Bibliotecas PUC-SP - Busca Integrada

Correction for Brennan et al., “Maximizing the potential of high-throughput next-generation sequencing through precise normalization based on read count distribution”

por Caitriona Brennan, Rodolfo A. Salido, Pedro Belda-Ferre, MacKenzie Bryant, Charles Cowart, Maria D. Tiu, Antonio Gonzalez, Daniel McDonald, Caitlin Tribelhorn, Amir Zarrinpar, Rob Knight
Publicado en mSystems (2025-01-01)

Maximizing the potential of high-throughput next-generation sequencing through precise normalization based on read count distribution

por Caitriona Brennan, Rodolfo A. Salido, Pedro Belda-Ferre, MacKenzie Bryant, Charles Cowart, Maria D. Tiu, Antonio González, Daniel McDonald, Caitlin Tribelhorn, Amir Zarrinpar, Rob Knight
Publicado en mSystems (2023-08-01)

A comparison of six DNA extraction protocols for 16S, ITS and shotgun metagenomic sequencing of microbial communities

por Justin P Shaffer, Carolina S Carpenter, Cameron Martino, Rodolfo A Salido, Jeremiah J Minich, MacKenzie Bryant, Karenina Sanders, Tara Schwartz, Gregory Humphrey, Austin D Swafford, Rob Knight
Publicado en BioTechniques (2022-06-01)

Calculating fast differential genome coverages among metagenomic sources using micov

por Yuhan Weng, Caitlin Guccione, Daniel McDonald, Renee Oles, Suzanne Devkota, Evguenia Kopylova, Gregory D. Sepich-Poore, Rodolfo A. Salido, M. Omar Din, Se Jin Song, Kit Curtius, Hiutung Chu, Andrew Bartko, Jeff Hasty, Rob Knight
Publicado en Communications Biology (2025-11-01)

Handwashing and Detergent Treatment Greatly Reduce SARS-CoV-2 Viral Load on Halloween Candy Handled by COVID-19 Patients

por Rodolfo A. Salido, Sydney C. Morgan, Maria I. Rojas, Celestine G. Magallanes, Clarisse Marotz, Peter DeHoff, Pedro Belda-Ferre, Stefan Aigner, Deborah M. Kado, Gene W. Yeo, Jack A. Gilbert, Louise Laurent, Forest Rohwer, Rob Knight
Publicado en mSystems (2020-12-01)

The genetic basis for adaptation of model-designed syntrophic co-cultures.

por Colton J Lloyd, Zachary A King, Troy E Sandberg, Ying Hefner, Connor A Olson, Patrick V Phaneuf, Edward J O'Brien, Jon G Sanders, Rodolfo A Salido, Karenina Sanders, Caitriona Brennan, Gregory Humphrey, Rob Knight, Adam M Feist
Publicado en PLoS Computational Biology (2019-03-01)

Association Between the Gut Microbiota and Blood Pressure in a Population Cohort of 6953 Individuals

por Joonatan Palmu, Aaro Salosensaari, Aki S. Havulinna, Susan Cheng, Michael Inouye, Mohit Jain, Rodolfo A. Salido, Karenina Sanders, Caitriona Brennan, Gregory C. Humphrey, Jon G. Sanders, Erkki Vartiainen, Tiina Laatikainen, Pekka Jousilahti, Veikko Salomaa, Rob Knight, Leo Lahti, Teemu J. Niiranen
Publicado en Journal of the American Heart Association: Cardiovascular and Cerebrovascular Disease (2020-08-01)

Clearing the plate: a strategic approach to mitigate well-to-well contamination in large-scale microbiome studies

por Caitriona Brennan, Pedro Belda-Ferre, Simone Zuffa, Vincent Charron-Lamoureux, Ipsita Mohanty, Gail Ackermann, Celeste Allaband, Madison Ambre, Tara Boyer, MacKenzie Bryant, Kalen Cantrell, Antonio Gonzalez, Daniel McDonald, Rodolfo A. Salido, Se Jin Song, Gillian Wright, Pieter C. Dorrestein, Rob Knight
Publicado en mSystems (2024-10-01)

A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities

por Justin P Shaffer, Clarisse Marotz, Pedro Belda-Ferre, Cameron Martino, Stephen Wandro, Mehrbod Estaki, Rodolfo A Salido, Carolina S Carpenter, Livia S Zaramela, Jeremiah J Minich, MacKenzie Bryant, Karenina Sanders, Serena Fraraccio, Gail Ackermann, Gregory Humphrey, Austin D Swafford, Sandrine Miller-Montgomery, Rob Knight
Publicado en BioTechniques (2021-03-01)

Gut microbiome and atrial fibrillation—results from a large population-based studyResearch in context

por Joonatan Palmu, Christin S. Börschel, Alfredo Ortega-Alonso, Lajos Markó, Michael Inouye, Pekka Jousilahti, Rodolfo A. Salido, Karenina Sanders, Caitriona Brennan, Gregory C. Humphrey, Jon G. Sanders, Friederike Gutmann, Dominik Linz, Veikko Salomaa, Aki S. Havulinna, Sofia K. Forslund, Rob Knight, Leo Lahti, Teemu Niiranen, Renate B. Schnabel
Publicado en EBioMedicine (2023-05-01)

Taxonomic signatures of cause-specific mortality risk in human gut microbiome

por Aaro Salosensaari, Ville Laitinen, Aki S. Havulinna, Guillaume Meric, Susan Cheng, Markus Perola, Liisa Valsta, Georg Alfthan, Michael Inouye, Jeramie D. Watrous, Tao Long, Rodolfo A. Salido, Karenina Sanders, Caitriona Brennan, Gregory C. Humphrey, Jon G. Sanders, Mohit Jain, Pekka Jousilahti, Veikko Salomaa, Rob Knight, Leo Lahti, Teemu Niiranen
Publicado en Nature Communications (2021-05-01)

Streamlined extraction of nucleic acids and metabolites from low- and high-biomass samples using isopropanol and matrix tubes

por Caitriona Brennan, Justin P. Shaffer, Pedro Belda-Ferre, Ipsita Mohanty, Yuhan Weng, Kalen Cantrell, Gail Ackermann, Celeste Allaband, MacKenzie Bryant, Sawyer Farmer, Antonio González, Daniel McDonald, Cameron Martino, Michael J. Meehan, Gibraan Rahman, Rodolfo A. Salido, Tara Schwartz, Se Jin Song, Caitlin Tribelhorn, Helena M. Tubb, Pieter C. Dorrestein, Rob Knight
Publicado en Microbiology Spectrum (2025-11-01)

Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads

por Jon G. Sanders, Sergey Nurk, Rodolfo A. Salido, Jeremiah Minich, Zhenjiang Z. Xu, Qiyun Zhu, Cameron Martino, Marcus Fedarko, Timothy D. Arthur, Feng Chen, Brigid S. Boland, Greg C. Humphrey, Caitriona Brennan, Karenina Sanders, James Gaffney, Kristen Jepsen, Mahdieh Khosroheidari, Cliff Green, Marlon Liyanage, Jason W. Dang, Vanessa V. Phelan, Robert A. Quinn, Anton Bankevich, John T. Chang, Tariq M. Rana, Douglas J. Conrad, William J. Sandborn, Larry Smarr, Pieter C. Dorrestein, Pavel A. Pevzner, Rob Knight
Publicado en Genome Biology (2019-10-01)

Sentinel Cards Provide Practical SARS-CoV-2 Monitoring in School Settings

por Victor J. Cantú, Karenina Sanders, Pedro Belda-Ferre, Rodolfo A. Salido, Rebecca Tsai, Brett Austin, William Jordan, Menka Asudani, Amanda Walster, Celestine G. Magallanes, Holly Valentine, Araz Manjoonian, Carrissa Wijaya, Vinton Omaleki, Stefan Aigner, Nathan A. Baer, Maryann Betty, Anelizze Castro-Martínez, Willi Cheung, Peter De Hoff, Emily Eisner, Abbas Hakim, Alma L. Lastrella, Elijah S. Lawrence, Toan T. Ngo, Tyler Ostrander, Ashley Plascencia, Shashank Sathe, Elizabeth W. Smoot, Aaron F. Carlin, Gene W. Yeo, Louise C. Laurent, Anna Liza Manlutac, Rebecca Fielding-Miller, Rob Knight
Publicado en mSystems (2022-08-01)

SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment

por 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
Publicado en Microbiome (2021-06-01)

Implementation of Practical Surface SARS-CoV-2 Surveillance in School Settings

por Victor J. Cantú, Pedro Belda-Ferre, Rodolfo A. Salido, Rebecca Tsai, Brett Austin, William Jordan, Menka Asudani, Amanda Walster, Celestine G. Magallanes, Holly Valentine, Araz Manjoonian, Carrissa Wijaya, Vinton Omaleki, Karenina Sanders, Stefan Aigner, Nathan A. Baer, Maryann Betty, Anelizze Castro-Martínez, Willi Cheung, Evelyn S. Crescini, Peter De Hoff, Emily Eisner, Abbas Hakim, Bhavika Kapadia, Alma L. Lastrella, Elijah S. Lawrence, Toan T. Ngo, Tyler Ostrander, Shashank Sathe, Phoebe Seaver, Elizabeth W. Smoot, Aaron F. Carlin, Gene W. Yeo, Louise C. Laurent, Anna Liza Manlutac, Rebecca Fielding-Miller, Rob Knight
Publicado en mSystems (2022-08-01)

SARS-CoV-2 Distribution in Residential Housing Suggests Contact Deposition and Correlates with Rothia sp.

por Victor J. Cantú, Rodolfo A. Salido, Shi Huang, Gibraan Rahman, Rebecca Tsai, Holly Valentine, Celestine G. Magallanes, Stefan Aigner, Nathan A. Baer, Tom Barber, Pedro Belda-Ferre, Maryann Betty, MacKenzie Bryant, Martín Casas Maya, Anelizze Castro-Martínez, Marisol Chacón, Willi Cheung, Evelyn S. Crescini, Peter De Hoff, Emily Eisner, Sawyer Farmer, Abbas Hakim, Laura Kohn, Alma L. Lastrella, Elijah S. Lawrence, Sydney C. Morgan, Toan T. Ngo, Alhakam Nouri, Ashley Plascencia, Christopher A. Ruiz, Shashank Sathe, Phoebe Seaver, Tara Shwartz, Elizabeth W. Smoot, R. Tyler Ostrander, Thomas Valles, Gene W. Yeo, Louise C. Laurent, Rebecca Fielding-Miller, Rob Knight
Publicado en mSystems (2022-06-01)

Analysis of SARS-CoV-2 RNA Persistence across Indoor Surface Materials Reveals Best Practices for Environmental Monitoring Programs

por Rodolfo A. Salido, Victor J. Cantú, Alex E. Clark, Sandra L. Leibel, Anahid Foroughishafiei, Anushka Saha, Abbas Hakim, Alhakam Nouri, Alma L. Lastrella, Anelizze Castro-Martínez, Ashley Plascencia, Bhavika K. Kapadia, Bing Xia, Christopher A. Ruiz, Clarisse A. Marotz, Daniel Maunder, Elijah S. Lawrence, Elizabeth W. Smoot, Emily Eisner, Evelyn S. Crescini, Laura Kohn, Lizbeth Franco Vargas, Marisol Chacón, Maryann Betty, Michal Machnicki, Min Yi Wu, Nathan A. Baer, Pedro Belda-Ferre, Peter De Hoff, Phoebe Seaver, R. Tyler Ostrander, Rebecca Tsai, Shashank Sathe, Stefan Aigner, Sydney C. Morgan, Toan T. Ngo, Tom Barber, Willi Cheung, Aaron F. Carlin, Gene W. Yeo, Louise C. Laurent, Rebecca Fielding-Miller, Rob Knight
Publicado en mSystems (2021-12-01)

Phylogeographic and genetic network assessment of COVID-19 mitigation protocols on SARS-CoV-2 transmission in university campus residencesResearch in context

por Joel O. Wertheim, Tetyana I. Vasylyeva, Robert J. Wood, Kalen Cantrell, Soraya Piña Contreras, Aryeh Feldheim, Ravi Goyal, Jennifer L. Havens, Rob Knight, Louise C. Laurent, Niema Moshiri, Robert Neuhard, Shashank Sathe, Alysson Satterlund, Angela Scioscia, Angela Y. Song, Robert T. Schooley, Cheryl M. Anderson, Natasha K. Martin, Stefan Aigner, Kristian G. Andersen, Nathan A. Baer, Maryann Betty, Amanda Birmingham, Anelizze Castro-Martinez, Willi Cheung, Peter De Hoff, Kathleen M. Fisch, Alison J. King, Karthik Gangavarapu, Abbas Hakim, Benjamin Henson, Kristen Jepsen, Christina H. Mac, Toan T. Ngo, Kelly N. Nguyen, Tyler R. Ostrander, Sarah Perkins, Ashley Plascencia, Andrea Rivera, Ariana Rivera, Rodolfo A. Salido, Kieran C. Saucedo, Madison Schwab, Allison L. Steedman, Anthony Veder, Alana Weiss, Gene W. Yeo, Mark Zeller
Publicado en EBioMedicine (2025-06-01)

SARS-CoV-2 infectivity can be modulated through bacterial grooming of the glycocalyx

por Cameron Martino, Benjamin P. Kellman, Daniel R. Sandoval, Thomas Mandel Clausen, Robert Cooper, Alhosna Benjdia, Feryel Soualmia, Alex E. Clark, Aaron F. Garretson, Clarisse A. Marotz, Se Jin Song, Stephen Wandro, Livia S. Zaramela, Rodolfo A. Salido, Qiyun Zhu, Erick Armingol, Yoshiki Vázquez-Baeza, Daniel McDonald, James T. Sorrentino, Bryn Taylor, Pedro Belda-Ferre, Promi Das, Farhana Ali, Chenguang Liang, Yujie Zhang, Luca Schifanella, Alice Covizzi, Alessia Lai, Agostino Riva, Christopher Basting, Courtney Ann Broedlow, Aki S. Havulinna, Pekka Jousilahti, Mehrbod Estaki, Tomasz Kosciolek, Rayus Kuplicki, Teresa A. Victor, Martin P. Paulus, Kristen E. Savage, Jennifer L. Benbow, Emma S. Spielfogel, Cheryl A. M. Anderson, Maria Elena Martinez, James V. Lacey, Shi Huang, Niina Haiminen, Laxmi Parida, Ho-Cheol Kim, Jack A. Gilbert, Daniel A. Sweeney, Sarah M. Allard, Austin D. Swafford, Susan Cheng, Michael Inouye, Teemu Niiranen, Mohit Jain, Veikko Salomaa, Karsten Zengler, Nichole R. Klatt, Jeff Hasty, Olivier Berteau, Aaron F. Carlin, Jeffrey D. Esko, Nathan E. Lewis, Rob Knight
Publicado en mBio (2025-04-01)