2020 Computational Sciences 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

6.  Shefchek KA, Harris NL, Gargano M, Matentzoglu N, Unni D, Brush M, Keith D, Conlin T, Vasilevsky N, Zhang XA, Balhoff JP, Babb L, Bello SM, Blau H, Bradford Y, Carbon S, Carmody L, Chan LE, Cipriani V, Cuzick A, Della Rocca M, Dunn N, Essaid S, Fey P, Grove C, Gourdine JP, Hamosh A, Harris M, Helbig I, Hoatlin M, Joachimiak M, Jupp S, Lett KB, Lewis SE, McNamara C, Pendlington ZM, Pilgrim C, Putman T, Ravanmehr V, Reese J, Riggs E, Robb S, Roncaglia P, Seager J, Segerdell E, Similuk M, Storm AL, Thaxon C, Thessen A, Jacobsen JOB, McMurry JA, Groza T, Köhler S, Smedley D, Robinson PN, Mungall CJ, Haendel MA, Munoz-Torres MC, Osumi-Sutherland D.  The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species.   Nucleic Acids Res. 2020 Jan 8;48(D1):D704-D715. doi: 10.1093/nar/gkz997.PMID: 31701156 

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

5.  Zhu, D., Rostami, M.R., Zuo, W.L., Leopold, P.L., Crystal, R.G. (2020). Single-Cell Transcriptome Analysis of Mouse Liver Cell- Specific Tropism and Transcriptional Dysregulation Following Intravenous Administration of AAVrh.10 Vectors. Human Gene Therapy. 31(9-10):590-604. doi: 10.1089/hum.2019.366.

6.  Evrard, Y. A., Srivastava, A., Randjelovic, J., NCI PDXNet Consortium, Lloyd, M.W., Woo, X., 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

3Q - 2020

1. 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.   

2. Jung, M., Gao, J., Cheung, L., George, J., 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

3. 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

4.  Robinson PN, Ravanmehr V, Jacobsen JOB, Danis D, Zhang XA, Carmody LC, Gargano MA, Thaxton CL; UNC Biocuration Core, Karlebach G, Reese J, Holtgrewe M, Köhler S, McMurry JA, Haendel MA, Smedley D. Interpretable Clinical Genomics with a Likelihood Ratio Paradigm.   Am J Hum Genet. 2020 Sep 3;107(3):403-417. doi: 10.1016/j.ajhg.2020.06.021. Epub 2020 Aug 4.PMID: 32755546

5.  Lin, J., & Ouyang, Z. (2020). Large-scale analysis of the position-dependent binding and regulation of human RNA binding proteins. Quantitative Biology, 1-11.

6.  Lin, J., Chen, Y., Zhang, Y., & Ouyang, Z. (2020). Identification and analysis of RNA structural disruptions induced by single nucleotide variants using Riprap and RiboSNitchDB. NAR Genomics and Bioinformatics, 2(3), lqaa057.

7.  Zuo, W.L., Rostami, M.R., Shenoy, S.A., LeBlanc, M.G., Salit, J., Strulovici-Barel, Y., O'Beirne, S.L., Kaner, R.J., Leopold, P.L., Mezey, J.G., Schymeinsky, J., Quast, K., Visvanathan, S., Fine, J.S., Thomas, M.J., Crystal, R.G. (2020) Cell-specific expression of lung disease risk-related genes in the human small airway epithelium.  Respiratory Research. 21(1):200. doi: 10.1186/s12931-020-01442-9.

8.  Zuo, W.L., Rostami, M.R., LeBlanc, M., Kaner, R.J., O'Beirne, S.L., Mezey, J.G., Leopold, P.L., Quast, K., Visvanathan, S., Fine, J.S., Thomas, M.J., & Crystal, R.G. (2020). Dysregulation of club cell biology in idiopathic pulmonary fibrosis.  Plos One, 15(9):e0237529. doi: 10.1371/journal.pone.0237529

9.  Lee SJ, Lehar A, Meir JU, Koch C, Morgan A, Warren LE, Rydzik R, Youngstrom DW, Chandok H, George J, Gogain J, Michaud M, Stoklasek TA, Liu Y, Germain-Lee EL. Copyright © 2020Targeting myostatin/activin A protects against skeletal muscle and bone loss during spaceflight. Published by PNAS. PMID: 32900939 DOI: 10.1073/pnas.2014716117

10. Kohar, V., Gordin, D., Katebi, A., Levine, H., Onuchic, J. N., & Lu, M. (2020). Gene Circuit Explorer (GeneEx): an interactive web-app for visualizing, simulating and analyzing gene regulatory circuits. Bioinformatics, doi:10.1093/bioinformatics/btaa785.

11. 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, doi:10.1186/s13059-020-02086-0

4Q - 2020

1. Zhao, Y., Pan, Z., Namburi, S., Pattison, A., Posner, A., Balachander, S., Paisie, C.A., Reddi, H.V., Rueter, J., Gill, A.J., Fox, S., Raghav, K.P.S., Flynn, W.F., Tothill, R.W., Li, S., Karuturi, R.K.M., George, J. (2020) CUP-AI-Dx: A tool for inferring cancer tissue of origin and molecular subtype using RNA gene-expression data and artificial intelligence EBioMedicine. doi: 10.1016/j.ebiom.2020.103030

2. Suh, Y.S., Na, D., Lee, J.S., Chae, J., Kim, E., Jang, G., Lee, J., Min, J., Ock, C.Y., Kong, S.H., George, J., Zhang, C., Lee, H.J., Kim, J.I., Kim, S.J., Kim, W.H., Lee, C., Yang, H.K. (2020) Comprehensive Molecular Characterization of Adenocarcinoma of the Gastroesophageal Junction Between Esophageal and Gastric Adenocarcinomas Annals of Surgery doi: 10.1097/SLA.0000000000004303.

3. Leclair, N.K., Brugiolo, M., Urbanski, L., Lawson, S.C., Thakar, K., Yurieva, M.,George, J., Hinson, J.T., Cheng, A., Graveley, B.R., Anczuków, O. (2020) Poison Exon Splicing Regulates a Coordinated Network of SR Protein Expression during Differentiation and Tumorigenesis Molecular Cell doi: 10.1016/j.molcel.2020.10.019.