Recent Scientific Publications from Morgridge Institute Researchers

Reflections on the cost of "low-cost" whole genome sequencing: framing the health policy debate.
November 2013 [Epub November 5, 2013]
Caulfield T., Evans J., McGuire A., McCabe C., Bubela T., Cook-Deegan R., Fishman J., Hogarth S., Miller F.A., Ravitsky V., Biesecker B., Borry P., Cho M.K., Carroll J.C., Etchegary H., Joly Y., Kato K., Lee S.S., Rothenberg K., Sankar P., Szego M.J., Ossorio P., Pullman D., Rousseau F., Ungar W.J. and Wilson B.
PLoS Biol. 11(11): e1001699.
Fan-beam intensity modulated proton therapy.
November 2013
Hill P., Westerly D. and Mackie T.
Med Phys. (11):111704.
Quantitative selection and parallel characterization of aptamers.
November 12, 2013 [Epub October 28, 2013]
Cho M., Soo Oh S., Nie J., Stewart R., Eisenstein M., Chambers J., Marth J.D., Walker F., Thomson J.A. and Soh H.T.
Proc Natl Acad Sci U S A. 110(46):18460-18465.
ZASC1 stimulates HIV-1 transcription elongation by recruiting P-TEFb and TAT to the LTR promoter.
October 2013 [Epub October 24, 2013]
Bruce J.W., Reddington R., Mathieu E., Bracken M., Young J.A. and Ahlquist P.
PLoS Pathog. 9(10):e1003712.
Vacuum seed sowing manifold: a novel device for high-throughput sowing of Arabidopsis seeds.
[Epub October 22, 2013]
Barker R., Cox B., Mackie T.R. and Masson P.
Plant Methods. 9(1): 41.
Integrated module and gene-specific regulatory inference implicates upstream signaling networks.
October 2013 [Epub October 17, 2013]
Roy S., Lagree S., Hou Z., Thomson J.A., Stewart R. and Gasch A.P.
PLoS Comput Biol. 9(10):e1003252.
Limited agreement of independent RNAi screens for virus-required host genes owes more to false-negative than false-positive factors.
September 2013 [Epub September 19, 2013]
Hao L., He Q., Wang Z., Craven M., Newton M.A. and Ahlquist P.
PLoS Comput. Biol. 9(9):e1003235.
Systematic analyses of the cytotoxic effects of compound 11a, a putative synthetic agonist of photoreceptor-specific nuclear receptor (PNR), in cancer cell lines.
September 2013 [Epub September 16, 2013]
Zhao Z., Wang L., Wen Z., Ayaz-Guner S., Wang Y., Ahlquist P. and Xu W.
PLoS One. 8(9):e75198.
Development of an efficient targeted cell-SELEX procedure for DNA aptamer reagents.
August 13, 2013
Meyer S., Maufort J.P., Nie J., Stewart R., McIntosh B.E., Conti L.R., Ahmad K.M., Soh H.T. and Thomson J.A.
PLoS One. 8(8):e71798.
Efficient genome engineering in human pluripotent stem cells using Cas9 from Neisseria meningitidis.
[Epub August 12, 2013]
Hou Z., Zhang Y., Propson N.E., Howden S.E., Chu L.F., Sontheimer E.J. and Thomson J.A.
Proc. Natl. Acad. Sci. USA. 110(39):15644-15649.
Comment on "When is better best? A multiobjective perspective" [Med. Phys. 38, 1635-1640 (2011)].
July 2013
Yartsev S. and Mackie T.R.
Med.Phys. 40(7):077101.
Epigenomic analysis of multilineage differentiation of human embryonic stem cells.
May 23, 2013 [Epub May 9, 2013]
Xie W., Schultz M.D., Lister R., Hou Z., Rajagopal N., Ray P., Whitaker J.W., Tian S., Hawkins R.D., Leung D., Yang H., Wang T., Lee A.Y., Swanson S.A., Zhang J., Zhu Y., Kim A., Nery J.R., Urich M.A., Kuan S., Yen C.A., Klugman S., Yu P., Suknuntha K., Propson N.E., Chen H., Edsall L.E., Wagner U., Li Y., Ye Z., Kulkarni A., Xuan Z., Chung W.Y., Chi N.C., Antosiewicz-Bourget J.E., Slukvin I., Stewart R., Zhang M.Q., Wang W., Thomson J.A., Ecker J.R. and Ren B.
Cell. 153(5):1134-1148.
ZASC1 knockout mice exhibit an early bone marrow-specific defect in murine leukemia virus replication.
April 24, 2013
Seidel S., Bruce J., Leblanc M., Lee K.F., Fan H., Ahlquist P. and Young J.A.
Virol. J. 10(1), 130.
EBSeq: An Empirical Bayes Hierarchical Model for Inference in RNA-seq Experiments.
April 15, 2013 [Epub February 21, 2013]
Leng N., Dawson J.A., Thomson J.A., Ruotti V., Rissman A.I., Smits B.M., Haag J.D., Gould M.N., Stewart R.M. and Kendziorski C.
Bioinformatics. 29(8), 1035-1043
Comparative RNA-seq Analysis in the Unsequenced Axolotl: The Oncogene Burst Highlights Early Gene Expression in the Blastema.
March 2013 [Epub March 7, 2013]
Stewart R., Rascón C.A., Tian S., Nie J., Barry C., Chu L.F., Ardalani H., Wagner R.J., Probasco M.D., Bolin J.M., Leng N., Sengupta S., Volkmer M., Habermann B., Tanaka E.M., Thomson J.A. and Dewey C.N.
PLoS Comput. Biol. 9(3), e1002936.