Publications

2017

Obexer R, Godina A, Garrabou X, Mittl PR, Baker D, Griffiths AD, Hilvert D.Emergence of a catalytic tetrad during evolution of a highly active artificial aldolase. Nat Chem, 9(1) 50-56

Beneyton T, Thomas S, Griffiths AD, Nicaud JM, Drevelle A, Rossignol T. Droplet-based microfluidic high-throughput screening of heterologous enzymes secreted by the yeast Yarrowia lipolytica. Microb Cell Fact, 16(1)18

2016

Matsumura S, Kun Á, Ryckelynck M, Coldren F, Szilágyi A, Jossinet F, Rick C, Nghe P, Szathmáry E, Griffiths AD. Transient compartmentalization maintains catalytically active RNA replicators and prevents functional collapse due to parasites. Science 354 (6317), 1293-1296

Obexer R, Pott M, Zeymer C, Griffiths AD, Hilvert D. Efficient laboratory evolution of computationally designed enzymes with low starting activities using fluorescence-activated droplet sorting. Protein Eng Des Sel, 29(9), 355-66

Beneyton T, Wijaya IP, Postros P, Najah M, Leblond P, Couvent A, Mayot E,Griffiths AD, Drevelle A. High-throughput screening of filamentous fungi using nanoliter-range droplet-based microfluidics. Sci Rep, 6

Cottinet D, Condamine F, Bremond N, Griffiths AD, Rainey PB, de Visser JA, Baudry J, Bibette J. Lineage Tracking for Probing Heritable Phenotypes at Single-Cell Resolution. PLoS One, 11(4):e0152395

Walker N, Nghe P, Tans SJ, Generation and filtering of gene expression noise by the bacterial cell cycle. BMC biology, 14(1), 1, 2016

Kennard AS, Osella M, Javer A, Grilli J, Nghe P, Tans, SJ, Lagomarsino MC. Individuality and universality in the growth-division laws of single E. coli cells. Physical Review E 93 (1), 012408

2015

Nghe P, Hordijk W, Kauffman SA, Walker SI, Schmidt FJ, Kemble H, Yeates JAM and Lehman N. Prebiotic network evolution : six key parameters. Mol. BioSyst., 2015,11, 3206-3217

Woronoff G, Ryckelynck M, Wessel J, Schicke O, Griffiths AD, Soumillion P. Activity-Fed Translation (AFT) Assay : A New High-Throughput Screening Strategy for Enzymes in Droplets. Chembiochem, 16(9), 1343-9

Ryckelynck M, Baudrey S, Rick C, Marin A, Coldren F, Westhof E, Griffiths AD. Using droplet-based microfluidics to improve the catalytic properties of RNA under multiple-turnover conditions. RNA, 21(3), 458-69

2014

Najah M, Calbrix R, Mahendra-Wijaya IP, Beneyton T, Griffiths AD, Drevelle A. Droplet-based microfluidics platform for ultra-high-throughput bioprospecting of cellulolytic microorganisms. Chem Biol, 21(12), 1722-32

Leman M, Abouakil F, Griffiths AD, Tabeling P. Droplet-based microfluidics at the femtolitre scale. Lab Chip, 15(3), 753-65

Beneyton T, Coldren F, Baret JC, Griffiths AD, Taly V (2014). CotA laccase : high-throughput manipulation and analysis of recombinant enzyme libraries expressed in E. coli using droplet-based microfluidics. Analyst. 2014 Apr 15

Fallah-Araghi A, Meguellati K, Baret JC, El Harrak A, Mangeat T, Karplus M, Ladame S, Marques CM, Griffiths AD (2014). Enhanced chemical synthesis at soft interfaces : a universal reaction-adsorption mechanism in microcompartments. Phys Rev Lett. 2014 Jan 17 ;112(2):028301

2013

Meguellati K, Fallah-Araghi A, Baret JC, El Harrak A, Mangeat T, Marques CM, Griffiths AD, Ladame S . Enhanced imine synthesis in water : from surfactant-mediated catalysis to host-guest mechanisms. Chem Commun (Camb). 2013 Dec 14 ;49(96):11332-4

Najah M, Mayot E, Mahendra-Wijaya IP, Griffiths AD, Ladame S, Drevelle A. New glycosidase substrates for droplet-based microfluidic screening. Anal Chem. 2013 Oct 15 ;85(20):9807-14

Taly V, Pekin D, Benhaim L, Kotsopoulos SK, Le Corre D, Li X, Atochin I, Link DR, Griffiths AD, Pallier K, Blons H, Bouché O, Landi B, Hutchison JB, Laurent-Puig P (2013). Multiplex picodroplet digital PCR to detect KRAS mutations in circulating DNA from the plasma of colorectal cancer patients. Clin Chem. 2013 Dec ;59(12):1722-31

L. Mazutis, J. Gilbert, W.L. Ung, D.A. Weitz, A.D. Griffiths, J.A. Heyman (2013). Single-cell analysis and sorting using droplet-based microfluidics Nat Protoc., 8, 870-91

T. Beneyton , I Putu Mahendra Wijaya , C. Ben Salem , A. D. Griffiths and V. Taly (2013). Membraneless glucose/O2 microfluidic biofuel cells using covalently bound enzymes
Chem. Commun., 49, 1094-1096

2012

O.J. Miller, A.E. Harrak, T. Mangeat, J.-C. Baret, L. Frenz, B. El Debs, E. Mayot, M.L. Samuels, E.K. Rooney, P. Dieu, M. Galvan, D.R. Link and A.D. Griffiths (2012). High-resolution dose-response screening using droplet-based microfluidics. Proc. Natl. Acad. Sci. USA, 109, 378–383.

A. Fallah-Araghi, J.-C. Baret, M. Ryckelynck, and A.D. Griffiths (2012). A completely in vitro ultrahigh-throughput droplet-based microfluidic screening system for protein engineering and directed evolution. Lab. Chip. 12, 882–891.

A.B. Theberge, E. Mayot, A. El-Harrak, F. Kleinschmidt, W.T.S. Huck and A.D. Griffiths (2012). Microfluidic platform for combinatorial synthesis in picolitre droplets. Lab Chip, 12, 1320–1326.

M. Najah, A.D. Griffiths and M. Ryckelynck (2012). Teaching Single-Cell Digital Analysis Using Droplet-Based Microfluidics. Anal. Chem., 84, 1202–1209.

L. Mazutis, and A.D. Griffiths (2012). Selective droplet coalescence using microfluidic systems. Lab Chip. 2012, 12, 1800-1806.

B. El Debs, R. Utharala, I.V. Balyasnikova, A.D. Griffiths and C.A. Merten (2012). Functional single-cell hybridoma screening using droplet-based microfluidics. Proc. Natl. Acad. Sci. USA, 109, 11570-11575.

Y. Skhiri, P. Gruner, B. Semin, Q. Brosseau, D. Pekin, L. Mazutis, V. Goust, F. Kleinschmidt, A. El Harrak, J.B. Hutchison, E. Mayot, J.-F. Bartolo, A.D. Griffiths, V. Taly and J.-C. Baret (2012). Dynamics of molecular transport by surfactants in emulsions. Soft Matter, 8, 10618–10627.

2011

T. Beneyton, A. El Harrak, A.D. Griffiths, P. Hellwig and V. Taly (2011). Immobilisation of CotA, an extremophilic laccase from Bacillus subtilis, on glassy carbon electrodes for biofuel cell applications. Electrochem. Comm., 13, 24-27.

L. Briseno-Roa, C.M. Timperley, A.D. Griffiths, A.R. Fersht (2011). Phosphotriesterase variants with high methylphosphonatase activity and strong negative trade-off against phosphotriesters. Protein Eng. Des. Sel. 24, 151-159.

L. Briseno-Roa, Z. Oliynyk, C.M. Timperley, A.D. Griffiths, A.R Fersht (2011). Highest paraoxonase turnover rate found in a bacterial phosphotriesterase variant. Protein Eng. Des. Sel. 24, 209-211.

G.Woronoff, A. El Harrak, E. Mayot, O. Schicke, O.J. Miller, P. Soumillion, A.D. Griffiths, M. Ryckelynck (2011). New generation of amino coumarin methyl sulfonate-based fluorogenic substrates for amidase assays in droplet-based microfluidic applications. Anal. Chem. 83, 2852-2857.

D. Pekin, Y. Skhiri, J.-C. Baret, D. Le Corre, L. Mazutis, C. Ben Salem, F. Millot, A. El Harrak, J.B. Hutchison, J.W. Larson, D.R. Link, P. Laurent-Puig, A.D. Griffiths and V. Taly (2011).
Quantitative and sensitive detection of rare mutations using droplet microfluidics. Lab. Chip. 11, 2156-2166.

Q. Zhong, S. Bhattacharya, S. Kotsopoulos, J. Olsen, V. Taly, A.D. Griffiths, D.R. Link and J.W. Larson (2011). Multiplex digital PCR : breaking the one target per color barrier of quantitative PCR. Lab. Chip. 11, 2167-2174.

T. Beneyton, Y. Beyl, D.A. Guschin, A.D. Griffiths, V. Taly and W. Schuhmann (2011). The thermophilic CotA laccase from Bacillus subtilis : bioelectrocatalytic evaluation of O2 reduction in the direct and mediated electron transfer regime. Electroanal. 23, 1781-1789.

B.W. El Debs, U. Tschulena, A.D. Griffiths and C.A. Merten (2011). A competitive co-cultivation assay for cancer drug specificity evaluation. J. Biomol. Screen. 16, 818-824.

2010

J.J. Agresti, E. Antipov, A.R. Abate, K. Ahn, A.C. Rowat, J.-C. Baret, M. Marquez, A.M. Klibanov, A.D. Griffiths, David A. Weitz (2010). Ultra-high-throughput screening in drop-based microfluidics for directed evolution of peroxidases. Proc. Natl. Acad. Sci. USA, 107, 4004-4009.

L. Granieri, J.-C. Baret, A.D. Griffiths and C.A Merten (2010). High-throughput screening of enzymes by retroviral display using droplet-based microfluidics. Chem. Biol. 17, 229-235.

J. Clausell-Tormos, A.D. Griffiths and C.A. Merten (2010). An automated two-phase microfluidic system for kinetic analyses and the screening of compound libraries. Lab Chip, 10, 1302-1307.

J. Clausell-Tormos, A.D. Griffiths and C.A. Merten (2010). Coupling the Inhibition of Viral Transduction with a Positive Fluorescence Signal. Comb. Chem. High Throughput Screen., 13, 352-357.

J.-C. Baret, Y. Beck, I. Billas-Massobrio, D. Moras and A.D. Griffiths (2010). Quantitative cell-based reporter gene assays using droplet-based microfluidics. Chem. Biol., 17, 528–536.

2009

L. Frenz, K. Blank, E. Brouzes and A.D. Griffiths. (2009). Reliable microfluidic on-chip incubation of droplets in delay-lines. Lab Chip, 9, 1344-1348.

J.-C. Baret, F. Kleinschmidt, A. El Harrak and A.D. Griffiths (2009). Kinetic aspects of emulsion stabilization by surfactants : a microfluidic analysis. Langmuir, 25, 6088–6093.

L. Granieri, O. Miller, A. Griffiths, C. Merten (2009). A competition-based assay for the screening of species-specific antibiotics. J Antimicrob Chemother, 64, 62–68.

L. Mazutis, A. Fallah Araghi, O.J. Miller, J.-C. Baret, L. Frenz, A. Janoshazi, V. Taly, B.J. Miller, J. B. Hutchison, D. Link, A.D. Griffiths and M. Ryckelynck (2009). Droplet-Based Microfluidic Systems for High-Throughput Single DNA Molecule Isothermal Amplification. Anal Chem, 81, 4813-21.

J.-C. Baret, O.J. Miller, V. Taly, M. Ryckelynck, A. El-Harrak, L. Frenz, C. Rick, M.L. Samuels, J. B. Hutchison, J.J. Agresti, D.R. Link, D.A. Weitz and A.D. Griffiths (2009). Flourescence-activated droplet sorting (FADS) : efficient microfluidic cell sorting based on enzymatic activity. Lab Chip, 9, 1850-1858.

L. Mazutis, J.-C. Baret and A.D. Griffiths (2009). A fast and efficient microfluidic system for highly selective one-to-one droplet fusion. Lab Chip, 9, 2665-2672.

L. Mazutis, J.-C. Baret, P. Treacy, Y. Skhiri, A. Fallah Araghi, M. Ryckelynck, V. Taly and A.D. Griffiths (2009). Multi-step microfluidic droplet processing : kinetic analysis of an in vitro translated enzyme. Lab Chip, 9, 2902-8.

L. Mazutis and A.D. Griffiths (2009). Preparation of monodisperse emulsions by hydrodynamic size fractionation. Appl. Phys. Lett. 95, 204103.

2008

J. Clausell-Tormos, D. Lieber, J.-C. Baret, A. El-Harrak, O.J. Miller, L. Frenz, J. Blouwolff, K.J. Humphry, S. Köster, H. Duan, C. Holtze, D.A. Weitz, A.D. Griffiths and C.A. Merten. (2008) ; Droplet-based microfluidic platforms for the encapsulation and screening of mammalian cells and multicellular organisms. Chemistry and Biology, 15, 427-437.

S. Köster, F.E. Angilè, H. Duan, J.J. Agresti, A. Wintner, C. Schmitz, A.C. Rowat, C.A. Merten, D. Pisignano, A.D. Griffiths and D.A. Weitz. (2008). Drop-based microfluidic devices for encapsulation of single cells. Lab Chip, 8, 1110-1115.

L. Frenz, A. El Harrak, M. Pauly, S. Bégin-Colin, A.D. Griffiths and J.-C. Baret. (2008). Droplet-based microreactors for the synthesis of magnetic iron oxide nanoparticles. Angewandte Chimie Int. Ed., 47, 6817-6820.

L. Frenz, J. Blouwolff, A.D. Griffiths and J.-C. Baret (2008). Microfluidic Production of Droplet Pairs. Langmuir, 24, 12073-12076.

2005-2007

B.T. Kelly and A.D. Griffiths. (2007). Selective gene amplification. Protein Engineering Design and Selection, 20, 577-581.

O.J. Miller, K. Bernath, J.J. Agresti G. Amitai, B.T. Kelly, E. Mastrobattista, V. Taly, S. Magdassi, D.S. Tawfik and A.D. Griffiths. (2006). Directed evolution by in vitro compartmentalization. Nature Methods, 3, 561-570.

R. Williams, S.G. Peisajovich, O.J. Miller, S. Magdassi, D.S. Tawfik and A.D. Griffiths. (2006). Amplification of complex gene libraries by emulsion PCR. Nature Methods, 3, 545-550.

L. Briseno-Roa, J. Hill, S. Notman, D. Sellers, A.P. Smith, C.M. Timperley, J. Wetherell, N.H. Williams, G.R. Williams, A.R. Fersht, and A.D. Griffiths. (2006). Analogues with fluorescent leaving groups for screening and selection of enzymes that efficiently hydrolyze organophosphorus nerve agents. J. Med. Chem. 49, 246-255.

H.M. Cohen, A.D. Griffiths, D.S. Tawfik and D. Loakes. (2005). Determinants of cofactor binding to DNA methyltransferases : insights from a systematic series of structural variants of S-adenosylhomocysteine. Org. Biomol. Chem., 3, 152–161.

J.J. Agresti, B.T. Kelly, A. Jäschke and A.D. Griffiths. (2005). Selection of ribozymes that catalyze multiple-turnover Diels-Alder cycloadditions by using in vitro compartmentalization. Proc. Natl. Acad. Sci. USA 102, 16170-16175.

E. Mastrobattista, V. Taly, E. Chanudet, P. Treacy, B.T. Kelly and A.D. Griffiths. (2005). High-throughput screening of enzyme libraries : in vitro evolution of a -galactosidase by fluorescence-activated sorting of double emulsions. Chem. Biol. 12, 1291-1300.

2000-2004

K. Bernath, M. Hai, E. Mastrobattista, A.D. Griffiths, S. Magdassi & D. Tawfik. (2004). In vitro compartmentalisation by double emulsions : sorting and gene enrichment by fluorescence activated cell sorting. Analytical Biochemistry, 325 : 151-157.

H.M. Cohen, D.S. Tawfik & A.D. Griffiths. (2004). Altering the sequence specificity of HaeIII methyltransferase by directed evolution using in vitro compartmentalisation. Protein Engineering Design and Selection, 17, 3-11.

A.D. Griffiths and D.S. Tawfik. (2003). Directed evolution of an extremely fast phosphotriesterase by in vitro compartmentalisation. EMBO J. 22 : 24-35.

A. Sepp, D.S. Tawfik and A.D. Griffiths. (2002). Microbead display by in vitro compartmentalisation : selection for binding using flow cytometry. FEBS Letters 532 : 455-458.

Y.-F. Lee, D.S. Tawfik and A.D. Griffiths. (2002). Investigating the target recognition of DNA cytosine-5 methyltransferase HhaI by library selelction using in vitro compartmentalisation. Nucleic Acids Res. 30, 4937-4944.

H.M. Cohen, D.S. Tawfik and A.D. Griffiths. (2002). Promiscuous methylation of non-canonical DNA sites by HaeIII methyltransferase. Nucleic Acids Res. 30, 3880-3885.

Before 2000

J. Chatellier, O. Hartley, A.D. Griffiths, A.R. Fersht, G. Winter and L. Riechmann. (1999). Interdomain interactions within the gene 3 protein of filamentous phage. FEBS Letters 463 : 371-374.

D.S. Tawfik and A.D. Griffiths. (1998). Man-made cell-like compartments for molecular evolution. Nature Biotechnol. 16 : 652-656.

G.P. Smith, S.U. Patel, J.D. Windass, J.M. Thornton, G. Winter and A.D. Griffiths. (1998). Small binding proteins selected from a combinatorial repertoire of knottins displayed on phage. J. Mol. Biol. 277, 317-332.

M. Figini, L. Obici, D. Mezzanzanica, A. Griffiths, M.I. Colnaghi, G. Winter and S. Canevari. (1998). Panning phage antibody libraries on cells : isolation of human Fab fragments against ovarian carcinoma using guided selection. Cancer Res. 58, 991-996.

M. Zaccolo, A.D. Griffiths, T.D. Prospero, G. Winter and E. Gherardi. (1997). Dimerization of Fab fragments enables ready screening of phage antibodies that affect hepatocyte growth factor/scatter factor activity on target cells. Eur. J. Immunol. 27, 618-623.

I. Fisch, R.E. Kontermann, R. Finnern, O. Hartley, A. S. Soler-Gonzalez, A.D. Griffiths and G. Winter. (1996). A strategy of exon shuffling for making large peptide repertoires displayed on filamentous bacteriophage. Proc. Natl. Acad. Sci. USA 93, 7761-7766.

J. Fan, A.D. Griffiths, A. Lockhart, R.A. Cross and L.A. Amos. (1996). Microtubule minus ends can be labelled with a phage display antibody specific to alpha-tubulin. J. Mol. Biol. 259 : 325-330.

R.M.T. de Wildt, R. Finnern, W.H. Ouwehand, A.D. Griffiths, W.J. van Venrooij, R.M.A. Hoet. (1996). Characterization of human variable domain antibody fragments against the U1 RNA-associated A-protein, selected from a synthetic and a patient-derived combinatorial V-gene library. Eur. J. Immunol. 26, 629-639.

M. Zaccolo, T.D. Prospero, A. Griffiths, G. Winter and E. Gherardi. (1995). Phage antibodies against HGF/SF and other kringle containing proteins. In Perspectives in Protein Engineering and Complementary Technologies. Ed. M.J. Geisow and R. Epton pp. 170-171. Mayflower Worldwide, Birmingham.

A.D. Griffiths, S.C. Williams, O. Hartley, I.M. Tomlinson, P. Waterhouse, W.L. Crosby, R.E. Kontermann, P.T. Jones, N.M. Low, T.J. Allison, T.D. Prospero, H.R. Hoogenboom, A. Nissim, J.P.L. Cox, J.L. Harrison, M. Zaccolo, E. Gherardi and G. Winter. (1994). Isolation of high affinity human antibodies directly from large synthetic repertoires. EMBO J., 13 : 3245-3260.

M. Figini, J.D. Marks, G. Winter and A.D. Griffiths. (1994). In vitro assembly of repertoires of antibody chains on the surface of phage by renaturation. J. Mol. Biol. 239 : 68-78.

P. Waterhouse, A.D. Griffiths, K.S. Johnson and G. Winter. (1993). Combinatorial infection and in vivo recombination : a strategy for making large antibody repertoires. Nucl. Acids Res. 21 : 2265-2266.

A.D. Griffiths, M. Malmqvist, J.D. Marks, J.M. Bye, M.J. Embleton, J. McCafferty, M. Baier, K.P. Holliger, B.D. Gorick, N.C. Hughes-Jones, H.R. Hoogenboom and G. Winter. (1993). Human anti-self antibodies with high specificities from phage display libraries. EMBO J. 12 : 725-734.

J.D. Marks, A.D. Griffiths, M. Malmqvist, T.P. Clackson, J.M. Bye and G. Winter. (1992). By-passing immunization : building high affinity human antibodies by chain shuffling. Bio/technology 10 : 779-783.

J.D. Marks, H.R. Hoogenboom, T.P. Bonnert, J. McCafferty, A.D. Griffiths and G. Winter. (1991). Human antibodies from V-gene libraries displayed on phage. J. Mol. Biol. 222 : 581-597.

H.R. Hoogenboom, A.D. Griffiths, K.S. Johnson, D.J. Chiswell, P. Hudson and Greg Winter. (1991). Multi-subunit proteins on the surface of filamentous phage : methodologies for displaying antibody (Fab) heavy and light chains. Nucl. Acids Res. 19 : 4133-4137.

T. Clackson, H.R. Hoogenboom, A.D. Griffiths and G. Winter. (1991). Making antibody fragments using phage display libraries. Nature 352 : 624-628.

J. McCafferty, A.D. Griffiths, G. Winter and D.J. Chiswell. (1990). Phage antibodies : filamentous phage displaying antibody variable domains. Nature 348 : 552-554.

E.S. Ward, D. Güssow, A.D. Griffiths, P.T. Jones and G. Winter. (1989). Binding activities of a repertoire of single immunoglobulin variable domains secreted from Escherichia coli. Nature 341 : 544-546.

L.P. Eperon, I.R. Graham, A.D. Griffiths and I.C. Eperon. (1988). Effects of RNA secondary structure on alternative splicing of pre-mRNA : is folding limited to a region behind the transcribing RNA polymerase ? Cell 54 : 393-401.

A.D. Griffiths, B.V.L. Potter and I.C. Eperon. (1988). Substitution of pre-mRNA with phosphorothioate linkages reveals a new splicing-related reaction. Journal of Biological Chemistry 263 : 12295-12304.

A.D. Griffiths, B.V.L. Potter and I.C. Eperon. (1987). Stereospecificity of nucleases towards phosphorothioate-substituted RNA : stereochemistry of transcription by T7 RNA polymerase. Nucleic Acids Res. 15 : 4145-4162.

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