Exploring the landscape of focal amplifications in cancer using AmpliconArchitect
Deshpande, Viraj, Luebeck, Jens, Nguyen, Nam-Phuong D., Bakhtiari, Mehrdad, Turner, Kristen M., Schwab, Richard, Carter, Hannah, Mischel, Paul S., Bafna, Vineet
Published in Nature communications (23.01.2019)
Published in Nature communications (23.01.2019)
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Journal Article
ViFi: accurate detection of viral integration and mRNA fusion reveals indiscriminate and unregulated transcription in proximal genomic regions in cervical cancer
Nguyen, Nam-phuong D, Deshpande, Viraj, Luebeck, Jens, Mischel, Paul S, Bafna, Vineet
Published in Nucleic acids research (20.04.2018)
Published in Nucleic acids research (20.04.2018)
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Journal Article
Longitudinal assessment of tumor development using cancer avatars derived from genetically engineered pluripotent stem cells
Koga, Tomoyuki, Chaim, Isaac A., Benitez, Jorge A., Markmiller, Sebastian, Parisian, Alison D., Hevner, Robert F., Turner, Kristen M., Hessenauer, Florian M., D’Antonio, Matteo, Nguyen, Nam-phuong D., Saberi, Shahram, Ma, Jianhui, Miki, Shunichiro, Boyer, Antonia D., Ravits, John, Frazer, Kelly A., Bafna, Vineet, Chen, Clark C., Mischel, Paul S., Yeo, Gene W., Furnari, Frank B.
Published in Nature communications (28.01.2020)
Published in Nature communications (28.01.2020)
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Journal Article
iBioSim: a tool for the analysis and design of genetic circuits
Myers, Chris J., Barker, Nathan, Jones, Kevin, Kuwahara, Hiroyuki, Madsen, Curtis, Nguyen, Nam-Phuong D.
Published in Bioinformatics (01.11.2009)
Published in Bioinformatics (01.11.2009)
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Journal Article
Ultra-large alignments using phylogeny-aware profiles
Nguyen, Nam-Phuong D, Mirarab, Siavash, Kumar, Keerthana, Warnow, Tandy
Published in Genome Biology (16.06.2015)
Published in Genome Biology (16.06.2015)
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Journal Article
Fully automated sequence alignment methods are comparable to, and much faster than, traditional methods in large data sets: an example with hepatitis B virus
Catanach, Therese A, Sweet, Andrew D, Nguyen, Nam-Phuong D, Peery, Rhiannon M, Debevec, Andrew H, Thomer, Andrea K, Owings, Amanda C, Boyd, Bret M, Katz, Aron D, Soto-Adames, Felipe N, Allen, Julie M
Published in PeerJ (San Francisco, CA) (03.01.2019)
Published in PeerJ (San Francisco, CA) (03.01.2019)
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Journal Article
Metagenomic Analysis Reveals Previously Undescribed Bat Coronavirus Strains in Eswatini
Shapiro, Julie Teresa, Mollerup, Sarah, Jensen, Randi Holm, Olofsson, Jill Katharina, Nguyen, Nam-phuong D., Hansen, Thomas Arn, Vinner, Lasse, Monadjem, Ara, McCleery, Robert A., Hansen, Anders J.
Published in EcoHealth (01.12.2021)
Published in EcoHealth (01.12.2021)
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Journal Article
Author Correction: Longitudinal assessment of tumor development using cancer avatars derived from genetically engineered pluripotent stem cells
Koga, Tomoyuki, Chaim, Isaac A., Benitez, Jorge A., Markmiller, Sebastian, Parisian, Alison D., Hevner, Robert F., Turner, Kristen M., Hessenauer, Florian M., D’Antonio, Matteo, Nguyen, Nam-phuong D., Saberi, Shahram, Ma, Jianhui, Miki, Shunichiro, Boyer, Antonia D., Ravits, John, Frazer, Kelly A., Bafna, Vineet, Chen, Clark C., Mischel, Paul S., Yeo, Gene W., Furnari, Frank B.
Published in Nature communications (20.04.2020)
Published in Nature communications (20.04.2020)
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Journal Article
Genetic design automation
Myers, C.J., Barker, N., Kuwahara, H., Jones, K., Madsen, C., Nguyen, N.-P.D.
Published in 2009 IEEE/ACM International Conference on Computer-Aided Design - Digest of Technical Papers (01.11.2009)
Published in 2009 IEEE/ACM International Conference on Computer-Aided Design - Digest of Technical Papers (01.11.2009)
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Conference Proceeding
The Design of a Genetic Muller C-Element
Nguyen, N.-P.D., Kuwahara, H., Myers, C.J., Keener, J.P.
Published in 13th IEEE International Symposium on Asynchronous Circuits and Systems (ASYNC'07) (01.03.2007)
Published in 13th IEEE International Symposium on Asynchronous Circuits and Systems (ASYNC'07) (01.03.2007)
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Conference Proceeding
Reconstructing and characterizing focal amplifications in cancer using AmpliconArchitect
Deshpande, Viraj, Luebeck, Jens, Bakhtiari, Mehrdad, Nguyen, Nam-Phuong D, Turner, Kristen M, Schwab, Richard, Carter, Hannah, Mischel, Paul S, Bafna, Vineet
Published in bioRxiv (30.10.2018)
Published in bioRxiv (30.10.2018)
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Paper
Cancer avatars derived from genetically engineered pluripotent stem cells allow for longitudinal assessment of tumor development
Koga, Tomoyuki, Benitez, Jorge A, Chaim, Isaac A, Markmiller, Sebastian, Parisian, Alison D, Hevner, Robert F, Turner, Kristen M, Hessenauer, Florian M, D'antonio, Matteo, Nguyen, Nam-Phuong D, Saberi, Shahram, Ma, Jianhui, Miki, Shunichiro, Boyer, Antonia D, Ravits, John, Frazer, Kelly A, Bafna, Vineet, Chen, Clark C, Mischel, Paul S, Yeo, Gene W, Furnari, Frank B
Published in bioRxiv (25.10.2019)
Published in bioRxiv (25.10.2019)
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Paper