Trainee Accomplishments

Awards and Fellowships

2024

Catalina Alvarez-Yela, ASPIRE Grant from the Susan Komen G. Foundation (IN THE NEWS)

Catalina Alvarez, UVA Engineering Endowed Graduate Fellowship

Mario Garcia, Wallace H.Coulter Center for Translational Research Scholar

Emma Glass, Achievement Rewards for College Scientists (ARCS) Foundation Scholar

Emma Glass, Evelyn Soucek Memorial Scholar of Metropolitan Washington Chapter of Achievement Rewards for College Scientists Foundation (MWC/ARCS)

Emma Glass, Sture G. Olsson Fellowship in Engineering

Emma Glass, UVA Engineering Endowed Graduate Fellowship

Rusty Hawes, UVA Cancer Center Fellowship

Shay Ladd, NSF GRFP Honorable Mention

Candace Lei, Croucher Foundation Fellow

Kris Pas, UVA Brain Institute Presidential Fellowship in Collaborative Neuroscience

Lionel Watkins, Wallace H.Coulter Center for Translational Research Scholar

Remziye Wessel, P.E.O. Foundation Scholar Award

Remziye Wessel, Travel Award from American Society for Reproductive Immunologists (ASRI)

2023

Nathan LeRoy, Double Hoo Research Award (ABOUT)

Emma Glass, One of four UVA nominees for the Google Fellowship

Publications/preprints

2024

Methods for constructing and evaluating consensus genomic interval sets.  Rymuza J, Sun Y, Zheng G, LeRoy NJ, Murach M, Phan N, Zhang A, Sheffield NC. Nucleic Acids Res. 2024 Sep 23;52(17):10119-10131. doi: 10.1093/nar/gkae685. PMID: 39180401 Free PMC article. 

Methods for evaluating unsupervised vector representations of genomic regions. Zheng G, Rymuza J, Gharavi E, LeRoy NJ, Zhang A, Sheffield NC.NAR Genom Bioinform. 2024 Aug 10;6(3):lqae086. doi: 10.1093/nargab/lqae086. eCollection 2024 Sep. PMID: 39131817 Free PMC article. 

PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata.  LeRoy NJ, Khoroshevskyi O, O'Brien A, Stępień R, Arslan A, Sheffield NC. Gigascience. 2024 Jan 2;13:giae033. doi: 10.1093/gigascience/giae033. PMID: 38991851 Free PMC article. 

Joint Representation Learning for Retrieval and Annotation of Genomic Interval Sets.  Gharavi E, LeRoy NJ, Zheng G, Zhang A, Brown DE, Sheffield NC. Bioengineering (Basel). 2024 Mar 8;11(3):263. doi: 10.3390/bioengineering11030263. PMID: 38534537 Free PMC article. 

Fast clustering and cell-type annotation of scATAC data using pre-trained embeddings. LeRoy NJ, Smith JP, Zheng G, Rymuza J, Gharavi E, Brown DE, Zhang A, Sheffield NC. NAR Genom Bioinform. 2024 Jul 5;6(3):lqae073. doi: 10.1093/nargab/lqae073. eCollection 2024 Sep. PMID: 38974799 Free PMC article. 

Distinct Type 1 Immune Networks Underlie the Severity of Restrictive Lung Disease after COVID-19. Canderan G, Muehling LM, Kadl A, Ladd S, Bonham C, Cross CE, Lima SM, Yin X, Sturek JM, Wilson JM, Keshavarz B, Bryant N, Murphy DD, Cheon IS, McNamara CA, Sun J, Utz PJ, Dolatshahi S, Irish JM, Woodfolk JA. bioRxiv [Preprint]. 2024 Apr 4:2024.04.03.587929. doi: 10.1101/2024.04.03.587929.   PMID: 38617217 Free PMC article. Preprint.

Modeling the Roles of Cohesotaxis, Cell-Intercalation, and Tissue Geometry in Collective Cell Migration of Xenopus Mesendoderm. Comlekoglu, Tien, Bette J. Dzamba, Gustavo G. Pacheco, David R. Shook, T. J. Sego, James A. Glazier, Shayn M. Peirce, and Douglas W. DeSimone. Biology Open 13, no. 8 (August 15, 2024): bio060615. https://doi.org/10.1242/bio.060615.

Spatial colocalization and combined survival benefit of natural killer and CD8 T cells despite profound MHC class I loss in non-small cell lung cancer. Wessel RE, Ageeb N, Obeid JM, Mauldin I, Goundry KA, Hanson GF, Hossain M, Lehman C, Gentzler RD, Wages NA, Slingluff CL Jr, Bullock TNJ, Dolatshahi S, Brown MG. bioRxiv [Preprint]. 2024 Jun 25:2024.02.20.581048. doi: 10.1101/2024.02.20.581048. Update in: J Immunother Cancer. 2024 Sep 18;12(9):e009126. doi: 10.1136/jitc-2024-009126.  PMID: 38979183 Free PMC article. Preprint. 

Regulators of placental antibody transfer through a modeling lens. Wessel RE, Dolatshahi S. Nature Immunology. (2024) In press.

Patient-derived response estimates from zero-passage organoids of luminal breast cancer. Przanowska, R., Labban, N., Przanowski, P., Hawes, R., Atkins, K., Showalter, S., & Janes, K. BioRxiv 2024.03.24.586432 [Preprint] March 27, 2024 [cited 2024 October 7]. Available from: https://doi.org/10.1101/2024.03.24.586432

2023

Reconstructor: a COBRApy compatible tool for automated genome-scale metabolic network reconstruction with parsimonious flux-based gap-filling. Jenior ML, Glass EM, Papin JA., Bioinformatics. 2023 Jun 1;39(6):btad367. doi: 10.1093/bioinformatics/btad367. PMID: 37279743 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. No abstract available. 

Integrative single-cell meta-analysis reveals disease-relevant vascular cell states and markers in human atherosclerosis. Mosquera JV, Auguste G, Wong D, Turner AW, Hodonsky CJ, Alvarez-Yela AC, Song Y, Cheng Q, Lino Cardenas CL, Theofilatos K, Bos M, Kavousi M, Peyser PA, Mayr M, Kovacic JC, Björkegren JLM, Malhotra R, Stukenberg PT, Finn AV, van der Laan SW, Zang C, Sheffield NC, Miller CL. Cell Rep. 2023 Nov 28;42(11):113380. doi: 10.1016/j.celrep.2023.113380. Epub 2023 Nov 10. PMID: 37950869 

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.

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.

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.

Quantitative mechanistic model reveals key determinants of placental IgG transfer and informs prenatal immunization strategies. Wessel RE, Dolatshahi S. PLoS Comput Biol. 2023 Nov 7;19(11):e1011109. doi: 10.1371/journal.pcbi.1011109. eCollection 2023 Nov. PMID: 37934786 Free PMC article.

Model-driven characterization of functional diversity of Pseudomonas aeruginosa clinical isolates with broadly representative phenotypes. Islam MM, Kolling GL, Glass EM, Goldberg JB, Papin JA. bioRxiv [Preprint]. 2023 Oct 10:2023.10.08.561426. doi: 10.1101/2023.10.08.561426. Update in: Microb Genom. 2024 Jun;10(6). doi: 10.1099/mgen.0.001259. PMID: 37873245 Free PMC article. Preprint