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Li YJ, Liu L, Zhang FC. [The clinical significance of SSA antigen and its different positive expressions]. Zhonghua Nei Ke Za Zhi. 2003 Mar;42(3):165-8. PubMed PMID: 12816697.
Cousins RJ, Blanchard RK, Popp MP, Liu L, Cao J, Moore JB, Green CL. A global view of the selectivity of zinc deprivation and excess on genes expressed in human THP-1 mononuclear cells. Proc Natl Acad Sci U S A. 2003 Jun 10;100(12):6952-7. doi: 10.1073/pnas.0732111100. Epub 2003 May 19. PubMed PMID: 12756304; PubMed Central PMCID: PMC165811.
Esson DW, Popp MP, Liu L, Schultz GS, Sherwood MB. Microarray analysis of the failure of filtering blebs in a rat model of glaucoma filtering surgery. Invest Ophthalmol Vis Sci. 2004 Dec;45(12):4450-62. doi: 10.1167/iovs.04-0375. PubMed PMID: 15557454.
Farmerie WG, Hammer J, Liu L, Sahni A, Schneider M. Biological Workflow with BlastQuest. Data and Knowledge Engineering. 2005; 53(1):75-97.
Gabriel DW, Allen C, Schell M, Denny TP, Greenberg JT, Duan YP, Flores-Cruz Z, Huang Q, Clifford JM, Presting G, González ET, Reddy J, Elphinstone J, Swanson J, Yao J, Mulholland V, Liu L, Farmerie W, Patnaikuni M, Balogh B, Norman D, Alvarez A, Castillo JA, Jones J, Saddler G, Walunas T, Zhukov A, Mikhailova N. Identification of open reading frames unique to a select agent: Ralstonia solanacearum race 3 biovar 2. Mol Plant Microbe Interact. 2006 Jan;19(1):69-79. doi: 10.1094/MPMI-19-0069. PubMed PMID: 16404955.
Sun Y, Liu L, Popp M, Farmerie WG. Estimation of Cross-hybridization Signals Using Support Vector Regression. Proc. IEEE Symp. of Computations in Bioinformatics and Bioscience (SCBB'06). 2006.
Cho EM, Liu L, Farmerie W, Keyhani NO. EST analysis of cDNA libraries from the entomopathogenic fungus Beauveria (Cordyceps) bassiana. I. Evidence for stage-specific gene expression in aerial conidia, in vitro blastospores and submerged conidia. Microbiology (Reading). 2006 Sep;152(Pt 9):2843-2854. doi: 10.1099/mic.0.28844-0. PubMed PMID: 16946278.
Moroz LL, Edwards JR, Puthanveettil SV, Kohn AB, Ha T, Heyland A, Knudsen B, Sahni A, Yu F, Liu L, Jezzini S, Lovell P, Iannucculli W, Chen M, Nguyen T, Sheng H, Shaw R, Kalachikov S, Panchin YV, Farmerie W, Russo JJ, Ju J, Kandel ER. Neuronal transcriptome of Aplysia: neuronal compartments and circuitry. Cell. 2006 Dec 29;127(7):1453-67. doi: 10.1016/j.cell.2006.09.052. PubMed PMID: 17190607; PubMed Central PMCID: PMC4024467.
Sun Y, Goodison S, Li J, Liu L, Farmerie W. Improved breast cancer prognosis through the combination of clinical and genetic markers. Bioinformatics. 2007 Jan 1;23(1):30-7. doi: 10.1093/bioinformatics/btl543. Epub 2006 Nov 26. PubMed PMID: 17130137; PubMed Central PMCID: PMC3431620.
Popp MP, Liu L, Timmers A, Esson DW, Shiroma L, Meyers C, Berceli S, Tao M, Wistow G, Schultz GS, Sherwood MB. Development of a microarray chip for gene expression in rabbit ocular research. Mol Vis. 2007 Feb 2;13:164-73. PubMed PMID: 17293780; PubMed Central PMCID: PMC2536532.
Larkin P, Villeneuve DL, Knoebl I, Miracle AL, Carter BJ, Liu L, Denslow ND, Ankley GT. Development and validation of a 2,000-gene microarray for the fathead minnow (Pimephales promelas). Environ Toxicol Chem. 2007 Jul;26(7):1497-506. doi: 10.1897/06-501r.1. PubMed PMID: 17665692.
Luo X, Pan Q, Liu L, Chegini N. Genomic and proteomic profiling II: comparative assessment of gene expression profiles in leiomyomas, keloids, and surgically-induced scars. Reprod Biol Endocrinol. 2007 Aug 24;5:35. doi: 10.1186/1477-7827-5-35. PubMed PMID: 17718906; PubMed Central PMCID: PMC2039739.
Garcia-Reyero N, Griffitt RJ, Liu L, Kroll KJ, Farmerie WG, Barber DS, Denslow ND. Construction of a robust microarray from a non-model species (largemouth bass) using pyrosequencing technology. J Fish Biol. 2008 Jun 28;72(9):2354-2376. doi: 10.1111/j.1095-8649.2008.01904.x. PubMed PMID: 19936325; PubMed Central PMCID: PMC2779536.
Garcia-Reyero N, Adelman I, Liu L, Denslow N. Gene expression profiles of fathead minnows exposed to surface waters above and below a sewage treatment plant in Minnesota. Mar Environ Res. 2008 Jul;66(1):134-6. doi: 10.1016/j.marenvres.2008.02.073. Epub 2008 Mar 7. PubMed PMID: 18417205; PubMed Central PMCID: PMC2531227.
Clement C, Popp MP, Bloom DC, Schultz G, Liu L, Neumann DM, Bhattacharjee PS, Hill JM. Microarray analysis of host gene expression for comparison between naïve and HSV-1 latent rabbit trigeminal ganglia. Mol Vis. 2008 Jul 3;14:1209-21. PubMed PMID: 18615202; PubMed Central PMCID: PMC2443748.
Rosser CJ, Liu L, Sun Y, Villicana P, McCullers M, Porvasnik S, Young PR, Parker AS, Goodison S. Bladder cancer-associated gene expression signatures identified by profiling of exfoliated urothelia. Cancer Epidemiol Biomarkers Prev. 2009 Feb;18(2):444-53. doi: 10.1158/1055-9965.EPI-08-1002. Epub 2009 Feb 3. PubMed PMID: 19190164; PubMed Central PMCID: PMC2729268.
Paul AL, Liu L, McClung S, Laughner B, Chen S, Ferl RJ. Comparative interactomics: analysis of arabidopsis 14-3-3 complexes reveals highly conserved 14-3-3 interactions between humans and plants. J Proteome Res. 2009 Apr;8(4):1913-24. doi: 10.1021/pr8008644. PubMed PMID: 19714877.
Garcia-Reyero N, Villeneuve DL, Kroll KJ, Liu L, Orlando EF, Watanabe KH, Sepúlveda MS, Ankley GT, Denslow ND. Expression signatures for a model androgen and antiandrogen in the fathead minnow (Pimephales promelas) ovary. Environ Sci Technol. 2009 Apr 1;43(7):2614-9. doi: 10.1021/es8024484. PubMed PMID: 19452925.
Sun Y, Cai Y, Liu L, Yu F, Farrell ML, McKendree W, Farmerie W. ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences. Nucleic Acids Res. 2009 Jun;37(10):e76. doi: 10.1093/nar/gkp285. Epub 2009 May 5. PubMed PMID: 19417062; PubMed Central PMCID: PMC2691849.
Garcia-Reyero N, Kroll KJ, Liu L, Orlando EF, Watanabe KH, Sepúlveda MS, Villeneuve DL, Perkins EJ, Ankley GT, Denslow ND. Gene expression responses in male fathead minnows exposed to binary mixtures of an estrogen and antiestrogen. BMC Genomics. 2009 Jul 13;10:308. doi: 10.1186/1471-2164-10-308. PubMed PMID: 19594897; PubMed Central PMCID: PMC2713996.
Duan Y, Zhou L, Hall DG, Li W, Doddapaneni H, Lin H, Liu L, Vahling CM, Gabriel DW, Williams KP, Dickerman A, Sun Y, Gottwald T. Complete genome sequence of citrus huanglongbing bacterium, 'Candidatus Liberibacter asiaticus' obtained through metagenomics. Mol Plant Microbe Interact. 2009 Aug;22(8):1011-20. doi: 10.1094/MPMI-22-8-1011. PubMed PMID: 19589076.
Yu F, Sun Y, Liu L, Farmerie W. GSTaxClassifier: a genomic signature based taxonomic classifier for metagenomic data analysis. Bioinformation. 2009 Aug 20;4(1):46-9. doi: 10.6026/97320630004046. PubMed PMID: 20011152; PubMed Central PMCID: PMC2770370.
Garcia-Reyero N, Adelman IR, Martinovic D, Liu L, Denslow ND. Site-specific impacts on gene expression and behavior in fathead minnows (Pimephales promelas) exposed in situ to streams adjacent to sewage treatment plants. BMC Bioinformatics. 2009 Oct 8;10 Suppl 11(Suppl 11):S11. doi: 10.1186/1471-2105-10-S11-S11. PubMed PMID: 19811676; PubMed Central PMCID: PMC2759673.
Van Aggelen G, Ankley GT, Baldwin WS, Bearden DW, Benson WH, Chipman JK, Collette TW, Craft JA, Denslow ND, Embry MR, Falciani F, George SG, Helbing CC, Hoekstra PF, Iguchi T, Kagami Y, Katsiadaki I, Kille P, Liu L, Lord PG, McIntyre T, O'Neill A, Osachoff H, Perkins EJ, Santos EM, Skirrow RC, Snape JR, Tyler CR, Versteeg D, Viant MR, Volz DC, Williams TD, Yu L. Integrating omic technologies into aquatic ecological risk assessment and environmental monitoring: hurdles, achievements, and future outlook. Environ Health Perspect. 2010 Jan;118(1):1-5. doi: 10.1289/ehp.0900985. PubMed PMID: 20056575; PubMed Central PMCID: PMC2831950.
Spade DJ, Griffitt RJ, Liu L, Brown-Peterson NJ, Kroll KJ, Feswick A, Glazer RA, Barber DS, Denslow ND. Queen conch (Strombus gigas) testis regresses during the reproductive season at nearshore sites in the Florida Keys. PLoS One. 2010 Sep 15;5(9):e12737. doi: 10.1371/journal.pone.0012737. PubMed PMID: 20856805; PubMed Central PMCID: PMC2939879.
Kumar S, Dudley JT, Filipski A, Liu L. Phylomedicine: an evolutionary telescope to explore and diagnose the universe of disease mutations. Trends Genet. 2011 Sep;27(9):377-86. doi: 10.1016/j.tig.2011.06.004. Epub 2011 Jul 20. Review. PubMed PMID: 21764165; PubMed Central PMCID: PMC3272884.
Dudley JT, Kim Y, Liu L, Markov GJ, Gerold K, Chen R, Butte AJ, Kumar S. Human genomic disease variants: a neutral evolutionary explanation. Genome Res. 2012 Aug;22(8):1383-94. doi: 10.1101/gr.133702.111. Epub 2012 Jun 4. Review. PubMed PMID: 22665443; PubMed Central PMCID: PMC3409252.
Kumar S, Sanderford M, Gray VE, Ye J, Liu L. Evolutionary diagnosis method for variants in personal exomes. Nat Methods. 2012 Sep;9(9):855-6. doi: 10.1038/nmeth.2147. PubMed PMID: 22936163; PubMed Central PMCID: PMC3810944.
Yin L, Liu L, Sun Y, Hou W, Lowe AC, Gardner BP, Salemi M, Williams WB, Farmerie WG, Sleasman JW, Goodenow MM. High-resolution deep sequencing reveals biodiversity, population structure, and persistence of HIV-1 quasispecies within host ecosystems. Retrovirology. 2012 Dec 17;9:108. doi: 10.1186/1742-4690-9-108. PubMed PMID: 23244298; PubMed Central PMCID: PMC3531307.
Liu L, Kumar S. Evolutionary balancing is critical for correctly forecasting disease-associated amino acid variants. Mol Biol Evol. 2013 Jun;30(6):1252-7. doi: 10.1093/molbev/mst037. Epub 2013 Mar 5. PubMed PMID: 23462317; PubMed Central PMCID: PMC3649672.
Yin L, Hou W, Liu L, Cai Y, Wallet MA, Gardner BP, Chang K, Lowe AC, Rodriguez CA, Sriaroon P, Farmerie WG, Sleasman JW, Goodenow MM. IgM Repertoire Biodiversity is Reduced in HIV-1 Infection and Systemic Lupus Erythematosus. Front Immunol. 2013;4:373. doi: 10.3389/fimmu.2013.00373. eCollection 2013. PubMed PMID: 24298273; PubMed Central PMCID: PMC3828670.
Stecher G, Liu L, Sanderford M, Peterson D, Tamura K, Kumar S. MEGA-MD: molecular evolutionary genetics analysis software with mutational diagnosis of amino acid variation. Bioinformatics. 2014 May 1;30(9):1305-7. doi: 10.1093/bioinformatics/btu018. Epub 2014 Jan 11. PubMed PMID: 24413669; PubMed Central PMCID: PMC3998139.
Kumar S, Liu L. No positive selection for G allele in a p53 response element in Europeans. Cell. 2014 Jun 19;157(7):1497-9. doi: 10.1016/j.cell.2014.05.033. PubMed PMID: 24949959.
Gray VE, Liu L, Nirankari R, Hornbeck PV, Kumar S. Signatures of natural selection on mutations of residues with multiple posttranslational modifications. Mol Biol Evol. 2014 Jul;31(7):1641-5. doi: 10.1093/molbev/msu137. Epub 2014 Apr 16. PubMed PMID: 24739307; PubMed Central PMCID: PMC4069621.
Kumar S, Ye J, Liu L. Reply to: "Proper reporting of predictor performance". Nat Methods. 2014 Aug;11(8):781-2. doi: 10.1038/nmeth.3039. PubMed PMID: 25075901.
Yang T, Wang J, Sun Q, Hibar D, Jahanshad N, Liu L, Wang Y, Zhan L, Thompson P, Ye J. Detecting genetic risk factors for Alzheimer’s disease in whole genome sequence data via lasso screening. Proceedings of International Symposium on Biomedical Imaging. 2015.
Gerek NZ, Liu L, Gerold K, Biparva P, Thomas ED, Kumar S. Evolutionary Diagnosis of non-synonymous variants involved in differential drug response. BMC Med Genomics. 2015;8 Suppl 1(Suppl 1):S6. doi: 10.1186/1755-8794-8-S1-S6. Epub 2015 Jan 15. PubMed PMID: 25952014; PubMed Central PMCID: PMC4315320.
Chastain-Gross RP, Xie G, Bélanger M, Kumar D, Whitlock JA, Liu L, Farmerie WG, Daligault HE, Han CS, Brettin TS, Progulske-Fox A. Genome Sequence of Porphyromonas gingivalis Strain A7436. Genome Announc. 2015 Sep 24;3(5). doi: 10.1128/genomeA.00927-15. PubMed PMID: 26404590; PubMed Central PMCID: PMC4582566.
Xie G, Chastain-Gross RP, Bélanger M, Kumar D, Whitlock JA, Liu L, Farmerie WG, Daligault HE, Han CS, Brettin TS, Progulske-Fox A. Genome Sequence of Porphyromonas gingivalis Strain AJW4. Genome Announc. 2015 Nov 5;3(6). doi: 10.1128/genomeA.01304-15. PubMed PMID: 26543127; PubMed Central PMCID: PMC4645212.
Liu L, Tamura K, Sanderford M, Gray VE, Kumar S. A Molecular Evolutionary Reference for the Human Variome. Mol Biol Evol. 2016 Jan;33(1):245-54. doi: 10.1093/molbev/msv198. Epub 2015 Oct 13. PubMed PMID: 26464126; PubMed Central PMCID: PMC5009994.
Szedlak A, Smith N, Liu L, Paternostro G, Piermarocchi C. Young and old, hot and cold: topological and evolutionary properties of gene modules and driver mutations in a leukemia gene regulatory network. PLoS computational biology. 2016.
Liu L, Chang Y, Yang T, Noren DP, Long B, Kornblau S, Qutub A, Ye J. Evolution-informed modeling improves outcome prediction for cancers. Evol Appl. 2017 Jan;10(1):68-76. doi: 10.1111/eva.12417. eCollection 2017 Jan. PubMed PMID: 28035236; PubMed Central PMCID: PMC5192825.
Chastain-Gross RP, Xie G, Bélanger M, Kumar D, Whitlock JA, Liu L, Raines SM, Farmerie WG, Daligault HE, Han CS, Brettin TS, Progulske-Fox A. Genome Sequence of Porphyromonas gingivalis Strain 381. Genome Announc. 2017 Jan 12;5(2). doi: 10.1128/genomeA.01467-16. PubMed PMID: 28082501; PubMed Central PMCID: PMC5256213.
Xie G, Chastain-Gross RP, Bélanger M, Kumar D, Whitlock JA, Liu L, Farmerie WG, Zeng CL, Daligault HE, Han CS, Brettin TS, Progulske-Fox A. Genome Sequence of Porphyromonas gingivalis Strain A7A1-28. Genome Announc. 2017 Mar 9;5(10). doi: 10.1128/genomeA.00021-17. PubMed PMID: 28280013; PubMed Central PMCID: PMC5347233.
Liu L, Sanderford MD, Patel R, Chandrashekar P, Gibson G, Kumar S. Biological relevance of computationally predicted pathogenicity of noncoding variants. Nat Commun. 2019 Jan 18;10(1):330. doi: 10.1038/s41467-018-08270-y. PubMed PMID: 30659175; PubMed Central PMCID: PMC6338804.
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