Computational Sciences Publications

2023 Publications

1Q - 2023

1. Bogue MA, Ball RL, Philip VM, Walton DO, Dunn MH, Kolishovski G, Lamoureux A, Gerring M, Liang H, Emerson J, Stearns T, He H, Mukherjee G, Bluis J, Desai S, Sundberg B, Kadakkuzha B, Kunde-Ramamoorthy G, Chesler EJ. Mouse Phenome Database: towards a more FAIR-compliant and TRUST-worthy data repository and tool suite for phenotypes and genotypes. Nucleic Acids Res. 2023;51(D1):D1067–D74. PubMed PMID: 36330959

2.  Reese JT, Blau H, Casiraghi E, Bergquist T, Loomba JJ, Callahan TJ, Laraway B, Antonescu C, Coleman B, Gargano M, Wilkins KJ, Cappelletti L, Fontana T, Ammar N, Antony B, Murali TM, Caufield JH, Karlebach G, McMurry JA, Williams A, Moffitt R, Banerjee J, Solomonides AE, Davis H, Kostka K, Valentini G, Sahner D, Chute CG, Madlock-Brown C, Haendel MA, Robinson PN, on behalf of the N3C Consortium and the RECOVER Consortium. Generalisable long COVID subtypes: Findings from the NIH N3C and RECOVER programmes. EBioMedicine. 2022;87:104413. PubMed PMID: 36563487; PMCID: PMC9769411

3.  SanMiguel JM, Eudy E, Loberg MA, Young KA, Mistry JJ, Mujica KD, Schwartz LS, Stearns TM, Challen GA, Trowbridge JJ. Distinct Tumor Necrosis Factor Alpha Receptors Dictate Stem Cell Fitness versus Lineage Output in Dnmt3a-Mutant Clonal Hematopoiesis. Cancer Discov. 2022;12(12):2763-73. PubMed PMID: 36169447; PMCID: PMC9716249

4. Binh Tran TD, Nguyen H, Sodergren E, Center for Systems Neurogenetics of Addiction, Dickson PE, Wright SN, Philip VM, Weinstock GM, Chesler EJ, Zhou Y, Bubier JA. Microbial glutamate metabolism predicts intravenous cocaine self-administration in diversity outbred mice. Neuropharmacology. 2022;226:109409. PubMed PMID: 36592885

5. Capobianco E. Overview of triple negative breast cancer prognostic signatures in the context of data science-driven clinico-genomics research. Ann Transl Med. 2022;10(24):1300. PubMed PMID: 36660729; PMCID: PMC9843365

6. Capobianco E, Dominietto M. Translating Data Science Results into Precision Oncology Decisions: A Mini Review. J Clin Med. 2023;12(2). PubMed PMID: 36675367; PMCID: PMC9862106

7. George J, Chen Y, Abdelfattah N, Yamamoto K, Gallup TD, Adamson SI, Rybinski B, Srivastava A, Kumar P, Lee MG, Baskin DS, Jiang W, Choi JM, Flavahan W, Chuang JH, Kim BY, Xu J, Jung SY, Yun K. Cancer stem cells, not bulk tumor cells, determine mechanisms of resistance to SMO inhibitors. Cancer Res Commun. 2022;2(6):402-16. PubMed PMID: 36688010; PMCID:

8. Rubinstein JC, Foroughi Pour A, Zhou J, Sheridan TB, White BS, Chuang JH. Deep learning image analysis quantifies tumor heterogeneity and identifies microsatellite instability in colon cancer. J Surg Oncol. 2023;127(3):426-33. PubMed PMID: 36251352

9.  Bagley JR, Bailey LS, Gagnon LH, He H, Philip VM, Reinholdt LG, Tarantino LM, Chesler EJ, Jentsch JD. Behavioral phenotypes revealed during reversal learning are linked with novel genetic loci in diversity outbred mice. Addict Neurosci. 2022 Dec;4:100045. doi: 10.1016/j.addicn.2022.100045. Epub 2022 Nov 4. PMID: 36714272; PMCID: PMC9879139.

10. Xu H, Bensalel J, Raju S, Capobianco E, Lu ML, Wei J. Characterization of huntingtin interactomes and their dynamic responses in living cells by proximity proteomics. J Neurochem. 2023;164(4):512-28. PubMed PMID: 36437609

11.Trivella MG, Capobianco E, L'Abbate A. Editorial: Physiology in extreme conditions: Adaptations and unexpected reactions, Volume II. Front Physiol. 2023;14:1181010. PubMed PMID: 36998988; PMCID: PMC10043470

12. Raza A, Diehl SA, Krementsov DN, Case LK, Li D, Kost J, Ball RL, Chesler EJ, Philip VM, Huang R, Chen Y, Ma R, Tyler AL, Mahoney JM, Blankenhorn EP, Teuscher C. A genetic locus complements resistance to Bordetella pertussis-induced histamine sensitization. Commun Biol. 2023;6(1):244. PubMed PMID: 36879097; PMCID: PMC9988836

13. Ladewig MS, Jacobsen JOB, Wagner AH, Danis D, El Kassaby B, Gargano M, Groza T, Baudis M, Steinhaus R, Seelow D, Bechrakis NE, Mungall CJ, Schofield PN, Elemento O, Smith L, McMurry JA, Munoz-Torres M, Haendel MA, Robinson PN. GA4GH Phenopackets: A Practical Introduction. Adv Genet (Hoboken). 2023;4(1):2200016. PubMed PMID: 36910590; PMCID: PMC10000265

2Q - 2023

1. Gerbenn Seraphin, Sandra Rieger, Martin Hewison, Enrico Capobianco, Thomas S. Lisse, The impact of vitamin D on cancer: A mini review. The Journal of Steroid Biochemistry and Molecular Biology. Volume 2023; 231: 106308, ISSN 0960-0760,

2. Cornes BK, Paisie C, Swanzey E, Fields PD, Schile A, Brackett K, Reinholdt LG, Srivastava A. Protein coding variation in the J:ARC and J:DO outbred laboratory mouse stocks provides a molecular basis for distinct research applications. G3 (Bethesda). 2023;13(4):jkad015. PubMed PMID: 36649207; PMCID: PMC10085793

3. Domanskyi S, Jocoy EL, Srivastava A, Bult CJ. ACDA: implementation of an augmented drug synergy prediction algorithm. Bioinform Adv. 2023;3(1):vbad051. PubMed PMID: 37113249; PMCID: PMC10125903

4.Rinchai D, Chaussabel D. Assessing the potential relevance of CEACAM6 as a blood transcriptional biomarker. F1000Research. 2022;11:1294

5. Li Y, Chen M, George J, Liu ET, Karuturi RKM. Adaptive Sentinel Testing in Workplace for COVID-19 Pandemic. J Comput Biol. 2023;30(4):376-90. PubMed PMID: 36445177

6. Capobianco E, McGaughey V, Seraphin G, Heckel J, Rieger S and Lisse TS Vitamin D inhibits osteosarcoma by reprogramming nonsense-mediated RNA decay and SNAI2-mediated epithelial-to-mesenchymal transition.

Front. Oncol. 2023; 13: 1188641.  doi: 10.3389/fonc.2023.1188641.