Jennifer Lu

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Ultrafast and accurate 16S rRNA microbial community analysis using Kraken 2

S. Salzberg, Jennifer Lu, 2020, Microbiome.

Improved metagenomic analysis with Kraken 2

Derrick E. Wood, B. Langmead, Jennifer Lu, 2019, Genome Biology.

Bracken: Estimating species abundance in metagenomics data

Steven L. Salzberg, Jennifer Lu, Peter Thielen, 2016 .

Characterization of desnutrin functional domains: critical residues for triacylglycerol hydrolysis in cultured cells[S]

H. Sul, R. Duncan, Maryam Ahmadian, 2010, Journal of Lipid Research.

Improved metagenomic analysis with Kraken 2

Jennifer Lu, Ben Langmead, Derrick E. Wood, 2019, Genome Biology.

Identifying Corneal Infections in Formalin-Fixed Specimens Using Next Generation Sequencing

S. Salzberg, A. Jun, C. Eberhart, 2018, Investigative ophthalmology & visual science.

Regulation of Canonical Oncogenic Signaling Pathways in Cancer via DNA Methylation

M. Trau, D. Korbie, Jennifer Lu, 2020, Cancers.

Comprehensive evaluation of targeted multiplex bisulphite PCR sequencing for validation of DNA methylation biomarker panels

R. Pidsley, S. Clark, Phuc-Loi Luu, 2020, Clinical Epigenetics.

Metagenome analysis using the Kraken software suite

Derrick E. Wood, S. Salzberg, B. Langmead, 2022, Nature Protocols.

Modelling clinical DNA fragmentation in the development of universal PCR-based assays for bisulfite-converted, formalin-fixed and cell-free DNA sample analysis

M. Trau, D. Korbie, Jennifer Lu, 2022, Scientific Reports.

The IFITM Proteins Inhibit HIV-1 Infection

L. Rong, C. Liang, Jennifer Lu, 2010, Journal of Virology.

Targeting a prokaryotic protein in a eukaryotic pathogen: identification of lead compounds against cryptosporidiosis.

Lisa Sharling, Jennifer Lu, L. Hedstrom, 2008, Chemistry & biology.

Identification of microbial agents in tissue specimens of ocular and periocular sarcoidosis using a metagenomics approach

S. Salzberg, A. Scott, A. Jedlicka, 2021, F1000Research.

A review of methods and databases for metagenomic classification and assembly

Florian P Breitwieser, Jennifer Lu, Steven L Salzberg, 2019, Briefings Bioinform..

Identifying Corneal Infections in Formalin-Fixed Specimens Using Next Generation Sequencing

Steven L. Salzberg, Jennifer Lu, Florian P. Breitwieser, 2018, Investigative ophthalmology & visual science.

Bracken: Estimating species abundance in metagenomics data

Steven Salzberg, Jennifer Lu, Peter Thielen, 2016, bioRxiv.

Evaluation of Different Oligonucleotide Base Substitutions at CpG Binding sites in Multiplex Bisulfite-PCR sequencing

A. Dobrovic, M. Trau, D. Korbie, 2017, Scientific Reports.

PrimerROC: accurate condition-independent dimer prediction using ROC analysis

M. Trau, D. Korbie, Jennifer Lu, 2019, Scientific Reports.

Risk SNP-Mediated Promoter-Enhancer Switching Drives Prostate Cancer through lncRNA PCAT19

P. Boutros, S. Thibodeau, S. McDonnell, 2018, Cell.

SkewIT: The Skew Index Test for large-scale GC Skew analysis of bacterial genomes

S. Salzberg, Jennifer Lu, 2020, PLoS Comput. Biol..

SkewIT: Skew Index Test for detecting mis-assembled bacterial genomes

S. Salzberg, Jennifer Lu, 2020, bioRxiv.

Comprehensive evaluation of targeted multiplex bisulphite PCR sequencing for validation of DNA methylation biomarker panels

R. Pidsley, S. Clark, Phuc-Loi Luu, 2020, Clinical Epigenetics.

Noncoding RNA for personalized prostate cancer treatment: utilizing the 'dark matters' of the genome.

H. He, Haiyang Guo, Keren Isaev, 2017, Personalized medicine.

A New Insect-Specific Flavivirus from Northern Australia Suppresses Replication of West Nile Virus and Murray Valley Encephalitis Virus in Co-infected Mosquito Cells

J. Hobson-Peters, S. Davis, R. Weir, 2013, PloS one.

An analytical pipeline for DNA Methylation Array Biomarker Studies

M. Trau, D. Korbie, Jennifer Lu, 2021, bioRxiv.

A global metagenomic map of urban microbiomes and antimicrobial resistance

Stephanie L. Hyland, Nora C. Toussaint, Paweł P. Łabaj, 2021, Cell.

Removing contaminants from databases of draft genomes

Steven Salzberg, Jennifer Lu, S. Salzberg, 2018, PLoS Comput. Biol..

The requirement of the DEAD-box protein DDX24 for the packaging of human immunodeficiency virus type 1 RNA.

Chen Liang, Jennifer Lu, Jing Ma, 2008, Virology.

PrimerSuite: A High-Throughput Web-Based Primer Design Program for Multiplex Bisulfite PCR

Jennifer Lu, Matt Trau, Darren Korbie, 2017, Scientific Reports.

Removing Contaminants from Metagenomic Databases

S. Salzberg, Jennifer Lu, 2018, bioRxiv.

Insulin-Like Growth Factor II mRNA Binding Protein 1 Associates with Gag Protein of Human Immunodeficiency Virus Type 1, and Its Overexpression Affects Virus Assembly

L. Rong, C. Liang, Jennifer Lu, 2008, Journal of Virology.

Ultrafast and accurate 16S microbial community analysis using Kraken 2

Jennifer Lu, Steven L Salzberg, S. Salzberg, 2020, bioRxiv.

The Transmembrane Domain of BST-2 Determines Its Sensitivity to Down-Modulation by Human Immunodeficiency Virus Type 1 Vpu

M. Wainberg, L. Rong, Fei Guo, 2009, Journal of Virology.

Detection of Penicillin Nonsusceptible Streptococcus agalactiae by Laboratories That Participate in the College of American Pathologist’s Proficiency Testing Program

R. Humphries, Jennifer Lu, P. Simner, 2023, Journal of clinical microbiology.

The IFITM Proteins Inhibit HIV-1 Infection

L. Rong, C. Liang, Wei He, 2011, Journal of Virology.

Multicentre genetic diversity study of carbapenem-resistant Enterobacterales: predominance of untypeable pUVA-like blaKPC bearing plasmids

M. Schatz, K. Carroll, W. Timp, 2023, JAC-antimicrobial resistance.

Major data analysis errors invalidate cancer microbiome findings

S. Salzberg, C. Cooper, D. Puiu, 2023, bioRxiv.