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Nam-phuong Nguyen
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Phylotranscriptomic analysis of the origin and early diversification of land plants
NJ Wickett, S Mirarab, N Nguyen, T Warnow, E Carpenter, N Matasci, ...
Proceedings of the National Academy of Sciences 111 (45), E4859-E4868, 2014
12012014
One thousand plant transcriptomes and the phylogenomics of green plants
Nature 574 (7780), 679-685, 2019
11812019
Data access for the 1,000 Plants (1KP) project
N Matasci, LH Hung, Z Yan, EJ Carpenter, NJ Wickett, S Mirarab, ...
Gigascience 3 (1), 2047-217X-3-17, 2014
5822014
PASTA: ultra-large multiple sequence alignment
S Mirarab, N Nguyen, T Warnow
Research in Computational Molecular Biology: 18th Annual International …, 2014
4742014
Circular ecDNA promotes accessible chromatin and high oncogene expression
S Wu, KM Turner, N Nguyen, R Raviram, M Erb, J Santini, J Luebeck, ...
Nature 575 (7784), 699-703, 2019
3792019
A perspective on 16S rRNA operational taxonomic unit clustering using sequence similarity
NP Nguyen, T Warnow, M Pop, B White
NPJ biofilms and microbiomes 2 (1), 1-8, 2016
3082016
Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers
H Kim, NP Nguyen, K Turner, S Wu, AD Gujar, J Luebeck, J Liu, ...
Nature genetics 52 (9), 891-897, 2020
2912020
SEPP: SATé-enabled phylogenetic placement
S Mirarab, N Nguyen, T Warnow
Biocomputing 2012, 247-258, 2012
2372012
Global phylogeography and ancient evolution of the widespread human gut virus crAssphage
RA Edwards, AA Vega, HM Norman, M Ohaeri, K Levi, EA Dinsdale, ...
Nature microbiology 4 (10), 1727-1736, 2019
2092019
Exploring the landscape of focal amplifications in cancer using AmpliconArchitect
V Deshpande, J Luebeck, NPD Nguyen, M Bakhtiari, KM Turner, ...
Nature communications 10 (1), 392, 2019
1912019
Ultra-large alignments using phylogeny-aware profiles
ND Nguyen, S Mirarab, K Kumar, T Warnow
Genome biology 16, 1-15, 2015
1392015
iBioSim: a tool for the analysis and design of genetic circuits
CJ Myers, N Barker, K Jones, H Kuwahara, C Madsen, NPD Nguyen
Bioinformatics 25 (21), 2848-2849, 2009
1272009
TIPP: taxonomic identification and phylogenetic profiling
N Nguyen, S Mirarab, B Liu, M Pop, T Warnow
Bioinformatics 30 (24), 3548-3555, 2014
1002014
MRL and SuperFine+ MRL: new supertree methods
N Nguyen, S Mirarab, T Warnow
Algorithms for Molecular Biology 7, 1-13, 2012
892012
Phylogenomics from whole genome sequences using aTRAM
JM Allen, B Boyd, NP Nguyen, P Vachaspati, T Warnow, DI Huang, ...
Systematic Biology 66 (5), 786-798, 2017
722017
Primates, lice and bacteria: speciation and genome evolution in the symbionts of hominid lice
BM Boyd, JM Allen, NP Nguyen, P Vachaspati, ZS Quicksall, T Warnow, ...
Molecular Biology and Evolution 34 (7), 1743-1757, 2017
562017
ViFi: accurate detection of viral integration and mRNA fusion reveals indiscriminate and unregulated transcription in proximal genomic regions in cervical cancer
NPD Nguyen, V Deshpande, J Luebeck, PS Mischel, V Bafna
Nucleic acids research 46 (7), 3309-3325, 2018
542018
Longitudinal assessment of tumor development using cancer avatars derived from genetically engineered pluripotent stem cells
T Koga, IA Chaim, JA Benitez, S Markmiller, AD Parisian, RF Hevner, ...
Nature communications 11 (1), 550, 2020
502020
Metastable nonextremal antibranes
J Armas, N Nguyen, V Niarchos, NA Obers, T Van Riet
Physical Review Letters 122 (18), 181601, 2019
442019
Simultaneous radiation of bird and mammal lice following the K-Pg boundary
KP Johnson, N Nguyen, AD Sweet, BM Boyd, T Warnow, JM Allen
Biology letters 14 (5), 20180141, 2018
432018
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Articles 1–20