Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 27

1.

Histopathological Image QTL Discovery of Immune Infiltration Variants.

Barry JD, Fagny M, Paulson JN, Aerts HJWL, Platig J, Quackenbush J.

iScience. 2018 Jul 27;5:80-89. doi: 10.1016/j.isci.2018.07.001. Epub 2018 Jul 6.

2.

Conventional wastewater treatment and reuse site practices modify bacterial community structure but do not eliminate some opportunistic pathogens in reclaimed water.

Kulkarni P, Olson ND, Paulson JN, Pop M, Maddox C, Claye E, Rosenberg Goldstein RE, Sharma M, Gibbs SG, Mongodin EF, Sapkota AR.

Sci Total Environ. 2018 Oct 15;639:1126-1137. doi: 10.1016/j.scitotenv.2018.05.178. Epub 2018 May 26.

PMID:
29929281
3.

Cancer subtype identification using somatic mutation data.

Kuijjer ML, Paulson JN, Salzman P, Ding W, Quackenbush J.

Br J Cancer. 2018 May 16. doi: 10.1038/s41416-018-0109-7. [Epub ahead of print]

4.

Meta-analysis of the lung microbiota in pulmonary tuberculosis.

Hong BY, Paulson JN, Stine OC, Weinstock GM, Cervantes JL.

Tuberculosis (Edinb). 2018 Mar;109:102-108. doi: 10.1016/j.tube.2018.02.006. Epub 2018 Feb 22.

PMID:
29559113
5.

Metaviz: interactive statistical and visual analysis of metagenomic data.

Wagner J, Chelaru F, Kancherla J, Paulson JN, Zhang A, Felix V, Mahurkar A, Elmqvist N, Corrada Bravo H.

Nucleic Acids Res. 2018 Apr 6;46(6):2777-2787. doi: 10.1093/nar/gky136.

6.

Multisystem Analysis of Mycobacterium tuberculosis Reveals Kinase-Dependent Remodeling of the Pathogen-Environment Interface.

Carette X, Platig J, Young DC, Helmel M, Young AT, Wang Z, Potluri LP, Moody CS, Zeng J, Prisic S, Paulson JN, Muntel J, Madduri AVR, Velarde J, Mayfield JA, Locher C, Wang T, Quackenbush J, Rhee KY, Moody DB, Steen H, Husson RN.

MBio. 2018 Mar 6;9(2). pii: e02333-17. doi: 10.1128/mBio.02333-17.

7.

Age-dependent alterations of glucose clearance and homeostasis are temporally separated and modulated by dietary fat.

Damgaard MTF, Pærregaard SI, Søgaard I, Agerholm M, Paulson JN, Treebak JT, Sina C, Holm JB, Kristiansen K, Jensen BAH.

J Nutr Biochem. 2018 Apr;54:66-76. doi: 10.1016/j.jnutbio.2017.09.026. Epub 2017 Oct 18.

PMID:
29268121
8.

Understanding Tissue-Specific Gene Regulation.

Sonawane AR, Platig J, Fagny M, Chen CY, Paulson JN, Lopes-Ramos CM, DeMeo DL, Quackenbush J, Glass K, Kuijjer ML.

Cell Rep. 2017 Oct 24;21(4):1077-1088. doi: 10.1016/j.celrep.2017.10.001.

9.

Smooth quantile normalization.

Hicks SC, Okrah K, Paulson JN, Quackenbush J, Irizarry RA, Bravo HC.

Biostatistics. 2018 Apr 1;19(2):185-198. doi: 10.1093/biostatistics/kxx028.

PMID:
29036413
10.

Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data.

Paulson JN, Chen CY, Lopes-Ramos CM, Kuijjer ML, Platig J, Sonawane AR, Fagny M, Glass K, Quackenbush J.

BMC Bioinformatics. 2017 Oct 3;18(1):437. doi: 10.1186/s12859-017-1847-x.

11.

Regulatory network changes between cell lines and their tissues of origin.

Lopes-Ramos CM, Paulson JN, Chen CY, Kuijjer ML, Fagny M, Platig J, Sonawane AR, DeMeo DL, Quackenbush J, Glass K.

BMC Genomics. 2017 Sep 12;18(1):723. doi: 10.1186/s12864-017-4111-x.

12.

Exploring regulation in tissues with eQTL networks.

Fagny M, Paulson JN, Kuijjer ML, Sonawane AR, Chen CY, Lopes-Ramos CM, Glass K, Quackenbush J, Platig J.

Proc Natl Acad Sci U S A. 2017 Sep 12;114(37):E7841-E7850. doi: 10.1073/pnas.1707375114. Epub 2017 Aug 29.

13.

Minimal genetic change in Vibrio cholerae in Mozambique over time: Multilocus variable number tandem repeat analysis and whole genome sequencing.

Garrine M, Mandomando I, Vubil D, Nhampossa T, Acacio S, Li S, Paulson JN, Almeida M, Domman D, Thomson NR, Alonso P, Stine OC.

PLoS Negl Trop Dis. 2017 Jun 16;11(6):e0005671. doi: 10.1371/journal.pntd.0005671. eCollection 2017 Jun.

14.

Estimating gene regulatory networks with pandaR.

Schlauch D, Paulson JN, Young A, Glass K, Quackenbush J.

Bioinformatics. 2017 Jul 15;33(14):2232-2234. doi: 10.1093/bioinformatics/btx139.

15.

Temporal Variations in Cigarette Tobacco Bacterial Community Composition and Tobacco-Specific Nitrosamine Content Are Influenced by Brand and Storage Conditions.

Chopyk J, Chattopadhyay S, Kulkarni P, Smyth EM, Hittle LE, Paulson JN, Pop M, Buehler SS, Clark PI, Mongodin EF, Sapkota AR.

Front Microbiol. 2017 Mar 7;8:358. doi: 10.3389/fmicb.2017.00358. eCollection 2017.

16.

Simplified and representative bacterial community of maize roots.

Niu B, Paulson JN, Zheng X, Kolter R.

Proc Natl Acad Sci U S A. 2017 Mar 21;114(12):E2450-E2459. doi: 10.1073/pnas.1616148114. Epub 2017 Mar 8.

17.

Mentholation affects the cigarette microbiota by selecting for bacteria resistant to harsh environmental conditions and selecting against potential bacterial pathogens.

Chopyk J, Chattopadhyay S, Kulkarni P, Claye E, Babik KR, Reid MC, Smyth EM, Hittle LE, Paulson JN, Cruz-Cano R, Pop M, Buehler SS, Clark PI, Sapkota AR, Mongodin EF.

Microbiome. 2017 Feb 15;5(1):22. doi: 10.1186/s40168-017-0235-0.

18.

Dynamic metabolic exchange governs a marine algal-bacterial interaction.

Segev E, Wyche TP, Kim KH, Petersen J, Ellebrandt C, Vlamakis H, Barteneva N, Paulson JN, Chai L, Clardy J, Kolter R.

Elife. 2016 Nov 18;5. pii: e17473. doi: 10.7554/eLife.17473.

19.

Longitudinal analysis of the lung microbiota of cynomolgous macaques during long-term SHIV infection.

Morris A, Paulson JN, Talukder H, Tipton L, Kling H, Cui L, Fitch A, Pop M, Norris KA, Ghedin E.

Microbiome. 2016 Jul 8;4(1):38. doi: 10.1186/s40168-016-0183-0.

20.

Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment.

Pop M, Paulson JN, Chakraborty S, Astrovskaya I, Lindsay BR, Li S, Bravo HC, Harro C, Parkhill J, Walker AW, Walker RI, Sack DA, Stine OC.

BMC Genomics. 2016 Jun 8;17:440. doi: 10.1186/s12864-016-2777-0.

21.

Privacy-preserving microbiome analysis using secure computation.

Wagner J, Paulson JN, Wang X, Bhattacharjee B, Corrada Bravo H.

Bioinformatics. 2016 Jun 15;32(12):1873-9. doi: 10.1093/bioinformatics/btw073. Epub 2016 Feb 11.

22.

Methylome Analysis in Chickens Immunized with Infectious Laryngotracheitis Vaccine.

Carrillo JA, He Y, Luo J, Menendez KR, Tablante NL, Zhao K, Paulson JN, Li B, Song J.

PLoS One. 2015 Jun 24;10(6):e0100476. doi: 10.1371/journal.pone.0100476. eCollection 2015.

23.

Microbiota that affect risk for shigellosis in children in low-income countries.

Lindsay B, Oundo J, Hossain MA, Antonio M, Tamboura B, Walker AW, Paulson JN, Parkhill J, Omore R, Faruque AS, Das SK, Ikumapayi UN, Adeyemi M, Sanogo D, Saha D, Sow S, Farag TH, Nasrin D, Li S, Panchalingam S, Levine MM, Kotloff K, Magder LS, Hungerford L, Sommerfelt H, Pop M, Nataro JP, Stine OC.

Emerg Infect Dis. 2015 Feb;21(2):242-50. doi: 10.3201/eid2101.140795.

24.

Reply to: "a fair comparison".

Paulson JN, Bravo HC, Pop M.

Nat Methods. 2014 Apr;11(4):359-60. doi: 10.1038/nmeth.2898. No abstract available.

PMID:
24681718
25.

Differential abundance analysis for microbial marker-gene surveys.

Paulson JN, Stine OC, Bravo HC, Pop M.

Nat Methods. 2013 Dec;10(12):1200-2. doi: 10.1038/nmeth.2658. Epub 2013 Sep 29.

26.

Survey of culture, goldengate assay, universal biosensor assay, and 16S rRNA Gene sequencing as alternative methods of bacterial pathogen detection.

Lindsay B, Pop M, Antonio M, Walker AW, Mai V, Ahmed D, Oundo J, Tamboura B, Panchalingam S, Levine MM, Kotloff K, Li S, Magder LS, Paulson JN, Liu B, Ikumapayi U, Ebruke C, Dione M, Adeyemi M, Rance R, Stares MD, Ukhanova M, Barnes B, Lewis I, Ahmed F, Alam MT, Amin R, Siddiqui S, Ochieng JB, Ouma E, Juma J, Mailu E, Omore R, O'Reilly CE, Hannis J, Manalili S, Deleon J, Yasuda I, Blyn L, Ranken R, Li F, Housley R, Ecker DJ, Hossain MA, Breiman RF, Morris JG, McDaniel TK, Parkhill J, Saha D, Sampath R, Stine OC, Nataro JP.

J Clin Microbiol. 2013 Oct;51(10):3263-9. doi: 10.1128/JCM.01342-13. Epub 2013 Jul 24.

27.

Anterior vaginal wall tenderness (AVWT) as a physical symptom in chronic pelvic pain.

Paulson JD, Paulson JN.

JSLS. 2011 Jan-Mar;15(1):6-9. doi: 10.4293/108680810X12924466008961.

Supplemental Content

Loading ...
Support Center