| Improved metagenomic analysis with Kraken 2 DE Wood, J Lu, B Langmead Genome Biology 20 (257), 2019 | 4206 | 2019 |
| Bracken: Estimating species abundance in metagenomics data J Lu, FP Breitwieser, P Thielen, SL Salzberg PeerJ Computer Science 3, e104, 2017 | 1325 | 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 | 589 | 2017 |
| Metagenome analysis using the Kraken software suite J Lu, N Rincon, DE Wood, FP Breitwieser, C Pockrandt, B Langmead, ... Nature Protocols, 2022 | 262 | 2022 |
| Ultrafast and accurate 16S rRNA microbial community analysis using Kraken 2 J Lu, SL Salzberg Microbiome 8 (1), 124, 2020 | 189 | 2020 |
| Bracken: estimating species abundance in metagenomics data. PeerJ Comput Sci 3: e104 J Lu, FP Breitwieser, P Thielen, SL Salzberg | 126 | 2017 |
| Removing contaminants from databases of draft genomes J Lu, SL Salzberg PLoS computational biology 14 (6), e1006277, 2018 | 117 | 2018 |
| 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 | 67 | 2023 |
| 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 | 65 | 2015 |
| 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 | 64 | 2018 |
| 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 | 52 | 2020 |
| 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 | 19 | 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 | 6 | 2021 |
| Novel metagenomics analysis of stony coral tissue loss disease JM Heinz, J Lu, LK Huebner, SL Salzberg, M Sommer, SM Rosales G3 Genes|Genomes|Genetics, 2024 | 1 | 2024 |
| 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 | 1 | 2023 |
| Metagenomic next generation sequencing of plasma RNA for diagnosis of unexplained, acute febrile illness in Uganda AJ Kandathil, PW Blair, J Lu, R Anantharam, K Kobba, ML Robinson, ... PLOS Neglected Tropical Diseases 18 (9), e0012451, 2024 | | 2024 |
| No Evidence of Chronic Infection in a Metagenomic Sequencing Study of the Keratoconus Corneal Epithelium P Kaur, L Moon, D Srikumaran, SL Salzberg, J Lu, PJ Simner, ... Journal of Clinical Medicine 13 (12), 3399, 2024 | | 2024 |
| 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 | | 2023 |
Steven SalzbergBloomberg Distinguished Professor, Johns Hopkins UniversityVerified email at jhu.edu
