Publications (2005-2019) (*Corresponding Author; **Co-Corresponding Author;++Graduate Student;+Undergraduate Student)

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. International Journal of Molecular Sciences, 20(4),958

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.

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 H++, 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++, Hoeksema J+,Liang C* (2018). piRNN: Deep Learning Algorithm for piRNA Prediction. PeerJ 6: e5429.

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.

Shi J++, Dong M++, Li L++, Liu L, Luz-Madrigal A, Tsonis PA, Rio-Tsonis KD, Liang C* (2015) mirPRo - a novel standalone program for differential expression and variation analysis of miRNAs, Scientific Reports, 5:14617.

Kumar PK++, Hoang TV++, Robinson ML, Tsonis PA, Liang C* (2015) CADBURE: A generic tool to evaluate the performance of spliced aligners on RNA-Seq data, Scientific Reports, 5:13443.

Li L++, Ji G, Ye C++, Shu C, Zhang J, Liang C** (2015) PlantOrDB: a genome-wide ortholog database for land plants and green algae, BMC Plant Biology, 15:161.

Guo C++, Li L, Wang X, Liang C** (2015) Alterations in siRNA and miRNA expression profiles detected by deep sequencing of transgenic rice with siRNA-mediated viral resistance, PLOS ONE, 10(1):e0116175.

Dong M++, Ji G, Li QQ, Liang C* (2015) Extraction of Poly(A) Sites from Large-Scale RNA-seq Data, Methods Mol Biol, 1255:25-37.

Wang K++, Liang C, Liu J, Xiao H, Huang S, Xu J, Li F (2014) Prediction of piRNAs using transposon interaction and a support vector machine. BMC Bioinformatics, 15:6593.

Ye C++, Ji G, Li L++, Liang C** (2014) detectIR: a novel program for detecting perfect and imperfect inverted repeats using complex numbers and vector calculation, PLOS ONE, 9(11):e0113349.

Geng L, Duan X, Liang C, Shu C, Song F, Zhang J (2014) Mining tissue-specific contigs from peanut for promoter cloning by deep transcriptome sequencing, Plant Cell Physiol, 55:1793-1801.

Hoang TV++, Raj Kumar PK++, Sreeskandarajan S++, Tsonis PA, Liang C, Robinson M (2014) Comparative transcriptome analysis of epithelial and fiber cells in newborn mouse lenses by RNA sequencing, Molecular Vision, 20:1491-1517.

Mao R++, Kumar PR++, Guo C++, Zhang Y, Liang C** (2014) Comparative analyses between retained introns and constitutively spliced introns in Arabidopsis thaliana using random forest and support vector machine, PLOS ONE, 9(8):e104049.

Morton TJ+, Abrudan P+, Figueroa N, Liang C**, Karro JE (2014) SCOPE++: Sequence Classification Of homoPolymer Emissions, Genomics, 104:157-162

Batesole K+, Wimalanathan K++, Liu L, Echt CS, Zhang F+, Liang C* (2014) YouGenMap: A web platform for dynamic multi-comparative mapping and visualization of genetic maps. Frontiers in Genetics, 5:183.

Ray WC, Wolock SL, Callahan NW, Dong M++, Li QQ, Liang C, Magliery T, Bartlett CW (2014) Addressing the unmet need for visualizing conditional random fields in biological data. BMC Bioinformatics, 15:202.

Sreeskandarajan S++, Flowers MM, Karro J, Liang C** (2014) A MATLAB-based tool for accurate detection of perfect overlapping and nested inverted repeats in DNA sequences. Bioinformatics, 30:887-8.

Zhao Z++, Guo C++, Sutharzan S++, Li P++, Echt CS, Zhang J, Liang C* (2014) Genome-wide analysis of tandem repeats in plants and green algae. G3: Genes, Genomics and Genetics, 4:67-78.

Zhao Z++, Wu X, Kumar PK++, Dong M++, Ji G, Li QQ, Liang C** (2014) Bioinformatics analysis of alternative polyadenylation in green alga Chlamydomonas reinhardtii using transcriptome sequences from three different sequencing platforms. G3: Genes, Genomics and Genetics, 4:871-83.

Ream DC, Murakami ST, Schmidt E+, Huang GH, Liang C, Friedberg I, Cheng XW (2013). Comparative analysis of error-prone replication mononucleotide repeats across baculovirus genomes. Virus Res, 178(2):217-225.

Li P++, Ji G, Dong M++, Schmidt E+, Lenox D+, Chen L++, Liu Q++, Liu L, Zhang J and Liang C** (2012) CBrowse: a SAM/BAM-based contig browser for transcriptome assembly visualization and analysis. Bioinformatics, 28(18):2382-2384.

Duan X++, Schmidt E+, Li P++, Lenox D+, Liu L, Shu C, Zhang J and Liang C** (2012) PeanutDB: An integrated bioinformatics web portal for Arachis hypogaea transcriptomics. BMC Plant Biology, 12:94.

Sun Zhou, Guoli Ji, Xiaolin Liu, Li P++, Moler J, Karro JE and Liang C** (2012) Pattern analysis approach reveals restriction enzyme cutting abnormalities and other cDNA library construction artifacts using raw EST data. BMC Biotechnology, 12:16.

Gong P, Guan X, Pirooznia M, Liang C, and Perkins EJ. (2012) Gene Expression Analysis of CL-20-Induced Reversible Neurotoxicity Reveals GABA(A) Receptors as Potential Targets in the Earthworm Eisenia fetida. Environ Sci Technol, 46(2):1223-32.

Wu X, Liu M, Downie B, Liang C, Ji G, Li QQ and Hunt AG (2011) Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation. PNAS, 108(30):12533-12538.

Specht M, Stanke M, Terashima M, Naumann-Busch B, Janssen I, Hohner R, Hom EFY, Liang C and Hippler M (2011) Concerted action of the new Genomic Peptide Finder and AUGUSTUS allows for automated proteogenomic annotation of the Chlamydomonas reinhardtii genome. Proteomics, 11(9):1814-1823.

Echt CS, Saha S, Krutovsky KV, Wimalanathan K++, Erpelding JE, Liang C and CD Nelson (2011) An annotated genetic map of loblolly pine based on microsatellite and cDNA markers. BMC Genetics, 12:17.

Rao DM, Moler JC++, Ozden M, Zhang Y++, Liang C** and JE Karro (2010) PEACE: Parallel Environment for Assembly and Clustering of Gene Expression. Nucleic Acids Research, 38:W737-W742.

Liang C*, Liu L and G Ji (2009) WebGMAP: a web service for mapping and aligning cDNA sequences to genomes. Nucleic Acids Research, 37:W77-W83.

Liang C*, Liu Y++, Liu L, Davis AC+, Shen Y++ and QQ Li (2008) ESTs with cDNA termini - previously overlooked resources for gene annotation and transcriptome exploration in Chlamydomonas reinhardtii. Genetics, 179:83-93.

Shen Y++, Liu Y++, Liu L, Liang C and QQ Li (2008) Unique features of nuclear mRNA poly(A) signals and alternative polyadenylation in Chlamydomonas reinhardtii. Genetics, 179:167-176.

Conner JA, Goel S, Gunawan G, Cordonnier-Pratt M-M, Johnson VE, Liang C, Wang H, Pratt LH, Mullet JE, DeBarry J, Yang L, Bennetzen JL, Klein PE, and P Ozias-Akins (2008) Sequence Analysis of Bacterial Artificial Chromosome Clones from the Apospory-Specific Genomic Region of Pennisetum and Cenchrus. Plant Physiology, 147: 1396-1411.

Liang C*, Wang G, Liu L, Ji G, Fang L, Liu Y++, Carter K+, Webb JS+ and JFD Dean (2007) ConiferEST: an integrated bioinformatics system for data reprocessing and mining of conifer expressed sequence tags (ESTs). BMC Genomics, 8:134.

Liang C*, Wang G, Liu L, Ji G, Liu Y++, Chen J++, Webb JS+, Reese G, and JFD Dean (2007) WebTraceMiner: a web service for processing and mining EST sequence trace files. Nucleic Acids Research, 35:W137-W142.

Liang C, Sun F, Wang H, Qu J, Freeman RM Jr, Pratt LH, M-M Cordonnier-Pratt (2006) MAGIC-SPP: a database-driven DNA sequence processing package with associated management tools. BMC Bioinformatics, 7:115.

Lorenz WW, Sun F, Liang C, Kolychev DS, Wang H, Zhao X, Cordonnier-Pratt M-M, Pratt LH, and JFD Dean (2006) Water stress-responsive genes in loblolly pine (Pinus taeda) roots identified by analysis of expressed sequence tag libraries. Tree Physiology, 26:1-16.

Pratt LH, Liang C, Shah M, Sun F, Wang H, Reid SP, Gingle AR, Paterson AH, Wing R, Dean R, Klein R, Nguyen HT, Ma H-M, Zhao X, Morishige DT, Mullet JE, and M-M Cordonnier-Pratt (2005) Sorghum Expressed Sequence Tags Identify Signature Genes for Drought, Pathogenesis and Skotomorphogenesis from a Milestone Set of 16,801 Unique Transcripts. Plant Physiology, 139:869-884.