Publications

Bioinformatics Neural Networks Machine Learning
Incorporating existing network information into gene network inference
Christley S, Nie Q and Xie X
PLoS ONE 4(8): e6799. doi:10.1371/journal.pone.0006799 (2009)

Genome-wide analysis of SREBP-1 binding in mouse liver chromatin reveals a preference for promoter proximal binding to a new motif
Seo YK, Chong HK, Infante AM, Im S, Xie X, and Osborne TF
Proc Natl Acad Sci USA doi:10.1073/pnas.0904246106 (2009)
Identifying novel constrained elements by exploiting biased substitution patterns
Garber M, Guttman1 M, Clamp M, Zody MG, Friedman N, and Xie X
Bioinformatics 25:i54-i62 (2009)
Supplementary Methods
SiPhy (SIte-specific PHYlogenetic analysis) Java software package


Comparative genomics allows the discovery of cis-regulatory elements in mosquitoes
Sieglaff DH, Dunn WA, Xie X, Megy K, Marinotti O, and James AA
Proc Natl Acad Sci USA doi:10.1073/pnas.0813264106 (2009)
PDF

Common polymorphic transcript variation in human disease
Fraser H and Xie X
Genome Research doi:10.1101/gr.083477.108 (2009)
PDF

MotifMap: a human genome-wide map of candidate regulatory motif sites
Xie X, Rigor P, and Baldi P
Bioinformatics 25: 167-174 (2009)
PDF Supplementary Methods
MotifMap Server

Human genomes as email attachments
Christley S, Lu Y, Li C, and Xie X
Bioinformatics 25: 274-275 (2009)
DNAzip: DNA sequence compression using a reference genome
PDF
News featured in genomeweb

Discovering regulatory motifs in the Plasmodium genome using comparative genomics
Wu J, Sieglaff DH, Gervin J, and Xie X
Bioinformatics 24:1843-9 (2008)
MDOS software: A method for Motif Discovery using Orthologous Sequences (alignment independent).
Supplementary Information on the MDOS algorithm

Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains
Ku M, Koche RP, Rheinbay E, Mendenhall EM, Endoh M, Mikkelsen TS, Presser A, Nusbaum C, Xie X, Chi AS, Adli M, Kasif S, Ptaszek LM, Cowan CA, Lander ES, Koseki H, Bernstein BE
PLoS Genetics 4(10):e1000242 (2008)


Distinguishing protein-coding and noncoding genes in the human genome
Clamp M, Fry B, Kamal M, Xie X, Cuff J, Lin MF, Kellis M, Lindblad-Toh K, and Lander ES.
Proc Natl Acad Sci USA 104(49):19428-33 (2007)


Genome-wide detection and characterization of positive selection in human populations
Sabeti PC, Varilly P, Fry B, Lohmueller J, Hostetter E, Cotsapas C, Xie X, Byrne EH, McCarroll SA, Gaudet R, Schaffner SF, Lander ES and International HapMap Consortium
Nature 449:913-918 (2007)
Geome-wide maps of chromatin state in pluripotent and lineage-committed cells
Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim TK, Koche RP, Lee W, Mendenhall E, O'Donovan A, Presser A, Russ C, Xie X, Meissner A, Wernig M, Jaenisch R, Nusbaum C, Lander ES, Bernstein BE.
Nature 448:553-60 (2007)
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)
Supplementary website     Supporting Information     News story
Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences
Mikkelsen TS, Wakefield MJ, et al.
Nature 447:167-177 (2007)
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)
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)
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)
Comparative sequence analysis reveals an intricate network among REST, CREB and miRNA in mediating neuronal gene expression
Wu J and Xie X
Genome Biology 7(9):R85 (2006) (Highly accessed)
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)
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
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)
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)
Learning curves for stochastic gradient descent in linear feedforward networks.
Werfel J, Xie X and Seung HS.
Neural Computation, 2005;17:2699-718
Genome sequence, comparative analysis and haplotype structure of the domestic dog
Lindblad-Toh K, Wade CM, et al.
Nature 438:803-19 2005
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.
Learning in neural networks by reinforcement of irregular spiking.
Xie X and Seung HS.
Phys Rev E, 2004;69:041909
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
The double-ring network modeling of the head-direction system
Xie X, Hahnloser RH, and Seung HS.
Physical Review E, 2002;66:041902
Nonlinear dynamics of direction-selective recurrent neural media
Xie X and Giese MA.
Physical Review E, 2002;65:051904
Exact solution of the nonlinear dynamics of recurrent neural mechanisms for direction selectivity
Giese MA and Xie X
Neurocomputing 2002;44:417-422
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
Generating velocity tuning by asymmetric recurrent connections
Xie X and Giese MA.
Advances in Neural Information Processing Systems 2002;13:325-332
Selectively Grouping Neurons in Recurrent Networks of Lateral Inhibition
Xie X, Hahnloser RH, and Seung HS.
Neural Computation, 2002;14:2627-2646
Equivalence of backpropagation and contrastive Hebbian learning in a layered network
Xie X and Seung HS.
Neural Computation, 2003;16:441-454
Threshold behavior of maximum likelihood method in population decoding
Xie X
Network: Comput. Neural Syst. 2002;13:447-456
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