Multivariable association discovery in population-scale meta-omics studies
Mallick, Himel, Rahnavard, Ali, McIver, Lauren J, Ma, Siyuan, Zhang, Yancong, Nguyen, Long H, Tickle, Timothy L, Weingart, George, Ren, Boyu, Schwager, Emma H, Chatterjee, Suvo, Thompson, Kelsey N, Wilkinson, Jeremy E, Subramanian, Ayshwarya, Lu, Yiren, Waldron, Levi, Paulson, Joseph N, Franzosa, Eric A, Bravo, Hector Corrada, Huttenhower, Curtis
Published in PLoS computational biology (16.11.2021)
Published in PLoS computational biology (16.11.2021)
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Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3
Beghini, Francesco, McIver, Lauren J, Blanco-Míguez, Aitor, Dubois, Leonard, Asnicar, Francesco, Maharjan, Sagun, Mailyan, Ana, Manghi, Paolo, Scholz, Matthias, Thomas, Andrew Maltez, Valles-Colomer, Mireia, Weingart, George, Zhang, Yancong, Zolfo, Moreno, Huttenhower, Curtis, Franzosa, Eric A, Segata, Nicola
Published in eLife (04.05.2021)
Published in eLife (04.05.2021)
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Gut microbiome structure and metabolic activity in inflammatory bowel disease
Franzosa, Eric A., Sirota-Madi, Alexandra, Avila-Pacheco, Julian, Fornelos, Nadine, Haiser, Henry J., Reinker, Stefan, Vatanen, Tommi, Hall, A. Brantley, Mallick, Himel, McIver, Lauren J., Sauk, Jenny S., Wilson, Robin G., Stevens, Betsy W., Scott, Justin M., Pierce, Kerry, Deik, Amy A., Bullock, Kevin, Imhann, Floris, Porter, Jeffrey A., Zhernakova, Alexandra, Fu, Jingyuan, Weersma, Rinse K., Wijmenga, Cisca, Clish, Clary B., Vlamakis, Hera, Huttenhower, Curtis, Xavier, Ramnik J.
Published in Nature microbiology (01.02.2019)
Published in Nature microbiology (01.02.2019)
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Dynamics of metatranscription in the inflammatory bowel disease gut microbiome
Schirmer, Melanie, Franzosa, Eric A., Lloyd-Price, Jason, McIver, Lauren J., Schwager, Randall, Poon, Tiffany W., Ananthakrishnan, Ashwin N., Andrews, Elizabeth, Barron, Gildardo, Lake, Kathleen, Prasad, Mahadev, Sauk, Jenny, Stevens, Betsy, Wilson, Robin G., Braun, Jonathan, Denson, Lee A., Kugathasan, Subra, McGovern, Dermot P. B., Vlamakis, Hera, Xavier, Ramnik J., Huttenhower, Curtis
Published in Nature microbiology (01.03.2018)
Published in Nature microbiology (01.03.2018)
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Divergence of Drosophila melanogaster repeatomes in response to a sharp microclimate contrast in Evolution Canyon, Israel
Kim, Young Bun, Oh, Jung Hun, McIver, Lauren J., Rashkovetsky, Eugenia, Michalak, Katarzyna, Garner, Harold R., Kang, Lin, Nevo, Eviatar, Korol, Abraham B., Michalak, Pawel
Published in Proceedings of the National Academy of Sciences - PNAS (22.07.2014)
Published in Proceedings of the National Academy of Sciences - PNAS (22.07.2014)
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A two-cohort study on the association between the gut microbiota and bone density, microarchitecture, and strength
Okoro, Paul C, Orwoll, Eric S, Huttenhower, Curtis, Morgan, Xochitl, Kuntz, Thomas M, McIver, Lauren J, Dufour, Alyssa B, Bouxsein, Mary L, Langsetmo, Lisa, Farsijani, Samaneh, Kado, Deborah M, Pacifici, Roberto, Sahni, Shivani, Kiel, Douglas P
Published in Frontiers in endocrinology (Lausanne) (21.09.2023)
Published in Frontiers in endocrinology (Lausanne) (21.09.2023)
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Species-level functional profiling of metagenomes and metatranscriptomes
Franzosa, Eric A., McIver, Lauren J., Rahnavard, Gholamali, Thompson, Luke R., Schirmer, Melanie, Weingart, George, Lipson, Karen Schwarzberg, Knight, Rob, Caporaso, J. Gregory, Segata, Nicola, Huttenhower, Curtis
Published in Nature methods (01.11.2018)
Published in Nature methods (01.11.2018)
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bioBakery: a meta'omic analysis environment
McIver, Lauren J, Abu-Ali, Galeb, Franzosa, Eric A, Schwager, Randall, Morgan, Xochitl C, Waldron, Levi, Segata, Nicola, Huttenhower, Curtis
Published in Bioinformatics (01.04.2018)
Published in Bioinformatics (01.04.2018)
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Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4
Blanco-Míguez, Aitor, Beghini, Francesco, Cumbo, Fabio, McIver, Lauren J., Thompson, Kelsey N., Zolfo, Moreno, Manghi, Paolo, Dubois, Leonard, Huang, Kun D., Thomas, Andrew Maltez, Nickols, William A., Piccinno, Gianmarco, Piperni, Elisa, Punčochář, Michal, Valles-Colomer, Mireia, Tett, Adrian, Giordano, Francesca, Davies, Richard, Wolf, Jonathan, Berry, Sarah E., Spector, Tim D., Franzosa, Eric A., Pasolli, Edoardo, Asnicar, Francesco, Huttenhower, Curtis, Segata, Nicola
Published in Nature biotechnology (01.11.2023)
Published in Nature biotechnology (01.11.2023)
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Transcriptional profile of isoproterenol-induced cardiomyopathy and comparison to exercise-induced cardiac hypertrophy and human cardiac failure
Galindo, Cristi L, Skinner, Michael A, Errami, Mounir, Olson, L Danielle, Watson, David A, Li, Jing, McCormick, John F, McIver, Lauren J, Kumar, Neil M, Pham, Thinh Q, Garner, Harold R
Published in BMC physiology (09.12.2009)
Published in BMC physiology (09.12.2009)
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Discovery of bioactive microbial gene products in inflammatory bowel disease
Zhang, Yancong, Bhosle, Amrisha, Bae, Sena, McIver, Lauren J., Pishchany, Gleb, Accorsi, Emma K., Thompson, Kelsey N., Arze, Cesar, Wang, Ya, Subramanian, Ayshwarya, Kearney, Sean M., Pawluk, April, Plichta, Damian R., Rahnavard, Ali, Shafquat, Afrah, Xavier, Ramnik J., Vlamakis, Hera, Garrett, Wendy S., Krueger, Andy, Huttenhower, Curtis, Franzosa, Eric A.
Published in Nature (London) (23.06.2022)
Published in Nature (London) (23.06.2022)
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High-sensitivity pattern discovery in large, paired multiomic datasets
Ghazi, Andrew R, Sucipto, Kathleen, Rahnavard, Ali, Franzosa, Eric A, McIver, Lauren J, Lloyd-Price, Jason, Schwager, Emma, Weingart, George, Moon, Yo Sup, Morgan, Xochitl C, Waldron, Levi, Huttenhower, Curtis
Published in Bioinformatics (24.06.2022)
Published in Bioinformatics (24.06.2022)
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Intestinal Blastocystis is linked to healthier diets and more favorable cardiometabolic outcomes in 56,989 individuals from 32 countries
Piperni, Elisa, Nguyen, Long H., Manghi, Paolo, Kim, Hanseul, Pasolli, Edoardo, Andreu-Sánchez, Sergio, Arrè, Alberto, Bermingham, Kate M., Blanco-Míguez, Aitor, Manara, Serena, Valles-Colomer, Mireia, Bakker, Elco, Busonero, Fabio, Davies, Richard, Fiorillo, Edoardo, Giordano, Francesca, Hadjigeorgiou, George, Leeming, Emily R., Lobina, Monia, Masala, Marco, Maschio, Andrea, McIver, Lauren J., Pala, Mauro, Pitzalis, Maristella, Wolf, Jonathan, Fu, Jingyuan, Zhernakova, Alexandra, Cacciò, Simone M., Cucca, Francesco, Berry, Sarah E., Ercolini, Danilo, Chan, Andrew T., Huttenhower, Curtis, Spector, Tim D., Segata, Nicola, Asnicar, Francesco
Published in Cell (22.08.2024)
Published in Cell (22.08.2024)
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Overview of the Microbiome Among Nurses study (Micro-N) as an example of prospective characterization of the microbiome within cohort studies
Everett, Christine, Li, Chengchen, Wilkinson, Jeremy E., Nguyen, Long H., McIver, Lauren J., Ivey, Kerry, Izard, Jacques, Palacios, Natalia, Eliassen, A. Heather, Willett, Walter C., Ascherio, Alberto, Sun, Qi, Tworoger, Shelley S., Chan, Andrew T., Garrett, Wendy S., Huttenhower, Curtis, Rimm, Eric B., Song, Mingyang
Published in Nature protocols (01.06.2021)
Published in Nature protocols (01.06.2021)
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Alterations in the gut microbiome implicate key taxa and metabolic pathways across inflammatory arthritis phenotypes
Thompson, Kelsey N, Bonham, Kevin S, Ilott, Nicholas E, Britton, Graham J, Colmenero, Paula, Bullers, Samuel J, McIver, Lauren J, Ma, Siyuan, Nguyen, Long H, Filer, Andrew, Brough, India, Pearson, Claire, Moussa, Caroline, Kumar, Vinod, Lam, Lilian H, Jackson, Matthew A, Pawluk, April, Kiriakidis, Serafim, Taylor, Peter C, Wedderburn, Lucy R, Marsden, Brian, Young, Stephen P, Littman, Dan R, Faith, Jeremiah J, Pratt, Arthur G, Bowness, Paul, Raza, Karim, Powrie, Fiona, Huttenhower, Curtis
Published in Science translational medicine (26.07.2023)
Published in Science translational medicine (26.07.2023)
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Publisher Correction: Overview of the Microbiome Among Nurses study (Micro-N) as an example of prospective characterization of the microbiome within cohort studies
Everett, Christine, Li, Chengchen, Wilkinson, Jeremy E., Nguyen, Long H., McIver, Lauren J., Ivey, Kerry, Izard, Jacques, Palacios, Natalia, Eliassen, A. Heather, Willett, Walter C., Ascherio, Alberto, Sun, Qi, Tworoger, Shelley S., Chan, Andrew T., Garrett, Wendy S., Huttenhower, Curtis, Rimm, Eric B., Song, Mingyang
Published in Nature protocols (01.09.2021)
Published in Nature protocols (01.09.2021)
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Large scale comparison of non-human sequences in human sequencing data
Tae, Hongseok, Karunasena, Enusha, Bavarva, Jasmin H., McIver, Lauren J., Garner, Harold R.
Published in Genomics (San Diego, Calif.) (01.12.2014)
Published in Genomics (San Diego, Calif.) (01.12.2014)
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Genomic leftovers: identifying novel microsatellites, over-represented motifs and functional elements in the human genome
Fonville, Natalie C., Velmurugan, Karthik Raja, Tae, Hongseok, Vaksman, Zalman, McIver, Lauren J., Garner, Harold R.
Published in Scientific reports (09.06.2016)
Published in Scientific reports (09.06.2016)
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Same work, twice the money?
Garner, Harold R., McIver, Lauren J., Waitzkin, Michael B.
Published in Nature (London) (01.01.2013)
Published in Nature (London) (01.01.2013)
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