2016 Computational Sciences Publications

4Q - 2016

• Kurum E, Benayoun BA,Malhotra A, George J, Ucar D. Computational inference of a genomic pluripotency signature in human and mouse stem cells.Biology direct. 2016;11:47. Epub 2016/09/19. doi: 10.1186/s13062-016-0148-z. PubMed PMID: 27639379;PubMedCentral PMCPMC5027095.
• Young K, Borikar S, Bell R, Kuffler L,Philip V, Trowbridge JJ. Progressive alterations in multipotent hematopoietic progenitors underlie lymphoid cell loss in aging.The Journal of experimental medicine. 2016. doi: 10.1084/jem.20160168.
• Soundararajan R,Stearns TM, Czachor A, Fukumoto J, Turn C, Westermann-Clark E, et al. Global gene profiling of aging lungs in Atp8b1 mutant mice.Aging. 2016;8(9):2232-52. Epub 2016/10/01. doi: 10.18632/aging.101056.PubMedPMID: 27689529.
• Sutphin GL, Mahoney JM, Sheppard K, Walton DO, Korstanje R. WORMHOLE: Novel Least Diverged Ortholog Prediction through Machine Learning. PLoS computational biology. 2016;12(11):e1005182. Epub 2016/11/05. doi: 10.1371/journal.pcbi.1005182. PubMed PMID: 27812085.
• Lawlor N, George J, Bolisetty M, Kursawe R, Sun L, V S, et al. Single cell transcriptomes identify human islet cell signatures and reveal cell-type-specific expression changes in type 2 diabetes.Genome research. 2016. Epub 2016/11/20. doi: 10.1101/gr.212720.116. PubMed PMID: 27864352.

3Q - 2016

• Dillon JL, Mockus SM,Ananda G, Spotlow V, Wells WA, Tsongalis GJ, et al. Somatic gene mutation analysis of triple negative breast cancers.Breast(Edinburgh, Scotland). 2016. Epub 2016/07/12. doi: 10.1016/j.breast.2016.06.018. PubMed PMID: 27397723.
• Szalaj P, Michalski PJ, Wroblewski P, Tang Z, Kadlof M, Mazzocco G, et al. 3D-GNOME: an integrated web service for structural modeling of the 3D genome.Nucleic acids research. 2016;44(W1):W288-93. Epub 2016/05/18. doi: 10.1093/nar/gkw437. PubMed PMID: 27185892.
• George J,Uyar A, Young K, Kuffler L, Waldron-Francis K, Marquez E, et al. Leukaemia cell of origin identified by chromatin landscape of bulk tumour cells.Nature communications.2016;7:12166. Epub 2016/07/12. doi: 10.1038/ncomms12166. PubMed PMID: 27397025.
• Pei S, Minhajuddin M, D'Alessandro A, Nemkov T,Yadav V, Stevens BM, Adane B, et al. Rational Design of a Parthenolide-based Drug Regimen that Selectively Eradicates Acute Myelogenous Leukemia Stem Cells.The Journal of biological chemistry. 2016. Epub 2016/08/31. doi: 10.1074/jbc.M116.750653. PubMed PMID: 27573247.
• Kotzin JJ, Spencer SP, McCright SJ, Kumar DB, Collet MA, Mowel WK,Uyar A, et al. The long non-coding RNA Morrbid regulates Bim and short-lived myeloid cell lifespan.Nature.2016;537(7619):239-43. Epub 2016/08/16. doi: 10.1038/nature19346. PubMed PMID: 27525555.
• Hintzsche J, Kim J,Yadav V, et. al., IMPACT: a whole-exome sequencing analysis pipeline for integrating molecular profiles with actionable therapeutics in clinical samples. Journal of the American Medical Informatics Association :JAMIA. 2016; 23(4):721-30. PMID: 27026619 PMCID: PMC4926746
• Yadav VK, Smith KS, Flinders C, Mumenthaler SM, De S. Significance of duon mutations in cancer genomes.Scientific reports. 2016; 6:27437. PMID: 27272679 PMCID: PMC4897603

2Q - 2016

• Bais P, Beebe K, Morelli KH, Currie ME, Norberg SN, Evsikov AV, et al. Metabolite profile of a mouse model of Charcot-Marie-Tooth type 2D neuropathy: implications for disease mechanisms and interventions.Biology open. 2016;5(7):908-20. Epub 2016/06/12. doi: 10.1242/bio.019273. PubMed PMID: 27288508.
• Bigdeli TB,Lee D, Webb BT, Riley BP, Vladimirov VI, Fanous AH, et al. A simple yet accurate correction for winner's curse can predict signals discovered in much larger genome scans.Bioinformatics(Oxford, England). 2016. Epub 2016/05/18. doi: 10.1093/bioinformatics/btw303. PubMed PMID: 27187203.
• Lawlor N, Fabbri A, Guan P,George J, Karuturi RK. multiClust: An R-package for Identifying Biologically Relevant Clusters in Cancer Transcriptome Profiles.Cancer informatics. 2016;15:103-14. Epub 2016/06/23. doi: 10.4137/cin.s38000. PubMed PMID: 27330269; PubMed Central PMCID: PMCPMC4907340.
• Menghi F, Inaki K,Woo X, Kumar PA, Grzeda KR,Malhotra A,Yadav V,et. al.,The tandem duplicator phenotype as a distinct genomic configuration in cancer.Proceedings of the National Academy of Sciences of the United States of America. 2016; 113(17):E2373-82. PMID: 27071093 PMCID: PMC4855596.
• Poznik GD, Xue Y, Mendez FL, Willems TF, Massaia A,Malhotra A, Wilson Sayres MA, et al. Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences.Nature genetics. 2016;48(6):593-Epub 2016/04/26. doi: 10.1038/ng.3559. PubMed PMID: 27111036; PubMed Central PMCID: PMCPMC4884158.
• Su KH, Cao J, Tang Z, Dai S,He Y, Sampson SB, et al. HSF1 critically attunes proteotoxic stress sensing by mTORC1 to combat stress and promote growth.Nature cell biology. 2016;18(5):527-39. Epub 2016/04/05. doi: 10.1038/ncb3335. PubMed PMID: 27043084.
• Alam SK,Yadav VK, Bajaj S, Datta A, et. al.,DNA damage-induced ephrin-B2 reverse signaling promotes chemoresistance and drives EMT in colorectal carcinoma harboring mutant p53.Cell death and differentiation. 2016; 23(4):707-22. PMID: 26494468 PMCID: PMC4986638.
• Tafe LJ, Muller KE, Ananda G, Mitchell T, Spotlow V, Patterson SE, et al. Molecular Genetic Analysis of Ovarian Brenner Tumors and Associated Mucinous Epithelial Neoplasms: High Variant Concordance and Identification of Mutually Exclusive RAS Driver Mutations and MYC Amplification.The American journal of pathology. 2016;186(3):671-7. Epub 2016/01/23. doi: 10.1016/j.ajpath.2015.11.008. PubMed PMID: 26797085.
• Sundberg JP, Pratt CH, Silva KA, Kennedy VE, Stearns TM, Sundberg BA, et al. Dermal lymphatic dilation in a mouse model of alopecia areata.Experimental and molecular pathology. 2016;100(2):332-6. Epub 2016/03/10. doi: 10.1016/j.yexmp.2016.03.001. PubMed PMID: 26960166; PubMed Central PMCID: PMCPMC4823156.
• Poznik GD, Xue Y, Mendez FL, Willems TF, Massaia A, Wilson Sayres MA, et al. Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences.Nature genetics. 2016;48(6):593-9. Epub 2016/04/26. doi: 10.1038/ng.3559. PubMed PMID: 27111036; PubMed Central PMCID: PMCPMC4884158.

1Q - 2016

• J. P. Sundberg, A. Berndt,B. A. Sundberg, K. A. Silva, V. Kennedy, R. S. Smith, T. K. Cooper, and P. N. Schofield. Approaches to Investigating Complex Genetic Traits in a Large-Scale Inbred Mouse Aging Study.Vet Path. 53(2): 456-67. 2016. DOI: 10.1177/0300985815612556. http://vet.sagepub.com/content/53/2/456.full.pdf+html
• Sundberg, J. P., Silva, K. A., Kennedy, V. E.,Sundberg, B. A., Li, Q., Uitto, J., and Berndt, A. Mouse genome-wide association study identifies polymorphisms on chromosomes 4, 11 and 15 for age-related cardiac fibrosis. Accepted for publication inMammalian Genome. January 2016.
• Sundberg, J. P., Pratt, C. H., Silva, K. A., Kennedy, V. E.,Stearns, T. M.,Sundberg, B. A.,King, L. E., and HogenEsch, H. Dermal lymphatic dilation in a mouse model of alopecia areata.Experimental and Molecular Pathology. March 7, 2016.
• Yadav VK, DeGregori J, De S. The landscape of somatic mutations in protein coding genes in apparently benign human tissues carries signatures of relaxed purifying selection.Nucleic acids research. 2016; 44(5):2075-84. PMID: 26883632 PMCID: PMC4797307.
• Tafe L, Muller KE,Ananda G, et al.Molecular Genetic Analysis of Ovarian Brenner Tumors and Associated Mucinous Epithelial Neoplasms: High Variant Concordance and Identification of Mutually Exclusive RAS and Driver Mutations and MYC Amplification.Am J Pathol. 2016 Mar;186(3):671-7
• Poczobutt JM, De S,Yadav VK, Nguyen TT, Li H, Sippel TR, Weiser-Evans MC, Nemenoff RA. Expression Profiling of Macrophages Reveals Multiple Populations with Distinct Biological Roles in an Immunocompetent Orthotopic Model of Lung Cancer.Journal of immunology.PMID: 26873985 PMCID: PMC4779748
• Smith KS,Yadav VK, Pei S, Pollyea DA, Jordan CT, De S. SomVarIUS: somatic variant identification from unpaired tissue samples.Bioinformatics. 2016; 32(6):808-13. PMID: 26589277