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). doi: 10.1038/srep38432. PubMed PMID: 27917931. [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. doi: 10.1016/j.anaerobe.2016.10.004. PubMed PMID: 27742572. [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. doi: 10.1371/journal.pone.0162442. PubMed PMID: 27632579; PubMed Central PMCID: PMC5025195. [Full Text]
  4. Hasan M, Zhang L. SPAI: an interactive platform for indel analysis. BMC Genomics. 2016 Aug 31; 17(5): 496. doi:10.1186/s12864-016-2824-x. PubMed PMID: 27585593; PubMed Central PMCID: PMC5009558. [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. doi: 10.1371/journal.pone.0151826. PubMed PMID: 27011215; PubMed Central PMCID: PMC4806927. [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. doi: 10.1186/1471-2164-16-S11-S2. PubMed PMID: 26576456; PubMed Central PMCID: PMC4652484. [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. doi: 10.1186/s12859-015-0781-z. PubMed PMID: 26518340; PubMed Central PMCID: PMC4628267. [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. Sci Rep. 2015 Sep 7;5:13859. doi: 10.1038/srep13859. PubMed PMID: 26343792; PubMed Central PMCID: PMC4561376. [Full Text]
  4. Hasan MS, Wu X, Zhang L. Performance evaluation of indel calling tools using real short-read data. Hum Genomics. 2015 Aug 19;9:20. doi: 10.1186/s40246-015-0042-2. PubMed PMID: 26286629; PubMed Central PMCID: PMC4545535. [Full Text]
  5. Liu M, Watson LT, Zhang L. Predicting the combined effect of multiple genetic variants. Hum Genomics. 2015 Jul 30;9:18. doi: 10.1186/s40246-015-0040-4. PubMed PMID: 26223264; PubMed Central PMCID: PMC4520001. [Full Text]
  6. Chen W, Zhang L. The pattern of DNA cleavage intensity around indels. Sci Rep. 2015 Feb 9;5:8333. doi: 10.1038/srep08333. PubMed PMID: 25660536; PubMed Central PMCID: PMC4321175. [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. doi: 10.1093/bioinformatics/btu602. PubMed PMID: 25231908. [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. doi: 10.1186/s12859-014-0359-1. PubMed PMID: 25407965; PubMed Central PMCID: PMC4245841. [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. doi:10.1155/2014/961823. [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. doi: 10.1186/1471-2105-15-5. PubMed PMID: 24405700; PubMed Central PMCID: PMC3893606. [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. PubMed PMID: 24839440; PubMed Central PMCID: PMC4009243. [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. doi: 10.1109/TST.2012.6374367. [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. doi: 10.1111/j.1365-2583.2012.01141.x. PubMed PMID: 22458920; PubMed Central PMCID: PMC3386798. [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. doi: 10.1007/s00726-010-0825-7. Epub 2010 Dec 30. PubMed PMID: 21191803. [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. doi: 10.1186/1471-2105-12-191. PubMed PMID: 21635719; PubMed Central PMCID: PMC3119068. [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. doi: 10.4137/CIN.S7135. PubMed PMID: 21695068; PubMed Central PMCID: PMC3118451. [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. doi: 10.1371/journal.pone.0027175. PubMed PMID: 22076134; PubMed Central PMCID: PMC3208586. [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. doi: 10.1016/S1673-8527(09)60087-4. PubMed PMID: 21035095. [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. doi: 10.1371/journal.pbio.1000475. PubMed PMID: 20838655; PubMed Central PMCID: PMC2935454. [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. doi: 10.1186/1471-2148-10-125. PubMed PMID: 20433764; PubMed Central PMCID: PMC2876160. [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. doi: 10.4061/2009/803142. PubMed PMID: 21350656; PubMed Central PMCID: PMC3042666. [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. doi: 10.1186/1471-2105-11-10. PubMed PMID: 20053291; PubMed Central PMCID: PMC2821317. [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. doi: 10.1371/journal.pone.0007342. PubMed PMID: 19851465; PubMed Central PMCID: PMC2761543. [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. doi: 10.1093/nar/gkp421. Epub 2009 May 31. PubMed PMID: 19487239; PubMed Central PMCID: PMC2724270. [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. doi: 10.1186/1471-2105-10-S1-S68. PubMed PMID: 19208172; PubMed Central PMCID: PMC2648782. [Full Text]
  4. Pan D, Zhang L. Burst of young retrogenes and independent retrogene formation in mammals. PLoS One. 2009;4(3):e5040. PubMed PMID: 19325906; PubMed Central PMCID: PMC2657826. [Full Text]
  5. Zhang L, Watson LT. Analysis of the fitness effect of compensatory mutations. HFSP J. 2009;3(1):47-54. doi: 10.2976/1.2990075. PubMed PMID: 19649156; PubMed Central PMCID: PMC2689613. [Full Text]
  6. Lawson MJ, Jiao J, Fan W, Zhang L. A pattern analysis of gene conversion literature. Comp Funct Genomics. 2009:761512. doi: 10.1155/2009/761512. PubMed PMID: 20148076; PubMed Central PMCID: PMC2817553. [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. doi: 10.1007/s00425-008-0748-7. PubMed PMID: 18493791. [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. doi: 10.1007/s10528-008-9148-8. PubMed PMID: 18236150. [Full Text]
  3. Sanna CR, Li WH, Zhang L. Overlapping genes in the human and mouse genomes. BMC Genomics. 2008 Apr 14;9:169. PubMed PMID: 18410680; PubMed Central PMCID: PMC2335118. [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. doi: 10.1093/nar/gkn075. Epub 2008 Feb 22. PubMed PMID: 18296485; PubMed Central PMCID: PMC2275138. [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. PubMed PMID: 17964742. [Full Text]
  6. Pan D, Zhang L. Tandemly arrayed genes in vertebrate genomes. Comp Funct Genomics. 2008:545269. doi: 10.1155/2008/545269. PubMed PMID: 18815629; PubMed Central PMCID: PMC2547482. [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. PubMed PMID: 17803372. [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. PubMed PMID: 17683522; PubMed Central PMCID: PMC2374989. [Full Text]
  3. Shoja V, Murali TM, Zhang L. Expression divergence of tandemly arrayed genes in human and mouse. Comp Funct Genomics. 2007:60964. doi: 10.1155/2007/60964. PubMed PMID: 18273387; PubMed Central PMCID: PMC2216068. [Full Text]

  1. 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. PubMed PMID: 16901985. [Full Text]
  2. Lawson MJ, Zhang L. Distinct patterns of SSR distribution in the Arabidopsis thaliana and rice genomes. Genome Biol. 2006;7(2):R14. PubMed PMID: 16507170; PubMed Central PMCID: PMC1431726. [Full Text]

  1. Zhang L, Li WH. Human SNPs reveal no evidence of frequent positive selection. Mol Biol Evol. 2005 Dec;22(12):2504-7. PubMed PMID: 16107590. [Full Text]
  2. 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. PubMed PMID: 15371527. [Full Text]

  1. Zhang L, Li WH. Mammalian housekeeping genes evolve more slowly than tissue-specific genes. Mol Biol Evol. 2004 Feb;21(2):236-9. PubMed PMID: 14595094. [Full Text]

  1. 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. PubMed PMID: 14656961; PubMed Central PMCID: PMC403795. [Full Text]

  1. 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. PubMed PMID: 12399395; PubMed Central PMCID: PMC1462307. [Full Text]
  2. 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. PubMed PMID: 12200474. [Full Text]

  1. 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. PubMed PMID: 11231894. [Full Text]
  2. Zhang L, Gaut BS, Vision TJ. The evolution of duplicated genes. Science . 2001; 293:1551-1552.