Publications

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2020

  1. Guan X, Runger G, Liu L. (2020) Dynamic incorporation of prior knowledge from multiple domains in biomarker discovery. BMC Bioinformatics (in press) 

  2. Liu Y, Fan J, Xu T, Ahmadinejad N, Hess K, Lin S, Zhang J, Liu L, Ning B, Liao Z, Hu, Y. (2020) Extracellular vesicle tetraspanin-8 expression predicts distant metastasis in non-small cell lung cancer after concurrent chemoradiation, Science Advances (in press) 


2019

  1. Chandrashekar P, Ahmadinejad N, Sekulic A, Wang J, Maley C, Liu L. (2019) Somatic selection distinguishes oncogenes and tumor suppressor genes. Bioinformatics (btz851)

  2. Liu L, Maxwell D, Patel R, Chandrashekar P, Gibson G, Kumar S. (2019) Biological relevance of predicted pathogenicity of noncoding variants. Nature Communications 10:330 


2018

  1. Liu L, Caselli R. (2018) Age stratification corrects bias in estimated hazards of APOE Genotype in Alzheimer’s disease. Alzheimer’s & Dementia TRCI 4:602–608


2016

  1. Liu L, Chang Y, Yang T, Noren DP, Amina Q, Kornblau S, Ye J. (2016) Evolution-informed Modeling Improves Outcome Prediction for Cancers. Evolutionary Applications 10(1):68-76 

  2. Liu L, Tamura K, Sanderford M, Gray VE, Kumar S (2016) A Molecular Evolutionary Reference for the Human Variome. Molecular Biology and Evolution 33(1):245-54 


2015

  1. Gerek ZN, Liu L§, Gerold K, Biparva P, Thomas ED, Kumar S. (2015) Evolutionary Diagnosis of non-synonymous variants involved in differential drug response. BMC Medical Genomics 8;Suppl 1:S6

  2. Chastain-Gross RP, Xie G, Belanger M, Kumar D, Whitlock JA, Liu L, Farmerie G, Daligault HE, Han CS, Brettin TS, Progulske-Fox A. (2015) Genome sequence of porphyromonas gingivalis strain A7436. Genome Announcements 3(5).e00927

  3. Xie G, Chastain-Gross RP, Belanger M, Kumar D, Whitlock JA, Liu L, Farmerie G, Daligault HE, Han CS, Brettin TS, Progulske-Fox A. (2015) Genome sequence of porphyromonas gingivalis strain AJW4. Genome Announcements 3(6).e01304


2014

  1. Kumar S, Liu L. (2014) No positive selection for G-allele in a p53 response element in Europeans. Cell 157(7):1497-1499

  2. Kumar S, Ye J, Liu L (2014) Reply to: “Proper reporting of predictor performance”. Nature Methods 11(8):781-2

  3. Gray VE, Liu L§, Nirankari R, Hornbeck P, Kumar S (2014) Signatures of natural selection on mutations of residues with multiple posttranslational modifications. Molecular Biology and Evolution 31(7):1641-5

  4. Stecher G, Liu L, Sanderford M, Peterson D, Tamura K, Kumar S. (2014) MEGA-MD: molecular evolutionary genetics analysis software with mutational diagnosis of amino acid variation. Bioinformatics 30(9):1305-7


2013

  1. Liu L, Kumar S. (2013) Evolutionary balancing is critical for correctly forecasting disease associated amino acid variants. Molecular Biology and Evolution 30(6):1252-7

  2. Wellensiek BP, Larsen AC, Stephens B, Kukurba K, Waern K, Briones N, Liu L, Snyder M, Jacobs BL, Kumar S, Chaput JC. (2013) Genome-wide profiling of human cap-independent translation-enhancing elements. Nature Methods 10(8):747-50

  3. 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 (2013) IgM repertoire biodiversity is reduced in HIV-1 infection and systemic lupus erythematosus. Frontiers in HIV and AIDS doi:10.3389/fimmu.2013.00373


2012

  1. Kumar S, Sanderford M, Gray VE, Ye J, Liu L (2012) Evolutionary Diagnosis Method for Variants in Personal Exomes. Nature Methods 9(9):855-6

  2. Yin L, Liu L, Sun Y, Hou W, Lowe AC, Gardner BP, Salemi M, Williams WB, Farmerie WG, Sleasman JW, Goodenow MM (2012) High-resolution deep sequencing reveals biodiversity, population structure, and persistence of HIV-1 quasispecies within host ecosystems. Retrovirology 9:108


2011

  1. Dudley JT, Kim Y, Liu L, Markov GJ, Gerold K, Chen R, Butte AJ, Kumar S (2011) Human Genomic Disease Variants: A Neutral Evolutionary Explanation. Genome Research doi:10.1101/gr.133702.111

  2. Kumar S, Dudley JT, Filipski A, Liu L (2011) Phylomedicine: an evolutionary telescope to explore and diagnose the universe of disease mutations. Trends in Genetics. 27(9):377-86.


2010

  1. Aggelen GV, 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 DJ, Santos EM, Skirrow RC, Snape JR, Tyler CR, Versteeg D, Viant M, Volz DC, Williams TD, Yu L, (2010) Integrating Omic Technologies into Aquatic Ecological Risk Assessment and Environmental Monitoring: Hurdles, Achievements, and Future Outlook, Environmental Health Perspectives. 118(1):1-5

  2. Spade DJ, Griffitt RJ, Liu L, Brown-Peterson NJ, Kroll KJ, Feswick a, Glazer RA, Barber DS, Denslow ND. (2010) Queen conch (Strombus gigas) testis regresses during the reproductive season at nearshore sites in the Florida Keys. PloS one 5(9):e12737


2009

  1. Paul A, Liu L, Laughner B, McClung S, Chen S, Ferl R. (2009) Comparative Interactomics: Analysis of Arabidopsis 14-3-3 complexes reveals highly conserved 14-3-3 interactions between humans and plants. Journal of Proteome Research. 8:1913-1924

  2. Rosser CJ, Liu L, Sun Y, Villicana P, McCullers M, Porvasnik S, Young PR, Parker AS, Goodison S. (2009) Bladder cancer-associated gene expression signatures identified by profiling of exfoliated urothelia. Cancer Epidemiology, Biomarkers and Prevention 18(2):444-53.

  3. Duan YP, Zhou LJ, Hall DG, Li WB, Doddapaneni H, Lin H, Liu L, Sun Y, Gabriel DW, Vahling CM, Williams K, Dickerman A, Gottwald T. (2009) Complete genome sequence of citrus huanglongbing bacterium, 'Candidatus Liberibacter asiaticus' obtained through metagenomics, Molecular Plant-Microbe Interaction 22(8):1011-20

  4. Garcia-Reyero N, Kroll KJ, Liu L, Orlando EF, Watanabe KH, Sepúlveda MS, Villeneuve DL, Perkins EJ, Ankley GT, Denslow ND. (2009) Gene expression responses in male fathead minnows exposed to binary mixtures of an estrogen and antiestrogen. BMC Genomics. 13;10:308

  5. Sun Y, Cai YP, Liu L, Yu F, Farrell M, McKendree W, Farmerie WG. (2009) ESPRIT: estimating species richness using large collections of 16S rRNA shotgun sequences. Nucleic Acid Research 37(10):e76

  6. Yu F, Sun Y, Liu L, Farmerie WG. (2009) GSTaxClassifier: a genomic signature based taxonomic classifier for metagenomics data analysis. Bioinformation. 4(1):46-49


2008

  1. Garcia-Reyero N, Adelman I, Liu L, Denslow N. (2008) Gene expression profiles of fathead minnows exposed to surface waters above and below a sewage treatment plant in Minnesota. Marine Environmental Research 66(1):134-6.

  2. Garcia-Reyero N, Griffitt RJ, Liu L, Kroll KJ, Farmerie WG, Barber DS, Denslow ND. (2008) Construction of a robust microarray from a non-model species (largemouth bass) using pyrosequencing technology. Journal of Fish Biology 72(9):2354-2376


2007

  1. Sun Y, Goodison S, Li J, Liu L, Farmerie WG. (2007) Improved breast cancer prognosis through the combination of clinical and genetic markers. Bioinformatics. 23(1):30-37

  2. Popp MP, Liu L, Timmers A, Esson DW, Shiroma L, Meyers C, Berceli S, Tao M,  Wistow G, Schultz GS,  Sherwood MB. (2007) Development of a Microarray Chip for Rabbit Ocular Research. Molecular Vision. 13:164-73

  3. Luo X, Pan Q, Liu L, Chegini N. (2007) Genomic and proteomic profiling II: Comparative assessment of gene expression profiles in leiomyomas, keloids, and surgically-induced scars. Reproductive Biology and Endocrinology 5(1):35

  4. Larkin P, Villeneuve DL, Knoebl I, Miracle AL, Carter BJ, Liu L, Denslow ND, Ankley GT. (2007) Development and validation of a 2,000-gene microarray for the fathead minnow (Pimephales promelas). Environmental Toxicology and Chemistry. 26(7):1497-506


2006

  1. Moroz LL, Edwards JR, Puthanveettil SV, Kohn A, Ha T, Heyland A, Knudsen B, Sahni A, Yu F, Liu L, Jezzini S, Sadreyev R, Lovell P, Iannucculli W, Chen M, Nguyen T, Sheng H, Shaw R, Kalachikov S, Panchin Y, Farmerie WG, Russo JJ, Ju J, Kandel ER. (2006) The Neuronal Transcriptome of Aplysia californica: A Platform for the Neurogenomics of Defined Neurons, Neuronal Compartments and Neuronal Circuitry. Cell.127(7):1453-1467

  2. Chao EM, Liu L, Farmerie WG, Keyhani NO (2006) 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. 152(Pt 9):2843-54.

  3. Gabriel DW, Allen C, Schell M, Denny TP, Greenberg JT, Duan Y, Flores-Cruz Z, Huang Q, Clifford JM, Presting G, Gonzalez ET, Reddy J, Elphinstone J, Swanson J, Yao J, Mulholland V, Liu L, Farmerie WG, Patnaikuni M, Balogh B, Norman D, Alvarez A, Castillo JA, Jones J, Saddler G, Walunas T, Zhukov A, Mikhailova N (2006) Identification of open reading frames unique to a Select Agent:  Ralstonia solanacearum race 3 biovar 2. Molecular Plant-Microbe Interaction 19(1):69-79


2005

  1. Farmerie WG, Hammer J, Liu L, Sahni A, Schneider M. (2005) Biological Workflow with BlastQuest. Data and Knowledge Engineering. 53(1):75-97

  2. Kornberg LJ, Villaret D, Popp MP, Liu L, McLaren R, Brown H, and McFadden M. (2005) Gene Expression Profiling in Squamous Cell Carcinoma of the Oral Cavity Shows Abnormalities in Several Signaling Pathways. Laryngoscope. 115(4):690-8


2004

Esson DW, Popp MP, Liu L, Schultz GS, Sherwood MB. (2004) Microarray analysis of the failure of filtering blebs in a rat model of glaucoma filtering surgery. Investigative Ophthalmology and Visual Science. 45(12):4450-62.


2003

  1. Cousins RJ, Blanchard RK, Popp MP, Liu L, Cao J, Moore JB and Green CL. (2003) A Global View of the Selectivity of Zinc Deprivation and Excess on Genes Expressed in Human THP-1 Mononuclear Cells. Proceedings of the National Academy of Science 100:6952-6957

  2. Li YJ, Liu L, Zhang FC. (2003) The clinical significance of SSA antigen and its different positive expressions. Zhonghua Nei Ke Za Zhi. 42(3):165-8