Jennifer Lu, Ph. D.
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Improved metagenomic analysis with Kraken 2
DE Wood, J Lu, B Langmead
Genome Biology 20 (257), 2019
Bracken: Estimating species abundance in metagenomics data
J Lu, FP Breitwieser, P Thielen, SL Salzberg
PeerJ Computer Science 3, e104, 2017
A review of methods and databases for metagenomic classification and assembly
FP Breitwieser, J Lu, SL Salzberg
Briefings in Bioinformatics 20 (4), 1125-1136, 2017
Ultrafast and accurate 16S rRNA microbial community analysis using Kraken 2
J Lu, SL Salzberg
Microbiome 8 (1), 124, 2020
Metagenome analysis using the Kraken software suite
J Lu, N Rincon, DE Wood, FP Breitwieser, C Pockrandt, B Langmead, ...
Nature Protocols, 2022
Removing contaminants from databases of draft genomes
J Lu, SL Salzberg
PLoS computational biology 14 (6), e1006277, 2018
Bracken: estimating species abundance in metagenomics data. PeerJ Comput Sci 3: e104
J Lu, FP Breitwieser, P Thielen, SL Salzberg
Identifying Corneal Infections in Formalin-Fixed Specimens Using Next Generation Sequencing
Z Li, FP Breitwieser, J Lu, AS Jun, L Asnaghi, SL Salzberg, CG Eberhart
Investigative Ophthalmology & Visual Science 59 (1), 280-288, 2018
Automated profiling of individual cell–cell interactions from high-throughput time-lapse imaging microscopy in nanowell grids (TIMING)
A Merouane, N Rey-Villamizar, Y Lu, I Liadi, G Romain, J Lu, H Singh, ...
Bioinformatics 31 (19), 3189-3197, 2015
SkewIT: The Skew Index Test for large-scale GC Skew analysis of bacterial genomes
J Lu, SL Salzberg
PLoS computational biology 16 (12), e1008439, 2020
Major data analysis errors invalidate cancer microbiome findings
A Gihawi, Y Ge, J Lu, D Puiu, A Xu, CS Cooper, DS Brewer, M Pertea, ...
bioRxiv, 2023.07. 28.550993, 2023
The Energy Landscape for the Self-Assembly of a Two-Dimensional DNA Origami Complex
J Fern, J Lu, R Schulman
ACS nano 10 (2), 1836-1844, 2016
Identification of microbial agents in tissue specimens of ocular and periocular sarcoidosis using a metagenomics approach
AS Shifera, C Pockrandt, N Rincon, Y Ge, J Lu, A Varabyou, AE Jedlicka, ...
F1000Research 10 (820), 820, 2021
Detection of Penicillin Nonsusceptible Streptococcus agalactiae by Laboratories That Participate in the College of American Pathologist’s Proficiency Testing Program
RM Humphries, J Lu, I Martin, CA Rauch, C Wojewoda, Y McCarter, ...
Journal of clinical microbiology 61 (8), e00595-23, 2023
Multicentre genetic diversity study of carbapenem-resistant Enterobacterales: predominance of untypeable pUVA-like blaKPC bearing plasmids
PJ Simner, Y Bergman, Y Fan, EB Jacobs, S Ramakrishnan, J Lu, S Lewis, ...
JAC-Antimicrobial Resistance 5 (3), dlad061, 2023
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