Here is a link to my Google Scholar page.

Journal Articles

  1. Topological properties of robust biological and computational networks.
    Navlakha S, He X, Faloutsos C, Bar-Joseph Z.
    J R Soc Interface, 2014 Apr 30;11(96) (Science Daily)

  2. DAWN: a framework to identify autism genes and subnetworks using gene expression and genetics.
    Liu L, Lei J, Sanders SJ, Willsey AJ, Kou Y, Cicek AE, Klei L, Lu C, He X, Li M, Muhle RA, Ma'ayan A, Noonan JP, Sestan N, McFadden KA, State MW, Buxbaum JD, Devlin B, Roeder K.
    Mol Autism, 2014 Mar 6;5(1):22.

  3. Coexpression networks implicate human midfetal deep cortical projection neurons in the pathogenesis of autism.
    Willsey AJ, Sanders SJ, Li M, Dong S, Tebbenkamp AT, Muhle RA, Reilly SK, Lin L, Fertuzinhos S, Miller JA, Murtha MT, Bichsel C, Niu W, Cotney J, Ercan-Sencicek AG, Gockley J, Gupta AR, Han W, He X, Hoffman EJ, Klei L, Lei J, Liu W, Liu L, Lu C, Xu X, Zhu Y, Mane SM, Lein ES, Wei L, Noonan JP, Roeder K, Devlin B, Sestan N, State MW.
    Cell, 2013 Nov 21;155(5):997-1007

  4. Predicting tissue specific transcription factor binding sites.
    Zhong S*, He X*, Bar-Joseph Z.
    BMC Genomics, 2013 Nov 15;14(1):796 (Highly accessed)

  5. Integrated model of de novo and inherited genetic variants yields greater power to identify risk genes.
    He X, Sanders SJ, Liu L, De Rubeis S, Lim ET, Sutcliffe JS, Schellenberg GD, Gibbs RA, Daly MJ, Buxbaum JD, State MW, Devlin B, Roeder K.
    PLoS Genetics, 2013 Aug;9(8):e1003671
    Reported by SFARI News (Simons Foundation Autism Research Initiative).
    Recommended by Faculty of 1000 Genomics & Genetics.

  6. Sherlock: Detecting Gene-Disease Associations by Matching Patterns of Expression QTL and GWAS.
    He X, Fuller CK, Song Y, Meng Q, Zhang B, Yang X, Li H.
    Am J Hum Genet, 2013 May 2;92(5):667-80
    Featured by Am. J Hum. Genet. and Genetics.

  7. Evolutionary Origins of Transcription Factor Binding Site Clusters.
    He X, Duque TS, Sinha S
    Mol Biol Evol, 2012, 29(3):1059-70

  8. Towards an evolutionary model of transcription networks
    Xie D*, Chen CC*, He X, Cao X, Zhong S
    PLoS Comput Biol, 2011 Jun;7(6):e1002064

  9. BeeSpace Navigator: exploratory analysis of gene function using semantic indexing of biological literature
    Sen Sarma M, Arcoleo D, Khetani RS, Chee B, Ling X, He X, Jiang J, Mei Q, Zhai C, Schatz B
    Nucleic Acids Res, 2011 Jul;39 W462-9

  10. Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression
    He X, Samee MA, Blatti C, Sinha S.
    PLoS Comput Biol, 2010 Sep 16;6(9). pii: e1000935

  11. BSQA: integrated text mining using entity relation semantics extracted from biological literature of insects
    He X, Li Y, Khetani R, Sanders B, Lu Y, Ling X, Zhai C, Schatz B.
    Nucleic Acids Res, 2010 Jul 1;38 W175-81.

  12. Identifying overrepresented concepts in gene lists from literature: a statistical approach based on Poisson mixture model
    He X, Sarma MS, Ling X, Chee B, Zhai C, Schatz B.
    BMC Bioinformatics, 2010 May 20;11:272.

  13. ChIPs and regulatory bits (invited News and Views article)
    He X, Sinha S.
    Nat Biotechnol, 2010 Feb;28(2):142-3

  14. A biophysical model for analysis of transcription factor interaction and binding site arrangement from genome-wide binding data
    He X, Chen CC, Hong F, Fang F, Sinha S, Ng HH, Zhong S.
    PLoS One 2009 Dec 1;4(12):e8155. (accepted by RECOMB Regulatory Genomics)

  15. Detecting gene clusters under evolutionary constraint in a large number of genomes
    Ling X, He X, Xin D.
    Bioinformatics, 2009 Mar 1;25(5):571-7

  16. Alignment and prediction of regulatory sequences based on a probabilistic model of evolution
    He X, Ling X, Sinha S.
    PLoS Comput Biol, 2009 Mar;5(3):e1000299

  17. Evolution of regulatory sequences in 12 Drosophila species
    Kim J*, He X*, Sinha S (*Equal contribution).
    PLoS Genet, 2009 Jan;5(1):e1000330

  18. Efficiently identifying max-gap clusters in pairwise genome comparison
    Ling X, He X, Xin D, Han J.
    J Comput Biol, 2008 Jul-Aug;15(6):593-609.

  19. MORPH: probabilistic alignment combined with hidden Markov models of cis-regulatory modules
    Sinha S, He X
    PLoS Comput Biol, 2007 Nov;3(11):e216

  20. Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses
    Li L, Zhu Q, He X, Sinha S, Halfon MS.
    Genome Biol, 2007;8(6):R101 (Highly accessed)

  21. Cross-species microarray analysis with the OSCAR system suggests an INSR-Pax6-NQO1 neuro-protective pathway in aging and Alzheimer's disease
    Lu Y, He X, Zhong S.
    Nucleic Acid Research, 2007 Jul;35:W105-14

  22. Generating gene summaries from biomedical literature: a study of semi-structured summarization
    Ling X, Jiang J, He X, Mei Q, Zhai C, Schatz B
    Information Processing and Management, 43, 2007, 1777-1791

  23. Identifying conserved gene clusters in the presence of homology families
    He X, Goldwasser M.
    J Comput Biol, RECOMB Special Issue, 2005 Jul-Aug;12(6):638-56

Refereed Conference Papers

  1. Automatically generating gene summaries from biomedical literature
    Ling X, Jiang J, He X, Mei Q, Zhai C, Schatz B
    Proceedings of Pacific Symposium on Biocomputing (PSB), 2006, pages 40-51

  2. Identifying conserved gene clusters in the presence of orthologous groups
    He X, Goldwasser M
    Proceedings of the Eighth Annual International Conferences on Research in Computational Molecular Biology (RECOMB), 2004, pp. 272-280

Book Chapters

  1. Evolution of cis-regulatory sequences in Drosophila
    He X, Sinha S
    Computational Biology of Transcription Factor Binding: Methods Mol Biol. Ed: Istvan Ladunga. Humana Press, 2010