Publications 2023

Gene duplications facilitate C4-CAM compatibility in common purslane

  • Xiaoliang Wang, Xuxu Ma, Ge Yan, Lei Hua, Han Liu, Wei Huang, Zhikai Liang, Qing Chao, Julian M Hibberd, Yuannian Jiao, Mei Zhang
  • Plant Physiology
  • Paper Link

Integrative Genome and Transcriptome Sequencing Analysis Indicates Genetic and Epigenetic Dysregulation in DS-AML

  • Xiaotu Ma, Rhonda E Ries, Quang Tran, Yanling Liu, Pandurang Kolekar, Ramzi Alsallaq, Zhikai Liang, Timothy Shaw, Meghana Devineni, Anne Deslattes Mays, Ching Lau, Johann K Hitzler, Soheil Meshinchi
  • Blood
  • Paper Link

Oligogalactolipid production during cold challenge is conserved in early diverging lineages

  • Allison C Barnes, Jennifer L Myers, Samantha M Surber, Zhikai Liang, Jeffrey P Mower, James C Schnable, Rebecca L Roston
  • Journal of Experimental Botany
  • Paper Link

A Transferable Machine Learning Framework for Predicting Transcriptional Responses of Genes Across Species

  • Zhikai Liang, Xiaoxi Meng, James C Schnable
  • Plant Gene Regulatory Networks: Methods and Protocols
  • Book Chapter Link

Conserved and variable heat stress responses of the Heat Shock Factor transcription factor family in maize and Setaria viridis

  • Zachary A Myers, Clair M Wootan, Zhikai Liang, Peng Zhou, Julia Engelhorn, Thomas Hartwig, Springer M Nathan
  • Plant Direct
  • Paper Link

SJPedPanel: A pan-cancer gene panel for childhood malignancies

  • Pandurang Kolekar, Vidya Balagopal, Li Dong, Yanling Liu, Scott Foy, Quang Tran, Heather Mulder, Anna LW Huskey, Emily Plyler, Zhikai Liang, Jingqun Ma, Joy Nakitandwe, Jiali Gu, Jamie Maciaszek, Debbie Payne-Turner, Saradhi Mallampati, Lu Wang, Elizabeth Stewart, John Easton, Jeffery M Klco, Xiaotu Ma
  • medRxiv
  • Preprint Link

Publications 2022

Mapping responsive genomic elements to heat stress in a maize diversity panel

  • Zhikai Liang#, Zachary A Myers, Dominic Petrella, Julia Engelhorn, Thomas Hartwig, Nathan M Springer#
  • Genome Biology
  • Paper Link

Genome‐wide loss of CHH methylation with limited transcriptome changes in Setaria viridis DOMAINS REARRANGED METHYLTRANSFERASE (DRM) mutants

  • Andrew Read, Trevor Weiss, Peter A Crisp, Zhikai Liang, Jaclyn Noshay, Claire C Menard, Chunfang Wang, Meredith Song, Candice N Hirsch, Nathan M Springer, Feng Zhang
  • The Plant Journal
  • Paper Link

Prediction of conserved and variable heat and cold stress response in maize using cis-regulatory information

  • Peng Zhou, Tara A Enders, Zachary A Myers, Erika Magnusson, Peter A Crisp, Jaclyn M Noshay, Fabio Gomez-Cano, Zhikai Liang, Erich Grotewold, Kathleen Greenham, Nathan M Springer
  • The Plant Cell
  • Paper Link

Publications 2021

Whole-genome variation of transposable element insertions in a maize diversity panel

  • Yinjie Qiu, Christine H O’Connor, Rafael Della Coletta, Jonathan S Renk, Patrick J Monnahan, Jaclyn M Noshay, Zhikai Liang, Amanda Gilbert, Sarah N Anderson, Suzanne E McGaugh, Nathan M Springer, Candice N Hirsch
  • G3: Genes, Genomes, Genetics
  • Paper Link

Stability of DNA methylation and chromatin accessibility in structurally diverse maize genomes

  • Jaclyn M Noshay, Zhikai Liang, Peng Zhou, Peter A Crisp, Alexandre P Marand, Candice N Hirsch, Robert J Schmitz, Nathan M Springer
  • G3: Genes, Genomes, Genetics
  • Paper Link

Genetic and epigenetic variation in transposable element expression responses to abiotic stress in maize

  • Zhikai Liang, Sarah N Anderson, Jaclyn M Noshay, Peter A Crisp, Tara A Enders, Nathan M Springer
  • Plant Physiology
  • Paper Link

Perioperative and oncological outcomes following minimally invasive versus open pancreaticoduodenectomy for pancreatic duct adenocarcinoma

  • Rui Sun, Jiawen Yu, Yifan Zhang, Zhika Liang, Xianlin Han
  • Surgical endoscopy
  • Paper Link

Predicting transcriptional responses to cold stress across plant species

  • Xiaoxi Meng*, Zhikai Liang*, Xiuru Dai, Yang Zhang, Samira Mahboub, Daniel W Ngu, Rebecca L Roston, James C Schnable
  • Proceedings of the National Academy of Sciences
  • Paper Link

Publications 2020

Hybrid of Restricted and Penalized Maximum Likelihood Method for Efficient Genome-wide Association Study

  • Wenlong Ren, Zhikai Liang, Shu He, Jing Xiao
  • Genes
  • Paper Link

A high-throughput phenotyping pipeline for image processing and functional growth curve analysis

  • Ronghao Wang, Yumou Qiu, Yuzhen Zhou, Zhikai Liang, James C Schnable
  • Plant Phenomics
  • Paper Link

Non‐homology‐based prediction of gene functions in maize (Zea mays ssp. mays)

  • Xiuru Dai, Zheng Xu, Zhikai Liang, Xiaoyu Tu, Silin Zhong, James C Schnable, Pinghua Li
  • The Plant Genome
  • Paper Link

Genome–phenome wide association in maize and arabidopsis identifies a common molecular and evolutionary signature

  • Zhikai Liang, Yumou Qiu, James C Schnable
  • Molecular Plant
  • Paper Link

Enhancing hybrid prediction in pearl millet using genomic and/or multi-environment phenotypic information of inbreds

  • Diego Jarquin, Reka Howard, Zhikai Liang, Shashi K Gupta, James C Schnable, Jose Crossa
  • Frontiers in Genetics
  • Paper Link

Publications 2019

New Approaches to Use Genomics, Field Traits, and High-throughput Phenotyping for Gene Discovery in Maize (Zea mays)

  • Zhikai Liang
  • University of Nebraska-Lincoln
  • Thesis Link

Genome wide analysis of Ga1-s modifiers in maize

  • Preston Hurst, Zhikai Liang, Christine Smith, Melinda Yerka, Brandi Sigmon, Oscar Rodriguez, James C Schnable
  • bioRxiv
  • Preprint Link

Publications 2018

Phenotypic data from inbred parents can improve genomic prediction in pearl millet hybrids

  • Zhikai Liang, Shashi K Gupta, Cheng-Ting Yeh, Yang Zhang, Daniel W Ngu, Ramesh Kumar, Hemant T Patil, Kanulal D Mungra, Dev Vart Yadav, Abhishek Rathore, Rakesh K Srivastava, Rajeev Gupta, Jinliang Yang, Rajeev K Varshney, Patrick S Schnable, James C Schnable
  • G3: Genes, Genomes, Genetics
  • Paper Link

Functional divergence between subgenomes and gene pairs after whole genome duplications

  • Zhikai Liang, James C Schnable
  • Molecular Plant
  • Paper Link

Conventional and hyperspectral time-series imaging of maize lines widely used in field trials

  • Zhikai Liang, Piyush Pandey, Vincent Stoerger, Yuhang Xu, Yumou Qiu, Yufeng Ge, James C Schnable
  • Gigascience
  • Paper Link

Publications 2017

Lessons From Paired Data From exPVP Maize Lines in Agronomic Field Trials and RGB And Hyperspectral Time-Series Imaging In Controlled Environments

  • James C Schnable, Piyush Pandey, Yufeng Ge, Yuhang Xu, Yumou Qiu, Zhikai Liang
  • AGU Fall Meeting Abstracts
  • Conference Processing Link

Differentially regulated orthologs in sorghum and the subgenomes of maize

  • Yang Zhang, Daniel W Ngu, Daniel Carvalho, Zhikai Liang, Yumou Qiu, Rebecca L Roston, James C Schnable
  • The Plant Cell
  • Paper Link

STAG-CNS: an order-aware conserved noncoding sequences discovery tool for arbitrary numbers of species

  • Xianjun Lai, Sairam Behera, Zhikai Liang, Yanli Lu, Jitender S Deogun, James C Schnable
  • Molecular Plant
  • Paper Link

Publications 2016

Genome-wide identification and functional prediction of nitrogen-responsive intergenic and intronic long non-coding RNAs in maize (Zea mays L.)

  • Yuanda Lv, Zhikai Liang, Min Ge, Weicong Qi, Tifu Zhang, Feng Lin, Zhaohua Peng and Han Zhao
  • BMC Genomics
  • Paper Link

Automated vegetative stage phenotyping analysis of maize plants using visible light images

  • Sruti Das Choudhury, Vincent Stoerger, Ashok Samal, James C Schnable, Zhikai Liang, Jin-Gang Yu
  • KDD workshop
  • Conference Processing Link

RNA-seq based analysis of population structure within the maize inbred B73

  • Zhikai Liang, James C Schnable
  • PloS One
  • Paper Link

Publications 2015

Verification and evaluation of grain QTLs using RILs from TD70 x Kasalath in rice

  • YD Zhang, J Zheng, ZK Liang, YL Liang, ZH Peng, CL Wang
  • Genet. Mol. Res
  • Paper Link