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Polar Effects of Transposon Insertion into a Minimal Bacterial Genome.

Hutchison CA 3rd, Merryman C, Sun L, Assad-Garcia N, Richter RA, Smith HO, Glass JI.

J Bacteriol. 2019 Sep 6;201(19). pii: e00185-19. doi: 10.1128/JB.00185-19. Print 2019 Oct 1.


Human Tumor-Associated Macrophage and Monocyte Transcriptional Landscapes Reveal Cancer-Specific Reprogramming, Biomarkers, and Therapeutic Targets.

Cassetta L, Fragkogianni S, Sims AH, Swierczak A, Forrester LM, Zhang H, Soong DYH, Cotechini T, Anur P, Lin EY, Fidanza A, Lopez-Yrigoyen M, Millar MR, Urman A, Ai Z, Spellman PT, Hwang ES, Dixon JM, Wiechmann L, Coussens LM, Smith HO, Pollard JW.

Cancer Cell. 2019 Apr 15;35(4):588-602.e10. doi: 10.1016/j.ccell.2019.02.009. Epub 2019 Mar 28.


Essential metabolism for a minimal cell.

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.

Elife. 2019 Jan 18;8. pii: e36842. doi: 10.7554/eLife.36842.


Direct Transfer of a Mycoplasma mycoides Genome to Yeast Is Enhanced by Removal of the Mycoides Glycerol Uptake Factor Gene glpF.

Karas BJ, Moreau NG, Deerinck TJ, Gibson DG, Venter JC, Smith HO, Glass JI.

ACS Synth Biol. 2019 Feb 15;8(2):239-244. doi: 10.1021/acssynbio.8b00449. Epub 2019 Jan 24.


Adjuvant Pelvic Radiation "Sandwiched" Between Paclitaxel/Carboplatin Chemotherapy in Women With Completely Resected Uterine Serous Carcinoma: Long-term Follow-up of a Prospective Phase 2 Trial.

Frimer M, Miller EM, Shankar V, Girda E, Mehta K, Smith HO, Kuo DYS, Goldberg GL, Einstein MH.

Int J Gynecol Cancer. 2018 Nov;28(9):1781-1788. doi: 10.1097/IGC.0000000000001359.


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

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 3rd, Smith HO, Tomita M, Venter JC, Glass JI, Piñol J, Suzuki Y.

ACS Synth Biol. 2018 Jun 15;7(6):1538-1552. doi: 10.1021/acssynbio.8b00028. Epub 2018 May 22.


Minimal Cells-Real and Imagined.

Glass JI, Merryman C, Wise KS, Hutchison CA 3rd, Smith HO.

Cold Spring Harb Perspect Biol. 2017 Dec 1;9(12). pii: a023861. doi: 10.1101/cshperspect.a023861. Review.


One step engineering of the small-subunit ribosomal RNA using CRISPR/Cas9.

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.

Sci Rep. 2016 Aug 4;6:30714. doi: 10.1038/srep30714.


Design and synthesis of a minimal bacterial genome.

Hutchison CA 3rd, 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.

Science. 2016 Mar 25;351(6280):aad6253. doi: 10.1126/science.aad6253. Erratum in: ACS Chem Biol. 2016 May 20;11(5):1463.


The Sequence of the Human Genome.

Venter JC, Smith HO, Adams MD.

Clin Chem. 2015 Sep;61(9):1207-8. doi: 10.1373/clinchem.2014.237016. Epub 2015 Jul 16. No abstract available.


Designer diatom episomes delivered by bacterial conjugation.

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 3rd, Smith HO, Venter JC, Allen AE, Dupont CL, Weyman PD.

Nat Commun. 2015 Apr 21;6:6925. doi: 10.1038/ncomms7925.


Bacterial genome reduction using the progressive clustering of deletions via yeast sexual cycling.

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 3rd, Gibson DG, Smith HO, Glass JI, Venter JC.

Genome Res. 2015 Mar;25(3):435-44. doi: 10.1101/gr.182477.114. Epub 2015 Feb 5.


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

Yonemoto IT, Smith HO, Weyman PD.

Int J Mol Sci. 2015 Jan 16;16(1):2020-33. doi: 10.3390/ijms16012020.


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

Karas BJ, Wise KS, Sun L, Venter JC, Glass JI, Hutchison CA 3rd, Smith HO, Suzuki Y.

Front Microbiol. 2014 Jul 23;5:369. doi: 10.3389/fmicb.2014.00369. eCollection 2014.


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

Yonemoto IT, Clarkson BR, Smith HO, Weyman PD.

BMC Biochem. 2014 Jun 17;15:10. doi: 10.1186/1471-2091-15-10.


Hemoglobin parameters from diffuse reflectance data.

Mourant JR, Marina OC, Hebert TM, Kaur G, Smith HO.

J Biomed Opt. 2014 Mar;19(3):37004. doi: 10.1117/1.JBO.19.3.037004.


Transferring whole genomes from bacteria to yeast spheroplasts using entire bacterial cells to reduce DNA shearing.

Karas BJ, Jablanovic J, Irvine E, Sun L, Ma L, Weyman PD, Gibson DG, Glass JI, Venter JC, Hutchison CA 3rd, Smith HO, Suzuki Y.

Nat Protoc. 2014 Apr;9(4):743-50. doi: 10.1038/nprot.2014.045. Epub 2014 Mar 6.


G protein-coupled estrogen receptor-selective ligands modulate endometrial tumor growth.

Petrie WK, Dennis MK, Hu C, Dai D, Arterburn JB, Smith HO, Hathaway HJ, Prossnitz ER.

Obstet Gynecol Int. 2013;2013:472720. doi: 10.1155/2013/472720. Epub 2013 Nov 27.


Assembly of eukaryotic algal chromosomes in yeast.

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 3rd, Smith HO, Venter JC, Weyman PD.

J Biol Eng. 2013 Dec 10;7(1):30. doi: 10.1186/1754-1611-7-30.


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

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

J Biol Eng. 2013 Jul 2;7(1):17. doi: 10.1186/1754-1611-7-17.


Assembly of large, high G+C bacterial DNA fragments in yeast.

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 3rd, Venter JC, Weyman PD.

ACS Synth Biol. 2012 Jul 20;1(7):267-73. doi: 10.1021/sb3000194. Epub 2012 May 21.


Direct transfer of whole genomes from bacteria to yeast.

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 3rd, Smith HO, Suzuki Y.

Nat Methods. 2013 May;10(5):410-2. doi: 10.1038/nmeth.2433. Epub 2013 Mar 31.


The clinical significance of inflammatory cytokines in primary cell culture in endometrial carcinoma.

Smith HO, Stephens ND, Qualls CR, Fligelman T, Wang T, Lin CY, Burton E, Griffith JK, Pollard JW.

Mol Oncol. 2013 Feb;7(1):41-54. doi: 10.1016/j.molonc.2012.07.002. Epub 2012 Aug 15.


Sequence analysis of a complete 1.66 Mb Prochlorococcus marinus MED4 genome cloned in yeast.

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 3rd.

Nucleic Acids Res. 2012 Nov 1;40(20):10375-83. doi: 10.1093/nar/gks823. Epub 2012 Aug 31.


High prevalence of high grade anal intraepithelial neoplasia in HIV-infected women screened for anal cancer.

Hou JY, Smotkin D, Grossberg R, Suhrland M, Levine R, Smith HO, Negassa A, McAndrew TC, Einstein MH.

J Acquir Immune Defic Syndr. 2012 Jun 1;60(2):169-72. doi: 10.1097/QAI.0b013e318251afd9.


Cloning the Acholeplasma laidlawii PG-8A genome in Saccharomyces cerevisiae as a yeast centromeric plasmid.

Karas BJ, Tagwerker C, Yonemoto IT, Hutchison CA 3rd, Smith HO.

ACS Synth Biol. 2012 Jan 20;1(1):22-8. doi: 10.1021/sb200013j. Epub 2012 Jan 10.


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

Weyman PD, Smith HO, Xu Q.

FEMS Microbiol Lett. 2011 Sep;322(2):180-7. doi: 10.1111/j.1574-6968.2011.02348.x. Epub 2011 Jul 19.


Heterologous expression of Alteromonas macleodii and Thiocapsa roseopersicina [NiFe] hydrogenases in Synechococcus elongatus.

Weyman PD, Vargas WA, Tong Y, Yu J, Maness PC, Smith HO, Xu Q.

PLoS One. 2011;6(5):e20126. doi: 10.1371/journal.pone.0020126. Epub 2011 May 26.


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

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

Microbiology. 2011 May;157(Pt 5):1363-74. doi: 10.1099/mic.0.044834-0. Epub 2011 Feb 24.


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

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

Appl Environ Microbiol. 2011 Mar;77(6):1990-8. doi: 10.1128/AEM.01559-10. Epub 2011 Jan 21.


Risk factors for poor prognosis in microinvasive adenocarcinoma of the uterine cervix (IA1 and IA2): a pooled analysis.

Hou J, Goldberg GL, Qualls CR, Kuo DY, Forman A, Smith HO.

Gynecol Oncol. 2011 Apr;121(1):135-42. doi: 10.1016/j.ygyno.2010.11.036. Epub 2010 Dec 30.


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

Ramon A, Smith HO.

Biotechnol Lett. 2011 Mar;33(3):549-55. doi: 10.1007/s10529-010-0455-x. Epub 2010 Nov 24.


Chemical synthesis of the mouse mitochondrial genome.

Gibson DG, Smith HO, Hutchison CA 3rd, Venter JC, Merryman C.

Nat Methods. 2010 Nov;7(11):901-3. doi: 10.1038/nmeth.1515. Epub 2010 Oct 10.


Detection of cervical intraepithelial neoplasias and cancers in cervical tissue by in vivo light scattering.

Mourant JR, Bocklage TJ, Powers TM, Greene HM, Dorin MH, Waxman AG, Zsemlye MM, Smith HO.

J Low Genit Tract Dis. 2009 Oct;13(4):216-223.


Co-expression of GPR30 and ERbeta and their association with disease progression in uterine carcinosarcoma.

Huang GS, Gunter MJ, Arend RC, Li M, Arias-Pulido H, Prossnitz ER, Goldberg GL, Smith HO.

Am J Obstet Gynecol. 2010 Sep;203(3):242.e1-5. doi: 10.1016/j.ajog.2010.04.046. Epub 2010 Jun 3.


Creation of a bacterial cell controlled by a chemically synthesized genome.

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 3rd, Smith HO, Venter JC.

Science. 2010 Jul 2;329(5987):52-6. doi: 10.1126/science.1190719. Epub 2010 May 20.


Insulin-like growth factor 2 expression modulates Taxol resistance and is a candidate biomarker for reduced disease-free survival in ovarian cancer.

Huang GS, Brouwer-Visser J, Ramirez MJ, Kim CH, Hebert TM, Lin J, Arias-Pulido H, Qualls CR, Prossnitz ER, Goldberg GL, Smith HO, Horwitz SB.

Clin Cancer Res. 2010 Jun 1;16(11):2999-3010. doi: 10.1158/1078-0432.CCR-09-3233. Epub 2010 Apr 19.


Cloning whole bacterial genomes in yeast.

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 3rd.

Nucleic Acids Res. 2010 May;38(8):2558-69. doi: 10.1093/nar/gkq119. Epub 2010 Mar 7.


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

Glass JI, Hutchison CA 3rd, Smith HO, Venter JC.

Mol Syst Biol. 2009;5:330. doi: 10.1038/msb.2009.89. Epub 2009 Dec 1. No abstract available.


A phase I study of flavopiridol in combination with gemcitabine and irinotecan in patients with metastatic cancer.

Fekrazad HM, Verschraegen CF, Royce M, Smith HO, Chyi Lee F, Rabinowitz I.

Am J Clin Oncol. 2010 Aug;33(4):393-7. doi: 10.1097/COC.0b013e3181b2043f.


The evolution of RecD outside of the RecBCD complex.

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

J Mol Evol. 2009 Oct;69(4):360-71. doi: 10.1007/s00239-009-9290-x. Epub 2009 Oct 20.


Creating bacterial strains from genomes that have been cloned and engineered in yeast.

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 3rd, Smith HO, Venter JC, Glass JI.

Science. 2009 Sep 25;325(5948):1693-6. doi: 10.1126/science.1173759. Epub 2009 Aug 20.


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

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

Appl Environ Microbiol. 2009 Sep;75(18):5821-30. doi: 10.1128/AEM.00580-09. Epub 2009 Jul 24.


Estrogen and progesterone receptor status and outcome in epithelial ovarian cancers and low malignant potential tumors.

Arias-Pulido H, Smith HO, Joste NE, Bocklage T, Qualls CR, Chavez A, Prossnitz ER, Verschraegen CF.

Gynecol Oncol. 2009 Sep;114(3):480-5. doi: 10.1016/j.ygyno.2009.05.045. Epub 2009 Jun 27.


GPR30 predicts poor survival for ovarian cancer.

Smith HO, Arias-Pulido H, Kuo DY, Howard T, Qualls CR, Lee SJ, Verschraegen CF, Hathaway HJ, Joste NE, Prossnitz ER.

Gynecol Oncol. 2009 Sep;114(3):465-71. doi: 10.1016/j.ygyno.2009.05.015. Epub 2009 Jun 6.


Southwest Oncology Group Trial S9912: intraperitoneal cisplatin and paclitaxel plus intravenous paclitaxel and pegylated liposomal doxorubicin as primary chemotherapy of small-volume residual stage III ovarian cancer.

Smith HO, Moon J, Wilczynski SP, Tiersten AD, Hannigan EV, Robinson WR, Rivkin SE, Anderson GL, Liu PY, Markman M.

Gynecol Oncol. 2009 Aug;114(2):206-9. doi: 10.1016/j.ygyno.2009.04.023. Epub 2009 May 23.


Enzymatic assembly of DNA molecules up to several hundred kilobases.

Gibson DG, Young L, Chuang RY, Venter JC, Hutchison CA 3rd, Smith HO.

Nat Methods. 2009 May;6(5):343-5. doi: 10.1038/nmeth.1318. Epub 2009 Apr 12.


In vivo light scattering for the detection of cancerous and precancerous lesions of the cervix.

Mourant JR, Powers TM, Bocklage TJ, Greene HM, Dorin MH, Waxman AG, Zsemlye MM, Smith HO.

Appl Opt. 2009 Apr 1;48(10):D26-35.


Phase II evaluation of neoadjuvant chemotherapy and debulking followed by intraperitoneal chemotherapy in women with stage III and IV epithelial ovarian, fallopian tube or primary peritoneal cancer: Southwest Oncology Group Study S0009.

Tiersten AD, Liu PY, Smith HO, Wilczynski SP, Robinson WR 3rd, Markman M, Alberts DS.

Gynecol Oncol. 2009 Mar;112(3):444-9. doi: 10.1016/j.ygyno.2008.10.028. Epub 2009 Jan 12.

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