levi waldron - PMC

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Select item 78159641.

SIMON: Open-Source Knowledge Discovery Platform

Adriana Tomic, Ivan Tomic, Levi Waldron, Ludwig Geistlinger, Max Kuhn, Rachel L. Spreng, Lindsay C. Dahora, Kelly E. Seaton, Georgia Tomaras, Jennifer Hill, Niharika A. Duggal, Ross D. Pollock, Norman R. Lazarus, Stephen D.R. Harridge, Janet M. Lord, Purvesh Khatri, Andrew J. Pollard, Mark M. Davis

Patterns (N Y) 2021 Jan 8; 2(1): 100178. Published online 2021 Jan 8. doi: 10.1016/j.patter.2020.100178

PMCID:: PMC7815964

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Select item 77815872.

SARS-CoV-2 Testing Service Preferences of Adults in the United States: Discrete Choice Experiment

Rebecca Zimba, Sarah Kulkarni, Amanda Berry, William You, Chloe Mirzayi, Drew Westmoreland, Angela Parcesepe, Levi Waldron, Madhura Rane, Shivani Kochhar, McKaylee Robertson, Andrew Maroko, Christian Grov, Denis Nash

JMIR Public Health Surveill. 2020 Oct-Dec; 6(4): e25546. Published online 2020 Dec 31. doi: 10.2196/25546

PMCID:: PMC7781587

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Select item 77246763.

Household factors and the risk of severe COVID-like illness early in the US pandemic

Denis Nash, Saba Qasmieh, McKaylee Robertson, Madhura Rane, Rebecca Zimba, Sarah Kulkarni, Amanda Berry, William You, Chloe Mirzayi, Drew Westmoreland, Angela Parcesepe, Levi Waldron, Shivani Kochhar, Andrew R Maroko, Christian Grov, CHASING COVID Cohort Study Team

Version 1. medRxiv. Preprint. 2020 Dec 4. doi: 10.1101/2020.12.03.20243683

PMCID:: PMC7724676

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Select item 76548634.

The relationship between anxiety, health, and potential stressors among adults in the United States during the COVID-19 pandemic

Angela M Parcesepe, McKaylee Robertson, Amanda Berry, Andrew Maroko, Rebecca Zimba, Christian Grov, Drew Westmoreland, Sarah Kulkarni, Madhura Rane, William Salgado-You, Chloe Mirzayi, Levi Waldron, Denis Nash

Version 1. medRxiv. Preprint. 2020 Nov 4. doi: 10.1101/2020.10.30.20221440

PMCID:: PMC7654863

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Select item 75726455.

Multi-omic analysis of subtype evolution and heterogeneity in high-grade serous ovarian carcinoma

Ludwig Geistlinger, Sehyun Oh, Marcel Ramos, Lucas Schiffer, Rebecca S. LaRue, Christine M. Henzler, Sarah A. Munro, Claire Daughters, Andrew C. Nelson, Boris J. Winterhoff, Zenas Chang, Shobhana Talukdar, Mihir Shetty, Sally A. Mullaney, Martin Morgan, Giovanni Parmigiani, Michael J. Birrer, Li-Xuan Qin, Markus Riester, Timothy K. Starr, Levi Waldron

Cancer Res. Author manuscript; available in PMC 2021 Apr 15.

Published in final edited form as: Cancer Res. 2020 Oct 15; 80(20): 4335–4345. Published online 2020 Aug 3. doi: 10.1158/0008-5472.CAN-20-0521

PMCID:: PMC7572645

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Select item 73980766.

Assessment of statistical methods from single cell, bulk RNA-seq, and metagenomics applied to microbiome data

Matteo Calgaro, Chiara Romualdi, Levi Waldron, Davide Risso, Nicola Vitulo

Genome Biol. 2020; 21: 191. Published online 2020 Aug 3. doi: 10.1186/s13059-020-02104-1

PMCID:: PMC7398076

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Select item 72657877.

Global Alliance for Genomics and Health Meets Bioconductor: Toward Reproducible and Agile Cancer Genomics at Cloud Scale

Vincent J. Carey, Marcel Ramos, Benjamin J. Stubbs, Shweta Gopaulakrishnan, Sehyun Oh, Nitesh Turaga, Levi Waldron, Martin Morgan

JCO Clin Cancer Inform. 2020; 4: CCI.19.00111. Published online 2020 May 26. doi: 10.1200/CCI.19.00111

PMCID:: PMC7265787

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Select item 78208598.

Toward a gold standard for benchmarking gene set enrichment analysis

Ludwig Geistlinger, Gergely Csaba, Mara Santarelli, Marcel Ramos, Lucas Schiffer, Nitesh Turaga, Charity Law, Sean Davis, Vincent Carey, Martin Morgan, Ralf Zimmer, Levi Waldron

Brief Bioinform. 2021 Jan; 22(1): 545–556. Published online 2020 Mar 9. doi: 10.1093/bib/bbz158

PMCID:: PMC7820859

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Select item 73580589.

Orchestrating Single-Cell Analysis with Bioconductor

Robert A. Amezquita, Aaron T. L. Lun, Etienne Becht, Vince J. Carey, Lindsay N. Carpp, Ludwig Geistlinger, Federico Marini, Kevin Rue-Albrecht, Davide Risso, Charlotte Soneson, Levi Waldron, Hervé Pagès, Mike L. Smith, Wolfgang Huber, Martin Morgan, Raphael Gottardo, Stephanie C. Hicks

Nat Methods. Author manuscript; available in PMC 2020 Aug 1.

Published in final edited form as: Nat Methods. 2020 Feb; 17(2): 137–145. Published online 2019 Dec 2. doi: 10.1038/s41592-019-0654-x

Correction in:: Nat Methods. 2019 Dec 11

PMCID:: PMC7358058

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Select item 654863710.

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

Francesco Beghini, Audrey Renson, Christine P. Zolnik, Ludwig Geistlinger, Mykhaylo Usyk, Thomas U. Moody, Lorna Thorpe, Jennifer B. Dowd, Robert Burk, Nicola Segata, Heidi E. Jones, Levi Waldron

Ann Epidemiol. Author manuscript; available in PMC 2020 Jun 1.

Published in final edited form as: Ann Epidemiol. 2019 Jun; 34: 18–25.e3. Published online 2019 Mar 28. doi: 10.1016/j.annepidem.2019.03.005

PMCID:: PMC6548637

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Select item 636550411.

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

Jennifer Rosenbaum, Mykhaylo Usyk, Zigui Chen, Christine P. Zolnik, Heidi E. Jones, Levi Waldron, Jennifer B. Dowd, Lorna E. Thorpe, Robert D. Burk

Sci Rep. 2019; 9: 1531. Published online 2019 Feb 6. doi: 10.1038/s41598-018-38049-6

PMCID:: PMC6365504

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Select item 654527412.

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

Levi Waldron, Lucas Schiffer, Rimsha Azhar, Marcel Ramos, Ludwig Geistlinger, Nicola Segata

Am J Epidemiol. 2019 Jun; 188(6): 1031–1032. Published online 2019 Jan 23. doi: 10.1093/aje/kwz008

PMCID:: PMC6545274

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Select item 615297113.

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

Denis Nash, McKaylee M. Robertson, Kate Penrose, Stephanie Chamberlin, Rebekkah S. Robbins, Sarah L. Braunstein, Julie E. Myers, Bisrat Abraham, Sarah Kulkarni, Levi Waldron, Bruce Levin, Mary K. Irvine

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

PMCID:: PMC6152971

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Select item 620708114.

Consensus on Molecular Subtypes of High-grade Serous Ovarian Carcinoma

Gregory M Chen, Lavanya Kannan, Ludwig Geistlinger, Victor Kofia, Zhaleh Safikhani, Deena MA Gendoo, Giovanni Parmigiani, Michael Birrer, Benjamin Haibe-Kains, Levi Waldron

Clin Cancer Res. Author manuscript; available in PMC 2019 Oct 15.

Published in final edited form as: Clin Cancer Res. 2018 Oct 15; 24(20): 5037–5047. Published online 2018 Jul 3. doi: 10.1158/1078-0432.CCR-18-0784

PMCID:: PMC6207081

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Select item 585008115.

Data and Statistical Methods To Analyze the Human Microbiome

Levi Waldron

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

PMCID:: PMC5850081

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Select item 603094716.

bioBakery: a meta’omic analysis environment

Lauren J McIver, Galeb Abu-Ali, Eric A Franzosa, Randall Schwager, Xochitl C Morgan, Levi Waldron, Nicola Segata, Curtis Huttenhower

Bioinformatics. 2018 Apr 1; 34(7): 1235–1237. Published online 2017 Nov 29. doi: 10.1093/bioinformatics/btx754

PMCID:: PMC6030947

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Select item 567924117.

Software for the integration of multi-omics experiments in Bioconductor

Marcel Ramos, Lucas Schiffer, Angela Re, Rimsha Azhar, Azfar Basunia, Carmen Rodriguez, Tiffany Chan, Phil Chapman, Sean R. Davis, David Gomez-Cabrero, Aedin C. Culhane, Benjamin Haibe-Kains, Kasper D. Hansen, Hanish Kodali, Marie S. Louis, Arvind S. Mer, Markus Riester, Martin Morgan, Vince Carey, Levi Waldron

Cancer Res. Author manuscript; available in PMC 2018 Nov 1.

Published in final edited form as: Cancer Res. 2017 Nov 1; 77(21): e39–e42. doi: 10.1158/0008-5472.CAN-17-0344

PMCID:: PMC5679241

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Select item 586203918.

Accessible, curated metagenomic data through ExperimentHub

Edoardo Pasolli, Lucas Schiffer, Paolo Manghi, Audrey Renson, Valerie Obenchain, Duy Tin Truong, Francesco Beghini, Faizan Malik, Marcel Ramos, Jennifer B Dowd, Curtis Huttenhower, Martin Morgan, Nicola Segata, Levi Waldron

Nat Methods. Author manuscript; available in PMC 2018 Mar 21.

Published in final edited form as: Nat Methods. 2017 Oct 31; 14(11): 1023–1024. doi: 10.1038/nmeth.4468