Peng Liu

Selected Publications:

• Z. Qiao, E. Barnes, S. Tringe, D. Schachtman, and P. Liu* (2023), Hurdle Poisson model-based clustering for microbiome data, Bioinformatics, 39(1), btac782, https://doi.org/10.1093/bioinformatics/btac782  
• 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, https://doi.org/10.3389/fgene.2023.1178508
• 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 https://doi.org/10.1038/s41396-022-01245-4
• 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 https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-021-08251-4
• 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, 2021, DOI: 10.1080/02664763.2021.2004581
• 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. https://doi.org/10.1186/s12859-021-04232-2
• 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, https://doi.org/10.1002/pld3.241
• 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, https://doi.org/10.1002/pld3.122
• E. Goren, P. Liu*, C. Wang, and C. Wang  (2018), BinQuasi: a peak detection method for ChIP-sequencing data with biological replicates, Bioinformatics, 34(17), 2909–2917, https://doi.org/10.1093/bioinformatics/bty227
• 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: 1701-1708, doi: 10.1093/bioinformatics/btw061
• R. Bi and P. Liu* (2016), Sample size calculation for designing RNA-sequencing experiments, BMC Bioinformatics, 17 :146, doi: 10.1186/s12859-016-0994-9
• 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, doi: 10.1007/s13253-015-0227-0