Liu M, Su YR, Liu Y, Hsu L*, He Q*. Structured testing of genetic association with mixed clinical outcomes. (2024) Genetic Epidemiology, doi: 10.1002/gepi.22560, Online ahead of print. PMID: 38606632 [Co-corresponding author]

Liu M, Liu Y, Hsu L, He Q*. TCR-pred:  incorporating T-cell receptor repertoire for clinical outcome prediction. (2024) Frontiers in Genetics, 15: 1345559. PMCID: PMC10965803 [*Corresponding author]

Burnett-Hartman A, Ton M, He Q, Malen R, Potter JD, Reedy AM, Phipps AI, Newcomb PA. Dietary factors differ between young-onset and older-onset colorectal cancer patients. (2024) Nutrition and Cancer, 76: 352-355.  PMID: 38347682

Pietrosanu M, Shu H, Jiang B, Kong L, Heo G, He Q, Gilmore J, Zhu H. Estimation for the bivariate quantile varying coefficient model with application to diffusion tensor imaging data analysis. (2023) Biostatistics, 24:465-480. PMCID: PMC10102902

Vutien P, Berry K, ..., He Q, ..., Ioannou G. Combining FIB-4 and liver stiffness into the FIB-5, a single model that accurately predicts complications of portal hypertension. (2022) American Journal of Gastroenterology, 117: 1999. PMCID: PMC9741846

Peng K, Deng N, ..., He Q, ..., Shen F.  Alpha-momorcharin inhibits proinflammatory cytokine expression by M1 macrophage but not anti-inflammatory cytokine expression by M2 macrophages. (2022) Journal of Inflammation Research,15: 4853. PMCID: PMC9420447

Liu M, Goo J, Liu Y, Sun W, MC Wu, Hsu L, He Q*. TCR-L: an analysis tool for evaluating the association between the T-cell receptor repertoire and clinical phenotypes. (2022) BMC Bioinformatics, 23: 152. PMCID: PMC9052542 [*Corresponding author]

Liu Y, Sun W, Hsu L, He Q*. Statistical inference for high-dimensional pathway analysis with multiple responses. (2022) Computational Statistics and Data Analysis, 169: 107418. PMCID: PMC8813039 [*Corresponding author]

Schroeder B, Zhang Y, ..., He Q*, Pollack S*. Immunologic gene signature analysis correlates myeloid cells and M2 macrophages with time to trabectedin failure in sarcoma patients. (2022) Cancers, 14: 1290. PMCID: PMC8909887 [*Co-corresponding author]

Wang A, Hai R, Rider P, He Q. Noncoding RNAs and deep learning neural network discriminate multi-cancer types. (2022) Cancers, 14: 352. PubMed PMCID: PMC8774129

Wagner M, ..., He Q, ..., Pollack S. A Phase I/II Trial Combining Avelumab and Trabectedin for Advanced Liposarcoma and Leiomyosarcoma. (2022) Clinical Cancer Research, 28:2306-2312. doi: 10.1158/1078-0432.CCR-22-0240. PMCID: PMC9249583

Goff P, ..., He Q, ..., Pollack S. Neoadjuvant therapy induces a potent immune response to sarcoma, dominated by myeloid and B-cells. (2022) Clinical Cancer Research, 28: 1701-1711. PMCID: PMC9953754

He Q, Liu Y, Liu M, Wu MC, Hsu L. Random effect based tests for multinomial logistic regression in genetic association studies. (2021) Genetic Epidemiology, 45: 736-740. PMCID: PMC9209005

Turner J, He Q, ..., Flowers M, Cheng GS.  Home spirometry telemonitoring for early detection of bronchiolitis obliterans syndrome in patients with chronic graft versus host disease. (2021) Transplantation and cellular therapy,  21: 801. 
PMCID: PMC8423348

Thomas M, Sakoda L, ..., He Q,..., Hsu L.  Response to Li and Hopper. (2021) American Journal of Human Genetics, 108: 527-529.  PMCID: PMC8008475

Liu M, Liu Y, Wu M, Hsu L, He Q*. A Method for subtype analysis with somatic mutations. (2021) Bioinformatics. doi: 10.1093/bioinformatics/btaa1090. Online ahead of print. PMID: 33416828. [*Co-corresponding author]

Dighe S, Chen J, . . . , He Q, . . . , Buas M. Germline variation in the insulin-like growth factor pathway and risk of Barrett’s esophagus and esophageal adenocarcinoma. (2021) Carcinogenesis. 42(3):369-377. doi: 10.1093/carcin/bgaa132. Online ahead of print. PMCID: PMC8052954

Thomas M, Sakoda L, ..., He Q,..., Hsu L. Genome-wide modeling of polygenic risk score in colorectal cancer risk. (2020) American Journal of Human Genetics, 107: 432-444. PMCID: PMC7477007

Dong X, Su YR, ..., He Q, ..., Hsu L. A general framework for functionally informed set-based analysis: Application to a large-scale colorectal cancer study. (2020) PLoS Genetics, 16: e1008947. PMCID: PMC7470748

Cheng GS, Bondeelle L, Gooley T, He Q, Jamani K, Krakow EF, Flowers MED, de Latour RP, Michonneau D, Socié G, Chien JW, Chevret S, Bergeron A. Azithromycin use and increased cancer risk among patients with bronchiolitis obliterans after hematopoietic cell transplantation. (2020) Biol Blood Marrow Transplant. 26(2):392-400. doi: 10.1016/j.bbmt.2019.10.025. Epub 2019 Nov 1. PMCID: PMC7430235.

Liu B, Zhang Z, Lu S, He Q, Deng N, Meng H, Pan C, Li H, Liu M, Huang A, Shen F. In-silico analysis of ligand-receptor binding patterns of α-MMC, TCS and MAP30 protein to LRP1 receptor.  (2020) J Mol Graph Model. 98:107619. doi: 10.1016/j.jmgm.2020.107619.  Apr 10. PMID: 32311663.

Jamani K, He Q, Liu Y, Davis C, Hubbard J, Schoch G, Lee SJ, Gooley T, Flowers MED, Cheng GS. Early post-transplantation spirometry is associated with the development of bronchiolitis obliterans syndrome after allogeneic hematopoietic cell transplantation. (2020) Biol Blood Marrow Transplant. 26(5):943-948.  PMCID: PMC7255698

Zhang S, Kohli K, Black RG, Yao L, Spadinger SM, He Q, Pillarisetty VG, Cranmer LD, Van Tine BA, Yee C, Pierce RH, Riddell SR, Jones RL, Pollack SM. Systemic interferon-γ increases MHC class I expression and T-cell infiltration in cold tumors: Results of a phase 0 clinical trial. (2019) Cancer Immunol Res.  doi: 10.1158/2326-6066.CIR-18-0940. [Epub ahead of print] PMCID: PMC6677581.

Deng N, Li M, Shen D, He Q, et al. LRP1 Receptor-mediated Immunosuppression of alpha-MMC on monocytes. (2019) International Immunopharmacology, 90: 80-8. PMID: 30785094.

Liu Y,  Sun W, Reiner A, Kooperberg C, He Q*. Statistical inference for genetic pathway analysis under high dimensions. (2019) Biometrika, 106(3):651. PMCID: PMC6690174 [*Corresponding author].

Deng N, Sun Y, Liu M, He Q, et al. Alpha-momorcharin regulates cytokine expression and induces apoptosis in monocytes. (2019) Immunopharmacology and Immunotoxicology, 7: 1-9. PMID: 31062632.

Liu Y, He Q, Sun W. Association analysis using somatic mutations. PLoS Genet. 2018 Nov 2;14(11):e1007746. eCollection 2018 Nov. Erratum in: PLoS Genet. 2018 Dec 6;14(12):e1007848. PMCID: PMC6235399.

He Q, Liu Y, Sun W. Statistical analysis of non-coding RNA data. Cancer Lett. 2018 Mar 28;417:161-167. Review. PMCID: PMC5826599.

He Q, Liu Y, Peters U, Hsu L. Multivariate association analysis with somatic mutation data. Biometrics. 2018 Mar;74(1):176-184. PMCID: PMC5967890.

Buas MF, He Q, Johnson LG, Onstad L, Levine DM, Thrift AP, Gharahkhani P, Palles C, Lagergren J, Fitzgerald RC, Ye W, Caldas C, Bird NC, Shaheen NJ, Bernstein L, Gammon MD, Wu AH, Hardie LJ, Pharoah PD, Liu G, Iyer P, Corley DA, Risch HA, Chow WH, Prenen H, Chegwidden L, Love S, Attwood S, Moayyedi P, MacDonald D, Harrison R, Watson P, Barr H, deCaestecker J, Tomlinson I, Jankowski J, Whiteman DC, MacGregor S, Vaughan TL, Madeleine MM. Germline variation in inflammation-related pathways and risk of Barrett's oesophagus and oesophageal adenocarcinoma. Gut. 2017 Oct;66(10):1739-1747. PMCID: PMC5296402.

Pollack SM, He Q, Yearley JH, Emerson R, Vignali M, Zhang Y, Redman MW, Baker KK, Cooper S, Donahue B, Loggers ET, Cranmer LD, Spraker MB, Seo YD, Pillarisetty VG, Ricciotti RW, Hoch BL, McClanahan TK, Murphy E, Blumenschein WM, Townson SM, Benzeno S, Riddell SR, Jones RL. T-cell infiltration and clonality correlate with programmed cell death protein 1 and programmed death-ligand 1 expression in patients with soft tissue sarcomas. Cancer. 2017 Sep 1;123(17):3291-3304. PMCID: PMC5568958.

Xun P and He Q. Multivariate Analysis, Chapter 4 In Handbook of Medical Statistics (Fang, Ji-Qian, Eds.), World Scientific Co., Singapore, 2017. ISBN-10: 9813148950

He Q, Cai T, Liu Y, Zhao N, Harmon QE, Almli LM, Binder EB, Engel SM, Ressler KJ, Conneely KN, Lin X, Wu MC. Prioritizing individual genetic variants after kernel machine testing using variable selection. Genet Epidemiol. 2016 Dec;40(8):722-731. PMCID: PMC5118060.

He Q, Zhang HH, Avery CL, Lin DY. Sparse meta-analysis with high-dimensional data. Biostatistics. 2016 Apr;17(2):205-20. PMCID: PMC4834947.

He Q, Kong L, Wang Y, Wang S, Chan TA, Holland E. Regularized quantile regression under heterogeneous sparsity with application to quantitative genetic traits. Comput Stat Data Anal. 2016 Mar;95:222-239. PMCID: PMC5267342.

Deng N, Wang L, He Q, Zheng J, Meng Y, Meng Y, Zhang C, Shen F. PEGylation alleviates the non-specific toxicities of alpha-momorcharin and preserves its antitumor efficacy in vivo.  (2016) Drug Delivery, 23: 95-100.

Wang L, Shen F, Zhang M, He Q, Yu X, Deng F, Yang S, Liu Y, Deng N, Zheng J, Zhu L, Liu X.  Cytotoxicity mechanism of a-MMC in normal liver cells through LRP1 mediated endocytosis and JNK activation. (2016) Toxicology, 357: 33-43.

Karyadi DM, Zhao S, He Q, McIntosh L, Wright JL, Ostrander EA, Feng Z, Stanford JL. Confirmation of genetic variants associated with lethal prostate cancer in a cohort of men from hereditary prostate cancer families. Int J Cancer. 2015 May 1;136(9):2166- 71. PMCID: PMC4331209.

Nyante SJ, Gammon MD, Kaufman JS, Bensen JT, Lin DY, Barnholtz-Sloan JS, Hu Y, He Q, Luo J, Millikan RC. Genetic variation in estrogen and progesterone pathway genes and breast cancer risk: an exploration of tumor subtype-specific effects. Cancer Causes Control. 2015 Jan;26(1):121-31. PMCID: PMC4291841.

Cao D, Sun Y, Wang L, He Q, Zheng J, Deng S, Li M, Meng Y, Jin J, Shen F, Chang S, Yu X. Alpha-momorcharin exerts effective anti-human breast tumor activities but has a narrow therapeutic window in vivo. (2015) Fitoterapia, 100: 139-149.

Wang L, Zheng J, He Q, Yu X, Hu X, Deng S, Chang S, and Shen F. TOA02, a recombinant adenovirus with tumor-specific GM-CSF expression, has limited biodistribution and low toxicity in Rhesus monkeys. (2015) Human Gene Therapy, 26: 62-70.

 Wang A*, He Q*, Zhong Y. Systematically dissecting the global mechanism of miRNA functions in mouse pluripotent stem cells. (2015) BMC Genomics, 16: 490. [*Co-corresponding author] PMCID: PMC4488055

Wang A, Yan Zhong, Yanhua Wang, He Q. A web-server of Cell Type Discrimination System. (2014). The Scientific World Journal, 2014: 1-5. PMCID: PMC3919083

He Q, Avery CL, Lin DY. A general framework for association tests with multivariate traits in large-scale genomics studies. Genet Epidemiol. 2013 Dec;37(8):759-67. PMCID: PMC3926135.

Peng Y, Dai Y, Hitchcock C, Yang X, Kassis ES, Liu L, Luo Z, Sun HL, Cui R, Wei H, Kim T, Lee TJ, Jeon YJ, Nuovo GJ, Volinia S, He Q, Yu J, Nana-Sinkam P, Croce CM. Insulin growth factor signaling is regulated by microRNA-486, an underexpressed microRNA in lung cancer. Proc Natl Acad Sci U S A. 2013 Sep 10;110(37):15043-8. PMCID: PMC3773758.

Wang A, Du Y, He Q, Zhou C. A quantitative system for discriminating induced pluripotent stem cells, embryonic stem cells and somatic cells. (2013). PLoS ONE, 8(2): e56095.

Xun P, Wu Y, He Q, and He K. Fasting insulin levels and incidence of hypertension stroke and coronary heart disease: a meta-analysis of prospective cohort studies. (2013). American Journal of Clinical Nutrition, 98(6): 1543-54.

Avery CL, Sethupathy P, Buyske S, He Q, Lin DY, Arking DE, Carty CL, Duggan D, Fesinmeyer MD, Hindorff LA, Jeff JM, Klein L, Patton KK, Peters U, Shohet RV, Sotoodehnia N, Young AM, Kooperberg C, Haiman CA, Mohlke KL, Whitsel EA, North KE. Fine-mapping and initial characterization of QT interval loci in African Americans. PLoS Genet. 2012;8(8):e1002870. PMCID: PMC3415454.

Meng Y, Liu B, Lei N, Zheng JC, He Q, Li D, Zhao X, Shen F. Alpha-momorcharin possessing high immunogenicity, immunotoxicity and hepatotoxicity in rats. (2012). Journal of Ethnopharmacology, 139(2): 590-598.

Zheng J, Lei N, He Q, Hu W, Jin J, Meng Y, Deng N, Meng Y, Zhang C, Shen F. PEGylation is effective in reducing immunogenicity, immunotoxicity and hepatotoxicity of alpha-momorcharin in vivo. (2012). Immunopharmacology and Immunotoxicology, 34(5): 866-873.

Avery CL, He Q, North KE, Ambite JL, Boerwinkle E, Fornage M, Hindorff LA, Kooperberg C, Meigs JB, Pankow JS, Pendergrass, SA, Psaty BM, Ritchie MD, Rotter JI, Taylor KD, Wilkens LR, Heiss G, Lin DY. A phenomics-based strategy identifies loci on APOC1, BRAP, and PLCG1 associated with metabolic syndrome phenotype domains. PLoS Genet. 2011 Oct;7(10):e1002322. PMCID: PMC3192835.

Nyante SJ, Gammon MD, Kaufman JS, Bensen JT, Lin DY, Barnholtz-Sloan JS, Hu Y, He Q, Luo J, Millikan RC. Common genetic variation in adiponectin, leptin, and leptin receptor and association with breast cancer subtypes. Breast Cancer Res Treat. 2011 Sep;129(2):593-606. PMCID: PMC3355661.

He Q, Lin DY. A variable selection method for genome-wide association studies. Bioinformatics. 2011 Jan 1;27(1):1-8. PMCID: PMC3025714.

Sullivan PF, de Geus EJ, Willemsen G, James MR, Smit JH, Zandbelt T, Arolt V, Baune BT, Blackwood D, Cichon S, Coventry, WL, Domschke K, Farmer A, Fava M, Gordon SD, He Q, Heath AC, Heutink P, Holsboer F, Hoogendijk WJ, Hottenga JJ, Hu Y, Kohli M, Lin D, Lucae S, Macintyre DJ, Maier W, McGhee KA, McGuffin P, Montgomery GW, Muir WJ, Nolen WA, Nöthen MM, Perlis RH, Pirlo K, Posthuma D, Rietschel M, Rizzu P, Schosser A, Smit AB, Smoller JW, Tzeng JY, van Dyck R, Verhage M, Zitman FG, Martin NG, Wray NR, Boomsma DI, Penninx BW. Genome-wide association for major depressive disorder: a possible role for the presynaptic protein piccolo. Mol Psychiatry. 2009 Apr;14(4):359-75. PMCID: PMC2717726.

He Q, Madsen M, Kilkenney A, Gregory B, Christensen EI, Vorum H, Hojrup P, Schaffer AA, Kirkness EF, Tanner SM, de la Chapelle A, Giger U, Moestrup SK, Fyfe JC. Amnionless function is required for cubilin brush-border expression and intrinsic factor-cobalamin (vitamin B12) absorption in vivo. (2005). Blood, 106(4): 1447-53. (with discussion.)

Fyfe JC, Madsen M, Hørup P, Christensen EI, Tanner SM, de la Chapelle A, He Q, Moestrup SK. The functional cobalamin (vitamin B12)-intrinsic factor receptor is a novel complex of cubilin and amnionless. (2004). Blood, 103(5): 1573-1579. (with discussion.)

He Q, Lowrie C, Shelton GD, Castellani RJ, Menotti-Raymond M, Murphy W, O'Brien SJ, Swanson WF, Fyfe JC. Inherited motor neuron disease in domestic cats: a model of spinal muscular atrophy. (2005).  Pediatric Research, 57(3): 324-30.

Fyfe JC, Kampschmidt K, Dang V, Poteet BA, He Q, Lowrie C, Graham PA, Fetro VM. Congenital hypothyroidism with goiter in toy fox terriers. (2003). Journal of Veterinarian Internal Medicine, 17(1): 50-57.

He Q, Fyfe JC, Schaffer AA, Kilkenney A, Werner P, Kirkness EF, Henthorn PS. Canine Imerslund-Gräsbeck syndrome maps to a region orthologous to HSA14q. (2003). Mammalian Genome, 14(11): 758-764.