1. Connor L Brown, Ishi M Keenum, Dongjuan Dai, Liqing Zhang, Peter J Vikesland, Amy Pruden. Critical evaluation of short, long, and hybrid assembly for contextual analysis of antibiotic resistance genes in complex environmental metagenomes. Scientific reports. 2021 Feb 12; 11(1): 1-12. [Full Text]

  1. Karley K Mahalak, Jenni Firrman, Jung-Jin Lee, Kyle Bittinger, Alberto Nuñez, Lisa M Mattei, Huanjia Zhang, Bryton Fett, Jamshed Bobokalonov, Gustavo Arango-Argoty, Liqing Zhang, Guodong Zhang, Lin Shu Liu. Triclosan has a robust, yet reversible impact on human gut microbial composition in vitro. Plos one. 2020 Jun 25; 15(6): e0234046. [Full Text]
  2. GA Arango-Argoty, GKP Guron, Emily Garner, Maria V Riquelme, LS Heath, Amy Pruden, PJ Vikesland, Liqing Zhang. ARGminer: a web platform for the crowdsourcing-based curation of antibiotic resistance genes. Bioinformatics. 2020 May 1; 36(9):2966-2973. [Full Text]
  3. Min Oh, Liqing Zhang. DeepMicro: deep representation learning for disease prediction based on microbiome data. Scientific reports. 2020 Apr 7; 10(1):1-9. [Full Text]
  4. Latania K Logan, Liqing Zhang, Stefan J Green, Samuel Dorevitch, Gustavo A Arango-Argoty, Kendrick Reme, Emily Garner, Jared Aldstadt, Yvette J Johnson-Walker, Mary K Hayden, Robert A Weinstein, Amy Pruden. A Pilot Study of Chicago Waterways as Reservoirs of Multidrug-Resistant Enterobacteriaceae (MDR-Ent) in a High-Risk Region for Community-Acquired MDR-Ent Infection in Children. Antimicrobial Agents and Chemotherapy. 2020 Mar 24; 64(4):e02310-19. [Full Text]

  1. Emily Garner, Connor L Brown, David Otto Schwake, William J Rhoads, Gustavo Arango-Argoty, Liqing Zhang, Guillaume Jospin, David A Coil, Jonathan A Eisen, Marc A Edwards, Amy Pruden. Comparison of Whole-Genome Sequences of Legionella pneumophila in Tap Water and in Clinical Strains, Flint, Michigan, USA, 2016. Emerging infectious diseases. 2019 Nov; 25(11):2013. [Full Text]
  2. Shaohua Lei, Erica L Twitchell, Ashwin K Ramesh, Tammy Bui, Elizabeth Majette, Christine M Tin, Roger Avery, Gustavo Arango-Argoty, Liqing Zhang, Sylvia Becker-Dreps, M Andrea Azcarate-Peril, Xi Jiang, Lijuan Yuan. Enhanced GII. 4 human norovirus infection in gnotobiotic pigs transplanted with a human gut microbiota. Journal of General Virology. 2019 Nov 1; 100(11):1530-1540. [Full Text]
  3. Qinglai Bian, Jiaxu Chen, Wenqi Qiu, Chenxi Peng, Meifang Song, Xuebin Sun, Yueyun Liu, Fengmin Ding, Jianbei Chen, Liqing Zhang. Four targeted genes for predicting the prognosis of colorectal cancer: A bioinformatics analysis case. Oncology letters. 2019 Sep 13; 18(5):5043-5054. [Full Text]
  4. Suraj Gupta, Gustavo Arango-Argoty, Liqing Zhang, Amy Pruden, Peter Vikesland. Identification of discriminatory antibiotic resistance genes among environmental resistomes using extremely randomized tree algorithm. Microbiome. 2019 Aug 29; 7(1):123. [Full Text]
  5. Mohammad Shabbir Hasan, Xiaowei Wu, Liqing Zhang. Uncovering missed indels by leveraging unmapped reads. Scientific reports. 2019 Jul 31; 9(1):1-14. [Full Text]
  6. Chaoqi Chen, Christine A Pankow, Min Oh, Lenwood S Heath, Liqing Zhang, Pang Du, Kang Xia, Amy Pruden. Effect of antibiotic use and composting on antibiotic resistance gene abundance and resistome risks of soils receiving manure-derived amendments. Environment international. 2019 Jul 1; 128:233-243. [Full Text]
  7. Gustavo A Arango-Argoty, Dongjuan Dai, Amy Pruden, Peter Vikesland, Lenwood S Heath, Liqing Zhang. NanoARG: a web service for detecting and contextualizing antimicrobial resistance genes from nanopore-derived metagenomes. Microbiome. 2019 Jun 7; 7(1):1-18. [Full Text]
  8. Giselle KP Guron, Gustavo Arango-Argoty, Liqing Zhang, Amy Pruden, Monica A Ponder. Effects of Dairy Manure-Based Amendments and Soil Texture on Lettuce-and Radish-Associated Microbiota and Resistomes. mSphere. 2019 May 8; 4(3):e00239-19. [Full Text]
  9. Man Tang, Mohammad Shabbir Hasan, Hongxiao Zhu, Liqing Zhang, Xiaowei Wu. vi-HMM: a novel HMM-based method for sequence variant identification in short-read data. Human genomics. 2019 Feb 13; 13(1):9. [Full Text]

  1. Eric W. Getz, Saima Sultana Tithi, Liqing Zhang, Frank O. Aylward. Parallel Evolution of Genome Streamlining and Cellular Bioenergetics across the Marine Radiation of a Bacterial Phylum. mBio. 2018 Sep 18; 9(5):e01089-18. [Full Text]
  2. Yonggang Zhang, Gustavo Arango, Fang Li, Xiao Xiao, Raj Putatunda, Jun Yu, Xiao-Feng Yang, Hong Wang, Layne T Watson, Liqing Zhang, Wenhui Hu. Comprehensive off-target analysis of dCas9-SAM-mediated HIV reactivation via long noncoding RNA and mRNA profiling BioMed Central. 2018 Sep 10; 11(1):78. [Full Text]
  3. Firrman J, Liu L, Argoty GA, Zhang L, Tomasula P, Wang M, Pontious S, Kobori M, Xiao W. Analysis of Temporal Changes in Growth and Gene Expression for Commensal Gut Microbes in Response to the Polyphenol Naringenin. Microbiology Insights. 2018 May 30; 11:1178636118775100. [Full Text]
  4. Oh M, Pruden A, Chen C, Heath LS, Xia K, Zhang L. MetaCompare: A computational pipeline for prioritizing environmental resistome risk. FEMS microbiology ecology. 2018 Apr 26; 94(7) [Full Text]
  5. Guo S, Pridham KJ, Virbasius CM, He B, Zhang L, Varmark H, Green MR, Sheng Z. A large-scale RNA interference screen identifies genes that regulate autophagy at different stages. Scientific Reports. 2018 Feb 12; 8(1):2822. [Full Text]
  6. Tran H, Zhu H, Wu X, Kim G, Clarke CR, Larose H, Haak DC, Askew SD, Barney JN, Westwood JH, Zhang L. Identification of Differentially Methylated Sites with Weak Methylation Effects. Genes. 2018 Feb 8; 9(2):75. [Full Text]
  7. Arango-Argoty, G., Garner, E., Pruden, A., Heath, L.S., Vikesland, P.and Zhang, L. DeepARG: A deep learning approach for predicting antibiotic resistance genes from metagenomic data. Microbiome. 2018 Feb 1; 6(1):23. [Full Text]
  8. Tithi SS, Aylward FO, Jensen RV, Zhang L. FastViromeExplorer: a pipeline for virus and phage identification and abundance profiling in metagenomics data. PeerJ. 2018 Jan 12; 6:e4227. [Full Text]

  1. Hasan MS, Wu X, Watson LT, Zhang L. UPS-indel: a Universal Positioning System for Indels. Scientific Reports.2017 Oct 26; 7(1):14106. [Full Text]
  2. Vijayan V, Yiu SM, Zhang L. Improving somatic variant identification through integration of genome and exome data. BMC genomics. 2017 Oct; 18(7):63. [Full Text]
  3. Wang M, Firrman J, Zhang L, Arango-Argoty G, Tomasula P, Liu L, Xiao W, Yam K. Apigenin Impacts the Growth of the Gut Microbiota and Alters the Gene Expression of Enterococcus. Molecules. 2017 Aug 3; 22(8):1292. [Full Text]
  4. Kim G, Clarke CR, Larose H, Tran HT, Haak DC, Zhang L, Askew S, Barney J, Westwood JH. Herbicide injury induces DNA methylome alterations in Arabidopsis. PeerJ. 2017 Jul 20; 5:e3560. [Full Text]
  5. Zhang S, Zhang L. Combining weighted adaptive CS-LBP and local linear discriminant projection for gait recognition. Multimedia Tools and Applications. 2017 Jun 3; 1-17. [Full Text]
  6. Zhang S, Wu X, You Z, Zhang L. Leaf image based cucumber disease recognition using sparse representation classification. Computers and electronics in agriculture. 2017 Mar 1;134:135-41. [Full Text]

  1. Garner E, Wallace JS, Argoty GA, Wilkinson C, Fahrenfeld N, Heath LS, Zhang L, Arabi M, Aga DS, Pruden A. Metagenomic profiling of historic Colorado Front Range flood impact on distribution of riverine antibiotic resistance genes. Scientific Reports. 2016 Dec 5; 6(38432). [Full Text]
  2. Firrman J, Liu L, Zhang L, Arango Argoty G, Wang M, Tomasula P, Kobori M, Pontious S, Xiao W. The effect of quercetin on genetic expression of the commensal gut microbes Bifidobacterium catenulatum, Enterococcus caccae and Ruminococcus gauvreauii. Anaerobe. 2016 Dec; 42:130-141. [Full Text]
  3. Arango-Argoty G, Singh G, Heath LS, Pruden A, Xiao W, Zhang L. MetaStorm: A Public Resource for Customizable Metagenomics Annotation. PLoS One. 2016 Sep 15; 11(9):e0162442. [Full Text]
  4. Hasan M, Zhang L. SPAI: an interactive platform for indel analysis. BMC Genomics. 2016 Aug 31; 17(5): 496. [Full Text]
  5. Tran H, Wu X, Tithi S, Sun MA, Xie H, Zhang L. A Bayesian Assignment Method for Ambiguous Bisulfite Short Reads. PloS One. 2016 Mar 24; 11(3):e0151826. [Full Text]

  1. Porter J, Sun MA, Xie H, Zhang L. Investigating bisulfite short-read mapping failure with hairpin bisulfite sequencing data. BMC Genomics.2015 Nov 10; 16 Suppl 11:S2. [Full Text]
  2. Liu M, Watson LT, Zhang L. HMMvar-func: a new method for predicting the functional outcome of genetic variants. BMC Bioinformatics.2015 Oct 30; 16:351. [Full Text]
  3. Chen W, Tran H, Liang Z, Lin H, Zhang L. Identification and analysis of the N(6)-methyladenosine in the Saccharomyces cerevisiae transcriptome. Scientific Reports.2015 Sep 7; 5:13859. [Full Text]
  4. Hasan MS, Wu X, Zhang L. Performance evaluation of indel calling tools using real short-read data. Human Genomics.2015 Aug 19; 9:20. [Full Text]
  5. Liu M, Watson LT, Zhang L. Predicting the combined effect of multiple genetic variants. Human Genomics.2015 Jul 30; 9:18. [Full Text]
  6. Chen W, Zhang L. The pattern of DNA cleavage intensity around indels. Scientific Reports.2015 Feb 9; 5:8333. [Full Text]
  7. Chen W, Zhang X, Brooker J, Lin H, Zhang L, Chou KC. PseKNC-General: a cross-platform package for generating various modes of pseudo nucleotide compositions. Bioinformatics.2015 Jan 1; 31(1):119-20. [Full Text]

  1. Li Z, Wu X, He B, Zhang L. Vindel: a simple pipeline for checking indel redundancy. BMC Bioinformatics. 2014 Nov 19; 15:359. [Full Text]
  2. Liu M, Adelman ZN, Myles K, Zhang L. TransPS: A Transcriptome Post Scaffolding Method for Assembling High Quality Contigs. Computational Biology Journal. 2014 May 28; 2014. [Full Text]
  3. Liu M, Watson LT, Zhang L. Quantitative prediction of the effect of genetic variation using hidden Markov models. BMC Bioinformatics. 2014 Jan 9; 15:5. [Full Text]
  4. Tran H, Porter J, Sun MA, Xie H, Zhang L. Objective and comprehensive evaluation of bisulfite short read mapping tools. Adv Bioinformatics. 2014; 2014:472045. [Full Text]

  1. Zhang L, Liu M, Watson LT. Status of Research on Insertion and Deletion Variations in the Human Population. Models and algorithms for genome evolution. 2013 Nov 19; 15:359. [Full Text]

  1. Huang Y, Zhang L. Gene Selection for Classifications by Multiple PCA with Sparsity. Tsinghua Science and Technology. 2012 Dec 12; 17(6):659 - 665. [Full Text]
  2. Adelman ZN, Anderson MA, Liu M, Zhang L, Myles KM. Sindbis virus induces the production of a novel class of endogenous siRNAs in Aedes aegypti mosquitoes. Insect Mol Biol. 2012 Jun; 21(3):357-68. [Full Text]
  3. Chen YL, Li QZ, Zhang LQ. Using increment of diversity to predict mitochondrial proteins of malaria parasite: integrating pseudo-amino acid composition and structural alphabet. Amino Acids. 2012 Apr; 42(4):1309-16. [Full Text]

  1. Zhang L, Watson LT, Heath LS. A network of SCOP hidden Markov models and its analysis. BMC Bioinformatics. 2011 May 23; 12:191. [Full Text]
  2. Zhang J, Zhao H, Zhang L, Lu B. An Empirical Comparative Study on Two Large-Scale Hierarchical Text Classification Approaches. International Journal on Computer Processing of Oriental Languages. 2011; 23(4):309-326. [Full Text]
  3. Urgard E, Vooder T, Võsa U, Välk K, Liu M, Luo C, Hoti F, Roosipuu R, Annilo T, Laine J, Frenz CM, Zhang L, Metspalu A. Metagenes associated with survival in non-small cell lung cancer. Cancer Inform.2011; 10:175-83. [Full Text]
  4. Lewis SN, Nsoesie E, Weeks C, Qiao D, Zhang L. Prediction of disease and phenotype associations from genome-wide association studies. PLoS One.2011; 6(11):e27175. [Full Text]
  5. Lewis SN, Nsoesie EO, Weeks C, Qiao D, Zhang L. Meta-Analysis of Genome-Wide Association Studies to Understand Disease Relatedness. Type 1 Diabetes-Complications, Pathogenesis, and Alternative Treatments.IntechOpen.2011 Nov 21; [Full Text]

  1. Li Y, Zhang L, Zhang D, Zhang X, Lu X. Faster evolution of Z-linked duplicate genes in chicken. J Genet Genomics. 2010 Oct; 37(10):695-702. [Full Text]
  2. Dalloul RA, Long JA, Zimin AV, Aslam L, Beal K, Blomberg Le Ann, Bouffard P, Burt DW, Crasta O, Crooijmans RP, Cooper K, Coulombe RA, De S, Delany ME, Dodgson JB, Dong JJ, Evans C, Frederickson KM, Flicek P, Florea L, Folkerts O, Groenen MA, Harkins TT, Herrero J, Hoffmann S, Megens HJ, Jiang A, de Jong P, Kaiser P, Kim H, Kim KW, Kim S, Langenberger D, Lee MK, Lee T, Mane S, Marcais G, Marz M, McElroy AP, Modise T, Nefedov M, Notredame C, Paton IR, Payne WS, Pertea G, Prickett D, Puiu D, Qioa D, Raineri E, Ruffier M, Salzberg SL, Schatz MC, Scheuring C, Schmidt CJ, Schroeder S, Searle SM, Smith EJ, Smith J, Sonstegard TS, Stadler PF, Tafer H, Tu ZJ, Van Tassell CP, Vilella AJ, Williams KP, Yorke JA, Zhang L, Zhang HB, Zhang X, Zhang Y, Reed KM. Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biol. 2010 Sep 7; 8(9).pii: e1000475. [Full Text]
  3. Warren AS, Anandakrishnan R, Zhang L. Functional bias in molecular evolution rate of Arabidopsis thaliana. BMC Evol Biol. 2010 May 1; 10:125. [Full Text]
  4. Beck DC, Jiang H, Zhang L. Elucidating the Evolutionary Relationships among Bos taurus Digestive Organs Using Unigene Expression Data. Int J Evol Biol. 2010 Feb 8; 2010:803142. [Full Text]
  5. Shi G, Zhang L, Jiang T. MSOAR 2.0: Incorporating tandem duplications into ortholog assignment based on genome rearrangement. BMC Bioinformatics. 2010 Jan 6; 11:10. [Full Text]
  6. Zhang L, Watson LT. The expected fitness cost Of a mutation fixation under the one-dimensional Fisher model. International Journal of Pure and Applied Mathematics : IJPAM. 2010; 62(2):21. [Full Text]

  1. Pan D, Zhang L. An atlas of the speed of copy number changes in animal gene families and its implications. PLoS One. 2009 Oct 23; 4(10):e7342. [Full Text]
  2. Lawson MJ, Zhang L. Sexy gene conversions: locating gene conversions on the X-chromosome. Nucleic Acids Res. 2009 Aug; 37(14):4570-9. [Full Text]
  3. Huang W, Wang P, Liu Z, Zhang L. Identifying disease associations via genome-wide association studies. BMC Bioinformatics. 2009 Jan 30; 10 Suppl 1:S68. [Full Text]
  4. Pan D, Zhang L. Burst of young retrogenes and independent retrogene formation in mammals. PLoS One. 2009; 4(3):e5040. [Full Text]
  5. Zhang L, Watson LT. Analysis of the fitness effect of compensatory mutations. HFSP J. 2009; 3(1):47-54. [Full Text]
  6. Lawson MJ, Jiao J, Fan W, Zhang L. A pattern analysis of gene conversion literature. Comp Funct Genomics. 2009:761512. [Full Text]

  1. Yang K, Zhang L. Performance comparison of gene family clustering methods with expert curated gene family data set in Arabidopsis thaliana. Planta. 2008 Aug; 228(3):439-47. [Full Text]
  2. Zhang L. Adaptive evolution and frequent gene conversion in the brain expressed X-linked gene family in mammals. Biochem Genet. 2008 Jun; 46(5-6):293-311. [Full Text]
  3. Sanna CR, Li WH, Zhang L. Overlapping genes in the human and mouse genomes. BMC Genomics. 2008 Apr 14; 9:169. [Full Text]
  4. Yang K, Zhang L. Performance comparison between k-tuple distance and four model-based distances in phylogenetic tree reconstruction. Nucleic Acids Res. 2008 Mar; 36(5):e33. [Full Text]
  5. Lawson MJ, Zhang L. Housekeeping and tissue-specific genes differ in simple sequence repeats in the 5'-UTR region. Gene. 2008 Jan 15; 407(1-2):54-62. [Full Text]
  6. Pan D, Zhang L. Tandemly arrayed genes in vertebrate genomes. Comp Funct Genomics. 2008:545269. [Full Text]

  1. Zhang L, Watson LT. Note on the computation of critical effective population sizes. J Comput Biol. 2007 Sep; 14(7):950-60. [Full Text]
  2. Pan D, Zhang L. Quantifying the major mechanisms of recent gene duplications in the human and mouse genomes: a novel strategy to estimate gene duplication rates. Genome Biol. 2007; 8(8):R158. [Full Text]
  3. Shoja V, Murali TM, Zhang L. Expression divergence of tandemly arrayed genes in human and mouse. Comp Funct Genomics. 2007:60964. [Full Text]
  4. Shoja V, Zhang L. A roadmap of tandemly arrayed genes in the genomes of human, mouse, and rat. Mol Biol Evol. 2006 Nov; 23(11):2134-41. [Full Text]
  5. Lawson MJ, Zhang L. Distinct patterns of SSR distribution in the Arabidopsis thaliana and rice genomes. Genome Biol. 2006; 7(2):R14. [Full Text]
  6. Zhang L, Li WH. Human SNPs reveal no evidence of frequent positive selection. Mol Biol Evol. 2005 Dec; 22(12):2504-7. [Full Text]
  7. Zhang L, Lu HH, Chung WY, Yang J, Li WH. Patterns of segmental duplication in the human genome. Mol Biol Evol. 2005 Jan; 22(1):135-41. [Full Text]
  8. Zhang L, Li WH. Mammalian housekeeping genes evolve more slowly than tissue-specific genes. Mol Biol Evol. 2004 Feb; 21(2):236-9. [Full Text]
  9. Zhang L, Gaut BS. Does recombination shape the distribution and evolution of tandemly arrayed genes (TAGs) in the Arabidopsis thaliana genome? Genome Res. 2003 Dec; 13(12):2533-40. [Full Text]
  10. Zhang L, Peek AS, Dunams D, Gaut BS. Population genetics of duplicated disease-defense genes, hm1 and hm2, in maize (Zea mays ssp.mays L.) and its wild ancestor (Zea mays ssp.parviglumis). Genetics. 2002 Oct; 162(2):851-60. [Full Text]
  11. Zhang L, Vision TJ, Gaut BS. Patterns of nucleotide substitution among simultaneously duplicated gene pairs in Arabidopsis thaliana. Mol Biol Evol. 2002 Sep; 19(9):1464-73. [Full Text]
  12. Zhang L, Pond SK, Gaut BS. A survey of the molecular evolutionary dynamics of twenty-five multigene families from four grass taxa. J Mol Evol. 2001 Feb; 52(2):144-56. [Full Text]
  13. Zhang L, Gaut BS, Vision TJ. The evolution of duplicated genes. Science. 2001; 293:1551-1552.