44.  Wang G, Wang Y, Shen C, Huang Y, Huang K, Huang T H-M, Nephew KP, Li L, Liu Y, RNA Polymerase II binding patterns reveal genomic regions involved in microRNA gene regulation, Plos One, in press

43.  Jiang, Q., Hao, Y., Wang, G., Juan, L., Zhang, T., Teng, M., Liu, Y., Wang, Y. Prioritization of disease microRNAs through a human phenome-microRNAome network. BMC Syst Biol 2010;4 Suppl 1:S2

42.  Alam, I., Carr, LG., Liang, T., Liu, Y., Edenberg, HJ., Econs, MJ., Turner, CH. Identification of genes influencing skeletal phenotypes in congenic P/NP rats. Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research 2010 Jan 8:

41.  Di Leva, G., Gasparini, P., Piovan, C., Ngankeu, A., Garofalo, M., Taccioli, C., Iorio, MV., Li, M., Volinia, S., Alder, H., Nakamura, T., Nuovo, G., Liu, Y., Nephew, KP., Croce, CM. MicroRNA Cluster 221-222 and Estrogen Receptor {alpha} Interactions in Breast Cancer. Journal of the National Cancer Institute 2010 Apr 13:

40.  Cheng, BH., Liu, Y., Xuei, X., Liao, CP., Lu, D., Lasbury, ME., Durant, PJ., Lee, CH. Microarray studies on effects of Pneumocystis carinii infection on global gene expression in alveolar macrophages. BMC microbiology 2010 Apr 8;10(1):103

39.  Wang, G., Wang, Y., Teng, M., Zhang, D., Li, L., Liu, Y. Signal transducers and activators of transcription-1 (STAT1) regulates microRNA transcription in interferon gamma-stimulated HeLa cells. PLoS ONE 2010;5(7):e11794

38.  Wang, G., Wang, Y., Teng, M., Zhang, D., Li, L., Liu, Y. Signal transducers and activators of transcription-1 (STAT1) regulates microRNA transcription in interferon gamma-stimulated HeLa cells. PLoS ONE 2010;5(7):e11794

37.  Mantila Roosa, SM., Liu, Y., Turner, CH. Gene expression patterns in bone following mechanical loading. Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research 2010 Jul 23:

36.  Jiang, Q., Wang, Y., Hao, Y., Juan, L., Teng, M., Zhang, X., Li, M., Wang, G., Liu, Y. miR2Disease: a manually curated database for microRNA deregulation in human disease. Nucleic Acids Res. 2009 Jan;37(Database issue):D98-104

35.  Sanford, JR., Wang, X., Mort, M., Vanduyn, N., Cooper, DN., Mooney, SD., Edenberg, HJ., Liu, Y. Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts. Genome Res. 2009 Mar;19(3):381-94

34.  Xin, F., Li, M., Balch, C., Thomson, M., Fan, M., Liu, Y., Hammond, SM., Kim, S., Nephew, KP. Computational analysis of microRNA profiles and their target genes suggests significant involvement in breast cancer antiestrogen resistance. Bioinformatics 2009 Feb 15;25(4):430-4

33.  Wang X., Teng M., Wang G., Zhao Y., Feng W., Li L., Sanford J.R., and Liu Y., xIP-seq platform: an integrative framework for high-throughput sequencing data analysis, the Ohio Collaborative Conference on Bioinformatics (OCCBIO), Cleveland, OH, 2009, June 15

32.  Bhat-Nakshatri, P., Wang, G., Collins, NR., Thomson, MJ., Geistlinger, TR., Carroll, JS., Brown, M., Hammond, S., Srour, EF., Liu, Y., Nakshatri, H. Estradiol-regulated microRNAs control estradiol response in breast cancer cells. Nucleic Acids Res. 2009 Aug;37(14):4850-61

31.  He, B., Wang, K., Liu, Y., Xue, B., Uversky, VN., Dunker, AK. Predicting intrinsic disorder in proteins: an overview. Cell Res. 2009 Aug;19(8):929-49

30.  Wang, X., Wang, K., Radovich, M., Wang, Y., Wang, G., Feng, W., Sanford, JR., Liu, Y. Genome-wide prediction of cis-acting RNA elements regulating tissue-specific pre-mRNA alternative splicing. BMC Genomics 2009;10 Suppl 1:S4

29.  Wang, Y., Wang, G., Yang, B., Tao, H., Yang, JY., Deng, Y., Liu, Y. Reconstruct gene regulatory network using slice pattern model. BMC Genomics 2009;10 Suppl 1:S2

28.  Edenberg H.J. and Liu Y., Methods for high throughput analysis, Genetics of Complex Human Diseases, Editors: Ammar Al-Chalabi and Laura Almasy, Publisher: Cold Spring Harbor Press (book chapter)

27.  Camerlengo T., Ozer H.G., Teng M., Perez F., Yang P., Li L., Parvin J., Huang T., Kurc T., Liu Y., Huang K., Enabling Data Analysis on High-throughput Data in Large Data Depository Using Web-based Analysis Platform – A Case Study on Integrating QUEST with GenePattern in Epigenetics Research. Proceedings of IEEE International Conference on Bioinformatics & Biomedicine (BIBM'09), Washington DC, Nov. 2009.

26.  Alam, I., Sun, Q., Koller, DL., Liu, L., Liu, Y., Edenberg, HJ., Foroud, T., Turner, CH. Genes influencing spinal bone mineral density in inbred F344, LEW, COP, and DA rats. Functional & integrative genomics 2009 Oct 15:

25.  Edenberg, HJ., Liu, Y. Laboratory methods for high-throughput genotyping. CSH Protoc 2009 Nov;2009(11):pdb.top62

24.  Liu, Y., Balaraman, Y., Wang, G., Nephew, KP., Zhou, FC. Alcohol exposure alters DNA methylation profiles in mouse embryos at early neurulation. Epigenetics 2009 Oct;4(7):500-11

23.  Wang, X., Wang, G., Shen, C., Li, L., Edenberg, H.J., Sanford, J., Liu, Y., Refining Detection of Protein Binding Regions Using Pyrosequencing-derived RNA Fragments, BMC Genomics, 9 (S1):S17 (2008)

22.  Wang, G., Wang, X., Li, L., Nephew, N.P., Edenberg, H.J., Zhou, F.C., Liu, Y. Identification of Transcription Factor and microRNA Binding Sites from Array-derived Gene Expression Data, BMC Genomics, 9 (S1):S19 (2008)

21.  Hamamura K., Liu Y., and Yokota H. Microarray Analysis of Thapsigargin-Induced Stress to Endoplasmic Reticulum of Mouse Osteoblasts, Journal of Bone and Mineral Metabolism, 2008;26(3):231-40. Epub 2008 May 11.

20.  Feng, W.*, Liu, Y.*, Wu, J., Nephew, K.P., Huang, T.H., and Li, L., A Poisson mixture model to identify changes in RNA polymerase II binding quantity using high-throughput sequencing technology, BMC Genomics 2008, 9(S2):S23. * co-first author

19.  Wang, G., Wang, Y., Feng, W., Wang, X., Yang, J.Y., Zhao, Y, Wang, Y., Liu, Y., Transcription factor and microRNA regulation in androgen-dependent and -independent prostate cancer cells, BMC Genomics 2008, 9(S2):S22

18.  Wang X., Wang K., Wang G., Sanford, J.R., Liu Y., Model-based prediction of cis-acting RNA elements regulating tissue-specifc alternative splicing, 8th IEEE International Conference on BioInformatics and BioEngineering, Athens, Greece, October 2008.

17.  Alam I, Sun Q, Liu L, Koller DL, Liu Y, Edenberg HJ, Econs MJ, Foroud T, Turner CH., Genomic expression analysis of rat chromosome 4 for skeletal traits at femoral neck, Physiol Genomics. 2008 Aug 26.

16.  Bhat-Nakshatri, P., Wang, G., Appaiah, H., Luktuke, N., Carroll, JS., Geistlinger, TR., Brown, M., Badve, S., Liu, Y., Nakshatri, H. AKT alters genome-wide estrogen receptor alpha binding and impacts estrogen signaling in breast cancer. Mol. Cell. Biol. 2008 Dec;28(24):7487-503

15.  Zhang, P., Su, M., Liu, Y., Hsu, A. and Yokota, H. Knee Loading Dynamically Alters Intramedullary Pressure in Mouse Femora. Bone 40(2):538-43 (2007).

14.  Liu, Y., Computational Genome Analysis: an Introduction (book review), Briefings in Bioinformatics, doi:10.1093/bib/bbm020

13.  Chen, A., Hamamura, K., Wang, G., Xing, W., Mohan, S., Yokota, H, and Liu, Y., Model-Based Comparative Prediction of Transcription-Factor Binding Motifs in Anabolic Responses in Bone, Genomics, Proteomics and Bioinformatics, Aug-Nov 5 (3-4), 158-65 (2007).

12.  McClintick, J.N.*, Liu, Y.*, Edenberg, H.J., Mapping of trans-acting regulatory factors from microarray data, BMC Genetics, BMC Proceedings 2007, 1 (Suppl 1):S155 (18 December 2007). *co-first author.

11.  Liu, Y. & Yokota, H. Artificial Ants Deposit Pheromone to Search for Regulatory DNA Elements. BMC Genomics, Aug 30;7:221 (2006)

10.  Su, M., Jiang, H., Zhang, P., Liu, Y., Tanaka, S., and Yokota, H. Load-Driven Molecular Transport Using FRAP, Annals of Biomedical Engineering, Oct;34(10):1600-1606. (2006).

9.  Liu, Y. & Edenberg, H. Identification and Evaluation of Transcription Factor Binding Sites Responsive to PEG-IFN-alpha in PBMC in vitro. Genomics 2006, 88: 452-461.

8.  Liu, Y., Vincenti, M. P. & Yokota, H. Principal Component Analysis for Predicting Transcription-Factor Binding Motifs from Array-Derived Data. BMC Bioinformatics 2005, 6:276.

7.  Liu, Y. and Yokota, H. Modeling Transcriptional Regulation in Chondrogenesis Using Particle Swarm Optimization. 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology 311-317, San Diego, CA (2005).

6.  Liu, Y. & Yokota, H. Modeling of Dynamic Transcriptional Regulation in Human Chondrogenesis. Systems Biology 1, 85-92 (2004).

5.  Sun, I., Liu, Y., Tanaka, S., Sun, H. & Yokota, H. Biochemical Aspects of High-Impact Exercises in Joint Degradation. Journal of Sports Sci. and Med 3, 37-43 (2004).

4.  Liu, Y., Sun, H. B. & Yokota, H. Regulating Gene Expression Using Optimal Control Theory. Third IEEE Symposium Bioinformatics and Bioengineering 313 -318, Bethesda, MD (2003).

3.  Sun, H. B., Liu, Y., Qian, L. & Yokota, H. Model-based analysis of matrix metalloproteinase expression under mechanical shear. Ann Biomed Eng 31, 171-80 (2003).

2.  Qian, L., Liu, Y., Sun, H. B. & Yokota, H. Systems analysis of matrix metalloproteinase mRNA expression in skeletal tissues. Front Biosci 7, a126-34 (2002).

1.  Du, X. & Liu, Y. Network Management for Enterprise Intranet, Journal of Automation (1999).