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Yong Lu, Ph.D.
Postdoctoral Fellow
Harvard Medical School
250 Longwood Avenue, SGMB-322 Boston, MA 02115
...@hms.harvard.edu
(My name in Chinese: 吕邕)

I am a Postdoctoral Fellow working with Dr. Fritz Roth at Harvard Medical School.

I received my Ph.D. in Computer Science from Carnegie Mellon University. My advisors at CMU were Drs. Ziv Bar-Joseph and Roni Rosenfeld. I was a member of the CMU Systems Biology Group.

My OpenPGP Public Key ID is B397E6F6, and the fingerprint is

689D 99E1 0D99 3062 18D1  
0424 8A91 84D6 B397 E6F6


Publications

Journal Publications

  1. A.M.F. Heilmann, M.A. Calderwood, D. Portal, Y. Lu, E.C. Johannsen,
    Genome wide analysis of Epstein-Barr virus Rta-DNA interactions, Journal of Virology, 2012.
    [abstract ]

  2. Y. Liu, A. Niculescu-Mizil, A.C. Lozano and Y. Lu,
    Temporal Graphical Models for Cross-Species Gene Regulatory Network Discovery, Journal of Bioinformatics and Computational Biology, 9(2):231-250, 2011.
    [abstract ]

  3. E. Kugelberg, E.C. Kofoid, D.I. Andersson, Y. Lu, J. Mellor, F.P. Roth and J.R. Roth,
    The Tandem Inversion Duplication in Salmonella enterica: Selection Drives Unstable Precursors to Final Mutation Types, Genetics, 185:65-80, 2010.
    [abstract | pdf | ...]

  4. Y. Lu, R. Rosenfeld, G.J. Nau and Z. Bar-Joseph,
    Cross species expression analysis of innate immune response, Journal of Computational Biology March 2010, 17(3): 253-268.
    [abstract | pdf | ...]

  5. L. Li, Y. Lu, L.X. Qin, Z. Bar-Joseph, M. Werner-Washburne and L.L. Breeden,
    Budding yeast SSD1-V regulates transcript levels of many longevity genes and extends chronological life span in purified quiescent cells, Mol Biol Cell, 20(17):3851-3864, 2009.
    [abstract | pdf | ... ]

  6. Y. Lu, P. Huggins and Z. Bar-Joseph,
    Cross species analysis of microarray expression data, Bioinformatics 25(12):1476-1483, 2009.
    [ abstract | pdf | ... ]

  7. Y. Lu, R. Rosenfeld, I. Simon, G.J. Nau and Z. Bar-Joseph,
    A Probabilistic Generative Model for GO Enrichment Analysis, Nucleic Acids Research 36(17):e109, 2008.
    [ abstract | html | pdf | ... ]

  8. Y. Lu, S. Mahony, P.V. Benos, R. Rosenfeld, I. Simon, L.L. Breeden and Z. Bar-Joseph,
    Selecting a threshold for identifying cell cycle genes, Genome Biology, 9:403, 2008.
    [ html | pdf | ... ]

  9. Z. Bar-Joseph, Z. Siegfried, M. Brandeis, B. Brors, Y. Lu, R. Eils, B. D. Dynlacht and I. Simon,
    Genome-wide transcriptional analysis of the human cell cycle identifies genes differentially regulated in normal and cancer cells, Proc Natl Acad Sci U S A, 105:955-960, 2008
    (Also accepted to ISMB 2008 Highlights Track)
    [ html | pdf | supporting information | ... ]

  10. Y. Lu, S. Mahony, P.V. Benos, R. Rosenfeld, I. Simon, L.L. Breeden and Z. Bar-Joseph,
    Combined Analysis Reveals a Core Set of Cycling Genes, Genome Biology, 8:R146, 2007
    (Also presented at ISMB 2008 Highlights Track, Jul 19-23, Toronto)
    [ pdf | html | supplements | supporting website | ... ] Must Read(Ranked 2nd in Hidden Jewels)

  11. Y. Lu, R. Rosenfeld and Z. Bar-Joseph,
    Identifying Cycling Genes by Combining Sequence Homology and Expression Data, Bioinformatics (Proceedings of ISMB 2006), 22(14):e314-322, 2006.
    [ bib | .pdf | http | ... ]

Refereed Conference Publications

  1. Y. Liu, A. Niculescu-Mizil, A.C. Lozano and Y. Lu
    Learning Temporal Causal Graphs for Relational Time-Series Analysis, in Proceedings of the 27th International Conference on Machine Learning (ICML 2010).
    [conference website | pdf]


  2. Y. Liu, A. Niculescu-Mizil, A.C. Lozano and Y. Lu
    Temporal Graphical Models for Cross-Species Gene Regulatory Network Discovery, in Proceedings of the 9th International Conference on Computational Systems Bioinformatics (CSB 2010).
    [conference website | pdf | ...]


  3. Y. Lu, R. Rosenfeld, G.J. Nau and Z. Bar-Joseph,
    Cross species expression analysis of innate immune response, in Proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2009).
    [ conference website | proceedings | ... ]

  4. Y. Lu, R. Rosenfeld, I. Simon, G.J. Nau and Z. Bar-Joseph,
    A Probabilistic Generative Model for GO Enrichment Analysis, RECOMB Satellite Conference on Systems Biology, 2007.
    [ conference website ]

Book Chapters

Teaching

Press



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