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  • Yunlong Liu
2018

Presymptomatic change in microRNAs modulates Tau pathology

Sharma, S., Khadimallah, I., Corya, A. W., Ali, Y. O., Rao, X., Liu, Y. & Lu, H. C., Dec 1 2018, In : Scientific reports. 8, 1, 9251.

Research output: Contribution to journalArticle

Open Access
4 Scopus citations

Rifampin modulation of xeno- and endobiotic conjugating enzyme mRNA expression and associated microRNAs in human hepatocytes

Gufford, B. T., Robarge, J. D., Eadon, M. T., Gao, H., Lin, H., Liu, Y., Desta, Z. & Skaar, T. C., Apr 2018, In : Pharmacology Research and Perspectives. 6, 2, e00386.

Research output: Contribution to journalArticle

5 Scopus citations

Simultaneous inhibition of MEK and Hh signaling reduces pancreatic cancer metastasis

Gu, D., Lin, H., Zhang, X., Fan, Q., Chen, S., Shahda, S., Liu, Y., Sun, J. & Xie, J., Nov 2018, In : Cancers. 10, 11, 403.

Research output: Contribution to journalArticle

5 Scopus citations

Variants in the CYP2B6 3′UTR Alter In Vitro and In Vivo CYP2B6 Activity: Potential Role of MicroRNAs

Burgess, K. S., Ipe, J., Swart, M., Metzger, I. F., Lu, J., Gufford, B. T., Thong, N., Desta, Z., Gaedigk, R., Pearce, R. E., Gaedigk, A., Liu, Y. & Skaar, T. C., Jul 2018, In : Clinical Pharmacology and Therapeutics. 104, 1, p. 130-138 9 p.

Research output: Contribution to journalArticle

10 Scopus citations
2017

A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra

Kou, Q., Wu, S., Tolić, N., Paša-Tolić, L., Liu, Y. & Liu, X., May 1 2017, In : Bioinformatics. 33, 9, p. 1309-1316 8 p.

Research output: Contribution to journalArticle

12 Scopus citations

Both MisR (CpxR) and MisS (CpxA) are required for Neisseria gonorrhoeae infection in a murine model of lower genital tract infection

Gangaiah, D., Raterman, E. L., Wu, H., Fortney, K. R., Gao, H., Liu, Y., Jerse, A. E. & Spinola, S. M., Sep 1 2017, In : Infection and immunity. 85, 9, e00307-17.

Research output: Contribution to journalArticle

11 Scopus citations

Characterizing the roles of long non-coding RNA in rat alcohol preference

Zhou, A., Wang, Y., Liu, Y., Feng, W. & Edenberg, H., Jan 17 2017, Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016. Institute of Electrical and Electronics Engineers Inc., p. 167-173 7 p. 7822513

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Complete Transcriptome RNA-Seq

Miller, D. F. B., Yan, P., Fang, F., Buechlein, A., Kroll, K., Frankhouser, D., Stump, C., Stump, P., Ford, J. B., Tang, H., Michaels, S., Matei, D., Huang, T. H., Chien, J., Liu, Y., Rusch, D. B. & Nephew, K. P., 2017, Methods in Molecular Biology. Humana Press Inc., p. 141-162 22 p. (Methods in Molecular Biology; vol. 1513).

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Scopus citations

Editorial

Ruan, J., Huang, K., Zhao, Z. & Liu, Y., 2017, In : International Journal of Computational Biology and Drug Design. 10, 2, p. 87-90 4 p.

Research output: Contribution to journalEditorial

ExonImpact: Prioritizing Pathogenic Alternative Splicing Events

Li, M., Feng, W., Zhang, X., Yang, Y., Wang, K., Mort, M., Cooper, D. N., Wang, Y., Zhou, Y. & Liu, Y., Jan 1 2017, In : Human Mutation. 38, 1, p. 16-24 9 p.

Research output: Contribution to journalArticle

8 Scopus citations

Investigating DNA-, RNA-, and protein-based features as a means to discriminate pathogenic synonymous variants

Livingstone, M., Folkman, L., Yang, Y., Zhang, P., Mort, M., Cooper, D. N., Liu, Y., Stantic, B. & Zhou, Y., Oct 2017, In : Human Mutation. 38, 10, p. 1336-1347 12 p.

Research output: Contribution to journalArticle

13 Scopus citations

Novel serine 176 phosphorylation of YBX1 activates NF-κB in colon cancer

Martin, M., Hua, L., Wang, B., Wei, H., Prabhu, L., Hartley, A. V., Jiang, G., Liu, Y. & Lu, T., Feb 24 2017, In : Journal of Biological Chemistry. 292, 8, p. 3433-3444 12 p.

Research output: Contribution to journalArticle

16 Scopus citations

Polo-like kinase 1 (Plk1) overexpression enhances ionizing radiation-induced cancer formation in mice

Li, Z., Liu, J., Li, J., Kong, Y., Sandusky, G., Rao, X., Liu, Y., Wan, J. & Liu, X., Oct 20 2017, In : Journal of Biological Chemistry. 292, 42, p. 17461-17472 12 p.

Research output: Contribution to journalArticle

15 Scopus citations

Preface

Wang, Y., Burrage, K., Liu, Y., Morishita, S., Tian, T., Jiang, Q., Song, J., Wang, G., Zhu, Q. & Hu, X. T., Jan 17 2017, In : Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016. 7822473.

Research output: Contribution to journalEditorial

RareVar: A Framework for Detecting Low-Frequency Single-Nucleotide Variants

Hao, Y., Xuei, X., Li, L., Nakshatri, H., Edenberg, H. J. & Liu, Y., Jul 1 2017, In : Journal of Computational Biology. 24, 7, p. 637-646 10 p.

Research output: Contribution to journalArticle

3 Scopus citations

Reduction in Migratory Phenotype in a Metastasized Breast Cancer Cell Line via Downregulation of S100A4 and GRM3

Chen, A., Wang, L., Li, B. Y., Sherman, J., Ryu, J. E., Hamamura, K., Liu, Y., Nakshatri, H. & Yokota, H., Dec 1 2017, In : Scientific reports. 7, 1, 3459.

Research output: Contribution to journalArticle

11 Scopus citations

regSNPs-splicing: a tool for prioritizing synonymous single-nucleotide substitution

Zhang, X., Li, M., Lin, H., Rao, X., Feng, W., Yang, Y., Mort, M., Cooper, D. N., Wang, Y., Wang, Y., Wells, C., Zhou, Y. & Liu, Y., Sep 1 2017, In : Human genetics. 136, 9, p. 1279-1289 11 p.

Research output: Contribution to journalArticle

5 Scopus citations

Renal tubular cell-derived extracellular vesicles accelerate the recovery of established renal ischemia reperfusion injury

Dominguez, J., Liu, Y., Gao, H., Dominguez, J. M., Xie, D. & Kelly, K., Dec 1 2017, In : Journal of the American Society of Nephrology. 28, 12, p. 3533-3544 12 p.

Research output: Contribution to journalArticle

29 Scopus citations

RGRNA: prediction of RNA secondary structure based on replacement and growth of stems

Li, J., Xu, C., Liang, H., Cong, W., Wang, Y., Luan, K. & Liu, Y., Sep 10 2017, In : Computer Methods in Biomechanics and Biomedical Engineering. 20, 12, p. 1261-1272 12 p.

Research output: Contribution to journalArticle

1 Scopus citations

Roles of alternative splicing in modulating transcriptional regulation

Li, J., Wang, Y., Rao, X., Wang, Y., Feng, W., Liang, H. & Liu, Y., Oct 3 2017, In : BMC Systems Biology. 11, 89.

Research output: Contribution to journalArticle

7 Scopus citations

System modeling reveals the molecular mechanisms of HSC cell cycle alteration mediated by Maff and Egr3 under leukemia

Li, R., Wang, Y., Cheng, H., Liu, G., Cheng, T., Liu, Y. & Liu, L., Oct 3 2017, In : BMC Systems Biology. 11, 91.

Research output: Contribution to journalArticle

4 Scopus citations

Validation and Utilization of a Clinical Next-Generation Sequencing Panel for Selected Cardiovascular Disorders

Celestino-Soper, P. B. S., Gao, H., Lynnes, T. C., Lin, H., Liu, Y., Spoonamore, K. G., Chen, P. S. & Vatta, M., Mar 15 2017, In : Frontiers in Cardiovascular Medicine. 4, 11.

Research output: Contribution to journalArticle

Open Access
6 Scopus citations
2016

Advancing Systems Biology in the International Conference on Intelligent Biology and Medicine (ICIBM) 2015

Zhao, Z., Liu, Y., Huang, Y., Huang, K. & Ruan, J., Aug 26 2016, In : BMC Systems Biology. 10, 61.

Research output: Contribution to journalArticle

Altered mRNA splicing in SMN-depleted motor neuron-like cells

Custer, S. K., Gilson, T. D., Li, H., Todd, A. G., Astroski, J. W., Lin, H., Liu, Y. & Androphy, E. J., Oct 2016, In : PloS one. 11, 10, e0163954.

Research output: Contribution to journalArticle

8 Scopus citations

A study of alterations in DNA epigenetic modifications (5mC and 5hmC) and gene expression influenced by simulated microgravity in human lymphoblastoid cells

Chowdhury, B., Seetharam, A., Wang, Z., Liu, Y., Lossie, A. C., Thimmapuram, J. & Irudayaraj, J., Jan 1 2016, In : PloS one. 11, 1, e0147514.

Research output: Contribution to journalArticle

17 Scopus citations

Chemotherapy-related cachexia is associated with mitochondrial depletion and the activation of ERK1/2 and p38 MAPKs

Barreto, R., Waning, D. L., Gao, H., Liu, Y., Zimmers, T. A. & Bonetto, A., 2016, In : Oncotarget. 7, 28, p. 43442-43460 19 p.

Research output: Contribution to journalArticle

55 Scopus citations

Comprehensive comparison of molecular portraits between cell lines and tumors in breast cancer

Jiang, G., Zhang, S., Yazdanparast, A., Li, M., Pawar, A. V., Liu, Y., Inavolu, S. M. & Cheng, L., Aug 22 2016, In : BMC genomics. 17, 525.

Research output: Contribution to journalArticle

51 Scopus citations

Correction: Evaluation of the genetic basis of familial aggregation of pacemaker implantation by a large next generation sequencing panel

Celestino-Soper, P. B. S., Doytchinova, A., Steiner, H. A., Uradu, A., Lynnes, T. C., Groh, W. J., Miller, J. M., Lin, H., Gao, H., Wang, Z., Liu, Y., Chen, P. S. & Vatta, M., Jan 1 2016, In : PLoS One. 11, 1, e0147455.

Research output: Contribution to journalArticle

1 Scopus citations

Garcinol inhibits GCN5-mediated lysine acetyltransferase activity and prevents replication of the parasite Toxoplasma gondii

Jeffers, V., Gao, H., Checkley, L. A., Liu, Y., Ferdig, M. T. & Sullivan, W. J., Apr 2016, In : Antimicrobial Agents and Chemotherapy. 60, 4, p. 2164-2170 7 p.

Research output: Contribution to journalArticle

17 Scopus citations
20 Scopus citations

Haemophilus ducreyi seeks alternative carbon sources and adapts to nutrient stress and anaerobiosis during experimental infection of human volunteers

Gangaiah, D., Zhang, X., Baker, B., Fortney, K. R., Gao, H., Holley, C. L., Munson, R. S., Liu, Y. & Spinola, S. M., May 1 2016, In : Infection and immunity. 84, 5, p. 1514-1525 12 p.

Research output: Contribution to journalArticle

5 Scopus citations

High Resolution Genomic Scans Reveal Genetic Architecture Controlling Alcohol Preference in Bidirectionally Selected Rat Model

Lo, C. L., Lossie, A. C., Liang, T., Liu, Y., Xuei, X., Lumeng, L., Zhou, F. C. & Muir, W. M., Aug 2016, In : PLoS Genetics. 12, 8, e1006178.

Research output: Contribution to journalArticle

13 Scopus citations

Identification of rifampin-regulated functional modules and related microRNAs in human hepatocytes based on the protein interaction network

Li, J., Wang, Y., Wang, L., Dai, X., Cong, W., Feng, W., Xu, C., Deng, Y., Wang, Y., Skaar, T. C., Liang, H. & Liu, Y., Aug 22 2016, In : BMC genomics. 17, 517.

Research output: Contribution to journalArticle

3 Scopus citations

Improving alignment accuracy on homopolymer regions for semiconductor-based sequencing technologies

Feng, W., Zhao, S., Xue, D., Song, F., Li, Z., Chen, D., He, B., Hao, Y., Wang, Y. & Liu, Y., Aug 22 2016, In : BMC genomics. 17, 521.

Research output: Contribution to journalArticle

7 Scopus citations

Intelligent biology and medicine in 2015: Advancing interdisciplinary education, collaboration, and data science

Huang, K., Liu, Y., Huang, Y., Li, L., Cooper, L., Ruan, J. & Zhao, Z., Aug 22 2016, In : BMC genomics. 17, 524.

Research output: Contribution to journalArticle

7 Scopus citations

Lipopolysaccharide treatment induces genome-wide pre-mRNA splicing pattern changes in mouse bone marrow stromal stem cells

Zhou, A., Li, M., He, B., Feng, W., Huang, F., Xu, B., Dunker, A. K., Balch, C., Li, B., Liu, Y. & Wang, Y., Aug 22 2016, In : BMC genomics. 17, 509.

Research output: Contribution to journalArticle

3 Scopus citations

Mass graphs and their applications in top-down proteomics

Kou, Q., Wu, S., Tolić, N., Liu, Y., Paša-Tolić, L. & Liu, X., 2016, Algorithms in Bioinformatics - 16th International Workshop, WABI 2016, Proceedings. Springer Verlag, Vol. 9838. p. XII (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 9838).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

NF-κB-HOTAIR axis links DNA damage response, chemoresistance and cellular senescence in ovarian cancer

Özeş, A. R., Miller, D. F., Özeş, O. N., Fang, F., Liu, Y., Matei, D., Huang, T. & Nephew, K. P., Oct 13 2016, In : Oncogene. 35, 41, p. 5350-5361 12 p.

Research output: Contribution to journalArticle

126 Scopus citations

PSRna: Prediction of small RNA secondary structures based on reverse complementary folding method

Li, J., Xu, C., Wang, L., Liang, H., Feng, W., Cai, Z., Wang, Y., Cong, W. & Liu, Y., 2016, (Accepted/In press) In : Journal of Bioinformatics and Computational Biology.

Research output: Contribution to journalArticle

Rifampin regulation of drug transporters gene expression and the association of microRNAs in human hepatocytes

Benson, E., Eadon, M., Desta, Z., Liu, Y., Lin, H., Burgess, K. S., Segar, M. W., Gaedigk, A. & Skaar, T., Apr 26 2016, In : Frontiers in Pharmacology. 7, APR, 111.

Research output: Contribution to journalArticle

20 Scopus citations

Statistical modeling for sensitive detection of low-frequency single nucleotide variants

Hao, Y., Zhang, P., Xuei, X., Nakshatri, H., Edenberg, H. J., Li, L. & Liu, Y., Aug 22 2016, In : BMC genomics. 17, 514.

Research output: Contribution to journalArticle

3 Scopus citations

Tissue-specific Co-expression of Long Non-coding and Coding RNAs Associated with Breast Cancer

Wu, W., Wagner, E. K., Hao, Y., Rao, X., Dai, H., Han, J., Chen, J., Storniolo, A. M. V., Liu, Y. & He, C., Sep 6 2016, In : Scientific reports. 6, 32731.

Research output: Contribution to journalArticle

16 Scopus citations

Transmembrane protein 88 (TMEM88) promoter hypomethylation is associated with platinum resistance in ovarian cancer

de Leon, M., Cardenas, H., Vieth, E., Emerson, R., Segar, M., Liu, Y., Nephew, K. & Matei, D., Sep 1 2016, In : Gynecologic oncology. 142, 3, p. 539-547 9 p.

Research output: Contribution to journalArticle

17 Scopus citations

Whole-exome sequencing in familial Parkinson disease

Farlow, J. L., Robak, L. A., Hetrick, K., Bowling, K., Boerwinkle, E., Coban-Akdemir, Z. H., Gambin, T., Gibbs, R. A., Gu, S., Jain, P., Jankovic, J., Jhangiani, S., Kaw, K., Lai, D., Lin, H., Ling, H., Liu, Y., Lupski, J. R., Muzny, D., Porter, P. & 6 others, Pugh, E., White, J., Doheny, K., Myers, R. M., Shulman, J. M. & Foroud, T., Jan 2016, In : JAMA Neurology. 73, 1, p. 68-75 8 p.

Research output: Contribution to journalArticle

32 Scopus citations