2015 Computational Sciences Publications

Q4 – 2015

  1. Tongjun Gu, Daniel M. Gatti, Anuj Srivastava, Elizabeth M. Snyder, Narayanan Raghupathy, Petr Simecek, Karen L. Svenson, Ivan Dotu, Jeffrey H. Chuang, Mark P. Keller, Alan D. Attie, Robert E. Braun, Gary A. Churchill, Genetics Early online November 27, 2015; DOI: 10.1534/genetics.115.179481
  2. 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. Modern Pathol. Manuscript accepted for publication in American Journal of Pathology. 2015
  3. Sinha D, Chong L, George J, et al. (2015).  “Pericytes promote malignant ovarian cancer progression in mice and predict poor prognosis in serous ovarian cancer patients”. Clinical Cancer Research, Nov 20 2015
  4. Tang Z, OJ Luo, X Li, M Zheng, JJ Zhu, P Szalaj, P Trzaskoma, A Magalska, J Wlodarczyk, B Ruszczycki, P Michalski, E Piecuch, P Wang, D Wang, SZ Tian, M Penrad-Mobayed, LM Sachs, X Ruan, C-L Wei, ET Liu, GM Wilczynski, D Plewczynski, G Li, and Y Ruan. CTCF-mediated human 3D genome architecture reveals chromatin topology for transcription. 2015 Cell 163, 1611-1627.
  5. Sundberg, J. P., Berndt, A., Sundberg, B. A., Silva, K. A., Kennedy, V., Smith, R. S., Cooper, T.  K., and Schofield, P. N.Approaches to Investigating Complex Genetic Traits in a Large Scale Inbred Mouse Aging Study. Galleys for this manuscript accepted for publication in Veterinary Pathology. December 2015.

Q3 – 2015

  1. Turcotte M, Spring K, Sandra Pmmey, Choudinard G, Cousineau I, George J et al. (2015).  CD73 is associated with poor prognosis in high-grade serous ovarian cancer. Cancer Research. Published Online Sept 11, 2015
  2. Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Hsi-Yang Fritz M, Konkel MK, Malhotra A, Stütz AM, Shi X, Paolo Casale F, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJ, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HY, Jasmine Mu X, Alkan C, Antaki D, Bae T, Cerveira E, Chines P, Chong Z, Clarke L, Dal E, Ding L, Emery S, Fan X, Gujral M, Kahveci F, Kidd JM, Kong Y, Lameijer EW, McCarthy S, Flicek P, Gibbs RA, Marth G, Mason CE, Menelaou A, Muzny DM, Nelson BJ, Noor A, Parrish NF, Pendleton M, Quitadamo A, Raeder B, Schadt EE, Romanovitch M, Schlattl A, Sebra R, Shabalin AA, Untergasser A, Walker JA, Wang M, Yu F, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer MA, McCarroll SA; 1000 Genomes Project Consortium, Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO. An integrated map of structural variation in 2,504 human genomes. Nature. 2015 Oct 1;526(7571):75-81. doi: 10.1038/nature15394. PMID: 26432246
  3. 1000 Genomes Project Consortium, Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA, Abecasis GR. A global reference for human genetic variation. Nature. 2015 Oct 1;526(7571):68-74. doi: 10.1038/nature15393. PMID: 26432245 (Malhotra A, part of the 1000G consortium, and co-project lead for JAX part of 1000G analysis group)

Q2 – 2015

  1. Minor genomic differences between related B6 and B10 mice affect severity of schistosome infection by governing the mode of dendritic cell activation.Smith PM, Sproule TJ, Philip VM, Roopenian DC, Stadecker MJ. Eur J Immunol. 2015 May 9. doi: 10.1002/eji.201545547. PMID: 25959828
  2. Fairfield H, Srivastava A*, Ananda G*, Liu R*, Martin Kircher, Anuradha Lakshminarayana, Belinda S. Harris, Son Yong Karst, Louise A. Dionne, Colleen C. Kane, Michelle Curtain, Melissa L. Berry, Patricia F. Ward-Bailey, Ian Greenstein, Candice Byers, Anne Czechanski, Jocelyn Sharp, Kristina Palmer, Polyxeni Gudis, Whitney Martin, Abby Tadenev, Laurent Bogdanik, C. Herbert Pratt, Bo Chang, David G. Schroeder, Gregory A. Cox, Paul Cliften, Jeffrey Milbrandt, Stephen Murray, Robert Burgess, David E. Bergstrom, Leah Rae Donahue, Hanan Hamamy, Amira Masri, Federico A. Santoni, Periklis Makrythanasis, Stylianos E. Antonarakis, Jay Shendure, Laura G. Reinholdt. ‘Exome sequencing reveals pathogenic mutations in 91 strains of mice with Mendelian disorders.’ Genome Research 2015 Jul;25(7):948-57 (* = equal contribution)
  3. Wenning Qin, Stephanie L Dion, Peter M Kutny, Yingfan Zhang, Albert Cheng, Nathaniel L Jillette, Ankit Malhotra, Aron M Geurts, Yi-Guang Chen, Haoyi Wang. Efficient CRISPR/Cas9-Mediated Genome Editing in Mice by Zygote Electroporation of Nuclease. Genetics, 115.176594, 2015
  4. Patch, A. M., Christie, E. L., Etemadmoghadam, D., Garsed, D. W., George, J., Fereday, S., . . . Bowtell, D. D. (2015). Whole-genome characterization of chemoresistant ovarian cancer. Nature, 521(7553), 489-494. doi: 10.1038/nature14410
  5. Peter H. Sudmant, Tobias Rausch, Eugene J. Gardner, Robert E. Handsaker, Alexej Abyzov, John Huddleston, Yan Zhang, Kai Ye, Goo Jun, Markus Hsi-Yang Fritz, Miriam K. Konkel, Ankit Malhotra, et al, An integrated map of structural variation in 2,504 human genomes, Nature, accepted.

Q1 – 2015

  1. Guruprasad Ananda, Susan Mockus, Micaela Lundquist, Vanessa Spotlow, Al Simons, Talia Mitchell, Grace Stafford, Vivek Philip, Timothy Stearns, Anuj Srivastava, Mary Barter, Lucy Rowe, Joan Malcolm, Carol Bult, Radha Krishna Murthy Karuturi, Karen Rasmussen and Douglas Hinerfeld, Development and validation of the JAX Cancer Treatment Profile™ for detection of clinically actionable mutations in solid tumors, Experimental and Molecular Pathology, 2015.
  2. Preeti Bais, Kirk Bebee, Alexi Esikov, Kathy E. Miers, Kevin L. Seburn, Gregory C. Cox, Carol J. Bult, and Robert W. Burgess.  A metabolite profile and implications for disease mechanisms from a mouse model of Charcot-Marie-Tooth type 2D; Accepted at Metabolomics Society Conference 2015
  3. Jayendra Kumar Krishnaswamy, Arpita Singh, …. Anuj Srivastava….. Adam Williamsi, Richard A. Flavellb and Stephanie C. Eisenbartha, Coincidental loss of DOCK8 function in NLRP10-deficient and C3H/HeJ mice results in defective dendritic cell migration, PNAS, 2015
  4. Huei San Leong, Laura Galletta, Dariush Etemadmoghadam, Joshy George, Martin Köbel, Susan J Ramus, David Bowtell: Efficient molecular subtype classification of high-grade serous ovarian cancer. The Journal of Pathology 03/2015;  DOI:10.1002/path.4536
  5. Fungtammasan A*, Ananda G*, Hile S, Su M, Sun C, Harris R, Medvedev P, Eckert K, Makova K. Accurate typing of short tandem repeats from genome-wide sequencing data and its applications. Genome Res. 2015 Mar 30 (* = equal contribution)
  6. Tang Z., Dai S., He Y., Doty R.A., Shultz L.D., Sampson S.B., and Dai C. 2015. MEK guards proteome stability and inhibits tumor-suppressive amyloidogenesis via HSF1. Cell. 160(4):729-744.
  7. Sigrid Rouam, Lance D. Miller and R. Krishna Murthy Karuturi, Identifying Driver Genes in Cancer by Triangulating Gene Expression, Gene Location, and Survival Data. Cancer Informatics, Feb’2015