My Bibliography

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Moghal N, Li Q, Stewart EL, Navab R, Mikubo M, D'Arcangelo E, Martins-Filho SN, Raghavan V, Pham NA, Li M, Shepherd FA, Liu G, Tsao MS. Single-Cell Analysis Reveals Transcriptomic Features of Drug-Tolerant Persisters and Stromal Adaptation in a Patient-Derived EGFR-Mutated Lung Adenocarcinoma Xenograft Model. J Thorac Oncol. 2023 Apr;18(4):499-515. doi: 10.1016/j.jtho.2022.12.003. Epub 2022 Dec 16. PubMed PMID: 36535627.

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Eder L, Li Q, Rahmati S, Rahman P, Jurisica I, Chandran V. Defining imaging sub-phenotypes of psoriatic arthritis: integrative analysis of imaging data and gene expression in a PsA patient cohort. Rheumatology (Oxford). 2022 Nov 28;61(12):4952-4961. doi: 10.1093/rheumatology/keac078. PubMed PMID: 35157043; PubMed Central PMCID: PMC9707284.

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Guo L, Park J, Yi E, Marchi E, Hsieh TC, Kibalnyk Y, Moreno-Sáez Y, Biskup S, Puk O, Beger C, Li Q, Wang K, Voronova A, Krawitz PM, Lyon GJ. KBG syndrome: videoconferencing and use of artificial intelligence driven facial phenotyping in 25 new patients. Eur J Hum Genet. 2022 Nov;30(11):1244-1254. doi: 10.1038/s41431-022-01171-1. Epub 2022 Aug 15. PubMed PMID: 35970914; PubMed Central PMCID: PMC9626563.

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Li Q, Ren Z, Cao K, Li MM, Wang K, Zhou Y. CancerVar: An artificial intelligence-empowered platform for clinical interpretation of somatic mutations in cancer. Sci Adv. 2022 May 6;8(18):eabj1624. doi: 10.1126/sciadv.abj1624. Epub 2022 May 6. PubMed PMID: 35544644; PubMed Central PMCID: PMC9075800.

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Mirhadi S, Tam S, Li Q, Moghal N, Pham NA, Tong J, Golbourn BJ, Krieger JR, Taylor P, Li M, Weiss J, Martins-Filho SN, Raghavan V, Mamatjan Y, Khan AA, Cabanero M, Sakashita S, Huo K, Agnihotri S, Ishizawa K, Waddell TK, Zadeh G, Yasufuku K, Liu G, Shepherd FA, Moran MF, Tsao MS. Integrative analysis of non-small cell lung cancer patient-derived xenografts identifies distinct proteotypes associated with patient outcomes. Nat Commun. 2022 Apr 5;13(1):1811. doi: 10.1038/s41467-022-29444-9. PubMed PMID: 35383171; PubMed Central PMCID: PMC8983714.

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Huo KG, Notsuda H, Fang Z, Liu NF, Gebregiworgis T, Li Q, Pham NA, Li M, Liu N, Shepherd FA, Marshall CB, Ikura M, Moghal N, Tsao MS. Lung Cancer Driven by BRAF^G469V Mutation Is Targetable by EGFR Kinase Inhibitors. J Thorac Oncol. 2022 Feb;17(2):277-288. doi: 10.1016/j.jtho.2021.09.008. Epub 2021 Oct 12. PubMed PMID: 34648945.

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Ly D, Li Q, Navab R, Zeltz C, Fang L, Cabanero M, Zhu CQ, Tsao MS, Zhang L. Tumor-Associated Regulatory T Cell Expression of LAIR2 Is Prognostic in Lung Adenocarcinoma. Cancers (Basel). 2021 Dec 31;14(1). doi: 10.3390/cancers14010205. PubMed PMID: 35008369; PubMed Central PMCID: PMC8744930.

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Rosen JC, Weiss J, Pham NA, Li Q, Martins-Filho SN, Wang Y, Tsao MS, Moghal N. Antitumor efficacy of XPO1 inhibitor Selinexor in KRAS-mutant lung adenocarcinoma patient-derived xenografts. Transl Oncol. 2021 Oct;14(10):101179. doi: 10.1016/j.tranon.2021.101179. Epub 2021 Jul 17. PubMed PMID: 34284202; PubMed Central PMCID: PMC8313753.

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Pham NA, Radulovich N, Ibrahimov E, Martins-Filho SN, Li Q, Pintilie M, Weiss J, Raghavan V, Cabanero M, Denroche RE, Wilson JM, Metran-Nascente C, Borgida A, Hutchinson S, Dodd A, Begora M, Chadwick D, Serra S, Knox JJ, Gallinger S, Hedley DW, Muthuswamy L, Tsao MS. Patient-derived tumor xenograft and organoid models established from resected pancreatic, duodenal and biliary cancers. Sci Rep. 2021 May 19;11(1):10619. doi: 10.1038/s41598-021-90049-1. PubMed PMID: 34011980; PubMed Central PMCID: PMC8134568.

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Rahmati S, Li Q, Rahman P, Chandran V. Insights into the pathogenesis of psoriatic arthritis from genetic studies. Semin Immunopathol. 2021 Apr;43(2):221-234. doi: 10.1007/s00281-021-00843-2. Epub 2021 Mar 12. Review. PubMed PMID: 33712923.

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Iafolla MAJ, Yang C, Chandran V, Pintilie M, Li Q, Bedard PL, Hansen A, Lheureux S, Spreafico A, Razak AA, Hakgor S, Giesler A, Pugh TJ, Siu LL. Predicting Toxicity and Response to Pembrolizumab Through Germline Genomic HLA Class 1 Analysis. JNCI Cancer Spectr. 2021 Feb;5(1). doi: 10.1093/jncics/pkaa115. eCollection 2021 Feb. PubMed PMID: 33554038; PubMed Central PMCID: PMC7853183.

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Rahmati S, O'Rielly DD, Li Q, Codner D, Dohey A, Jenkins K, Jurisica I, Gladman DD, Chandran V, Rahman P. Rho-GTPase pathways may differentiate treatment response to TNF-alpha and IL-17A inhibitors in psoriatic arthritis. Sci Rep. 2020 Dec 10;10(1):21703. doi: 10.1038/s41598-020-78866-2. PubMed PMID: 33303908; PubMed Central PMCID: PMC7728744.

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Li Q, Cao Z, Rahman P. Genetic variability of human angiotensin-converting enzyme 2 (hACE2) among various ethnic populations. Mol Genet Genomic Med. 2020 Aug;8(8):e1344. doi: 10.1002/mgg3.1344. Epub 2020 Jun 18. PubMed PMID: 32558308; PubMed Central PMCID: PMC7323111.

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Shi R, Filho SNM, Li M, Fares A, Weiss J, Pham NA, Ludkovski O, Raghavan V, Li Q, Ravi D, Cabanero M, Moghal N, Leighl NB, Bradbury P, Sacher A, Shepherd FA, Yasufuku K, Tsao MS, Liu G. BRAF V600E mutation and MET amplification as resistance pathways of the second-generation anaplastic lymphoma kinase (ALK) inhibitor alectinib in lung cancer. Lung Cancer. 2020 Aug;146:78-85. doi: 10.1016/j.lungcan.2020.05.018. Epub 2020 May 21. PubMed PMID: 32521388.

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Martins-Filho SN, Weiss J, Pham NA, Li Q, Cabanero M, Fares A, Stewart EL, Shi R, Patel D, Pal P, McConnell J, Bradbury PA, Sacher AG, Leighl NB, Grindlay A, Allison F, Li M, Yasufuku K, Shepherd FA, Moghal N, Tsao MS, Liu G. EGFR-mutated lung adenocarcinomas from patients who progressed on EGFR-inhibitors show high engraftment rates in xenograft models. Lung Cancer. 2020 Jul;145:144-151. doi: 10.1016/j.lungcan.2020.03.022. Epub 2020 May 11. PubMed PMID: 32447118.

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Li Q, Chandran V, Tsoi L, O'Rielly D, Nair RP, Gladman D, Elder JT, Rahman P. Quantifying Differences in Heritability among Psoriatic Arthritis (PsA), Cutaneous Psoriasis (PsC) and Psoriasis vulgaris (PsV). Sci Rep. 2020 Mar 18;10(1):4925. doi: 10.1038/s41598-020-61981-5. PubMed PMID: 32188927; PubMed Central PMCID: PMC7080781.

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Shi R, Radulovich N, Ng C, Liu N, Notsuda H, Cabanero M, Martins-Filho SN, Raghavan V, Li Q, Mer AS, Rosen JC, Li M, Wang YH, Tamblyn L, Pham NA, Haibe-Kains B, Liu G, Moghal N, Tsao MS. Organoid Cultures as Preclinical Models of Non-Small Cell Lung Cancer. Clin Cancer Res. 2020 Mar 1;26(5):1162-1174. doi: 10.1158/1078-0432.CCR-19-1376. Epub 2019 Nov 6. PubMed PMID: 31694835.

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Lyon GJ, Marchi E, Ekstein J, Meiner V, Hirsch Y, Scher S, Yang E, De Vivo DC, Madrid R, Li Q, Wang K, Haworth A, Chilton I, Chung WK, Velinov M. VAC14 syndrome in two siblings with retinitis pigmentosa and neurodegeneration with brain iron accumulation. Cold Spring Harb Mol Case Stud. 2019 Dec;5(6). doi: 10.1101/mcs.a003715. Print 2019 Dec. PubMed PMID: 31387860; PubMed Central PMCID: PMC6913149.

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Alriyami M, Marchand L, Li Q, Du X, Olivier M, Polychronakos C. Clonal copy-number mosaicism in autoreactive T lymphocytes in diabetic NOD mice. Genome Res. 2019 Dec;29(12):1951-1961. doi: 10.1101/gr.247882.118. Epub 2019 Nov 6. PubMed PMID: 31694869; PubMed Central PMCID: PMC6886509.

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Cheng H, Capponi S, Wakeling E, Marchi E, Li Q, Zhao M, Weng C, Stefan PG, Ahlfors H, Kleyner R, Rope A, Lumaka A, Lukusa P, Devriendt K, Vermeesch J, Posey JE, Palmer EE, Murray L, Leon E, Diaz J, Worgan L, Mallawaarachchi A, Vogt J, de Munnik SA, Dreyer L, Baynam G, Ewans L, Stark Z, Lunke S, Gonçalves AR, Soares G, Oliveira J, Fassi E, Willing M, Waugh JL, Faivre L, Riviere JB, Moutton S, Mohammed S, Payne K, Walsh L, Begtrup A, Guillen Sacoto MJ, Douglas G, Alexander N, Buckley MF, Mark PR, Adès LC, Sandaradura SA, Lupski JR, Roscioli T, Agrawal PB, Kline AD, Wang K, Timmers HTM, Lyon GJ. Missense variants in TAF1 and developmental phenotypes: challenges of determining pathogenicity. Hum Mutat. 2019 Oct 23;. doi: 10.1002/humu.23936. [Epub ahead of print] PubMed PMID: 31646703; PubMed Central PMCID: PMC7187541.

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He MM, Li Q, Yan M, Cao H, Hu Y, He KY, Cao K, Li MM, Wang K. Variant Interpretation for Cancer (VIC): a computational tool for assessing clinical impacts of somatic variants. Genome Med. 2019 Aug 23;11(1):53. doi: 10.1186/s13073-019-0664-4. PubMed PMID: 31443733; PubMed Central PMCID: PMC6708137.

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Hao J, Zeltz C, Pintilie M, Li Q, Sakashita S, Wang T, Cabanero M, Martins-Filho SN, Wang DY, Pasko E, Venkat K, Joseph J, Raghavan V, Zhu CQ, Wang YH, Moghal N, Tsao MS, Navab R. Characterization of Distinct Populations of Carcinoma-Associated Fibroblasts from Non-Small Cell Lung Carcinoma Reveals a Role for ST8SIA2 in Cancer Cell Invasion. Neoplasia. 2019 May;21(5):482-493. doi: 10.1016/j.neo.2019.03.009. Epub 2019 Apr 9. PubMed PMID: 30978569; PubMed Central PMCID: PMC6458340.

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Li Q, Wang K. InterVar: Clinical Interpretation of Genetic Variants by the 2015 ACMG-AMP Guidelines. Am J Hum Genet. 2017 Feb 2;100(2):267-280. doi: 10.1016/j.ajhg.2017.01.004. Epub 2017 Jan 26. PubMed PMID: 28132688; PubMed Central PMCID: PMC5294755.

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Pater JA, Benteau T, Griffin A, Penney C, Stanton SG, Predham S, Kielley B, Squires J, Zhou J, Li Q, Abdelfatah N, O'Rielly DD, Young TL. A common variant in CLDN14 causes precipitous, prelingual sensorineural hearing loss in multiple families due to founder effect. Hum Genet. 2017 Jan;136(1):107-118. doi: 10.1007/s00439-016-1746-7. Epub 2016 Nov 12. PubMed PMID: 27838790; PubMed Central PMCID: PMC5215284.

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He KY, Zhao Y, McPherson EW, Li Q, Xia F, Weng C, Wang K, He MM. Pathogenic Mutations in Cancer-Predisposing Genes: A Survey of 300 Patients with Whole-Genome Sequencing and Lifetime Electronic Health Records. PLoS One. 2016;11(12):e0167847. doi: 10.1371/journal.pone.0167847. eCollection 2016. PubMed PMID: 27930734; PubMed Central PMCID: PMC5145192.

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Shi L, Guo Y, Dong C, Huddleston J, Yang H, Han X, Fu A, Li Q, Li N, Gong S, Lintner KE, Ding Q, Wang Z, Hu J, Wang D, Wang F, Wang L, Lyon GJ, Guan Y, Shen Y, Evgrafov OV, Knowles JA, Thibaud-Nissen F, Schneider V, Yu CY, Zhou L, Eichler EE, So KF, Wang K. Long-read sequencing and de novo assembly of a Chinese genome. Nat Commun. 2016 Jun 30;7:12065. doi: 10.1038/ncomms12065. PubMed PMID: 27356984; PubMed Central PMCID: PMC4931320.

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Li Q, Liu X, Gibbs RA, Boerwinkle E, Polychronakos C, Qu HQ. Gene-specific function prediction for non-synonymous mutations in monogenic diabetes genes. PLoS One. 2014;9(8):e104452. doi: 10.1371/journal.pone.0104452. eCollection 2014. PubMed PMID: 25136813; PubMed Central PMCID: PMC4138110.

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Zouk H, Marchand L, Li Q, Polychronakos C. Functional characterization of the Thr946Ala SNP at the type 1 diabetes IFIH1 locus. Autoimmunity. 2014 Feb;47(1):40-5. doi: 10.3109/08916934.2013.832758. Epub 2013 Oct 14. PubMed PMID: 24117221.

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Li Q, Qu HQ. Human coding synonymous single nucleotide polymorphisms at ramp regions of mRNA translation. PLoS One. 2013;8(3):e59706. doi: 10.1371/journal.pone.0059706. Epub 2013 Mar 19. PubMed PMID: 23527255; PubMed Central PMCID: PMC3602041.

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Li Q, Makri A, Lu Y, Marchand L, Grabs R, Rousseau M, Ounissi-Benkalha H, Pelletier J, Robert F, Harmsen E, Hudson TJ, Pastinen T, Polychronakos C, Qu HQ. Genome-wide search for exonic variants affecting translational efficiency. Nat Commun. 2013;4:2260. doi: 10.1038/ncomms3260. PubMed PMID: 23900168; PubMed Central PMCID: PMC3749366.

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Qu HQ, Li Q, Lu Y, Hanis CL, Fisher-Hoch SP, McCormick JB. Ancestral effect on HOMA-IR levels quantitated in an American population of Mexican origin. Diabetes Care. 2012 Dec;35(12):2591-3. doi: 10.2337/dc12-0636. Epub 2012 Aug 13. PubMed PMID: 22891255; PubMed Central PMCID: PMC3507582.

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Qu HQ, Li Q, Grove ML, Lu Y, Pan JJ, Rentfro AR, Bickel PE, Fallon MB, Hanis CL, Boerwinkle E, McCormick JB, Fisher-Hoch SP. Population-based risk factors for elevated alanine aminotransferase in a South Texas Mexican-American population. Arch Med Res. 2012 Aug;43(6):482-8. doi: 10.1016/j.arcmed.2012.08.005. Epub 2012 Sep 5. PubMed PMID: 22959976; PubMed Central PMCID: PMC3590902.

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Li Q, Qu HQ, Rentfro AR, Grove ML, Mirza S, Lu Y, Hanis CL, Fallon MB, Boerwinkle E, Fisher-Hoch SP, McCormick JB. PNPLA3 polymorphisms and liver aminotransferase levels in a Mexican American population. Clin Invest Med. 2012 Aug 4;35(4):E237-45. doi: 10.25011/cim.v35i4.17153. PubMed PMID: 22863562; PubMed Central PMCID: PMC3441048.

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Qu HQ, Li Q, Lu Y, Fisher-Hoch SP, McCormick JB. Translational genomic medicine: common metabolic traits and ancestral components of Mexican Americans. J Med Genet. 2012 Aug;49(8):544-5. doi: 10.1136/jmedgenet-2012-100966. Epub 2012 Jun 20. PubMed PMID: 22717649; PubMed Central PMCID: PMC3419327.

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Moosavi M, Séguin J, Li Q, Polychronakos C. The effect of type 2 diabetes risk loci on insulin requirements in type 1 diabetes. Horm Res Paediatr. 2012;77(5):305-8. doi: 10.1159/000338665. Epub 2012 May 15. PubMed PMID: 22584884.

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Qu HQ, Li Q, Xu S, McCormick JB, Fisher-Hoch SP, Xiong M, Qian J, Jin L. Ancestry informative marker set for han chinese population. G3 (Bethesda). 2012 Mar;2(3):339-41. doi: 10.1534/g3.112.001941. Epub 2012 Mar 1. PubMed PMID: 22413087; PubMed Central PMCID: PMC3291503.

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Polychronakos C, Li Q. Understanding type 1 diabetes through genetics: advances and prospects. Nat Rev Genet. 2011 Oct 18;12(11):781-92. doi: 10.1038/nrg3069. Review. PubMed PMID: 22005987.

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Mirza S, Qu HQ, Li Q, Martinez PJ, Rentfro AR, McCormick JB, Fisher-Hoch SP. Adiponectin/leptin ratio and metabolic syndrome in a Mexican American population. Clin Invest Med. 2011 Oct 1;34(5):E290. doi: 10.25011/cim.v34i5.15672. PubMed PMID: 21968271; PubMed Central PMCID: PMC3256930.

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Qu HQ, Li Q, Rentfro AR, Fisher-Hoch SP, McCormick JB. The definition of insulin resistance using HOMA-IR for Americans of Mexican descent using machine learning. PLoS One. 2011;6(6):e21041. doi: 10.1371/journal.pone.0021041. Epub 2011 Jun 14. PubMed PMID: 21695082; PubMed Central PMCID: PMC3114864.

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Qu HQ, Li Q, McCormick JB, Fisher-Hoch SP. What did we learn from the genome-wide association study for tuberculosis susceptibility?. J Med Genet. 2011 Apr;48(4):217-8. doi: 10.1136/jmg.2010.087361. Epub 2011 Jan 14. PubMed PMID: 21239447; PubMed Central PMCID: PMC3179256.

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Qu HQ, Bradfield JP, Li Q, Kim C, Frackelton E, Grant SF, Hakonarson H, Polychronakos C. In silico replication of the genome-wide association results of the Type 1 Diabetes Genetics Consortium. Hum Mol Genet. 2010 Jun 15;19(12):2534-8. doi: 10.1093/hmg/ddq133. Epub 2010 Apr 8. PubMed PMID: 20378605.

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Li Q, Cao Z, Liu H. Improve the prediction of RNA-binding residues using structural neighbours. Protein Pept Lett. 2010 Mar;17(3):287-96. doi: 10.2174/092986610790780279. PubMed PMID: 19508202.

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Li Q, Zhou C, Liu H. Fragment-based local statistical potentials derived by combining an alphabet of protein local structures with secondary structures and solvent accessibilities. Proteins. 2009 Mar;74(4):820-36. doi: 10.1002/prot.22191. PubMed PMID: 18704928.