NiemaGraphGen: A memory-efficient global-scale contact network simulation toolkit by Niema Moshiri

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CompactTree: a lightweight header-only C++ library and Python wrapper for ultra-large phylogenetics by Niema Moshiri

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An Evaluation of Phylogenetic Workflows in Viral Molecular Epidemiology by Colin Young, Sarah Meng, Niema Moshiri

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TreeCluster: Clustering biological sequences using phylogenetic trees. by Metin Balaban, Niema Moshiri, Uyen Mai, Xingfan Jia, Siavash Mirarab

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SEPIA: simulation-based evaluation of prioritization algorithms by Kimberly Almaraz, Tyler Jang, McKenna Lewis, Titan Ngo, Miranda Song, Niema Moshiri

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The ViReflow pipeline enables user friendly large scale viral consensus genome reconstruction by Niema Moshiri, Kathleen M. Fisch, Amanda Birmingham, Peter DeHoff, Gene W. Yeo, Kristen Jepsen, Louise C. Laurent, Rob Knight

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HDBind: encoding of molecular structure with hyperdimensional binary representations by Derek Jones, Xiaohua Zhang, Brian J. Bennion, Sumukh Pinge, Weihong Xu, Jaeyoung Kang, Behnam Khaleghi, Niema Moshiri, Jonathan E. Allen, Tajana S. Rosing

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Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks. by Adam Rule, Amanda Birmingham, Cristal Zuniga, Ilkay Altintas, Shih-Cheng Huang, Rob Knight, Niema Moshiri, Mai H Nguyen, Sara Brin Rosenthal, Fernando Pérez, Peter W Rose

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Swapping Metagenomics Preprocessing Pipeline Components Offers Speed and Sensitivity Increases by George Armstrong, Cameron Martino, Justin Morris, Behnam Khaleghi, Jaeyoung Kang, Jeff DeReus, Qiyun Zhu, Daniel Roush, Daniel McDonald, Antonio Gonazlez, Justin P. Shaffer, Carolina Carpenter, Mehrbod Estaki, Stephen Wandro, Sean Eilert, Ameen Akel, Justin Eno, Ken Curewitz, Austin D. Swafford, Niema Moshiri, Tajana Rosing, Rob Knight

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Safer at school early alert: an observational study of wastewater and surface monitoring to detect COVID-19 in elementary schoolsResearch in context by Rebecca Fielding-Miller, Smruthi Karthikeyan, Tommi Gaines, Richard S. Garfein, Rodolfo A. Salido, Victor J. Cantu, Laura Kohn, Natasha K. Martin, Adriane Wynn, Carrissa Wijaya, Marlene Flores, Vinton Omaleki, Araz Majnoonian, Patricia Gonzalez-Zuniga, Megan Nguyen, Anh V. Vo, Tina Le, Dawn Duong, Ashkan Hassani, Samantha Tweeten, Kristen Jepsen, Benjamin Henson, Abbas Hakim, Amanda Birmingham, Peter De Hoff, Adam M. Mark, Chanond A. Nasamran, Sara Brin Rosenthal, Niema Moshiri, Kathleen M. Fisch, Greg Humphrey, Sawyer Farmer, Helena M. Tubb, Tommy Valles, Justin Morris, Jaeyoung Kang, Behnam Khaleghi, Colin Young, Ameen D. Akel, Sean Eilert, Justin Eno, Ken Curewitz, Louise C. Laurent, Tajana Rosing, Rob Knight, Nathan A. Baer, Tom Barber, Anelizze Castro-Martinez, Marisol Chacón, Willi Cheung, Evelyn S. Crescini, Emily R. Eisner, Lizbeth Franco Vargas, Abbas Hakim, Charlotte Hobbs, Alma L. Lastrella, Elijah S. Lawrence, Nathaniel L. Matteson, Karthik Gangavarapu, Toan T. Ngo, Phoebe Seaver, Elizabeth W. Smoot, Rebecca Tsai, Bing Xia, Stefan Aigner, Catelyn Anderson, Pedro Belda-Ferre, Shashank Sathe, Mark Zeller, Kristian G. Andersen, Gene W. Yeo, Ezra Kurzban

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