Genome-wide analysis of hepatic LRH-1 reveals a promoter binding preference and suggests a role in regulating genes of lipid metabolism in concert with FXR
Kim Chong H, Biesinger J, Seo YK, Xie X, Osborne TF
BMC Genomics, 2012
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Hobbes: optimized gram-based methods for efficient read alignment
Ahmadi A, Behm A, Honnalli N, Li C, Weng L, and Xie X
Nucleic Acids Research, 2011
Software: Hobbes
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Efficient latent variable graphical model selection via split Bregman method
Ye G, Wang Y, Chen Y, and Xie X
arXiv:1110.3076v1, 2011
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MotifMap: integrative genome-wide maps of regulatory motif sites for model species.
Daily K, Patel VR, Rigor P, Xie X, Baldi P.
BMC Bioinformatics, 2011
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A high-resolution map of human evolutionary constraint using 29
mammals
Lindblad-Toh, Barber, Zuk, Lin, et al.
Nature, 2011
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SNP-based pathway
enrichment analysis for genome-wide association studies
Weng L, Macciardi F, Subramanian A, Guffanti G, Potkin SG, Yu Z, and
Xie X
BMC Bioinformatics, 2011
Software: SNP Set Enrichment Analysis (SSEA)
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Genome-wide Positioning of SREBP-2 in Hepatic Chromatin Predicts a
Novel Role in Autophagy
Seo Y, Jeon T , Chong H, Beisinger J, Xie X, and Osborne TF
Cell Metabolism, 13:367-75, 2011
Science
Daily coverage
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AREM: aligning short reads from ChIP-sequencing by expectation
maximization
Newkirk D, Biesinger, J, Chon A, Yokomori K, and Xie X
J Comput Biol., 2011
Software: AREM
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Querying large similar sequences in a compressed format efficiently
Yang X, Wang B, Li C, and Xie X
Submitted, 2011
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Efficient variable selection in support vector machines via the
alternating direction method of multipliers
Ye G, Chen Y, and Xie X
AI & STATS , 2011
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Split
Bregman method for sparse inverse covariance estimation with matrix
iteration acceleration
Ye G, Cai J, and Xie X
arXiv:1012.0975v1, 2010
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Split Bregman method for
large scale fused Lasso
Ye G-B and Xie X
Computational Statistics and Data Analysis,
doi:10.1016/j.csda.2010.10.021, 2010
arXiv version
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Data Structures and Compression Algorithms for High-Throughput Sequencing Technologies
Daily K, Rigor P, Christley S, Xie X and Baldi P
BMC Bioinformatics,11:514, 2010
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Interactive and fuzzy search: a dynamic way to explore MEDLINE
Wang J, Cetindil I, Ji S, Li C*, Xie X*, Li G and Feng J
Bioinformatics, 26(18):2321-2327, 2010
iPubMed Search
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Variable selection and dimension reduction via sparse gradients
Ye G-B and Xie X
arXiv:1006.5060v2, 2010
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Identifying gene regulatory networks in Schizophrenia
Potkin SG, Macciardi F, Guffanti G, Wang Q,
Turner JA, Lakatos A, Miles MF, Lander A, Vawter MP, Xie X
NeuroImage 53:839-847, 2010
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Parameter inference for discretely observed stochastic kinetic models
using stochastic gradient descent
Wang Y, Christley S, Mjolsness E, and Xie X
BMC Systems Biology, 4:99doi:10.1186/1752-0509-4-99, 2010
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Site-frequency Spectrum of Linked Sites
Xie X
Bulletin of Mathematical Biology, DOI: 10.1007/s11538-010-9534-3, 2010
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Genome-Wide Interrogation of Hepatic FXR Reveals an Asymmetric IR-1
Motif and Synergy with LRH-1
Chong H, Infante A, Seo Y, Jeon T, Ahang Y, Edwards P, Xie X, and
Osborne TF
Nucleic Acids Research, doi:10.1093/nar/gkq397, 2010
Online Supplementary Materials
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Systematic discovery of regulatory motifs in Fusarium graminearum by
comparing four Fusarium genomes
Kumar L, Breakspear A, Kistler HC, Ma L-J, and Xie X
BMC Genomics 11:208, 2010
Supplementary Information
Fusarium Comparative Database
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Comparative genomics reveals mobile pathogenicity chromosomes in
Fusarium oxysporum
Ma L-J, et al.
Nature 464:367-373, 2010
The chromosomal
secrets of a plant pathogen
Comparative
genomics reveals horizontal gene transfer in pathogenic
fungus
Fusarium Comparative Database
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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)
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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)
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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
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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
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Common polymorphic transcript variation in human disease
Fraser H and Xie X
Genome Research doi:10.1101/gr.083477.108 (2009)
PDF
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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
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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
News featured in bio-itworld
One of the 20 most important papers in Translational
Bioinformatics in 2009 as reviewed by Russ Altman of Stanford
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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
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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)
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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)
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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)
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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)
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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
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Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences
Mikkelsen TS, Wakefield MJ, et al.
Nature 447:167-177 (2007)
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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
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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
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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)
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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
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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)
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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
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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)
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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)
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Learning curves for stochastic gradient descent in linear feedforward networks.
Werfel J, Xie X and Seung HS.
Neural Computation, 2005;17:2699-718
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Genome sequence, comparative analysis and haplotype structure of the
domestic dog
Lindblad-Toh K, Wade CM, et al.
Nature 438:803-19 2005
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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.
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Learning in neural networks by reinforcement of irregular spiking.
Xie X and Seung HS.
Phys Rev E, 2004;69:041909
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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
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The double-ring network modeling of the head-direction system
Xie X, Hahnloser RH, and Seung HS.
Physical Review E, 2002;66:041902
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Nonlinear dynamics of direction-selective recurrent neural media
Xie X and Giese MA.
Physical Review E, 2002;65:051904
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Exact solution of the nonlinear dynamics of recurrent neural mechanisms for direction selectivity
Giese MA and Xie X
Neurocomputing 2002;44:417-422
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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
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Generating velocity tuning by asymmetric recurrent connections
Xie X and Giese MA.
Advances in Neural Information Processing Systems 2002;13:325-332
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Selectively Grouping Neurons in Recurrent Networks of Lateral Inhibition
Xie X, Hahnloser RH, and Seung HS.
Neural Computation, 2002;14:2627-2646
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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
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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
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