CPH Publications

1. Jia P, Zhao Z, Hulgan T, Bush W, Samuels DC, Bloss C, Heaton R, Ellis R, Schork N, Marra C, Collier AC, Clifford D, Gelman B, Sacktor N, Morgello S, Simpson D, McCutchan JA, Letendre S, Barnholtz-Sloan J, Franklin DR, and Grant I for the CHARTER Study Group, Kallianpur, AR (accepted) Genome-wide association study of HIV-Associated Neurocognitive Disorder (HAND): a CHARTER Group Study. American Journal of Medical Genetics
2. Fang J, Cai C, Wang Q, Lin P, Zhao Z*, Cheng F* (2017) Systems pharmacology-based discovery of natural products for precision oncology through targeting cancer mutated genes. CPT: Pharmacometrics & Systems Pharmacology 6:177-187
3. Cao Y, Zhu J, Han G, Jia P, Zhao Z* (2017) scRNASeqDB: a database for gene expression profiling in human single cell by RNA-seq. bioRxiv, 104810
4. Zhao Z, Liu Z, Zheng W, Ruan J (2017) The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: summary and innovation in genomics. BMC Genomics 18(4):S1 (in press)
5. Patton SM, Wang Q, Hulgan T, Connor JR, Jia P, Zhao Z, Letendre S, Ellis R, Bush WS, Samuels DC, Franklin DR, Kaur H, Iudicello J, Grant I, Kallianpur A (accepted) Cerebrospinal Fluid (CSF) Iron and Biomarkers of Iron Transport are Associated with Age, Sex, Ancestry, and CSF Viral Load in HIV-Infected Adults. Fluids and Barriers of the CNS
6. Zhao J, Cheng F, Zhao Z* (2017) Tissue-specific signaling networks rewired by major somatic mutations in human cancer revealed by proteome-wide discovery. Cancer Research. Advanced online access March 31, 2017. DOI:10.1158/0008-5472.CAN-16-2460
7. Han G, Zhao W, Ng KS, Karama JA, Jonasch E, Smith GB, Zhao Z*, Ding Z*, Jia P* (accepted) Unique protein expression signatures of survival time in kidney renal clear cell carcinoma through a pan-cancer screening. BMC Genomics
8. Kim P, Zhao J, Lu P, Zhao Z* (2017) mutLBSgeneDB: mutated Ligand Binding Site gene DataBase. Nucleic Acids Research Online advanced access October 7, 2016, doi: 10.1093/nar/gkw905
9. Liu S, Mitra R, Zhao MM, Fan W, Eischen CM, Yin F, Zhao Z* (2016) The potential roles of long non-coding RNAs (lncRNAs) in glioblastoma development. Molecular Cancer Therapeutics 15(12):2977-2986
10. Shen Q, Cheng F, Song H, Lu W, Zhao Z* (co-corresponding author), Zhang J* (2016) Proteome-scale investigation of protein allosteric regulation perturbed by somatic mutations in 7,000 cancer genomes. American Journal of Human Genetics. 2016 Nov 24. pii: S0002-9297(16)30401-3. doi: 10.1016/j.ajhg.2016.09.020. [Epub ahead of print]
11. Chen, J., Bacanu, S. A., Yu, H., Zhao, Z., Jia, P., Kendler, K. S., Kranzler, H. R., Gelernter, J., Farrer, L., Minica, C., Pool, R., Milaneschi, Y., Boomsma, D. I., Penninx, B. W., Tyndale, R. F., Ware, J. J., Vink, J. M., Kaprio, J., Munafo, M., & Chen, X. (2016). Genetic Relationship between Schizophrenia and Nicotine Dependence. Sci Rep, 6, 25671. doi: 10.1038/srep25671
12. Cheng, F., Liu, C., Shen, B., & Zhao, Z. (2016). Investigating cellular network heterogeneity and modularity in cancer: a network entropy and unbalanced motif approach. BMC Syst Biol, 10 Suppl 3, 65. doi: 10.1186/s12918-016-0309-9
13. Cheng, F., Murray, J. L., Zhao, J., Sheng, J., Zhao, Z., & Rubin, D. H. (2016). Systems Biology-Based Investigation of Cellular Antiviral Drug Targets Identified by Gene-Trap Insertional Mutagenesis. PLoS Comput Biol, 12(9), e1005074. doi: 10.1371/journal.pcbi.1005074
14. Cheng, F., Zhao, J., Fooksa, M., & Zhao, Z. (2016). A network-based drug repositioning infrastructure for precision cancer medicine through targeting significantly mutated genes in the human cancer genomes. J Am Med Inform Assoc, 23(4), 681-691. doi: 10.1093/jamia/ocw007
15. Cheng, F., Zhao, J., & Zhao, Z. (2016). Advances in computational approaches for prioritizing driver mutations and significantly mutated genes in cancer genomes. Brief Bioinform, 17(4), 642-656. doi: 10.1093/bib/bbv068
16. Edmonds, M. D., Boyd, K. L., Moyo, T., Mitra, R., Duszynski, R., Arrate, M. P., Chen, X., Zhao, Z., Blackwell, T. S., Andl, T., & Eischen, C. M. (2016). MicroRNA-31 initiates lung tumorigenesis and promotes mutant KRAS-driven lung cancer. J Clin Invest, 126(1), 349-364. doi: 10.1172/jci82720
17. Hart, T., Dider, S., Han, W., Xu, H., Zhao, Z., & Xie, L. (2016). Toward Repurposing Metformin as a Precision Anti-Cancer Therapy Using Structural Systems Pharmacology. Sci Rep, 6, 20441. doi: 10.1038/srep20441
18. Heist, R. S., Shim, H. S., Gingipally, S., Mino-Kenudson, M., Le, L., Gainor, J. F., Zheng, Z., Aryee, M., Xia, J., Jia, P., Jin, H., Zhao, Z., Pao, W., Engelman, J. A., & Iafrate, A. J. (2016). MET Exon 14 Skipping in Non-Small Cell Lung Cancer. Oncologist, 21(4), 481-486. doi: 10.1634/theoncologist.2015-0510
19. Hemnes, A. R., Zhao, M., West, J., Newman, J. H., Rich, S., Archer, S. L., Robbins, I. M., Blackwell, T. S., Cogan, J., Loyd, J. E., Zhao, Z., Gaskill, C., Jetter, C., Kropski, J. A., Majka, S. M., & Austin, E. D. (2016). Critical Genomic Networks and Vasoreactive Variants in Idiopathic Pulmonary Arterial Hypertension. Am J Respir Crit Care Med, 194(4), 464-475. doi: 10.1164/rccm.201508-1678OC
20. Huang, K., Liu, Y., Huang, Y., Li, L., Cooper, L., Ruan, J., & Zhao, Z. (2016). Intelligent biology and medicine in 2015: advancing interdisciplinary education, collaboration, and data science. BMC Genomics, 17 Suppl 7, 524. doi: 10.1186/s12864-016-2893-x
21. Jia, P., & Zhao, Z. (2016). Impacts of somatic mutations on gene expression: an association perspective. Brief Bioinform. doi: 10.1093/bib/bbw037
22. Kallianpur, A. R., Wang, Q., Jia, P., Hulgan, T., Zhao, Z., Letendre, S. L., Ellis, R. J., Heaton, R. K., Franklin, D. R., Barnholtz-Sloan, J., Collier, A. C., Marra, C. M., Clifford, D. B., Gelman, B. B., McArthur, J. C., Morgello, S., Simpson, D. M., McCutchan, J. A., & Grant, I. (2016). Anemia and Red Blood Cell Indices Predict HIV-Associated Neurocognitive Impairment in the Highly Active Antiretroviral Therapy Era. J Infect Dis, 213(7), 1065-1073. doi: 10.1093/infdis/jiv754
23. Kim, P., Cheng, F., Zhao, J., & Zhao, Z. (2016). ccmGDB: a database for cancer cell metabolism genes. Nucleic Acids Res, 44(D1), D959-968. doi: 10.1093/nar/gkv1128
24. Liu, S., Yin, F., Zhao, M., Zhou, C., Ren, J., Huang, Q., Zhao, Z., Mitra, R., Fan, W., & Fan, M. (2016). The homing and inhibiting effects of hNSCs-BMP4 on human glioma stem cells. Oncotarget, 7(14), 17920-17931. doi: 10.18632/oncotarget.7472
25. Pardo, L., Schluter, A., Valor, L. M., Barco, A., Giralt, M., Golbano, A., Hidalgo, J., Jia, P., Zhao, Z., Jove, M., Portero-Otin, M., Ruiz, M., Gimenez-Llort, L., Masgrau, R., Pujol, A., & Galea, E. (2016). Targeted activation of CREB in reactive astrocytes is neuroprotective in focal acute cortical injury. Glia, 64(5), 853-874. doi: 10.1002/glia.22969
26. Tenenbaum, J. D., Avillach, P., Benham-Hutchins, M., Breitenstein, M. K., Crowgey, E. L., Hoffman, M. A., Jiang, X., Madhavan, S., Mattison, J. E., Nagarajan, R., Ray, B., Shin, D., Visweswaran, S., Zhao, Z., & Freimuth, R. R. (2016). An informatics research agenda to support precision medicine: seven key areas. J Am Med Inform Assoc, 23(4), 791-795. doi: 10.1093/jamia/ocv213
27. Wang, Y., Guo, X., Bray, M. J., Ding, Z., & Zhao, Z. (2016). An integrative genomics approach for identifying novel functional consequences of PBRM1 truncated mutations in clear cell renal cell carcinoma (ccRCC). BMC Genomics, 17 Suppl 7, 515. doi: 10.1186/s12864-016-2906-9
28. Zhao, J., Cheng, F., Wang, Y., Arteaga, C. L., & Zhao, Z. (2016). Systematic Prioritization of Druggable Mutations in approximately 5000 Genomes Across 16 Cancer Types Using a Structural Genomics-based Approach. Mol Cell Proteomics, 15(2), 642-656. doi: 10.1074/mcp.M115.053199
29. Zhao, M., Kim, P., Mitra, R., Zhao, J., & Zhao, Z. (2016). TSGene 2.0: an updated literature-based knowledgebase for tumor suppressor genes. Nucleic Acids Res, 44(D1), D1023-1031. doi: 10.1093/nar/gkv1268
30. Zhao, M., & Zhao, Z. (2016). Concordance of copy number loss and down-regulation of tumor suppressor genes: a pan-cancer study. BMC Genomics, 17 Suppl 7, 532. doi: 10.1186/s12864-016-2904-y
31. Zhao, Z., Liu, Y., Huang, Y., Huang, K., & Ruan, J. (2016). Advancing Systems Biology in the International Conference on Intelligent Biology and Medicine (ICIBM) 2015. BMC Syst Biol, 10 Suppl 3, 61. doi: 10.1186/s12918-016-0305-0

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1. Wang H., Cade B., Chen H., Gleason K., Saxena R., Feng T., Larkin E., Ramachandran V., Patel S., Tracy R., Lin Y., Wood L., Rotter J., Post W., Gottlieb D., Below J.E., Hanis C., Petty L., Sunyaev S., Lin X., Redline S.*,  Zhu X.* Variants in ANGPT2 contribute to variation in Nocturnal Oxyhemoglobin Saturation Level. Human Molecular Genetics. Accepted.
2. Xue C., Raveendran M., Harris R.A., Fawcett G.L., White S., Dahdouli M., Liu X., Deiros D.R., Below J.E., Salerno W., Cox L., Fan G., Ferguson B., Horvath J., Johnson Z., Kanthaswamy S., Kubisch H.M., Liu D., Platt M., Smith D.G., Sun B., Vallender E.J., Wang F., Wiseman R.W., Chen R., Muzny D.M., Gibbs R.A., Yu F., Rogers J. The population genomics of rhesus macaques (Macaca mulatta) based on whole genome sequences. Genome Research. Accepted.
3. Below, J. E., & Parra, E. J. (2016). Genome-Wide Studies of Type 2 Diabetes and Lipid Traits in Hispanics. Curr Diab Rep, 16(5), 41. doi: 10.1007/s11892-016-0737-3
4. Below, J. E., Parra, E. J., Gamazon, E. R., Torres, J., Krithika, S., Candille, S., Lu, Y., Manichakul, A., Peralta-Romero, J., Duan, Q., Li, Y., Morris, A. P., Gottesman, O., Bottinger, E., Wang, X. Q., Taylor, K. D., Ida Chen, Y. D., Rotter, J. I., Rich, S. S., Loos, R. J., Tang, H., Cox, N. J., Cruz, M., Hanis, C. L., & Valladares-Salgado, A. (2016). Meta-analysis of lipid-traits in Hispanics identifies novel loci, population-specific effects, and tissue-specific enrichment of eQTLs. Sci Rep, 6, 19429. doi: 10.1038/srep19429
5. Cade, B. E., Chen, H., Stilp, A. M., Gleason, K. J., Sofer, T., Ancoli-Israel, S., Arens, R., Bell, G. I., Below, J. E., Bjonnes, A. C., Chun, S., Conomos, M. P., Evans, D. S., Johnson, W. C., Frazier-Wood, A. C., Lane, J. M., Larkin, E. K., Loredo, J. S., Post, W. S., Ramos, A. R., Rice, K., Rotter, J. I., Shah, N. A., Stone, K. L., Taylor, K. D., Thornton, T. A., Tranah, G. J., Wang, C., Zee, P. C., Hanis, C. L., Sunyaev, S. R., Patel, S. R., Laurie, C. C., Zhu, X., Saxena, R., Lin, X., & Redline, S. (2016). Genetic Associations with Obstructive Sleep Apnea Traits in Hispanic/Latino Americans. Am J Respir Crit Care Med. doi: 10.1164/rccm.201512-2431OC
6. Chen, D. H., Below, J. E., Shimamura, A., Keel, S. B., Matsushita, M., Wolff, J., Sul, Y., Bonkowski, E., Castella, M., Taniguchi, T., Nickerson, D., Papayannopoulou, T., Bird, T. D., & Raskind, W. H. (2016). Ataxia-Pancytopenia Syndrome Is Caused by Missense Mutations in SAMD9L. Am J Hum Genet, 98(6), 1146-1158. doi: 10.1016/j.ajhg.2016.04.009
7. Fuchsberger, C., Flannick, J., Teslovich, T. M., Mahajan, A., Agarwala, V., Gaulton, K. J., Ma, C., Fontanillas, P., Moutsianas, L., McCarthy, D. J., Rivas, M. A., Perry, J. R., Sim, X., Blackwell, T. W., Robertson, N. R., Rayner, N. W., Cingolani, P., Locke, A. E., Fernandez Tajes, J., Highland, H. M., Dupuis, J., Chines, P. S., Lindgren, C. M., Hartl, C., Jackson, A. U., Chen, H., Huyghe, J. R., van de Bunt, M., Pearson, R. D., Kumar, A., Muller-Nurasyid, M., Grarup, N., Stringham, H. M., Gamazon, E. R., Lee, J., Chen, Y., Scott, R. A., Below, J. E., Chen, P., Huang, J., Go, M. J., Stitzel, M. L., Pasko, D., Parker, S. C., Varga, T. V., Green, T., Beer, N. L., Day-Williams, A. G., Ferreira, T., Fingerlin, T., Horikoshi, M., Hu, C., Huh, I., Ikram, M. K., Kim, B. J., Kim, Y., Kim, Y. J., Kwon, M. S., Lee, J., Lee, S., Lin, K. H., Maxwell, T. J., Nagai, Y., Wang, X., Welch, R. P., Yoon, J., Zhang, W., Barzilai, N., Voight, B. F., Han, B. G., Jenkinson, C. P., Kuulasmaa, T., Kuusisto, J., Manning, A., Ng, M. C., Palmer, N. D., Balkau, B., Stancakova, A., Abboud, H. E., Boeing, H., Giedraitis, V., Prabhakaran, D., Gottesman, O., Scott, J., Carey, J., Kwan, P., Grant, G., Smith, J. D., Neale, B. M., Purcell, S., Butterworth, A. S., Howson, J. M., Lee, H. M., Lu, Y., Kwak, S. H., Zhao, W., Danesh, J., Lam, V. K., Park, K. S., Saleheen, D., So, W. Y., Tam, C. H., Afzal, U., Aguilar, D., Arya, R., Aung, T., Chan, E., Navarro, C., Cheng, C. Y., Palli, D., Correa, A., Curran, J. E., Rybin, D., Farook, V. S., Fowler, S. P., Freedman, B. I., Griswold, M., Hale, D. E., Hicks, P. J., Khor, C. C., Kumar, S., Lehne, B., Thuillier, D., Lim, W. Y., Liu, J., van der Schouw, Y. T., Loh, M., Musani, S. K., Puppala, S., Scott, W. R., Yengo, L., Tan, S. T., Taylor, H. A., Jr., Thameem, F., Wilson, G., Sr., Wong, T. Y., Njolstad, P. R., Levy, J. C., Mangino, M., Bonnycastle, L. L., Schwarzmayr, T., Fadista, J., Surdulescu, G. L., Herder, C., Groves, C. J., Wieland, T., Bork-Jensen, J., Brandslund, I., Christensen, C., Koistinen, H. A., Doney, A. S., Kinnunen, L., Esko, T., Farmer, A. J., Hakaste, L., Hodgkiss, D., Kravic, J., Lyssenko, V., Hollensted, M., Jorgensen, M. E., Jorgensen, T., Ladenvall, C., Justesen, J. M., Karajamaki, A., Kriebel, J., Rathmann, W., Lannfelt, L., Lauritzen, T., Narisu, N., Linneberg, A., Melander, O., Milani, L., Neville, M., Orho-Melander, M., Qi, L., Qi, Q., Roden, M., Rolandsson, O., Swift, A., Rosengren, A. H., Stirrups, K., Wood, A. R., Mihailov, E., Blancher, C., Carneiro, M. O., Maguire, J., Poplin, R., Shakir, K., Fennell, T., DePristo, M., Hrabe de Angelis, M., Deloukas, P., Gjesing, A. P., Jun, G., Nilsson, P., Murphy, J., Onofrio, R., Thorand, B., Hansen, T., Meisinger, C., Hu, F. B., Isomaa, B., Karpe, F., Liang, L., Peters, A., Huth, C., O'Rahilly, S. P., Palmer, C. N., Pedersen, O., Rauramaa, R., Tuomilehto, J., Salomaa, V., Watanabe, R. M., Syvanen, A. C., Bergman, R. N., Bharadwaj, D., Bottinger, E. P., Cho, Y. S., Chandak, G. R., Chan, J. C., Chia, K. S., Daly, M. J., Ebrahim, S. B., Langenberg, C., Elliott, P., Jablonski, K. A., Lehman, D. M., Jia, W., Ma, R. C., Pollin, T. I., Sandhu, M., Tandon, N., Froguel, P., Barroso, I., Teo, Y. Y., Zeggini, E., Loos, R. J., Small, K. S., Ried, J. S., DeFronzo, R. A., Grallert, H., Glaser, B., Metspalu, A., Wareham, N. J., Walker, M., Banks, E., Gieger, C., Ingelsson, E., Im, H. K., Illig, T., Franks, P. W., Buck, G., Trakalo, J., Buck, D., Prokopenko, I., Magi, R., Lind, L., Farjoun, Y., Owen, K. R., Gloyn, A. L., Strauch, K., Tuomi, T., Kooner, J. S., Lee, J. Y., Park, T., Donnelly, P., Morris, A. D., Hattersley, A. T., Bowden, D. W., Collins, F. S., Atzmon, G., Chambers, J. C., Spector, T. D., Laakso, M., Strom, T. M., Bell, G. I., Blangero, J., Duggirala, R., Tai, E. S., McVean, G., Hanis, C. L., Wilson, J. G., Seielstad, M., Frayling, T. M., Meigs, J. B., Cox, N. J., Sladek, R., Lander, E. S., Gabriel, S., Burtt, N. P., Mohlke, K. L., Meitinger, T., Groop, L., Abecasis, G., Florez, J. C., Scott, L. J., Morris, A. P., Kang, H. M., Boehnke, M., Altshuler, D., & McCarthy, M. I. (2016). The genetic architecture of type 2 diabetes. Nature, 536(7614), 41-47. doi: 10.1038/nature18642
8. Hanis, C. L., Redline, S., Cade, B. E., Bell, G. I., Cox, N. J., Below, J. E., Brown, E. L., & Aguilar, D. (2016). Beyond type 2 diabetes, obesity and hypertension: an axis including sleep apnea, left ventricular hypertrophy, endothelial dysfunction, and aortic stiffness among Mexican Americans in Starr County, Texas. Cardiovasc Diabetol, 15, 86. doi: 10.1186/s12933-016-0405-6
9. Horikoshi, M., Pasquali, L., Wiltshire, S., Huyghe, J. R., Mahajan, A., Asimit, J. L., Ferreira, T., Locke, A. E., Robertson, N. R., Wang, X., Sim, X., Fujita, H., Hara, K., Young, R., Zhang, W., Choi, S., Chen, H., Kaur, I., Takeuchi, F., Fontanillas, P., Thuillier, D., Yengo, L., Below, J. E., Tam, C. H., Wu, Y., Abecasis, G., Altshuler, D., Bell, G. I., Blangero, J., Burtt, N. P., Duggirala, R., Florez, J. C., Hanis, C. L., Seielstad, M., Atzmon, G., Chan, J. C., Ma, R. C., Froguel, P., Wilson, J. G., Bharadwaj, D., Dupuis, J., Meigs, J. B., Cho, Y. S., Park, T., Kooner, J. S., Chambers, J. C., Saleheen, D., Kadowaki, T., Tai, E. S., Mohlke, K. L., Cox, N. J., Ferrer, J., Zeggini, E., Kato, N., Teo, Y. Y., Boehnke, M., McCarthy, M. I., & Morris, A. P. (2016). Transancestral fine-mapping of four type 2 diabetes susceptibility loci highlights potential causal regulatory mechanisms. Hum Mol Genet. doi: 10.1093/hmg/ddw048
10. Staples, J., Ekunwe, L., Lange, E., Wilson, J. G., Nickerson, D. A., & Below, J. E. (2016). PRIMUS: improving pedigree reconstruction using mitochondrial and Y haplotypes. Bioinformatics, 32(4), 596-598. doi: 10.1093/bioinformatics/btv618
11. Staples, J., Witherspoon, D. J., Jorde, L. B., Nickerson, D. A., Below, J. E., & Huff, C. D. (2016). PADRE: Pedigree-Aware Distant-Relationship Estimation. Am J Hum Genet, 99(1), 154-162. doi: 10.1016/j.ajhg.2016.05.020

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1. Lin X, Lee S, Wu MC, Wang C, Chen H, Li Z, Lin X. Test for rare variants by environment interactions in sequencing association studies. Biometrics 2016, 72 (1): 156-164.
2. Chen H*, Wang C*, Conomos MP, Stilp AM, Li Z, Sofer T, Szpiro AA, Chen W, Brehm JM, Celedón JC, Redline S, Papanicolaou GJ, Thornton TA, Laurie CC, Rice K, Lin X. Control for population structure and relatedness for binary traits in genetic association studies via logistic mixed models. The American Journal of Human Genetics 2016, 98 (4): 653-666.
   * Equal contribution
3. Hobbs BD, Parker MM, Chen H, Lao T, Hardin M, Qiao D, Hawrylkiewicz I, Sliwinski P, Yim JJ, Kim WJ et al. Exome array analysis identifies a common variant in IL27 associated with chronic obstructive pulmonary disease. The American Journal of Respiratory and Critical Care Medicine 2016, 194 (1): 48-57.
4. Liang J, Cade BE, Wang H, Chen H, Gleason KJ, Larkin EK, Saxena R, Lin X, Redline S, Zhu X. Comparison of heritability estimation and linkage analysis for multiple traits using principal component analyses. Genetic Epidemiology 2016, 40 (3): 222-232.
5. Fuchsberger C, Flannick J, Teslovich TM, Mahajan A, Agarwala V, Gaulton KJ, Ma C, Fontanillas P, Moutsianas L, McCarthy DJ, Rivas MA, Perry JRB, Sim X, Blackwell TW, Robertson NR, Rayner NW, Cingolani P, Locke AE, Fernandez Tajes J, Highland HM, Dupuis J, Chines PS, Lindgren CM, Hartl C, Jackson AU, Chen H et al. The genetic architecture of type 2 diabetes. Nature 2016, 536 (7614): 41-47.
6. Horikoshi M, Pasquali L, Wiltshire S, Huyghe JR, Mahajan A, Asimit JL, Ferreira T, Locke AE, Robertson NR, Wang X, Sim X, Fujita H, Hara K, Young R, Zhang W, Choi S, Chen H et al. Transancestral fine-mapping of four type 2 diabetes susceptibility loci highlights potential causal regulatory mechanisms. Human Molecular Genetics 2016, 25 (10): 2070-2081.
7. Cade BE, Chen H, Stilp AM, Gleason KJ, Sofer T, Ancoli-Israel S, Arens R, Bell GI, Below JE, Bjonnes AC et al. Genetic associations with obstructive sleep apnea traits in Hispanic/Latino Americans. The American Journal of Respiratory and Critical Care Medicine 2016, 194 (7): 886-897.
8. Walford GA, Gustafsson S, Rybin D, Stan?áková A, Chen H, Liu CT, Hong J, Jensen RA, Rice K, Morris AP et al. Genome-wide association study of the modified Stumvoll insulin sensitivity index identifies BCL2 and FAM19A2 as novel insulin sensitivity loci. Diabetes 2016, 65 (10): 3200-3211.
9. Liu C, Kraja AT, Smith JA, Brody JA, Franceschini N, Bis JC, Rice K, Morrison AC, Lu Y, Weiss S, Guo X, Palmas W, Martin LW, Chen YDI, Surendran P, Drenos F, Cook JP, Auer PL, Chu AY, Tsosie KS, Zhao W, Jakobsdóttir J, Lin LA, Stafford JM, Amin N, Mei H, Yao J, Voorman A, Larson MG, Grove ML, Smith AV, Hwang SJ, Chen H et al. Meta-analysis identifies common and rare variants influencing blood pressure and overlapping with metabolic trait loci. Nature Genetics 2016, 48 (10): 1162-1170.
10. Wang H, Cade BE, Chen H, Gleason KJ, Saxena R, Feng T, Larkin EK, Ramachandran VS, Lin H, Patel SR et al. Variants in Angiopoietin-2 (ANGPT2) contribute to variation in Nocturnal Oxyhemoglobin Saturation Level. Human Molecular Genetics 2016, Oct 18 [Epub ahead of print].

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1. Arroyo-Gallego, T., Ledesma-Carbayo, M, Sanchez-Ferro, A., Butterworth, I., Mendoza, C., Matarazzo, M., Montero, P., Lopez-Blanco, R., Puertas-Martin, V., Trincado, R. & Giancardo, L*. Detection of Motor Impairment in Parkinson’s Disease via Mobile Touchscreen Typing. IEEE Trans Biomed Eng in press, (2017).
2. L Giancardo, A Sanchez-Ferro, T Arroyo-Gallego, I Butterworth, C Sanchez-Mendoza, P Montero, M Matarazzo, J A Obeso, M L Gray and R. San José Estépar, “Computer keyboard interaction as an indicator of early Parkinson’s disease”, Scientific Reports 6, Article number: 34468, 2016.
3. T Arroyo-Gallego, M Ledesma-Carbayo, A Sanchez-Ferro, C Sanchez-Mendoza, I Butterworth, M Matarazzo, P Montero, R López-Blanco, V Puertas-Martín, R Trincado and L Giancardo, “Detection of Motor Impairment in Parkinson’s Disease via Mobile Touchscreen Typing”, IEEE Biomedical Engineering (under review).
4. A Crimi, L Giancardo, A Gozzi, F Sambataro, V Murino, D Sona, “Multi-Link Discrimination: Brain Network Comparison via Sparse Connectivity Analysis”, Neuroimaging (under review).

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1. Feng Y, Ge X, Meng L, Scull J, Li J, Tian X, Zhang T, Jin W, Cheng H, Wang X, Tokita M, Liu P, Mei H, Wang Y, Li F, Schmitt ES, Zhang WV, Muzny D, Wen S, Chen Z, Yang Y, Beaudet AL, Liu X, Eng CM, Xia F, Wong L-J, Zhang J. (2017) The Next-Generation of Spinal Muscular Atrophy Carrier Screening: Comprehensive Pan-ethnic SMN1 Copy Number and Sequence Variant Analysis by Massively Parallel Sequencing. Genetics in Medicine advance online publication, January 26, 2017; doi:10.1038/gim.2016.215
2. Morrison AC, Huang Z, Yu B, Metcalf G, Liu X, Ballantyne C, Coresh J, Yu F, Muzny D, Feofanova E, Rustagi N, Gibbs R, Boerwinkle E. (2017) Practical Approaches for Whole Genome Sequence Analysis of Complex Traits. American Journal of Human Genetics 100:205–215.
3. Liu X*, Li C and Boerwinkle E. (2017) The performance of deleteriousness prediction scores for rare non-protein-changing single nucleotide variants in human genomes. Journal of Medical Genetics 54:134-144. *corresponding author
4. Dong C, Guo Y, He Z, Yang H, Liu X, Wang K. (2016) iCAGES: integrated CAncer GEnome Score for comprehensively prioritizing driver genes in personal cancer genomes. Genome Medicine 8:135.
5. Xue C, Raveendran M, Harris RA, Fawcett GL, Liu X, White S, Dahdouli M, Rio Deiros D, Below JE, Salerno W, Cox L, Fan D, Ferguson B, Horvath J, Johnson Z, Kanthaswamy S, Kubisch HM, Liu D, Platt M, Smith DG, Sun B, Vallender EJ, Wang F, Wiseman R, Chen R, Muzny DM, Gibbs RA, Yu F and Rogers J. (2016) The population genomics of rhesus macaques (Macaca mulatta) based on whole genome sequences. Genome Research 26(12):1651-1662.
6. Yu B, de Vries P, Metcalf G, Wang Z, Feofanova E, Liu X, Muzny D, Wagenknecht L, Gibbs R, Morrison A, Boerwinkle E. (2016) Whole genome sequence analysis of serum amino acid levels. Genome Biology 17:237.
7. Yazdani A, Yazdani A, Liu X, Boerwinkle E. (2016) Identification of Rare Variants in Metabolites of the Carnitine Pathway by Whole Genome Sequencing Analysis. Genetic Epidemiology. 40(6):486-91.
8. Huang J, Wang K, Wei P, Liu X, Liu X, Tan K, Boerwinkle E, Potash JB and Han S. (2016) FLAGS: A Flexible and Adaptive Association Test for Gene Sets Using Summary Statistics. Genetics. 202(3):919-929.
9. Liu X*, Wu C, Li C and Boerwinkle E. (2016) dbNSFP v3.0: A One-Stop Database of Functional Predictions and Annotations for Human Non-synonymous and Splice Site SNVs. Human Mutation. 37(3):235-241. *corresponding author
10. Liu X*, White S, Peng B, Johnson AD, Brody JA, Li AH, Huang Z, Carroll A, Wei P, Gibbs R, Klein RJ and Boerwinkle E. (2016) WGSA: an annotation pipeline for human genome sequencing studies. Journal of Medical Genetics. 53:111-112. *corresponding author

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1. Chen, J., Bacanu, S. A., Yu, H., Zhao, Z., Jia, P., Kendler, K. S., Kranzler, H. R., Gelernter, J., Farrer, L., Minica, C., Pool, R., Milaneschi, Y., Boomsma, D. I., Penninx, B. W., Tyndale, R. F., Ware, J. J., Vink, J. M., Kaprio, J., Munafo, M., & Chen, X. (2016). Genetic Relationship between Schizophrenia and Nicotine Dependence. Sci Rep, 6, 25671. doi: 10.1038/srep25671
2. Heist, R. S., Shim, H. S., Gingipally, S., Mino-Kenudson, M., Le, L., Gainor, J. F., Zheng, Z., Aryee, M., Xia, J., Jia, P., Jin, H., Zhao, Z., Pao, W., Engelman, J. A., & Iafrate, A. J. (2016). MET Exon 14 Skipping in Non-Small Cell Lung Cancer. Oncologist, 21(4), 481-486. doi: 10.1634/theoncologist.2015-0510
3. Jia, P., & Zhao, Z. (2016). Impacts of somatic mutations on gene expression: an association perspective. Brief Bioinform. doi: 10.1093/bib/bbw037
4. Kallianpur, A. R., Wang, Q., Jia, P., Hulgan, T., Zhao, Z., Letendre, S. L., Ellis, R. J., Heaton, R. K., Franklin, D. R., Barnholtz-Sloan, J., Collier, A. C., Marra, C. M., Clifford, D. B., Gelman, B. B., McArthur, J. C., Morgello, S., Simpson, D. M., McCutchan, J. A., & Grant, I. (2016). Anemia and Red Blood Cell Indices Predict HIV-Associated Neurocognitive Impairment in the Highly Active Antiretroviral Therapy Era. J Infect Dis, 213(7), 1065-1073. doi: 10.1093/infdis/jiv754
5. Pardo, L., Schluter, A., Valor, L. M., Barco, A., Giralt, M., Golbano, A., Hidalgo, J., Jia, P., Zhao, Z., Jove, M., Portero-Otin, M., Ruiz, M., Gimenez-Llort, L., Masgrau, R., Pujol, A., & Galea, E. (2016). Targeted activation of CREB in reactive astrocytes is neuroprotective in focal acute cortical injury. Glia, 64(5), 853-874. doi: 10.1002/glia.22969

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1. Akila Subramaniam, Ranjit Kumar, Suzanne P Cliver, Degui Zhi, Jeff M Szychowski, Adi Abramovici, Joseph R Biggio, Elliot J Lefkowitz, Casey Morrow and Rodney K Edwards. “Vaginal microbiota in pregnancy: evaluation based on vaginal flora, birth outcome.” American Journal of Perinatology, 2016;33(4):401-8. PMCID: 26479170
2. S. Pennathur, A. Vivekanandan-Giri, M. L. Locy, T. Kulkarni, D. Zhi, L. Zeng, J. Byun, J. A. de Andrade and V. J. Thannickal. "Oxidative Modifications of Protein Tyrosyl Residues are Increased in Plasma of Human Subjects with Interstitial Lung Disease." Am J Respir Crit Care Med 2016193(8): 861-868. PMCID: PMC4849179.
3. Mithun Das; Jin Sha; Bertha Hidalgo; Stella Aslibekyan; Anh N Do; Degui Zhi; Dianjianyi Sun; Tao Zhang; Shengxu Li; Wei Chen; Hemant K Tiwari; Devin Absher; Jose M Ordovas; Gerald S Berenson; Donna K Arnett; Marguerite Ryan Irvin. “Association of DNA Methylation at CPT1A Locus with Metabolic Syndrome in the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) Study.” PLoS ONE, 11 (1), e0145789, 2016. PMCID; PMC4726462
4. Balu K Chacko, Degui Zhi, Victor M Darley-Usmar, Tanecia Mitchell. “The Bioenergetic Health Index is a Sensitive Measure of Oxidative Stress in Human Monocytes.” Redox Biology Journal, 8, 43-50, 2016. PMCID: 4712317.
5. Yiyi Ma, Jack L Follis, Caren E Smith, Toshiko Tanaka, Ani W Manichaikul, Audrey Y Chu, Cecilia Samieri, Xia Zhou, Weihua Guan, Lu Wang, Mary L Biggs, Yii-Der I Chen, Dena G Hernandez, Ingrid Borecki, Daniel I Chasman, Stephen S Rich, Luigi Ferrucci, Marguerite Ryan Irvin, Stella Aslibekyan, Degui Zhi, Hemant K Tiwari, Steven A Claas, Jin Sha, Edmond K Kabagambe, Chao-Qiang Lai, Laurence D Parnell, Yu-Chi Lee, Philippe Amouyel, Jean-Charles Lambert, Bruce M Psaty, Irena B King, Dariush Mozaffarian, Barbara McKnight, Stefania Bandinelli, Michael Y Tsai, Paul M Ridker, Jingzhong Ding, Kurt Lohmant Mstat, Yongmei Liu, Nona Sotoodehnia, Pascale Barberger-Gateau, Lyn M Steffen, David S Siscovick, Devin Absher, Donna K Arnett, José M Ordovás, Rozenn N Lemaitre. “Interaction of methylation-related genetic variants with circulating fatty acids on plasma lipids: a meta-analysis of 7 studies and methylation analysis of 3 studies in the Cohorts for Heart and Aging Research in Genomic Epidemiology consortium.” The American Journal of Clinical Nutrition, ajcn112987; First published online January 20, 2016.
6. Rodney K Edwards, Ranjit Kumar, Degui Zhi, Jeffrey Szychowski, Akila Subramaniam, Elliot J Lefkowitz, Casey Morrow. “Gravidas with class III obesity: evaluating the abdominal skin microbiota above and below the panniculus.” J Matern Fetal Neonatal Med. 2015 Dec 23:1-5. [Epub ahead of print] PMCID: 4975423 [Available on 2017-10-01].
7. Sonja I. Berndt, Nicola J. Camp, Christine F. Skibola, Joseph Vijai, Zhaoming Wang, Jian Gu, Alexandra Nieters, Rachel S. Kelly, Karin E. Smedby, Alain Monnereau, Wendy Cozen, Angela Cox, Sophia S. Wang, Qing Lan, Lauren R. Teras, Moara Machado, Meredith Yeager, Angela R. Brooks-Wilson, Patricia Hartge, Mark P. Purdue, Brenda M. Birmann, Claire M. Vajdic, Pierluigi Cocco, Yawei Zhang, Graham G. Giles, Anne Zeleniuch-Jacquotte, Charles Lawrence, Rebecca Montalvan, Laurie Burdett, Amy Hutchinson, Yuanqing Ye, Timothy G. Call, Tait D. Shanafelt, Anne J. Novak, Neil E. Kay, Mark Liebow, Julie M. Cunningham, Cristine Allmer, Henrik Hjalgrim, Hans-Olov Adami, Mads Melbye, Bengt Glimelius, Ellen T. Chang, Martha Glenn, Karen Curtin, Lisa A. Cannon-Albright, W Ryan Diver, Brian K. Link, George J. Weiner, Lucia Conde, Paige M. Bracci, Jacques Riby, Donna K. Arnett, Degui Zhi, Justin M. Leach, Elizabeth A. Holly, Rebecca D. Jackson, Lesley F. Tinker, Yolanda Benavente, Núria Sala, Delphine Casabonne, Nikolaus Becker, Paolo Boffetta, Paul Brennan, Lenka Foretova, Marc Maynadie, James McKay, Anthony Staines, Kari G. Chaffee, Sara J. Achenbach, Celine M. Vachon, Lynn R. Goldin, Sara S. Strom, Jose F. Leis, J. Brice Weinberg, Neil E. Caporaso, Aaron D. Norman, Anneclaire J. De Roos, Lindsay M. Morton, Richard K. Severson, Elio Riboli, Paolo Vineis, Rudolph Kaaks, Giovanna Masala, Elisabete Weiderpass, María- Dolores Chirlaque, Roel C. H. Vermeulen, Ruth C. Travis, Melissa C. Southey, Roger L. Milne, Demetrius Albanes, Jarmo Virtamo, Stephanie Weinstein, Jacqueline Clavel, Tongzhang Zheng, Theodore R. Holford, Danylo J. Villano, Ann Maria, John J. Spinelli, Randy D. Gascoyne, Joseph M. Connors, Kimberly A. Bertrand, Edward Giovannucci, Peter Kraft, Anne Kricker, Jenny Turner, Maria Grazia Ennas, Giovanni M. Ferri, Lucia Miligi, Liming Liang, Baoshan Ma, Jinyan Huang, Simon Crouch, Ju-Hyun Park, Nilanjan Chatterjee, Kari E. North, John A. Snowden, Josh Wright, Joseph F. Fraumeni, Kenneth Offit, Xifeng Wu, Silvia de Sanjose, James R. Cerhan, Stephen J. Chanock, Nathaniel Rothman & Susan L. Slager. “Meta-analysis of genome-wide association studies discovers multiple loci for chronic lymphocytic leukemia.” Nat Commun. 2016 Mar 9;7:10933. PMCID: 4786871.
8. Irvin, Marguerite R.; Rotroff, Daniel M.; Aslibekyan, Stella; Zhi, Degui; Hidalgo, Bertha; Motsinger-Reif, Alison; Marvel, Skylar; Srinivasasainagendra, Vinodh; Claas, Steven A.; Buse, John B.; Straka, Robert J.; Ordovas, Jose M.; Borecki, Ingrid B.; Guo, Xiuqing; Chen, Ida Y.D.; Rotter, Jerome I.; Wagner, Michael J.; Arnett, Donna K. “A genome-wide study of lipid response to fenofibrate in Caucasians: a combined analysis of the GOLDN and ACCORD studies” Pharmacogenetics and Genomics. 2016. PMCID: 4986826 [Available on 2017-07-01].
9. Hongying Dai, Guodong Wu, Michael Wu, Degui Zhi. “An Optimal Bahadur-Efficient Method in Detection of Sparse Signals with Applications to Pathway Analysis in Sequencing Association Studies.” PLoS One. 2016;11(7):e0152667. PMCID: PMC4933358.
10. Machiela, M. J., Q. Lan, S. L. Slager, R. C. Vermeulen, L. R. Teras, N. J. Camp, J. R. Cerhan, J. J. Spinelli, S. S. Wang, A. Nieters, J. Vijai, M. Yeager, Z. Wang, H. Ghesquieres, J. McKay, L. Conde, P. I. de Bakker, D. G. Cox, L. Burdett, A. Monnereau, C. R. Flowers, A. J. De Roos, A. R. Brooks-Wilson, G. G. Giles, M. Melbye, J. Gu, R. D. Jackson, E. Kane, M. P. Purdue, C. M. Vajdic, D. Albanes, R. S. Kelly, M. Zucca, K. A. Bertrand, A. Zeleniuch-Jacquotte, C. Lawrence, A. Hutchinson, D. Zhi, T. M. Habermann, B. K. Link, A. J. Novak, A. Dogan, Y. W. Asmann, M. Liebow, C. A. Thompson, S. M. Ansell, T. E. Witzig, H. Tilly, C. Haioun, T. J. Molina, H. Hjalgrim, B. Glimelius, H. O. Adami, G. Roos, P. M. Bracci, J. Riby, M. T. Smith, E. A. Holly, W. Cozen, P. Hartge, L. M. Morton, R. K. Severson, L. F. Tinker, K. E. North, N. Becker, Y. Benavente, P. Boffetta, P. Brennan, L. Foretova, M. Maynadie, A. Staines, T. Lightfoot, S. Crouch, A. Smith, E. Roman, W. R. Diver, K. Offit, A. Zelenetz, R. J. Klein, D. J. Villano, T. Zheng, Y. Zhang, T. R. Holford, J. Turner, M. C. Southey, J. Clavel, J. Virtamo, S. Weinstein, E. Riboli, P. Vineis, R. Kaaks, H. Boeing, A. Tjonneland, E. Angelucci, S. Di Lollo, M. Rais, I. De Vivo, E. Giovannucci, P. Kraft, J. Huang, B. Ma, Y. Ye, B. C. Chiu, L. Liang, J. H. Park, C. C. Chung, D. D. Weisenburger, J. F. Fraumeni, Jr., G. Salles, M. Glenn, L. Cannon-Albright, K. Curtin, X. Wu, K. E. Smedby, S. de Sanjose, C. F. Skibola, S. I. Berndt, B. M. Birmann, S. J. Chanock and N. Rothman (2016). "Genetically predicted longer telomere length is associated with increased risk of B-cell lymphoma subtypes." Hum Mol Genet 25(8): 1663-1676. PMCID: 4854019 [Available on 2017-04-15].
11. Xin Geng, Shikai Liu, Jun Yao, Lisui Bao, Jiaren Zhang, Chao Li, Ruijia Wang, Jin Sha, Peng Zeng, Degui Zhi and Zhanjiang Liu (2016). A Genome Wide Association Study Identifies Multiple Regions Associated with Head Size in Catfish. G3: 116.032201. PMCID: 5068958.
12. Roby Joehanes, Allan C. Just, Riccardo E. Marioni, Luke C. Pilling, Lindsay M. Reynolds, Pooja R. Mandaviya, Weihua Guan, Tao Xu, Cathy E. Elks, Stella Aslibekyan, Hortensia Moreno-Macias, Jennifer A. Smith, Jennifer A. Brody, Radhika Dhingra, Paul Yousefi, James S. Pankow, Sonja Kunze, Sonia Shah, Allan F. McRae, Kurt Lohman, Jin Sha, Devin M. Absher, Luigi Ferrucci, Wei Zhao, Ellen W. Demerath, Jan Bressler, Megan L. Grove, Tianxiao Huan, Chunyu Liu, Michael M. Mendelson, Chen Yao, Douglas P. Kiel, Annette Peters, Rui Wang-Sattler, Peter M. Visscher, Naomi R. Wray, John M. Starr, Jingzhong Ding, Carlos J. Rodriguez, Nicholas J. Wareham, Marguerite R. Irvin, Degui Zhi, Myrto Barrdahl, Paolo Vineis, Srikant Ambatipudi, André G. Uitterlinden, Albert Hofman, Joel Schwartz, Elena Colicino, Lifang Hou, Pantel S. Vokonas, Dena G. Hernandez, Andrew B. Singleton, Stefania Bandinelli, Stephen T. Turner, Erin B. Ware, Alicia K. Smith, Torsten Klengel, Elisabeth B. Binder, Bruce M. Psaty, Kent D. Taylor, Sina A. Gharib, Brenton R. Swenson, Liming Liang, Dawn L. DeMeo, George T. O'Connor, Zdenko Herceg, Kerry J. Ressler, Karen N. Conneely, Nona Sotoodehnia, Sharon L.R. Kardia, David Melzer, Andrea A. Baccarelli, Joyce B.J. van Meurs, Isabelle Romieu, Donna K. Arnett, Ken K. Ong, Yongmei Liu, Melanie Waldenberger, Ian J. Deary, Myriam Fornage, Daniel Levy, and Stephanie J. London (2016). Epigenetic Signatures of Cigarette Smoking, Circ Cardiovasc Genet 2016, first published on September 20 2016 as doi:10.1161/CIRCGENETICS.116.001506. PMCID, in process.
13. Chunyu Liu, Riccardo E Marioni, Åsa K Hedman, Liliane Pfeiffer, Pei-Chien Tsai, Lindsay M Reynolds, Allan C Just, Qing Duan, Cindy G Boer, Toshiko Tanaka, Cathy E Elks, Stella Aslibekyan, Jennifer A Brody, BA, Brigitte Kühnel, Christian Herder, Degui Zhi, Yujie Wang, Tianxiao Huan, Chen Yao, Michael M Mendelson, Roby Joehanes, Liming Liang, Shelly-Ann Love, Weihua Guan, Sonia Shah, Allan F McRae, Anja Kretschmer, Holger Prokisch, Konstantin Strauch, Annette Peters, Peter M Visscher, Naomi R Wray, Xiuqing Guo, Kerri L Wiggins, Lynn M Almli, Alicia K Smith, Elisabeth B Binder, Kerry J Ressler, Ryan Irvin, Devin M Absher, Dena Hernandez, Luigi Ferrucci, Stefania Bandinelli, Kurt Lohman, Jingzhong Ding, Letizia Trevisi, Stefan Gustafsson, Johanna Sandling, Lisette Stolk, André G Uitterlinden, Idil Yet, Juan Castillo-Fernandez, BS, Timothy D Spector, Joel D Schwartz, Pantel Vokonas, Lars Lind, Yun Li, Myriam Fornage, Donna K Arnett, Nona Sotoodehnia, Ken K Ong, Joyce BJ van Meurs, Karen N Conneely, Andrea A Baccarelli, Ian J Deary, Jordana T Bell, Kari E North, Yongmei Liu, Melanie Waldenberger, Stephanie J London, Erik Ingelsson, Daniel Levy. “A DNA Methylation Biomarker of Alcohol Consumption” accepted to Molecular Psychiatry. 2016. PMCID: in process.
14. Gene Sher, Degui Zhi, Shaojie Zhang. “DRREP: Deep Ridge Regressed Epitope Predictor”, Accepted to International Conference on Intelligent Biology and Medicine (ICIBM) (2016), to be appear in a special issue of BMC Genomics.
15. Kenneth Day, Lindsay L Waite, Arnald Alonso, Marguerite R Irvin, Degui Zhi, Krista S Thibeault, Stella Aslibekyan, Bertha Hidalgo, Ingrid B Borecki, Jose M Ordovas, Donna K Arnett, Hemant K Tiwari, Devin M Absher (2016). "Heritable DNA Methylation in CD4+ Cells among Complex Families Displays Genetic and Non-Genetic Effects." PLoS One 11(10): e0165488.
16. Ardalan Naseri, Xiaoming Liu, Shaojie Zhang, Degui Zhi*, (2017). " Ultra-fast Identity by Descent Detection in Biobank-Scale Cohorts using Positional Burrows–Wheeler Transform." RECOMB accepted.
17. S. Aslibekyan, A.N. Do, H. Xu, S. Li, M.R. Irvin, D. Zhi, H.K. Tiwari, D.M. Absher, A.R. Shuldiner, T. Zhang, W. Chen, K. Tanner, C. Hong, B.D. Mitchell, G. Berenson, D.K. Arnett. (2017) “Cpt1a Methylation is Associated with Plasma Adiponectin”. Nutrition, Metabolism and Cardiovascular Diseases, accepted.
18. Mendelson, M. M., R. E. Marioni, R. Joehanes, C. Liu, A. K. Hedman, S. Aslibekyan, E. W. Demerath, W. Guan, D. Zhi, C. Yao, T. Huan, C. Willinger, B. Chen, P. Courchesne, M. Multhaup, M. R. Irvin, A. Cohain, E. E. Schadt, M. L. Grove, J. Bressler, K. North, J. Sundstrom, S. Gustafsson, S. Shah, A. F. McRae, S. E. Harris, J. Gibson, P. Redmond, J. Corley, L. Murphy, J. M. Starr, E. Kleinbrink, L. Lipovich, P. M. Visscher, N. R. Wray, R. M. Krauss, D. Fallin, A. Feinberg, D. M. Absher, M. Fornage, J. S. Pankow, L. Lind, C. Fox, E. Ingelsson, D. K. Arnett, E. Boerwinkle, L. Liang, D. Levy and I. J. Deary (2017). "Association of Body Mass Index with DNA Methylation and Gene Expression in Blood Cells and Relations to Cardiometabolic Disease: A Mendelian Randomization Approach." PLoS Med 14(1): e1002215.

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1. Ergin S, Lee HJ, Zhang Y, Huang LC, Chen X, Wei Q, Zheng JW, Chang JT, Cohen T, Sun J, and Xu H.  CATTLE (CAncer Treatment Treasury with Linked Evidence) - An Integrated Knowledgebase for Personalized Oncology Research and Practice.  Accepted, CPT: Pharmacometrics & Systems Pharmacology.
2. Boyle G, Priest HD, Richter K, Traver D, Chang JT, Mockler TC, Kay SA, and Breton G.  Comparative analysis of vertebrate diurnal/circadian transcriptomes.  PLoS One, accepted.
3. Chen X and Chang JT.  Planning bioinformatics workflows using an expert system. Bioinformatics, accepted.
4. Tsai WB, Long Y, Estecio M, Chang JT, Savaraj N, Feun LG, and Kuo MT.  Cisplatin-induced Argininosuccinate
5. Synthetase Downregulation Resulting in Synthetic Lethal to Arginine-Depleting Agent Is Mediated by Transcriptional Upregulation of HIF-1a and Downregulation of c-Myc and Independent of DNA Methylation.  Oncotarget, accepted.
6. Tang X, Wu J, Ding CK, Sjol J, Lu M, Lin CA, Keenan M, Lin CC, Wang CC, Wardell S, George D, McDonnell DP, Hsu DS, Chang JT, and Chi JT.  Cell-type specific cystine addiction associated with distinct signaling amplification of programmed necrosis. Oncogene, accepted.
7. Mansouri S, Singh S, Alamsahebpour A, Burrell K, Li M, Karabork M, Ekinci C, Solaroglu I, Chang J, Aldape K, and Zadeh G.  DICER Governs Characteristics of Glioma Stem Cells and the Resulting Tumors in Xenograft Mouse Models of GBM. Oncotarget, 2016.
8. Werden SJ*, Sphyris N*, Sarkar TR, Paranjape AN, LaBaff AM, Taube JH, Hollier BG, Ramirez-Peña EQ, Soundararajan R, Den Hollander P, Powell E, Echeverria G, Miura N, Chang JT, Piwnica-Worms H, Rosen JM, and Mani SA.  Phosphorylation of serine 367 of FOXC2 by p38 regulates ZEB1 and breast cancer metastasis, without impacting primary tumor growth.  Oncogene, 2016.
9. Tisza MJ, Fuentes JSR, Zhao W, Chen X, Levental I*, and Chang JT*.  Motility and stem cell properties induced by the Epithelial-Mesenchymal Transition require destabilization of lipid rafts.  Oncotarget, 2016.
   * Co-Corresponding Authors
10. Chen CY, Chang JT, Ho YF, and Shyu AB.  MiR-26 down-regulates TNF-?/NF-?B signaling and IL-6 expression by silencing HMGA1 and MALT1.  NAR 44(8), 2016.
11. Xu Y, Chang JT, Myers MG, Xu Y, and Tong Q.  Euglycemia restoration by central leptin in type 1 diabetes requires STAT3 signaling but not fast-acting neurotransmitter release.  Diabetes, 2016.
12. Zhao W, Prijic W, Urban BC, Tisza MJ, Li L, Tan Z, Chen X, Mani SA, and Chang JT. Candidate anti-metastasis drugs suppress the metastatic capacity of breast cancer cells by reducing membrane fluidity.  Cancer Research 76(7):2037-49, 2016.
13. Tsai WB, Long Y, Park JR, Chang JT, Liu H, Rodriguez-Canales J, Savaraj N, Feun LG, Davies MA, Wistuba II, and Kuo MT.  Gas6/Axl is the sensor of Arginine-Auxotrophic Response in Targeted Chemotherapy with Arginine-Depleting Agents.  Oncogene 35(13):1632-42, 2016.
14. Paranjape AN, Soundararajan R, Werden SJ, Joseph R, Taube JH, Liu H, Rodriguez-Canales J, Sphyris N, Wistuba I, Dhillon J, Mahajan N, Mahajan K, Chang JT, Ittmann M, Maity SN, Logothetis C, Miura N, Tang DG, and Mani SA.  Inhibition of FOXC2 restores epithelial phenotype and drug-sensitivity in prostate cancer cells with stem-like properties.  Oncogene, 2016.

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1. Lei L, Xia S, Liu D, Li X, Feng J, Zhu Y, Hu J, Xia L, Guo L, Chen F, Cheng H, Chen K, Hu H, Chen X, Li F, Zhong S, Mittal N, Yang G, Qian Z, Han L#, He C#: Genome-wide characterization of lncRNAs in acute myeloid leukemia. Briefings in Bioinformatics, 2017, bbx007
2. Lin A, Hu Q, Li C, Xing Z, Ma G, Wang C, Li J, Yao J, Liang K, Wang S, Park P, Marks J, Zhou Y, Zhou J, Hung MC, Liang H, Hu Z, Shen H, Hawke DH, Han L, Zhou Y, Lin C, Yang L: PtdIns (3,4,5)P3-lncRNA interaction exaggerates AKT activation and confers resistance to AKT inhibitors. Nature Cell Biology (Accepted)
3. Li C, Wang S, Xing Z, Lin A, Liang K, Song J, Hu Q, Yao J, Chen Z, Park P, Hawke DH, Zhou J,  Zhou Y, Zhang S, Liang H, Hung MC, Gallick G, Han L, Lin C, and Yang L: A ROR1-HER3-LncRNA signaling axis modulates the Hippo-YAP pathway to regulate bone metastasis. Nature Cell Biology (In press)
4. Song A, Zhang Y, Han L, Yegutkin G, Liu H, Sun K, D'Alessandro A, Li J, Karmouty-Quintana H, Iriyama T, Weng T, Zhao S, Wang W, Wu H, Nemkov T, Subudhi A, Jameson-Van Houten S, Julian CG, Lovering AT, Hansen KC, Zhang H, Bogdanov M, Dowhan W, Jin J, Kellems RE, Eltzschig HK, Blackburn M, Roach RC, Xia Y: Erythrocytes retain hypoxic adenosine response for faster acclimatization upon re-ascent. Nature Communications (In press)
5. Gong J, Liu C, Liu W, Xiang Y, Diao L, Guo AY#, Han L#: LNCediting: a database for functional effects of RNA editing in lncRNAs. Nucleaid Acid Research. 2016, gkw835
6. Xia S, Feng J, Lei L, Hu J, Xia L, Wang J, Xiang Y, Liu L, Zhong S, Han L#, He C#: Comprehensive characterization of tissue-specific circular RNAs in the human and mouse genomes. Briefings in Bioinformatics. 2016, bbw081.
7. Jiang HJ, Lee HS, Burt BM, Lee GK, Yoon KA, Park YY, Sohn BH, Kim SB, Kim MS, Lee JM, Joo J, Kim SC, Yoo JS, Na KJ, Choi YL, Oark JL, Kim SY, Lee YS, Han L, Liang H, Mak D, Burks JK, Zo J, Sugarbaker DJ, Shim YM, Lee JS: Integrated Genomic Analysis of Recurrence-Associated Small Non-coding RNAs in Oesophageal Cancer. Gut. 2016, pii: gutjnl-2015-311238
8. Marini A, Lena AM, Panatta E, Ivan C, Han L, Liang H, Annicchiarico-Petruzzelli M, Di Daniele N, Calin GA, Candi E, Melino G: Ultraconserved long non-coding RNA uc.63 in breast cancer. Oncotarget. 2016 (In press)
9. Zhou B, Wang L, Zhang S, Bennett BD, He F, Zhang Y, Xiong C, Han L, Diao L, Li P, Fargo DC, Cox AD, Hu G: INO80 governs superenhancer-mediated oncogenic transcription and tumor growth in melanoma. Genes & Development. 2016, 30:1440-53
10. Liu X, Xiao ZD, Han L, Zhang J, Lee SW, Wang W, Lee H, Zhuang L, Chen J, Lin HK, Wang J, Liang H, Gan B: LncRNA NBR2 engages a metabolic checkpoint by regulating AMPK under energy stress. Nature Cell Biology, 2016, 18: 431-442
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1. Savarraj J, Parsha KN, Hergenroeder G, Zhu L, Bajgur S, Ahn S, Lee K, Chang T, Kim D, Liu Y, and Choi H. Systematic Model of Peripheral Inflammation after Subarachnoid Hemorrhage. Neurology, in press.
2. Moussa H, Baha S, Blackwell S, Leon M, Redell, J, Liu Y, Dash P, and Longo M. Contribution of Maternal Hypertension to Autism Etiology in a Murine Model; Cerebellar Gene Expression. Future Neurology, in press.
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5. Woodfield S, Zhang L, Scorsone K, Liu Y, and Zage P. Binimetinib inhibits MEK and is effective against neuroblastoma tumor cells with low NF1 expression. BMC Cancer, 16: 172, 2016.
6. Wang Z. Xu W, and Liu Y. Systematic and integrative analysis of gene expression to identify feature genes underlying human diseases. In: Translational Bioinformatics in Transcriptomic and Gene Regulation (Wu, J., ed), pp: 161-185, Springer, 2016.

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1. Tu J, Huo Z, Gingold J, Zhao R, Shen J, Lee DF. The histogenesis of Ewing Sarcoma. Cancer Rep Rev. 1(2):1-2, 2017.
2. Lu J, Song G, Tang Q, Yin J, Zou C, Zhao Z, Xie X, Xu H, Huang G, Wang J, Lee DF, Khokha R, Yang H, Shen J. MiR-26a inhibits stem cell-like phenotype and tumor growth of osteosarcoma by targeting Jagged1. Oncogene. 36(2):231-241, 2017.
3. Li C, Wang S, Xing Z, Lin A, Liang K, Song J, Hu Q, Yao J, Chen Z, Park P, Hawke DH, Zhou J, Zhou Y, Zhang S, Liang H, Hung MC, Gallick G, Lee DF, Lin C, and Yang L: A ROR1-HER3-LncRNA signaling axis modulates the Hippo-YAP pathway to regulate bone metastasis. Nature Cell Biology (In press)
4. Gingold J, Zhou R, Lemischka IR, Lee DF. Modeling cancer with pluripotent stem cells. Trends Cancer. 2(9):485-494, 2016
5. Lee DF, Walsh MJ, Aguilo F. ZNF217/ZFP217 meets chromatin and RNA (2016). Trends Biochem Sci. 41(12):986-988, 2016.
6. Li CW, Xia W, Lim SO, Hsu JL, Huo L, Wu Y, Li LY, Lai CC, Chang SS, Hsu YH, Sun HL, Kim J, Yamaguchi H, Lee DF, Wang H, Wang Y, Chou CK, Hsu JM, Lai YJ, LaBaff AM, Ding Q, Ko HW, Tsai FJ, Tsai CH, Hortobagyi GN, Hung MC. AKT1 Inhibits Epithelial-to-Mesenchymal Transition in Breast Cancer through Phosphorylation-Dependent Twist1 Degradation.Cancer Res. 76(6):1451-62, 2016.

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