2016 Computational Sciences Publications

4Q - 2016

  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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

  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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
  7. 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

  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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

  1. 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
  2. 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.
  3. 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.
  4. 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.
  5. 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
  6. 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
  7. 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