TreeCluster: Clustering biological sequences using phylogenetic trees
Balaban, Metin, Moshiri, Niema, Mai, Uyen, Jia, Xingfan, Mirarab, Siavash
Published in PloS one (22.08.2019)
Published in PloS one (22.08.2019)
Get full text
Journal Article
The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2
Pekar, Jonathan E, Magee, Andrew, Parker, Edyth, Moshiri, Niema, Izhikevich, Katherine, Havens, Jennifer L, Gangavarapu, Karthik, Malpica Serrano, Lorena Mariana, Crits-Christoph, Alexander, Matteson, Nathaniel L, Zeller, Mark, Levy, Joshua I, Wang, Jade C, Hughes, Scott, Lee, Jungmin, Park, Heedo, Park, Man-Seong, Ching Zi Yan, Katherine, Lin, Raymond Tzer Pin, Mat Isa, Mohd Noor, Noor, Yusuf Muhammad, Vasylyeva, Tetyana I, Garry, Robert F, Holmes, Edward C, Rambaut, Andrew, Suchard, Marc A, Andersen, Kristian G, Worobey, Michael, Wertheim, Joel O
Published in Science (American Association for the Advancement of Science) (26.08.2022)
Published in Science (American Association for the Advancement of Science) (26.08.2022)
Get full text
Journal Article
Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks
Rule, Adam, Birmingham, Amanda, Zuniga, Cristal, Altintas, Ilkay, Huang, Shih-Cheng, Knight, Rob, Moshiri, Niema, Nguyen, Mai H, Rosenthal, Sara Brin, Pérez, Fernando, Rose, Peter W
Published in PLoS computational biology (01.07.2019)
Published in PLoS computational biology (01.07.2019)
Get full text
Journal Article
The ViReflow pipeline enables user friendly large scale viral consensus genome reconstruction
Moshiri, Niema, Fisch, Kathleen M., Birmingham, Amanda, DeHoff, Peter, Yeo, Gene W., Jepsen, Kristen, Laurent, Louise C., Knight, Rob
Published in Scientific reports (24.03.2022)
Published in Scientific reports (24.03.2022)
Get full text
Journal Article
Ten simple rules for attending your first conference
Leininger, Elizabeth, Shaw, Kelly, Moshiri, Niema, Neiles, Kelly, Onsongo, Getiria, Ritz, Anna
Published in PLoS computational biology (01.07.2021)
Published in PLoS computational biology (01.07.2021)
Get full text
Journal Article
HDBind: encoding of molecular structure with hyperdimensional binary representations
Jones, Derek, Zhang, Xiaohua, Bennion, Brian J., Pinge, Sumukh, Xu, Weihong, Kang, Jaeyoung, Khaleghi, Behnam, Moshiri, Niema, Allen, Jonathan E., Rosing, Tajana S.
Published in Scientific reports (23.11.2024)
Published in Scientific reports (23.11.2024)
Get full text
Journal Article
SEPIA: simulation-based evaluation of prioritization algorithms
Almaraz, Kimberly, Jang, Tyler, Lewis, McKenna, Ngo, Titan, Song, Miranda, Moshiri, Niema
Published in BMC medical informatics and decision making (03.06.2021)
Published in BMC medical informatics and decision making (03.06.2021)
Get full text
Journal Article
Swapping Metagenomics Preprocessing Pipeline Components Offers Speed and Sensitivity Increases
Armstrong, George, Martino, Cameron, Morris, Justin, Khaleghi, Behnam, Kang, Jaeyoung, DeReus, Jeff, Zhu, Qiyun, Roush, Daniel, McDonald, Daniel, Gonazlez, Antonio, Shaffer, Justin P, Carpenter, Carolina, Estaki, Mehrbod, Wandro, Stephen, Eilert, Sean, Akel, Ameen, Eno, Justin, Curewitz, Ken, Swafford, Austin D, Moshiri, Niema, Rosing, Tajana, Knight, Rob
Published in mSystems (26.04.2022)
Published in mSystems (26.04.2022)
Get full text
Journal Article
ViralWasm: a client-side user-friendly web application suite for viral genomics
Ji, Daniel, Aboukhalil, Robert, Moshiri, Niema
Published in Bioinformatics (Oxford, England) (02.01.2024)
Published in Bioinformatics (Oxford, England) (02.01.2024)
Get full text
Journal Article
Timing the SARS-CoV-2 index case in Hubei province
Pekar, Jonathan, Worobey, Michael, Moshiri, Niema, Scheffler, Konrad, Wertheim, Joel O
Published in Science (23.04.2021)
Published in Science (23.04.2021)
Get full text
Journal Article
Web Resource
HyperSpec: Ultrafast Mass Spectra Clustering in Hyperdimensional Space
Xu, Weihong, Kang, Jaeyoung, Bittremieux, Wout, Moshiri, Niema, Rosing, Tajana
Published in Journal of proteome research (02.06.2023)
Published in Journal of proteome research (02.06.2023)
Get full text
Journal Article
HIV Care Prioritization Using Phylogenetic Branch Length
Moshiri, Niema, Smith, Davey M, Mirarab, Siavash
Published in Journal of acquired immune deficiency syndromes (1999) (15.04.2021)
Published in Journal of acquired immune deficiency syndromes (1999) (15.04.2021)
Get more information
Journal Article
HyperGen: Compact and Efficient Genome Sketching using Hyperdimensional Vectors
Xu, Weihong, Hsu, Po-Kai, Moshiri, Niema, Yu, Shimeng, Rosing, Tajana
Published in Bioinformatics (Oxford, England) (16.07.2024)
Published in Bioinformatics (Oxford, England) (16.07.2024)
Get full text
Journal Article