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Items: 1 to 50 of 108

1.

CNVRanger: association analysis of CNVs with gene expression and quantitative phenotypes.

da Silva V, Ramos M, Groenen M, Crooijmans R, Johansson A, Regitano L, Coutinho L, Zimmer R, Waldron L, Geistlinger L.

Bioinformatics. 2019 Aug 8. pii: btz632. doi: 10.1093/bioinformatics/btz632. [Epub ahead of print]

PMID:
31392308
2.

MetaGxData: Clinically Annotated Breast, Ovarian and Pancreatic Cancer Datasets and their Use in Generating a Multi-Cancer Gene Signature.

Gendoo DMA, Zon M, Sandhu V, Manem VSK, Ratanasirigulchai N, Chen GM, Waldron L, Haibe-Kains B.

Sci Rep. 2019 Jun 19;9(1):8770. doi: 10.1038/s41598-019-45165-4.

3.

Sociodemographic variation in the oral microbiome.

Renson A, Jones HE, Beghini F, Segata N, Zolnik CP, Usyk M, Moody TU, Thorpe L, Burk R, Waldron L, Dowd JB.

Ann Epidemiol. 2019 Jul;35:73-80.e2. doi: 10.1016/j.annepidem.2019.03.006. Epub 2019 May 8.

PMID:
31151886
4.

Tobacco exposure associated with oral microbiota oxygen utilization in the New York City Health and Nutrition Examination Study.

Beghini F, Renson A, Zolnik CP, Geistlinger L, Usyk M, Moody TU, Thorpe L, Dowd JB, Burk R, Segata N, Jones HE, Waldron L.

Ann Epidemiol. 2019 Jun;34:18-25.e3. doi: 10.1016/j.annepidem.2019.03.005. Epub 2019 Mar 28.

PMID:
31076212
5.

Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation.

Thomas AM, Manghi P, Asnicar F, Pasolli E, Armanini F, Zolfo M, Beghini F, Manara S, Karcher N, Pozzi C, Gandini S, Serrano D, Tarallo S, Francavilla A, Gallo G, Trompetto M, Ferrero G, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Wirbel J, Schrotz-King P, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G, Cordero F, Dias-Neto E, Setubal JC, Tett A, Pardini B, Rescigno M, Waldron L, Naccarati A, Segata N.

Nat Med. 2019 Apr;25(4):667-678. doi: 10.1038/s41591-019-0405-7. Epub 2019 Apr 1.

PMID:
30936548
6.

Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer.

Wirbel J, Pyl PT, Kartal E, Zych K, Kashani A, Milanese A, Fleck JS, Voigt AY, Palleja A, Ponnudurai R, Sunagawa S, Coelho LP, Schrotz-King P, Vogtmann E, Habermann N, Niméus E, Thomas AM, Manghi P, Gandini S, Serrano D, Mizutani S, Shiroma H, Shiba S, Shibata T, Yachida S, Yamada T, Waldron L, Naccarati A, Segata N, Sinha R, Ulrich CM, Brenner H, Arumugam M, Bork P, Zeller G.

Nat Med. 2019 Apr;25(4):679-689. doi: 10.1038/s41591-019-0406-6. Epub 2019 Apr 1.

PMID:
30936547
7.

restfulSE: A semantically rich interface for cloud-scale genomics with Bioconductor.

Gopaulakrishnan S, Pollack S, Stubbs BJ, Pagès H, Readey J, Davis S, Waldron L, Morgan M, Carey V.

F1000Res. 2019 Jan 7;8:21. doi: 10.12688/f1000research.17518.1. eCollection 2019.

8.

Evaluation of Oral Cavity DNA Extraction Methods on Bacterial and Fungal Microbiota.

Rosenbaum J, Usyk M, Chen Z, Zolnik CP, Jones HE, Waldron L, Dowd JB, Thorpe LE, Burk RD.

Sci Rep. 2019 Feb 6;9(1):1531. doi: 10.1038/s41598-018-38049-6.

9.

Waldron et al. Reply to "Commentary on the HMP16SData Bioconductor Package".

Waldron L, Schiffer L, Azhar R, Ramos M, Geistlinger L, Segata N.

Am J Epidemiol. 2019 Jun 1;188(6):1031-1032. doi: 10.1093/aje/kwz008. No abstract available.

PMID:
30689687
10.

HMP16SData: Efficient Access to the Human Microbiome Project Through Bioconductor.

Schiffer L, Azhar R, Shepherd L, Ramos M, Geistlinger L, Huttenhower C, Dowd JB, Segata N, Waldron L.

Am J Epidemiol. 2019 Jun 1;188(6):1023-1026. doi: 10.1093/aje/kwz006.

PMID:
30649166
11.

Orchestrating a community-developed computational workshop and accompanying training materials.

Davis S, Ramos M, Shepherd L, Turaga N, Geistlinger L, Morgan MT, Haibe-Kains B, Waldron L.

F1000Res. 2018 Oct 17;7:1656. doi: 10.12688/f1000research.16516.1. eCollection 2018.

12.

Impact of an HIV Care Coordination Program on Durable Viral Suppression.

Robertson MM, Penrose K, Irvine MK, Robbins RS, Kulkarni S, Braunstein SL, Waldron L, Harriman G, Nash D.

J Acquir Immune Defic Syndr. 2019 Jan 1;80(1):46-55. doi: 10.1097/QAI.0000000000001877.

PMID:
30299346
13.

Continuity of transcriptomes among colorectal cancer subtypes based on meta-analysis.

Ma S, Ogino S, Parsana P, Nishihara R, Qian Z, Shen J, Mima K, Masugi Y, Cao Y, Nowak JA, Shima K, Hoshida Y, Giovannucci EL, Gala MK, Chan AT, Fuchs CS, Parmigiani G, Huttenhower C, Waldron L.

Genome Biol. 2018 Sep 25;19(1):142. doi: 10.1186/s13059-018-1511-4.

14.

Short-term effectiveness of HIV care coordination among persons with recent HIV diagnosis or history of poor HIV outcomes.

Nash D, Robertson MM, Penrose K, Chamberlin S, Robbins RS, Braunstein SL, Myers JE, Abraham B, Kulkarni S, Waldron L, Levin B, Irvine MK.

PLoS One. 2018 Sep 24;13(9):e0204017. doi: 10.1371/journal.pone.0204017. eCollection 2018.

15.

The impact of different sources of heterogeneity on loss of accuracy from genomic prediction models.

Zhang Y, Bernau C, Parmigiani G, Waldron L.

Biostatistics. 2018 Sep 6. doi: 10.1093/biostatistics/kxy044. [Epub ahead of print]

PMID:
30202918
16.

Consensus on Molecular Subtypes of High-Grade Serous Ovarian Carcinoma.

Chen GM, Kannan L, Geistlinger L, Kofia V, Safikhani Z, Gendoo DMA, Parmigiani G, Birrer M, Haibe-Kains B, Waldron L.

Clin Cancer Res. 2018 Oct 15;24(20):5037-5047. doi: 10.1158/1078-0432.CCR-18-0784. Epub 2018 Jul 3.

PMID:
30084834
17.

Using Registry Data to Construct a Comparison Group for Programmatic Effectiveness Evaluation: The New York City HIV Care Coordination Program.

Robertson MM, Waldron L, Robbins RS, Chamberlin S, Penrose K, Levin B, Kulkarni S, Braunstein SL, Irvine MK, Nash D.

Am J Epidemiol. 2018 Sep 1;187(9):1980-1989. doi: 10.1093/aje/kwy103.

18.

Calcineurin Regulatory Subunit Calcium-Binding Domains Differentially Contribute to Calcineurin Signaling in Saccharomyces cerevisiae.

Connolly S, Quasi-Woode D, Waldron L, Eberly C, Waters K, Muller EM, Kingsbury TJ.

Genetics. 2018 Jul;209(3):801-813. doi: 10.1534/genetics.118.300911. Epub 2018 May 7.

19.

Data and Statistical Methods To Analyze the Human Microbiome.

Waldron L.

mSystems. 2018 Mar 13;3(2). pii: e00194-17. doi: 10.1128/mSystems.00194-17. eCollection 2018 Mar-Apr.

20.

Beetroot supplementation improves the physiological responses to incline walking.

Waldron M, Waldron L, Lawlor C, Gray A, Highton J.

Eur J Appl Physiol. 2018 Jun;118(6):1131-1141. doi: 10.1007/s00421-018-3843-x. Epub 2018 Mar 15.

PMID:
29546639
21.

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.

22.

bioBakery: a meta'omic analysis environment.

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

Bioinformatics. 2018 Apr 1;34(7):1235-1237. doi: 10.1093/bioinformatics/btx754.

23.

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.

24.

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.

25.

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. 2018 Apr;22(2):279-280. doi: 10.1111/hdi.12614. Epub 2017 Oct 3. No abstract available.

PMID:
28972691
26.

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.

27.

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.

28.

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.

29.

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.

30.

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.

31.

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.

32.

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.

33.

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
34.

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
35.

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.

36.

Management and Outcome of Mucosal Injury During Pyloromyotomy--An Analytical Survey Study.

Waldron LS, St Peter SD, Muensterer OJ.

J Laparoendosc Adv Surg Tech A. 2015 Dec;25(12):1044-6. doi: 10.1089/lap.2015.0117. Epub 2015 Nov 23.

PMID:
26595590
37.

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.

38.

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.

39.

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.

40.

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.

41.

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.

42.

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.

43.

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.

44.

B-vitamin status in relation to bone mineral density in treated celiac disease patients.

Clarke M, Ward M, Dickey W, Hoey L, Molloy AM, Waldron L, Varghese A, McCann A, Blayney JK, McNulty H.

Scand J Gastroenterol. 2015 Aug;50(8):975-84. doi: 10.3109/00365521.2015.1015603. Epub 2015 Apr 10.

PMID:
25861707
45.

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.

46.

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
47.

Lineage-specific interface proteins match up the cell cycle and differentiation in embryo stem cells.

Re A, Workman CT, Waldron L, Quattrone A, Brunak S.

Stem Cell Res. 2014 Sep;13(2):316-28. doi: 10.1016/j.scr.2014.07.008. Epub 2014 Aug 4.

48.

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.

49.

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.

50.

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.

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