Publications
- Wyllie RM, Jensen PA
The MutRS quorum sensing system controls lantibiotic mutacin production in the human pathogen Streptococcus mutans.
bioRxiv. 2024; 10.01.616031.
[Preprint] - Richardson JD, Guo E, Wyllie RM, Jensen PA, Dawid S
The pneumococcal bacteriocin streptococcin B is produced as part of the early competence cascade and promotes intraspecies competition.
bioRxiv. 2024; 10.01.616058.
[Preprint] - Suresh DE, Martin JP, Lunkes A, Jensen PA
Modeling career paths in biomedical quality engineering.
Biomedical Engineering Education. 2024; 4(2), 339–359.
[Journal] - Martin JP, Suresh DE, Jensen PA.
Using collaborative autoethnography to investigate mentoring relationships for novice engineering education researchers.
International Journal of STEM Education. 2024; 11(1), 13.
[Journal] - Dama AC, Kim KS, Leyva DM, Lunkes AP, Schmid NS, Jijakli K, Jensen PA.
BacterAI maps microbial metabolism without prior knowledge.
Nature Microbiology. 2023; 8:1018-1025.
[PubMed] [Journal]
News & Views: Gaming bacterial metabolism. - Li JW, Wyllie RM, Jensen PA.
Crosstalk between paralogous ComRS quorum-sensing systems diversifies the competence/bacteriocin networks of oral streptococci.
bioRxiv. 2022; doi:10.1101/2022.10.14.512260.
[Preprint] - David BM, Jensen PA.
Improving an rRNA depletion protocol with statistical design of experiments.
SLAS Technology. 2023; 28:16-21.
[Journal] - Martin JP, Suresh DE, Jensen PA.
Perceptions of shared experiences in mentoring relationships: a collaborative autoethnography.
2022 ASEE Annual Conference & Exposition.
[Proceedings] - David BM, Wyllie RM, Harouaka R, Jensen PA.
A reinforcement learning framework for pooled oligonucleotide design.
Bioinformatics. 2022; 38(8):2219–2225.
[PubMed] [Journal] - David BM, Li JW, Masood F, Blassick C, Jensen PA, Jensen KJ.
Laboratory exercise to measure plasmid copy number by qPCR.
Journal of Microbiology & Biology Education. 2021; 22:e00125-21.
[PubMed] [Journal] - Li W*, Wyllie RM*, Jensen PA.
A novel competence pathway in the oral pathogen Streptococcus sobrinus.
Journal of Dental Research. 2021 May; 100(5):542-548.
[PubMed] [Journal] - Keaty TC, Jensen PA.
Gapsplit: Efficient random sampling for non-convex constraint-based models.
Bioinformatics. 2020; 36(8): 2623-2625.
[PubMed] [Journal] - Pradhan D, Papin JA, Jensen PA.
Efficient enzyme coupling algorithms identify functional pathways in genome-scale metabolic models.
bioRxiv. 2019, doi:10.1101/608430.
[bioRxiv] - Thibault DT, Jensen PA, Wood S, Qabar C, Clark S, Shainheit MG, Isberg RR, van Opijnen T.
droplet-Tn-Seq combines microfluidics with Tn-Seq for identifying complex single-cell phenotypes.
Nature Communications. 2019, 10:5729.
[PubMed] [Journal] - Blassick C, David B, Storm A, Jensen PA, Jensen KJ.
Laboratory exercise to measure restriction enzyme kinetics.
Journal of Microbiology & Biology Education. 2019, 20:3.
[PubMed] [Journal] - Jijakli K, Jensen PA.
Metabolic modeling of Streptococcus mutans reveals complex nutrient requirements of an oral pathogen.
mSystems. 2019; 4:e00529-19.
[PubMed] [Journal] - Shields RC*, Jensen PA.
The bare necessities: Uncovering essential and condition‐critical genes with transposon sequencing.
Molecular Oral Microbiology. 2019; 1-12. Review.
[PubMed] [Journal] - Sales MJ, Herbert WG, Du Y, Sandur AS, Stanley NM, Jensen PA.
Complete genome sequences of Streptococcus sobrinus SL1 (ATCC 33478 = DSM 20742), NIDR 6715-7 (ATCC 27351), NIDR 6715-15 (ATCC 27352), and NCTC 10919 (ATCC 33402).
Microbiology Resource Announcements. 2018, doi:10.1128/MRA.00804-18.
[PubMed] [Journal] - Jensen PA.
Coupling fluxes, enzymes, and regulation in genome-scale metabolic models.
Methods in Molecular Biology. 2018; 1716:337-351. Review.
[PubMed] [Publisher] - Storm AJ, Jensen PA.
Designing randomized DNA sequences free of restriction enzyme recognition sites.
Biotechnology Journal. 2017, doi:10.1002/biot.201700326.
[PubMed] [Journal] - Jensen PA*, Zhu Z*, van Opijnen T.
Antibiotics disrupt coordination between transcriptional and phenotypic stress responses in pathogenic bacteria.
Cell Reports. 2017, 20 1705-1716.
[PubMed] [Journal] - Jensen PA.
Hands-on Assembly of DNA Sequencing Reads as a Gateway to Bioinformatics.
Journal of Microbiology & Biology Education. 2017, 18:2.
[PubMed] [Journal] - Jensen PA, Dougherty BV, Moutinho TJ, Papin JA.
Miniaturized plate readers for low-cost, high-throughput phenotypic screening.
Journal of Laboratory Automation. 2015, Feb;20(1):51-5.
[PubMed] [Journal] - Jensen PA, Papin JA.
MetDraw: Automated visualization of genome-scale metabolic models and high-throughput data.
Bioinformatics. 2014, 30(9): 1327-1328.
[PubMed] [Journal] - Chavali AK, Tlaxca JL, Blazier AS, Jensen PA, Pearson RD, Papin JA.
Metabolic network analysis predicts efficacy of FDA-approved drugs targeting the causative agent of a neglected tropical disease.
BMC Systems Biology. 2012, 6:27.
[PubMed] [Journal] - Jensen PA, Lutz KA, Papin JA.
TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks.
BMC Systems Biology. 2011, 5:147.
[PubMed] [Journal] - Jensen PA, Papin JA.
Functional integration of a metabolic network model and expression data without arbitrary thresholding.
Bioinformatics. 2011, 27(4):541-7.
[PubMed] [Journal]