2023 Computational Sciences Publications

1. Carmody LCGargano MA, Toro S, Vasilevsky NA, Adam MP, Blau H, Chan LE, Gomez-Andres D, Horvath R, Kraus ML, Ladewig MS, Lewis-Smith D, Lochmüller H, Matentzoglu NA, Munoz-Torres MC, Schuetz C, Seitz B, Similuk MN, Sparks TN, Strauss T, Swietlik EM, Thompson R, Zhang XA, Mungall CJ, Haendel MA, Robinson PN. The Medical Action Ontology: A tool for annotating and analyzing treatments and clinical management of human disease. Med. 2023;4(12):913-27. PMID: 37963467. https://libkey.io/libraries/3075/37963467

2. Choudhary A, Radhakrishnan A, Lindner JF, Sinha S, Ditto WL. Neuronal diversity can improve machine learning for physics and beyond. Sci Rep. 2023;13(1):13962. PMID: 37634029; PMCID: PMC10460398. https://libkey.io/libraries/3075/37634029

3. Capobianco E, Dominietto M. Assessment of brain cancer atlas maps with multimodal imaging features. J Transl Med. 2023;21(1):385. PubMed PMID: 37308956; PMCID: PMC10262565. https://libkey.io/libraries/3075/37308956

4. Capobianco E, Moretti PF. Complexity of the marine ecosystem in view of the human health factors: role of network science. Frontiers in Marine Science. 2023;10:1076258. PMID: 10.3389/fmars.2023.1076258. https://libkey.io/libraries/3075/10.3389/fmars.2023.1076258

5. 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: 12.3389/fonc.2023.1188641.  https://www.frontiersin.org/articles/10.3389/fonc.2023.1188641/full#h10

6. Cornes BKPaisie 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 https://libkey.io/libraries/3075/36649207

7. 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 https://libkey.io/libraries/3075/37113249 

8. Li YChen MGeorge 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 https://libkey.io/libraries/3075/36445177

9. Philip VMHe HSaul MC, Dickson PE, Bubier JA, Chesler EJ. Gene expression genetics of the striatum of Diversity Outbred mice. Sci Data. 2023;10(1):522. PMID: 37543624; PMCID: PMC10404230. https://libkey.io/libraries/3075/37543624

10. Kearney SK, Berger A, Baker E. Aon: a service to augment Alliance Genome Resource data with additional species. BMC Res Notes. 2023;16(1):297. PMID: 37891644; PMCID: PMC10604687. https://libkey.io/libraries/3075/37891644

11. Sheehan, S., Mawe, S., Chen, Met al. A machine learning approach for quantifying age-related histological changes in the mouse kidney. GeroScience (2023). https://doi.org/10.1007/s11357-023-01013-y

12. Sproule TJ, Philip VM, Chaudhry NA, Roopenian DC, Sundberg JP. Seven naturally variant loci serve as genetic modifiers of Lamc2jeb induced non-Herlitz junctional Epidermolysis Bullosa in mice. PLoS One. 2023;18(7):e0288263. PubMed PMID: 37437067; PMCID: PMC10337971. https://libkey.io/libraries/3075/37437067

13. Perez MF, Yurieva M, Poddutoori S, Mortensen EM, Crotty Alexander LE, Williams A. Transcriptomic responses in the blood and sputum of cigarette smokers compared to e-cigarette vapers. Respir Res. 2023;24(1):134. PubMed PMID: 37208747; PMCID: PMC10196320 https://libkey.io/libraries/3075/37208747

14. Song Y, Chen MZhang Y, Li J, Liu B, Li N, Chen M, Qiao M, Wang N, Cao Y, Lu S, Chen J, Sun W, Gao F, Wang H. Loss of circSRY reduces γH2AX level in germ cells and impairs mouse spermatogenesis. Life Sci Alliance. 2023;6(2). PubMed PMID: 36414375; PMCID: PMC9684031https://libkey.io/libraries/3075/36414375

15. 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 https://libkey.io/libraries/3075/36998988

16. Hu N, Hale H, Sanderson B, Feng G, Guo M, Gambhir D, Olson M. Reproductive Sexual Dimorphisms in Two Willow Species, Salix exigua Nutt. and Salix nigra Marshall. International Journal of Plant Sciences. 2023;184(9):688-95. PMID: 10.1086/726623. https://libkey.io/libraries/3075/10.1086/726623

17. Bogue MA, Ball RL, Walton DODunn MHKolishovski GBerger ALamoureux AGrubb SCGerring M, Kim M, Liang H, Emerson JStearns THe H, Mukherjee G, Bluis JDavis SDesai SSundberg BKadakkuzha BKunde-Ramamoorthy GPhilip VM, Chesler EJ. Mouse phenome database: curated data repository with interactive multi-population and multi-trait analyses. Mamm Genome. 2023;34(4):509-19. PMID: 37581698; PMCID: PMC10627943. https://libkey.io/libraries/3075/37581698

18. Castaneda DC, Jangra S, Yurieva M, Martinek J, Callender M, Coxe M, Choi A, García-Bernalt Diego J, Lin J, Wu TC, Marches F, Chaussabel D, Yu P, Salner A, Aucello G, Koff J, Hudson B, Church SE, Gorman K, Anguiano E, García-Sastre A, Williams A, Schotsaert M, Palucka K. Spatiotemporally organized immunomodulatory response to SARS-CoV-2 virus in primary human broncho-alveolar epithelia. iScience. 2023;26(8):107374. PubMed PMID: 37520727; PMCID: PMC10374611. https://libkey.io/libraries/3075/37520727

19. Staff NP, Hrstka SC, Dasari S, Capobianco E, Rieger S. Skin Extracellular Matrix Breakdown Following Paclitaxel Therapy in Patients with Chemotherapy-Induced Peripheral Neuropathy. Cancers. 2023;15(16):4191. PMID: 37627219; PMCID: PMC10453667. https://libkey.io/libraries/3075/37627219

20. 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 https://libkey.io/libraries/3075/36437609

21. 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, https://doi.org/10.1016/j.jsbmb.2023.106308.

22. SundaramurthiJC, Bagley AM, Blau H, Carmody L, Crandall A,Danis D, Gargano M, Gustafson AG, Raney EM, Shingle M, Davids JR, Robinson PN. De novo TRPM3 missense variant associated with neurodevelopmental delay and manifestations of cerebral palsy. Cold Spring Harb Mol Case Stud. 2023;9(4):a006293. PMID: 37684057. https://libkey.io/libraries/3075/37684057

23. Nehar-Belaid D, Sokolowski M, Ravichandran S, Banchereau J, Chaussabel D, Ucar D. Baseline immune states (BIS) associated with vaccine responsiveness and factors that shape the BIS. Semin Immunol. 2023;70:101842. PMID: 37717525. https://libkey.io/libraries/3075/37717525

24. 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 https://libkey.io/libraries/3075/36251352 

25. Ladewig MS, Jacobsen JOB, Wagner AH, Danis D, El Kassaby BGargano 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 https://libkey.io/libraries/3075/36910590

26. Hughes K, Evans K, Earley EJ, Smith CM, Erickson SW, Stearns TPhilip VM, Neuhauser SB, Chuang JH, Jocoy EL, Bult CJ, Teicher BA, Smith MA, Lock RB. In vivo activity of the dual SYK/FLT3 inhibitor TAK-659 against pediatric acute lymphoblastic leukemia xenografts. Pediatr Blood Cancer. 2023;70(9):e30503. PubMed PMID: 37339930. https://libkey.io/libraries/3075/37339930

27. Liu W, Wang Y, Ulivi P, Tavolari S, Rizvi SAA, Capobianco E, Navarro A, Zhang Y. A signature of five 7-methylguanosine-related genes is a prognostic marker for lung squamous cell carcinoma.  J Thorac Dis 2023;15(11):6265-6278. doi: 10.21037/jtd-23-1504. https://jtd.amegroups.org/article/view/80806/html

28. Toufiq M, Rinchai D, Bettacchioli E, Kabeer BSA, Khan T, Subba B, White OYurieva MGeorge J, Jourde-Chiche N, Chiche L, Palucka K, Chaussabel D. Harnessing large language models (LLMs) for candidate gene prioritization and selection. J Transl Med. 2023;21(1):728. PMID: 37845713; PMCID: PMC10580627. https://libkey.io/libraries/3075/37845713

29. Wilson JJ, Wei J, Daamen AR,Sears JD, Bechtel E, Mayberry CL, Stafford GA, Bechtold L, Grammer AC, Lipsky PE, Roopenian DC, Chang CH. Glucose oxidation-dependent survival of activated B cells provides a putative novel therapeutic target for lupus treatment. iScience. 2023;26(9):107487. PMID: 37636066; PMCID: PMC10448027. https://libkey.io/libraries/3075/37636066

30. 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 https://libkey.io/libraries/3075/36879097

31. Tyler AL, Spruce C, Kursawe R, Haber A, Ball RL, Pitman WA, Fine AD, Raghupathy N, Walker M, Philip VM, Baker CL, Mahoney JM, ChurchillGA, Trowbridge JJ, Stitzel ML, Paigen K, Petkov PM, Carter GW. Variation in histone configurations correlates with gene expression across nine inbred strains of mice. Genome Res. 2023;33(6):857-71. PubMed PMID: 37217254. https://libkey.io/libraries/3075/37217254

32. Rashid A, Brusletto BS, Al-Obeidat F, Toufiq M, Benakatti G, Brierley J, Malik ZA, Hussain Z, Alkhazaimi H, Sharief J, Kadwa R, Sarpal A, Chaussabel D, Malik RA, Quraishi N, Khilnani P, Zaki SA, Nadeem R, Shaikh G, Al-Dubai A, Hafez W, Hussain A. A Transcriptomic Appreciation of Childhood Meningococcal and Polymicrobial Sepsis from a Pro-Inflammatory and Trajectorial Perspective, a Role for Vascular Endothelial Growth Factor a and B Modulation? Shock. 2023;60(4):503-16. PMID: 37553892; PMCID: PMC10581425. https://libkey.io/libraries/3075/37553892

33. Xie F, Armand EJ, Yao Z, Liu H, Bartlett A, Behrens MM, Li YE, Lucero JD, Luo C, Nery JR, Pinto-Duarte A, Poirion OB, Preissl S, Rivkin AC, Tasic B, Zeng H, Ren B, Ecker JR, Mukamel EA. Robust enhancer-gene regulation identified by single-cell transcriptomes and epigenomes. Cell Genom. 2023;3(7):100342. PubMed PMID: 37492103; PMCID: PMC10363915. https://libkey.io/libraries/3075/37492103

34. Roelands J, Kuppen PJK, Ahmed EI, Mall R, Masoodi T, Singh P, Monaco G, Raynaud C, de Miranda N, Ferraro L, Carneiro-Lobo TC, Syed N, Rawat A, Awad A, Decock J, Mifsud W, Miller LD, Sherif S, Mohamed MG, Rinchai D, Van den Eynde M, Sayaman RW, Ziv E, Bertucci F, Petkar MA, Lorenz S, Mathew LS, Wang K, Murugesan S, Chaussabel D, Vahrmeijer AL, Wang E, Ceccarelli A, Fakhro KA, Zoppoli G, Ballestrero A, Tollenaar R, Marincola FM, Galon J, Khodor SA, Ceccarelli M, Hendrickx W, Bedognetti D. An integrated tumor, immune and microbiome atlas of colon cancer. Nat Med. 2023;29(5):1273-86. PubMed PMID: 37202560; PMCID: PMC10202816 https://libkey.io/libraries/3075/37202560

35. Stefancsik R, Balhoff JP, Balk MA, Ball RL, Bello SM, Caron AR, Chesler EJ, de Souza V, Gehrke S, Haendel M, Harris LW, Harris NL, Ibrahim A, Koehler S, Matentzoglu N, McMurry JA, Mungall CJ, Munoz-Torres MC, Putman T, Robinson P, Smedley D, Sollis E, Thessen AE, Vasilevsky N, Walton DO, Osumi-Sutherland D. The Ontology of Biological Attributes (OBA)-computational traits for the life sciences. Mamm Genome. 2023;34(3):364-78. PMID: 37076585; PMCID: PMC10382347. https://libkey.io/libraries/3075/37076585