L
Lauren J. McIver
Researcher at Harvard University
Publications - 23
Citations - 13907
Lauren J. McIver is an academic researcher from Harvard University. The author has contributed to research in topics: Metagenomics & Microbiome. The author has an hindex of 12, co-authored 16 publications receiving 5758 citations. Previous affiliations of Lauren J. McIver include Broad Institute.
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Journal ArticleDOI
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
Evan Bolyen,Jai Ram Rideout,Matthew R. Dillon,Nicholas A. Bokulich,Christian C. Abnet,Gabriel A. Al-Ghalith,Harriet Alexander,Harriet Alexander,Eric J. Alm,Manimozhiyan Arumugam,Francesco Asnicar,Yang Bai,Jordan E. Bisanz,Kyle Bittinger,Asker Daniel Brejnrod,Colin J. Brislawn,C. Titus Brown,Benjamin J. Callahan,Andrés Mauricio Caraballo-Rodríguez,John Chase,Emily K. Cope,Ricardo Silva,Christian Diener,Pieter C. Dorrestein,Gavin M. Douglas,Daniel M. Durall,Claire Duvallet,Christian F. Edwardson,Madeleine Ernst,Madeleine Ernst,Mehrbod Estaki,Jennifer Fouquier,Julia M. Gauglitz,Sean M. Gibbons,Sean M. Gibbons,Deanna L. Gibson,Antonio Gonzalez,Kestrel Gorlick,Jiarong Guo,Benjamin Hillmann,Susan Holmes,Hannes Holste,Curtis Huttenhower,Curtis Huttenhower,Gavin A. Huttley,Stefan Janssen,Alan K. Jarmusch,Lingjing Jiang,Benjamin D. Kaehler,Benjamin D. Kaehler,Kyo Bin Kang,Kyo Bin Kang,Christopher R. Keefe,Paul Keim,Scott T. Kelley,Dan Knights,Irina Koester,Tomasz Kosciolek,Jorden Kreps,Morgan G. I. Langille,Joslynn S. Lee,Ruth E. Ley,Ruth E. Ley,Yong-Xin Liu,Erikka Loftfield,Catherine A. Lozupone,Massoud Maher,Clarisse Marotz,Bryan D Martin,Daniel McDonald,Lauren J. McIver,Lauren J. McIver,Alexey V. Melnik,Jessica L. Metcalf,Sydney C. Morgan,Jamie Morton,Ahmad Turan Naimey,Jose A. Navas-Molina,Jose A. Navas-Molina,Louis-Félix Nothias,Stephanie B. Orchanian,Talima Pearson,Samuel L. Peoples,Samuel L. Peoples,Daniel Petras,Mary L. Preuss,Elmar Pruesse,Lasse Buur Rasmussen,Adam R. Rivers,Michael S. Robeson,Patrick Rosenthal,Nicola Segata,Michael Shaffer,Arron Shiffer,Rashmi Sinha,Se Jin Song,John R. Spear,Austin D. Swafford,Luke R. Thompson,Luke R. Thompson,Pedro J. Torres,Pauline Trinh,Anupriya Tripathi,Peter J. Turnbaugh,Sabah Ul-Hasan,Justin J. J. van der Hooft,Fernando Vargas,Yoshiki Vázquez-Baeza,Emily Vogtmann,Max von Hippel,William A. Walters,Yunhu Wan,Mingxun Wang,Jonathan Warren,Kyle C. Weber,Kyle C. Weber,Charles H. D. Williamson,Amy D. Willis,Zhenjiang Zech Xu,Jesse R. Zaneveld,Yilong Zhang,Qiyun Zhu,Rob Knight,J. Gregory Caporaso +123 more
TL;DR: QIIME 2 development was primarily funded by NSF Awards 1565100 to J.G.C. and R.K.P. and partial support was also provided by the following: grants NIH U54CA143925 and U54MD012388.
Journal ArticleDOI
Species-level functional profiling of metagenomes and metatranscriptomes.
Eric A. Franzosa,Eric A. Franzosa,Lauren J. McIver,Lauren J. McIver,Gholamali Rahnavard,Gholamali Rahnavard,Luke R. Thompson,Melanie Schirmer,Melanie Schirmer,George Weingart,Karen Schwarzberg Lipson,Rob Knight,J. Gregory Caporaso,Nicola Segata,Curtis Huttenhower,Curtis Huttenhower +15 more
TL;DR: HUMAnN2 is developed, a tiered search strategy that enables fast, accurate, and species-resolved functional profiling of host-associated and environmental communities and introduces ‘contributional diversity’ to explain patterns of ecological assembly across different microbial community types.
Journal ArticleDOI
Gut microbiome structure and metabolic activity in inflammatory bowel disease
Eric A. Franzosa,Eric A. Franzosa,Alexandra Sirota-Madi,Julian Avila-Pacheco,Nadine Fornelos,Henry J. Haiser,Stefan Reinker,Tommi Vatanen,A. Brantley Hall,Himel Mallick,Himel Mallick,Lauren J. McIver,Lauren J. McIver,Jenny Sauk,Robin G. Wilson,Betsy W. Stevens,Justin M. Scott,Kerry A. Pierce,Amy Deik,Kevin Bullock,Floris Imhann,Jeffrey A. Porter,Alexandra Zhernakova,Jingyuan Fu,Rinse K. Weersma,Cisca Wijmenga,Cisca Wijmenga,Clary B. Clish,Hera Vlamakis,Curtis Huttenhower,Curtis Huttenhower,Ramnik J. Xavier +31 more
TL;DR: Using metabolomics and shotgun metagenomics on stool samples from individuals with and without inflammatory bowel disease, metabolites, microbial species and genes associated with disease were identified and validated in an independent cohort, providing an improved understanding of perturbations of the microbiome–metabolome interface in IBD.
Posted ContentDOI
QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science
Evan Bolyen,Jai Ram Rideout,Matthew R. Dillon,Nicholas A. Bokulich,Christian C. Abnet,Gabriel A. Al-Ghalith,Harriet Alexander,Harriet Alexander,Eric J. Alm,Manimozhiyan Arumugam,Francesco Asnicar,Yang Bai,Jordan E. Bisanz,Kyle Bittinger,Asker Daniel Brejnrod,Colin J. Brislawn,C. Titus Brown,Benjamin J. Callahan,Andrés Mauricio Caraballo-Rodríguez,John Chase,Emily K. Cope,Ricardo Silva,Pieter C. Dorrestein,Gavin M. Douglas,Daniel M. Durall,Claire Duvallet,Christian F. Edwardson,Madeleine Ernst,Mehrbod Estaki,Jennifer Fouquier,Julia M. Gauglitz,Deanna L. Gibson,Antonio Gonzalez,Kestrel Gorlick,Jiarong Guo,Benjamin Hillmann,Susan Holmes,Hannes Holste,Curtis Huttenhower,Curtis Huttenhower,Gavin A. Huttley,Stefan Janssen,Alan K. Jarmusch,Lingjing Jiang,Benjamin D. Kaehler,Kyo Bin Kang,Kyo Bin Kang,Christopher R. Keefe,Paul Keim,Scott T. Kelley,Dan Knights,Irina Koester,Irina Koester,Tomasz Kosciolek,Jorden Kreps,Morgan G. I. Langille,Joslynn S. Lee,Ruth E. Ley,Ruth E. Ley,Yong-Xin Liu,Erikka Loftfield,Catherine A. Lozupone,Massoud Maher,Clarisse Marotz,Bryan D Martin,Daniel McDonald,Lauren J. McIver,Lauren J. McIver,Alexey V. Melnik,Jessica L. Metcalf,Sydney C. Morgan,Jamie Morton,Ahmad Turan Naimey,Jose A. Navas-Molina,Jose A. Navas-Molina,Louis-Félix Nothias,Stephanie B. Orchanian,Talima Pearson,Samuel L. Peoples,Samuel L. Peoples,Daniel Petras,Mary L. Preuss,Elmar Pruesse,Lasse Buur Rasmussen,Adam R. Rivers,Ii Michael S Robeson,Patrick Rosenthal,Nicola Segata,Michael Shaffer,Arron Shiffer,Rashmi Sinha,Se Jin Song,John R. Spear,Austin D. Swafford,Luke R. Thompson,Luke R. Thompson,Pedro J. Torres,Pauline Trinh,Anupriya Tripathi,Anupriya Tripathi,Peter J. Turnbaugh,Sabah Ul-Hasan,Justin J. J. van der Hooft,Fernando Vargas,Yoshiki Vázquez-Baeza,Emily Vogtmann,Max von Hippel,William A. Walters,Yunhu Wan,Mingxun Wang,Jonathan Warren,Kyle C. Weber,Kyle C. Weber,Chase Hd Williamson,Amy D. Willis,Zhenjiang Zech Xu,Jesse R. Zaneveld,Yilong Zhang,Rob Knight,J. Gregory Caporaso +119 more
TL;DR: QIIME 2 provides new features that will drive the next generation of microbiome research, including interactive spatial and temporal analysis and visualization tools, support for metabolomics and shotgun metagenomics analysis, and automated data provenance tracking to ensure reproducible, transparent microbiome data science.
Journal ArticleDOI
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with biobakery 3
Francesco Beghini,Lauren J. McIver,Aitor Blanco-Míguez,Leonard Dubois,Francesco Asnicar,Sagun Maharjan,Sagun Maharjan,Ana Mailyan,Ana Mailyan,Paolo Manghi,Matthias Scholz,Andrew Maltez Thomas,Mireia Valles-Colomer,George Weingart,George Weingart,Yancong Zhang,Yancong Zhang,Moreno Zolfo,Curtis Huttenhower,Curtis Huttenhower,Eric A. Franzosa,Eric A. Franzosa,Nicola Segata,Nicola Segata +23 more
TL;DR: BioBakery 3 as mentioned in this paper is a set of integrated, improved methods for taxonomic, strain-level, functional, and phylogenetic profiling of metagenomes newly developed to build on the largest set of reference sequences now available.