Functional profiling of COVID-19 respiratory tract microbiomes by Niina Haiminen, Filippo Utro, Ed Seabolt, Laxmi Parida

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Correction: Evaluation of Methods for Genome Assembly from High-Throughput Sequencing Reads Reveals Dependencies That Affect the Quality of the Results. by Niina Haiminen, David N. Kuhn, Laxmi Parida, Isidore Rigoutsos

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Correction: Evaluation of Methods for Genome Assembly from High-Throughput Sequencing Reads Reveals Dependencies That Affect the Quality of the Results. by Niina Haiminen, David N. Kuhn, Laxmi Parida, Isidore Rigoutsos

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Signal enrichment with strain-level resolution in metagenomes using topological data analysis by Aldo Guzmán-Sáenz, Niina Haiminen, Saugata Basu, Laxmi Parida

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Evaluation of methods for de novo genome assembly from high-throughput sequencing reads reveals dependencies that affect the quality of the results. by Niina Haiminen, David N Kuhn, Laxmi Parida, Isidore Rigoutsos

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Efficient in silico Chromosomal Representation of Populations via Indexing Ancestral Genomes by Zivan Karaman, Pascal Flament, Claude Lebreton, Filippo Utro, Niina Haiminen, Laxmi Parida

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Re-purposing software for functional characterization of the microbiome by Laura-Jayne Gardiner, Niina Haiminen, Filippo Utro, Laxmi Parida, Ed Seabolt, Ritesh Krishna, James H. Kaufman

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Hierarchically Labeled Database Indexing Allows Scalable Characterization of Microbiomes by Filippo Utro, Niina Haiminen, Enrico Siragusa, Laura-Jayne Gardiner, Ed Seabolt, Ritesh Krishna, James H. Kaufman, Laxmi Parida

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Development and evaluation of statistical and artificial intelligence approaches with microbial shotgun metagenomics data as an untargeted screening tool for use in food production by Kristen L. Beck, Niina Haiminen, Akshay Agarwal, Anna Paola Carrieri, Matthew Madgwick, Jennifer Kelly, Victor Pylro, Ban Kawas, Martin Wiedmann, Erika Ganda

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DNA Extraction and Host Depletion Methods Significantly Impact and Potentially Bias Bacterial Detection in a Biological Fluid by Erika Ganda, Kristen L. Beck, Niina Haiminen, Justin D. Silverman, Ban Kawas, Brittany D. Cronk, Renee R. Anderson, Laura B. Goodman, Martin Wiedmann

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Human Skin, Oral, and Gut Microbiomes Predict Chronological Age by Shi Huang, Niina Haiminen, Anna-Paola Carrieri, Rebecca Hu, Lingjing Jiang, Laxmi Parida, Baylee Russell, Celeste Allaband, Amir Zarrinpar, Yoshiki Vázquez-Baeza, Pedro Belda-Ferre, Hongwei Zhou, Ho-Cheol Kim, Austin D. Swafford, Rob Knight, Zhenjiang Zech Xu

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Human Skin, Oral, and Gut Microbiomes Predict Chronological Age by Shi Huang, Niina Haiminen, Anna-Paola Carrieri, Rebecca Hu, Lingjing Jiang, Laxmi Parida, Baylee Russell, Celeste Allaband, Amir Zarrinpar, Yoshiki Vázquez-Baeza, Pedro Belda-Ferre, Hongwei Zhou, Ho-Cheol Kim, Austin D. Swafford, Rob Knight, Zhenjiang Zech Xu

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Monitoring the microbiome for food safety and quality using deep shotgun sequencing by Kristen L. Beck, Niina Haiminen, David Chambliss, Stefan Edlund, Mark Kunitomi, B. Carol Huang, Nguyet Kong, Balasubramanian Ganesan, Robert Baker, Peter Markwell, Ban Kawas, Matthew Davis, Robert J. Prill, Harsha Krishnareddy, Ed Seabolt, Carl H. Marlowe, Sophie Pierre, André Quintanar, Laxmi Parida, Geraud Dubois, James Kaufman, Bart C. Weimer

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Explainable AI reveals changes in skin microbiome composition linked to phenotypic differences by Anna Paola Carrieri, Niina Haiminen, Sean Maudsley-Barton, Laura-Jayne Gardiner, Barry Murphy, Andrew E. Mayes, Sarah Paterson, Sally Grimshaw, Martyn Winn, Cameron Shand, Panagiotis Hadjidoukas, Will P. M. Rowe, Stacy Hawkins, Ashley MacGuire-Flanagan, Jane Tazzioli, John G. Kenny, Laxmi Parida, Michael Hoptroff, Edward O. Pyzer-Knapp

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Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy by Qiyun Zhu, Shi Huang, Antonio Gonzalez, Imran McGrath, Daniel McDonald, Niina Haiminen, George Armstrong, Yoshiki Vázquez-Baeza, Julian Yu, Justin Kuczynski, Gregory D. Sepich-Poore, Austin D. Swafford, Promi Das, Justin P. Shaffer, Franck Lejzerowicz, Pedro Belda-Ferre, Aki S. Havulinna, Guillaume Méric, Teemu Niiranen, Leo Lahti, Veikko Salomaa, Ho-Cheol Kim, Mohit Jain, Michael Inouye, Jack A. Gilbert, Rob Knight

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Correction for Zhu et al., “Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy” by Qiyun Zhu, Shi Huang, Antonio Gonzalez, Imran McGrath, Daniel McDonald, Niina Haiminen, George Armstrong, Yoshiki Vázquez-Baeza, Julian Yu, Justin Kuczynski, Gregory D. Sepich-Poore, Austin D. Swafford, Promi Das, Justin P. Shaffer, Franck Lejzerowicz, Pedro Belda-Ferre, Aki S. Havulinna, Guillaume Méric, Teemu Niiranen, Leo Lahti, Veikko Salomaa, Ho-Cheol Kim, Mohit Jain, Michael Inouye, Jack A. Gilbert, Rob Knight

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EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets by Kalen Cantrell, Marcus W. Fedarko, Gibraan Rahman, Daniel McDonald, Yimeng Yang, Thant Zaw, Antonio Gonzalez, Stefan Janssen, Mehrbod Estaki, Niina Haiminen, Kristen L. Beck, Qiyun Zhu, Erfan Sayyari, James T. Morton, George Armstrong, Anupriya Tripathi, Julia M. Gauglitz, Clarisse Marotz, Nathaniel L. Matteson, Cameron Martino, Jon G. Sanders, Anna Paola Carrieri, Se Jin Song, Austin D. Swafford, Pieter C. Dorrestein, Kristian G. Andersen, Laxmi Parida, Ho-Cheol Kim, Yoshiki Vázquez-Baeza, Rob Knight

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SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment by Clarisse Marotz, Pedro Belda-Ferre, Farhana Ali, Promi Das, Shi Huang, Kalen Cantrell, Lingjing Jiang, Cameron Martino, Rachel E. Diner, Gibraan Rahman, Daniel McDonald, George Armstrong, Sho Kodera, Sonya Donato, Gertrude Ecklu-Mensah, Neil Gottel, Mariana C. Salas Garcia, Leslie Y. Chiang, Rodolfo A. Salido, Justin P. Shaffer, Mac Kenzie Bryant, Karenina Sanders, Greg Humphrey, Gail Ackermann, Niina Haiminen, Kristen L. Beck, Ho-Cheol Kim, Anna Paola Carrieri, Laxmi Parida, Yoshiki Vázquez-Baeza, Francesca J. Torriani, Rob Knight, Jack Gilbert, Daniel A. Sweeney, Sarah M. Allard

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