Publications

  1. Wu, Q, Morrow EM, Gamsiz Uzun, ED, A deep learning model for prediction of autism status using whole-exome sequencing data, PLOS Computational Biology, Accepted
  2. VanHelene, AD, Khatri, I, Hilton, CB, Mishra, S, Gamsiz Uzun, ED, Warner, JL, Inferring Gender from First Names: Comparing the Accuracy of Genderize, Gender API, and the gender R Package on Authors of Diverse Nationality, PLOS Digital Health, Accepted
  3. Li, J, Yang, A , Carneiro, BA , Gamsiz Uzun, ED , Massingham, L , Uzun, A. Variant Graph Craft (VGC): A Comprehensive Tool for Analyzing Genetic Variation and Identifying Disease-Causing Variants, BMC Bioinformatics, 2024
  4. Nenninger, EK, Geffert, S, Charla, S, Chou, C, Gamsiz Uzun, ED, Sawyer, D, Badeel, R, Chargualaf, C, Almaghlouth, NK, Hong, T, Recurrent joint infection caused by a multidrug-resistant capnophilic Escherichia coli ST131 O25H4 strain, IDCases, 2024
  5. Walton, NA, Nagarajan, R, Wang, C, Sincan , M, Freimuth, RR, Everman, DB, Walton, DC, Lemas, DJ, Benos, PV, Alekseyenko, AV, Song, Q, Gamsiz Uzun, ED, Taylor, CO, Uzun, A, Person, TN, Rappoport, N, Zhao, Z, McGrath, SP, Williams, MS, Enabling the Clinical Application of Artificial Intelligence in Genomics: A Perspective of the AMIA Genomics and Translational Bioinformatics Workgroup, Journal of the American Medical Informatics Association, 2024
  6. Baykara, Y, Gamsiz Uzun, ED, Jackson, C, Kurt, H, Exon 19 deletion in EGFR in a patient with a high-grade glioma: a case report, Annals of Clinical & Laboratory Science, 2023
  7. Wu, Q, Ma, L, Joesch-Cohen, L, Schmidt, M, Gamsiz Uzun, ED#, Morrow, EM#, Targeting NHE6 gene expression identifies lysosome and neurodevelopmental mechanisms in Christianson Syndrome cell model, Biology Open, 2023
  8. Gamsiz Uzun, ED, Introducing JMIR Bioinformatics and Biotechnology: A Platform for Interdisciplinary Collaboration and Cutting-Edge Research, JMIR Bioinformatics and Biotechnology, 2023
  9. Hacking, S, Karam, J, Singh, K, Gamsiz Uzun, ED, Brickman, A, Yakirevich, E, Taliano, R, Wang, Y “Whole slide image features predict pathologic complete response and poor clinical outcomes in triple-negative breast cancer” Pathology-Research and Practice, 2023
  10. Hacking, S, Chou, C, Baykara, Y, Wang, Y, Uzun, A, Gamsiz Uzun, ED “MMR Deficiency Defines Distinct Molecular Subtype of Breast Cancer with Histone Proteomic Networks” International Journal of Molecular Science, 2023, 24(6)
  11. Leung, C, Rosenweig, S, Yoon, B, Marinelli, NA, Hollingsworth, EW, Maguire, AM, Cowen, MM, Schmidt, M, Imitola, J, Gamsiz Uzun, ED#, Lizarraga, SB# “Dysregulation of the chromatin environment leads to differential alternative splicing as a mechanism of disease in a human model of Autism Spectrum Disorder”, Accepted to Human Molecular Genetics, 2023
  12. De Souza, A, Charissa, C, Mega, AE, Douglass J, Olszewski A, Gamsiz Uzun ED, Uzun A, Duan F, Wang J, Amin A, Golijanin D, Holder S, Lagos G, Safran H, El-Deiry WS, Carneiro BA “Clinical features of patients with MTAP-deleted bladder cancer”, American Journal of Cancer Research, 2023
  13. Lai, J, Yang J, Gamsiz Uzun ED, Rubenstein, B, Sarkar, IN, “LYRUS: A Machine Learning Model for Predicting the Pathogenicity of Missense Variants”, Bioinformatics Advances, 2021
  14. Brodsky, AS, Khurana, J, Guo, KS, Wu, EY, Yang, D,  Siddique, AS, Wong, IY, Gamsiz Uzun, ED, Resnick, MB, Somatic Mutations in Collagens are Associated with a Distinct Tumor Environment and Overall Survival in Gastric Cancer, BMC Cancer, 2021
  15. Lizarraga, SB, Maguire AM, Ma L, van Dyck, LI, Wu, Q, Nagda, D, Livi, LL, Pescosolido, MF, Schmidt, M, Alabi, S, Cowen, MH, Brito-Vargas, P, Hoffman-Kim, D, Gamsiz Uzun, ED, Schlessinger, A, Jones, RN, Morrow, EM, “Human neurons from Christianson syndrome iPSCs reveal allele-specific responses to rescue strategies”, Science Translational Medicine, 2021, 13(580), PMID: 33568516
  16. Howard, M, Kane, B, Lepry, M, Stey, P, Ragevandran, A, Gamsiz Uzun, ED, “VarStack: a web tool for data retrieval to interpret somatic variants in cancer”, Database, 2020, Volume 2020. PMID: 33247936
  17. McCormick, CEB,  Kavanaugh , BC, , Sipsock, D, Righi, G, Oberman, LM, Moreno De Luca, D, Gamsiz Uzun,  ED, Best, CR, Jerskey, BA, Quinn, JG, Jewel, SB, Wu, PC, McLean, RL, Levine, TP, Tokadjian, H, Perkins, KA,  Clarke, EB, Dunn, B, Gerber , AH, Tenenbaum, EJ,  Anders, TF, Rhode Island Consortium for Autism Research and Treatment (RI-CART), Sheinkopf, SJ and Morrow, EM, “Autism Heterogeneity in a Densely Sampled U.S. Population: Results From the First 1,000 Participants in the RI‐CART Study”, Autism Research, 2020 Mar;13(3):474-488. PMID:31957984
  18. Von Werra, L, Schongens, M, Gamsiz Uzun, ED, Eickhoff, C, “Generative adversarial networks in precision oncology”, ICTIR 2019 Meeting Proceedings, Short Paper
  19. Xu, M, Ouyang, Q, Gong, J, Pescosolido, MF, Pruett, BS, Mishra, S, Schmidt, M, Jones, RN, Gamsiz Uzun, ED, Lizarraga, SB, Morrow, EM, “Mixed neurodevelopmental and neurodegenerative pathology in Nhe6-null mouse model of Christianson syndrome”, eNeuro 2017, 4(6).
  20. Gamsiz ED, Sciarra LN, Maguire AM, Pescosolido MF, van Dyck LI, Morrow EM, “Discovery of Rare Mutations in Autism: Elucidating Neurodevelopmental Mechanisms”, Neurotherapeutics, 2015 Jul;12(3):553-71. PMID: 26105128
  21. Harrison, AJ, Gamsiz, ED, Berkowitz, IC, Nagpal, S, Jerskey, BA, “Genetic Variation in the Oxytocin Receptor Gene is Associated with a Social Phenotype in Autism Spectrum Disorders, American Journal of Medical Genetics B: Neuropsychiatric Genetics 2015, 168(8). PMID: 26365303
  22. Gamsiz, ED, Viscidi, EW, Nagpal, S, Sanders, SJ, Murtha, MT, Simons Simplex Collection Genetics Consortium, Istrail, S, Triche, EW, State, MW, Cook Jr, EH, Devlin, B Morrow, EM,
    “Intellectual Disability is Associated with Increased Runs of Homozygosity in Simplex Autism”, American Journal of Human Genetics 2013, 93(1):103-109. PMID: 23830515; PMC3710760
  23. Pescosolido M, Schwede, M, Ashley, J, Schmidt, M, Gamsiz, ED, Phornphutkul, C, Morrow, EM, “Expansion of the Clinical Phenotype Associated with Mutations in Activity- Dependent Neuroprotective Protein”, Journal of Medical Genetics 2014, 51(9):587-9, PMID: 25057125; PMC4135390
  24. Pescosolido, MF, Gamsiz ED, Nagpal, S, Morrow, EM, “Distribution of Disease- associated Copy Number Variants Across Distinct Disorders of Cognitive Development”. Journal of American Academy of Child and Adolescent Psychiatry 2013, 52(4):414-430. PMID: 23582872; PMC3774163
  25. Gamsiz, ED, Ouyang, Q, Schmidt, M, Nagpal, S, Morrow, EM, “Genome-wide Transcriptome Analysis in Murine Neural Retina Using High-throughput RNA Sequencing”, Genomics 2012, 99(1):44-51. PMID:22032952; PMC3392719
  26. Gamsiz, ED, Thombre, A, Ahmed, I, Carrier, RL, “Model Predicting Impact of Complication with Cyclodextrins on Oral Absorption”. Biotechnology and Bioengineering 2013, 110(9);2536-47. PMID:23592239
  27. Gamsiz, ED, Thombre, A, Ahmed, I, Carrier, RL, “Drug Salts and Solubilization: Modeling the Influence of Cyclodextrins on Oral Absorption”, Annuals of Biomedical Engineering
    2011, 39(1);455-68 PMID: 20960062
  28. Gamsiz, ED, Ashtikar, M, Crison, J, Woltosz, W, Carrier, RL “Predicting the Effect of Fed State Intestinal Contents on Drug Dissolution”, Pharmaceutical Research 2010, 27(12):2646-56. PMID:20963629
  29. Gamsiz, ED, Thombre, A, Miller, LA, Ahmed, I, Carrier, RL “Modeling the Influence of Cyclodextrins on Oral Absorption of Insoluble Drugs: 1. Model Development, Biotechnology and Bioengineering 2010, 105(2):409-420. PMID: 19725042
  30. Gamsiz, ED, Thombre, A, Miller, LA, Ahmed, I Carrier, RL, “Modeling the Influence of Cyclodextrins on Oral Absorption of Insoluble Drugs: 2. Model Validation, Biotechnology and Bioengineering 2010, 105(2):421-430. PMID: 197250431
  31. Gamsiz, ED, Shah, L, Amiji, M, Carrier, RL, “A Model Predicting Delivery of Saquinavir in Nanoparticles to Human Monocyte/macrophage (Mo/Mac) cells”, Biotechnology and Bioengineering 2008, 101(5):1072-1082. PMID: 18553495