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Items: 47

1.

An in situ high-throughput screen identifies inhibitors of intracellular Burkholderia pseudomallei with therapeutic efficacy.

Bulterys PL, Toesca IJ, Norris MH, Maloy JP, Fitz-Gibbon ST, France B, Toffig B, Morselli M, Somprasong N, Pellegrini M, Schweizer HP, Tuanyok A, Damoiseaux R, French CT, Miller JF.

Proc Natl Acad Sci U S A. 2019 Sep 10;116(37):18597-18606. doi: 10.1073/pnas.1906388116. Epub 2019 Aug 22.

2.

Landscape genomics provides evidence of climate-associated genetic variation in Mexican populations of Quercus rugosa.

Martins K, Gugger PF, Llanderal-Mendoza J, González-Rodríguez A, Fitz-Gibbon ST, Zhao JL, Rodríguez-Correa H, Oyama K, Sork VL.

Evol Appl. 2018 Aug 31;11(10):1842-1858. doi: 10.1111/eva.12684. eCollection 2018 Dec.

3.

Improving Gene Editing Outcomes in Human Hematopoietic Stem and Progenitor Cells by Temporal Control of DNA Repair.

Lomova A, Clark DN, Campo-Fernandez B, Flores-Bjurström C, Kaufman ML, Fitz-Gibbon S, Wang X, Miyahira EY, Brown D, DeWitt MA, Corn JE, Hollis RP, Romero Z, Kohn DB.

Stem Cells. 2019 Feb;37(2):284-294. doi: 10.1002/stem.2935. Epub 2018 Nov 27.

PMID:
30372555
4.

Metabolic repair through emergence of new pathways in Escherichia coli.

Pontrelli S, Fricke RCB, Teoh ST, Laviña WA, Putri SP, Fitz-Gibbon S, Chung M, Pellegrini M, Fukusaki E, Liao JC.

Nat Chem Biol. 2018 Nov;14(11):1005-1009. doi: 10.1038/s41589-018-0149-6. Epub 2018 Oct 16.

PMID:
30327558
5.

Assessment of shared alleles in drought-associated candidate genes among southern California white oak species (Quercus sect. Quercus).

Oney-Birol S, Fitz-Gibbon S, Chen JM, Gugger PF, Sork VL.

BMC Genet. 2018 Oct 1;19(1):88. doi: 10.1186/s12863-018-0677-9.

6.

RADseq data reveal ancient, but not pervasive, introgression between Californian tree and scrub oak species (Quercus sect. Quercus: Fagaceae).

Kim BY, Wei X, Fitz-Gibbon S, Lohmueller KE, Ortego J, Gugger PF, Sork VL.

Mol Ecol. 2018 Nov;27(22):4556-4571. doi: 10.1111/mec.14869. Epub 2018 Oct 12.

PMID:
30226013
7.

Directed strain evolution restructures metabolism for 1-butanol production in minimal media.

Pontrelli S, Fricke RCB, Sakurai SSM, Putri SP, Fitz-Gibbon S, Chung M, Wu HY, Chen YJ, Pellegrini M, Fukusaki E, Liao JC.

Metab Eng. 2018 Sep;49:153-163. doi: 10.1016/j.ymben.2018.08.004. Epub 2018 Aug 11.

PMID:
30107263
8.

Site-Specific Gene Editing of Human Hematopoietic Stem Cells for X-Linked Hyper-IgM Syndrome.

Kuo CY, Long JD, Campo-Fernandez B, de Oliveira S, Cooper AR, Romero Z, Hoban MD, Joglekar AV, Lill GR, Kaufman ML, Fitz-Gibbon S, Wang X, Hollis RP, Kohn DB.

Cell Rep. 2018 May 29;23(9):2606-2616. doi: 10.1016/j.celrep.2018.04.103.

9.

Complete genomic sequences of Propionibacterium freudenreichii phages from Swiss cheese reveal greater diversity than Cutibacterium (formerly Propionibacterium) acnes phages.

Cheng L, Marinelli LJ, Grosset N, Fitz-Gibbon ST, Bowman CA, Dang BQ, Russell DA, Jacobs-Sera D, Shi B, Pellegrini M, Miller JF, Gautier M, Hatfull GF, Modlin RL.

BMC Microbiol. 2018 Mar 1;18(1):19. doi: 10.1186/s12866-018-1159-y.

10.
11.

Phylogenomic inferences from reference-mapped and de novo assembled short-read sequence data using RADseq sequencing of California white oaks (Quercus section Quercus).

Fitz-Gibbon S, Hipp AL, Pham KK, Manos PS, Sork VL.

Genome. 2017 Sep;60(9):743-755. doi: 10.1139/gen-2016-0202. Epub 2017 Mar 29.

12.

Human Embryonic Stem Cells Do Not Change Their X Inactivation Status during Differentiation.

Patel S, Bonora G, Sahakyan A, Kim R, Chronis C, Langerman J, Fitz-Gibbon S, Rubbi L, Skelton RJP, Ardehali R, Pellegrini M, Lowry WE, Clark AT, Plath K.

Cell Rep. 2017 Jan 3;18(1):54-67. doi: 10.1016/j.celrep.2016.11.054. Epub 2016 Dec 16.

13.

First Draft Assembly and Annotation of the Genome of a California Endemic Oak Quercus lobata Née (Fagaceae).

Sork VL, Fitz-Gibbon ST, Puiu D, Crepeau M, Gugger PF, Sherman R, Stevens K, Langley CH, Pellegrini M, Salzberg SL.

G3 (Bethesda). 2016 Nov 8;6(11):3485-3495. doi: 10.1534/g3.116.030411.

14.

CRISPR/Cas9-Mediated Correction of the Sickle Mutation in Human CD34+ cells.

Hoban MD, Lumaquin D, Kuo CY, Romero Z, Long J, Ho M, Young CS, Mojadidi M, Fitz-Gibbon S, Cooper AR, Lill GR, Urbinati F, Campo-Fernandez B, Bjurstrom CF, Pellegrini M, Hollis RP, Kohn DB.

Mol Ther. 2016 Sep;24(9):1561-9. doi: 10.1038/mt.2016.148. Epub 2016 Jul 29.

15.

Ni induces the CRR1-dependent regulon revealing overlap and distinction between hypoxia and Cu deficiency responses in Chlamydomonas reinhardtii.

Blaby-Haas CE, Castruita M, Fitz-Gibbon ST, Kropat J, Merchant SS.

Metallomics. 2016 Jul 13;8(7):679-91. doi: 10.1039/c6mt00063k.

16.

Epigenetic changes mediated by polycomb repressive complex 2 and E2a are associated with drug resistance in a mouse model of lymphoma.

Flinders C, Lam L, Rubbi L, Ferrari R, Fitz-Gibbon S, Chen PY, Thompson M, Christofk H, B Agus D, Ruderman D, Mallick P, Pellegrini M.

Genome Med. 2016 May 4;8(1):54. doi: 10.1186/s13073-016-0305-0.

17.

Species-wide patterns of DNA methylation variation in Quercus lobata and their association with climate gradients.

Gugger PF, Fitz-Gibbon S, PellEgrini M, Sork VL.

Mol Ecol. 2016 Apr;25(8):1665-80. doi: 10.1111/mec.13563. Epub 2016 Mar 14.

PMID:
26833902
18.

An Indexed, Mapped Mutant Library Enables Reverse Genetics Studies of Biological Processes in Chlamydomonas reinhardtii.

Li X, Zhang R, Patena W, Gang SS, Blum SR, Ivanova N, Yue R, Robertson JM, Lefebvre PA, Fitz-Gibbon ST, Grossman AR, Jonikas MC.

Plant Cell. 2016 Feb;28(2):367-87. doi: 10.1105/tpc.15.00465. Epub 2016 Jan 13.

19.

Genome-wide analysis on Chlamydomonas reinhardtii reveals the impact of hydrogen peroxide on protein stress responses and overlap with other stress transcriptomes.

Blaby IK, Blaby-Haas CE, Pérez-Pérez ME, Schmollinger S, Fitz-Gibbon S, Lemaire SD, Merchant SS.

Plant J. 2015 Dec;84(5):974-988. doi: 10.1111/tpj.13053.

20.

Dynamic Changes in the Transcriptome and Methylome of Chlamydomonas reinhardtii throughout Its Life Cycle.

Lopez D, Hamaji T, Kropat J, De Hoff P, Morselli M, Rubbi L, Fitz-Gibbon S, Gallaher SD, Merchant SS, Umen J, Pellegrini M.

Plant Physiol. 2015 Dec;169(4):2730-43. doi: 10.1104/pp.15.00861. Epub 2015 Oct 8.

21.

Distinct Shifts in Microbiota Composition during Drosophila Aging Impair Intestinal Function and Drive Mortality.

Clark RI, Salazar A, Yamada R, Fitz-Gibbon S, Morselli M, Alcaraz J, Rana A, Rera M, Pellegrini M, Ja WW, Walker DW.

Cell Rep. 2015 Sep 8;12(10):1656-67. doi: 10.1016/j.celrep.2015.08.004. Epub 2015 Aug 28.

22.

Chlamydomonas Genome Resource for Laboratory Strains Reveals a Mosaic of Sequence Variation, Identifies True Strain Histories, and Enables Strain-Specific Studies.

Gallaher SD, Fitz-Gibbon ST, Glaesener AG, Pellegrini M, Merchant SS.

Plant Cell. 2015 Sep;27(9):2335-52. doi: 10.1105/tpc.15.00508. Epub 2015 Aug 25.

23.

Genome-wide gene order distances support clustering the gram-positive bacteria.

House CH, Pellegrini M, Fitz-Gibbon ST.

Front Microbiol. 2015 Jan 20;5:785. doi: 10.3389/fmicb.2014.00785. eCollection 2014.

24.

Cloning of a functional 25-hydroxyvitamin D-1α-hydroxylase in zebrafish (Danio rerio).

Chun RF, Blatter E, Elliott S, Fitz-Gibbon S, Rieger S, Sagasti A, Adams JS, Hewison M.

Cell Biochem Funct. 2014 Dec;32(8):675-82. doi: 10.1002/cbf.3071. Epub 2014 Oct 7.

25.

Systems-level analysis of nitrogen starvation-induced modifications of carbon metabolism in a Chlamydomonas reinhardtii starchless mutant.

Blaby IK, Glaesener AG, Mettler T, Fitz-Gibbon ST, Gallaher SD, Liu B, Boyle NR, Kropat J, Stitt M, Johnson S, Benning C, Pellegrini M, Casero D, Merchant SS.

Plant Cell. 2013 Nov;25(11):4305-23. doi: 10.1105/tpc.113.117580. Epub 2013 Nov 26.

26.

Analysis of complete genomes of Propionibacterium acnes reveals a novel plasmid and increased pseudogenes in an acne associated strain.

Kasimatis G, Fitz-Gibbon S, Tomida S, Wong M, Li H.

Biomed Res Int. 2013;2013:918320. doi: 10.1155/2013/918320. Epub 2013 May 13.

27.

Propionibacterium acnes strain populations in the human skin microbiome associated with acne.

Fitz-Gibbon S, Tomida S, Chiu BH, Nguyen L, Du C, Liu M, Elashoff D, Erfe MC, Loncaric A, Kim J, Modlin RL, Miller JF, Sodergren E, Craft N, Weinstock GM, Li H.

J Invest Dermatol. 2013 Sep;133(9):2152-60. doi: 10.1038/jid.2013.21. Epub 2013 Jan 21.

28.

Propionibacterium acnes bacteriophages display limited genetic diversity and broad killing activity against bacterial skin isolates.

Marinelli LJ, Fitz-Gibbon S, Hayes C, Bowman C, Inkeles M, Loncaric A, Russell DA, Jacobs-Sera D, Cokus S, Pellegrini M, Kim J, Miller JF, Hatfull GF, Modlin RL.

MBio. 2012 Sep 25;3(5). pii: e00279-12. doi: 10.1128/mBio.00279-12. Print 2012.

29.

Amino acid signatures of salinity on an environmental scale with a focus on the Dead Sea.

Rhodes ME, Fitz-Gibbon ST, Oren A, House CH.

Environ Microbiol. 2010 Sep;12(9):2613-23. doi: 10.1111/j.1462-2920.2010.02232.x. Epub 2010 May 7.

PMID:
20482588
30.

Metagenomic signatures of the Peru Margin subseafloor biosphere show a genetically distinct environment.

Biddle JF, Fitz-Gibbon S, Schuster SC, Brenchley JE, House CH.

Proc Natl Acad Sci U S A. 2008 Jul 29;105(30):10583-8. doi: 10.1073/pnas.0709942105. Epub 2008 Jul 23.

31.

Terminal addition, the Cambrian radiation and the Phanerozoic evolution of bilaterian form.

Jacobs DK, Hughes NC, Fitz-Gibbon ST, Winchell CJ.

Evol Dev. 2005 Nov-Dec;7(6):498-514. Review.

PMID:
16336405
32.

The euryarchaeota, nature's medium for engineering of single-stranded DNA-binding proteins.

Robbins JB, McKinney MC, Guzman CE, Sriratana B, Fitz-Gibbon S, Ha T, Cann IK.

J Biol Chem. 2005 Apr 15;280(15):15325-39. Epub 2005 Jan 24.

33.

A novel uracil-DNA glycosylase with broad substrate specificity and an unusual active site.

Sartori AA, Fitz-Gibbon S, Yang H, Miller JH, Jiricny J.

EMBO J. 2002 Jun 17;21(12):3182-91.

34.

Using homolog groups to create a whole-genomic tree of free-living organisms: an update.

House CH, Fitz-Gibbon ST.

J Mol Evol. 2002 Apr;54(4):539-47.

PMID:
11956692
35.

Direct interaction between uracil-DNA glycosylase and a proliferating cell nuclear antigen homolog in the crenarchaeon Pyrobaculum aerophilum.

Yang H, Chiang JH, Fitz-Gibbon S, Lebel M, Sartori AA, Jiricny J, Slupska MM, Miller JH.

J Biol Chem. 2002 Jun 21;277(25):22271-8. Epub 2002 Apr 1.

36.

Genome sequence of the hyperthermophilic crenarchaeon Pyrobaculum aerophilum.

Fitz-Gibbon ST, Ladner H, Kim UJ, Stetter KO, Simon MI, Miller JH.

Proc Natl Acad Sci U S A. 2002 Jan 22;99(2):984-9. Epub 2002 Jan 15.

37.

Biochemical characterization of uracil processing activities in the hyperthermophilic archaeon Pyrobaculum aerophilum.

Sartori AA, Schär P, Fitz-Gibbon S, Miller JH, Jiricny J.

J Biol Chem. 2001 Aug 10;276(32):29979-86. Epub 2001 Jun 8.

38.

Leaderless transcripts of the crenarchaeal hyperthermophile Pyrobaculum aerophilum.

Slupska MM, King AG, Fitz-Gibbon S, Besemer J, Borodovsky M, Miller JH.

J Mol Biol. 2001 Jun 1;309(2):347-60.

PMID:
11371158
39.

A thermostable endonuclease III homolog from the archaeon Pyrobaculum aerophilum.

Yang H, Phan IT, Fitz-Gibbon S, Shivji MK, Wood RD, Clendenin WM, Hyman EC, Miller JH.

Nucleic Acids Res. 2001 Feb 1;29(3):604-13.

40.

Cloning and characterization of a new member of the Nudix hydrolases from human and mouse.

Yang H, Slupska MM, Wei YF, Tai JH, Luther WM, Xia YR, Shih DM, Chiang JH, Baikalov C, Fitz-Gibbon S, Phan IT, Conrad A, Miller JH.

J Biol Chem. 2000 Mar 24;275(12):8844-53.

41.

Selecting protein targets for structural genomics of Pyrobaculum aerophilum: validating automated fold assignment methods by using binary hypothesis testing.

Mallick P, Goodwill KE, Fitz-Gibbon S, Miller JH, Eisenberg D.

Proc Natl Acad Sci U S A. 2000 Mar 14;97(6):2450-5.

42.
43.
44.

Whole genome-based phylogenetic analysis of free-living microorganisms.

Fitz-Gibbon ST, House CH.

Nucleic Acids Res. 1999 Nov 1;27(21):4218-22.

45.

A novel Rieske iron-sulfur protein from the hyperthermophilic crenarchaeon Pyrobaculum aerophilum: sequencing of the gene, expression in E. coli and characterization of the protein.

Henninger T, Anemüller S, Fitz-Gibbon S, Miller JH, Schäfer G, Schmidt CL.

J Bioenerg Biomembr. 1999 Apr;31(2):119-28.

PMID:
10449238
46.

A fosmid-based genomic map and identification of 474 genes of the hyperthermophilic archaeon Pyrobaculum aerophilum.

Fitz-Gibbon S, Choi AJ, Miller JH, Stetter KO, Simon MI, Swanson R, Kim UJ.

Extremophiles. 1997 Feb;1(1):36-51.

PMID:
9680335
47.

Genomic and cDNA sequence tags of the hyperthermophilic archaeon Pyrobaculum aerophilum.

Völkl P, Markiewicz P, Baikalov C, Fitz-Gibbon S, Stetter KO, Miller JH.

Nucleic Acids Res. 1996 Nov 15;24(22):4373-8.

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