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Items: 1 to 20 of 48

1.

Widespread modulation of gene expression by copy number variation in skeletal muscle.

Geistlinger L, da Silva VH, Cesar ASM, Tizioto PC, Waldron L, Zimmer R, Regitano LCA, Coutinho LL.

Sci Rep. 2018 Jan 23;8(1):1399. doi: 10.1038/s41598-018-19782-4.

2.

bioBakery: A meta'omic analysis environment.

McIver LJ, Abu-Ali G, Franzosa EA, Schwager R, Morgan XC, Waldron L, Segata N, Huttenhower C.

Bioinformatics. 2017 Nov 29. doi: 10.1093/bioinformatics/btx754. [Epub ahead of print]

PMID:
29194469
3.

Software for the Integration of Multiomics Experiments in Bioconductor.

Ramos M, Schiffer L, Re A, Azhar R, Basunia A, Rodriguez C, Chan T, Chapman P, Davis SR, Gomez-Cabrero D, Culhane AC, Haibe-Kains B, Hansen KD, Kodali H, Louis MS, Mer AS, Riester M, Morgan M, Carey V, Waldron L.

Cancer Res. 2017 Nov 1;77(21):e39-e42. doi: 10.1158/0008-5472.CAN-17-0344.

PMID:
29092936
4.

Accessible, curated metagenomic data through ExperimentHub.

Pasolli E, Schiffer L, Manghi P, Renson A, Obenchain V, Truong DT, Beghini F, Malik F, Ramos M, Dowd JB, Huttenhower C, Morgan M, Segata N, Waldron L.

Nat Methods. 2017 Oct 31;14(11):1023-1024. doi: 10.1038/nmeth.4468. No abstract available.

PMID:
29088129
5.

Meta-analysis and commentary: Preemptive correction of arteriovenous access stenosis.

Raimann JG, Waldron L, Koh E, Miller GA, Sor MH, Gray RJ, Kotanko P.

Hemodial Int. 2017 Oct 3. doi: 10.1111/hdi.12614. [Epub ahead of print] No abstract available.

PMID:
28972691
6.

Multiparametric Quantitative Ultrasound Imaging in Assessment of Chronic Kidney Disease.

Gao J, Perlman A, Kalache S, Berman N, Seshan S, Salvatore S, Smith L, Wehrli N, Waldron L, Kodali H, Chevalier J.

J Ultrasound Med. 2017 Nov;36(11):2245-2256. doi: 10.1002/jum.14209. Epub 2017 Apr 13.

PMID:
28407281
7.

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.

8.

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.

9.

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.

10.

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.

11.

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.

12.

Shear Wave Elastography of the Spleen for Monitoring Transjugular Intrahepatic Portosystemic Shunt Function: A Pilot Study.

Gao J, Zheng X, Zheng YY, Zuo GQ, Ran HT, Auh YH, Waldron L, Chan T, Wang ZG.

J Ultrasound Med. 2016 May;35(5):951-8. doi: 10.7863/ultra.15.07009. Epub 2016 Apr 1.

PMID:
27036168
13.

Meta-Analysis in Gene Expression Studies.

Waldron L, Riester M.

Methods Mol Biol. 2016;1418:161-76. doi: 10.1007/978-1-4939-3578-9_8.

PMID:
27008014
14.

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. Review.

15.

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.

16.

Creation of a Human Secretome: A Novel Composite Library of Human Secreted Proteins: Validation Using Ovarian Cancer Gene Expression Data and a Virtual Secretome Array.

Vathipadiekal V, Wang V, Wei W, Waldron L, Drapkin R, Gillette M, Skates S, Birrer M.

Clin Cancer Res. 2015 Nov 1;21(21):4960-9. doi: 10.1158/1078-0432.CCR-14-3173. Epub 2015 May 5.

17.

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.

18.

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.

19.

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.

20.

Molecular subtypes of high-grade serous ovarian cancer: the holy grail?

Waldron L, Riester M, Birrer M.

J Natl Cancer Inst. 2014 Sep 30;106(10). pii: dju297. doi: 10.1093/jnci/dju297. Print 2014 Oct. No abstract available.

PMID:
25269490

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