Rozhdestvensky TS, Schmolke M, Resa-Infante P, Robeck T, Randau G, Wolff T, Gabriel G, Brosius J, Ludwig S. 2015. Evidence for a novel mechanism of influenza virus-induced type I interferon expression by a defective RNA-encoded protein. PLoS Pathog 11:e1004924. https://doi.org/10.1371/journal.ppat.1004924.
-
(2015)
PLoS Pathog
, vol.11
, pp. e1004924
-
-
Boergeling, Y1
Rozhdestvensky, TS2
Schmolke, M3
Resa-Infante, P4
Robeck, T5
Randau, G6
Wolff, T7
Gabriel, G8
Brosius, J9
Ludwig, S.10
-
41
-
-
84936931510
-
Cloned defective interfering influenza RNA and a possible pan-specific treatment of respiratory virus diseases
-
Dimmock NJ, Easton AJ. 2015. Cloned defective interfering influenza RNA and a possible pan-specific treatment of respiratory virus diseases. Viruses 7:3768–3788. https://doi.org/10.3390/v7072796.
-
(2015)
Viruses
, vol.7
, pp. 3768-3788
-
-
Dimmock, NJ1
Easton, AJ.2
-
42
-
-
85062641949
-
Inhibition of ongoing influenza A virus replication reveals different mechanisms of RIG-I activation
-
Liu G, Lu Y, Liu Q, Zhou Y. 2019. Inhibition of ongoing influenza A virus replication reveals different mechanisms of RIG-I activation. J Virol 93: e02066-18. https://doi.org/10.1128/JVI.02066-18.
-
(2019)
J Virol
, vol.93
, pp. e02066-18
-
-
Liu, G1
Lu, Y2
Liu, Q3
Zhou, Y.4
-
43
-
-
84874702494
-
Most influenza A virions fail to express at least one essential viral protein
-
Brooke CB, Ince WL, Wrammert J, Ahmed R, Wilson PC, Bennink JR, Yewdell JW. 2013. Most influenza A virions fail to express at least one essential viral protein. J Virol 87:3155–3162. https://doi.org/10.1128/JVI .02284-12.
-
(2013)
J Virol
, vol.87
, pp. 3155-3162
-
-
Brooke, CB1
Ince, WL2
Wrammert, J3
Ahmed, R4
Wilson, PC5
Bennink, JR6
Yewdell, JW.7
-
44
-
-
85034112659
-
Single-cell virology: on-chip investigation of viral infection dynamics
-
Guo F, Li S, Caglar MU, Mao Z, Liu W, Woodman A, Arnold JJ, Wilke CO, Huang TJ, Cameron CE. 2017. Single-cell virology: on-chip investigation of viral infection dynamics. Cell Rep 21:1692–1704. https://doi.org/10.1016/j.celrep.2017.10.051.
-
(2017)
Cell Rep
, vol.21
, pp. 1692-1704
-
-
Guo, F1
Li, S2
Caglar, MU3
Mao, Z4
Liu, W5
Woodman, A6
Arnold, JJ7
Wilke, CO8
Huang, TJ9
Cameron, CE.10
-
45
-
-
85043513977
-
Single-cell transcriptional dynamics of flavivirus infection
-
Zanini F, Pu SY, Bekerman E, Einav S, Quake SR. 2018. Single-cell transcriptional dynamics of flavivirus infection. Elife 7:e32942. https://doi.org/10.7554/eLife.32942.
-
(2018)
Elife
, vol.7
, pp. e32942
-
-
Zanini, F1
Pu, SY2
Bekerman, E3
Einav, S4
Quake, SR.5
-
46
-
-
85059214054
-
Virus-inclusive single-cell RNA sequencing reveals molecular signature predictive of progression to severe dengue infection
-
Zanini F, Robinson M, Croote D, Sahoo MK, Sanz AM, Ortiz-Lasso E, Albornoz LL, Suarez FR, Montoya JG, Pinsky BA, Quake S, Einav S. 2018. Virus-inclusive single-cell RNA sequencing reveals molecular signature predictive of progression to severe dengue infection. Proc Natl Acad Sci U S A 115:E12363–E12369. https://doi.org/10.1073/pnas.1813819115.
-
(2018)
Proc Natl Acad Sci U S A
, vol.115
, pp. E12363-E12369
-
-
Zanini, F1
Robinson, M2
Croote, D3
Sahoo, MK4
Sanz, AM5
Ortiz-Lasso, E6
Albornoz, LL7
Suarez, FR8
Montoya, JG9
Pinsky, BA10
Quake, S11
Einav, S.12
-
47
-
-
85058839075
-
Simultaneous multiplexed amplicon sequencing and transcriptome profiling in single cells
-
Saikia M, Burnham P, Keshavjee SH, Wang MF, Heyang M, Moral-Lopez P, Hinchman MM, Danko CG, Parker JS, De Vlaminck I. 2019. Simultaneous multiplexed amplicon sequencing and transcriptome profiling in single cells. Nat Methods 16:59–62. https://doi.org/10.1038/s41592-018-0259-9.
-
(2019)
Nat Methods
, vol.16
, pp. 59-62
-
-
Saikia, M1
Burnham, P2
Keshavjee, SH3
Wang, MF4
Heyang, M5
Moral-Lopez, P6
Hinchman, MM7
Danko, CG8
Parker, JS9
De Vlaminck, I.10
-
48
-
-
85062631583
-
West Nile virus-inclusive single-cell RNA sequencing reveals heterogeneity in the type I interferon response within single cells
-
O’Neal JT, Upadhyay AA, Wolabaugh A, Patel NB, Bosinger SE, Suthar MS. 2019. West Nile virus-inclusive single-cell RNA sequencing reveals heterogeneity in the type I interferon response within single cells. J Virol 93:e01778-18. https://doi.org/10.1128/JVI.01778-18.
-
(2019)
J Virol
, vol.93
, pp. e01778-18
-
-
O’Neal, JT1
Upadhyay, AA2
Wolabaugh, A3
Patel, NB4
Bosinger, SE5
Suthar, MS.6
-
49
-
-
85064879786
-
Single-cell virus sequencing of influenza infections that trigger innate immunity
-
Russell AB, Kowalsky JR, Bloom JD. 2018. Single-cell virus sequencing of influenza infections that trigger innate immunity. bioRxiv https://doi.org/10.1101/437277.
-
(2018)
bioRxiv
-
-
Russell, AB1
Kowalsky, JR2
Bloom, JD.3
-
50
-
-
0030843493
-
HSV-TK gene transfer into donor lymphocytes for control of allogeneic graft-versus leukemia
-
Bonini C, Ferrari G, Verzeletti S, Servida P, Zappone E, Ruggieri L, Ponzoni M, Rossini S, Mavilio F, Traversari C, Bordignon C. 1997. HSV-TK gene transfer into donor lymphocytes for control of allogeneic graft-versus leukemia. Science 276:1719 –1724. https://doi.org/10.1126/science.276.5319.1719.
-
(1997)
Science
, vol.276
, pp. 1719-1724
-
-
Bonini, C1
Ferrari, G2
Verzeletti, S3
Servida, P4
Zappone, E5
Ruggieri, L6
Ponzoni, M7
Rossini, S8
Mavilio, F9
Traversari, C10
Bordignon, C.11
-
51
-
-
0030660432
-
Cell-surface marking of CD34-restricted phenotypes of human hematopoietic progenitor cells by retrovirus-mediated gene transfer
-
Ruggieri L, Aiuti A, Salomoni M, Zappone E, Ferrari G, Bordignon C. 1997. Cell-surface marking of CD34-restricted phenotypes of human hematopoietic progenitor cells by retrovirus-mediated gene transfer. Hum Gene Ther 8:1611–1623. https://doi.org/10.1089/hum.1997.8.13-1611.
-
(1997)
Hum Gene Ther
, vol.8
, pp. 1611-1623
-
-
Ruggieri, L1
Aiuti, A2
Salomoni, M3
Zappone, E4
Ferrari, G5
Bordignon, C.6
-
52
-
-
33745839246
-
Sendai virus defective-interfering genomes and the activation of interferon-beta
-
Strahle L, Garcin D, Kolakofsky D. 2006. Sendai virus defective-interfering genomes and the activation of interferon-beta. Virology 351:101–111. https://doi.org/10.1016/j.virol.2006.03.022.
-
(2006)
Virology
, vol.351
, pp. 101-111
-
-
Strahle, L1
Garcin, D2
Kolakofsky, D.3
-
53
-
-
0034705225
-
A DNA transfection system for generation of influenza A virus from eight plasmids
-
Hoffmann E, Neumann G, Kawaoka Y, Hobom G, Webster RG. 2000. A DNA transfection system for generation of influenza A virus from eight plasmids. Proc Natl Acad Sci U S A 97:6108–6113. https://doi.org/10.1073/pnas.100133697.
-
(2000)
Proc Natl Acad Sci U S A
, vol.97
, pp. 6108-6113
-
-
Hoffmann, E1
Neumann, G2
Kawaoka, Y3
Hobom, G4
Webster, RG.5
-
54
-
-
84964329278
-
Propagation and characterization of influenza virus stocks that lack high levels of defective viral genomes and hemagglutinin mutations
-
Xue J, Chambers BS, Hensley SE, Lopez CB. 2016. Propagation and characterization of influenza virus stocks that lack high levels of defective viral genomes and hemagglutinin mutations. Front Microbiol 7:326. https://doi.org/10.3389/fmicb.2016.00326.
-
(2016)
Front Microbiol
, vol.7
, pp. 326
-
-
Xue, J1
Chambers, BS2
Hensley, SE3
Lopez, CB.4
-
55
-
-
85009446777
-
Massively parallel digital transcriptional profiling of single cells
-
Zheng GX, Terry JM, Belgrader P, Ryvkin P, Bent ZW, Wilson R, Ziraldo SB, Wheeler TD, McDermott GP, Zhu J, Gregory MT, Shuga J, Montesclaros L, Underwood JG, Masquelier DA, Nishimura SY, Schnall-Levin M, Wyatt PW, Hindson CM, Bharadwaj R, Wong A, Ness KD, Beppu LW, Deeg HJ, McFarland C, Loeb KR, Valente WJ, Ericson NG, Stevens EA, Radich JP, Mikkelsen TS, Hindson BL, Bielas JH. 2017. Massively parallel digital transcriptional profiling of single cells. Nat Commun 8:14049. https://doi.org/10.1038/ncomms14049.
-
(2017)
Nat Commun
, vol.8
, pp. 14049
-
-
Zheng, GX1
Terry, JM2
Belgrader, P3
Ryvkin, P4
Bent, ZW5
Wilson, R6
Ziraldo, SB7
Wheeler, TD8
McDermott, GP9
Zhu, J10
Gregory, MT11
Shuga, J12
Montesclaros, L13
Underwood, JG14
Masquelier, DA15
Nishimura, SY16
Schnall-Levin, M17
Wyatt, PW18
Hindson, CM19
Bharadwaj, R20
Wong, A21
Ness, KD22
Beppu, LW23
Deeg, HJ24
McFarland, C25
Loeb, KR26
Valente, WJ27
Ericson, NG28
Stevens, EA29
Radich, JP30
Mikkelsen, TS31
Hindson, BL32
Bielas, JH.33
more..
-
56
-
-
0019470363
-
Polyadenylation sites for influenza virus mRNA
-
Robertson J, Schubert M, Lazzarini R. 1981. Polyadenylation sites for influenza virus mRNA. J Virol 38:157–163.
-
(1981)
J Virol
, vol.38
, pp. 157-163
-
-
Robertson, J1
Schubert, M2
Lazzarini, R.3
-
57
-
-
84931275587
-
Sequencing the cap-snatching repertoire of H1N1 influenza provides insight into the mechanism of viral transcription initiation
-
Koppstein D, Ashour J, Bartel DP. 2015. Sequencing the cap-snatching repertoire of H1N1 influenza provides insight into the mechanism of viral transcription initiation. Nucleic Acids Res 43:5052–5064. https://doi.org/10.1093/nar/gkv333.
-
(2015)
Nucleic Acids Res
, vol.43
, pp. 5052-5064
-
-
Koppstein, D1
Ashour, J2
Bartel, DP.3
-
58
-
-
77956125365
-
A flexible and efficient template format for circular consensus sequencing and SNP detection
-
Travers KJ, Chin CS, Rank DR, Eid JS, Turner SW. 2010. A flexible and efficient template format for circular consensus sequencing and SNP detection. Nucleic Acids Res 38:e159. https://doi.org/10.1093/nar/ gkq543.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. e159
-
-
Travers, KJ1
Chin, CS2
Rank, DR3
Eid, JS4
Turner, SW.5
-
59
-
-
85052891535
-
Estimating the frequency of multiplets in single-cell RNA sequencing from cell-mixing experiments
-
Bloom JD. 2018. Estimating the frequency of multiplets in single-cell RNA sequencing from cell-mixing experiments. PeerJ 6:e5578. https://doi.org/10.7717/peerj.5578.
-
(2018)
PeerJ
, vol.6
, pp. e5578
-
-
Bloom, JD.1
-
60
-
-
85027696020
-
A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications
-
Haque A, Engel J, Teichmann SA, Lonnberg T. 2017. A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications. Genome Med 9:75. https://doi.org/10.1186/s13073-017-0467-4.
-
(2017)
Genome Med
, vol.9
, pp. 75
-
-
Haque, A1
Engel, J2
Teichmann, SA3
Lonnberg, T.4
-
61
-
-
85021823834
-
Analysis of IAV replication and co-infection dynamics by a versatile RNA viral genome labeling method
-
Dou D, Hernandez-Neuta I, Wang H, Ostbye H, Qian X, Thiele S, Resa-Infante P, Kouassi NM, Sender V, Hentrich K, Mellroth P, Henriques-Normark B, Gabriel G, Nilsson M, Daniels R. 2017. Analysis of IAV replication and co-infection dynamics by a versatile RNA viral genome labeling method. Cell Rep 20:251–263. https://doi.org/10.1016/j.celrep .2017.06.021.
-
(2017)
Cell Rep
, vol.20
, pp. 251-263
-
-
Dou, D1
Hernandez-Neuta, I2
Wang, H3
Ostbye, H4
Qian, X5
Thiele, S6
Resa-Infante, P7
Kouassi, NM8
Sender, V9
Hentrich, K10
Mellroth, P11
Henriques-Normark, B12
Gabriel, G13
Nilsson, M14
Daniels, R.15
-
62
-
-
85067402257
-
Incomplete influenza A virus genomes are abundant but readily complemented during spatially structured viral spread
-
Jacobs NT, Onuoha NO, Antia A, Antia R, Steel J, Lowen AC. 2019. Incomplete influenza A virus genomes are abundant but readily complemented during spatially structured viral spread. bioRxiv https://doi.org/10.1101/529065.
-
(2019)
bioRxiv
-
-
Jacobs, NT1
Onuoha, NO2
Antia, A3
Antia, R4
Steel, J5
Lowen, AC.6
-
63
-
-
0024535928
-
Control of influenza virus gene expression: quantitative analysis of each viral RNA species in infected cells
-
Hatada E, Hasegawa M, Mukaigawa J, Shimizu K, Fukuda R. 1989. Control of influenza virus gene expression: quantitative analysis of each viral RNA species in infected cells. J Biochem 105:537–546. https://doi.org/10.1093/oxfordjournals.jbchem.a122702.
-
(1989)
J Biochem
, vol.105
, pp. 537-546
-
-
Hatada, E1
Hasegawa, M2
Mukaigawa, J3
Shimizu, K4
Fukuda, R.5
-
64
-
-
85019101126
-
Plaques formed by mutagenized viral populations have elevated coinfection frequencies
-
Aguilera ER, Erickson AK, Jesudhasan PR, Robinson CM, Pfeiffer JK. 2017. Plaques formed by mutagenized viral populations have elevated coinfection frequencies. mBio 8:e02020-16. https://doi.org/10.1128/mBio.02020-16.
-
(2017)
mBio
, vol.8
, pp. e02020-16
-
-
Aguilera, ER1
Erickson, AK2
Jesudhasan, PR3
Robinson, CM4
Pfeiffer, JK.5
-
65
-
-
84944213433
-
Single-cell analysis of RNA virus infection identifies multiple genetically diverse viral genomes within single infectious units
-
Combe M, Garijo R, Geller R, Cuevas JM, Sanjuan R. 2015. Single-cell analysis of RNA virus infection identifies multiple genetically diverse viral genomes within single infectious units. Cell Host Microbe 18:424 – 432. https://doi.org/10.1016/j.chom.2015.09.009.
-
(2015)
Cell Host Microbe
, vol.18
, pp. 424-432
-
-
Combe, M1
Garijo, R2
Geller, R3
Cuevas, JM4
Sanjuan, R.5
-
66
-
-
85051246722
-
Mitochondrial double-stranded RNA triggers antiviral signalling in humans
-
238 –242
-
Dhir A, Dhir S, Borowski LS, Jimenez L, Teitell M, Rotig A, Crow YJ, Rice GI, Duffy D, Tamby C, Nojima T, Munnich A, Schiff M, de Almeida CR, Rehwinkel J, Dziembowski A, Szczesny RJ, Proudfoot NJ. 2018. Mitochondrial double-stranded RNA triggers antiviral signalling in humans. Nature 560:238 –242. https://doi.org/10.1038/s41586-018-0363-0.
-
(2018)
Nature
, vol.560
-
-
Dhir, A1
Dhir, S2
Borowski, LS3
Jimenez, L4
Teitell, M5
Rotig, A6
Crow, YJ7
Rice, GI8
Duffy, D9
Tamby, C10
Nojima, T11
Munnich, A12
Schiff, M13
de Almeida, CR14
Rehwinkel, J15
Dziembowski, A16
Szczesny, RJ17
Proudfoot, NJ.18
-
67
-
-
84937639038
-
In vivo RNAi screening identifies MDA5 as a significant contributor to the cellular defense against influenza A virus
-
Benitez AA, Panis M, Xue J, Varble A, Shim JV, Frick AL, Lopez CB, Sachs D, tenOever BR. 2015. In vivo RNAi screening identifies MDA5 as a significant contributor to the cellular defense against influenza A virus. Cell Rep 11:1714–1726. https://doi.org/10.1016/j.celrep.2015.05.032.
-
(2015)
Cell Rep
, vol.11
, pp. 1714-1726
-
-
Benitez, AA1
Panis, M2
Xue, J3
Varble, A4
Shim, JV5
Frick, AL6
Lopez, CB7
Sachs, D8
tenOever, BR.9
-
68
-
-
85035083737
-
Viral unmasking of cellular 5S rRNA pseudogene transcripts induces RIG-I-mediated immunity
-
Chiang JJ, Sparrer KMJ, van Gent M, Lässig C, Huang T, Osterrieder N, Hopfner K-P, Gack MU. 2018. Viral unmasking of cellular 5S rRNA pseudogene transcripts induces RIG-I-mediated immunity. Nat Immunol 19: 53–62. https://doi.org/10.1038/s41590-017-0005-y.
-
(2018)
Nat Immunol
, vol.19
, pp. 53-62
-
-
Chiang, JJ1
Sparrer, KMJ2
van Gent, M3
Lässig, C4
Huang, T5
Osterrieder, N6
Hopfner, K-P7
Gack, MU.8
-
69
-
-
57249084011
-
Visualizing data using t-SNE
-
Maaten L, Hinton G. 2008. Visualizing data using t-SNE. J Mach Learn Res 9:2579–2605.
-
(2008)
J Mach Learn Res
, vol.9
, pp. 2579-2605
-
-
Maaten, L1
Hinton, G.2
-
70
-
-
84897403748
-
Comparison of somatic mutation calling methods in amplicon and whole exome sequence data
-
Xu H, DiCarlo J, Satya RV, Peng Q, Wang Y. 2014. Comparison of somatic mutation calling methods in amplicon and whole exome sequence data. BMC Genomics 15:244. https://doi.org/10.1186/1471-2164-15-244.
-
(2014)
BMC Genomics
, vol.15
, pp. 244
-
-
Xu, H1
DiCarlo, J2
Satya, RV3
Peng, Q4
Wang, Y.5
-
71
-
-
84874025843
-
Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples
-
Cibulskis K, Lawrence MS, Carter SL, Sivachenko A, Jaffe D, Sougnez C, Gabriel S, Meyerson M, Lander ES, Getz G. 2013. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol 31:213–222. https://doi.org/10.1038/nbt.2514.
-
(2013)
Nat Biotechnol
, vol.31
, pp. 213-222
-
-
Cibulskis, K1
Lawrence, MS2
Carter, SL3
Sivachenko, A4
Jaffe, D5
Sougnez, C6
Gabriel, S7
Meyerson, M8
Lander, ES9
Getz, G.10
-
72
-
-
0012057129
-
Measurement of inequality of incomes
-
Gini C. 1921. Measurement of inequality of incomes. Econ J (London) 31:124–126. https://doi.org/10.2307/2223319.
-
(1921)
Econ J (London)
, vol.31
, pp. 124-126
-
-
Gini, C.1
-
73
-
-
0037452618
-
Selective incorporation of influenza virus RNA segments into virions
-
Fujii Y, Goto H, Watanabe T, Yoshida T, Kawaoka Y. 2003. Selective incorporation of influenza virus RNA segments into virions. Proc Natl Acad Sci U S A 100:2002–2007. https://doi.org/10.1073/pnas.0437772100.
-
(2003)
Proc Natl Acad Sci U S A
, vol.100
, pp. 2002-2007
-
-
Fujii, Y1
Goto, H2
Watanabe, T3
Yoshida, T4
Kawaoka, Y.5
-
74
-
-
35348814973
-
Specific residues of the influenza A virus hemagglutinin viral RNA are important for efficient packaging into budding virions
-
Marsh GA, Hatami R, Palese P. 2007. Specific residues of the influenza A virus hemagglutinin viral RNA are important for efficient packaging into budding virions. J Virol 81:9727–9736. https://doi.org/10.1128/JVI.01144-07.
-
(2007)
J Virol
, vol.81
, pp. 9727-9736
-
-
Marsh, GA1
Hatami, R2
Palese, P.3
-
75
-
-
60349083295
-
Growth of an RNA virus in single cells reveals a broad fitness distribution
-
Zhu Y, Yongky A, Yin J. 2009. Growth of an RNA virus in single cells reveals a broad fitness distribution. Virology 385:39–46. https://doi.org/10.1016/j.virol.2008.10.031.
-
(2009)
Virology
, vol.385
, pp. 39-46
-
-
Zhu, Y1
Yongky, A2
Yin, J.3
-
76
-
-
84899811665
-
Single-cell analysis uncovers extensive biological noise in poliovirus replication
-
Schulte M, Andino R. 2014. Single-cell analysis uncovers extensive biological noise in poliovirus replication. J Virol 88:6205–6212. https://doi.org/10.1128/JVI.03539-13.
-
(2014)
J Virol
, vol.88
, pp. 6205-6212
-
-
Schulte, M1
Andino, R.2
-
77
-
-
84958078465
-
High-throughput single-cell kinetics of virus infections in the presence of defective interfering particles
-
Akpinar F, Timm A, Yin J. 2016. High-throughput single-cell kinetics of virus infections in the presence of defective interfering particles. J Virol 90:1599–1612. https://doi.org/10.1128/JVI.02190-15.
-
(2016)
J Virol
, vol.90
, pp. 1599-1612
-
-
Akpinar, F1
Timm, A2
Yin, J.3
-
78
-
-
85058796569
-
Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells
-
Gupta I, Collier PG, Haase B, Mahfouz A, Joglekar A, Floyd T, Koopmans F, Barres B, Smit AB, Sloan SA, Luo W, Fedrigo O, Ross ME, Tilgner HU. 2018. Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells. Nat Biotechnol 36:1197–1202. https://doi.org/10.1038/nbt.4259.
-
(2018)
Nat Biotechnol
, vol.36
, pp. 1197-1202
-
-
Gupta, I1
Collier, PG2
Haase, B3
Mahfouz, A4
Joglekar, A5
Floyd, T6
Koopmans, F7
Barres, B8
Smit, AB9
Sloan, SA10
Luo, W11
Fedrigo, O12
Ross, ME13
Tilgner, HU.14
-
79
-
-
77957773125
-
Lentiviral vector delivery of human interleukin-7 (hIL-7) to human immune system (HIS) mice expands T lymphocyte populations
-
O’Connell RM, Balazs AB, Rao DS, Kivork C, Yang L, Baltimore D. 2010. Lentiviral vector delivery of human interleukin-7 (hIL-7) to human immune system (HIS) mice expands T lymphocyte populations. PLoS One 5:e12009. https://doi.org/10.1371/journal.pone.0012009.
-
(2010)
PLoS One
, vol.5
, pp. e12009
-
-
O’Connell, RM1
Balazs, AB2
Rao, DS3
Kivork, C4
Yang, L5
Baltimore, D.6
-
80
-
-
79955707349
-
High cleavage efficiency of a 2A peptide derived from porcine teschovirus-1 in human cell lines, zebrafish and mice
-
Kim JH, Lee SR, Li LH, Park HJ, Park JH, Lee KY, Kim MK, Shin BA, Choi SY. 2011. High cleavage efficiency of a 2A peptide derived from porcine teschovirus-1 in human cell lines, zebrafish and mice. PLoS One 6:e18556. https://doi.org/10.1371/journal.pone.0018556.
-
(2011)
PLoS One
, vol.6
, pp. e18556
-
-
Kim, JH1
Lee, SR2
Li, LH3
Park, HJ4
Park, JH5
Lee, KY6
Kim, MK7
Shin, BA8
Choi, SY.9
-
81
-
-
33745158157
-
A simple method of estimating fifty per cent endpoints
-
Reed LJ, Muench H. 1938. A simple method of estimating fifty per cent endpoints. Am J Epidemiol 27:493–497. https://doi.org/10.1093/oxfordjournals.aje.a118408.
-
(1938)
Am J Epidemiol
, vol.27
, pp. 493-497
-
-
Reed, LJ1
Muench, H.2
-
82
-
-
85016515562
-
Complete mapping of viral escape from neutralizing antibodies
-
Doud MB, Hensley SE, Bloom JD. 2017. Complete mapping of viral escape from neutralizing antibodies. PLoS Pathog 13:e1006271. https://doi.org/10.1371/journal.ppat.1006271.
-
(2017)
PLoS Pathog
, vol.13
, pp. e1006271
-
-
Doud, MB1
Hensley, SE2
Bloom, JD.3
-
83
-
-
84941761377
-
Micelle PCR reduces chimera formation in 16S rRNA profiling of complex microbial DNA mixtures
-
Boers SA, Hays JP, Jansen R. 2015. Micelle PCR reduces chimera formation in 16S rRNA profiling of complex microbial DNA mixtures. Sci Rep 5:14181. https://doi.org/10.1038/srep14181.
-
(2015)
Sci Rep
, vol.5
, pp. 14181
-
-
Boers, SA1
Hays, JP2
Jansen, R.3
-
84
-
-
84896950946
-
Activation of the interferon induction cascade by influenza A viruses requires viral RNA synthesis and nuclear export
-
Killip MJ, Smith M, Jackson D, Randall RE. 2014. Activation of the interferon induction cascade by influenza A viruses requires viral RNA synthesis and nuclear export. J Virol 88:3942–3952. https://doi.org/10.1128/JVI.03109-13.
-
(2014)
J Virol
, vol.88
, pp. 3942-3952
-
-
Killip, MJ1
Smith, M2
Jackson, D3
Randall, RE.4
-
85
-
-
85025409225
-
The quantitative determination of influenza virus and antibodies by means of red cell agglutination
-
Hirst GK. 1942. The quantitative determination of influenza virus and antibodies by means of red cell agglutination. J Exp Med 75:49–64. https://doi.org/10.1084/jem.75.1.49.
-
(1942)
J Exp Med
, vol.75
, pp. 49-64
-
-
Hirst, GK.1
-
86
-
-
77953262416
-
Permissive secondary mutations enable the evolution of influenza oseltamivir resistance
-
Bloom JD, Gong LI, Baltimore D. 2010. Permissive secondary mutations enable the evolution of influenza oseltamivir resistance. Science 328: 1272–1275. https://doi.org/10.1126/science.1187816.
-
(2010)
Science
, vol.328
, pp. 1272-1275
-
-
Bloom, JD1
Gong, LI2
Baltimore, D.3
-
87
-
-
84867306721
-
Snakemake–a scalable bioinformatics workflow engine
-
Koster J, Rahmann S. 2012. Snakemake–a scalable bioinformatics workflow engine. Bioinformatics 28:2520–2522. https://doi.org/10.1093/bioinformatics/ bts480.
-
(2012)
Bioinformatics
, vol.28
, pp. 2520-2522
-
-
Koster, J1
Rahmann, S.2
-
88
-
-
85054132627
-
Minimap2: pairwise alignment for nucleotide sequences
-
Li H. 2018. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34:3094–3100. https://doi.org/10.1093/bioinformatics/bty191.
-
(2018)
Bioinformatics
, vol.34
, pp. 3094-3100
-
-
Li, H.1
-
89
-
-
84930207201
-
Software for the analysis and visualization of deep mutational scanning data
-
Bloom JD. 2015. Software for the analysis and visualization of deep mutational scanning data. BMC Bioinformatics 16:168. https://doi.org/10.1186/s12859-015-0590-4.
-
(2015)
BMC Bioinformatics
, vol.16
, pp. 168
-
-
Bloom, JD.1
-
90
-
-
84961289551
-
Orchestrating high-throughput genomic analysis with Bioconductor
-
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oles´ AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M. 2015. Orchestrating high-throughput genomic analysis with Bioconductor. Nat Methods 12:115. https://doi.org/10.1038/nmeth.3252.
-
(2015)
Nat Methods
, vol.12
, pp. 115
-
-
Huber, W1
Carey, VJ2
Gentleman, R3
Anders, S4
Carlson, M5
Carvalho, BS6
Bravo, HC7
Davis, S8
Gatto, L9
Girke, T10
Gottardo, R11
Hahne, F12
Hansen, KD13
Irizarry, RA14
Lawrence, M15
Love, MI16
MacDonald, J17
Obenchain, V18
Oles´, AK19
Pagès, H20
Reyes, A21
Shannon, P22
Smyth, GK23
Tenenbaum, D24
Waldron, L25
Morgan, M.26
more..
-
91
-
-
85031017685
-
Reversed graph embedding resolves complex single-cell trajectories
-
Qiu X, Mao Q, Tang Y, Wang L, Chawla R, Pliner HA, Trapnell C. 2017. Reversed graph embedding resolves complex single-cell trajectories. Nat Methods 14:979. https://doi.org/10.1038/nmeth.4402.
-
(2017)
Nat Methods
, vol.14
, pp. 979
-
-
Qiu, X1
Mao, Q2
Tang, Y3
Wang, L4
Chawla, R5
Pliner, HA6
Trapnell, C.7
-
92
-
-
84900873950
-
The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells
-
Trapnell C, Cacchiarelli D, Grimsby J, Pokharel P, Li S, Morse M, Lennon NJ, Livak KJ, Mikkelsen TS, Rinn JL. 2014. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nat Biotechnol 32:381. https://doi.org/10.1038/nbt.2859.
-
(2014)
Nat Biotechnol
, vol.32
, pp. 381
-
-
Trapnell, C1
Cacchiarelli, D2
Grimsby, J3
Pokharel, P4
Li, S5
Morse, M6
Lennon, NJ7
Livak, KJ8
Mikkelsen, TS9
Rinn, JL.10
-
93
-
-
84922245983
-
Structural insight into cap-snatching and RNA synthesis by influenza polymerase
-
Reich S, Guilligay D, Pflug A, Malet H, Berger I, Crepin T, Hart D, Lunardi T, Nanao M, Ruigrok RW, Cusack S. 2014. Structural insight into cap-snatching and RNA synthesis by influenza polymerase. Nature 516: 361–366. https://doi.org/10.1038/nature14009.
-
(2014)
Nature
, vol.516
, pp. 361-366
-
-
Reich, S1
Guilligay, D2
Pflug, A3
Malet, H4
Berger, I5
Crepin, T6
Hart, D7
Lunardi, T8
Nanao, M9
Ruigrok, RW10
Cusack, S.11
-
94
-
-
85019837743
-
An in vitro fluorescence based study of initiation of RNA synthesis by influenza B polymerase
-
Reich S, Guilligay D, Cusack S. 2017. An in vitro fluorescence based study of initiation of RNA synthesis by influenza B polymerase. Nucleic Acids Res 45:3353–3368. https://doi.org/10.1093/nar/gkx043.
-
(2017)
Nucleic Acids Res
, vol.45
, pp. 3353-3368
-
-
Reich, S1
Guilligay, D2
Cusack, S.3
-
95
-
-
0036720769
-
A single amino acid mutation in the PA subunit of the influenza virus RNA polymerase inhibits endonucleolytic cleavage of capped RNAs
-
Fodor E, Crow M, Mingay LJ, Deng T, Sharps J, Fechter P, Brownlee GG. 2002. A single amino acid mutation in the PA subunit of the influenza virus RNA polymerase inhibits endonucleolytic cleavage of capped RNAs. J Virol 76:8989–9001. https://doi.org/10.1128/JVI.76.18.8989-9001.2002.
-
(2002)
J Virol
, vol.76
, pp. 8989-9001
-
-
Fodor, E1
Crow, M2
Mingay, LJ3
Deng, T4
Sharps, J5
Fechter, P6
Brownlee, GG.7
-
96
-
-
4143153932
-
Model suggesting that replication of influenza virus is regulated by stabilization of replicative intermediates
-
Vreede FT, Jung TE, Brownlee GG. 2004. Model suggesting that replication of influenza virus is regulated by stabilization of replicative intermediates. J Virol 78:9568–9572. https://doi.org/10.1128/JVI.78.17.9568-9572.2004.
-
(2004)
J Virol
, vol.78
, pp. 9568-9572
-
-
Vreede, FT1
Jung, TE2
Brownlee, GG.3
-
97
-
-
85010686232
-
The role of the priming loop in influenza A virus RNA synthesis
-
Velthuis A. t, Robb NC, Kapanidis AN, Fodor E. 2016. The role of the priming loop in influenza A virus RNA synthesis. Nat Microbiol 1:16029. https://doi.org/10.1038/nmicrobiol.2016.29.
-
(2016)
Nat Microbiol
, vol.1
, pp. 16029
-
-
Velthuis, A. t1
Robb, NC2
Kapanidis, AN3
Fodor, E.4
|