2019 Computational Sciences Publications

1Q - 2019

1.  Chae YK, Anker JF, Oh MS, Bais P, Namburi S, Agte S, Giles FJ, Chuang JH.Mutations in DNA repair genes are associated with increased neoantigen burden and a distinct immunophenotype in lung squamous cell carcinoma. Sci Rep. 2019 Mar 1;9(1):3235. doi: 10.1038/s41598-019-39594-4.

2.  Goodwin LO, Splinter E, Davis TL, Urban R, He H, Braun RE, Chesler EJ, Kumar V, van Min M, Ndukum J, Philip VM, Reinholdt LG, Svenson K, White JK, Sasner M, Lutz C, Murray SA. Large-scale discovery of mouse transgenic integration sites reveals frequent structural variation and insertional mutagenesis. Genome Res. 2019 Mar;29(3):494-505. doi: 0.1101/gr.233866.117. Epub 2019 Jan 18.

2Q - 2019

1.  Malcolm JE, Stearns TM, Airhart SD, Graber JH, Bult CJ., Factors that influenceresponseclassifications in chemotherapytreatedpatient-derivedxenografts (PDX). PeerJ. 2019 Mar 28;7:e6586. doi: 10.7717/peerj.6586. eCollection 2019.

2.  Miller RA, Harrison DE, Astle CM, Bogue MA, Brind J, Fernandez E, Flurkey K, Javors M, Ladiges W, Leeuwenburgh C, Macchiarini F, Nelson J, Ryazanov AG, Snyder J, Stearns TM, Vaughan DE, Strong R. Glycine supplementation extends lifespan of male and female mice.Aging Cell. 2019 Jun;18(3):e12953. doi: 10.1111/acel.12953. Epub 2019

3.  Nicaise AM, Wagstaff LJ, Willis CM, Paisie C, Chandok H, Robson P, Fossati V, Williams A, Crocker SJ. Cellular senescence in progenitor cells contributes to diminished remyelination potential in progressive multiple sclerosis.Proc Natl Acad Sci U S A. 2019 Apr 30;116(18):9030-9039. doi: 10.1073/pnas.1818348116. Epub 2019 Mar 25.

4.  Alghamdi SM, Sundberg BA, Sundberg JP, Schofield PN, Hoehndorf R. Quantitative evaluation of ontology design patterns for combining pathology and anatomy ontologies.Sci Rep. 2019 Mar 11;9(1):4025. doi: 10.1038/s41598-019-40368-1.

5.  Srivastava A, Kumar Sarsani V, Fiddes I, Sheehan SM, Seger RL, Barter ME, Neptune-Bear S, Lindqvist C, Korstanje R. Genome assembly and gene expression in the American black bear provides new insights into the renal response to hibernation.  DNA Res. 2019 Feb 1;26(1):37-44. doi: 10.1093/dnares/dsy036.

6.  Cooper TK, Silva KA, Kennedy VE, Alghamdi S, Hoehndorf R, Sundberg BA, Schofield PN, Sundberg JP. Hyaline Arteriolosclerosis in 30 Strains of Aged Inbred Mice.Vet Pathol. 2019 May 6:300985819844822. doi: 10.1177/0300985819844822.

7.  Harrison DE, Strong R, Alavez S, Astle CM, DiGiovanni J, Fernandez E, Flurkey K, Garratt M, Gelfond JAL, Javors MA, Levi M, Lithgow GJ, Macchiarini F, Nelson JF, Sukoff Rizzo SJ, Slaga TJ, Stearns T, Wilkinson JE, Miller RA. Acarbose improves health and lifespan in aging HET3 mice.Aging Cell. 2019 Apr;18(2):e12898. doi: 10.1111/acel.12898. Epub 2019 Jan 27.

8.  Sarsani VK, Raghupathy N, Fiddes IT, Armstrong J, Thibaud-Nissen F, Zinder O, Bolisetty M, Howe K, Hinerfeld D, Ruan X, Rowe L, Barter M, Ananda G, Paten B, Weinstock GM, Churchill GA, Wiles MV, Schneider VA, Srivastava A, Reinholdt LG. The Genome of C57BL/6J "Eve", the Mother of the Laboratory Mouse Genome Reference Strain.G3 (Bethesda). 2019 Apr 17. pii: g3.400071.2019. doi: 10.1534/g3.119.400071

9.Li Q, Philip VM, Stearns TM, Bubier JA, King BL, Low BE, Wiles MV, Saeidian AH, Sundberg BA, Uitto J, Sundberg JP. Quantitative Trait Locus and Integrative Genomics Revealed Candidate Modifier Genes for Ectopic Mineralization in Mouse Models of Pseudoxanthoma Elasticum. J Invest Dermatol. 2019 Jun 14. pii: S0022-202X(19)31761-0. doi: 10.1016/j.jid.2019.04.023

10. Graham LC, Grabowska WA, Chun Y, Risacher SL, Philip VM, Saykin AJ; Alzheimer's Disease Neuroimaging Initiative (ADNI), Sukoff Rizzo SJ, Howell GR. Exercise prevents obesity-induced cognitive decline and white matter damage in mice Neurobiol Aging. 2019 May 3;80:154-172. doi: 10.1016/j.neurobiolaging.2019.03.018

11.Abrams D, Kumar P, Karuturi RKM, George J. A computational method to aid the design and analysis of single cell RNA-seq experiments for cell type identification. BMC Bioinformatics. 2019 Jun 6;20 (Suppl 11):275. doi: 10.1186/s12859-019-2817-2.

12.  Sharma M, Srivastava A, Fairfield HE, Bergstrom D, Flynn WF, Braun RE.Identification of EOMES-expressing spermatogonial stem cells and their regulation by PLZF. Elife. 2019 May 31;8. pii: e43352. doi: 10.7554/eLife.43352.

13.  Saul MC, Philip VM, Reinholdt LG; Center for Systems Neurogenetics of Addiction, Chesler EJ. High-Diversity Mouse Populations for Complex Traits. Trends Genet. 2019 Jul;35(7):501-514. doi: 10.1016/j.tig.2019.04.003. Epub 2019 May 24.

3Q - 2019

1. Zeiss CJ, Gatti DM, Toro-Salazar O, Davis C, Lutz CM, Spinale F, Stearns T, Furtado MB, Churchill GA.Doxorubicin-Induced Cardiotoxicity in Collaborative Cross (CC) Mice Recapitulates Individual Cardiotoxicity in Humans. G3 (Bethesda) 2019 Jul 1. pii: g3.400232.2019. doi: 10.1534/g3.119.400232

2. Woo XY, Srivastava A, Graber JH, Yadav V, Sarsani VK, Simons A, Beane G, Grubb S, Ananda G, Liu R, Stafford G, Chuang JH, Airhart SD, Karuturi RKM, George J, Bult CJ.Genomic data analysis workflows for tumors from patient-derived xenografts (PDXs): challenges and guidelines., BMC Med Genomics 2019 Jul 1;12(1):92. doi: 10.1186/s12920-019-0551-2.

3.Sundberg JP, Pratt CH, Silva KA, Kennedy VE, Qin W, Stearns TM, Frost J, Sundberg BA, Bowcock AM. Gain of function p.E138A alteration in Card14 leads to psoriasiform skin inflammation and implicates genetic modifiers in disease severity.Exp Mol Pathol. 2019 Jul 16:104286. doi: 10.1016/j.yexmp.2019.104286

4. Elyada E., Bolisetty M., Laise P., Flynn W.F., Courtois E.T., Burkhart R.A., Teinor J.A., Belleau P., Biffi G., Lucito M.S., Sivajothi S., Armstrong T.D., Engle D.D., Kenneth H.Y., Hao Y., Wolfgang C.L., Park Y., Preall J., Jaffee E.M., Califano A., Robson P., & Tuveson D.A. (2019) Cross-species single-cell analysis of pancreatic ductal adenocarcinoma reveals antigen-presenting cancer-associated fibroblasts. Cancer Discovery, 9(8):1102-1123. https://doi.org/10.1158/2159-8290.CD-19-0094.

5. Gowthaman U., Chen J.S., Zhang B., Flynn W.F., Lu Y., Song W., Joseph J., Gertie J.A., Xu L., Collet M.A., Grassmann J.D.S., Simoneau T., Chiang D., Berin M.C., Craft J.E., Weinstein J.S., Williams A., & Eisenbarth S.C. (2019) Identification of a T follicular helper cell subset that drives anaphylactic IgE. Science, 365(6456): eaaw6433. https://doi.org/10.1126/science.aaw6433

4Q - 2019

1. Noorbakhsh, J., Chandok, H., Karuturi, R. K. M., & George, J. (2019). Machine Learning in Biology and Medicine. Advances in Molecular Pathology.

2. Garrett, A. M., Bosch, P. J., Steffen, D. M., Fuller, L. C., Marcucci, C. G., Koch, A. A., Bais P., Weiner A.J. ,Burgess, R. W. (2019). CRISPR/Cas9 interrogation of the mouse Pcdhg gene cluster reveals a crucial isoform-specific role for Pcdhgc4. PLOS Genetics, 15(12), e1008554. https://doi.org/10.1371/journal.pgen.1008554

3. Hansen, P., Gargano, M., Hecht, J., Ibn-Salem, J., Karlebach, G., Roehr, J. T., & Robinson, P. N. (2019). Computational Processing and Quality Control of Hi-C, Capture Hi-C and Capture-C Data. Genes, 10(7), 548. https://doi.org/10.3390/genes10070548

4. Shefchek, K. A., Harris, N. L., Gargano, M., Matentzoglu, N., Unni, D., Brush, M., Osumi-Sutherland, D. (2019). The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species. Nucleic Acids Research. https://doi.org/10.1093/nar/gkz997

5. Köhler, S., Øien, N. C., Buske, O. J., Groza, T., Jacobsen, Gargano, M., J. O. B., McNamara, C., Robinson, P. N. (2019). Encoding Clinical Data with the Human Phenotype Ontology for Computational Differential Diagnostics. Current Protocols in Human Genetics, 103(1). https://doi.org/10.1002/cphg.92

6. Li Q, Philip VM, Stearns TM, Bubier JA, King BL, Low BE, Wiles MV, Saeidian AH, Sundberg BA, Uitto J, Sundberg JP (2019).Quantitative Trait Locus and Integrative Genomics Revealed Candidate Modifier Genes for Ectopic Mineralization in Mouse Models of Pseudoxanthoma Elasticum. Journal of Investigative Dermatology, 139(12), 2447–2457.e7. https://doi.org/10.1016/j.jid.2019.04.023

7. Zeiss CJ, Gatti DM, Toro-Salazar O, Davis C, Lutz CM, Spinale F, Stearns T, Furtado MB, Churchill GA.Doxorubicin-Induced Cardiotoxicity in Collaborative Cross (CC) Mice Recapitulates Individual Cardiotoxicity in Humans.G3 (Bethesda). 2019 Aug 8;9(8):2637-2646. doi: 10.1534/g3.119.400232. PubMed PMID: 31263061; PubMed Central PMCID: PMC6686936.