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UT Southwestern Medical Center

The Altschuler & Wu Computational and Systems Biology Laboratory

Publications

  1. A simple image correction method for high-throughput microscopy. Coster A.D., Wichaidit C., Rajaram S., Altschuler S.J., Wu L.F. Nature Methods, 2014 June; Vol. 11 No. 6, 602
  2. Rapid Analysis and Exploration of Fluorescence Images Pavie B., Rajaram S., Ouyang A., Altschuler J.M., Steininger R.J., Wu L.F., Altschuler S.J., JoVE, 2014 March 3.
  3. Envisioning migration: Mathematics in both experimental analysis and modeling of cell behavior. Zhang E.R., Wu L.F., Altschuler S.J., Current Opinion in Cell Biology, 2013 May 6.
  4. Identifying network motifs that buffer front-to-back signaling in polarized neutrophils. Wang Y., Ku C.J., Zhang E.R., Artyukhin A.B., Weiner O.D., Wu L.F., Altschuler S.J., Cell Reports, 2013 May 30;3(5):1607-16.
  5. The Zoo of Solitons for Curve Shortening in ℝn. Altschuler D.J., Altschuler S.J., Angenent S.B., Wu L.F. Nonlinearity, 2013 May; Vol. 26, No. 5: 1189-1226. DOI:10.1088/0951-7715/26/5/1189 (PDF) (Videos).
  6. PhenoRipper: software for rapidly profiling microscopy images. Rajaram S., Pavie B., Wu L.F. & Altschuler S.J. Nature Methods 2012 July; Vol. 9 No. 7, 635-637
  7. SimuCell: a flexible framework for creating synthetic microscopy images. Rajaram S., Pavie B., Hac N.E.F, Wu L.F. & Altschuler S.J. Nature Methods 2012 July; Vol. 9 No. 7, 634-635.
  8. Network Crosstalk Dynamically Changes during Neutrophil Polarization. Ku C.J., Wang Y., Weiner O.D., Altschuler S.J., Wu L.F. Cell, 2012 May 25; Volume 149, Issue 5, 1073-1083. (News article)
  9. Identification of F-actin as the Dynamic Hub in a Microbial-Induced GTPase Polarity Circuit. Orchard R.C., Kittisopikul M., Altschuler S.J., Wu L.F., Suel G.M., Alto N.M. Cell, 2012 Feb 17;148(4):803-815
  10. Membrane Tension Maintains Cell Polairty by Confining Signals to the leading edge during Neutrophil Migration. Houk A.R., Jilkine A., Mejean C., Boltyanskiy R., Dufresne E., Angenent S.B., Altschuler S.J., Wu L.F., Weiner O.D. Cell, 2012 Jan 20;148(1-2):175-88.
  11. A Density-Dependent Switch Drives Stochastic Clustering and Polarization of Signaling Molecules. Jilkine A., Angenent S.B., Wu L.F.& Altschuler S.J. PLoS Computational Biology, 2011 Nov;7(11):e1002271.
  12. Cellular Heterogeneity: Do Differences Make a Difference? Altschuler S.J. & Wu L.F. Cell, May 2010; Volume 141, Issue 4, 559-563.
  13. Patterns of basal signaling heterogeneity can distinguish cellular populations with different drug sensitivities. Singh D.K., Ku C.J., Wichaidit C., Steininger R.J. 3rd, Wu L.F., Altschuler S.J. Mol Syst Biol., 2010 May; 6:369.
  14. On identifying information from image-based spatial polarity phenotypes in neutrophils. Ku C.J., Wang Y., Pavie B., Altschuler S.J., Wu L.F. Proc IEEE Int Symp Biomed Imaging, 2010 Apr 1;14-17:1029-1032., PMCID: PMC2921656
  15. An approach for extensibly profiling the molecular states of cellular subpopulations Loo L.H., Lin H.J., Steininger III R.J., Wang Y., Wu L.F. & Altschuler S.J. Nature Methods, Volume 6, 759-765 (2009) , October 2009
  16. Heterogeneity in the physiological states and pharmacological responses of differentiating 3T3-L1 preadipocytes Loo L.H., Lin H.J., Singh D. K., Lyons K. M., Altschuler S.J. & Wu L.F. The Journal of Cell Biology, jcb.200904140, September 2009.
  17. Only two ways to achieve perfection Artyukhin A.B., Wu L.F., Altschuler S.J. Cell, Volume 138, Issue 4, 619-621, 21 August 2009
  18. Characterizing heterogeneous cellular responses to perturbations Slack, M.D., Martinez, E.D., Wu, L.F., Altschuler, S.J. PNAS, 2008 December 9; vol. 105, no. 49, 19305-19310.
  19. On the spontaneous emergence of cell polarity Altschuler, S.J., Angenent, S.B., Wang, Y., Wu, L.F. Nature, 2008 Aug 14; 454:886-890.
  20. An actin-based wave generator organizes cell motility Weiner, O.D., Marganski, W.A., Wu, L.F., Altschuler, S.J., Krischner, M.W. PLOS Biology, 2007 Aug 14; 5(9):e221.
  21. Image-based multivariate profiling of drug responses from single cells Loo, L.H., Wu, L., Altschuler, S.J. Nature Methods, 2007 May; 4(5):445-53.
  22. Endocytosis optimizes the dynamic localization of membrane proteins that regulate cortical polarity Marco, E., Wedlich-Soldner, R., Li, R., Altschuler, S.J., Wu, L.F. Cell, 2007 Apr 20; 129:411-22. (PDF)
  23. 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.
  24. 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. (news article)
  25. 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.
  26. 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.
  27. 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. (PDF) (profiling code) (news article)
  28. A panoramic view of yeast non-coding RNA processing Peng, W.T. et al. Cell, 2003 Jun 27; 113(7):919-33.
  29. 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. (news article)
  30. 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. (PDF) (Supplemental) (news article)
  31. Experimental annotation of the human genome using microarray technology Shoemaker, D.D., et al. Nature, 2001; 409(6822):922-7
  32. 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. (PDF)
  33. On deforming confoliations Altschuler, S.J., Wu, L.F. Journal of Differential Geometry, 2000; 54(1):75-97.
  34. Clustering finite discrete markov chains Ridgeway, G., Altschuler, S.J. Proceedings of the Section on Physical and Engineering Sciences, 1998; 228-9. (PDF)
  35. Generating Signal Processing Software Altschuler, S.J., Kim, W. Proceedings of the ICSR5, 1998.
  36. 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.
  37. A geometric heat flow for one-forms on three dimensional manifolds Altschuler, S.J. Illinois Journal of Mathematics, 1995; 39(1):98-118.
  38. 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.
  39. The Ricci Flow on complete R2 Wu, L.F. Comm. in Analysis and Geometry, 1993; 1:439-72.
  40. 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.
  41. Convergence to translating solitons for a class of quasilinear parabolic boundary problems Altschuler, S.J., Wu, L.F. Math. Annalen, 1993; 295:761-5.
  42. Shortening space curves and flow through singularities Altschuler, S.J., Grayson, M. Journal of Differential Geometry, 1992; 35(2):283-98. (PDF)
  43. The Ricci Flow on 2-orbifolds with positive curvature Wu, L.F. Journal of Differential Geometry, 1991; 33:575-96. (PDF)
  44. 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.
  45. 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. (Abstract)
  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. (Abstact) (Supplemental)
  3. Mass Action Networks and the Deficiency Zero Theorem Jonathan M. Guberman presented to the Department of Mathematics, Harvard University, 2003. (PDF)