Xiaohui Xie, Ph.D.

Broad Institute of MIT and Harvard
7 Cambridge Center
Cambridge, MA 02142
Phone: 1-617-452-4134
Email: xhx@broad.mit.edu

Update: I have moved to University of California at Irvine. Here is my new website: http://www.ics.uci.edu/~xhx


Research Interests

Computational Biology, Genomics, Neural Computation, Recurrent Neural Networks, and Machine Learning
Search for my publications at Google Scholar


Selected Publications

Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites
Xie X, Mikkelsen TS, Gnirke A, Lindblad-Toh K, Kellis M and Lander ES.
Proc Natl Acad Sci USA 104:7145-7150 (2007) (PDF)
Supplementary website     Supporting Information     News story
A family of conserved noncoding elements derived from an ancient transposable element
Xie X, Kamal M, and Lander ES.
Proc Natl Acad Sci USA 103:11659-11664 (2006) (PDF)
Supplementary website     Supporting Information     News story
A large family of ancient repeat elements in the human genome is under strong selection
Kamal M, Xie X, and Lander ES.
Proc Natl Acad Sci USA 103:2740-2745 (2006) (PDF)
Supplementary website     Supporting Information     News story
A Bivalent Chromatin Structure Marks Key Developmental Genes in Embryonic Stem Cells
Bernstein BE, Mikkelsen TS, Xie X, Kamal M et al.
Cell 125:315-26 (2006) (PDF)
Comparative sequence analysis reveals an intricate network among REST, CREB and miRNA in mediating neuronal gene expression
Wu J and Xie X*.    (*Corresponding author)
Genome Biology 7(9):R85 (2006) (Highly accessed)   (PDF)     Supplementary website
Systematic identification of human mitochondrial disease genes through integrative genomics
Calvo S, Jain M, Xie X, Chang B, Spinazzola A, Zeviani M, Carr S, and Mootha VK.
Nature Genetics, 38:576-82 (2006) (PDF)
Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals
Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha VK, Lindblad-Toh K, Lander ES, Kellis M.
Nature 2005; 434:338-45 (PDF)
Supplementary Website     Supplementary Information     News story
A molecular-properties-based approach to understanding PDZ domain proteins and PDZ ligands
Giallourakis C, Cao Z, Green T, Wachtel H, Xie X, Lopez-Illasaca M, Daly M, Rioux J, Xavier R.
Genome Resesarch 16:1056-72 (2006) (PDF)
A Mammalian Organelle Map by Protein Correlation Profiling
Foster LJ, de Hoog CL, Zhang Y, Zhang Y, Xie X, Mootha VK, and Mann M.
Cell 125:187-99 (2006) (PDF)
Learning curves for stochastic gradient descent in linear feedforward networks.
Werfel J, Xie X and Seung HS.
Neural Computation, 2005;17:2699-718 (PDF)
Genome sequence, comparative analysis and haplotype structure of the domestic dog
Lindblad-Toh K, Wade CM, et al.
Nature 438:803-19 2005 (PDF)
Disease gene discovery through integrative genomics.
Giallourakis C, Henson C, Reich M, Xie X, and Mootha VK.
Annu. Rev. Genomics Hum. Genet. 2005:22:381-406. (PDF)
Learning in neural networks by reinforcement of irregular spiking.
Xie X and Seung HS.
Phys Rev E, 2004;69:041909 (PDF)
Erralpha and Gabpa/b specify PGC-1alpha-dependent oxidative phosphorylation gene expression that is altered in diabetic muscle
Mootha VK, Handschin C, Arlow D, Xie X, St Pierre J et al.
Proc Natl Acad Sci USA, 2004;101:6570-5 (PDF)
The double-ring network modeling of the head-direction system
Xie X, Hahnloser RH, and Seung HS.
Physical Review E, 2002;66:041902 (PDF)
Nonlinear dynamics of direction-selective recurrent neural media
Xie X and Giese MA.
Physical Review E, 2002;65:051904 (PDF)
Exact solution of the nonlinear dynamics of recurrent neural mechanisms for direction selectivity
Giese MA Xie X,
Neurocomputing 2002;44:417-422 (PDF)
Learning winner-take-all competition between groups of neurons in lateral inhibitory networks
Xie X, Hahnloser HR, and Seung HS.
Advances in Neural Information Processing Systems 2001;13:350-356 (PDF)
Generating velocity tuning by asymmetric recurrent connections
Xie X and Giese MA.
Advances in Neural Information Processing Systems 2002;13:325-332 (PDF)
Selectively Grouping Neurons in Recurrent Networks of Lateral Inhibition
Xie X, Hahnloser RH, and Seung HS.
Neural Computation, 2002;14:2627-2646 (PDF)
Equivalence of backpropagation and contrastive Hebbian learning in a layered network
Xie X and Seung HS.
Neural Computation, 2003;16:441-454 (PDF)
Threshold behavior of maximum likelihood method in population decoding
Xie X.
Network: Comput. Neural Syst. 2002;13:447-456 (PDF)
Spike-based learning rules and stabilization of persistent neural activity
Xie X and Seung HS.
Advances in Neural Information Processing Systems 2000;12:199-205 (PDF)