Computational Sciences Publications

2020 Publications

1Q - 2020

1. Bogue, M. A., Philip, V. M., Walton, D. O., Grubb, S. C., Dunn, M. H., Kolishovski, G., Emerson, J., Mukherjee, G., Stearns, T., He, H., Sinha, V., Kadakkuzha, B., Kunde-Ramamoorthy, G., & Chesler, E. J. (2020). Mouse Phenome Database: a data repository and analysis suite for curated primary mouse phenotype data. Nucleic acids research, 48(D1), D716–D723. https://doi.org/10.1093/nar/gkz1032

2. Ngan, C. Y., Wong, C. H., Tjong, H., Wang, W., Goldfeder, R. L., Choi, C., He, H., Gong, L., Lin, J., Urban, B., Chow, J., Li, M., Lim, J., Philip, V., Murray, S. A., Wang, H., & Wei, C. L. (2020). Chromatin interaction analyses elucidate the roles of PRC2-bound silencers in mouse development. Nature genetics, 10.1038/s41588-020-0581-x. Advance online publication. https://doi.org/10.1038/s41588-020-0581-x

3. Schoenrock, S. A., Kumar, P., Gómez-A, A., Dickson, P. E., Kim, S. M., Bailey, L., Neira, S., Riker, K. D., Farrington, J., Gaines, C. H., Khan, S., Wilcox, T. D., Roy, T. A., Leonardo, M. R., Olson, A. A., Gagnon, L. H., Philip, V. M., Valdar, W., de Villena, F. P., Jentsch, J. D., Logan, R.W., McClung, A.A, Chesler, E.J. & Tarantino, L. M. (2020). Characterization of genetically complex Collaborative Cross mouse strains that model divergent locomotor activating and reinforcing properties of cocaine. Psychopharmacology, 10.1007/s00213-019-05429-3. Advance online publication. https://doi.org/10.1007/s00213-019-05429-3

4. Bubier, J. A., Philip, V. M., Quince, C., Campbell, J., Zhou, Y., Vishnivetskaya, T., Duvvuru, S., Hageman Blair, R., Ndukum, J., Donohue, K. D., Foster, C. M., Mellert, D. J., Weinstock, G., Culiat, C. T., O'Hara, B., Palumbo, A. V., Podar, M., & Chesler, E. J. (2020). A Microbe Associated with Sleep Revealed by a Novel Systems-Genetic Analysis of the Microbiome in Collaborative Cross Mice. Genetics, genetics.303013.2019. Advance online publication. https://doi.org/10.1534/genetics.119.303013

5. Batista, A. R., King, O. D., Reardon, C. P., Davis, C., Shankaracharya, Philip, V., Gray-Edwards, H., Aronin, N., Lutz, C., Landers, J., & Sena-Esteves, M. (2020). Ly6a Differential Expression in Blood-Brain Barrier Is Responsible for Strain Specific Central Nervous System Transduction Profile of AAV-PHP.B. Human gene therapy, 31(1-2), 90–102. https://doi.org/10.1089/hum.2019.186

2Q - 2020

1. Yvonne A. Evrard, Srivastava, A., Randjelovic, J., NCI PDXNet Consortium, Doroshow, J.H., Dean, D.A., Morris, J.S., Chuang, J. H. (2020)Systematic Establishment of Robustness and Standards in Patient-Derived Xenograft Experiments and Analysis Cancer Research DOI: 10.1158/0008-5472.CAN-19-3101

2. Ashoor, H., Chen, X., Rosikiewicz, W., Wang J., Cheng A, Wang P., Raun Y, & Li S. Graph embedding and unsupervised learning predict genomic sub-compartments from HiC chromatin interaction data. Nat Commun 11, 1173 (2020). https://doi.org/10.1038/s41467-020-14974-x

3. Dragon, J., Gates, C., Sui, S., Hutchinson, J., Karuturi, R., Kucukural, A., Polson, S., Riva, A., Settles, M., Thimmapuram, J. and Levine, S., 2020. Bioinformatics Core Survey Highlights the Challenges Facing Data Analysis Facilities. J Biomol Tech. 2020 Apr 29, doi: 10.7171/jbt.20-3102-005

4. Kumuthini, J., Chimenti, M., Nahnsen, S., Peltzer, A., Meraba, R., McFadyen, R., Wells, G., Taylor, D., Maienschein-Cline, M., Li, J., Thimmapuram, J., Murthy-Karuturi, R. and Zass, L., 2020. Ten Simple Rules For Providing Effective Bioinformatics Research Support. PLOS Computational Biology, https://doi.org/10.1371/journal.pcbi.1007531

3Q - 2020

1. Hosur, V., Low, B. E., Li, D., Stafford, G. A., Kohar, V., Shultz, L. D., & Wiles, M. V. 2020. Genes adapt to outsmart gene-targeting strategies in mutant mouse strains by skipping exons to reinitiate transcription and translation. Genome biology 2020 Jul 9, doi: 10.1186/s13059-020-02086-0

2. Sundberg, J. P., Pratt, C. H., Goodwin, L. P., Silva, K. A., Kennedy, V. E., Potter, C. S., Dunham, A., Sundberg, B. A., HogenEsch, H. 2020. Keratinocyte-specific deletion of SHARPIN induces atopic dermatitis-like inflammation in mice. PLOS ONE 15(7) 2020 Jul 20, doi: 10.1371/journal.pone.0235295.   

3.  Consortium, I. T. P.-C. A. o. W. G. (2020). Pan-cancer analysis of whole genomes. Nature, 578(7793), 82-93. doi:10.1038/s41586-020-1969-6

4. Jung, M., Gao, J., Cheung, L., Bongers, A., Somers, K., Clifton, M., . . . Henderson, M. J. (2020). ABCC4/MRP4 contributes to the aggressiveness of Myc-associated epithelial ovarian cancer. Int J Cancer. doi:10.1002/ijc.33005

5. Millstein, J., Budden, T., Goode, E. L., Anglesio, M. S., Talhouk, A., Intermaggio, M. P., . . . Ramus, S. J. (2020). Prognostic gene expression signature for high-grade serous ovarian cancer. Ann Oncol. doi:10.1016/j.annonc.2020.05.019

6. Talhouk, A., George, J., Wang, C., Budden, T., Tan, T. Z., Chiu, D. S., . . . Anglesio, M. S. (2020). Development and Validation of the Gene Expression Predictor of High-grade Serous Ovarian Carcinoma Molecular SubTYPE (PrOTYPE). Clin Cancer Res. doi:10.1158/1078-0432.CCR-20-0103