Functional profiling of COVID-19 respiratory tract microbiomes

by Niina Haiminen, Filippo Utro, Ed Seabolt, Laxmi Parida
Published 2021-03-01

Correction: 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
Published 2011-01-01

Correction: 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
Published 2011-01-01

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
Published 2011-01-01

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

by Aldo Guzmán-Sáenz, Niina Haiminen, Saugata Basu, Laxmi Parida
Published 2019-04-01

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
Published 2011-01-01

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
Published 2011-01-01

Efficient in silico Chromosomal Representation of Populations via Indexing Ancestral Genomes

by Zivan Karaman, Pascal Flament, Claude Lebreton, Filippo Utro, Niina Haiminen, Laxmi Parida
Published 2013-07-01

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
Published 2021-01-01

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
Published 2020-04-01

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
Published 2021-06-01

Application of Genome Wide Association and Genomic Prediction for Improvement of Cacao Productivity and Resistance to Black and Frosty Pod Diseases

by J. Alberto Romero Navarro, Wilbert Phillips-Mora, Adriana Arciniegas-Leal, Allan Mata-Quirós, Niina Haiminen, Guiliana Mustiga, Donald Livingstone III, Harm van Bakel, David N. Kuhn, Laxmi Parida, Andrew Kasarskis, Juan C. Motamayor
Published 2017-11-01

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
Published 2020-02-01

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
Published 2021-02-01

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
Published 2021-02-01

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
Published 2021-04-01

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
Published 2021-06-01