2017 Computational Sciences Publications

1Q - 2017

• Potter CS, Silva KA, Kennedy VE, Stearns TM, HogenEsch H, J. P. Sundberg, Loss of FAS/FASL signaling does not reduce apoptosis in Sharpin null mice.Experimental dermatology. 2017. Epub 2017/01/18. DOI: 10.1111/exd. 13289. PubMed PMID: 28094869
• Peterson KA, Beane GL, Goodwin LO, Kutny PM, Reinholdt LG, Murray SA. CRISPRtools: a flexible computational platform for performing CRISPR/Cas9 experiments in the mouse.Mammalian genome: official journal of the International Mammalian Genome Society. 2017. Epub 2017/03/11. DOI: 10.1007/s00335-017-9681-z. PubMed PMID: 28280930.
• Min H, Turner S, Coronado S de, Davis B, Whetzel T, Freimuth RR, Solbrig HR, Kiefer R, Riben M,Stafford GA, Wright L, Ohira R. Towards a standard ontology metadata model.International Conference on Biomedical Ontology and BioCreative (ICBO BioCreative 2016) (Internet) CEUR-ws.org Volume 1747; 2016.

2Q - 2017

• Parker CC, Dickson PE, Philip VM, Thomas M, Chesler EJ. Systems Genetic Analysis in GeneNetwork.org.Current protocols in neuroscience. 2017;79:8 39 1-8 20. Epub 2017/04/12. doi: 10.1002/cpns.23. PubMed PMID: 28398643.
• Williams PA, Harder JM, Foxworth NE, Cochran KE, Philip VM, Porciatti V, et al. Vitamin B3 modulates mitochondrial vulnerability and prevents glaucoma in aged mice.Science (New York, NY). 2017;355(6326):756-60. Epub 2017/02/18. doi: 10.1126/science.aal0092. PubMed PMID: 28209901.
• Emery IF, Gopalan A, Wood S, Chow KH, Battelli C, George J, et al. Expression and function of ABCG2 and XIAP in glioblastomas. Journal of neuro-oncology. 2017. Epub 2017/04/23. doi: 10.1007/s11060-017-2422-z. PubMed PMID: 28432589.
• Mondo SJ, Dannebaum RO, Kuo RC, Louie KB, Bewick AJ, LaButti K, Haridas S, Kuo A, Salamov A, Ahrendt SR, Lau R, Bowen BP, Lipzen A, Sullivan W, Andreopoulos BB, Clum A, Lindquist E, Daum C, Northen TR, Kunde-Ramamoorthy G, et al. Widespread adenine N6-methylation of active genes in fungi.Nature genetics. 2017;49(6):964-8. Epub 2017/05/10. doi: 10.1038/ng.3859. PubMed PMID: 28481340.
• Srivastava A, Morgan AP, Najarian ML, Sarsani VK, Sigmon JS, Shorter JR, et al. Genomes of the Mouse Collaborative Cross.Genetics. 2017;206(2):537-56. Epub 2017/06/09. doi: 10.1534/genetics.116.198838. PubMed PMID: 28592495.
• Philip, V, Ratiu JJ, Racine JJ, Hasham MG, Wang Q, Branca JA, Chapman HD, et al. Genetic and Small Molecule Disruption of the AID/RAD51 Axis Similarly Protects Nonobese Diabetic Mice from Type 1 Diabetes through Expansion of Regulatory B Lymphocytes.Journal of immunology (Baltimore, Md : 1950). 2017;198(11):4255-67. Epub 2017/05/04. doi: 10.4049/jimmunol.1700024. PubMed PMID: 28461573; PubMed Central PMCID: PMCPMC5474749.
• Etemadmoghadam D, Azar WJ, Lei Y, Moujaber T, Garsed DW, Kennedy C,George J, et al. EIF1AX and NRAS mutations co-occur and cooperate in low-grade serous ovarian carcinomas.Cancer research. 2017. Epub 2017/06/25. doi: 10.1158/0008-5472.can-16-2224. PubMed PMID: 28646021

• Bais P, Namburi S, Gatti DM, Zhang X, Chuang JH. CloudNeo: A cloud pipeline for identifying patient-specific tumor neoantigens.Bioinformatics (Oxford, England). 2017. Epub 2017/06/13. doi: 10.1093/bioinformatics/btx375. PubMed PMID: 28605406.

3Q - 2017

• Sundberg BA, Dadras SS, Silva KA, Kennedy VE, Garland G, Murray SA, et al. Systematic screening for skin, hair, and nail abnormalities in a large-scale knockout mouse program. PloS one. 2017;12(7):e0180682. Epub 2017/07/13. doi: 10.1371/journal.pone.0180682. PubMed PMID: 28700664; PubMed Central PMCID: PMCPMC5503261.
• Chow KH, Park HJ, George J, Yamamoto K, Gallup AD, Graber JH, et al. S100A4 is a biomarker and regulator of glioma stem cells that is critical for mesenchymal transition in glioblastoma. Cancer research. 2017. Epub 2017/08/16. doi: 10.1158/0008-5472.can-17-1294. PubMed PMID: 28807938
• Etemadmoghadam D, Azar WJ, Lei Y, Moujaber T, Garsed DW, Kennedy CJ,George, J.,EIF1AX and NRAS Mutations Co-occur and Cooperate in Low-Grade Serous Ovarian Carcinomas.Cancer research. 2017;77(16):4268-78. Epub 2017/06/25. doi: 10.1158/0008-5472.can-16-2224. PubMed PMID: 28646021.

• Chatzinakos C, Lee D, Webb BT, Vladimirov VI, Kendler KS, Bacanu SA. JEPEGMIX2: improved gene-level joint analysis of eQTLs in cosmopolitan cohorts.Bioinformatics (Oxford, England). 2017. Epub 2017/10/03. doi: 10.1093/bioinformatics/btx509. PubMed PMID: 28968763.

4Q - 2017

• Garsed DW, Alsop K, Fereday S, Emmanuel C, Kennedy C, Etemadmoghadam D,George J, et al. Homologous Recombination DNA Repair Pathway Disruption and Retinoblastoma Protein Loss are Associated with Exceptional Survival in High-Grade Serous Ovarian Cancer.Clinical cancer research : an official journal of the American Association for Cancer Research. 2017. Epub 2017/10/25. doi: 10.1158/1078-0432.ccr-17-1621. PubMed PMID: 29061645
• Ucar D, Marquez EJ, Chung CH, Marches R, Rossi RJ, Uyar A, George J, et al. The chromatin accessibility signature of human immune aging stems from CD8+ T cells.The Journal of experimental medicine. 2017;214(10):3123-44. Epub 2017/09/15. doi: 10.1084/jem.20170416. PubMed PMID: 28904110; PubMed Central PMCID: PMCPMC5626401.
• Bogue MA, Grubb SC, Walton DO, Philip VM, Kolishovski G, Stearns T, Dunn M, Kadakkuzha B, TeHennepe G, Ramamoorthy G, et al. Mouse Phenome Database: an integrative database and analysis suite for curated empirical phenotype data from laboratory mice.Nucleic acids research. 2017. Epub 2017/11/15. doi: 10.1093/nar/gkx1082. PubMed PMID: 29136208.

• Olayan RS, Ashoor H, Bajic VB. DDR: Efficient computational method to predict drug-target interactions using graph mining and machine learning approaches. Bioinformatics (Oxford, England). 2017. Epub 2017/12/01. doi: 10.1093/bioinformatics/btx731. PubMed PMID: 29186331.

• Liany H, Rajapakse JC, Karuturi RKM. MultiDCoX: Multi-factor analysis of differential co-expression.BMC Bioinformatics. 2017;18(16):576. doi: 10.1186/s12859-017-1963-7.

• Evans J, Sanciangco MD, Lau KH, Crisovan E, Barry K, Daum C,G. Kunde-Ramamoorthy. Extensive Genetic Diversity is Present within North American Switchgrass Germplasm. The Plant Genome. 2017. doi: 10.3835/plantgenome2017.06.0055.