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Selected Publications in Computational Biology

  1. Automated Multivariate Profiling of Drug Effects from Fluorescence Microscopy Images
    Loo, L.H., Wu, L., Altschuler, S.J.
    IEEE International Symposium on Biomedical Imaging, 2006; 251-54.

  2. Systems-level analyses identify extensive coupling among gene expression machines
    Maciag, K., Altschuler, S.J., Slack, M.D., Krogan, N.J., Emili, A., Greenblatt, J.F., Maniatis, T., Wu, L.F.
    Molecular Systems Biology, 2006 Jan 17; 2(1):msb400045-E1-msb400045-E14.
  3. Genome-scale identification of nucleosome positions in S. cerevisiae.
    Yuan G.C., Liu Y.J., Dion M.F., Slack M.D., Wu L.F., Altschuler S.J., Rando O.J.
    Science, 2005 Jul 22; 309(5734):626-30.
  4. Genomic characterization reveals a simple histone H4 acetylation code
    Dion, M.F., Altschuler, S.J., Wu L.F., Rando, O.J.
    PNAS, 2005 April 12; 102(15):5501-5506.
  5. Multi-dimensional Drug Profiling By Automated Microscopy
    Perlman, Z.E., Slack, M.D., Feng, Y., Mitchison, T.J., Wu, L.F., Altschuler, S.J.
    Science, 2004 Nov 12; 306(5699):1194-8.
  6. A panoramic view of yeast non-coding RNA processing
    Peng, W.T., Robinson, M.D., Mnaimneh, S., Krogan, N.J., Cagney, G., Morris, Q., Davierwala, A.P., Grigull, J., Yang, X., Zhang, W., Mitsakakis, N., Ryan, O.W., Datta, N., Jojic, V., Pal, C., Canadien, V., Richards, D., Beattie, B., Wu, L.F., Altschuler, S.J., Roweis, S., Frey, B.J., Emili, A., Greenblatt, J.F., Hughes, T.R.
    Cell, 2003 Jun 27; 113(7):919-33.
  7. Spontaneous cell polarization through actomyosin-based delivery of the Cdc42 GTPase
    Wedlich-Soldner R., Altschuler S., Wu L., Li R.
    Science, 2003 Feb 21; 299(5610):1231-5.
  8. Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters
    Wu, L.F., Hughes, T.R., Davierwala, A.P., Robinson, M.D., Stoughton, R., and Altschuler, S.J.
    Nature Genetics, 2002; 31(3):255-65.
  9. Experimental annotation of the human genome using microarray technology
    Shoemaker, D.D., Schadt, E.E., Armour, C.D., He, Y.D., Garrett-Engele, P., McDonagh, P.D., Loerch, P.M., Leonardson, A., Lum, P.Y., Cavet, G., Wu, L.F., Altschuler, S.J., Edwards, S., King, J., Tsang, J.S., Schimmack, G., Schelter, J.M., Koch, J., Ziman, M., Marton, M.J., Li, B., Cundiff, P., Ward, T., Castle, J., Krolewski, M., Meyer, M.R., Mao, M., Burchard, J., Kidd, M.J., Dai, H., Phillips, J.W., Linsley, P.S., Stoughton, R., Scherer, S., Boguski, M.S.
    Nature, 2001; 409(6822):922-7

Selected Publications in Engineering and Mathematics

  1. Speech/Noise Separation Using Two Microphones and a VQ Model of Speech Signals
    Acero, A., Altschuler S.J., Wu L.F.
    Proceedings of the ICSLP 2000, 2002.
  2. On deforming confoliations
    Altschuler, S.J., Wu, L.F.
    Journal of Differential Geometry, 2000; 54(1):75-97.

  3. Clustering finite discrete markov chains
    Ridgeway, G., Altschuler, S.J.
    Proceedings of the Section on Physical and Engineering Sciences, 1998; 228-9.
  4. Generating Signal Processing Software
    Altschuler, S.J., Kim, W.
    Proceedings of the ICSR5, 1998.

  5. Mean curvature flow through singularities for surfaces of rotation
    Altschuler, S.J., Angenet, S., Giga, Y.
    Journal of Geometric Analysis, 1995; 5(3):293-358.

  6. A geometric heat flow for one-forms on three dimensional manifolds
    Altschuler, S.J.
    Illinois Journal of Mathematics, 1995; 39(1):98-118.

  7. Translating surfaces of the non-parametric mean curvature flow with prescribed contact angle
    Altschuler, S.J., Wu, L.F.
    Calc. Var. Partial Diff. Eq., 1994; 2(1):101-11.

  8. The Ricci Flow on complete R2
    Wu, L.F.
    Comm. in Analysis and Geometry, 1993; 1:439-72.

  9. A new result for the porous medium equation on R2 derived from the Ricci flow
    Wu, L.F.
    Bulletin of the American Mathematical Society, 1993; 28:90-94.

  10. Convergence to translating solitons for a class of quasilinear parabolic boundary problems
    Altschuler, S.J., Wu, L.F.
    Math. Annalen, 1993; 295:761-5.

  11. Shortening space curves and flow through singularities
    Altschuler, S.J., Grayson, M.
    Journal of Differential Geometry, 1992; 35(2):283-98.
  12. The Ricci Flow on 2-orbifolds with positive curvature
    Wu, L.F.
    Journal of Differential Geometry, 1991; 33:575-96.
  13. The Ricci Flow on compact 2-orbifolds with curvature negative somewhere
    Chow, B., Wu, L.F.
    Communications on Pure and Applied Mathematics, 1991; 44:275-86.

  14. Singularities for the curve shortening flow for space curves
    Altschuler, S.J.
    Journal of Differential Geometry, 1991. 34(2): p. 491-514.

Undergraduate Theses

  1. An Oligonucleotide Microarray-Based Method for Determining Nucleosome Positioning in Saccharomyces cerevisiae
    Yuen-Jong Liu
    presented to the Department of Computer Science and the Department of Biochemical Sciences, Harvard University, 2004.

  2. A Computational Approach to the Identification of Protein Network Elements Involved in the Coupling of Gene Expression Machines in Eukaryotic Cells
    Karolina Maciag
    presented to the Department of Biochemical Sciences, Harvard University, 2004.
  3. Mass Action Networks and the Deficiency Zero Theorem
    Jonathan M. Guberman
    presented to the Department of Mathematics, Harvard University, 2003.
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