Daniel Gibson, PhD

Professor

Daniel Gibson is an Professor in the Synthetic Biology group at the JCVI. Since joining the JCVI as a postdoc in 2004, Gibson led the JCVI efforts to synthesize two complete bacterial genomes. Those projects resulted in creation of the first synthetic bacterial cell and development of an enabling suite of DNA synthesis and assembly methods.

Prior to joining the JCVI, Gibson earned his PhD in Molecular Biology from the University of Southern California. While there, he used yeast as the model system for studying cell cycle surveillance mechanisms (checkpoints), which are significant in our understanding of cancer development. Before earning his Ph.D., he earned his Bachelor's degree in Biological Sciences from the State University of New York at Buffalo.

Publications

Ding L, Macdonald HD, Smith HO, Hutchison Iii CA, Merryman C, Michael TP, Abramson BW, Kannan K, Liang J, Gill J, Gibson DG, Glass JI
Gross Chromosomal Rearrangements in Kluyveromyces marxianus Revealed by Illumina and Oxford Nanopore Sequencing.
International journal of molecular sciences. 2020-09-26; 21.19:
PMID: 32993167
Karas BJ, Moreau N, Deernick TJ, Gibson DG, Venter JC, Smith H, Glass J
Direct transfer of a Mycoplasma mycoides genome to yeast is enhanced by removal of the mycoides glycerol uptake factor gene glpF.
ACS synthetic biology. 2019-01-15;
PMID: 30645947
Kannan K, Tsvetanova B, Chuang RY, Noskov VN, Assad-Garcia N, Ma L, Hutchison Iii CA, Smith HO, Glass JI, Merryman C, Venter JC, Gibson DG
One step engineering of the small-subunit ribosomal RNA using CRISPR/Cas9.
Scientific reports. 2016-08-04; 6.30714.
PMID: 27489041
Hutchison CA, Chuang RY, Noskov VN, Assad-Garcia N, Deerinck TJ, Ellisman MH, Gill J, Kannan K, Karas BJ, Ma L, Pelletier JF, Qi ZQ, Richter RA, Strychalski EA, Sun L, Suzuki Y, Tsvetanova B, Wise KS, Smith HO, Glass JI, Merryman C, Gibson DG, Venter JC
Design and synthesis of a minimal bacterial genome.
Science (New York, N.Y.). 2016-03-25; 351.6280: aad6253.
PMID: 27013737
Suzuki Y, Assad-Garcia N, Kostylev M, Noskov VN, Wise KS, Karas BJ, Stam J, Montague MG, Hanly TJ, Enriquez NJ, Ramon A, Goldgof GM, Richter RA, Vashee S, Chuang RY, Winzeler EA, Hutchison CA, Gibson DG, Smith HO, Glass JI, Venter JC
Bacterial genome reduction using the progressive clustering of deletions via yeast sexual cycling.
Genome research. 2015-03-01; 25.3: 435-44.
PMID: 25654978
Gibson DG, Venter JC
Synthetic biology: Construction of a yeast chromosome.
Nature. 2014-05-08; 509.7499: 168-9.
PMID: 24805340
Gibson DG
Programming biological operating systems: genome design, assembly and activation.
Nature methods. 2014-05-01; 11.5: 521-6.
PMID: 24781325
Karas BJ, Jablanovic J, Irvine E, Sun L, Ma L, Weyman PD, Gibson DG, Glass JI, Venter JC, Hutchison CA, Smith HO, Suzuki Y
Transferring whole genomes from bacteria to yeast spheroplasts using entire bacterial cells to reduce DNA shearing.
Nature protocols. 2014-04-01; 9.4: 743-50.
PMID: 24603933
Karas BJ, Jablanovic J, Sun L, Ma L, Goldgof GM, Stam J, Ramon A, Manary MJ, Winzeler EA, Venter JC, Weyman PD, Gibson DG, Glass JI, Hutchison CA, Smith HO, Suzuki Y
Direct transfer of whole genomes from bacteria to yeast.
Nature methods. 2013-05-01; 10.5: 410-2.
PMID: 23542886
Tagwerker C, Dupont CL, Karas BJ, Ma L, Chuang RY, Benders GA, Ramon A, Novotny M, Montague MG, Venepally P, Brami D, Schwartz A, Andrews-Pfannkoch C, Gibson DG, Glass JI, Smith HO, Venter JC, Hutchison CA
Sequence analysis of a complete 1.66 Mb Prochlorococcus marinus MED4 genome cloned in yeast.
Nucleic acids research. 2012-11-01; 40.20: 10375-83.
PMID: 22941652
Noskov VN, Karas BJ, Young L, Chuang RY, Gibson DG, Lin YC, Stam J, Yonemoto IT, Suzuki Y, Andrews-Pfannkoch C, Glass JI, Smith HO, Hutchison CA, Venter JC, Weyman PD
Assembly of large, high G+C bacterial DNA fragments in yeast.
ACS synthetic biology. 2012-07-20; 1.7: 267-73.
PMID: 23651249
Gibson DG
Gene and genome construction in yeast.
Current protocols in molecular biology. 2011-04-01; Chapter 3.Unit3.22.
PMID: 21472698
Noskov VN, Chuang RY, Gibson DG, Leem SH, Larionov V, Kouprina N
Isolation of circular yeast artificial chromosomes for synthetic biology and functional genomics studies.
Nature protocols. 2011-01-01; 6.1: 89-96.
PMID: 21212778
Gibson DG
Enzymatic assembly of overlapping DNA fragments.
Methods in enzymology. 2011-01-01; 498.349-61.
PMID: 21601685
Gibson DG, Smith HO, Hutchison CA, Venter JC, Merryman C
Chemical synthesis of the mouse mitochondrial genome.
Nature methods. 2010-11-01; 7.11: 901-3.
PMID: 20935651
Gibson DG, Glass JI, Lartigue C, Noskov VN, Chuang RY, Algire MA, Benders GA, Montague MG, Ma L, Moodie MM, Merryman C, Vashee S, Krishnakumar R, Assad-Garcia N, Andrews-Pfannkoch C, Denisova EA, Young L, Qi ZQ, Segall-Shapiro TH, Calvey CH, Parmar PP, Hutchison CA, Smith HO, Venter JC
Creation of a bacterial cell controlled by a chemically synthesized genome.
Science (New York, N.Y.). 2010-07-02; 329.5987: 52-6.
PMID: 20488990
Benders GA, Noskov VN, Denisova EA, Lartigue C, Gibson DG, Assad-Garcia N, Chuang RY, Carrera W, Moodie M, Algire MA, Phan Q, Alperovich N, Vashee S, Merryman C, Venter JC, Smith HO, Glass JI, Hutchison CA
Cloning whole bacterial genomes in yeast.
Nucleic acids research. 2010-05-01; 38.8: 2558-69.
PMID: 20211840
Gibson DG
Synthesis of DNA fragments in yeast by one-step assembly of overlapping oligonucleotides.
Nucleic acids research. 2009-11-01; 37.20: 6984-90.
PMID: 19745056
Lartigue C, Vashee S, Algire MA, Chuang RY, Benders GA, Ma L, Noskov VN, Denisova EA, Gibson DG, Assad-Garcia N, Alperovich N, Thomas DW, Merryman C, Hutchison CA, Smith HO, Venter JC, Glass JI
Creating bacterial strains from genomes that have been cloned and engineered in yeast.
Science (New York, N.Y.). 2009-09-25; 325.5948: 1693-6.
PMID: 19696314
Gibson DG, Young L, Chuang RY, Venter JC, Hutchison CA, Smith HO
Enzymatic assembly of DNA molecules up to several hundred kilobases.
Nature methods. 2009-05-01; 6.5: 343-5.
PMID: 19363495
Gibson DG, Benders GA, Axelrod KC, Zaveri J, Algire MA, Moodie M, Montague MG, Venter JC, Smith HO, Hutchison CA
One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome.
Proceedings of the National Academy of Sciences of the United States of America. 2008-12-23; 105.51: 20404-9.
PMID: 19073939
Gibson DG, Benders GA, Andrews-Pfannkoch C, Denisova EA, Baden-Tillson H, Zaveri J, Stockwell TB, Brownley A, Thomas DW, Algire MA, Merryman C, Young L, Noskov VN, Glass JI, Venter JC, Hutchison CA, Smith HO
Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome.
Science (New York, N.Y.). 2008-02-29; 319.5867: 1215-20.
PMID: 18218864

Minimization and Modularization of the Genome of the Eukaryote, Kluyveromyces marxianus

Past Project

Toward Re-Programming the Gut Microbiome

Past Project
04-Aug-2016
Press Release

Teams at Venter Institute and Synthetic Genomics, Inc. Successfully Engineer 16S rRNA using One Step Process Combining CRISPR/Cas9 Systems and Yeast Recombination Machinery

24-Mar-2016
Press Release

First Minimal Synthetic Bacterial Cell Designed and Constructed by Scientists at Venter Institute and Synthetic Genomics, Inc.

Cell, JCVI-syn3.0, was minimized to just 473 genes

20-May-2010
Press Release

First Self-Replicating, Synthetic Bacterial Cell Constructed by J. Craig Venter Institute Researchers

24-Jan-2008
Press Release

Venter Institute Scientists Create First Synthetic Bacterial Genome

Publication Represents Largest Chemically Defined Structure Synthesized in the Lab

Team Completes Second Step in Three Step Process to Create Synthetic Organism