Jean Peccoud Publications: Dynamic Bibliography

Jean Peccoud Publications: Static Bibliography

I try to keep this list current but I suggest look at my Googe Scholar profile for a more current list of publications.

Peer-Reviewed Publications

  1. Dellabona, P., Peccoud, J., Benoist, C., and Mathis, D. (1989). T-cell recognition of superantigens: inside or outside the groove? Cold. Spring. Harb. Symp. Quant. Biol. 54 Pt 1, 375-381.
  2. Pierres, M., Marchetto, S., Naquet, P., Landais, D., Peccoud, J., Benoist, C., and Mathis, D. (1989). I-A alpha polymorphic residues that determine alloreactive T cell recognition. J Exp. Med. 169, 1655-1668.
  3. Reske Kunz, A.B., Landais, D., Peccoud, J., Benoist, C., and Mathis, D. (1989). Functional sites on the A alpha-chain. Polymorphic residues involved in antigen presentation to insulin-specific, Ab alpha:Ak beta-restricted T cells. J Immunol. 143, 1472-1481.
  4. Peccoud, J., Dellabona, P., Allen, P., Benoist, C., and Mathis, D. (1990). Delineation of antigen contact residues on an MHC class II molecule. EMBO J. 9, 4215-4223.
  5. Warren, A.P., Paschedag, I., Benoist, C., Peccoud, J., Mathis, D., and Thomas, D.B. (1990). Defects in antigen presentation of mutant influenza haemagglutinins are reversed by mutations in the MHC class II molecule. EMBO J. 9, 3849-3856.
  6. Dellabona, P., Peccoud, J., Kappler, J., Marrack, P., Benoist, C., and Mathis, D. (1990). Superantigens interact with MHC class II molecules outside of the antigen groove. Cell 62, 1115-1121.
  7. Gervois N, Wei BY, Dellabona P, Peccoud J, Benoist C, and Mathis D (1992) Structure of the TCR-AG-MHC complex NATO Advanced Science Institute Series, Series A, 233, 17-23
  8. Peccoud, J. and Ycart, B. (1995). Markovian modelling of gene products synthesis. Theor. Pop. Biol. 48, 222-234.
  9. Peccoud, J. (1995). Automating molecular biology: A question of communication. Bio/Technology 13, 741-745.
  10. Jacob, C. and Peccoud, J. (1996). Inference on the initial size of a supercritical branching process from partial and migrating observations. C. R. Acad. Sci. Paris Série I 322, 875-880.
  11. Jacob, C. and Peccoud, J. (1996). Estimation of the offspring mean for a supercritical branching process from partial and migrating observations. C. R. Acad. Sci. Paris Série I 322, 736-768.
  12. Peccoud, J. and Jacob, C. (1996). Theoretical uncertainty of measurements using quantitative polymerase chain reaction. Biophys. J 71, 101-108.
  13. Jacob, C., Breton, N., Daegelen, P., and Peccoud, J. (1997). Probability distribution of the chemical states of a closed system and thermodynamic law of mass action from kinetics: The RNA example. J Chem. Phys. 107, 2913-29 19.
  14. Goss, P.J. and Peccoud, J. (1998). Quantitative modeling of stochastic systems in molecular biology using stochastic Petri nets. Proc. Natl. Acad. Sci. U. S. A. 95, 6750-6755
  15. Jacob, C. and Peccoud, J. (1998). Estimation of the parameters of a branching process from migrating binomial observations. Adv. Appl. Prob. 30, 948-967.
  16. Goss, P.J. and Peccoud, J. (1999). Analysis of the stabilizing effect of ROM on the genetic network controlling ColE1 plasmid replication. In Pacific Symposium on Biocomputing ’99. R.B Altam, A.K. Dunker, L. Hunter, T.E. Klein, and K. Lauderdale, eds. (Singapore New Jersey London Hong-Kong: World Scientific), pp. 65-76.
  17. Peccoud,J., Velden,K.V., Podlich,D.W., Winkler,C.R., Arthur,W.L., and Cooper,M. (2004). The Selective Values of Alleles in a Molecular Network Model Are Context Dependent.Genetics 166, 1715-1725.
  18. Peccoud, J. and Vander Velden, K. (2005) Parameterization of a non-linear genotype to phenotype map using molecular network. Pac.Symp.Biocomput. 284-95
  19. Griffith, M.; Courtney,T. ; Peccoud,J. ; Sanders,W.H. (2006) Dynamic partitioning for hybrid simulation of the bistable HIV-1 transactivation network Bioinformatics 22, 2782-2789
  20. Cai Y, Hartnett B, Gustafsson C, Peccoud J. (2007) A syntactic model to design and verify synthetic genetic constructs derived from standard biological parts. Bioinformatics. 23, 2760-7.
  21. Peccoud J, Courtney T, Sanders WH. (2007) Möbius: an integrated discrete-event modeling environment. Bioinformatics. 23, 3412-4
  22. Goler J.A., Bramlett B, Peccoud J (2008) Genetic designing rising above the sequence Trends in Biotechnology 26, 538-44
  23. Peccoud J, Blauvelt MF, Cai Y, Cooper KL, Crasta O, DeLalla EC, Evans C, Folkerts O, Lyons BM, Mane SP, Shelton R, Sweede MA, Waldon SA (2008) Targeted development of registries of biological parts PLoS ONE.;3 (7):e2671.
  24. Czar MJ, Anderson JC, Bader J, Peccoud J (2009) Gene synthesis demystified, Trends in Biotechnology 27, 63-72
  25. Czar M, Cai Y, Peccoud J (2009) Writing DNA with GenoCAD, Nucleic Acids Research 37, W40-47
  26. Cai Y, Lux MW, Adam L, Peccoud J (2009) Modeling structure-function relationships in synthetic DNA sequences using attribute grammars, PLoS Comp Bio 5(10):e1000529
  27. Ball DA, Lux MW, Graef RR, Peterson MW, Valenti JD, Dileo J, Peccoud J (2010) Co-design in synthetic biology, a system-level analysis of the development of an environmental sensing device Pac.Symp.Biocomput. 385-96
  28. Cai Y, Wilson ML, Peccoud J (2010) GenoCAD for iGEM: a grammatical approach to the design of standard-compliant constructs Nucleic Acids Research 38 (8): 2637-2644
  29. Adam L., Kozar M., Letort G., Mirat O., Srivastava A, Stewart T, Wilson ML, Peccoud J (2011) Strengths and limitations of the federal guidance on synthetic DNA Nature Biotechnology 29 (3) : 208-210 doi:10.1038/nbt.1802
  30. Ball DA, Ahn TH, Wang P, Chen KC, Cao Y, Tyson JJ, Peccoud J, Baumann WT (2011) Stochastic Exit from Mitosis in Budding Yeast: Model Predictions and Experimental Observations Cell Cycle 10 (6):999-1009 doi:10.4161/cc.10.6.14966
  31. Ball DA, Marchand J, Poulet M, Baumann WT, Chen KC, Tyson JJ, Peccoud J. (2011) Oscillatory dynamics of cell cycle proteins in single yeast cells analyzed by imaging cytometry. PLoS ONE 6:e26272 doi:10.1371/journal.pone.0026272
  32. Peccoud J, Anderson JC, Chandran D, Densmore D, Galdzicki M, Lux MW, Rodriguez CA, Stan GB, Sauro HM (2011) Essential information for synthetic DNA sequences Nature Biotechnology 28, 22 doi:10.1038/nbt.1753
  33. Lux MW, Bramlett BW, Ball DA, Peccoud J (2012) Genetic Design Automation: engineering fantasy or scientific renewal? Trends in Biotechnology 30:120-126 doi:10.1016/j.tibtech.2011.09.001
  34. Overend C, Yuan L, Peccoud J (2012) The synthetic futures of vesicular stomatitis virus Trends in Biotechnology 30:497-8 doi:10.1016/j.tibtech.2012.06.002
  35. Peccoud J, Isalan M (2012) The PLoS ONE Synthetic Biology Collection: Six Years and Counting PLoS ONE 8:e43231 doi:10.1371/journal.pone.0043231
  36. Wilson ML, Cai Y, Hanlon R, Taylor S, Chevreux B, Setubal JC, Tyler BM, Peccoud J. (2013) Sequence verification of synthetic DNA by assembly of sequencing reads Nucleic Acids Research 41:e25. doi:10.1093/nar/gks908
  37. Ball DA, Adames NR, Reischmann N, Barik D, Franck CT, Tyson JJ, Peccoud J (2013) Measurement and modeling of transcriptional noise in the cell cycle regulatory network Cell Cycle 12 (19), 3203 – 3218 doi:10.4161/cc.26257
  38. ML Wilson, S Okumoto, L Adam, J Peccoud (2014) Development of a domain-specific genetic language to design Chlamydomonas reinhardtii expression vectors Bioinformatics 30 (2) 251-257 doi:10.1093/bioinformatics/btt646
  39. O Purcell, J Peccoud, TK Lu (2014) Rule-based design of synthetic transcription factors in eukaryotes ACS Synthetic Biology 3 (10) 737–744 doi:10.1021/sb400134k
  40. Peccoud J (2014) If you cannot measure it, you cannot manage it PLoS Computational Biology 10 (3): e1003462 doi:10.1371/journal.pcbi.1003462
  41. Michal Galdzicki, Mandy Wilson, Cesar Rodriguez, Ernst Oberortner, Matthew Pocock, Laura Adam, J. Christopher Anderson, Bryan Bartley, Jacob Beal, Deepak Chandran, Joanna Chen, Douglas Densmore, Drew Endy, Raik Gruenberg, Jennifer Hallinan, Nathan Hillson, Cassie Huang, Jeffrey Johnson, Allan Kuchinsky, Matthew Lux, Goksel Misirli, Chris Myers, Jean Peccoud, Hector Plahar, Nicholas Roehner, Evren Sirin, Guy-Bart Stan, Alan Villalobos, Anil Wipat, John H. Gennari, and Herbert M. Sauro (2014) SBOL: A community standard for communicating designs in synthetic biology Nature Biotechnology 32 (6):545-50. doi:10.1038/nbt.2891
  42. Ball DA, Lux MW, Adames NR, Peccoud J (2014) Adaptive Imaging Cytometry to Estimate Parameters of Gene Networks Models in Systems and Synthetic Biology PloS ONE 9 (9), e107087 doi:10.1371/journal.pone.0107087
  43. Adames NR. Wilson ML, Fang G, Lux MW, Glick BS, Peccoud J (2015) GenoLIB: a database of biological parts derived from a library of common plasmid features Nucleic Acids Research 43 (10) 4823–4832 doi:10.1093/nar/gkv272
  44. Coll  A, Wilson ML, Gruden K, Peccoud J (2015) Rule-Based Design of Plant Expression Vectors Using GenoCAD PLoS ONE 10 (7): e0132502. doi:10.1371/journal.pone.0132502
  45. Adames NR, Schuck PL, Chen KC, Murali TM, Tyson JJ, Peccoud J. (2015) Experimental testing of a new integrated model of the budding yeast START transition. Mol Biol Cell. 26 (22)3966-3984. doi:10.1091/mbc.E15-06-0358
  46. Peccoud J (2016) Synthetic biology: fostering the cyber-biological revolution. Synthetic Biology 1 (1) ysw001 doi:10.1093/synbio/ysw001
  47. Barik D, Ball DA, Peccoud J, Tyson JJ (2016) A Stochastic Model of the Yeast Cell Cycle Reveals Roles for Feedback Regulation in Limiting Cellular Variability PLoS Comp. Bio. 12 (12): e1005230. doi:10.1371/journal.pcbi.1005230
  48. Bharadwaj A, Singh DP, Ritz A, Tegge AN, Poirel CL, Kraikivski P, Adames N, Luther K, Kale SD, Peccoud J, Tyson JJ, Murali TM (2017) GraphSpace: stimulating interdisciplinary collaborations in network biology. Bioinformatics In press doi:10.1093/bioinformatics/btx382
  49. Purdy GT, Camelio JA, Ellis KP, Peccoud J (2017) Opportunities to apply manufacturing systems analysis techniques in genetic manufacturing systems Manufacturing Letters 13, 34-38 doi:10.1016/j.mfglet.2017.06.003 
  50. Peccoud J, Gallegos JE, Murch R, Buchholtz W, Raman S (2018) Cyberbiosecurity: from naïve trust to risk awareness Trends in Biotechnology 36(1):4-7 doi:10.1016/j.tibtech.2017.10.012
  51. Pratapa A, Adames A, Kraikivski P, Franzese N, Tyson JJ, Peccoud J, Murali TM (2018) CrossPlan: Systematic planning of genetic crosses to validate mathematical models Bioinformatics (in press) doi:10.1093/bioinformatics/bty072
  52. Murch RS, So KL, Raman S, Buchholz WG , Peccoud J (2018) Cyberbiosecurity: An Emerging New Discipline to Help Safeguard the Bioeconomy Frontiers in Bioengineering and Biotechnology 6:39 doi:10.3389/fbioe.2018.00039

Other Publications

  1. Peccoud, J. (1993). Quantitative PCR – A New Tool for Clinical Investigations. MS-Med. Sci. 9, 1378-1385.
  2. Peccoud, J. (1994). Valeur heuristique de la modélisation en biologie. MS-Med. Sci. 10, 606.
  3. Peccoud, J. and Viville, S. (1994). Aspects aléatoires de la dynamique de la differenciation cellulaire. MS-Med. Sci. 10, 877-883.
  4. Peccoud, J. (1995). Intricate loops: a pragmatic approach. Bioessays 17, 183.
  5. Peccoud, J. and Damour, D. (1997) MathLink for LabVIEW: a new environment to control and interact with instruments; application to robotics in Innovations in mathematics(Keranen V and Mitic P eds) pp.391-399.
  6. Peccoud, J. and Jacob, C. (1998). Statistical estimation of PCR amplification rates. In Gene Quantification. F. Ferré, ed. (New-York: Birkhauser), pp. 111-128.
  7. Peccoud, J. (1998). Stochastic Petri nets for genetic networks. M S-Medecine Sciences 14, 991-993.
  8. Vander Velden, K. and Peccoud, J. Modeling networks of molecular interactions in the living cell: structure, dynamics, and applications. Sanders, W. H. and Ciardo, G. eds 10, 2-10. 2003. Los Alamitos, CA, IEEE Computer Society. International Workshop on Petri Nets and Performance Models.
  9. Peccoud, J and Coulombel, L (2007) A competition of synthetic biology or how to create the “water of E. coli” and nano-barbiesM S-Medecine Sciences 23, 551-2
  10. Ball, D.A., Moody, S.E., Peccoud, J. (2010) “Cyto•IQ: an adaptive cytometer for extracting the noisy dynamics of molecular interactions in live cells.” Imaging, Manipulation, and Analysis of Biomolecules, Cells, and Tissues VIII, SPIE BiOS: Biomedical Optics, January 23-28, 2010, San Francisco, CA.
  11. Lux, M.W., Ball, D.A., Graef, R.R., Peterson, M.W., Valenti, J.D., Dileo,J., Peccoud, J. (2010) Co-design in synthetic biology, Proceedings of the 27th Army Science Conference, November 29-December 2 2010, Orlando, FL
  12. Wilson ML, Hertzberg R, Adam L, Peccoud J. (2011) A step-by-step introduction to rule-based design of synthetic genetic constructs using GenoCAD. Methods in Enzymology 498:173-88
  13. Marchand JA, Peccoud J (2012) Building block synthesis using the polymerase chain assembly method, Methods in Molecular Biology 852:3:10
  14. Gene synthesis: methods and protocols (2012) Methods in Molecular Biology Vol 852 Humana Press Peccoud J Ed.
  15. Coll A, Wilson ML, Gruden K, Peccoud J (2016) GenoCAD Plant Grammar to Design Plant Expression Vectors for Promoter Analysis. Methods in Molecular Biology 1482:219-232 
  16. Gallegos JE, Peccoud J (2017) DNA has gone digital – what could possibly go wrong? The Conversation