Chun Liang

Chun Liang


350 Pearson Hall
Bioinfo Laboratory

Biographical Information

My bioinformatics lab focuses on three primary research areas: (1) develop bioinformatics software tools, (2) build and maintain biological databases, and (3) conduct data analysis and data mining to address interesting biological questions.  Currently, we are working with many different bioinformatics projects, including genome-wide detection and functional characterization of DNA and RNA transposons, In silico exploration of DNA repeats (e.g., inverted repeats) and their potential roles in gene expression regulation, CRISPR-based DNA and RNA editing: target design and specificity, genome-wide detection of CRISPRs in prokaryotic genomes, DNA methylation and its role in tissue regeneration, RNA-Seq based transcriptome analysis and differentially expressed gene analysis, small non-coding RNAs (miRNAs, siRNAs and piRNAs) biogenesis and their differential expression analysis, genome-wide analysis of alternative polyadenylation and alternative splicing in eukaryotes, cancer genomics, etc.

Courses Taught

  • BIO/CHM/CSE/MBI 466-566: Bioinformatics Computing Skills
  • BIO/MBI 485-585 CSE 456-556: Bioinformatics Principles
  • BIO/CSE/MBI 256: Introduction to Programming for the Life Sciences
  • BIO 131: Plants, Humanity, and the Environment

Recent Publications

  • Li M+ and Liang C (2022). LncDC: a machine learning-based tool for long non-coding RNA detection from RNA-Seq data. Scientific Reports, 12:19083
  • Wang C+ and Liang C (2022). The insertion and dysregulation of transposable elements in osteosarcoma and their association with patient event‑free survival. Scientific Reports, 12:377.

  • Tangeman JA, Pérez-Estrada JR, Van Zeeland E, Liu L, Danciutiu A, Grajales-Esquivel E, Smucker B, Liang C, & Del Rio-Tsonis K (2022). A stage-specific OTX2 regulatory network and maturation-associated gene programs are inherent barriers to RPE neural competency.  Frontiers in Cell and Developmental Biology. 10:875155
  • Tangeman JA+, Luz-Madrigal A, Sreeskandarajan S+, Grajales-Esquivel E, Liu L, Liang C, Tsonis PA, Del Rio-Tsonis K  (2021). Transcriptome Profiling of Embryonic Retinal Pigment Epithelium Reprogramming. Genes. 2021, 12(6): 840.

  • Tangeman J, Luz-Madrigal A, Sreeskandarajan S, Grajales-Esquivel E, Liu L, Liang C, Tsonis PA and Del Rio-Tsonis K (2020). Transcriptome Profiling of Embryonic Retinal PigmentEpithelium Reprogramming. Genes. DOI: 10.3390/genes12060840.

  • Liu B, Iwata‐Otsubo A, Yang D, Baker RL, Liang C, Jackson SA, Liu S, Ma J, Zhao M. (2020). Analysis of CACTA transposase genes unveils the mechanism of intron loss and distinct small RNA silencing pathways underlying divergent evolution of Brassica genomes. The Plant Journal.

  • Luz-Madrigal A, Grajales-Esquivel E, Tangeman J, Kosse S, Liu L, Wang K, Fausey A, Liang C, Tsonis PA and Del Rio-Tsonis KD. (2020). DNA demethylation is a driver for chick retina regeneration. Epigenetics. 15(9):998-1019.

  • Padula SL, Anand D, Hoang TV, Chaffee BR, Liu Lin, Liang C, Lachke SA and ML Robinson (2019). High-throughput transcriptome analysis reveals that the loss of Pten activates a novel NKX6-1/RASGRP1 regulatory module to rescue microphthalmia caused by Fgfr2-deficient lenses, Human Genetics, 138:1391-1407

  • Rao D, Sreeskandarajan S++, Liang C (2019). Accelerating clustering using approximate spanning tree and prime number based filter. Conference Proceedings - 2019 IEEE 33rd International Parallel and Distributed Processing Symposium Workshops, IPDPSW 2019 (2019), 166-174

  • Shi J++ and Liang C* (2019). Generic Repeat Finder: a high-sensitivity tool for genome-wide de novo repeat detection. Plant Physiology,

  • Qi Z, Glazier BJ, Hinkel BC, Cao J, Liu L, Liang C and H Shi* (2019). Neuroendocrine Regulation of Energy Metabolism Involving Different Types of Adipose Tissues. Int. J. Mol. Sci.,

  • Zhu H++ and Liang C* (2019). CRISPR-DT: designing gRNAs for the CRISPR-Cpf1 system with improved target efficiency and specificity. Bioinformatics, bty1061

  • Lam PT, Padula SL, Hoang TV, Poth JE, Liu L, Liang C, LeFever AS, Wallace LM, Ashery-Padan R, Riggs PK, Shields JE, Shaham O, Rowan S, Brown NL, Glaser T and Robinson ML (2019) Considerations for the use of Cre recombinase for conditional gene deletion in the mouse lens. Human Genomics, 13:10

  • Zhao Z++, Wu X, Ji G, Liang C and Li, QQ (2019). Genome-Wide Comparative Analyses of Polyadenylation Signals in Eukaryotes Suggest a Possible Origin of the AAUAAA Signal. Int. J. Mol. Sci., 20(4):958

  • Zhu H and Liang C. (2019) CRISPR-DT: designing gRNAs for the CRISPR-Cpf1 system with improved target efficiency and specificity. Bioinformatics, 35(16):2763-2789

  • Wang C and Liang C. (2018) MSIpred: A Python Package for Tumor Microsatellite Instability Classification from Tumor Mutation Annotation Data Using a Support Vector Machine. Scientific Reports, 8: 17546. PMC6277498.

  • Wang K, Hoeksema J and Liang C. (2018) piRNN: Deep Learning Algorithm for piRNA Prediction. PeerJ, 6: e5429. PMC6078063.

  • Cao J, Zhu Q, Liu L, Glazier BJ, Hinke BC, Liang C and Shi H (2018). Global Transcriptome Analysis of Brown Adipose Tissue of Diet-Induced Obese Mice. Int. J. Mol. Sci., 19(4):1095

  • Zhu, Richmond E, Liang C (2018). CRISPR-RT: A web application for designing CRISPR-C2c2 crRNA with improved target specificity. Bioinformatics, 34(1):117-119

  • Wang K, Liang C. (2017) CRF: detection of CRISPR arrays using random forest. PeerJ, 2017; 5:e3219. PMC5407274.

  • Mao R, Liang C, Zhang Y, Hao X, Li J (2017). 50/50 Expressional Odds of Retention Signifies the Distinction between Retained Introns and Constitutively Spliced Introns in Arabidopsis thaliana. Front Plant Sci, 8:1728

  • Moller AG, Liang C (2017) MetaCRAST: reference-guided extraction of CRISPR spacers from unassembled metagenomes. PeerJ, 5:e3788

  • Shi J, Li X, Dong M, Graham M+, Yadav N, Liang C (2017) JNSViewer - a JavaScript-based Nucleotide Sequence Viewer for DNA/RNA secondary structures. PLOS ONE, 12(6):e0179040

  • Guo C, Spinelli M, Ye C, Li QQ**, Liang C(2017) Genome-Wide Comparative Analysis of Miniature Inverted Repeat Transposable Elements in 19 Arabidopsis thaliana Ecotype Accessions. Scientific Reports, 7:2634

  • Wang K, Liang C (2017) CRF: detection of CRISPR arrays using random forest. PeerJ, 5:e3219

  • Raj-Kumar P, Vallon O, Liang C (2017) In silico analysis of the sequence features responsible for alternatively spliced introns in the model green alga Chlamydomonas reinhardtii. Plant Mol Biol, 94:253-265

  • Moller AG, Liang C (2017) Determining virus-host interactions and glycerol metabolism profiles in geographically diverse solar salterns with metagenomics. PeerJ, 5:e2844.

  • Guo C, Spinelli M, Liu M, Li QQ, Liang C (2016) A Genome-wide Study of "Non-3UTR" Polyadenylation Sites in Arabidopsis thaliana, Scientific Reports, 6:28060.

  • Li L, Guo C, Wang B, Zhou T, Lei Y, Dai Y, He W, Liang C, Wang X (2016) RNAi-mediated transgenic rice resistance to Rice stripe virus, Journal of Integrative Agriculture, 15:60345-7.

  • Zhu H, Misel L, Graham M, Robinson ML, Liang C (2016) CT-Finder: A Web Service for CRISPR Optimal Target Prediction and Visualization, Scientific Reports, 6:25516.

  • Ye C, Ji G, Liang C (2016) detectMITE: A novel approach to detect miniature inverted repeat transposable elements in genomes, Scientific Reports, 6:19688.