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
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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, 2011
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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
RECOMB, 2011
Software: AREM
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Storing and querying large similar sequences efficiently
Yang et al.
Submitted, 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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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 XS
Bioinformatics doi:10.1093/bioinformatics/btn348 (2008)
MDOS software: A method for Motif Discovery using Orthologous Sequences
(alignment independent).
Supplementary Information on the MDOS algorithm
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Genome-wide detection and characterization of positive
selection in human populations
Sabeti, Varilly, Fry, Lohmueller, Hostetter, Sotsapos, Xie, Byrne,
et al.
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, et al.
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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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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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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