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Yunlong Liu Lab
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Publications - Yunlong Liu Lab

In Press 

79.  Zhang X., Dangaiah D., Muson RS Jr., Spinola SM, and Liu Y., Correcting imbalanced reads coverage in a bacterial transcriptome sequencing with extreme deep coverage, in press

78.  Arindom C., Jiang G., Boustani M., Skaar T., Liu Y., and Li L., Simultaneous inferences based on empirical Bayes methods and false discovery rates in eQTL data analysis, in press

2014 

77.  Radovich, M., Clare, SE., Atale, R., Pardo, I., Hancock, BA., Solzak, JP., Kassem, N., Mathieson, T., Storniolo, AM., Rufenbarger, C., Lillemoe, HA., Blosser, RJ., Choi, MR., Sauder, CA., Doxey, D., Henry, JE., Hilligoss, EE., Sakarya, O., Hyland, FC., Hickenbotham, M., Zhu, J., Glasscock, J., Badve, S., Ivan, M., Liu, Y., Sledge, GW., Schneider, BP. Characterizing the heterogeneity of triple-negative breast cancers using microdissected normal ductal epithelium and RNA-sequencing. Breast Cancer Res. Treat. 2014 Jan;143(1):57-68

76.  Gangaiah, D., Labandeira-Rey, M., Zhang, X., Fortney, KR., Ellinger, S., Zwickl, B., Baker, B., Liu, Y., Janowicz, DM., Katz, BP., Brautigam, CA., Munson, RS., Hansen, EJ., Spinola, SM. Haemophilus ducreyi Hfq contributes to virulence gene regulation as cells enter stationary phase. MBio 2014;5(1):e01081-13

2013 

75.  Todd, AG., Lin, H., Ebert, AD., Liu, Y., Androphy, EJ. COPI transport complexes bind to specific RNAs in neuronal cells. Hum. Mol. Genet. 2013 Feb 15;22(4):729-36

74.  Wang, G., Qi, K., Zhao, Y., Li, Y., Juan, L., Teng, M., Li, L., Liu, Y., Wang, Y. Identification of regulatory regions of bidirectional genes in cervical cancer. BMC Med Genomics 2013;6 Suppl 1:S5

73.  Juan, L., Wang, G., Radovich, M., Schneider, BP., Clare, SE., Wang, Y., Liu, Y. Potential roles of microRNAs in regulating long intergenic noncoding RNAs. BMC Med Genomics 2013;6 Suppl 1:S7

72.  Breese, MR., Liu, Y. NGSUtils: a software suite for analyzing and manipulating next-generation sequencing datasets. Bioinformatics 2013 Feb 15;29(4):494-6

71.  Zhao, H., Yang, Y., Lin, H., Zhang, X., Mort, M., Cooper, DN., Liu, Y., Zhou, Y. DDIG-in: discriminating between disease-associated and neutral non-frameshifting micro-indels. Genome Biol. 2013 Mar 13;14(3):R23

70.  Kelly, KJ., Liu, Y., Zhang, J., Goswami, C., Lin, H., Dominguez, JH. Comprehensive genomic profiling in diabetic nephropathy reveals the predominance of proinflammatory pathways. Physiol. Genomics 2013 Aug 15;45(16):710-9

69.  Gangaiah, D., Zhang, X., Fortney, KR., Baker, B., Liu, Y., Munson, RS., Spinola, SM. Activation of CpxRA in Haemophilus ducreyi primarily inhibits the expression of its targets, including major virulence determinants. J. Bacteriol. 2013 Aug;195(15):3486-502

68.  Jiang, G., Chakraborty, A., Wang, Z., Boustani, M., Liu, Y., Skaar, T., Li, L. New aQTL SNPs for the CYP2D6 identified by a novel mediation analysis of genome-wide SNP arrays, gene expression arrays, and CYP2D6 activity. Biomed Res Int 2013;2013:493019

67.  Hsu, PY., Hsu, HK., Lan, X., Juan, L., Yan, PS., Labanowska, J., Heerema, N., Hsiao, TH., Chiu, YC., Chen, Y., Liu, Y., Li, L., Li, R., Thompson, IM., Nephew, KP., Sharp, ZD., Kirma, NB., Jin, VX., Huang, TH. Amplification of distant estrogen response elements deregulates target genes associated with tamoxifen resistance in breast cancer. Cancer Cell 2013 Aug 12;24(2):197-212

66.  Ramamoorthy, A., Liu, Y., Philips, S., Desta, Z., Lin, H., Goswami, C., Gaedigk, A., Li, L., Flockhart, DA., Skaar, TC. Regulation of microRNA expression by rifampin in human hepatocytes. Drug Metab. Dispos. 2013 Oct;41(10):1763-8

65.  Lin, J., Welker, NC., Zhao, Z., Li, Y., Zhang, J., Reuss, SA., Zhang, X., Lee, H., Liu, Y., Bronner, MP. Novel specific microRNA biomarkers in idiopathic inflammatory bowel disease unrelated to disease activity. Mod. Pathol. 2013 Sep 20:

64.  Lin, J., Welker, NC., Zhao, Z., Li, Y., Zhang, J., Reuss, SA., Zhang, X., Lee, H., Liu, Y., Bronner, MP. Novel specific microRNA biomarkers in idiopathic inflammatory bowel disease unrelated to disease activity. Mod. Pathol. 2013 Sep 20:

2012 

63.  Teng M., Ichikawa S., Padgett L.R., Wang Y., Mort M., Cooper D.N., Koller D.L., Foroud T., Edenberg H.J., Econs M.J., and Liu Y., regSNPs: A tool for prioritizing regulatory single nucleotide substitutions, Bioinformatics, 2012 Jul 15;28(14):1879-86. Epub 2012 May 18.

62.  Direnzo, D., Hess, DA., Damsz, B., Hallet, JE., Marshall, B., Goswami, C., Liu, Y., Deering, T., Macdonald, RJ., Konieczny, SF. Induced Mist1 Expression Promotes Remodeling of Mouse Pancreatic Acinar Cells. Gastroenterology 2012 Apr 14:

61.  Teng, M., Balch, C., Liu, Y., Li, M., Huang, TH., Wang, Y., Nephew, KP., Li, L. The influence of cis-regulatory elements on DNA methylation fidelity. PLoS ONE 2012;7(3):e32928

60.  Mantila Roosa, SM., Turner, CH., Liu, Y. Regulatory mechanisms in bone following mechanical loading. Gene Regul Syst Bio 2012;6:43-53

59.  Zhang, P., Mourad, R., Xiang, Y., Huang, K., Huang, T., Nephew, K., Liu, Y., Li, L. A dynamic time order network for time-series gene expression data analysis. BMC Syst Biol 2012;6 Suppl 3:S9

58.  Teng M., Balch C., Liu Y., Li M., Huang T.H., Wang Y., Nephew K.P., Li L., The Influence of cis-Regulatory Elements on DNA Methylation Fidelity, PLoS One. 2012;7(3):e32928. Epub 2012 Mar 6. PMID: 22412954

57.  Zhou, A., Breese, MR., Hao, Y., Edenberg, HJ., Li, L., Skaar, TC., Liu, Y. Alt Event Finder: a tool for extracting alternative splicing events from RNA-seq data. BMC Genomics 2012;13 Suppl 8:S10

56.  Wu, HY., Zheng, P., Jiang, G., Liu, Y., Nephew, KP., Huang, TH., Li, L. A modulator based regulatory network for ERα signaling pathway. BMC Genomics 2012;13 Suppl 6:S6

2011 

55.  Wang, X., Juan, L., Lv, J., Wang, K., Sanford, JR., Liu, Y. Predicting sequence and structural specificities of RNA binding regions recognized by splicing factor SRSF1. BMC Genomics 2011 Dec 23;12 Suppl 5:S8

54.  Hu, Y., Liu, Y., Jung, J., Dunker, AK., Wang, Y. Changes in predicted protein disorder tendency may contribute to disease risk. BMC Genomics 2011 Dec 23;12 Suppl 5:S2

53.  Teng, M., Wang, Y., Wang, G., Jung, J., Edenberg, HJ., Sanford, JR., Liu, Y. Prioritizing single-nucleotide variations that potentially regulate alternative splicing. BMC proceedings 2011 Nov 29;5 Suppl 9:S40

52.  Jung, J., Dantzer, J., Liu, Y. Identification of multiple rare variants associated with a disease. BMC proceedings 2011 Nov 29;5 Suppl 9:S103

51.  Namkung, J., Raska, P., Kang, J., Liu, Y., Lu, Q., Zhu, X. Analysis of exome sequences with and without incorporating prior biological knowledge. Genet. Epidemiol. 2011;35 Suppl 1:S48-55

50.  Appaiah, HN., Goswami, CP., Mina, LA., Badve, S., Sledge, GW., Liu, Y., Nakshatri, H. Persistent upregulation of U6:SNORD44 small RNA ratio in the serum of breast cancer patients. Breast Cancer Res. 2011;13(5):R86

49.  Shen, C., Huang, Y., Liu, Y., Wang, G., Zhao, Y., Wang, Z., Teng, M., Wang, Y., Flockhart, DA., Skaar, TC., Yan, P., Nephew, KP., Huang, TH., Li, L. A modulated empirical Bayes model for identifying topological and temporal estrogen receptor α regulatory networks in breast cancer. BMC Syst Biol 2011;5:67

48.  Zhou, FC., Zhao, Q., Liu, Y., Goodlett, CR., Liang, T., McClintick, JN., Edenberg, HJ., Li, L. Alteration of gene expression by alcohol exposure at early neurulation. BMC Genomics 2011;12:124

47.  Zhou, FC., Balaraman, Y., Teng, M., Liu, Y., Singh, RP., Nephew, KP. Alcohol alters DNA methylation patterns and inhibits neural stem cell differentiation. Alcohol. Clin. Exp. Res. 2011 Apr;35(4):735-46

2010 

46.  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

45.  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:

44.  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:

43.  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

42.  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

41.  Yang, JY., Niemierko, A., Bajcsy, R., Xu, D., Athey, BD., Zhang, A., Ersoy, OK., Li, GZ., Borodovsky, M., Zhang, JC., Arabnia, HR., Deng, Y., Dunker, AK., Liu, Y., Ghafoor, A. 2K09 and thereafter : the coming era of integrative bioinformatics, systems biology and intelligent computing for functional genomics and personalized medicine research. BMC Genomics 2010;11 Suppl 3:I1

40.  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:

39.  Jeong, J., Li, L., Liu, Y., Nephew, KP., Huang, TH., Shen, C. An empirical Bayes model for gene expression and methylation profiles in antiestrogen resistant breast cancer. BMC Med Genomics 2010;3:55

38.  Wang, G., Wang, Y., Shen, C., Huang, YW., Huang, K., Huang, TH., Nephew, KP., Li, L., Liu, Y. RNA polymerase II binding patterns reveal genomic regions involved in microRNA gene regulation. PLoS ONE 2010;5(11):e13798

37.  Herbert, BS., Chanoux, RA., Liu, Y., Baenziger, PH., Goswami, CP., McClintick, JN., Edenberg, HJ., Pennington, RE., Lipkin, SM., Kopelovich, L. A molecular signature of normal breast epithelial and stromal cells from Li-Fraumeni syndrome mutation carriers. Oncotarget 2010 Oct;1(6):405-22

2009 

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

2008 

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

2007 

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.

2006 

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.

2005 

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).

2004 

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).

2003 

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).

2002 

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).

1999 

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