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Jean Peccoud, PhD - Publications

Affiliations: 
2006-2015 Virginia Bioinformatics Institute Virginia Polytechnic Institute and State University, Blacksburg, VA, United States 
 2016- Department of Chemical & Biological Engineering Colorado State University, Fort Collins, CO 
Area:
Biomedical Engineering, General Biophysics, Molecular Biology, synthetic biology, bioinformatics
Website:
http://www.peccoud.org
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39 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Gallegos JE, Kar DM, Ray I, Ray I, Peccoud J. Securing the Exchange of Synthetic Genetic Constructs Using Digital Signatures. Acs Synthetic Biology. PMID 32916048 DOI: 10.1021/Acssynbio.0C00401  0.371
2020 Gallegos JE, Rogers MF, Cialek CA, Peccoud J. Rapid, robust plasmid verification by de novo assembly of short sequencing reads. Nucleic Acids Research. PMID 32890398 DOI: 10.1093/Nar/Gkaa727  0.347
2020 Kar DM, Ray I, Gallegos J, Peccoud J, Ray I. Synthesizing DNA molecules with identity-based digital signatures to prevent malicious tampering and enabling source attribution Journal of Computer Security. 28: 437-467. DOI: 10.3233/Jcs-191383  0.303
2018 Adames NR, Gallegos JE, Peccoud J. Yeast genetic interaction screens in the age of CRISPR/Cas. Current Genetics. PMID 30255296 DOI: 10.1007/S00294-018-0887-8  0.339
2018 Murch RS, So WK, Buchholz WG, Raman S, Peccoud J. Cyberbiosecurity: An Emerging New Discipline to Help Safeguard the Bioeconomy. Frontiers in Bioengineering and Biotechnology. 6: 39. PMID 29675411 DOI: 10.3389/Fbioe.2018.00039  0.307
2018 Peccoud J, Gallegos JE, Murch R, Buchholz WG, Raman S. Cyberbiosecurity: From Naive Trust to Risk Awareness. Trends in Biotechnology. 36: 4-7. PMID 29224719 DOI: 10.1016/J.Tibtech.2017.10.012  0.301
2017 Purdy GT, Camelio JA, Ellis KP, Peccoud J. Opportunities to apply manufacturing systems analysis techniques in genetic manufacturing systems Manufacturing Letters. 13: 34-38. DOI: 10.1016/J.Mfglet.2017.06.003  0.322
2016 Peccoud J. : fostering the cyber-biological revolution. Synthetic Biology (Oxford, England). 1: ysw001. PMID 32995500 DOI: 10.1093/Synbio/Ysw001  0.379
2015 Coll A, Wilson ML, Gruden K, Peccoud J. Correction: Rule-Based Design of Plant Expression Vectors Using GenoCAD. Plos One. 10: e0136004. PMID 26270038 DOI: 10.1371/Journal.Pone.0136004  0.317
2015 Coll A, Wilson ML, Gruden K, Peccoud J. Rule-Based Design of Plant Expression Vectors Using GenoCAD. Plos One. 10: e0132502. PMID 26148190 DOI: 10.1371/Journal.Pone.0132502  0.349
2015 Adames NR, Wilson ML, Fang G, Lux MW, Glick BS, Peccoud J. GenoLIB: a database of biological parts derived from a library of common plasmid features. Nucleic Acids Research. 43: 4823-32. PMID 25925571 DOI: 10.1093/Nar/Gkv272  0.714
2014 Ball DA, Lux MW, Adames NR, Peccoud J. Adaptive imaging cytometry to estimate parameters of gene networks models in systems and synthetic biology. Plos One. 9: e107087. PMID 25210731 DOI: 10.1371/Journal.Pone.0107087  0.687
2014 Purcell O, Peccoud J, Lu TK. Rule-based design of synthetic transcription factors in eukaryotes. Acs Synthetic Biology. 3: 737-44. PMID 24933274 DOI: 10.1021/Sb400134K  0.386
2014 Galdzicki M, Clancy KP, Oberortner E, Pocock M, Quinn JY, Rodriguez CA, Roehner N, Wilson ML, Adam L, Anderson JC, Bartley BA, Beal J, Chandran D, Chen J, Densmore D, ... ... Peccoud J, et al. The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology. Nature Biotechnology. 32: 545-50. PMID 24911500 DOI: 10.1038/Nbt.2891  0.724
2014 Wilson ML, Okumoto S, Adam L, Peccoud J. Development of a domain-specific genetic language to design Chlamydomonas reinhardtii expression vectors. Bioinformatics (Oxford, England). 30: 251-7. PMID 24215020 DOI: 10.1093/Bioinformatics/Btt646  0.727
2014 Ball DA, Lux MW, Adames NR, Peccoud J. Adaptive imaging cytometry to estimate parameters of gene networks models in systems and synthetic biology Plos One. 9. DOI: 10.1371/journal.pone.0107087  0.659
2013 Wilson ML, Cai Y, Hanlon R, Taylor S, Chevreux B, Setubal JC, Tyler BM, Peccoud J. Sequence verification of synthetic DNA by assembly of sequencing reads. Nucleic Acids Research. 41: e25. PMID 23042248 DOI: 10.1093/Nar/Gks908  0.329
2012 Peccoud J, Isalan M. The PLOS ONE synthetic biology collection: six years and counting. Plos One. 7: e43231. PMID 22916228 DOI: 10.1371/Journal.Pone.0043231  0.354
2012 Marchand JA, Peccoud J. Building block synthesis using the polymerase chain assembly method. Methods in Molecular Biology (Clifton, N.J.). 852: 3-10. PMID 22328421 DOI: 10.1007/978-1-61779-564-0_1  0.371
2012 Lux MW, Bramlett BW, Ball DA, Peccoud J. Genetic design automation: engineering fantasy or scientific renewal? Trends in Biotechnology. 30: 120-6. PMID 22001068 DOI: 10.1016/J.Tibtech.2011.09.001  0.718
2011 Wilson ML, Hertzberg R, Adam L, Peccoud J. A step-by-step introduction to rule-based design of synthetic genetic constructs using GenoCAD. Methods in Enzymology. 498: 173-88. PMID 21601678 DOI: 10.1016/B978-0-12-385120-8.00008-5  0.742
2011 Adam L, Kozar M, Letort G, Mirat O, Srivastava A, Stewart T, Wilson ML, Peccoud J. Strengths and limitations of the federal guidance on synthetic DNA. Nature Biotechnology. 29: 208-10. PMID 21390018 DOI: 10.1038/Nbt.1802  0.692
2011 Peccoud J, Anderson JC, Chandran D, Densmore D, Galdzicki M, Lux MW, Rodriguez CA, Stan GB, Sauro HM. Essential information for synthetic DNA sequences. Nature Biotechnology. 29: 22; discussion 22-3. PMID 21221092 DOI: 10.1038/Nbt.1753  0.68
2010 Cai Y, Wilson ML, Peccoud J. GenoCAD for iGEM: a grammatical approach to the design of standard-compliant constructs. Nucleic Acids Research. 38: 2637-44. PMID 20167639 DOI: 10.1093/Nar/Gkq086  0.363
2010 Ball DA, Lux MW, Graef RR, Peterson MW, Valenti JD, Dileo J, Peccoud J. Co-design in synthetic biology: a system-level analysis of the development of an environmental sensing device. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 385-96. PMID 19908391  0.693
2010 Ball DA, Moody SE, Peccoud J. Cyto•IQ: An adaptive cytometer for extracting the noisy dynamics of molecular interactions in live cells Progress in Biomedical Optics and Imaging - Proceedings of Spie. 7568. DOI: 10.1117/12.842342  0.315
2009 Cai Y, Lux MW, Adam L, Peccoud J. Modeling structure-function relationships in synthetic DNA sequences using attribute grammars. Plos Computational Biology. 5: e1000529. PMID 19816554 DOI: 10.1371/Journal.Pcbi.1000529  0.741
2009 Czar MJ, Cai Y, Peccoud J. Writing DNA with GenoCAD. Nucleic Acids Research. 37: W40-7. PMID 19429897 DOI: 10.1093/Nar/Gkp361  0.454
2009 Czar MJ, Anderson JC, Bader JS, Peccoud J. Gene synthesis demystified. Trends in Biotechnology. 27: 63-72. PMID 19111926 DOI: 10.1016/J.Tibtech.2008.10.007  0.373
2008 Goler JA, Bramlett BW, Peccoud J. Genetic design: rising above the sequence. Trends in Biotechnology. 26: 538-44. PMID 18687496 DOI: 10.1016/J.Tibtech.2008.06.003  0.425
2008 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. Targeted development of registries of biological parts. Plos One. 3: e2671. PMID 18628824 DOI: 10.1371/Journal.Pone.0002671  0.373
2007 Cai Y, Hartnett B, Gustafsson C, Peccoud J. A syntactic model to design and verify synthetic genetic constructs derived from standard biological parts. Bioinformatics (Oxford, England). 23: 2760-7. PMID 17804435 DOI: 10.1093/Bioinformatics/Btm446  0.404
2004 Peccoud J, Velden KV, Podlich D, Winkler C, Arthur L, Cooper M. The selective values of alleles in a molecular network model are context dependent. Genetics. 166: 1715-25. PMID 15126392 DOI: 10.1534/Genetics.166.4.1715  0.324
1998 Goss PJ, Peccoud J. Quantitative modeling of stochastic systems in molecular biology by using stochastic Petri nets. Proceedings of the National Academy of Sciences of the United States of America. 95: 6750-5. PMID 9618484 DOI: 10.1073/Pnas.95.12.6750  0.31
1990 Dellabona P, Peccoud J, Benoist C, Mathis D. T-cell recognition of superantigens: inside or outside the groove? Cold Spring Harbor Symposia On Quantitative Biology. 375-81. PMID 2639759 DOI: 10.1101/Sqb.1989.054.01.046  0.557
1990 Dellabona P, Peccoud J, Kappler J, Marrack P, Benoist C, Mathis D. Superantigens interact with MHC class II molecules outside of the antigen groove. Cell. 62: 1115-21. PMID 2401011 DOI: 10.1016/0092-8674(90)90388-U  0.581
1990 Peccoud J, Dellabona P, Allen P, Benoist C, Mathis D. Delineation of antigen contact residues on an MHC class II molecule. The Embo Journal. 9: 4215-4223. DOI: 10.1002/J.1460-2075.1990.Tb07869.X  0.578
1990 Warren AP, Paschedag I, Benoist C, Peccoud J, Mathis D, Thomas DB. Defects in antigen presentation of mutant influenza haemagglutinins are reversed by mutations in the MHC class II molecule. The Embo Journal. 9: 3849-3856. DOI: 10.1002/J.1460-2075.1990.Tb07603.X  0.578
1989 Pierres M, Marchetto S, Naquet P, Landais D, Peccoud J, Benoist C, Mathis D. I-A alpha polymorphic residues that determine alloreactive T cell recognition. The Journal of Experimental Medicine. 169: 1655-68. PMID 2469763 DOI: 10.1084/Jem.169.5.1655  0.583
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