Hamilton Smith, MD

Distinguished Professor Emeritus

Hamilton Smith, M.D. is a professor emeritus at the J. Craig Venter Institute and former director of the Synthetic Biology and Bioenergy Group that created the first synthetic cell in 2010 and designed and synthesized the first minimal bacterial genome in 2016. He received an A.B. degree in Mathematics from the University of California, Berkeley in 1952 and the M.D. degree from the Johns Hopkins School of Medicine in 1956. He completed a residency in Internal Medicine in 1962. From 1962-67, he did research on lysogeny in phage P22 at the University of Michigan. In 1967, he was appointed Assistant Professor of Microbiology at Johns Hopkins. In 1970, he discovered the first Type II restriction enzyme, HindII. He received the Nobel Prize in Medicine in 1978 for that work. From 1975 to 1998, he studied the DNA transformation mechanism in Haemophilus Inflluenzae Rd. In 1993, Dr. Smith began his long association with Craig Venter. In 1995, they collaborated to sequence the genome of H. Inflluenzae Rd, and from 1998 to 2002, at Celera Genomics they sequenced Drosophila and the human genome. After leaving Celera, Smith and Venter began their work in synthetic biology.

Publications

Thornburg ZR, Bianchi DM, Brier TA, Gilbert BR, Earnest TM, Melo MCR, Safronova N, Sáenz JP, Cook AT, Wise KS, Hutchison CA, Smith HO, Glass JI, Luthey-Schulten Z

Fundamental behaviors emerge from simulations of a living minimal cell.

Cell. 2022-01-20; 185.2: 345-360.e28.

PMID: 35063075

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

Thornburg ZR, Melo MCR, Bianchi D, Brier TA, Crotty C, Breuer M, Smith HO, Hutchison CA, Glass JI, Luthey-Schulten Z

Kinetic Modeling of the Genetic Information Processes in a Minimal Cell.

Frontiers in molecular biosciences. 2019-11-28; 6.130.

PMID: 31850364

Hutchison CA, Merryman C, Sun L, Assad-Garcia N, Richter RA, Smith HO, Glass JI

Polar Effects of Transposon Insertion into a Minimal Bacterial Genome.

Journal of bacteriology. 2019-10-01; 201.19:

PMID: 31262838

Breuer M, Earnest TM, Merryman C, Wise KS, Sun L, Lynott MR, Hutchison CA, Smith HO, Lapek JD, Gonzalez DJ, de Crécy-Lagard V, Haas D, Hanson AD, Labhsetwar P, Glass JI, Luthey-Schulten Z

Essential metabolism for a minimal cell.

eLife. 2019-01-18; 8.

PMID: 30657448

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

Mariscal AM, Kakizawa S, Hsu JY, Tanaka K, González-González L, Broto A, Querol E, Lluch-Senar M, Piñero-Lambea C, Sun L, Weyman PD, Wise KS, Merryman C, Tse G, Moore AJ, Hutchison CA, Smith HO, Tomita M, Venter JC, Glass JI, Piñol J, Suzuki Y

Tuning Gene Activity by Inducible and Targeted Regulation of Gene Expression in Minimal Bacterial Cells.

ACS synthetic biology. 2018-06-15; 7.6: 1538-1552.

PMID: 29786424

Glass JI, Merryman C, Wise KS, Hutchison CA, Smith HO

Minimal Cells-Real and Imagined.

Cold Spring Harbor perspectives in biology. 2017-12-01; 9.12:

PMID: 28348033

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

Venter JC, Smith HO, Adams MD

The Sequence of the Human Genome.

Clinical chemistry. 2015-09-01; 61.9: 1207-8.

PMID: 26185218

Karas BJ, Diner RE, Lefebvre SC, McQuaid J, Phillips AP, Noddings CM, Brunson JK, Valas RE, Deerinck TJ, Jablanovic J, Gillard JT, Beeri K, Ellisman MH, Glass JI, Hutchison CA, Smith HO, Venter JC, Allen AE, Dupont CL, Weyman PD

Designer diatom episomes delivered by bacterial conjugation.

Nature communications. 2015-04-21; 6.6925.

PMID: 25897682

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

Waldor MK, Tyson G, Borenstein E, Ochman H, Moeller A, Finlay BB, Kong HH, Gordon JI, Nelson KE, Dabbagh K, Smith H

Where next for microbiome research?

PLoS biology. 2015-01-20; 13.1: e1002050.

PMID: 25602283

Yonemoto IT, Smith HO, Weyman PD

Designed surface residue substitutions in [NiFe] hydrogenase that improve electron transfer characteristics.

International journal of molecular sciences. 2015-01-16; 16.1: 2020-33.

PMID: 25603181

Yonemoto IT, Clarkson BR, Smith HO, Weyman PD

A broad survey reveals substitution tolerance of residues ligating FeS clusters in [NiFe] hydrogenase.

BMC biochemistry. 2014-06-17; 15.10.

PMID: 24934472

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, Wise KS, Sun L, Venter JC, Glass JI, Hutchison CA, Smith HO, Suzuki Y

Rescue of mutant fitness defects using in vitro reconstituted designer transposons in Mycoplasma mycoides.

Frontiers in microbiology. 2014-01-01; 5.369.

PMID: 25101070

Karas BJ, Molparia B, Jablanovic J, Hermann WJ, Lin YC, Dupont CL, Tagwerker C, Yonemoto IT, Noskov VN, Chuang RY, Allen AE, Glass JI, Hutchison CA, Smith HO, Venter JC, Weyman PD

Assembly of eukaryotic algal chromosomes in yeast.

Journal of biological engineering. 2013-12-10; 7.1: 30.

PMID: 24325901

Yonemoto IT, Matteri CW, Nguyen TA, Smith HO, Weyman PD

Dual organism design cycle reveals small subunit substitutions that improve [NiFe] hydrogenase hydrogen evolution.

Journal of biological engineering. 2013-07-02; 7.1: 17.

PMID: 23819621

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

Weyman PD, Smith HO, Xu Q

Genetic analysis of the Alteromonas macleodii [NiFe]-hydrogenase.

FEMS microbiology letters. 2011-09-01; 322.2: 180-7.

PMID: 21718346

Weyman PD, Vargas WA, Chuang RY, Chang Y, Smith HO, Xu Q

Heterologous expression of Alteromonas macleodii and Thiocapsa roseopersicina [NiFe] hydrogenases in Escherichia coli.

Microbiology (Reading, England). 2011-05-01; 157.Pt 5: 1363-74.

PMID: 21349975

Vargas WA, Weyman PD, Tong Y, Smith HO, Xu Q

[NiFe] hydrogenase from Alteromonas macleodii with unusual stability in the presence of oxygen and high temperature.

Applied and environmental microbiology. 2011-03-01; 77.6: 1990-8.

PMID: 21257809

Ramon A, Smith HO

Single-step linker-based combinatorial assembly of promoter and gene cassettes for pathway engineering.

Biotechnology letters. 2011-03-01; 33.3: 549-55.

PMID: 21107654

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

Montague M, Barnes C, Smith HO, Chuang RY, Vashee S

The evolution of RecD outside of the RecBCD complex.

Journal of molecular evolution. 2009-10-01; 69.4: 360-71.

PMID: 19841849

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

Maróti G, Tong Y, Yooseph S, Baden-Tillson H, Smith HO, Kovács KL, Frazier M, Venter JC, Xu Q

Discovery of [NiFe] hydrogenase genes in metagenomic DNA: cloning and heterologous expression in Thiocapsa roseopersicina.

Applied and environmental microbiology. 2009-09-01; 75.18: 5821-30.

PMID: 19633107

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

Glass JI, Hutchison CA, Smith HO, Venter JC

A systems biology tour de force for a near-minimal bacterium.

Molecular systems biology. 2009-01-01; 5.330.

PMID: 19953084

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

Lartigue C, Glass JI, Alperovich N, Pieper R, Parmar PP, Hutchison CA, Smith HO, Venter JC

Genome transplantation in bacteria: changing one species to another.

Science (New York, N.Y.). 2007-08-03; 317.5838: 632-8.

PMID: 17600181

Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, Yooseph S, Wu D, Eisen JA, Hoffman JM, Remington K, Beeson K, Tran B, Smith H, Baden-Tillson H, Stewart C, Thorpe J, Freeman J, Andrews-Pfannkoch C, Venter JE, Li K, Kravitz S, Heidelberg JF, Utterback T, Rogers YH, Falcón LI, Souza V, Bonilla-Rosso G, Eguiarte LE, Karl DM, Sathyendranath S, Platt T, Bermingham E, Gallardo V, Tamayo-Castillo G, Ferrari MR, Strausberg RL, Nealson K, Friedman R, Frazier M, Venter JC

The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific.

PLoS biology. 2007-03-01; 5.3: e77.

PMID: 17355176

Glass JI, Assad-Garcia N, Alperovich N, Yooseph S, Lewis MR, Maruf M, Hutchison CA, Smith HO, Venter JC

Essential genes of a minimal bacterium.

Proceedings of the National Academy of Sciences of the United States of America. 2006-01-10; 103.2: 425-30.

PMID: 16407165

Hutchison CA, Smith HO, Pfannkoch C, Venter JC

Cell-free cloning using phi29 DNA polymerase.

Proceedings of the National Academy of Sciences of the United States of America. 2005-11-29; 102.48: 17332-6.

PMID: 16286637

Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO

Environmental genome shotgun sequencing of the Sargasso Sea.

Science (New York, N.Y.). 2004-04-02; 304.5667: 66-74.

PMID: 15001713

Smith HO, Hutchison CA, Pfannkoch C, Venter JC

Generating a synthetic genome by whole genome assembly: phiX174 bacteriophage from synthetic oligonucleotides.

Proceedings of the National Academy of Sciences of the United States of America. 2003-12-23; 100.26: 15440-5.

PMID: 14657399

Heidelberg JF, Paulsen IT, Nelson KE, Gaidos EJ, Nelson WC, Read TD, Eisen JA, Seshadri R, Ward N, Methe B, Clayton RA, Meyer T, Tsapin A, Scott J, Beanan M, Brinkac L, Daugherty S, Deboy RT, Dodson RJ, Durkin AS, Haft DH, Kolonay JF, Madupu R, Peterson JD, Umayam LA, White O, Wolf AM, Vamathevan J, Weidman J, Impraim M, Lee K, Berry K, Lee C, Mueller J, Khouri H, Gill J, Utterback TR, McDonald LA, Feldblyum TV, Smith HO, Venter JC, Nealson KH, Fraser CM

Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis.

Nature biotechnology. 2002-11-01; 20.11: 1118-23.

PMID: 12368813

Holt RA, Subramanian GM, Halpern A, Sutton GG, Charlab R, Nusskern DR, Wincker P, Clark AG, Ribeiro JM, Wides R, Salzberg SL, Loftus B, Yandell M, Majoros WH, Rusch DB, Lai Z, Kraft CL, Abril JF, Anthouard V, Arensburger P, Atkinson PW, Baden H, de Berardinis V, Baldwin D, Benes V, Biedler J, Blass C, Bolanos R, Boscus D, Barnstead M, Cai S, Center A, Chaturverdi K, Christophides GK, Chrystal MA, Clamp M, Cravchik A, Curwen V, Dana A, Delcher A, Dew I, Evans CA, Flanigan M, Grundschober-Freimoser A, Friedli L, Gu Z, Guan P, Guigo R, Hillenmeyer ME, Hladun SL, Hogan JR, Hong YS, Hoover J, Jaillon O, Ke Z, Kodira C, Kokoza E, Koutsos A, Letunic I, Levitsky A, Liang Y, Lin JJ, Lobo NF, Lopez JR, Malek JA, McIntosh TC, Meister S, Miller J, Mobarry C, Mongin E, Murphy SD, O'Brochta DA, Pfannkoch C, Qi R, Regier MA, Remington K, Shao H, Sharakhova MV, Sitter CD, Shetty J, Smith TJ, Strong R, Sun J, Thomasova D, Ton LQ, Topalis P, Tu Z, Unger MF, Walenz B, Wang A, Wang J, Wang M, Wang X, Woodford KJ, Wortman JR, Wu M, Yao A, Zdobnov EM, Zhang H, Zhao Q, Zhao S, Zhu SC, Zhimulev I, Coluzzi M, della Torre A, Roth CW, Louis C, Kalush F, Mural RJ, Myers EW, Adams MD, Smith HO, Broder S, Gardner MJ, Fraser CM, Birney E, Bork P, Brey PT, Venter JC, Weissenbach J, Kafatos FC, Collins FH, Hoffman SL

The genome sequence of the malaria mosquito Anopheles gambiae.

Science (New York, N.Y.). 2002-10-04; 298.5591: 129-49.

PMID: 12364791

Gardner MJ, Shallom SJ, Carlton JM, Salzberg SL, Nene V, Shoaibi A, Ciecko A, Lynn J, Rizzo M, Weaver B, Jarrahi B, Brenner M, Parvizi B, Tallon L, Moazzez A, Granger D, Fujii C, Hansen C, Pederson J, Feldblyum T, Peterson J, Suh B, Angiuoli S, Pertea M, Allen J, Selengut J, White O, Cummings LM, Smith HO, Adams MD, Venter JC, Carucci DJ, Hoffman SL, Fraser CM

Sequence of Plasmodium falciparum chromosomes 2, 10, 11 and 14.

Nature. 2002-10-03; 419.6906: 531-4.

PMID: 12368868

Carlton JM, Angiuoli SV, Suh BB, Kooij TW, Pertea M, Silva JC, Ermolaeva MD, Allen JE, Selengut JD, Koo HL, Peterson JD, Pop M, Kosack DS, Shumway MF, Bidwell SL, Shallom SJ, Van Aken SE, Riedmuller SB, Feldblyum TV, Cho JK, Quackenbush J, Sedegah M, Shoaibi A, Cummings LM, Florens L, Yates JR, Raine JD, Sinden RE, Harris MA, Cunningham DA, Preiser PR, Bergman LW, Vaidya AB, van Lin LH, Janse CJ, Waters AP, Smith HO, White OR, Salzberg SL, Venter JC, Fraser CM, Hoffman SL, Gardner MJ, Carucci DJ

Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii.

Nature. 2002-10-03; 419.6906: 512-9.

PMID: 12368865

Mural RJ, Adams MD, Myers EW, Smith HO, Miklos GL, Wides R, Halpern A, Li PW, Sutton GG, Nadeau J, Salzberg SL, Holt RA, Kodira CD, Lu F, Chen L, Deng Z, Evangelista CC, Gan W, Heiman TJ, Li J, Li Z, Merkulov GV, Milshina NV, Naik AK, Qi R, Shue BC, Wang A, Wang J, Wang X, Yan X, Ye J, Yooseph S, Zhao Q, Zheng L, Zhu SC, Biddick K, Bolanos R, Delcher AL, Dew IM, Fasulo D, Flanigan MJ, Huson DH, Kravitz SA, Miller JR, Mobarry CM, Reinert K, Remington KA, Zhang Q, Zheng XH, Nusskern DR, Lai Z, Lei Y, Zhong W, Yao A, Guan P, Ji RR, Gu Z, Wang ZY, Zhong F, Xiao C, Chiang CC, Yandell M, Wortman JR, Amanatides PG, Hladun SL, Pratts EC, Johnson JE, Dodson KL, Woodford KJ, Evans CA, Gropman B, Rusch DB, Venter E, Wang M, Smith TJ, Houck JT, Tompkins DE, Haynes C, Jacob D, Chin SH, Allen DR, Dahlke CE, Sanders R, Li K, Liu X, Levitsky AA, Majoros WH, Chen Q, Xia AC, Lopez JR, Donnelly MT, Newman MH, Glodek A, Kraft CL, Nodell M, Ali F, An HJ, Baldwin-Pitts D, Beeson KY, Cai S, Carnes M, Carver A, Caulk PM, Center A, Chen YH, Cheng ML, Coyne MD, Crowder M, Danaher S, Davenport LB, Desilets R, Dietz SM, Doup L, Dullaghan P, Ferriera S, Fosler CR, Gire HC, Gluecksmann A, Gocayne JD, Gray J, Hart B, Haynes J, Hoover J, Howland T, Ibegwam C, Jalali M, Johns D, Kline L, Ma DS, MacCawley S, Magoon A, Mann F, May D, McIntosh TC, Mehta S, Moy L, Moy MC, Murphy BJ, Murphy SD, Nelson KA, Nuri Z, Parker KA, Prudhomme AC, Puri VN, Qureshi H, Raley JC, Reardon MS, Regier MA, Rogers YH, Romblad DL, Schutz J, Scott JL, Scott R, Sitter CD, Smallwood M, Sprague AC, Stewart E, Strong RV, Suh E, Sylvester K, Thomas R, Tint NN, Tsonis C, Wang G, Wang G, Williams MS, Williams SM, Windsor SM, Wolfe K, Wu MM, Zaveri J, Chaturvedi K, Gabrielian AE, Ke Z, Sun J, Subramanian G, Venter JC, Pfannkoch CM, Barnstead M, Stephenson LD

A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome.

Science (New York, N.Y.). 2002-05-31; 296.5573: 1661-71.

PMID: 12040188

Myers EW, Sutton GG, Smith HO, Adams MD, Venter JC

On the sequencing and assembly of the human genome.

Proceedings of the National Academy of Sciences of the United States of America. 2002-04-02; 99.7: 4145-6.

PMID: 11904395

Tettelin H, Nelson KE, Paulsen IT, Eisen JA, Read TD, Peterson S, Heidelberg J, Deboy RT, Haft DH, Dodson RJ, Durkin AS, Gwinn M, Kolonay JF, Nelson WC, Peterson JD, Umayam LA, White O, Salzberg SL, Lewis MR, Radune D, Holtzapple E, Khouri H, Wolf AM, Utterback TR, Hansen CL, McDonald LA, Feldblyum TV, Angiuoli S, Dickinson T, Hickey EK, Holt IE, Loftus BJ, Yang F, Smith HO, Venter JC, Dougherty BA, Morrison DA, Hollingshead SK, Fraser CM

Complete genome sequence of a virulent isolate of Streptococcus pneumoniae.

Science (New York, N.Y.). 2001-07-20; 293.5529: 498-506.

PMID: 11463916

Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, Levine AJ, Roberts RJ, Simon M, Slayman C, Hunkapiller M, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu-Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R, Chaturvedi K, Deng Z, Di Francesco V, Dunn P, Eilbeck K, Evangelista C, Gabrielian AE, Gan W, Ge W, Gong F, Gu Z, Guan P, Heiman TJ, Higgins ME, Ji RR, Ke Z, Ketchum KA, Lai Z, Lei Y, Li Z, Li J, Liang Y, Lin X, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK, Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S, Shao W, Shue B, Sun J, Wang Z, Wang A, Wang X, Wang J, Wei M, Wides R, Xiao C, Yan C, Yao A, Ye J, Zhan M, Zhang W, Zhang H, Zhao Q, Zheng L, Zhong F, Zhong W, Zhu S, Zhao S, Gilbert D, Baumhueter S, Spier G, Carter C, Cravchik A, Woodage T, Ali F, An H, Awe A, Baldwin D, Baden H, Barnstead M, Barrow I, Beeson K, Busam D, Carver A, Center A, Cheng ML, Curry L, Danaher S, Davenport L, Desilets R, Dietz S, Dodson K, Doup L, Ferriera S, Garg N, Gluecksmann A, Hart B, Haynes J, Haynes C, Heiner C, Hladun S, Hostin D, Houck J, Howland T, Ibegwam C, Johnson J, Kalush F, Kline L, Koduru S, Love A, Mann F, May D, McCawley S, McIntosh T, McMullen I, Moy M, Moy L, Murphy B, Nelson K, Pfannkoch C, Pratts E, Puri V, Qureshi H, Reardon M, Rodriguez R, Rogers YH, Romblad D, Ruhfel B, Scott R, Sitter C, Smallwood M, Stewart E, Strong R, Suh E, Thomas R, Tint NN, Tse S, Vech C, Wang G, Wetter J, Williams S, Williams M, Windsor S, Winn-Deen E, Wolfe K, Zaveri J, Zaveri K, Abril JF, Guigó R, Campbell MJ, Sjolander KV, Karlak B, Kejariwal A, Mi H, Lazareva B, Hatton T, Narechania A, Diemer K, Muruganujan A, Guo N, Sato S, Bafna V, Istrail S, Lippert R, Schwartz R, Walenz B, Yooseph S, Allen D, Basu A, Baxendale J, Blick L, Caminha M, Carnes-Stine J, Caulk P, Chiang YH, Coyne M, Dahlke C, Mays A, Dombroski M, Donnelly M, Ely D, Esparham S, Fosler C, Gire H, Glanowski S, Glasser K, Glodek A, Gorokhov M, Graham K, Gropman B, Harris M, Heil J, Henderson S, Hoover J, Jennings D, Jordan C, Jordan J, Kasha J, Kagan L, Kraft C, Levitsky A, Lewis M, Liu X, Lopez J, Ma D, Majoros W, McDaniel J, Murphy S, Newman M, Nguyen T, Nguyen N, Nodell M, Pan S, Peck J, Peterson M, Rowe W, Sanders R, Scott J, Simpson M, Smith T, Sprague A, Stockwell T, Turner R, Venter E, Wang M, Wen M, Wu D, Wu M, Xia A, Zandieh A, Zhu X

The sequence of the human genome.

Science (New York, N.Y.). 2001-02-16; 291.5507: 1304-51.

PMID: 11181995

Ermolaeva MD, Khalak HG, White O, Smith HO, Salzberg SL

Prediction of transcription terminators in bacterial genomes.

Journal of molecular biology. 2000-08-04; 301.1: 27-33.

PMID: 10926490

Heidelberg JF, Eisen JA, Nelson WC, Clayton RA, Gwinn ML, Dodson RJ, Haft DH, Hickey EK, Peterson JD, Umayam L, Gill SR, Nelson KE, Read TD, Tettelin H, Richardson D, Ermolaeva MD, Vamathevan J, Bass S, Qin H, Dragoi I, Sellers P, McDonald L, Utterback T, Fleishmann RD, Nierman WC, White O, Salzberg SL, Smith HO, Colwell RR, Mekalanos JJ, Venter JC, Fraser CM

DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae.

Nature. 2000-08-03; 406.6795: 477-83.

PMID: 10952301

Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF, George RA, Lewis SE, Richards S, Ashburner M, Henderson SN, Sutton GG, Wortman JR, Yandell MD, Zhang Q, Chen LX, Brandon RC, Rogers YH, Blazej RG, Champe M, Pfeiffer BD, Wan KH, Doyle C, Baxter EG, Helt G, Nelson CR, Gabor GL, Abril JF, Agbayani A, An HJ, Andrews-Pfannkoch C, Baldwin D, Ballew RM, Basu A, Baxendale J, Bayraktaroglu L, Beasley EM, Beeson KY, Benos PV, Berman BP, Bhandari D, Bolshakov S, Borkova D, Botchan MR, Bouck J, Brokstein P, Brottier P, Burtis KC, Busam DA, Butler H, Cadieu E, Center A, Chandra I, Cherry JM, Cawley S, Dahlke C, Davenport LB, Davies P, de Pablos B, Delcher A, Deng Z, Mays AD, Dew I, Dietz SM, Dodson K, Doup LE, Downes M, Dugan-Rocha S, Dunkov BC, Dunn P, Durbin KJ, Evangelista CC, Ferraz C, Ferriera S, Fleischmann W, Fosler C, Gabrielian AE, Garg NS, Gelbart WM, Glasser K, Glodek A, Gong F, Gorrell JH, Gu Z, Guan P, Harris M, Harris NL, Harvey D, Heiman TJ, Hernandez JR, Houck J, Hostin D, Houston KA, Howland TJ, Wei MH, Ibegwam C, Jalali M, Kalush F, Karpen GH, Ke Z, Kennison JA, Ketchum KA, Kimmel BE, Kodira CD, Kraft C, Kravitz S, Kulp D, Lai Z, Lasko P, Lei Y, Levitsky AA, Li J, Li Z, Liang Y, Lin X, Liu X, Mattei B, McIntosh TC, McLeod MP, McPherson D, Merkulov G, Milshina NV, Mobarry C, Morris J, Moshrefi A, Mount SM, Moy M, Murphy B, Murphy L, Muzny DM, Nelson DL, Nelson DR, Nelson KA, Nixon K, Nusskern DR, Pacleb JM, Palazzolo M, Pittman GS, Pan S, Pollard J, Puri V, Reese MG, Reinert K, Remington K, Saunders RD, Scheeler F, Shen H, Shue BC, Sidén-Kiamos I, Simpson M, Skupski MP, Smith T, Spier E, Spradling AC, Stapleton M, Strong R, Sun E, Svirskas R, Tector C, Turner R, Venter E, Wang AH, Wang X, Wang ZY, Wassarman DA, Weinstock GM, Weissenbach J, Williams SM, WoodageT, Worley KC, Wu D, Yang S, Yao QA, Ye J, Yeh RF, Zaveri JS, Zhan M, Zhang G, Zhao Q, Zheng L, Zheng XH, Zhong FN, Zhong W, Zhou X, Zhu S, Zhu X, Smith HO, Gibbs RA, Myers EW, Rubin GM, Venter JC

The genome sequence of Drosophila melanogaster.

Science (New York, N.Y.). 2000-03-24; 287.5461: 2185-95.

PMID: 10731132

Tettelin H, Saunders NJ, Heidelberg J, Jeffries AC, Nelson KE, Eisen JA, Ketchum KA, Hood DW, Peden JF, Dodson RJ, Nelson WC, Gwinn ML, DeBoy R, Peterson JD, Hickey EK, Haft DH, Salzberg SL, White O, Fleischmann RD, Dougherty BA, Mason T, Ciecko A, Parksey DS, Blair E, Cittone H, Clark EB, Cotton MD, Utterback TR, Khouri H, Qin H, Vamathevan J, Gill J, Scarlato V, Masignani V, Pizza M, Grandi G, Sun L, Smith HO, Fraser CM, Moxon ER, Rappuoli R, Venter JC

Complete genome sequence of Neisseria meningitidis serogroup B strain MC58.

Science (New York, N.Y.). 2000-03-10; 287.5459: 1809-15.

PMID: 10710307

Hutchison CA, Peterson SN, Gill SR, Cline RT, White O, Fraser CM, Smith HO, Venter JC

Global transposon mutagenesis and a minimal Mycoplasma genome.

Science (New York, N.Y.). 1999-12-10; 286.5447: 2165-9.

PMID: 10591650

White O, Eisen JA, Heidelberg JF, Hickey EK, Peterson JD, Dodson RJ, Haft DH, Gwinn ML, Nelson WC, Richardson DL, Moffat KS, Qin H, Jiang L, Pamphile W, Crosby M, Shen M, Vamathevan JJ, Lam P, McDonald L, Utterback T, Zalewski C, Makarova KS, Aravind L, Daly MJ, Minton KW, Fleischmann RD, Ketchum KA, Nelson KE, Salzberg S, Smith HO, Venter JC, Fraser CM

Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1.

Science (New York, N.Y.). 1999-11-19; 286.5444: 1571-7.

PMID: 10567266

Smith HO, Gwinn ML, Salzberg SL

DNA uptake signal sequences in naturally transformable bacteria.

Research in microbiology. 1999-11-01; 150.9-10: 603-16.

PMID: 10673000

Gardner MJ, Tettelin H, Carucci DJ, Cummings LM, Smith HO, Fraser CM, Venter JC, Hoffman SL

The malaria genome sequencing project: complete sequence of Plasmodium falciparum chromosome 2.

Parassitologia. 1999-09-01; 41.1-3: 69-75.

PMID: 10697835

Nelson KE, Clayton RA, Gill SR, Gwinn ML, Dodson RJ, Haft DH, Hickey EK, Peterson JD, Nelson WC, Ketchum KA, McDonald L, Utterback TR, Malek JA, Linher KD, Garrett MM, Stewart AM, Cotton MD, Pratt MS, Phillips CA, Richardson D, Heidelberg J, Sutton GG, Fleischmann RD, Eisen JA, White O, Salzberg SL, Smith HO, Venter JC, Fraser CM

Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima.

Nature. 1999-05-27; 399.6734: 323-9.

PMID: 10360571

Gardner MJ, Tettelin H, Carucci DJ, Cummings LM, Aravind L, Koonin EV, Shallom S, Mason T, Yu K, Fujii C, Pederson J, Shen K, Jing J, Aston C, Lai Z, Schwartz DC, Pertea M, Salzberg S, Zhou L, Sutton GG, Clayton R, White O, Smith HO, Fraser CM, Adams MD, Venter JC, Hoffman SL

Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum.

Science (New York, N.Y.). 1998-11-06; 282.5391: 1126-32.

PMID: 9804551

Fraser CM, Norris SJ, Weinstock GM, White O, Sutton GG, Dodson R, Gwinn M, Hickey EK, Clayton R, Ketchum KA, Sodergren E, Hardham JM, McLeod MP, Salzberg S, Peterson J, Khalak H, Richardson D, Howell JK, Chidambaram M, Utterback T, McDonald L, Artiach P, Bowman C, Cotton MD, Fujii C, Garland S, Hatch B, Horst K, Roberts K, Sandusky M, Weidman J, Smith HO, Venter JC

Complete genome sequence of Treponema pallidum, the syphilis spirochete.

Science (New York, N.Y.). 1998-07-17; 281.5375: 375-88.

PMID: 9665876

Venter JC, Adams MD, Sutton GG, Kerlavage AR, Smith HO, Hunkapiller M

Shotgun sequencing of the human genome.

Science (New York, N.Y.). 1998-06-05; 280.5369: 1540-2.

PMID: 9644018

Gwinn ML, Ramanathan R, Smith HO, Tomb JF

A new transformation-deficient mutant of Haemophilus influenzae Rd with normal DNA uptake.

Journal of bacteriology. 1998-02-01; 180.3: 746-8.

PMID: 9457884

Fraser CM, Casjens S, Huang WM, Sutton GG, Clayton R, Lathigra R, White O, Ketchum KA, Dodson R, Hickey EK, Gwinn M, Dougherty B, Tomb JF, Fleischmann RD, Richardson D, Peterson J, Kerlavage AR, Quackenbush J, Salzberg S, Hanson M, van Vugt R, Palmer N, Adams MD, Gocayne J, Weidman J, Utterback T, Watthey L, McDonald L, Artiach P, Bowman C, Garland S, Fuji C, Cotton MD, Horst K, Roberts K, Hatch B, Smith HO, Venter JC

Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi.

Nature. 1997-12-11; 390.6660: 580-6.

PMID: 9403685

Gwinn ML, Stellwagen AE, Craig NL, Tomb JF, Smith HO

In vitro Tn7 mutagenesis of Haemophilus influenzae Rd and characterization of the role of atpA in transformation.

Journal of bacteriology. 1997-12-01; 179.23: 7315-20.

PMID: 9393695

Klenk HP, Clayton RA, Tomb JF, White O, Nelson KE, Ketchum KA, Dodson RJ, Gwinn M, Hickey EK, Peterson JD, Richardson DL, Kerlavage AR, Graham DE, Kyrpides NC, Fleischmann RD, Quackenbush J, Lee NH, Sutton GG, Gill S, Kirkness EF, Dougherty BA, McKenney K, Adams MD, Loftus B, Peterson S, Reich CI, McNeil LK, Badger JH, Glodek A, Zhou L, Overbeek R, Gocayne JD, Weidman JF, McDonald L, Utterback T, Cotton MD, Spriggs T, Artiach P, Kaine BP, Sykes SM, Sadow PW, D'Andrea KP, Bowman C, Fujii C, Garland SA, Mason TM, Olsen GJ, Fraser CM, Smith HO, Woese CR, Venter JC

The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus.

Nature. 1997-11-27; 390.6658: 364-70.

PMID: 9389475

Tomb JF, White O, Kerlavage AR, Clayton RA, Sutton GG, Fleischmann RD, Ketchum KA, Klenk HP, Gill S, Dougherty BA, Nelson K, Quackenbush J, Zhou L, Kirkness EF, Peterson S, Loftus B, Richardson D, Dodson R, Khalak HG, Glodek A, McKenney K, Fitzegerald LM, Lee N, Adams MD, Hickey EK, Berg DE, Gocayne JD, Utterback TR, Peterson JD, Kelley JM, Cotton MD, Weidman JM, Fujii C, Bowman C, Watthey L, Wallin E, Hayes WS, Borodovsky M, Karp PD, Smith HO, Fraser CM, Venter JC

The complete genome sequence of the gastric pathogen Helicobacter pylori.

Nature. 1997-08-07; 388.6642: 539-47.

PMID: 9252185

Venter JC, Smith HO, Hood L

A new strategy for genome sequencing.

Nature. 1996-05-30; 381.6581: 364-6.

PMID: 8632789

Fraser CM, Gocayne JD, White O, Adams MD, Clayton RA, Fleischmann RD, Bult CJ, Kerlavage AR, Sutton G, Kelley JM, Fritchman RD, Weidman JF, Small KV, Sandusky M, Fuhrmann J, Nguyen D, Utterback TR, Saudek DM, Phillips CA, Merrick JM, Tomb JF, Dougherty BA, Bott KF, Hu PC, Lucier TS, Peterson SN, Smith HO, Hutchison CA, Venter JC

The minimal gene complement of Mycoplasma genitalium.

Science (New York, N.Y.). 1995-10-20; 270.5235: 397-403.

PMID: 7569993

Smith HO, Tomb JF, Dougherty BA, Fleischmann RD, Venter JC

Frequency and distribution of DNA uptake signal sequences in the Haemophilus influenzae Rd genome.

Science (New York, N.Y.). 1995-07-28; 269.5223: 538-40.

PMID: 7542802

Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM

Whole-genome random sequencing and assembly of Haemophilus influenzae Rd.

Science (New York, N.Y.). 1995-07-28; 269.5223: 496-512.

PMID: 7542800

Smith HO, Wilcox KW

A restriction enzyme from Hemophilus influenzae. I. Purification and general properties. 1970.

Biotechnology (Reading, Mass.). 1992-01-01; 24.38-50.

PMID: 1330118

Smith HO, Annau TM, Chandrasegaran S

Finding sequence motifs in groups of functionally related proteins.

Proceedings of the National Academy of Sciences of the United States of America. 1990-01-01; 87.2: 826-30.

PMID: 1689055

Kelly TJ, Smith HO

A restriction enzyme from Hemophilus influenzae. II.

Journal of molecular biology. 1970-07-28; 51.2: 393-409.

PMID: 5312501

Salk Intitute Lecture — 2016 DOE JGI Genomics of Energy & Environment Meeting

Johns Hopkins Medicine — The Hamilton Smith Award for Innovative Research

UW-Madison Lecture

Salk Intitute Lecture — Making miniature machines - with Hamilton Smith

The Nobel Prize — Interview with Hamilton Smith and Richard Roberts

22-Dec-2020

Press Release

Hamilton O. Smith, M.D., Synthetic Biology Pioneer and Nobel Laureate, to Step Down from Daily Duties at J. Craig Venter Institute

Dr. Smith will maintain advisory role as professor emeritus

19-Dec-2020

The San Diego Union-Tribune

After saving countless lives, Nobel laureate Hamilton Smith retires as his own health falters

He has been a fixture in San Diego science for decades

17-May-2018

Blog

J. Craig Venter Institute Education Program Fosters Learning Opportunities with Salisbury University Students and Faculty

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

31-May-2016

Blog

Unlocking the Mysteries of the Microbiome

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

09-Nov-2015

Blog

JCVI Researchers, as Part of NIH Human Microbiome Project Consortium, Publish Papers Detailing the Variety and Abundance of Microbes Living on and in the Human Body

Study Represents Largest Group of Healthy Individuals Studied to Date

JCVI also Details its Metagenomics Reports (METAREP) Open Source Bioinformatics Tool

20-May-2010

Press Release

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

20-May-2010

Blog

Scientist Spotlight: Hamilton O. Smith and Clyde A. Hutchison III

20-Aug-2009

Press Release

J. Craig Venter Institute Researchers Clone and Engineer Bacterial Genomes in Yeast and Transplant Genomes Back into Bacterial Cells

New methods allow for the rapid engineering of bacterial chromosomes and the creation of extensively modified bacterial species; should also play key role in boot up of synthetic cell

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

28-Jun-2007

Press Release

JCVI Scientists Publish First Bacterial Genome Transplantation Changing One Species to Another

Research is important step in further advancing field of synthetic genomics

27-Sep-2006

Press Release

His Royal Highness Prince Andrew, The Duke of York, to Tour J. Craig Venter Institute

29-Sep-2004

Press Release

J. Craig Venter Announces Consolidation of Three Research Organizations Into One New Not-For-Profit Organization — The J. Craig Venter Institute

The Center for Advancement of Genomics (TCAG), Institute for Biological Energy Alternatives (IBEA), and J. Craig Venter Science Foundation Joint Technology Center (JTC) consolidated to form J. Craig Venter Institute

13-Nov-2003

Press Release

IBEA Researchers Make Significant Advance in Methodology Toward Goal of a Synthetic Genome

Group Synthesizes Biologically Active Genome of Bacteriophage φX174

IBEA research, funded by Dept. of Energy, is an important advance toward the goal of a completely synthetic genome that could aid in carbon sequestration and energy production

21-Nov-2002

Press Release

Hamilton Smith, MD

Related

Research Priorities

Deciphering the genetic requirements for minimal bacterial life

Designing a minimal yeast cell

Understanding the mechanism of DNA cassette insertional mutagenesis in yeast

Publications

Dr. Smith will maintain advisory role as professor emeritus

He has been a fixture in San Diego science for decades

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

Study Represents Largest Group of Healthy Individuals Studied to Date

JCVI also Details its Metagenomics Reports (METAREP) Open Source Bioinformatics Tool

New methods allow for the rapid engineering of bacterial chromosomes and the creation of extensively modified bacterial species; should also play key role in boot up of synthetic cell

Publication Represents Largest Chemically Defined Structure Synthesized in the Lab

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

Research is important step in further advancing field of synthetic genomics

The Center for Advancement of Genomics (TCAG), Institute for Biological Energy Alternatives (IBEA), and J. Craig Venter Science Foundation Joint Technology Center (JTC) consolidated to form J. Craig Venter Institute

Group Synthesizes Biologically Active Genome of Bacteriophage φX174

IBEA research, funded by Dept. of Energy, is an important advance toward the goal of a completely synthetic genome that could aid in carbon sequestration and energy production

Hamilton Smith, M.D., Nobel Laureate, Named Scientific Director of IBEA

In the News

Synthetic genomics advances and promise

What's Happening

Leg 2: exploring the Mid-Cayman Spreading Center

Recently Published

MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters.