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Items: 1 to 20 of 47

1.

Evolution of class 1 integrons: Mobilization and dispersal via food-borne bacteria.

Ghaly TM, Chow L, Asher AJ, Waldron LS, Gillings MR.

PLoS One. 2017 Jun 6;12(6):e0179169. doi: 10.1371/journal.pone.0179169. eCollection 2017.

2.

Control of Gene Expression by RNA Binding Protein Action on Alternative Translation Initiation Sites.

Re A, Waldron L, Quattrone A.

PLoS Comput Biol. 2016 Dec 6;12(12):e1005198. doi: 10.1371/journal.pcbi.1005198. eCollection 2016 Dec.

3.

CellMapper: rapid and accurate inference of gene expression in difficult-to-isolate cell types.

Nelms BD, Waldron L, Barrera LA, Weflen AW, Goettel JA, Guo G, Montgomery RK, Neutra MR, Breault DT, Snapper SB, Orkin SH, Bulyk ML, Huttenhower C, Lencer WI.

Genome Biol. 2016 Sep 29;17(1):201.

4.

Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights.

Pasolli E, Truong DT, Malik F, Waldron L, Segata N.

PLoS Comput Biol. 2016 Jul 11;12(7):e1004977. doi: 10.1371/journal.pcbi.1004977. eCollection 2016 Jul.

5.

The Doppelgänger Effect: Hidden Duplicates in Databases of Transcriptome Profiles.

Waldron L, Riester M, Ramos M, Parmigiani G, Birrer M.

J Natl Cancer Inst. 2016 Jul 5;108(11). doi: 10.1093/jnci/djw146. Print 2016 Nov.

6.

Racial/Ethnic Disparities in Genomic Sequencing.

Spratt DE, Chan T, Waldron L, Speers C, Feng FY, Ogunwobi OO, Osborne JR.

JAMA Oncol. 2016 Aug 1;2(8):1070-4. doi: 10.1001/jamaoncol.2016.1854.

7.

The Cardiac TBX5 Interactome Reveals a Chromatin Remodeling Network Essential for Cardiac Septation.

Waldron L, Steimle JD, Greco TM, Gomez NC, Dorr KM, Kweon J, Temple B, Yang XH, Wilczewski CM, Davis IJ, Cristea IM, Moskowitz IP, Conlon FL.

Dev Cell. 2016 Feb 8;36(3):262-75. doi: 10.1016/j.devcel.2016.01.009.

8.

Public data and open source tools for multi-assay genomic investigation of disease.

Kannan L, Ramos M, Re A, El-Hachem N, Safikhani Z, Gendoo DM, Davis S, Gomez-Cabrero D, Castelo R, Hansen KD, Carey VJ, Morgan M, Culhane AC, Haibe-Kains B, Waldron L.

Brief Bioinform. 2016 Jul;17(4):603-15. doi: 10.1093/bib/bbv080. Epub 2015 Oct 12.

9.

Potential impacts of aquatic pollutants: sub-clinical antibiotic concentrations induce genome changes and promote antibiotic resistance.

Chow L, Waldron L, Gillings MR.

Front Microbiol. 2015 Aug 5;6:803. doi: 10.3389/fmicb.2015.00803. eCollection 2015.

10.

A reproducible approach to high-throughput biological data acquisition and integration.

Börnigen D, Moon YS, Rahnavard G, Waldron L, McIver L, Shafquat A, Franzosa EA, Miropolsky L, Sweeney C, Morgan XC, Garrett WS, Huttenhower C.

PeerJ. 2015 Mar 31;3:e791. doi: 10.7717/peerj.791. eCollection 2015.

11.

Screening Foodstuffs for Class 1 Integrons and Gene Cassettes.

Waldron LS, Gillings MR.

J Vis Exp. 2015 Jun 19;(100):e52889. doi: 10.3791/52889.

12.

Comparing Platforms for Messenger RNA Expression Profiling of Archival Formalin-Fixed, Paraffin-Embedded Tissues.

Tyekucheva S, Martin NE, Stack EC, Wei W, Vathipadiekal V, Waldron L, Fiorentino M, Lis RT, Stampfer MJ, Loda M, Parmigiani G, Mucci LA, Birrer M.

J Mol Diagn. 2015 Jul;17(4):374-81. doi: 10.1016/j.jmoldx.2015.02.002. Epub 2015 Apr 30.

13.

Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease.

Morgan XC, Kabakchiev B, Waldron L, Tyler AD, Tickle TL, Milgrom R, Stempak JM, Gevers D, Xavier RJ, Silverberg MS, Huttenhower C.

Genome Biol. 2015 Apr 8;16:67. doi: 10.1186/s13059-015-0637-x.

14.

Orchestrating high-throughput genomic analysis with Bioconductor.

Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M.

Nat Methods. 2015 Feb;12(2):115-21. doi: 10.1038/nmeth.3252. Review.

15.

Más-o-menos: a simple sign averaging method for discrimination in genomic data analysis.

Zhao SD, Parmigiani G, Huttenhower C, Waldron L.

Bioinformatics. 2014 Nov 1;30(21):3062-9. doi: 10.1093/bioinformatics/btu488. Epub 2014 Jul 23.

16.

Cross-study validation for the assessment of prediction algorithms.

Bernau C, Riester M, Boulesteix AL, Parmigiani G, Huttenhower C, Waldron L, Trippa L.

Bioinformatics. 2014 Jun 15;30(12):i105-12. doi: 10.1093/bioinformatics/btu279.

17.

Relating the metatranscriptome and metagenome of the human gut.

Franzosa EA, Morgan XC, Segata N, Waldron L, Reyes J, Earl AM, Giannoukos G, Boylan MR, Ciulla D, Gevers D, Izard J, Garrett WS, Chan AT, Huttenhower C.

Proc Natl Acad Sci U S A. 2014 Jun 3;111(22):E2329-38. doi: 10.1073/pnas.1319284111. Epub 2014 May 19.

18.

Risk prediction for late-stage ovarian cancer by meta-analysis of 1525 patient samples.

Riester M, Wei W, Waldron L, Culhane AC, Trippa L, Oliva E, Kim SH, Michor F, Huttenhower C, Parmigiani G, Birrer MJ.

J Natl Cancer Inst. 2014 Apr 3;106(5). pii: dju048. doi: 10.1093/jnci/dju048.

19.

Comparative meta-analysis of prognostic gene signatures for late-stage ovarian cancer.

Waldron L, Haibe-Kains B, Culhane AC, Riester M, Ding J, Wang XV, Ahmadifar M, Tyekucheva S, Bernau C, Risch T, Ganzfried BF, Huttenhower C, Birrer M, Parmigiani G.

J Natl Cancer Inst. 2014 Apr 3;106(5). pii: dju049. doi: 10.1093/jnci/dju049. Review.

20.

Two-stage microbial community experimental design.

Tickle TL, Segata N, Waldron L, Weingart U, Huttenhower C.

ISME J. 2013 Dec;7(12):2330-9. doi: 10.1038/ismej.2013.139. Epub 2013 Aug 15.

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