Dr. Chaochun Wei, Department of Bioinformatics and Biostatistics

Publications

(* corresponding author)

2024

• Carrasco-Villanueva, M., Wang, C., Wei, C., "Identification of diversity-generating retroelements in host-associated and environmental genomes: prevalence, diversity, and roles", BMC Genomics, 2024, 25:1227, [artical ].

• Xue, H., Zhao, K., Zhao, K., Han, S., Chitkineni, A., Zhang, L., Qiu, D., Ren, R., Gong, R., Li, Z., Ma, X., zhang, X., Varshney, R., Zhang, X., Wei, C.* , Yin, D.*, "A new complete genome of Arachis monticola, an allotetraploid wild peanut", Plant Biotechnolgoy Journal, 2024, [article].

• Liu, M., Zhang, F., Lu, H., Xue, H., Li, Z., Xu, J., Wang, W.*, Wei, C.*, "PPanG: a pre1cision pangenome browser enabling nucleotide-level analysis of genomic variations in individual genomes and their graph-based pangenome", BMC Genomics, 2024, 25:405, [article].

2023

• Gao, Y., et al., "A pangenome reference of 36 Chinese populations", Nature, 14 June, 2023, [article].

2022

• Zhang, F., Xue, H., Dong, X., Li, M., Zheng, X., Li, Z., Xu, J., Wang, W., and Wei, C.*, "Long-read sequencing of 111 rice genomes reveals significantly larger pan-genomes", Genome Research , 2022,32:853-863, [ article].

• Yu, Y., Zhang, Z., Dong, X., Yang, R., Duan, Z., Xiang, Z., Li, J., Li, G., Yan, F., Xue, H., Jiao, D., Lu, J., Lu, H., Zhang, W., Wei, Y., Fan, S., Li, J., Jia, J., Zhang, J., Ji, J., Liu, P., Lu, H., Zhao, H., Chen, S., Wei, C.*, Chen, H.*, Zhu, Z.*, "Pangenomic analysis of Chinese gastric cancer", Nature Communications , 2022, 13:5412.1, [article ].

• Zeng, Y., Li, J., Wei, C, Zhao, H., Wang, T., "mbDenoise: microbiome data denoising using zero-inflated probabilistic principal components analysis", Genome Biology , 2022,23: 94.

• Zhai, Y. and Wei.C, "Open pangenome of Lactococcus lactis generated by a combination of metagenome-assembled genomes and isolate genomes", Frontiers in Microbiology , 2022, 10.3389.

2021

• Jiao, D., Dong, X., Yu, Y.*, Wei, C.*, "Gene Presence/Absence Variation analysis of coronavirus family displays its pan-genomic diversity", International Journal of Biological Sciences , 2021, 17(14):3717-3727.

• Li, J., Xue, H., Xiang, Z., Song, S., Yan, R., Ji, J, Zhu, Z., Wei, C., Yu, Y.,"Genetic Profiles Affect the Biological Effects of Serine on Gastric Cancer Cells", Frontiers in Pharmacology , 2021, 11:1183.

• Lyu, R., Sun, J., Jiang, Q., Wei, C., Zhang, Y.*, "GESLM algorithm for detecting causal SNPs in GWAS with multiple phenotypes", Briefings in Bioinformatics, 2021, 22(6), 1-12.

• Dong, X., Xue, H., Wei, C., "ivTerm An R package for interactive visualization of functional analysis results of meta-omics data", Journal of Cellular Biochemistry, 2021, 122:1428-1434.

• Xu, P., Zhang, L., Xiao, Y., Li, W., Hu, Z., Zhang, R., Li, J., Wu, F., Xi, Y., Zou, Q., Wang, Z., Guo, R., Ma, H., Dong, S., Xiao, M., Yang, Z., Ren, X., Wei, C.*, , Yu, W.*, "UHRF1 regulates alternative splicing by binding to splicing factors and U snRNAs", Human Molecular Genetics , 2021, 30(22)2110-2122.

2020

• Yu, Y. and Wei, C., "A powerful HUPAN on a pan-genome study: significance and perspectives", Cancer Biology & Medicine, 2020, 17(1):1-5.

• Bui, V. and Wei, C., "CDKAM: a taxonomic classification tool using discriminative k mers and approximate matching strategies", BMC Bioinformatics, 2020, 21:468.

2019

• Duan, Z., Qiao, Y., Lu, J., Lu, H., Zhang, W., Yan, F., Sun, C., Hu, Z., Zhang, Z., Li, G., Chen, H., Xiang, Z., Zhu, Z., Zhao, H., Yu, Y.*, Wei, C.*, "HUPAN: a pan-genome analysis pipeline for human genomes", Genome Biology, 2019, 20:149, [ article].

• Jia, B., Li, X., Liu, W., Lu, C., Lu, X., Ma, L., Li, Y.*, Wei, C.*, "GLAPD:Whole genome based LAMP Primer Design for a set of target genomes", Frontiers in Microbiology , 2019, 10:2860. [ article].

• Yan, F., Yu, X., Duan, Z., Lu, J., Jia, B., Qiao, Y, Sun, C., Wei, C.*, "Discovery and characterization of the evolution, variation and functions of Diversity-Generating Retroelements using thousands of genomes and metagenomes. BMC Genomics , 2019, 20:595, [ Article].

• Zhang, W., Jia, B., Wei, C.*, "PaSS: a sequencing simulator for PacBio Sequencing", BMC Bioinformatics 2019, 20:352, [ article ].

• Wang, C., Yu, H., Huang, J., Wang, W., Faruquee, M., Zhang, F., Zhao, X., Fu, B., Chen, K., Zhang, H., Tai, S., Wei, C., Li, J., McNally, K., Alexandrov, N., Gao, X., Li, Z., Xu, J., Zheng, T., "Towards a deeper haplotype mining of complex traits in rice with RFGB v2.0", Plant Biotechnology Journal , 2019, 18(1):14-16.

2018

• Wang, W., et al., "Genomic variation in 3,010 diverse accessions of Asian cultivated rice", Nature, 2018,557:43-49 (co-corresponding author) [article].

• Qiao, Y., Jia, B., Hu, Z., Sun, C., Xiang, Y., Wei, C.*, "MetaBinG2: a fast and accurate metagenomic sequence classification system for samples with many unknown organisms", Biology Direct, 2018, 13(1):15[article].

• Zeng, L., Pederson, S., Cao, D., Qu, Z., Hu, Z., Adelson, D.*, Wei, C.*, " Genome-wide analysis of the association of transposable elements with gene regulation suggests that Alu elements have the largest overall regulatory impact", Journal of Computational Biology, 2018,6:551-562 [article].

• Giri, B., Ye, J., Chen, Y., Wei, C.*, Cheng, G.*, "In silico analysis of endogenous siRNAs associated transposable elements and NATs in Schistosoma japonicum reveals their putative roles during reproductive development", Parasitology Research, 2018, 117(5):1549-1558 [article].

• Hu, Z., Wang, W., Wu, Z., Sun, C., Li, M., Lu, J., Fu, B., Shi, J., Xu, J., Wei, C., Li, Z., "Novel sequences, structural variations and gene presence variations of Asian cultivated rice", Scientific Data ,2018, 5:180079 [article].

2017

• Li, X., Hu, Z., Yu, X., Ma, B., Zhang, C., Wei, C.*, and Wu, J.*, "RNA-seq of embryonic cells and germ cells shows direct evidence for dosage compensation in mammals", Scientific Reports, 2017, 7:3729, [article].


• Hu, Z., Sun, C., Lu, K., Chu, X., Zhao, Y., Lu, J., Shi, J.*, Wei, C.*, "EUPAN enables pan-genome studies of a large number of eukaryotic genomes", Bioinformatics, 2017,33(15)2408-2409 [article].


• Huang, W., Tsai L., Li, Y., Hua, N., Sun, C., Wei, C.*, "Widespread of Horizontal Gene Transfer in the Human Genome", BMC Genomics, 2017, 18:274, [article]. (IF:3.73)


• Zhu, H., Xu, W., Hu, Z., Zhang, H., Shen, Y., Lu, S., Wei, C.*, Wang, Z.*, "RNA virus receptor Rig-I monitors gut microbiota and inhibits colitis-associated colorectal cancer", Journal of Experimental & Clinical Cancer Research, 2017, 36:2.[ article]. (IF: 5.19)

2016

• Sun, C., Hu, Z., Lu, K., Zhao, Y., Lu, J., Zheng, T., Wang, W., Shi, J., Zhang, D., Li, Z.*, Wei, C.*, "RPAN: Rice Pan-genome Browser for ~3,000 rice genomes", Nucleic Acids Research, 2016, doi: 10.1093/nar/gkw958. [ article ]. (IF: 10.16)

2015

• Hu, Z., Scott, H., Qin, G., Zheng, G, Chu, X., Xie, L., Adelson, D., Oftedal, B., Venugopal, P., Babic, M., Hahn, C., Zhang, B., Wang, X., Li, N., Wei, C.*, " Revealing missing human protein isoforms based on ab initio prediction, RNA-seq and proteomics", Scientific Reports, 2015, 5:10940.[article]. (IF: 4.26)


• Zhang, Y., He, Y., Zheng, G., Wei, C.*, "MOST+: A de novo motif finder combining genomic sequence and heterogeneous genome-wide signatures", BMC Genomics , 2015, 16(Suppl 7):S13. [article]. (IF: 3.73)

2014

• Xiao, G. et al., "Whole genome sequencing of six dog breeds from continuous altitudes reveals adaption to high-altitude hypoxia", Genome Research, 2014, 24:1308-1315. [ artical]. (IF: 11.25)


• Hou, T., Zheng, G., Zhang P., Jia, J., Li, J., Xie, L., Wei, C.*, Li, Y., "LAceP: lysine acetylation sites prediction using logistic regression classifier", 2014, PLoS ONE, 9(2):e89575.[ article ]. (IF: 2.86)

2013

• Xu, H., Yu, H., Tu, K., Shi, Q., Wei, C., Li, Y., Li, Y., "cGRNB: a web server for building combinatorial gene regulatory networks through integrated engineering of seed-matching sequence information and gene expression datasets", 2013, BMC Systems Biology , 7(Suppl 2):S7. [ article ]. (IF: 2.21)


• Jia, B., Xuan, L., Cai, K., Hu, Z., Ma, L., Wei, C.*, "NeSSM: a Next-generation Sequencing Simulator for Metagenomics", 2013, PLoS ONE , 8(10):e75448. [ article ]. (IF: 2.86)

2012

• Cui, X., Wang, Q., Yin, W., Xu, H., Wilson, Z., Pan, S., Wei, C. and Zhang, D., "PMRD: a curated database for genes and mutants involved in plant male reproduction", 2012, BMC Plant Biology , 12:215[ article ]. (IF: 3.63)


• He, Y., Zhang, Y., Zheng, G., Wei, C.*, "CTF: A CRF-based Transcription Factor Binding Sites Finding System", 2012, BMC Genomics , 13(Suppl 8):S18 [ article ]. (IF: 3.73)


• Zheng, G., Liu, Q., Ding, G., Wei, C. * , Li, Y., "Towards Biological Characters of Interactions between Transcription Factors and their DNA Targets in Mammals", 2012, BMC Genomics ,13:388.[ article ]. (IF: 3.73)

2011

• Zheng, G., Wang, H., Wei, C.*, Li, Y., "iGepros: An integrated gene and protein annotation server for biological nature exploration", BMC Bioinformatics, 2011, 12(Suppl 14): S6.[ article ]. (IF: 2.44)



• Jia, P., Liu, L., Wei, C.*, "MetaBinG: Using GPUs to accelerate metagenomic sequence classification", PLoS ONE, 2011, 6(11):e25353.[ article ]. (IF: 2.86)

2010

• Ling, Z., Kong, J., Jia, P., Wei, C., Wang, Y., Pan, Z., Huang, W., Chen, H., Xiang, C., "Analsysis of oral microbiota in children with dental caries by PCR-DGGE and Barcoded Pyrosequencing", 2010, Microbial Ecology, 60(3):677-90.[ article ]. (IF: 3.23)


• Zhang, C., Zhang, M., Wang, S., Han R., Cao, Y., Hua, W., Mao, Y., Zhang X., Pang X., Wei, C., Zhao, G., Chen, Y., Zhao, L., "Interactions between gut microbiota, host genetics, and diet relevant to development of metabolic syndromes in mice", ISME J, 2010, 4(2)232-241.[ article ]. (IF: 9.33)

2009

• The MGC Project Team, "The Completion of the Mammalian Gene Collection (MGC)", Genome Research, 2009, 19:2324-2333.[ artile ]. (IF: 11.35)


• Yang, X., Xie, L., Li, Y., Wei, C*. "More than 9,000,000 Unique Genes in Human Gut Bacterial Community: Estimating Gene Numbers Inside a Human Body", PLoS ONE, 2009, 4(6): e6074.[ article ]. (IF: 2.86)

2008

• Zheng, G., Qian, Z., Yang, Q., Wei, C., Xie, L., Zhu, Y. and Li, Y., "The Combination Approach of SVM and ECOC for Powerful Identification and Classification of Transcription Factor", BMC Bioinformatics, 2008 Jun 16;9(1):282.[ article]. (IF: 2.44)


• Zheng, G., Tu, K., Yang, Q., Xiong, Y., Wei, C., Xie, L., Zhu, Y. and Li, Y., "ITFP: an integrated platform of mammalian transcription factors", Bioinformatics, 2008, 24(20):2416-2417.[ article ]. (IF: 7.30)

2006

• Arumugam, M., Wei, C., Brown, R. H. and Brent, M. R., "PAIRAGON + N-SCAN_EST: A Model-Based Gene Annotation Pipeline", Genome Biology, 2006, 7(Suppl I):S5.[ article ]. (IF: 11.25)

• Wei, C. and Brent, M. R., "Using ESTs to Improve the Accuracy of de novo Gene Prediction", BMC Bioinformatics, 2006, 7:327.[ article] . (IF: 2.44)

2005

• Wei, C., Lamesch, P., Arumugam M., Rosenberg, J., Hu, P., Vidal, M., and Brent, M. R., "Closing in on the C.elegans ORFeome by Cloning TWINSCAN predictions", Genome Research , 2005, 15:577-582.[ article]. (IF: 11.35)
  Reported by Nature Reviews Genetics as Research Highlight .

2003

• Stein, L. D., Z. Bao, ..., Wei, C., ..., Waterston, R. H., "The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics", PLoS Biology , 2003, 1(2): E45.[ article ]. (IF: 8.67)

 

©2011 Chaochun Wei