Y.N. Chai, Y. Qi*, E. Goren*, D. Chiniquy, A.M. Sheflin, S.G. Tringe, J.E. Prenni, P. Liu*, D.P. Schachtman (2024). Root-associated bacterial communities and root metabolite composition are linked to nitrogen use efficiency in sorghum. mSystems 9:e01190-23
J. Pang, W. Ju, M. Welch, P. Gauger, P. Liu*, Q. Zhang, and C. Wang (2023). Nonparametric bootstrap methods for interval estimation of the area under the ROC curve with correlated diagnostic test data: Application to whole-virus ELISA testing in swine. Frontiers in Veterinary Science, 10, 1274786.
D. C. Walker*, Z. R. Lozier, R. Bi*, P. Kanodia, W. A. Miller and P. Liu* (2023). Variational inference for detecting differential translation in ribosome profiling studies, Frontiers in Genetics, Volume 14.
J. C. Berry, M. Qi, B. V. Sonawane, A. Sheflin, A. B. Cousins, J. Prenni, D. P. Schachtman, P. Liu*, R. S. Bart (2022). Increased signal to noise ratios within experimental field trials by regressing spatially distributed soil properties as principal components, eLife 11:e70056.
M. Qi, J. C. Berry, K. Veley, L. O’Connor, O. M. Finkel, I. Salas-González, M. Kuhs, J. Jupe, E. Holcomb, T.G. del Rio, C. Creech, P. Liu*, S. Tringe, J. L. Dangl, D. Schachtman, R. S. Bart (2022). Identification of beneficial and detrimental bacteria impacting sorghum responses to drought using multi-scale and multi-system microbiome comparisons, ISME J.
M. I. Natukundaa, M. B. Mantilla-Pereza,b, M. A. Grahama,c, P. Liu*, and M. G. Salas-Fernandez (2022). Dissection of canopy layer-specific genetic control of leaf angle in Sorghum bicolor by RNA sequencing, BMC Genomics, 23, 95.
R. Bi* and P. Liu* (2021). A Semi-parametric Bayesian Approach for Detection of Gene Expression Heterosis with RNA-Seq Data, Journal of Applied Statistics, 50(1): 214–230, DOI: 10.1080/02664763.2021.2004581
J. Wang, X. Li, T. Guo, M. Dzievit, X. Yu, P. Liu*, K. P. Price, J. Yu (2021). Genetic Dissection of Seasonal Vegetation Index Dynamics in Maize through Aerial Based High-throughput Phenotyping, The Plant Genome, 14(3), e20155.
E. Goren*, C. Wang, Z. He, A. Sheflin, D. Chiniquy, J. Prenni, S. Tringe, D. Schachtman, P. Liu* (2021). Feature selection and causal analysis for microbiome studies in the presence of confounding using standardization. BMC Bioinformatics 22, 362
J. Zhao, Y. Qi*, P. Liu*, A. Severin, M. Sayadi, I. Paetau-Robinson, W.S. White, (2021). Prebiotic Effects of a Cranberry Beverage in a Randomized, Placebo-Controlled, Crossover Clinical Trial. Current Developments in Nutrition, 5(2), 1190.
P. Liu*, E. Goren*, P. Morris, D. Walker*, and C. Wang, Statistical Methods for Feature Selection in Microbiome Studies (2021), invited book chapter for Statistical Analysis of Microbiome Data, Springer
P. Kanodia, V. Paramasivan, R. Srivastava, R. Bi*, P. Liu*, W. A. Miller, S. H. Howell (2020). Control of translation during the unfolded protein response in maize seedlings: Life without PERKs, Plant Direct.
J. Bao, Y. Yu, H. Li, J. Hawks, G. Szatkowski, B. Dade, H. Wang*, P. Liu*, T. Brutnell, B. Spehar, N. Tye-Murray (2020). Evidence for Independent Peripheral and Central Age-Related Hearing Impairment, Journal of Neuroscience Research.
L. A. Laboissonniere, J. J. Goetz, G. M. Martin, R. Bi, T. J.S. Lund, L. Ellson, M. R. Lynch, B. Mooney, H. Wickham, A. Mani, P. Liu, G. W. Schwartz, and J. M. Trimarchi (2019). Molecular signatures of retinal ganglion cells revealed through single cell profiling, Scientific Reports.
L. Dong, L. Qin, X.Dai, Z. Ding, R. Bi*, P. Liu*, Y. Chen, T. Brutnell, X. Wang, and P. Li (2019). Transcriptomic Analysis of Leaf Sheath Maturation in Maize, International Journal of Molecular Sciences, 20(10), 2472.
M. He, K. Wimalanathan, P. Liu*, C.J. Lawrence-Dill (2019). Compare Expression Profiles for Pre-defined Gene Groups with C-REx. Journal of Open Source Software, 4(37), 1255.
A. Sheflin, D. Chiniquy, C. Yuan*, E. Goren*, I. Kumar, M. Braud, T. Brutnell, A. Eveland, S. Tringe, P. Liu*, S. Kresovich, E. Marsh, D. Schachtman, and J. Prenni (2019). Metabolomics of sorghum roots during nitrogen stress reveals compromised metabolic capacity for defense response, Plant Direct.
Y. Zhang, R. Giuliani, Y. Zhang, W. L. Araujo, B. Wang, P. Liu, Q. Sun, A. Cousins, G. Edwards, A. Fernie, A. Barkan, T. Brutnell, and P. Li (2018). Characterization of maize leaf Pyurvate Orthophosphate Dikinase using high throughput sequencing. Accepted by the Journal of Integrative Plant Biology.
R. Srivastava, Z. Li, G. Russo, J. Tang, R. Bi, U. Muppirala, S. Chudalayandi, A. Severin, M. He, S. Vaitkevicius, C. Lawrence-Dill, P. Liu, A.E. Stapleton, D. Bassham, F. Brandizzi, and S. Howell (2018). Persistent ER stress in maize seedlings engages ZmIRE1 in a multiphasic process that transitions from prosurvival activities to cell death. Accepted by The Plant Cell.
E. Goren*, P. Liu*, C. Wang, and C. Wang (2018). BinQuasi: a peak detection method for ChIP-sequencing data with biological replicates. Bioinformatics.
M. He, P. Liu, and C.J. Lawrence-Dill (2017). A hypothesis-driven approach assessing significance of differences in RNA expression levels among specific groups of genes. Current Plant Biology, 11–12 (2017), pp. 46-51.
C. Zhang, S. Fei, P. Liu, T. Ji, J. Peng, U. Frei, and D. Hannapel (2017). Transcriptome changes in response to cold acclimation in perennial ryegrass as revealed by a cross-species microarray analysis. Crop Science, 57(Suppl1):S-179-S-191.
L. Laboissonniere, G. M. Martin, J. J Goetz, R. Bi, B. Pope, K. Weinand, L. Ellson, D. Fru, M. Lee, A. K Wester, P. Liu, and J. M Trimarchi (2017). Single cell transcriptome profiling of developing chick retinal cells. The Journal of Comparative Neurology, 2017 Aug 15; 525(12): 2735-2781.
S. Hu, C. Wang, D. Sanchez, A. Lipka, P. Liu*, Y. Yin, M. Blanco, and T. Lubberstedt (2017). Gibberellins promote brassinosteroids action and both increase heterosis for plant height in maize (Zea mays L.). Frontiers in Plant Science, 8:1039.
N. Cray, Y. Zhao, Y. Fang, P. Liu, L. Pollak, S. Duvick, D. F. Birt, and E. M. Whitley (2017), Effects of dietary resistant starch on the WNT signaling pathway and preneoplastic cells in the colons of azoxymethane-treated rats. Nutrition and Cancer, 69(4):632-642.
H. Sun, P. Liu, L. Nolan, and S. Lamont (2016). Thymus Transcriptome Reveals Novel Pathways in Response to Avian Pathogenic Escherichia coli (APEC) Infection. Poultry Science, 95(12): 2803-2814.
Z. Ding, Y. Zhang, Y. Xiao, F. Liu, M. Wang, X. Zhu, P. Liu, Qi Sun, W. Wang, M. Peng, T. Brutnell, and P. Li (2016). Transcriptome response of cassava leaves under natural shade. Scientific Reports, 6:31673.
B. Nelson, N. Cray, Y. Ai, Y. Fang, P. Liu, E. M. Whitley, and D. Birt (2016). Effect of Dietary Resistant Starch on Inhibition of Colonic Preneoplasia and Wnt Signaling in Azoxymethane-Induced Rodent Models. Nutrition and Cancer, 68(6):1052-63.
F. Liu*, C. Wang, Z. Wu, Q. Zhang, and P. Liu* (2016). A Zero-Inflated Poisson Model for Insertion Tolerance Analysis of Genes Based on Tn-seq Data. Bioinformatics, 32(11): 1701-1708.
H. Sun, R. Bi, P. Liu, L. Nolan, and S. Lamont (2016). Combined Analysis of Primary Lymphoid Tissues' Transcriptomic Response to Extra-intestinal Escherichia coli (ExPEC) Infection. Developmental and Comparative Immunology, 57:99-106.
F. Liu, C. Wang, and P. Liu* (2015). A Semi-parametric Bayesian Approach for Differential Expression Analysis of RNA-seq Data. Journal of Agricultural, Biological, and Environmental Statistics, 20(4):555-576.
H. Sun, P. Liu, L. Nolan, and S. Lamont (2015). Novel Pathways Revealed in Bursa of Fabricius Transcriptome in Response to Extraintestinal Pathogenic Escherichia coli (ExPEC) Infection. PLoS ONE, 10(11):e0142570.
H. Sun, P. Liu, L. Nolan, and S. Lamont (2015). Avian pathogenic Escherichia coli (APEC) infection alters the bone marrow transcriptome in chickens. BMC Genomics, 16:690.
J. E. Koltes, E. Fritz-Waters, C. J. Eisley, I. Choi, H. Bao, A. Kommadath, N. V. L. Serão, N. J. Boddicker, S. M. Abrams, M. Schroyen, H. Loyd, C. K. Tuggle, G. S. Plastow, L. Guan, P. Stothard, J. K. Lunney, P. Liu, S. Carpenter, R. R. R. Rowland, J. C. M. Dekkers, and J. M. Reecy (2015). Identification of a putative quantitative trait nucleotide in guanylate binding protein 5 for host response to PRRS virus infection. BMC Genomics, 16:412.
M. Orr*, P. Liu*, and D. Nettleton (2014). An Improved Method for Computing Q-values when the Distribution of Effect Sizes is Asymmetric. Bioinformatics, 30(21):3044-3053.
L. Wang, A. Czedik-Eysenberg, R. A. Mertz, Y. Si, T. Tohge, A. Nunes-Nesi, S. Arrivault, L. K. Dedow, D. W. Bryant, W. Zhou, J. Xu, S. Weissmann, A. Studer, P. Li, C. Zhang, T. LaRue, Y. Shao, Z. Ding, Q. Sun, R. V. Patel, R. Turgeon, X. Zhu, N. J. Provart, T. C. Mockler, A. R. Fernie, M. Stitt, P. Liu, T. P. Brutnell (2014). Comparative analyses of C₄ and C₃ photosynthesis in developing leaves of maize and rice. Nature Biotechnology, 32(11):1158-1165.
T. Ji, P. Liu, and D. Nettleton (2014). Estimation and Testing of Gene Expression Heterosis. Journal of Agricultural, Biological, and Environmental Statistics, 19(3):319-337.
Y. Du, C. Wang, and P. Liu (2014). A Permutation Test of Genetic Association between Salmonella Isolated On-farm and At-abattoir using Amplified Fragment Length Polymorphism. Journal of Biometrics and Biostatistics, 5:204.
S. L. Taustra, P. Li, Y. Si, N. Gandotra, P. Liu, Q. Sun, T. P. Brutnell, and T. Nelson (2014). Developmental dynamics of Kranz cell transcriptional specificity in maize leaf reveals early onset of C4-related processes. Journal of Experimental Botany, 65(13):3543-3555.
W. Landau, and P. Liu (2013). Dispersion Estimation and Its Effect on Test Performance in RNA-seq Data Analysis: A Simulation-Based Comparison of Methods. PLoS ONE, 8(12):e81415.
Z. Wu, O. Sahin, Z. Shen, P. Liu, W. G. Miller, and Q. Zhang (2013). Multi-omics approaches to deciphering a hypervirulent strain of Campylobacter jejuni. Genome Biology and Evolution, 5(11):2217-2230.
Q. Xia, W. T. Muraola, Z. Shen, O. Sahin, H. Wang, Z. Wu, P. Liu, and Q. Zhang (2013). Adaptive mechanisms of Campylobacter jejuni to erythromycin treatment. BMC Microbiology, 13:133.
H. Hao, Z. Yuan, Z. Shen, J. Han, O. Sahin, P. Liu, and Q. Zhang (2013). Mutational and transcriptomic changes involved in the development of macrolide resistance in Campylobacter jejuni. Antimicrobial Agents and Chemotherapy, 57(3):1369-1378.
E. E. Sandford, M. Orr, X. Li, H. Zhou, T. J. Johnson, S. Kariyawasam, P. Liu, L. K. Nolan, and S. J. Lamont (2012). Strong Concordance Between Transcriptomic Patterns of Spleen and Peripheral Blood Leukocytes in Response to Avian Pathogenic Escherichia coli Infection. Avian Diseases, 56(4):732-736.
H. Lin, C. Wang, P. Liu, and D.J. Holtkamp (2012). Construction of Disease Risk Scoring Systems using Logistic Group Lasso: Application to Porcine Reproductive and Respiratory Syndrome Survey Data. Journal of Applied Statistics, 40(4):736-746.
M. Orr, P. Liu, and D. Nettleton (2012). Estimating the Number of Genes that are Differentially Expressed in Both of Two Independent Experiments. The Journal of Agricultural, Biological, and Environmental Statistics. 17(4):583-600.
W. Fang, Y. Si, S. Douglass, D. Casero, S. Merchant, M. Pellegrini, I. Ladunga, P. Liu, and M. Spalding (2012). Transcriptome-Wide Changes in Chlamydomonas reinhardtii Gene Expression Regulated by Carbon Dioxide and the CO2-Concentrating Mechanism Regulator CIA5/CCM1. The Plant Cell, 24(5):1876-1893.
P. Liu*, and C. Wang (2012). Robust Semiparametric Optimal Testing Procedure for Multiple Normal Means. Journal of Probability and Statistics, Volume 2012, Article ID 913560.
T. Ji, P. Liu, and D. Nettleton (2012). Borrowing Information Across Genes and Experiments for Improved Error Variance Estimation in Microarray Data Analysis. Statistical Applications in Genetics and Molecular Biology, 11(3): Article 12.
T. Luangtongkum, Z. Shen, V. W. Seng, O. Sahin, B. Jeon, P. Liu, and Q. Zhang (2012). Impaired fitness and transmission of macrolide-resistant Campylobacter jejuni in its natural host. Antimicrobial Agents and Chemotherapy, 56(3):1300-1308.
E. E. Sandford, M. Orr, M. Shelby, X. Li, H. Zhou, T. J. Johnson, S. Kariyawasam, P. Liu, L. K. Nolan, and S. J. Lamont (2012). Leukocyte Transcriptome from Chickens Infected with Avian Pathogenic Escherichia coli Identifies Pathways Associated with Resistance. Results in Immunology, 2:44-53.
V. M. Kvam, P. Liu*, and Y. Si (2012). A comparison of statistical methods for detecting differentially expressed genes from RNA-seq data. American Journal of Botany, 99(2):248-256.
P. Liu, and Y. Si (2014), Book Chapter: Cluster Analysis of RNA-sequencing Data, in the book of Statistical Analysis of Next Generation Sequencing Data
L. Wang, Y. Si, L. K. Dedow, Y. Shao, P. Liu, and T. Brutnell (2011). A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq. PLoS ONE, 6(10):e26426.
E. E. Sandford, M. Orr, E. Balfanz, N. Bowerman, X. Li, H. Zhou, T. J. Johnson, S. Kariyawasam, P. Liu, L. K. Nolan, and S. J. Lamont (2011). Spleen transcriptome response to infection with avian pathogenic Escherichia coli in broiler chickens. BMC genomics, 12:469.
G. Li, K. Tivendale, P. Liu, Y. Feng, Y. Wannemuheler，W.Cai, P. Mangiamele, T. Johnson, C. Constantinidou, C. Penn, and L.K. Nolan (2011). Transcriptome Analysis of Avian Pathogenic Escherichia coli O1 in Chicken Serum Reveals Adaptive Responses to Systemic Infection. Infection and Immunity, 79(5):1951-1960.
X. Yu, L. Li, J. Zola, M. Aluru, H. Ye, A. Foudree, H. Guo, S. Anderson, S. Aluru, P. Liu, S. Rodermel, and Y. Yin (2011). A brassinosteroid transcriptional network revealed by genome-wide identification of bes1 target genes in Arabidopsis thaliana. The Plant Journal, 65(4):634-646.
P. Li, L. Ponnala, N. Gandotra, L. Wang, Y. Si, L. Tausta, T. Kebrom, N. Provart, R. Patel, C.R. Myers, E.J. Reidel, R. Turgeon, P. Liu, Q. Sun, T. Nelson, and T. Brutnell (2010). The developmental dynamics of the maize leaf transcriptome. Nature Genetics, 42(12):1060-1067.
J. T. G. Hwang, and P. Liu (2010). Optimal tests shrinking both means and variances applicable to microarray data analysis. Statistical Applications in Genetics and Molecular Biology, 9(1): Article 36.
M. Orr, and P. Liu* (2009). Sample size estimation while controlling false discovery rate for microarray experiments using the ssize.fdr package. The R Journal, 1(1): 47-53.
S. Covshoff, W. Majeran, P. Liu, J. M. Kolkman, K. J. van Wijk, and T. Brutnell (2008). Deregulation of maize C4 photosynthetic development in a mesophyll cell-defective mutant. Plant Physiology, 146:1469-1481.
X. Zheng, H-C Huang, W. Li, P. Liu*, Q-Z Li, and Y. Liu (2007). Modeling nonlinearity in dilution design microarray data. Bioinformatics, 23(11):1339-1347.
P. Liu*, and J. T. G. Hwang (2007). Quick estimation of sample size while controlling false discovery rate and application to microarray analysis. Bioinformatics, 23(6):739-746.
R. J. H. Sawers, P. Liu, K. Anufrikova, Q. Sun, G. Olsefski, J. T. G. Hwang, and T. Brutnell (2007). A multi-treatment experimental system to examine photosynthetic differentiation in the maize leaf. BMC genomics, 8:12.
S. A. Jesch, P. Liu, X. Zhao, M. T. Wells, and S. A. Henry (2006). Multiple Endoplasmic Reticulum-to-Nucleus Signaling Pathways Coordinate Phospholipid Metabolism with Gene Expression by Distinct Mechanisms. Journal of Biological Chemistry, 281:24070-24083.
N.-S. Tan, N. Shaw, N. Vinckenbosch, P. Liu*, R. Yasmin, B. Desvergne, W. Wahli, and N. Noy (2002). Selective cooperation between fatty acid binding proteins and peroxisome proliferator-activated receptors in regulating transcription. Molecular and Cellular Biology, 22(14): 5114-5127.
J. Ni, P. Liu, and H. Jia (2000). Binding Properties of M-CAT Element in the Chicken Nicotinic Acetylcholine Receptor γ-Subunit Promoter. Chinese Journal of Biochemistry and Molecular Biology, 16(5):580-585.