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 https://libkey.io/libraries/3075/36330959

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 https://libkey.io/libraries/3075/36563487

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 https://libkey.io/libraries/3075/36169447

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 https://libkey.io/libraries/3075/36592885

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 https://libkey.io/libraries/3075/36660729

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 https://libkey.io/libraries/3075/36675367

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: https://aacrjournals.org/cancerrescommun/article/2/6/402/699311/Cancer-Stem-Cells-not-Bulk-Tumor-Cells-Determine

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

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. https://pubmed.ncbi.nlm.nih.gov/36714272/

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

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

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

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 https://libkey.io/libraries/3075/36910590

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

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 https://libkey.io/libraries/3075/36649207

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

4.Rinchai D, Chaussabel D. Assessing the potential relevance of CEACAM6 as a blood transcriptional biomarker. F1000Research. 2022;11:1294 https://libkey.io/libraries/3075/10.12688/f1000research.126721.1

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 https://libkey.io/libraries/3075/36445177

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

7.  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

8. Rinchai D, Chaussabel D. A training curriculum for retrieving, structuring, and aggregating information derived from the biomedical literature and large-scale data repositories. F1000Research. 2022;11:994. PubMed PMID: 10.12688/f1000research.122811.1 https://libkey.io/libraries/3075/10.12688/f1000research.122811.1 

9.   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

10. 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

11. Hughes K, Evans K, Earley EJ, Smith CM, Erickson SW, Stearns T, Philip 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

12. 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

13. Tyler AL, Spruce C, Kursawe R, Haber A, Ball RL, Pitman WA, Fine AD, Raghupathy N, Walker M, Philip VM, Baker CL, Mahoney JM, Churchill GA, 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

14.   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

15. 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

3Q - 2023

1. Philip VM, He H, Saul 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

2. 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

3.  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

 4. 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

5.  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

6. 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