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Items: 1 to 20 of 96

1.
Machine learning for microbiologists
Francesco Asnicar, Andrew Maltez Thomas, Andrea Passerini, Levi Waldron, Nicola Segata
Nat Rev Microbiol. Author manuscript; available in PMC 2025 Apr 9.
Published in final edited form as: Nat Rev Microbiol. 2024 Apr; 22(4): 191–205. Published online 2023 Nov 15. doi: 10.1038/s41579-023-00984-1
PMCID:
PMC11980903
ArticlePDF–2.0M
2.
Large-scale metagenomic analysis of oral microbiomes reveals markers for autism spectrum disorders
Paolo Manghi, Michele Filosi, Moreno Zolfo, Lucas G. Casten, Albert Garcia-Valiente, Stefania Mattevi, Vitor Heidrich, Davide Golzato, Samuel Perini, Andrew M. Thomas, Simone Montalbano, Samuele Cancellieri, Levi Waldron, Jacob B. Hall, Simon Xu, Natalia Volfovsky, LeeAnne Green Snyder, Pamela Feliciano, Francesco Asnicar, Mireia Valles-Colomer, Jacob J. Michaelson, Nicola Segata, Enrico Domenici
Nat Commun. 2024; 15: 9743. Published online 2024 Nov 11. doi: 10.1038/s41467-024-53934-7
PMCID:
PMC11555315
ArticlePDF–3.1M
3.
AnVILWorkflow: A runnable workflow package for Cloud-implemented bioinformatics analysis pipelines
Sehyun Oh, Kai Gravel-Pucillo, Marcel Ramos, Michael C. Schatz, Sean Davis, Vincent Carey, Martin Morgan, Levi Waldron
Version 1. F1000Res. 2024; 13: 1257. Published online 2024 Oct 21. doi: 10.12688/f1000research.155449.1
PMCID:
PMC11635187
ArticlePDF–717K
4.
Best practices to evaluate the impact of biomedical research software—metric collection beyond citations
Awan Afiaz, Andrey A Ivanov, John Chamberlin, David Hanauer, Candace L Savonen, Mary J Goldman, Martin Morgan, Michael Reich, Alexander Getka, Aaron Holmes, Sarthak Pati, Dan Knight, Paul C Boutros, Spyridon Bakas, J Gregory Caporaso, Guilherme Del Fiol, Harry Hochheiser, Brian Haas, Patrick D Schloss, James A Eddy, Jake Albrecht, Andrey Fedorov, Levi Waldron, Ava M Hoffman, Richard L Bradshaw, Jeffrey T Leek, Carrie Wright
Bioinformatics. 2024 Aug; 40(8): btae469. Published online 2024 Jul 27. doi: 10.1093/bioinformatics/btae469
PMCID:
PMC11297485
ArticlePDF–1.5M
5.
AnVILWorkflow: A runnable workflow package for Cloud-implemented bioinformatics analysis pipelines
Sehyun Oh, Kai Gravel-Pucillo, Marcel Ramos, Sean Davis, Vince Carey, Martin Morgan, Levi Waldron
Version 1. Res Sq. Preprint. 2024 May 15. doi: 10.21203/rs.3.rs-4370115/v1
Published in:
F1000Res. 2024; 13: 1257.
PMCID:
PMC11118690
ArticlePDF–423K
6.
Longitudinal gut microbiome changes in immune checkpoint blockade-treated advanced melanoma
Johannes R. Björk, Laura A. Bolte, Andrew Maltez Thomas, Karla A. Lee, Niccolo Rossi, Thijs T. Wind, Lotte M. Smit, Federica Armanini, Francesco Asnicar, Aitor Blanco-Miguez, Ruth Board, Neus Calbet-Llopart, Lisa Derosa, Nathalie Dhomen, Kelly Brooks, Mark Harland, Mark Harries, Paul Lorigan, Paolo Manghi, Richard Marais, Julia Newton-Bishop, Luigi Nezi, Federica Pinto, Miriam Potrony, Susana Puig, Patricio Serra-Bellver, Heather M. Shaw, Sabrina Tamburini, Sara Valpione, Levi Waldron, Laurence Zitvogel, Moreno Zolfo, Elisabeth G. E. de Vries, Paul Nathan, Rudolf S. N. Fehrmann, Tim D. Spector, Véronique Bataille, Nicola Segata, Geke A. P. Hospers, Rinse K. Weersma
Nat Med. 2024; 30(3): 785–796. Published online 2024 Feb 16. doi: 10.1038/s41591-024-02803-3
PMCID:
PMC10957474
ArticlePDF–7.0M
7.
International Society for Extracellular Vesicles workshop. QuantitatEVs: Multiscale analyses, from bulk to single extracellular vesicle
Manuela Basso, Alessandro Gori, Caterina Nardella, Mari Palviainen, Marija Holcar, Ioannis Sotiropoulos, Sylwia Bobis‐Wozowicz, Vito G. D'Agostino, Elena Casarotto, Yari Ciani, Shiro Suetsugu, Alice Gualerzi, Lorena Martin‐Jaular, Daniela Boselli, Anna Kashkanova, Pietro Parisse, Lien Lippens, Martina Pagliuca, Martin Blessing, Roberto Frigerio, Thibaut Fourniols, Ana Meliciano, Anna Fietta, Paolo Vincenzo Fioretti, Karolina Soroczyńska, Silvia Picciolini, Amanda Salviano‐Silva, Paolo Bergese, Davide Zocco, Marcella Chiari, Guido Jenster, Levi Waldron, Aleksandar Milosavljevic, John Nolan, Marco P. Monopoli, Kenneth W. Witwer, Benedetta Bussolati, Dolores Di Vizio, Juan Falcon Perez, Metka Lenassi, Marina Cretich, Francesca Demichelis
J Extracell Biol. 2024 Jan; 3(1): e137. Published online 2024 Jan 24. doi: 10.1002/jex2.137
PMCID:
PMC10883470
ArticlePDF–988K
8.
Evaluation of software impact designed for biomedical research: Are we measuring what’s meaningful?
Awan Afiaz, Andrey A. Ivanov, John Chamberlin, David Hanauer, Candace L. Savonen, Mary J. Goldman, Martin Morgan, Michael Reich, Alexander Getka, Aaron Holmes, Sarthak Pati, Dan Knight, Paul C. Boutros, Spyridon Bakas, J. Gregory Caporaso, Guilherme Del Fiol, Harry Hochheiser, Brian Haas, Patrick D. Schloss, James A. Eddy, Jake Albrecht, Andrey Fedorov, Levi Waldron, Ava M. Hoffman, Richard L. Bradshaw, Jeffrey T. Leek, Carrie Wright
Version 1. ArXiv. Preprint. 2023 Jun 5: arXiv:2306.03255v1.
PMCID:
PMC10274942
ArticlePDF–647K
9.
RaggedExperiment: the missing link between genomic ranges and matrices in Bioconductor
Marcel Ramos, Martin Morgan, Ludwig Geistlinger, Vincent J Carey, Levi Waldron
Bioinformatics. 2023 Jun; 39(6): btad330. Published online 2023 May 19. doi: 10.1093/bioinformatics/btad330
PMCID:
PMC10272705
ArticlePDF–943K
10.
GenomicSuperSignature facilitates interpretation of RNA-seq experiments through robust, efficient comparison to public databases
Sehyun Oh, Ludwig Geistlinger, Marcel Ramos, Daniel Blankenberg, Marius van den Beek, Jaclyn N. Taroni, Vincent J. Carey, Casey S. Greene, Levi Waldron, Sean Davis
Nat Commun. 2022; 13: 3695. Published online 2022 Jun 27. doi: 10.1038/s41467-022-31411-3
PMCID:
PMC9237024
ArticlePDF–1.6M
11.
HGNChelper: identification and correction of invalid gene symbols for human and mouse
Sehyun Oh, Jasmine Abdelnabi, Ragheed Al-Dulaimi, Ayush Aggarwal, Marcel Ramos, Sean Davis, Markus Riester, Levi Waldron
Version 2. F1000Res. 2020; 9: 1493. Published online 2022 Jun 9. doi: 10.12688/f1000research.28033.2
PMCID:
PMC7856679
ArticlePDF–912K
12.
Refining colorectal cancer classification and clinical stratification through a single-cell atlas
Ateeq M. Khaliq, Cihat Erdogan, Zeyneb Kurt, Sultan Sevgi Turgut, Miles W. Grunvald, Tim Rand, Sonal Khare, Jeffrey A. Borgia, Dana M. Hayden, Sam G. Pappas, Henry R. Govekar, Audrey E. Kam, Jochen Reiser, Kiran Turaga, Milan Radovich, Yong Zang, Yingjie Qiu, Yunlong Liu, Melissa L. Fishel, Anita Turk, Vineet Gupta, Ram Al-Sabti, Janakiraman Subramanian, Timothy M. Kuzel, Anguraj Sadanandam, Levi Waldron, Arif Hussain, Mohammad Saleem, Bassel El-Rayes, Ameen A. Salahudeen, Ashiq Masood
Genome Biol. 2022; 23: 113. Published online 2022 May 11. doi: 10.1186/s13059-022-02677-z
Correction in:
Genome Biol. 2022; 23: 156.
PMCID:
PMC9092724
ArticlePDF–9.7M
13.
Cohort profile: a national, community-based prospective cohort study of SARS-CoV-2 pandemic outcomes in the USA—the CHASING COVID Cohort study
McKaylee M Robertson, Sarah Gorrell Kulkarni, Madhura Rane, Shivani Kochhar, Amanda Berry, Mindy Chang, Chloe Mirzayi, William You, Andrew Maroko, Rebecca Zimba, Drew Westmoreland, Christian Grov, Angela Marie Parcesepe, Levi Waldron, Denis Nash, CHASING COVID Cohort Study Team
BMJ Open. 2021; 11(9): e048778. Published online 2021 Sep 21. doi: 10.1136/bmjopen-2021-048778
PMCID:
PMC8458000
ArticlePDF–2.5M
14.
Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals
Francesco Asnicar, Sarah E. Berry, Ana M. Valdes, Long H. Nguyen, Gianmarco Piccinno, David A. Drew, Emily Leeming, Rachel Gibson, Caroline Le Roy, Haya Al Khatib, Lucy Francis, Mohsen Mazidi, Olatz Mompeo, Mireia Valles-Colomer, Adrian Tett, Francesco Beghini, Léonard Dubois, Davide Bazzani, Andrew Maltez Thomas, Chloe Mirzayi, Asya Khleborodova, Sehyun Oh, Rachel Hine, Christopher Bonnett, Joan Capdevila Pujol, Serge Danzanvilliers, Francesca Giordano, Ludwig Geistlinger, Levi Waldron, Richard Davies, George Hadjigeorgiou, Jonathan Wolf, José M. Ordovás, Christopher Gardner, Paul W. Franks, Andrew T. Chan, Curtis Huttenhower, Tim D. Spector, Nicola Segata
Nat Med. Author manuscript; available in PMC 2021 Aug 10.
Published in final edited form as: Nat Med. 2021 Feb; 27(2): 321–332. Published online 2021 Jan 11. doi: 10.1038/s41591-020-01183-8
PMCID:
PMC8353542
ArticlePDF–6.7M
15.
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
Article
16.
Patterns of SARS-CoV-2 testing preferences in a national cohort in the United States
Matthew L. Romo, Rebecca Zimba, Sarah Kulkarni, Amanda Berry, William You, Chloe Mirzayi, Drew Westmoreland, Angela M. Parcesepe, Levi Waldron, Madhura Rane, Shivani Kochhar, McKaylee Robertson, Andrew R. Maroko, Christian Grov, Denis Nash, CHASING COVID Cohort Study Team
Version 1. medRxiv. Preprint. 2020 Dec 24. doi: 10.1101/2020.12.22.20248747
Published in:
JMIR Public Health Surveill. 2021 Dec; 7(12): e32846.
PMCID:
PMC7781336
ArticlePDF–242K
17.
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
Published in:
PLoS One. 2022; 17(7): e0271786.
PMCID:
PMC7724676
ArticlePDF–1.0M
18.
Multiomic Integration of Public Oncology Databases in Bioconductor
Marcel Ramos, Ludwig Geistlinger, Sehyun Oh, Lucas Schiffer, Rimsha Azhar, Hanish Kodali, Ino de Bruijn, Jianjiong Gao, Vincent J. Carey, Martin Morgan, Levi Waldron
JCO Clin Cancer Inform. 2020; 4: CCI.19.00119. Published online 2020 Oct 29. doi: 10.1200/CCI.19.00119
PMCID:
PMC7608653
ArticlePDF–2.1M
19.
Transparency and reproducibility in artificial intelligence
Benjamin Haibe-Kains, George Alexandru Adam, Ahmed Hosny, Farnoosh Khodakarami, Massive Analysis Quality Control (MAQC) Society Board of Directors, Levi Waldron, Bo Wang, Chris McIntosh, Anna Goldenberg, Anshul Kundaje, Casey S. Greene, Tamara Broderick, Michael M. Hoffman, Jeffrey T. Leek, Keegan Korthauer, Wolfgang Huber, Alvis Brazma, Joelle Pineau, Robert Tibshirani, Trevor Hastie, John P.A. Ioannidis, John Quackenbush, Hugo J.W.L. Aerts, Thakkar Shraddha, Rebecca Kusko, Susanna-Assunta Sansone, Weida Tong, Russ D. Wolfinger, Christopher Mason, Wendell Jones, Joaquin Dopazo, Cesare Furlanello
Nature. Author manuscript; available in PMC 2021 May 25.
Published in final edited form as: Nature. 2020 Oct; 586(7829): E14–E16. Published online 2020 Oct 14. doi: 10.1038/s41586-020-2766-y
PMCID:
PMC8144864
ArticlePDF–55K
20.
Testing, Testing: What SARS-CoV-2 testing services do adults in the United States actually want?
Rebecca Zimba, Sarah Kulkarni, Amanda Berry, William You, Chloe Mirzayi, Drew Westmoreland, Angela Parcesepe, Levi Waldron, Madhura Rane, Shivani Kochhar, McKaylee Robertson, Andrew R Maroko, Christian Grov, Denis Nash, CHASING COVID Cohort Study Team
Version 1. medRxiv. Preprint. 2020 Sep 18. doi: 10.1101/2020.09.15.20195180
Published in:
JMIR Public Health Surveill. 2020 Oct-Dec; 6(4): e25546.
PMCID:
PMC7523137
ArticlePDF–912K

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