Publications

2017

HLA class I binding prediction via convolutional neural networks
Vang YS and Xie X
Bioinformatics, 2017

Foxh1 Occupies cis-Regulatory Modules Prior to Dynamic Transcription Factor Interactions Controlling the Mesendoderm Gene Program
Charney RM, Forouzmand E, Cho JS, Cheung J, Paraiso KD, Yasuoka Y, Takahashi S, Taira M, Blitz IL, Xie X, Cho KW
Dev Cell. 27;40(6):595-607.e4, 2017

2016

Deep Multi-instance Networks with Sparse Label Assignment for Whole Mammogram Classification
Wentao Zhu, Qi Lou, Yeeleng Scott Vang, Xiaohui Xie
arXiv:1612.05968

Adversarial Deep Structural Networks for Mammographic Mass Segmentation
Wentao Zhu, Xiaohui Xie
arXiv:1612.05970

Developmentally regulated long non-coding RNAs in Xenopus tropicalis
Forouzmand et al.
Developmental Biology, (16)30120-8 2016

Gene expression inference with deep learning
Chen Y, Li Y, Narayan R, Subramanian A, and Xie X
Bioinformatics, 2016

DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences
Quang D and Xie X
Nucleic Acids Research, 2016

Poly(A) code analyses reveal key determinants for tissue-specific mRNA alternative polyadenylation
Weng L, Li Y, Xie X, and Shi Y
RNA, 2016

Co-occurrence Feature Learning for Skeleton based Action Recognition using Regularized Deep LSTM Networks
Zhu W, et al.
AAAI Conference on Artificial Intelligence, 2016

2015

Hobbes3: Dynamic Generation of Variable-Length Signatures for Efficient Approximate Subsequence Mappings
Kim J, Chen L, and Xie X
32nd IEEE International Conference on Data Engineering - ICDE 2016

DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences
Quang D and Xie X

DANN: a deep learning approach for annotating the pathogenicity of genetic variants
Quang D, Chen Y and Xie X
Bioinformatics, 31(5):761-3, 2015

MixClone: a mixture model for inferring tumor subclonal populations
Li Y and Xie X
BMC Genomics, 2015

Identifying unanticipated genes and mechanisms in serious mental illness: GWAS based imaging genetics strategies
Potkin SG, van Erp TGM, Ling S, Macciardi F, and Xie X
Neuroimaging genetics : principles and practices, 2015

2014

Handwritten Hangul recognition using deep convolutional neural networks
Kim I and Xie X
International Journal on Document Analysis and Recognition, 2014
preprint

Genome-wide view of TGFbeta/Foxh1 regulation of the early mesendoderm program
Chiu WT, Le R, Blitz IL, Fish MB, Li Y, Biesinger J, Xie X, and Cho K
Development, 2014

Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity
Li Y and Xie X
Bioinformatics, 2014

EXTREME: An Online EM Algorithm for Motif Discovery
Quang D and Xie X
Bioinformatics, 2014

Improving Read Mapping Using Additional Prefix Grams
Kim J, Li C and Xie X
BMC Bioinformatics, 2014, 15(1):42

Integrative ChIP-seq/Microarray Analysis Identifies a CTNNB1 Target Signature Enriched in Intestinal Stem Cells and Colon Cancer
Watanabe K, Biesinger J, Salmans ML, Roberts BS, Arthur WT, Cleary M, Andersen B, Xie X, and Dai X
PLOS ONE, 2014, DOI: 10.1371/journal.pone.0092317

Inference of the Xenopus tropicalis embryonic regulatory network and spatial gene expression patterns
Zheng Z, Christley S, Chiu WT, Blitz IL, Xie X, Cho KW, Nie Q
BMC Systems Biology 2014, 8:3

Fip1 regulates mRNA alternative polyadenylation to promote stem cell self-renewal
Lackford B, Yao C, Charles GM, Weng L, Zheng X, Choi EA, Xie X, Wan J, Xing Y, Freudenberg JM, Yang P, Jothi R, Hu G, Shi Y
EMBO J. 2014 Mar 4.

2013

Low-Rank Regularization for Learning Gene Expression Programs
Ye G, Tang M, Nie Q and Xie X
PLOS ONE, 2013

A gradient boosting algorithm for survival analysis via direct optimization of concordance index
Chen Y, Jia Z, Mercola D and Xie X
Comput Math Methods Med., 2013

Biallelic genome modification in F0 Xenopus tropicalis embryos using the CRISPR/Cas system
Blitz I, Biesinger J, Xie X, and Cho K
Genesis, 2013.

Overlapping and distinct functions of CstF64 and CstF64t in mammalian mRNA 3′ processing
Yao C, Choi E, Weng L, Xie X, Wan J, Xing Y, Moresco JJ, Tu PG, Yates JR, and Shi Y
RNA, 2013

Inference in Kingman's Coalescent with Particle Markov Chain Monte Carlo Method
Chen Y and Xie X
arXiv, 2013

Discovering and Mapping Chromatin States Using a Tree Hidden Markov Model
Biesinger J, Wang Y, and Xie X
BMC Bioinformatics 2013, 14(S5):S4, 2013
Supplemental Information

A mixture model for expression deconvolution from RNA-seq in heterogeneous tissues
Li Y and Xie X
BMC Bioinformatics 2013, 14(Suppl 5):S11, 2013

Efficient direct search on compressed genomic data
Yang X, Wang B, Li C, Wang J, and Xie X
IEEE International Conference on Data Engineering (ICDE), 2013

2012

Learning sparse gradients for variable selection and dimension reduction
Ye G and Xie X
Machine Learning Journal, 87(3):303-355, 2012
Preprint

Transcriptome-wide analyses of CstF64-RNA interactions in global regulation of mRNA alternative polyadenylation
Yao C, Biesinger J,Wan J,Weng L, Busch A, Xing Y, Xie X, and Shi Y
PNAS, 109(46):18773-8, 2012

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

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, 40(6):e41, 2012
Software: Hobbes

2011

Efficient latent variable graphical model selection via split Bregman method
Ye G, Wang Y, Chen Y, and Xie X
arXiv:1110.3076v1, 2011

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

A high-resolution map of human evolutionary constraint using 29 mammals
Lindblad-Toh, Barber, Zuk, Lin, et al.
Nature, 2011

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)

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

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

Efficient variable selection in support vector machines via the alternating direction method of multipliers
Ye G, Chen Y, and Xie X
AI & STATS , 2011

2010

Split Bregman method for sparse inverse covariance estimation with matrix iteration acceleration
Ye G, Cai J, and Xie X
arXiv:1012.0975v1, 2010

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 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

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

Variable selection and dimension reduction via sparse gradients
Ye G-B and Xie X
arXiv:1006.5060v2, 2010

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

Parameter inference for discretely observed stochastic kinetic models using stochastic gradient descent
Wang Y, Christley S, Mjolsness E, and Xie X
BMC Systems Biology, 4:99 doi:10.1186/1752-0509-4-99, 2010

Site-frequency Spectrum of Linked Sites
Xie X
Bulletin of Mathematical Biology, DOI: 10.1007/s11538-010-9534-3, 2010

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

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

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

2009

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
Bioinformatics25: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)

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)
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
News featured in bio-itworld
One of the 20 most important papers in Translational Bioinformatics in 2009as reviewed by Russ Altman of Stanford

2008

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 Genetics4(10):e1000242 (2008)

2007

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 USA104(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
Nature449:913-918 (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 USA104:7145-7150 (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 USA103:11659-11664 (2006)
Supplementary website Supporting Information News story

2006 or before

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 USA103:2740-2745 (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 Biology7(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.
Nature2005; 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 Systems2001;13:350-356

Generating velocity tuning by asymmetric recurrent connections
Xie X and Giese MA.
Advances in Neural Information Processing Systems2002;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

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