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Items: 20

1.

Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis.

Johnson JS, Spakowicz DJ, Hong BY, Petersen LM, Demkowicz P, Chen L, Leopold SR, Hanson BM, Agresta HO, Gerstein M, Sodergren E, Weinstock GM.

Nat Commun. 2019 Nov 6;10(1):5029. doi: 10.1038/s41467-019-13036-1.

2.

Change in neutrophil to lymphocyte ratio during immunotherapy treatment is a non-linear predictor of patient outcomes in advanced cancers.

Li M, Spakowicz D, Burkart J, Patel S, Husain M, He K, Bertino EM, Shields PG, Carbone DP, Verschraegen CF, Presley CJ, Otterson GA, Kendra K, Owen DH.

J Cancer Res Clin Oncol. 2019 Oct;145(10):2541-2546. doi: 10.1007/s00432-019-02982-4. Epub 2019 Jul 31.

3.

Longitudinal multi-omics of host-microbe dynamics in prediabetes.

Zhou W, Sailani MR, Contrepois K, Zhou Y, Ahadi S, Leopold SR, Zhang MJ, Rao V, Avina M, Mishra T, Johnson J, Lee-McMullen B, Chen S, Metwally AA, Tran TDB, Nguyen H, Zhou X, Albright B, Hong BY, Petersen L, Bautista E, Hanson B, Chen L, Spakowicz D, Bahmani A, Salins D, Leopold B, Ashland M, Dagan-Rosenfeld O, Rego S, Limcaoco P, Colbert E, Allister C, Perelman D, Craig C, Wei E, Chaib H, Hornburg D, Dunn J, Liang L, Rose SMS, Kukurba K, Piening B, Rost H, Tse D, McLaughlin T, Sodergren E, Weinstock GM, Snyder M.

Nature. 2019 May;569(7758):663-671. doi: 10.1038/s41586-019-1236-x. Epub 2019 May 29.

4.

Integrative Personal Omics Profiles during Periods of Weight Gain and Loss.

Piening BD, Zhou W, Contrepois K, Röst H, Gu Urban GJ, Mishra T, Hanson BM, Bautista EJ, Leopold S, Yeh CY, Spakowicz D, Banerjee I, Chen C, Kukurba K, Perelman D, Craig C, Colbert E, Salins D, Rego S, Lee S, Zhang C, Wheeler J, Sailani MR, Liang L, Abbott C, Gerstein M, Mardinoglu A, Smith U, Rubin DL, Pitteri S, Sodergren E, McLaughlin TL, Weinstock GM, Snyder MP.

Cell Syst. 2018 Feb 28;6(2):157-170.e8. doi: 10.1016/j.cels.2017.12.013. Epub 2018 Jan 17.

5.

Volatile Metabolomic Composition of Vitex Species: Chemodiversity Insights and Acaricidal Activity.

de Sena Filho JG, Barreto IC, Soares Filho AO, Nogueira PCL, Teodoro AV, Cruz da Silva AV, Xavier HS, Rabbani ARC, Spakowicz DJ, Duringer JM.

Front Plant Sci. 2017 Nov 14;8:1931. doi: 10.3389/fpls.2017.01931. eCollection 2017.

6.

Genome of Diaporthe sp. provides insights into the potential inter-phylum transfer of a fungal sesquiterpenoid biosynthetic pathway.

de Sena Filho JG, Quin MB, Spakowicz DJ, Shaw JJ, Kucera K, Dunican B, Strobel SA, Schmidt-Dannert C.

Fungal Biol. 2016 Aug;120(8):1050-1063. doi: 10.1016/j.funbio.2016.04.001. Epub 2016 Apr 12.

7.

Erratum to: The real cost of sequencing: scaling computation to keep pace with data generation.

Muir P, Li S, Lou S, Wang D, Spakowicz DJ, Salichos L, Zhang J, Weinstock GM, Isaacs F, Rozowsky J, Gerstein M.

Genome Biol. 2016 Apr 28;17:78. doi: 10.1186/s13059-016-0961-9. No abstract available.

8.

The real cost of sequencing: scaling computation to keep pace with data generation.

Muir P, Li S, Lou S, Wang D, Spakowicz DJ, Salichos L, Zhang J, Weinstock GM, Isaacs F, Rozowsky J, Gerstein M.

Genome Biol. 2016 Mar 23;17:53. doi: 10.1186/s13059-016-0917-0. Erratum in: Genome Biol. 2016;17:78.

9.

Pyrrolocin A, a 3-Decalinoyltetramic Acid with Selective Biological Activity, Isolated from Amazonian Cultures of the Novel Endophyte Diaporthales sp. E6927E.

Patridge EV, Darnell A, Kucera K, Phillips GM, Bokesch HR, Gustafson KR, Spakowicz DJ, Zhou L, Hungerford WM, Plummer M, Hoyer D, Narváez-Trujillo A, Phillips AJ, Strobel SA.

Nat Prod Commun. 2015 Oct;10(10):1649-54.

PMID:
26669095
10.

Stelliosphaerols A and B, Sesquiterpene-Polyol Conjugates from an Ecuadorian Fungal Endophyte.

Forcina GC, Castro A, Bokesch HR, Spakowicz DJ, Legaspi ME, Kucera K, Villota S, Narváez-Trujillo A, McMahon JB, Gustafson KR, Strobel SA.

J Nat Prod. 2015 Dec 24;78(12):3005-10. doi: 10.1021/acs.jnatprod.5b00749. Epub 2015 Dec 14.

11.

The Biological Diversity and Production of Volatile Organic Compounds by Stem-Inhabiting Endophytic Fungi of Ecuador.

Rundell SM, Spakowicz DJ, Narváez-Trujillo A, Strobel SA.

J Fungi (Basel). 2015 Dec 2;1(3):384-396. doi: 10.3390/jof1030384.

12.

Biosynthesis of hydrocarbons and volatile organic compounds by fungi: bioengineering potential.

Spakowicz DJ, Strobel SA.

Appl Microbiol Biotechnol. 2015 Jun;99(12):4943-51. doi: 10.1007/s00253-015-6641-y. Epub 2015 May 10. Review.

13.

Biosynthesis and genomic analysis of medium-chain hydrocarbon production by the endophytic fungal isolate Nigrograna mackinnonii E5202H.

Shaw JJ, Spakowicz DJ, Dalal RS, Davis JH, Lehr NA, Dunican BF, Orellana EA, Narváez-Trujillo A, Strobel SA.

Appl Microbiol Biotechnol. 2015 Apr;99(8):3715-28. doi: 10.1007/s00253-014-6206-5. Epub 2015 Feb 12.

14.

Identification of a fungal 1,8-cineole synthase from Hypoxylon sp. with specificity determinants in common with the plant synthases.

Shaw JJ, Berbasova T, Sasaki T, Jefferson-George K, Spakowicz DJ, Dunican BF, Portero CE, Narváez-Trujillo A, Strobel SA.

J Biol Chem. 2015 Mar 27;290(13):8511-26. doi: 10.1074/jbc.M114.636159. Epub 2015 Feb 3.

15.

Genomic analysis of the hydrocarbon-producing, cellulolytic, endophytic fungus Ascocoryne sarcoides.

Gianoulis TA, Griffin MA, Spakowicz DJ, Dunican BF, Alpha CJ, Sboner A, Sismour AM, Kodira C, Egholm M, Church GM, Gerstein MB, Strobel SA.

PLoS Genet. 2012;8(3):e1002558. doi: 10.1371/journal.pgen.1002558. Epub 2012 Mar 1.

16.

Hypoxylon sp., an endophyte of Persea indica, producing 1,8-cineole and other bioactive volatiles with fuel potential.

Tomsheck AR, Strobel GA, Booth E, Geary B, Spakowicz D, Knighton B, Floerchinger C, Sears J, Liarzi O, Ezra D.

Microb Ecol. 2010 Nov;60(4):903-14. doi: 10.1007/s00248-010-9759-6. Epub 2010 Oct 17.

PMID:
20953951
17.

Volatile organic compound production by organisms in the genus Ascocoryne and a re-evaluation of myco-diesel production by NRRL 50072.

Griffin MA, Spakowicz DJ, Gianoulis TA, Strobel SA.

Microbiology. 2010 Dec;156(Pt 12):3814-29. doi: 10.1099/mic.0.041327-0. Epub 2010 Aug 12.

PMID:
20705658
18.

The production of myco-diesel hydrocarbons and their derivatives by the endophytic fungus Gliocladium roseum (NRRL 50072).

Strobel GA, Knighton B, Kluck K, Ren Y, Livinghouse T, Griffin M, Spakowicz D, Sears J.

Microbiology. 2008 Nov;154(Pt 11):3319-28. doi: 10.1099/mic.0.2008/022186-0. Erratum in: Microbiology. 2010 Dec;156(Pt 12):3830-3.

PMID:
18957585
19.

Changes in actin structural transitions associated with oxidative inhibition of muscle contraction.

Prochniewicz E, Spakowicz D, Thomas DD.

Biochemistry. 2008 Nov 11;47(45):11811-7. doi: 10.1021/bi801080x. Epub 2008 Oct 15.

20.

Functional, structural, and chemical changes in myosin associated with hydrogen peroxide treatment of skeletal muscle fibers.

Prochniewicz E, Lowe DA, Spakowicz DJ, Higgins L, O'Conor K, Thompson LV, Ferrington DA, Thomas DD.

Am J Physiol Cell Physiol. 2008 Feb;294(2):C613-26. Epub 2007 Nov 14.

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