Publications

David BM, Jensen PA

Planning and scheduling biological experiments across multiple liquid handling robots.

bioRxiv. 2025; 10.64898/2025.12.26.696584.

Preprint

Martin JP, Brown JS, Dunmoye ID, Smith LT, Suresh DE, Jensen PA

AI and engineering careers: recent graduates' outlook on opportunities and challenges.

International Journal of STEM Education. 2025; 10.1186/s40594-025-005830-x.

Journal

Sanders J, Mobley~IV J, Miller I, Sochacka NW, Jensen PA, Jensen KJ.

Affordances and limitations of using large language models to generate qualitative data about mental health perceptions in engineering.

Journal of Engineering Education. 2025; 10.1002/jee.70037.

Journal

Jensen PA, Al Habib S, Baker S, Bernstein D, David BM, DeBenedictis E, Eisen JA, Fitch L, Hoarfrost A, Knight-Connonni V, Koblitz J, Mahadevan R, Milshteyn S, Nattermann U, Reimer LC, Stork D, Surae S, Winnifrith A, Wood-Charlson EM, Kelly P

Genotype to Phenotype: Design of an extensible experimental platform for characterizing microbes.

Zenodo. 2025; 10.1038/s41564-023-01376-0.

Article

Herbert HG, Chia N, Jensen PA, Walther-Antonio MRS

Monotherapy cancer drug-blind response prediction is limited to intraclass generalization.

bioRxiv. 2025; 10.1101/2025.06.16.659838v1.

Preprint

Jensen PA

Ten species comprise half of the bacteriology literature, leaving most species unstudied.

bioRxiv. 2025; 10.1101/2025.01.04.631297v1.

Preprint | GitHub | Nature News & Views

Wyllie RM, Jensen PA

The MutRS quorum sensing system controls lantibiotic mutacin production in the human pathogen Streptococcus mutans.

PNAS. 2025, 122 (7) e2421164122.

PubMed | Journal

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.

mBio. 2025, 16:e02993-24.

PubMed | Journal

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 | Nature News & Views

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.

PubMed | 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