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ArticlesPeer ReviewedFull Text
Functional profiling of COVID-19 respiratory tract microbiomes
Author / Creator:Haiminen, Niina ; Utro, Filippo ; Seabolt, Ed ; Parida, Laxmi
Publisher:London: Nature Publishing Group UK
Journal title:Scientific reports, 2021-03, Vol.11 (1), p.6433-6433, Article 6433
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Challenges in benchmarking metagenomic profilers
Author / Creator:Sun, Zheng ; Huang, Shi ; Zhang, Meng ; Zhu, Qiyun ; Haiminen, Niina ; Carrieri, Anna Paola ; Vázquez-Baeza, Yoshiki ; Parida, Laxmi ; Kim, Ho-Cheol ; Knight, Rob ; Liu, Yang-Yu
Publisher:New York: Nature Publishing Group US
Journal title:Nature methods, 2021-06, Vol.18 (6), p.618-626
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Explainable AI reveals changes in skin microbiome composition linked to phenotypic differences
Author / Creator:Carrieri, Anna Paola ; Haiminen, Niina ; Maudsley-Barton, Sean ; Gardiner, Laura-Jayne ; Murphy, Barry ; Mayes, Andrew E. ; Paterson, Sarah ; Grimshaw, Sally ; Winn, Martyn ; Shand, Cameron ; Hadjidoukas, Panagiotis ; Rowe, Will P. M. ; Hawkins, Stacy ; MacGuire-Flanagan, Ashley ; Tazzioli, Jane ; Kenny, John G. ; Parida, Laxmi ; Hoptroff, Michael ; Pyzer-Knapp, Edward O.
Publisher:London: Nature Publishing Group UK
Journal title:Scientific reports, 2021-02, Vol.11 (1), p.4565-18, Article 4565
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ArticlesPeer ReviewedFull Text
Human Skin, Oral, and Gut Microbiomes Predict Chronological Age
Author / Creator:Huang, Shi ; Haiminen, Niina ; Carrieri, Anna-Paola ; Hu, Rebecca ; Jiang, Lingjing ; Parida, Laxmi ; Russell, Baylee ; Allaband, Celeste ; Zarrinpar, Amir ; Vázquez-Baeza, Yoshiki ; Belda-Ferre, Pedro ; Zhou, Hongwei ; Kim, Ho-Cheol ; Swafford, Austin D. ; Knight, Rob ; Xu, Zhenjiang Zech
Publisher:United States: American Society for Microbiology
Journal title:mSystems, 2020-02, Vol.5 (1)
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Signal enrichment with strain-level resolution in metagenomes using topological data analysis
Author / Creator:Guzmán-Sáenz, Aldo ; Haiminen, Niina ; Basu, Saugata ; Parida, Laxmi
Publisher:England: BioMed Central
Journal title:BMC genomics, 2019-04, Vol.20 (S2), p.194-34, Article 194
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DNA Extraction and Host Depletion Methods Significantly Impact and Potentially Bias Bacterial Detection in a Biological Fluid
Author / Creator:Ganda, Erika ; Beck, Kristen L. ; Haiminen, Niina ; Silverman, Justin D. ; Kawas, Ban ; Cronk, Brittany D. ; Anderson, Renee R. ; Goodman, Laura B. ; Wiedmann, Martin
Publisher:1752 N St., N.W., Washington, DC: American Society for Microbiology
Journal title:mSystems, 2021-06, Vol.6 (3), p.e0061921-e0061921
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Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy
Author / Creator:Zhu, Qiyun ; Huang, Shi ; Gonzalez, Antonio ; McGrath, Imran ; McDonald, Daniel ; Haiminen, Niina ; Armstrong, George ; Vázquez-Baeza, Yoshiki ; Yu, Julian ; Kuczynski, Justin ; Sepich-Poore, Gregory D. ; Swafford, Austin D. ; Das, Promi ; Shaffer, Justin P. ; Lejzerowicz, Franck ; Belda-Ferre, Pedro ; Havulinna, Aki S. ; Méric, Guillaume ; Niiranen, Teemu ; Lahti, Leo ; Salomaa, Veikko ; Kim, Ho-Cheol ; Jain, Mohit ; Inouye, Michael ; Gilbert, Jack A. ; Knight, Rob
Publisher:United States: American Society for Microbiology
Journal title:mSystems, 2022-04, Vol.7 (2), p.e0016722
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Monitoring the microbiome for food safety and quality using deep shotgun sequencing
Author / Creator:Beck, Kristen L. ; Haiminen, Niina ; Chambliss, David ; Edlund, Stefan ; Kunitomi, Mark ; Huang, B. Carol ; Kong, Nguyet ; Ganesan, Balasubramanian ; Baker, Robert ; Markwell, Peter ; Kawas, Ban ; Davis, Matthew ; Prill, Robert J. ; Krishnareddy, Harsha ; Seabolt, Ed ; Marlowe, Carl H. ; Pierre, Sophie ; Quintanar, André ; Parida, Laxmi ; Dubois, Geraud ; Kaufman, James ; Weimer, Bart C.
Publisher:London: Nature Publishing Group UK
Journal title:NPJ science of food, 2021-02, Vol.5 (1), p.3-12, Article 3
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Correction for Zhu et al., “Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy”
Author / Creator:Zhu, Qiyun ; Huang, Shi ; Gonzalez, Antonio ; McGrath, Imran ; McDonald, Daniel ; Haiminen, Niina ; Armstrong, George ; Vázquez-Baeza, Yoshiki ; Yu, Julian ; Kuczynski, Justin ; Sepich-Poore, Gregory D. ; Swafford, Austin D. ; Das, Promi ; Shaffer, Justin P. ; Lejzerowicz, Franck ; Belda-Ferre, Pedro ; Havulinna, Aki S. ; Méric, Guillaume ; Niiranen, Teemu ; Lahti, Leo ; Salomaa, Veikko ; Kim, Ho-Cheol ; Jain, Mohit ; Inouye, Michael ; Gilbert, Jack A. ; Knight, Rob
Publisher:United States: American Society for Microbiology
Journal title:mSystems, 2024-11, Vol.9 (11), p.e0128924
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ArticlesPeer ReviewedFull Text
Re-purposing software for functional characterization of the microbiome
Author / Creator:Gardiner, Laura-Jayne ; Haiminen, Niina ; Utro, Filippo ; Parida, Laxmi ; Seabolt, Ed ; Krishna, Ritesh ; Kaufman, James H.
Publisher:England: BioMed Central
Journal title:Microbiome, 2021-01, Vol.9 (1), p.4-4, Article 4
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The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color
Author / Creator:Motamayor, Juan C ; Mockaitis, Keithanne ; Schmutz, Jeremy ; Haiminen, Niina ; III, Donald Livingstone ; Cornejo, Omar ; Findley, Seth D ; Zheng, Ping ; Utro, Filippo ; Royaert, Stefan ; Saski, Christopher ; Jenkins, Jerry ; Podicheti, Ram ; Zhao, Meixia ; Scheffler, Brian E ; Stack, Joseph C ; Feltus, Frank A ; Mustiga, Guiliana M ; Amores, Freddy ; Phillips, Wilbert ; Marelli, Jean Philippe ; May, Gregory D ; Shapiro, Howard ; Ma, Jianxin ; Bustamante, Carlos D ; Schnell, Raymond J ; Main, Dorrie ; Gilbert, Don ; Parida, Laxmi ; Kuhn, David N
Publisher:England: BioMed Central Ltd
Journal title:Genome Biology (Online Edition), 2013-10, Vol.14 (6), p.r53-r53, Article r53
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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
Author / Creator:Beck, Kristen L. ; Haiminen, Niina ; Agarwal, Akshay ; Carrieri, Anna Paola ; Madgwick, Matthew ; Kelly, Jennifer ; Pylro, Victor ; Kawas, Ban ; Wiedmann, Martin ; Ganda, Erika
Publisher:United States: American Society for Microbiology
Journal title:mSystems, 2024-11, Vol.9 (11), p.e0084024
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EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets
Author / Creator:Cantrell, Kalen ; Fedarko, Marcus W. ; Rahman, Gibraan ; McDonald, Daniel ; Yang, Yimeng ; Zaw, Thant ; Gonzalez, Antonio ; Janssen, Stefan ; Estaki, Mehrbod ; Haiminen, Niina ; Beck, Kristen L. ; Zhu, Qiyun ; Sayyari, Erfan ; Morton, James T. ; Armstrong, George ; Tripathi, Anupriya ; Gauglitz, Julia M. ; Marotz, Clarisse ; Matteson, Nathaniel L. ; Martino, Cameron ; Sanders, Jon G. ; Carrieri, Anna Paola ; Song, Se Jin ; Swafford, Austin D. ; Dorrestein, Pieter C. ; Andersen, Kristian G. ; Parida, Laxmi ; Kim, Ho-Cheol ; Vázquez-Baeza, Yoshiki ; Knight, Rob
Publisher:United States: American Society for Microbiology
Journal title:mSystems, 2021-03, Vol.6 (2)
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ArticlesPeer ReviewedFull Text
Food authentication from shotgun sequencing reads with an application on high protein powders
Author / Creator:Haiminen, Niina ; Edlund, Stefan ; Chambliss, David ; Kunitomi, Mark ; Weimer, Bart C. ; Ganesan, Balasubramanian ; Baker, Robert ; Markwell, Peter ; Davis, Matthew ; Huang, B. Carol ; Kong, Nguyet ; Prill, Robert J. ; Marlowe, Carl H. ; Quintanar, André ; Pierre, Sophie ; Dubois, Geraud ; Kaufman, James H. ; Parida, Laxmi ; Beck, Kristen L.
Publisher:London: Nature Publishing Group UK
Journal title:NPJ science of food, 2019-01, Vol.3 (1), p.24-24, Article 24
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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
Author / Creator:Haiminen, Niina ; Kuhn, David N ; Parida, Laxmi ; Rigoutsos, Isidore ; Rzhetsky, Andrey
Publisher:United States: Public Library of Science
Journal title:PloS one, 2011-09, Vol.6 (9), p.e24182-e24182
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Randomization techniques for assessing the significance of gene periodicity results
Author / Creator:Kallio, Aleksi ; Vuokko, Niko ; Ojala, Markus ; Haiminen, Niina ; Mannila, Heikki
Publisher:England: BioMed Central Ltd
Journal title:BMC bioinformatics, 2011-08, Vol.12 (1), p.330-330, Article 330
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Assessing pooled BAC and whole genome shotgun strategies for assembly of complex genomes
Author / Creator:Haiminen, Niina ; Feltus, F Alex ; Parida, Laxmi
Publisher:England: BioMed Central Ltd
Journal title:BMC genomics, 2011-04, Vol.12 (1), p.194-194, Article 194
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Determining significance of pairwise co-occurrences of events in bursty sequences
Author / Creator:Haiminen, Niina ; Mannila, Heikki ; Terzi, Evimaria
Publisher:England: BioMed Central Ltd
Journal title:BMC bioinformatics, 2008-08, Vol.9 (1), p.336-336, Article 336
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Comparing segmentations by applying randomization techniques
Author / Creator:Haiminen, Niina ; Mannila, Heikki ; Terzi, Evimaria
Publisher:England: BioMed Central Ltd
Journal title:BMC bioinformatics, 2007-05, Vol.8 (1), p.171-171, Article 171
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ArticlesPeer ReviewedFull Text
EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets
Author / Creator:Cantrell, Kalen ; Fedarko, Marcus W. ; Rahman, Gibraan ; McDonald, Daniel ; Yang, Yimeng ; Zaw, Thant ; Gonzalez, Antonio ; Janssen, Stefan ; Estaki, Mehrbod ; Haiminen, Niina ; Beck, Kristen L. ; Zhu, Qiyun ; Sayyari, Erfan ; Morton, James T. ; Armstrong, George ; Tripathi, Anupriya ; Gauglitz, Julia M. ; Marotz, Clarisse ; Matteson, Nathaniel L. ; Martino, Cameron ; Sanders, Jon G. ; Carrieri, Anna Paola ; Song, Se Jin ; Swafford, Austin D. ; Dorrestein, Pieter C. ; Andersen, Kristian G. ; Parida, Laxmi ; Kim, Ho-Cheol ; Vázquez-Baeza, Yoshiki ; Knight, Rob
Publisher:1752 N St., N.W., Washington, DC: American Society for Microbiology
Journal title:mSystems, 2021-04, Vol.6 (2)
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Showing 1 to 20 of 49 results

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Functional profiling of COVID-19 respiratory tract microbiomes

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Challenges in benchmarking metagenomic profilers

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Explainable AI reveals changes in skin microbiome composition linked to phenotypic differences

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Human Skin, Oral, and Gut Microbiomes Predict Chronological Age

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Signal enrichment with strain-level resolution in metagenomes using topological data analysis

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DNA Extraction and Host Depletion Methods Significantly Impact and Potentially Bias Bacterial Detection in a Biological Fluid

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Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy

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Monitoring the microbiome for food safety and quality using deep shotgun sequencing

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Correction for Zhu et al., “Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy”

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Re-purposing software for functional characterization of the microbiome

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The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color

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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

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EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets

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Food authentication from shotgun sequencing reads with an application on high protein powders

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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

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Randomization techniques for assessing the significance of gene periodicity results

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Assessing pooled BAC and whole genome shotgun strategies for assembly of complex genomes

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Determining significance of pairwise co-occurrences of events in bursty sequences

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Comparing segmentations by applying randomization techniques

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EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets

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