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Projects and Publications

Projects and Publications

The Loyola Genomics Facility has a number of external and internal collaborations in both basic and clinical research.

Publications 

2022

  • Peter E. Larsen and Yang Dai (2022). Modeling interaction networks between host, diet, and bacteria predicts obesogenesis in a mouse model. Front. Mol. Biosci. https://doi.org/10.3389/fmolb.2022.1059094
  • Shuchen Feng, Mudassir S. Ali, Monika Evdokimova, Gail E. Reid, Nina M. Clark, Susan L. Uprichard, and Susan C. Baker (2022). Sequencing during Times of Change: Evaluating SARS-CoV-2 Clinical Samples during the Transition from the Delta to Omicron Wave. Viruses, 14(7), 1408; https://doi.org/10.3390/v14071408 [Using LGF-generated data]
  • Mark Sellin, Ryan Mack, Matthew C Rhodes, Lei Zhang, Stephanie Berg, Kanak Joshi, Shanhui Liu, Wei Wei, Peter Breslin, Peter Larsen, Richard E Taylor, Jiwang Zhang (2022). Molecular mechanisms by which splice modulator GEX1A inhibits leukaemia development and progression. Br J Cancer. Apr 14. doi: 10.1038/s41416-022-01796-5.
  • Hyun Gyu Lim, Kevin Rychel, Anand V Sastry, Gayle J Bentley, Joshua Mueller, Heidi S Schindel, Peter E Larsen, Philip D Laible, Adam M Guss, Wei Niu, Christopher W Johnson, Gregg T Beckham, Adam M Feist, Bernhard O Palsson (2022). Machine-learning from Pseudomonas putida KT2440 transcriptomes reveals its transcriptional regulatory network. Metabolic Engineering 72, 297-310.

2021

  • Carine R. Mores, Travis K. Price​, Birte Wolff​, Thomas Halverson​, Roberto Limeira, Linda Brubaker​, Elizabeth R. Mueller​, Catherine Putonti​, Alan J. Wolfe (2021). “Genomic relatedness and clinical significance of Streptococcus mitis strains isolated from the urogenital tract of sexual partners” Microb Genom. 7(3):mgen000535. doi: 10.1099/mgen.0.000535.
  • Kristin M Jacobs, Travis K Price, Krystal Thomas-White, Thomas Halverson, Abigail Davies, Deborah L Myers, Alan J Wolfe (2021) “Cultivable Bacteria in Urine of Women With Interstitial Cystitis: (Not) What We Expected”. Female Pelvic Med Reconstr Surg, 27(5):322-327. doi: 10.1097/SPV.0000000000000854. PMID: 32265402; PMCID: PMC8088819.

2020

  • Jarrad T Hampton-Marcell, Peter Larsen, Tifani Anton… (2020). “Detecting Personal Microbiota Signatures at Artificial Crime Scenes”.  Forensic Science International, 313 doi.org/10.1016/j.forsciint.2020.110351.
  • Daniele Armaleo, Olaf Müller, ... Peter E Larsen, ... Basil B Xavier (2019). “The lichen symbiosis re-viewed through the genomes of Cladonia grayi and its algal partner Asterochloris glomerata”. BMC Genomics 20 (1), 605.
  • Herbert ZT, Thimmapuram J, Xie S, et al. (2020). “Multisite Evaluation of Next-Generation Methods for Small RNA Quantification”. Journal of Biomolecular Techniques : DOI: 10.7171/jbt.20-3102-001. PMID: 31966025; PMCID: PMC6953595.
  • Taylor Miller-Ensminger,Rita Mormando,Laura Maskeri,Jason W. Shapiro, Alan J. Wolfe, Catherine Putonti (2020). “Introducing Lu-1, a Novel Lactobacillus jensenii Phage Abundant in the Urogenital Tract”. PLOS ONE, 15(6), e0234159.
  • Krystal Thomas-White,Susanne Taege,Roberto Limeira,Cynthia Brincat,Cara Joyce,Evann E Hilt,Laura Mac-Daniel,Katherine A Radek,Linda Brubaker,Elizabeth R Mueller, Alan J Wolfe (2020). “Vaginal Estrogen Therapy Is Associated with Increased Lactobacillus in the Urine of Post-Menopausal Women with Overactive Bladder Symptoms”. American Journal of Obstetrics & Gynecology, DOI:https://doi.org/10.1016/j.ajog.2020.08.006.
  • Roese Mores, Carine; Price, Travis K.; Brassil, Bridget; Putonti, Catherine; Wolfe, Alan J. (2020). “Complete Genome Sequences of Streptococcus mitis Strains Isolated from the Oral Cavity and Urogenital Tract of a Woman and Her Male Sexual Partner”. Microbiology Resource Announcements 9(1).
  • Zilliox MJ, Gange WS, Kuffel G, Mores CR, Joyce C, de Bustros P, Bouchard CS (2020). “Assessing the ocular surface microbiome in severe ocular surface diseases”. Ocul Surf. 18(4):706-712. doi: 10.1016/j.jtos.2020.07.007. Epub 2020 Jul 24. PMID: 32717380; PMCID: PMC7905829.

2019

  • MF Noirot-Gros, S Forrester, G Malato, PE Larsen, P Noirot (2019). ”CRISPR interference to interrogate genes that control biofilm formation in Pseudomonas fluorescens”. Scientific Reports 9 (1), 1-14.
  • Shinde, S., S. Zerbs, F. R. Collart, J. R. Cumming, P. Noirot and E. Larsen (2019). "Pseudomonas fluorescens increases mycorrhization and modulates expression of antifungal defense response genes in roots of aspen seedlings." BMC Plant Biol 19(1): 4.
  • Catherine Putonti, Virina Akhnoukh, Zoe Anagnostopoulos, Maria Bilek, John Colgan, Samir El Idrissi, Karolina Magnuszewski, Steven Marino, Matthew Szymulewski, Megan Tyahla, Viktoriya Yanchuk, Taylor Miller-Ensminger, Mary Batrich, Bridget Brassil, Rita Mormando, Genevieve Johnson, Alan J. Wolfe (2019). “Draft Genome Sequences of Six Lactobacillus gasseri and Three Lactobacillus paragasseri Strains Isolated from the Female Bladder”. Mirobiology Resource Announcements, Volume 8, Issue 37, e00973-19.

2018

  • Larsen, P. E., S. Zerbs, P. D. Laible, F. R. Collart, P. Korajczyk, Y. Dai and P. Noirot (2018). "Modeling the Pseudomonas Sulfur Regulome by Quantifying the Storage and Communication of Information." mSystems 3(3).
  • Cardona, C., S. Lax, Larsen, B. Stephens, J. Hampton-Marcell, C. F. Edwardson, C. Henry, B. Van Bonn and J. A. Gilbert (2018). "Environmental Sources of Bacteria Differentially Influence Host-Associated Microbial Dynamics." mSystems 3(3).
  • Holly Kramer, Gina Kuffel, Krystal Thomas-White, Alan J. Wolfe, Kavitha Vellanki, David J. Leehey, Vinod K. Bansal, Linda Brubaker, Robert Flanigan, Julia Koval, Anuradha Wadhwa & Michael J. Zilliox (2018). “Diversity of the midstream urine microbiome in adults with chronic kidney disease”. International Urology and Nephrology, volume 50, pages 1123–1130.
  • Peter E. Larsen (2018). “Statistical Tools for Study Design: Replication”. Springer Protocols Handbooks. Humana Press, 10.1007/8623_2015_95. http://dx.doi.org/10.1007/8623_2015_95).

2017

  • Lax, S., N. Sangwan, D. Smith, Larsen, K. M. Handley, M. Richardson, K. Guyton, M. Krezalek, B. D. Shogan, J. Defazio, I. Flemming, B. Shakhsheer, S. Weber, E. Landon, S. Garcia-Houchins, J. Siegel, J. Alverdy, R. Knight, B. Stephens and J. A. Gilbert (2017). "Bacterial colonization and succession in a newly opened hospital." Sci Transl Med 9(391).
  • Shinde, S., J. R. Cumming, F. R. Collart, P. H. Noirot and E. Larsen (2017). "Pseudomonas fluorescens Transportome Is Linked to Strain-Specific Plant Growth Promotion in Aspen Seedlings under Nutrient Stress." Frontiers in Plant Science 8.
  • Thompson, L. R., …E. Larsen… E. M. P. Consortiu (2017). "A communal catalogue reveals Earth's multiscale microbial diversity." Nature 551(7681): 457-+.

Other Publications

  • Association of Cardiomyopathy With MYBPC3 D389V and MYBPC3Δ25bpIntronic Deletion in South Asian Descendants
    Jun 2018, JAMA Cardiol.
  • Genetic Polymorphisms Associated with Risk of Developing Age-Related Macular Degeneration in Patients with Chronic Aspirin Usage
    May 14, 2018, Journal of Ophthalmology & Eye Care
  • Exosomal miR-21a-5p mediates cardioprotection by mesenchymal stem cells
    Apr 12, 2018, Journal of Molecular and Cellular Cardiology
  • An acetylatable lysine controls CRP function in E. coli
    Oct 31, 2017, Molecular Microbiology
  • Genomes of Gardnerella Strains Reveal an Abundance of Prophages within the Bladder Microbiome
    Nov 2016, PLoS ONE
  • Incontinence medication response relates to the female urinary microbiota
    May 2016, Int Urogynecol J

The Loyola Genomics Facility has a number of external and internal collaborations in both basic and clinical research.

Publications