Data Science Hub Publications

Highlighted authors are members of the Data Science Hub:

Computational biology

Jian Zhou, Claudia Cattoglio, Yingyao Shao, Harini P Tirumala, Carlo Vetralla, Sameer S Bajikar, Yan Li, Hu Chen, Qi Wang, Zhenyu Wu, Bing Tang, Mahla Zahabiyon, Aleksandar Bajic, Xiangling Meng, Jack J Ferrie, Anel LaGrone, Ping Zhang, Jean J Kim, Jianrong Tang, Zhandong Liu, Xavier Darzacq, Nathaniel Heintz, Robert Tjian, Huda Y Zoghbi, 2023. A novel pathogenic mutation of MeCP2 impairs chromatin association independent of protein levels. Genes & Development, 37(19-20), pp.883-900.

Zahra Anvar, Imen Chakchouk, Momal Sharif, Sangeetha Mahadevan, Eleni Theodora Nasiotis, Li Su, Zhandong Liu, Ying-Wooi Wan, Ignatia B Van den Veyver, 2023. Loss of the maternal effect gene Nlrp2 alters the transcriptome of ovulated mouse oocytes and impacts expression of histone demethylase KDM1B. Reproductive Sciences, 30(9), pp.2780-2793.

Sameer S Bajikar, Ashley G Anderson, Jian Zhou, Mark A Durham, Alexander J Trostle, Ying-Wooi Wan, Zhandong Liu, Huda Y Zoghbi, 2023. MeCP2 regulates Gdf11, a dosage-sensitive gene critical for neurological function. Elife, 12, p.e83806.

Jialin Sun, Sivan Osenberg, Austin Irwin, Li-Hua Ma, Nigel Lee, Yangfei Xiang, Feng Li, Ying-Wooi Wan, In-Hyun Park, Mirjana Maletic-Savatic, Nurit Ballas, 2023. Mutations in the transcriptional regulator MeCP2 severely impact key cellular and molecular signatures of human astrocytes during maturation. Cell reports, 42(1).

Tarik Seref Onur, Andrew Laitman, He Zhao, Ryan Keyho, Hyemin Kim, Jennifer Wang, Megan Mair, Huilan Wang, Lifang Li, Alma Perez, Maria de Haro, Ying-Wooi Wan, Genevera Allen, Boxun Lu, Ismael Al-Ramahi, Zhandong Liu, Juan Botas, 2021. Downregulation of glial genes involved in synaptic function mitigates Huntington's disease pathogenesis. elife, 10, p.e64564.

Machine learning

Liu, C., Wang, L. and Liu, Z., 2023. Single-cell multi-omics integration for unpaired data by a siamese network with graph-based contrastive loss. BMC bioinformatics, 24(1), p.5.

Wang, L., Wu, L., Liu, C., Wang, W., Zhang, X.H.F. and Liu, Z., 2022. Accurate cell type deconvolution in spatial transcriptomics using a batch effect-free strategy. bioRxiv, pp.2022-12.

Wang, W., Ma, L.H., Maletic-Savatic, M. and Liu, Z., 2023. NMRQNet: a deep learning approach for automatic identification and quantification of metabolites using Nuclear Magnetic Resonance (NMR) in human plasma samples. bioRxiv.

Jonnakuti, V.S., Wagner, E.J., Maletić-Savatić, M., Liu, Z. and Yalamanchili, H.K., 2024. PolyAMiner-Bulk is a deep learning-based algorithm that decodes alternative polyadenylation dynamics from bulk RNA-seq data. Cell Reports Methods, 4(2).

Biostatistics

Banerjee A, Stricker E. OralOpioids: Harnessing R Programming and Data Science to Combat Opioid Misuse. Health Serv Res Manag Epidemiol. 2023 Oct 27;10:23333928231208251. doi: 10.1177/23333928231208251. PMID: 37927819; PMCID: PMC10621401.

Patniyot I, Banerjee A, Nobleza KJ, Nguyen DT, Duggan D, Holick M, Dudley-Harrell H. A retrospective analysis of the use of candesartan for migraine prevention in adolescents. Headache. 2024 Jan;64(1):96-97. doi: 10.1111/head.14666. PMID: 38235835.

Wu R, Robayo V, Nguyen DT, Chan EY, Chihara R, Huang HJ, Graviss EA, Kim MP. Enhanced recovery after surgery may mitigate the risks associated with robotic-assisted fundoplication in lung transplant patients. Surg Endosc. 2024 Apr;38(4):2134-2141. doi: 10.1007/s00464-024-10719-9. Epub 2024 Mar 5. PMID: 38443500.

Amirkhosravi F, Nguyen DT, Del Rio RS, Graviss EA, Fida N, Guha A, Martin C, Suarez E, Chou LCP, Bhimaraj A. Outcomes Related to Hospital Characteristics of Heart Transplant Centers: A National Readmission Database Analysis. JHLT Open. Vol 4, 100085, May 2024.

Tayal B, Faza NN, Nguyen DT, Malahfji M, Little S, Saeed M, Goel SS, Guha A, El-Tallawi KC, Graviss EA, Shah DJ. Association of Secondary Mitral Regurgitation and Right Ventricular Dysfunction among Patients with Non-Ischemic Cardiomyopathy. Eur Heart J Cardiovasc Imaging. 2024 May 23:jeae134. doi: 10.1093/ehjci/jeae134. Epub ahead of print. PMID: 38781428.

Connor AA, Adelman MW, Mobley CM, Moaddab M, Erhardt AJ, Hsu DE, Brombosz EW, Sanghvi M, Cheah YL, Simon CJ, Hobeika MJ, Saharia AS, Victor DW 3rd, Kodali S, Basra T, Graviss EA, Nguyen DT, Elsaiey A, Moore LW, Nigo M, Drews AL, Grimes KA, Arias CA, Li XC, Gaber AO, Ghobrial RM. Single-center Outcomes After Liver Transplantation With SARS-CoV-2-Positive Donors: An Argument for Increased Utilization. Transplant Direct. 2024 Mar 7;10(4):e1590. doi: 10.1097/TXD.0000000000001590. PMID: 38464428; PMCID: PMC10923316.

Haddad C, Banerjee A, Eubanks J, Rana R, Rider NL, Pompeii L, Anvari S. A Second Slice of FPIES: A Single Center Reappraisal of Pediatric FPIES. J Allergy Clin Immunol Pract. 2024 Apr 27:S2213-2198(24)00423-9. doi: 10.1016/j.jaip.2024.04.038. Epub ahead of print. PMID: 38685476.

Williams E, White C, Banerjee A, Hellsten M, Nobleza KJ, Nguyen DT, Casas J, Jarrell JA. Quality of Outpatient Pediatric Palliative Care Telehealth: A Retrospective Chart Review. J Pain Symptom Manage. 2024 Jun;67(6):561-570.e1. doi: 10.1016/j.jpainsymman.2024.03.014. Epub 2024 Mar 19. Erratum in: J Pain Symptom Manage. 2024 Jun 18:S0885-3924(24)00803-0. doi: 10.1016/j.jpainsymman.2024.05.032. PMID: 38514022.

Biomedical informatics

Sahay S, Hernandez NV, Wang F, Wooten M, Nguyen DT, Fauvel C, Benza R, Graviss EA. Comparison Between REVEAL Lite 2 and COMPERA 2.0 for Risk Stratification in Pulmonary Arterial Hypertension. Chest. 2024 Mar 4:S0012-3692(24)00288-5. doi: 10.1016/j.chest.2024.02.052. Epub ahead of print. PMID: 38447640.

Nachiappa Ganesh R, Graviss EA, Nguyen DT, El-Zaatari Z, Gaber L, Barrios R, Truong L, Farris AB. Reproducibility and prognostic ability of chronicity parameters in kidney biopsy - Comprehensive evaluation comparing microscopy and artificial intelligence in digital pathology. Hum Pathol. 2024 Apr;146:75-85. doi: 10.1016/j.humpath.2024.04.006. Epub 2024 Apr 18. PMID: 38640986.

Banerjee A, Nobleza KJ, Haddad C, Eubanks j, Rana R, Rider NL, Pompeii L, Nguyen DT, Anvari S. Applying Market Basket Analysis to determine complex co-associations among food allergens in children with food protein-induced enterocolitis syndrome (FPIES). Health Services Research & Managerial Epidemiology. Accepted 06/06/2024.

Pehlivan, D., Aras, S., Glaze, D.G., Ak, M., Suter, B. and Motil, K.J., 2024. Development and validation of parent-reported gastrointestinal health scale in MECP2 duplication syndrome. Orphanet Journal of Rare Diseases, 19(1), p.52.