Alumni

Trainees

2023 Gabe Hanson

2023 Russell Hawes

2023 Shay Ladd

2023 Kris Pas

2023 Jamel Simpson

2023 Lionel Watkins

2023 Yonatan Degefu

2023 Candace Lei

2022 Catalina Alvarez Yela

2022 Tien Comlekoglu

2022 Remziye Erdogan

2022 Mario Garcia

2022 Emma Glass

2022 Nathan LeRoy

2022 Conner Moore

Awards and Fellowships

2023

Nathan LeRoy, Double Hoo Research Award (ABOUT)

Emma Glass, Selected as one of four UVA nominees for the Google Fellowship

2022

Emma Glass, National Science Foundation Graduate Research Fellow

Publications/preprints

2023

Dichotomous ovarian cancer-initiating potential of Pax8+ cells revealed by a mouse genetic mosaic model. Zeng J, Alvarez-Yela AC, Casarez E, Jiang Y, Wang L, Kelly BE, Jenkins T, Ke E, Atkins KA, Janes KA, Slack-Davis JK, Zong H. iScience. 2023 Apr 25;26(5):106742. doi: 10.1016/j.isci.2023.106742. eCollection 2023 May 19. PMID: 37207276 Free PMC article.

General, Open-Source Vertex Modeling in Biological Applications Using Tissue Forge. Sego TJ, Comlekoglu T, Peirce SM, Desimone D, Glazier JA. Res Sq. 2023 May 8:rs.3.rs-2886960. doi: 10.21203/rs.3.rs-2886960/v1. Preprint. PMID: 37214822 Free PMC article.

Metabolic modeling of sex-specific tissue predicts mechanisms of differences in toxicological responses. Moore CJ, Holstege CP, Papin JA. bioRxiv. 2023 Feb 7:2023.02.07.527430. doi: 10.1101/2023.02.07.527430. Preprint. PMID: 36798158 Free PMC article.

Quantitative mechanistic model reveals key determinants of placental IgG transfer and informs prenatal immunization strategies. Erdogan RR, Dolatshahi S. bioRxiv. 2023 Apr 19:2023.04.18.537285. doi: 10.1101/2023.04.18.537285. Preprint. PMID: 37131700 Free PMC article.

Challenges to sharing sample metadata in computational genomics. Sheffield NC, LeRoy NJ, Khoroshevskyi O. Front Genet. 2023 May 23;14:1154198. doi: 10.3389/fgene.2023.1154198. eCollection 2023. PMID: 37287537 Free PMC article.

Jenior M. †, Glass, E. M.†., and Papin, J.A., Reconstructor: A COBRApy compatible tool for automated genome-scale metabolic network reconstruction with parsimonious flux[1]based gap-filling. (2023) Bioinformatics. HTTPS://DOI.ORG/10.1093/BIOINFORMATICS/BTAD367. († denotes co-first authorship)

2022

Metabolic Network Models of the Gardnerella Pangenome Identify Key Interactions with the Vaginal Environment.  Dillard LR, Glass EM, Lewis AL, Thomas-White K, Papin JA.mSystems. 2023 Feb 23;8(1):e0068922. doi: 10.1128/msystems.00689-22. Epub 2022 Dec 13.PMID: 36511689 Free PMC article.