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1
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77956338533
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High-resolution mapping of protein sequence–function relationships
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1 Fowler, D.M., Araya, C.L., Fleishman, S.J., Kellogg, E.H., Stephany, J.J., Baker, D., Fields, S., High-resolution mapping of protein sequence–function relationships. Nat Methods 7 (2010), 741–746.
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Fowler, D.M.1
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Baker, D.6
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2
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Experimental illumination of a fitness landscape
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2 Hietpas, R.T., Jensen, J.D., Bolon, D.N.A., Experimental illumination of a fitness landscape. Proc Natl Acad Sci U S A 108 (2011), 7896–7901.
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Hietpas, R.T.1
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3
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84971636054
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Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting
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3 Mavor, D., Barlow, K., Thompson, S., Barad, B.A., Bonny, A.R., Cario, C.L., Gaskins, G., Liu, Z., Deming, L., Axen, S.D., et al. Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting. Elife, 5, 2016, e15802.
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Elife
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Mavor, D.1
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Liu, Z.8
Deming, L.9
Axen, S.D.10
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4
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Deep mutational scanning: a new style of protein science
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4 Fowler, D.M., Fields, S., Deep mutational scanning: a new style of protein science. Nat Methods 11 (2014), 801–807.
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Nat Methods
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Fowler, D.M.1
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Quantifying and understanding the fitness effects of protein mutations: laboratory versus nature
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5 Boucher, J.I., Bolon, D.N.A., Tawfik, D.S., Quantifying and understanding the fitness effects of protein mutations: laboratory versus nature. Protein Sci, 2016, 10.1002/pro.2928.
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Protein Sci
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Boucher, J.I.1
Bolon, D.N.A.2
Tawfik, D.S.3
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6
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84873605796
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High-throughput sequencing of the paired human immunoglobulin heavy and light chain repertoire
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6 Dekosky, B.J., Ippolito, G.C., Deschner, R.P., Lavinder, J.J., Wine, Y., Rawlings, B.M., Varadarajan, N., Giesecke, C., Dörner, T., Andrews, S.F., et al. High-throughput sequencing of the paired human immunoglobulin heavy and light chain repertoire. Nat Biotechnol 31 (2013), 166–169.
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Dekosky, B.J.1
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Varadarajan, N.7
Giesecke, C.8
Dörner, T.9
Andrews, S.F.10
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7
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84941236948
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Facile discovery of a diverse panel of anti-Ebola virus antibodies by immune repertoire mining
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7 Wang, B., Kluwe, C.A., Lungu, O.I., Dekosky, B.J., Kerr, S.A., Johnson, E.L., Tanno, H., Lee, C., Jung, J., Rezigh, A.B., et al. Facile discovery of a diverse panel of anti-Ebola virus antibodies by immune repertoire mining. Sci Rep, 2015, 5.
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Wang, B.1
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Tanno, H.7
Lee, C.8
Jung, J.9
Rezigh, A.B.10
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8
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84976329717
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Discovery of high affinity anti-ricin antibodies by B cell receptor sequencing and by yeast display of combinatorial VH: VL libraries from immunized animals
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8 Wang, B., Lee, C., Johnson, E.L., Kluwe, C.A., Cunningham, C., Tanno, H., Crooks, R.M., Georgiou, G., Ellington, A.D., Wang, B., et al. Discovery of high affinity anti-ricin antibodies by B cell receptor sequencing and by yeast display of combinatorial VH: VL libraries from immunized animals. MAbs, 2016, 10.1080/19420862.2016.1190059.
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MAbs
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Wang, B.1
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Tanno, H.6
Crooks, R.M.7
Georgiou, G.8
Ellington, A.D.9
Wang, B.10
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9
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84943615131
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Deep sequencing in library selection projects: what insight does it bring?
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9 Glanville, J., D'Angelo, S., Khan, T.A., Reddy, S.T., Naranjo, L., Ferrara, F., Bradbury, A.R.M., Deep sequencing in library selection projects: what insight does it bring?. Curr Opin Struct Biol 33 (2015), 146–160.
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Curr Opin Struct Biol
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Glanville, J.1
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Naranjo, L.5
Ferrara, F.6
Bradbury, A.R.M.7
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10
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84877583398
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Comprehensive interrogation of a minimalist synthetic CDR-H3 library and its ability to generate antibodies with therapeutic potential
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10 Mahon, C.M., Lambert, M.A., Glanville, J., Wade, J.M., Fennell, B.J., Krebs, M.R., Armellino, D., Yang, S., Liu, X., O'Sullivan, C.M., et al. Comprehensive interrogation of a minimalist synthetic CDR-H3 library and its ability to generate antibodies with therapeutic potential. J Mol Biol 425 (2013), 1712–1730.
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J Mol Biol
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Mahon, C.M.1
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Krebs, M.R.6
Armellino, D.7
Yang, S.8
Liu, X.9
O'Sullivan, C.M.10
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11
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84946594789
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High-throughput ligand discovery reveals a sitewise gradient of diversity in broadly evolved hydrophilic fibronectin domains
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An innovative use of NGS to design naïve protein binder libraries. NGS was used to uncover site-specific preferences for binders isolated from a fibronectin scaffold library. These preferences were hard-coded into a second, more robust library.
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11• Woldring, D.R., Holec, P.V., Zhou, H., Hackel, B.J., High-throughput ligand discovery reveals a sitewise gradient of diversity in broadly evolved hydrophilic fibronectin domains. PLOS ONE, 10, 2015, e0138956 An innovative use of NGS to design naïve protein binder libraries. NGS was used to uncover site-specific preferences for binders isolated from a fibronectin scaffold library. These preferences were hard-coded into a second, more robust library.
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(2015)
PLOS ONE
, vol.10
, pp. e0138956
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Woldring, D.R.1
Holec, P.V.2
Zhou, H.3
Hackel, B.J.4
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12
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84892615437
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Computational design of a pH-sensitive IgG binding protein
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12 Strauch, E.-M., Fleishman, S.J., Baker, D., Computational design of a pH-sensitive IgG binding protein. Proc Natl Acad Sci U S A 111 (2014), 675–680.
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Proc Natl Acad Sci U S A
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Strauch, E.-M.1
Fleishman, S.J.2
Baker, D.3
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13
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84903142850
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A computationally designed inhibitor of an Epstein-Barr viral Bcl-2 protein induces apoptosis in infected cells
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13 Procko, E., Berguig, G.Y., Shen, B.W., Song, Y., Frayo, S., Convertine, A.J., Margineantu, D., Booth, G., Correia, B.E., Cheng, Y., et al. A computationally designed inhibitor of an Epstein-Barr viral Bcl-2 protein induces apoptosis in infected cells. Cell 157 (2014), 1644–1656.
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Cell
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Procko, E.1
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Convertine, A.J.6
Margineantu, D.7
Booth, G.8
Correia, B.E.9
Cheng, Y.10
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14
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84862025262
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Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing
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14 Whitehead, T.A., Chevalier, A., Song, Y., Dreyfus, C., Fleishman, S.J., De Mattos, C., Myers, C.A., Kamisetty, H., Blair, P., Wilson, I.A., et al. Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing. Nat Biotechnol 30 (2012), 543–548.
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Whitehead, T.A.1
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Myers, C.A.7
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15
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84959485747
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A computationally designed hemagglutinin stem-binding protein provides in vivo protection from influenza independent of a host immune response
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15 Koday, M.T., Nelson, J., Chevalier, A., Koday, M., Kalinoski, H., Stewart, L., Carter, L., Nieusma, T., Lee, P.S., Ward, A.B., et al. A computationally designed hemagglutinin stem-binding protein provides in vivo protection from influenza independent of a host immune response. Plos Pathog, 12, 2016, e1005409.
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Koday, M.T.1
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Carter, L.7
Nieusma, T.8
Lee, P.S.9
Ward, A.B.10
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16
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84880097773
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Deep mutational scanning of an antibody against epidermal growth factor receptor using mammalian cell display and massively parallel pyrosequencing
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16 Forsyth, C.M., Juan, V., Akamatsu, Y., Dubridge, R.B., Doan, M., Ivanov, A.V., Ma, Z., Polakoff, D., Wilson, K., Powers, D.B., et al. Deep mutational scanning of an antibody against epidermal growth factor receptor using mammalian cell display and massively parallel pyrosequencing. MAbs, 2013, 5.
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MAbs
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Forsyth, C.M.1
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Ma, Z.7
Polakoff, D.8
Wilson, K.9
Powers, D.B.10
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17
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84869868746
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Robust in vitro affinity maturation strategy based on interface-focused high-throughput mutational scanning
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17 Fujino, Y., Fujita, R., Wada, K., Fujishige, K., Kanamori, T., Hunt, L., Shimizu, Y., Ueda, T., Robust in vitro affinity maturation strategy based on interface-focused high-throughput mutational scanning. Biochem Biophys Res Commun 428 (2012), 395–400.
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Biochem Biophys Res Commun
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Fujino, Y.1
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Kanamori, T.5
Hunt, L.6
Shimizu, Y.7
Ueda, T.8
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18
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84941333624
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Deep sequencing-guided design of a high affinity dual specificity antibody to target two angiogenic factors in neovascular age-related macular degeneration
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An excellent study combining NGS and structural information to design antibodies with potent affinity to two structurally unrelated conformational epitopes. A Fab with dual specificity for Ang2 and VEGF with high affinity for both was developed using DMS.
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18•• Koenig, P., Lee, C.V., Sanowar, S., Wu, P., Stinson, J., Harris, S.F., Fuh, G., Deep sequencing-guided design of a high affinity dual specificity antibody to target two angiogenic factors in neovascular age-related macular degeneration. J Biol Chem 290 (2015), 21773–21786 An excellent study combining NGS and structural information to design antibodies with potent affinity to two structurally unrelated conformational epitopes. A Fab with dual specificity for Ang2 and VEGF with high affinity for both was developed using DMS.
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(2015)
J Biol Chem
, vol.290
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Koenig, P.1
Lee, C.V.2
Sanowar, S.3
Wu, P.4
Stinson, J.5
Harris, S.F.6
Fuh, G.7
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19
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84962251178
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HIV-1 broadly neutralizing antibody precursor B cells revealed by germline-targeting immunogen
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A germline-targeting immunogen was engineered by exhaustive deep mutational scanning against dozens of germline-reverted and mature broadly neutralizing antibodies to HIV-1. This paper represents the most extensive NGS-aided protein engineering example to date.
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19•• Jardine, J.G., Kulp, D.W., Havenar-Daughton, C., Sarkar, A., Briney, B., Sok, D., Sesterhenn, F., Ereno-Orbea, J., Kalyuzhniy, O., Deresa, I., et al. HIV-1 broadly neutralizing antibody precursor B cells revealed by germline-targeting immunogen. Science 351 (2016), 1458–1463 A germline-targeting immunogen was engineered by exhaustive deep mutational scanning against dozens of germline-reverted and mature broadly neutralizing antibodies to HIV-1. This paper represents the most extensive NGS-aided protein engineering example to date.
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(2016)
Science
, vol.351
, pp. 1458-1463
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Jardine, J.G.1
Kulp, D.W.2
Havenar-Daughton, C.3
Sarkar, A.4
Briney, B.5
Sok, D.6
Sesterhenn, F.7
Ereno-Orbea, J.8
Kalyuzhniy, O.9
Deresa, I.10
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20
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84884166196
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Computational design of ligand-binding proteins with high affinity and selectivity
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20 Tinberg, C.E., Khare, S.D., Dou, J., Doyle, L., Nelson, J.W., Schena, A., Computational design of ligand-binding proteins with high affinity and selectivity. Nature 501 (2013), 212–216.
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Nature
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Tinberg, C.E.1
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Schena, A.6
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21
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84956609810
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Engineering an allosteric transcription factor to respond to new ligands
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21 Taylor, N.D., Garruss, A.S., Moretti, R., Chan, S., Arbing, M.A., Cascio, D., Rogers, J.K., Isaacs, F.J., Kosuri, S., Baker, D., et al. Engineering an allosteric transcription factor to respond to new ligands. Nat Methods 13 (2016), 177–183.
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Nat Methods
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Taylor, N.D.1
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Rogers, J.K.7
Isaacs, F.J.8
Kosuri, S.9
Baker, D.10
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22
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84920773999
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Conformation-dependent epitopes recognized by prion protein antibodies probed using mutational scanning and deep sequencing
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22 Doolan, K.M., Colby, D.W., Conformation-dependent epitopes recognized by prion protein antibodies probed using mutational scanning and deep sequencing. J Mol Biol 427 (2015), 328–340.
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J Mol Biol
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Doolan, K.M.1
Colby, D.W.2
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23
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84924117303
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Precise and efficient antibody epitope determination through library design, yeast display and next-generation sequencing
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23 Van Blarcom, T., Rossi, A., Foletti, D., Sundar, P., Pitts, S., Bee, C., Melton Witt, J., Melton, Z., Hasa-Moreno, A., Shaughnessy, L., et al. Precise and efficient antibody epitope determination through library design, yeast display and next-generation sequencing. J Mol Biol 427 (2015), 1513–1534.
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J Mol Biol
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Van Blarcom, T.1
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Bee, C.6
Melton Witt, J.7
Melton, Z.8
Hasa-Moreno, A.9
Shaughnessy, L.10
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24
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84946098489
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Rapid fine conformational epitope mapping using comprehensive mutagenesis and deep sequencing
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24 Kowalsky, C.A., Faber, M.S., Nath, A., Dann, H.E., Kelly, V.W., Liu, L., Shanker, P., Wagner, E.K., Maynard, J.A., Chan, C., et al. Rapid fine conformational epitope mapping using comprehensive mutagenesis and deep sequencing. J Biol Chem 290 (2015), 26457–26470.
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J Biol Chem
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Kowalsky, C.A.1
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Liu, L.6
Shanker, P.7
Wagner, E.K.8
Maynard, J.A.9
Chan, C.10
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25
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84862546176
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Critical features for biosynthesis, stability, and functionality of a G protein-coupled receptor uncovered by all-versus-all mutations
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An elegant early demonstration of NGS for uncovering the contribution of specific residues to the stability of a bacterial-expressed GPCR.
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25• Schlinkmann, K.M., Honegger, A., Türeci, E., Robison, K.E., Lipovšek, D., Plückthun, A., Critical features for biosynthesis, stability, and functionality of a G protein-coupled receptor uncovered by all-versus-all mutations. Proc Natl Acad Sci U S A 109 (2012), 9810–9815 An elegant early demonstration of NGS for uncovering the contribution of specific residues to the stability of a bacterial-expressed GPCR.
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(2012)
Proc Natl Acad Sci U S A
, vol.109
, pp. 9810-9815
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Schlinkmann, K.M.1
Honegger, A.2
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Robison, K.E.4
Lipovšek, D.5
Plückthun, A.6
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26
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84865068808
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Maximizing detergent stability and functional expression of a GPCR by exhaustive recombination and evolution
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26 Schlinkmann, K.M., Hillenbrand, M., Rittner, A., Künz, M., Strohner, R., Plückthun, A., Maximizing detergent stability and functional expression of a GPCR by exhaustive recombination and evolution. J Mol Biol 422 (2012), 414–428.
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J Mol Biol
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Schlinkmann, K.M.1
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Künz, M.4
Strohner, R.5
Plückthun, A.6
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27
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84893854581
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Structure of signaling-competent neurotensin receptor 1 obtained by directed evolution in Escherichia coli
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27 Egloff, P., Hillenbrand, M., Klenk, C., Batyuk, A., Heine, P., Balada, S., Schlinkmann, K.M., Scott, D.J., Schütz, M., Plückthun, A., Structure of signaling-competent neurotensin receptor 1 obtained by directed evolution in Escherichia coli. Proc Natl Acad Sci U S A 111 (2014), E655–E662.
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Egloff, P.1
Hillenbrand, M.2
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Batyuk, A.4
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Balada, S.6
Schlinkmann, K.M.7
Scott, D.J.8
Schütz, M.9
Plückthun, A.10
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28
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84947968739
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Comprehensive sequence-flux mapping of a levoglucosan utilization pathway in E. coli
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28 Klesmith, J.R., Bacik, J., Michalczyk, R., Whitehead, T.A., Comprehensive sequence-flux mapping of a levoglucosan utilization pathway in E. coli. ACS Synth Biol 4 (2015), 1235–1243.
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ACS Synth Biol
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Klesmith, J.R.1
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29
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84869080668
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Deep sequencing of systematic combinatorial libraries reveals β-lactamase sequence constraints at high resolution
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29 Deng, Z., Huang, W., Bakkalbasi, E., Brown, N.G., Adamski, C.J., Rice, K., Muzny, D., Gibbs, R.A., Palzkill, T., Deep sequencing of systematic combinatorial libraries reveals β-lactamase sequence constraints at high resolution. J Mol Biol 424 (2012), 150–167.
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J Mol Biol
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Deng, Z.1
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Gibbs, R.A.8
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30
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84901408859
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A comprehensive, high-resolution map of a gene's fitness landscape
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30 Firnberg, E., Labonte, J.W., Gray, J.J., Ostermeier, M., A comprehensive, high-resolution map of a gene's fitness landscape. Mol Biol Evol 31 (2014), 1581–1592.
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Mol Biol Evol
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Firnberg, E.1
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31
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84923321398
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Evolvability as a function of purifying selection in TEM-1 β-lactamase
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31 Stiffler, M.A., Hekstra, D.R., Ranganathan, R., Evolvability as a function of purifying selection in TEM-1 β-lactamase. Cell 160 (2015), 882–892.
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Cell
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Stiffler, M.A.1
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32
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84960428419
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Using mutability landscapes of a promiscuous tautomerase to guide the engineering of enantioselective Michaelases
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32 van der Meer, J.-Y., Poddar, H., Baas, B., Miao, Y., Rahimi, M., Kunzendorf, A., Merkerk, R.Van, Tepper, P.G., Geertsema, E.M., Thunnissen, A.W.H., et al. Using mutability landscapes of a promiscuous tautomerase to guide the engineering of enantioselective Michaelases. Nat Commun 7 (2016), 1–16.
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Nat Commun
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van der Meer, J.-Y.1
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Tepper, P.G.8
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Thunnissen, A.W.H.10
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33
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84906217475
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Comprehensive mutational scanning of a kinase in vivo reveals substrate-dependent fitness landscapes
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Innovative study where multiple fitness landscape for an aminoglycoside antibiotic resistance gene were generated with difference substrates at varying concentrations. The group leverage the fact that landcapes can vary dramatically with selection conditions and used differential analysis to generate enzymes with orthogonal substrate specificities.
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33• Melnikov, A., Rogov, P., Wang, L., Gnirke, A., Mikkelsen, T.S., Comprehensive mutational scanning of a kinase in vivo reveals substrate-dependent fitness landscapes. Nucleic Acids Res, 42, 2014, gku511 Innovative study where multiple fitness landscape for an aminoglycoside antibiotic resistance gene were generated with difference substrates at varying concentrations. The group leverage the fact that landcapes can vary dramatically with selection conditions and used differential analysis to generate enzymes with orthogonal substrate specificities.
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Nucleic Acids Res
, vol.42
, pp. gku511
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Melnikov, A.1
Rogov, P.2
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34
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Environmental changes bridge evolutionary valleys
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34 Steinberg, B., Ostermeier, M., Environmental changes bridge evolutionary valleys. Sci Adv, 2, 2016, e1500921.
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Sci Adv
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Steinberg, B.1
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Measuring the activity of protein variants on a large scale using deep mutational scanning
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35 Fowler, D.M., Stephany, J.J., Fields, S., Measuring the activity of protein variants on a large scale using deep mutational scanning. Nat Protoc 9 (2014), 2267–2284.
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