levi waldron - PMC

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Select item 63921521.

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

Shweta Gopaulakrishnan, Samuela Pollack, BJ Stubbs, Hervé Pagès, John Readey, Sean Davis, Levi Waldron, Martin Morgan, Vincent Carey

Version 1. F1000Res. 2019; 8: 21. Published online 2019 Jan 7. doi: 10.12688/f1000research.17518.1

PMCID:: PMC6392152

Article PubReader PDF–1.1M Citation

Select item 62347362.

Orchestrating a community-developed computational workshop and accompanying training materials

Sean Davis, Marcel Ramos, Lori Shepherd, Nitesh Turaga, Ludwig Geistlinger, Martin T. Morgan, Benjamin Haibe-Kains, Levi Waldron

Version 1. F1000Res. 2018; 7: 1656. Published online 2018 Oct 17. doi: 10.12688/f1000research.16516.1

PMCID:: PMC6234736

Article PubReader PDF–781K Citation

Select item 58500813.

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

Article PubReader PDF–177K Citation

Select item 56792414.

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

Article PubReader PDF–220K Citation

Select item 58620395.

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

PMCID:: PMC5862039

Article PubReader PDF–183K Citation

Select item 51400486.

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

Angela Re, Levi Waldron, Alessandro Quattrone

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

PMCID:: PMC5140048

Article PubReader PDF–2.6M Citation

Select item 51237557.

Racial/Ethnic Disparities in Genomic Sequencing

Daniel E. Spratt, Tiffany Chan, Levi Waldron, Corey Speers, Felix Y. Feng, Olorunseun O. Ogunwobi, Joseph R. Osborne

JAMA Oncol. Author manuscript; available in PMC 2016 Nov 25.

Published in final edited form as: JAMA Oncol. 2016 Aug 1; 2(8): 1070–1074. doi: 10.1001/jamaoncol.2016.1854

PMCID:: PMC5123755

Article PubReader PDF–287K Citation

Select item 49399628.

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

Edoardo Pasolli, Duy Tin Truong, Faizan Malik, Levi Waldron, Nicola Segata

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

PMCID:: PMC4939962

Article PubReader PDF–4.0M Citation

Select item 45095909.

Orchestrating high-throughput genomic analysis with Bioconductor

Wolfgang Huber, Vincent J. Carey, Robert Gentleman, Simon Anders, Marc Carlson, Benilton S. Carvalho, Hector Corrada Bravo, Sean Davis, Laurent Gatto, Thomas Girke, Raphael Gottardo, Florian Hahne, Kasper D. Hansen, Rafael A. Irizarry, Michael Lawrence, Michael I. Love, James MacDonald, Valerie Obenchain, Andrzej K. Oleś, Hervé Pagès, Alejandro Reyes, Paul Shannon, Gordon K. Smyth, Dan Tenenbaum, Levi Waldron, Martin Morgan

Nat Methods. Author manuscript; available in PMC 2015 Jul 21.

Published in final edited form as: Nat Methods. 2015 Feb; 12(2): 115–121. doi: 10.1038/nmeth.3252

PMCID:: PMC4509590

Article PubReader PDF–482K Citation

Select item 420115510.

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

Sihai Dave Zhao, Giovanni Parmigiani, Curtis Huttenhower, Levi Waldron

Bioinformatics. 2014 Nov 1; 30(21): 3062–3069. Published online 2014 Jul 23. doi: 10.1093/bioinformatics/btu488

PMCID:: PMC4201155

Article PubReader PDF–314K Citation

Select item 405892911.

Cross-study validation for the assessment of prediction algorithms

Christoph Bernau, Markus Riester, Anne-Laure Boulesteix, Giovanni Parmigiani, Curtis Huttenhower, Levi Waldron, Lorenzo Trippa

Bioinformatics. 2014 Jun 15; 30(12): i105–i112. Published online 2014 Jun 11. doi: 10.1093/bioinformatics/btu279

PMCID:: PMC4058929

Article PubReader PDF–494K Citation

Select item 405060612.

Relating the metatranscriptome and metagenome of the human gut

Eric A. Franzosa, Xochitl C. Morgan, Nicola Segata, Levi Waldron, Joshua Reyes, Ashlee M. Earl, Georgia Giannoukos, Matthew R. Boylan, Dawn Ciulla, Dirk Gevers, Jacques Izard, Wendy S. Garrett, Andrew T. Chan, Curtis Huttenhower

Proc Natl Acad Sci U S A. 2014 Jun 3; 111(22): E2329–E2338. Published online 2014 May 19. doi: 10.1073/pnas.1319284111

PMCID:: PMC4050606

Article PubReader PDF–1.4M Citation

Select item 458055613.

Risk Prediction for Late-Stage Ovarian Cancer by Meta-analysis of 1525 Patient Samples

Markus Riester, Wei Wei, Levi Waldron, Aedin C. Culhane, Lorenzo Trippa, Esther Oliva, Sung-hoon Kim, Franziska Michor, Curtis Huttenhower, Giovanni Parmigiani, Michael J. Birrer

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

PMCID:: PMC4580556

Article PubReader PDF–1.0M Citation

Select item 458055414.

Comparative Meta-analysis of Prognostic Gene Signatures for Late-Stage Ovarian Cancer

Levi Waldron, Benjamin Haibe-Kains, Aedín C. Culhane, Markus Riester, Jie Ding, Xin Victoria Wang, Mahnaz Ahmadifar, Svitlana Tyekucheva, Christoph Bernau, Thomas Risch, Benjamin Frederick Ganzfried, Curtis Huttenhower, Michael Birrer, Giovanni Parmigiani

J Natl Cancer Inst. 2014 May; 106(5): dju049. Published online 2014 Apr 3. doi: 10.1093/jnci/dju049

PMCID:: PMC4580554

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Select item 362595415.

curatedOvarianData: clinically annotated data for the ovarian cancer transcriptome

Benjamin Frederick Ganzfried, Markus Riester, Benjamin Haibe-Kains, Thomas Risch, Svitlana Tyekucheva, Ina Jazic, Xin Victoria Wang, Mahnaz Ahmadifar, Michael J. Birrer, Giovanni Parmigiani, Curtis Huttenhower, Levi Waldron

Database (Oxford) 2013; 2013: bat013. Published online 2013 Apr 2. doi: 10.1093/database/bat013

PMCID:: PMC3625954

Article PubReader PDF–758K Citation

Select item 354208016.

A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets

Omry Koren, Dan Knights, Antonio Gonzalez, Levi Waldron, Nicola Segata, Rob Knight, Curtis Huttenhower, Ruth E. Ley

PLoS Comput Biol. 2013 Jan; 9(1): e1002863. Published online 2013 Jan 10. doi: 10.1371/journal.pcbi.1002863

PMCID:: PMC3542080

Article PubReader PDF–3.6M Citation

Select item 334211917.

Report on emerging technologies for translational bioinformatics: a symposium on gene expression profiling for archival tissues

Levi Waldron, Peter Simpson, Giovanni Parmigiani, Curtis Huttenhower

BMC Cancer. 2012; 12: 124. Published online 2012 Mar 29. doi: 10.1186/1471-2407-12-124

PMCID:: PMC3342119

Article PubReader PDF–161K Citation

Select item 324870218.

The Murine Caecal MicroRNA Signature Depends on the Presence of the Endogenous Microbiota

Natasha Singh, Elize A. Shirdel, Levi Waldron, Regan-Heng Zhang, Igor Jurisica, Elena M. Comelli

Int J Biol Sci. 2012; 8(2): 171–186. Published online 2011 Dec 19. doi: 10.7150/ijbs.8.171

PMCID:: PMC3248702

Article PubReader PDF–735K Citation

Select item 321884819.

Metagenomic biomarker discovery and explanation

Nicola Segata, Jacques Izard, Levi Waldron, Dirk Gevers, Larisa Miropolsky, Wendy S Garrett, Curtis Huttenhower

Genome Biol. 2011; 12(6): R60. Published online 2011 Jun 24. doi: 10.1186/gb-2011-12-6-r60

PMCID:: PMC3218848

Article PubReader PDF–6.9M Citation

Select item 310342820.

mRNA transcript quantification in archival samples using multiplexed, color-coded probes

Patricia P Reis, Levi Waldron, Rashmi S Goswami, Wei Xu, Yali Xuan, Bayardo Perez-Ordonez, Patrick Gullane, Jonathan Irish, Igor Jurisica, Suzanne Kamel-Reid

BMC Biotechnol. 2011; 11: 46. Published online 2011 May 9. doi: 10.1186/1472-6750-11-46