个人简介

B.Sc., Fudan University, Shanghai Ph.D., Chinese Academy of Sciences, Qingdao

研究领域

Bioinformatics, Genome Architecture and Expression

My laboratory is interested in developing bioinformatics programs and genomics (and molecular) tools for understanding genome architecture and expression. In particular, we are interested in characterizing gene structures, transcription factors and regulatory elements, sequence and structural variations, and, more importantly, regulatory mechanisms. Ultimately, we are interested in understanding how genome sequences and their organization (including various modifications) direct development and biological functions. Currently, we primarily use the nematodeCaenorhabditis elegans as a model system. Bioinformatics programs and genomics tools, however, are generally readily applicable in all organisms, ranging from bacteria to humans. Current research projects fall into two major categories: (1) Identification and characterization of novel genes, synteny blocks, functional elements, genome variations and genome rearrangements; (2) Transcriptional regulation of genes and gene batteries. My research group provides an ideal environment for students who have interest in the emerging field of genomics and bioinformatics, an exciting field which is developing essentially everyday. Within this group, students have the opportunity to learn and apply computational skills, as well as advanced genomics and molecular techniques. Check current projects in my laboratory. If you find any one interesting to you, send me a message.

近期论文

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Hu J, Li J, Chen N, Zhang X. Conservation of hot regions in proteinprotein interaction in evolution. Methods. 2016. Champaigne NL, Leroy JG, Kishnani PS, Decaestecker J, Steenkiste E, Chaubey A, Li J, Verslype C, Van Dorpe J, Pollard L, Goldstein JL, Libbrecht L, Basehore M, Chen N, Hu H, Wood T, Friez MJ, Huizing M, Stevenson RE. New observation of sialuriaprompts detection of liver tumor in previously reported patient. Molecular Genetics and Metabolism. 2016. Dong L, Liu H, Zhang J, Yang S, Kong G, Chu JS, Chen N, Wang D, 2015. Single-molecule real-time transcript sequencing facilitates common wheat genome annotation and grain transcriptome research. (BMC Genomics) Ma L, Shan YL, Liao BJ, Kong GY, Wang C, Huang K, Zhang H, Cai XJ, Chen SB, Pei DQ, Chen N, Pan GJ. Factor-induced Reprogramming and Zinc Finger Nucleaseaided Gene Targeting Cause Different Genome Instability in -Thalassemia Induced Pluripotent Stem Cells (iPSCs). Joural of Biological Chemistry, 2015. Tarailo-Graovac M, Wong T, Qin Z, Flibotte S, Taylor J, Moerman DG, Rose AM, Chen N. Spectrum of variations in dog-1/FANCJ and mdf-1/MAD1 defective C. elegans strains after long-term propagation. BMC Genomics, 2015. Zou S, Li J, Zhou H, Frech C, Jiang X, Chu JS, Zhao X, Li Y, Li Q, Wang H, Hu J, Kong G, Wu M, Ding C, Chen N, Hu H. Mutational landscape of intrahepatic cholangiocarcinoma. Nature Communications, 2014. Tarailo-Graovac M, Wong T, Qin Z, Flibotte S, Taylor J, Moerman DG, Rose AM, Chen N. Cyclin B3 and dynein heavy chain cooperate to increase fitness in the absence of mdf-1/MAD1 in Caenorhabditis elegans. Cell Cycle, 2014. Wang S, Hao B, Li J, Peng J, Xie F, Zhao X, Frech C, Chen N, Ma B, and Li Y. Whole-genome sequencing of Mesorhizobium huakuii 7653R provides molecular insights into host specificity and symbiosis island dynamics. BMC Genomics, 2014. Vergara I, Tarailo-Graovac M, Frech C, Wang J, Qin Z, Zhang T, She R, Chu JSC, Wang K, Chen N. Genome-wide variations in a natural isolate of the nematode Caenorhabditis elegans. BMC Genomics, 2014. Frech C, Chen N*. Variant Surface Antigens of Malaria Parasites: Functional and Evolutionary Insights from Comparative Gene Family Classification and Analysis. BMC Genomics, 2013. Cheng XY, Tian XL, Wang YS, Lin RM, Mao ZC, Chen N*, Xie BY*. Metagenomic analysis of the pinewood nematode microbiome reveals a symbiotic relationship critical for xenobiotics degradation. Scientific Reports, 2013. (*Co-corresponding author). Clarke M, Lohan AJ, Liu B, Lagkouvardos I,Roy S, Zafar N, Bertelli C, Schilde C, Kianianmomeni A, Burglin TR, Frech C, Turcotte B, Kopec KO, Synnott JM, Choo C, Paponov I, Finkler A, Tan CSH, Hutchins AP, Weinmeier T, Rattei T, Chu JSC, Gimenez G, Irimia M, Rigden DJ, Fitzpatrick DA, Lorenzo-Morales J, Bateman A , Chiu C, Tang P, Hegemann P, Fromm H, Raoult D, Greub G, Miranda-Saavedra D, Chen N, Nash P, Ginger ML, Horn M, Schaap P, Caler L, Loftus BJ. Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling. Genome Biology, 2013. Vergara IA, Frech C, Chen N. CooVar: Co-occurring Variant Analyzer. BMC Research Notes, Tarailo-Graovac M, Chen N. Mos1-mediated transgenesis to probe consequences of single gene mutations in variation-rich isolates of Caenorhabditis elegans. PLoS ONE, 2012. Ding Z, Taneva SG, Huang H, Campbell SA, Semenec L, Chen N, Cornell RB. A 22mer segment in the structurally pliable regulatory domain of metazoan CTP: phosphocholine cytidylyltransferase facilitates both silencing and activating functions. Journal of Biological Chemistry, 2012. Frech C, Choo C, Chen N. FeatureStack: Perl module for comparative visualization of gene features. Bioinformatics, 2012. Tarailo-Graovac M, Chen N. Proper Cyclin B3 dosage is important for precision of metaphase-to-anaphase onset timing in Caenorhabditis elegans. G3: GENES, GENOMES, GENETICS, 2012, 2(8)865-871. Cover Uyar B, Chu JSC, Vergara IA, Chua SY, Jones MR, Wong T, Baillie, DL, and Chen N. RNA-seq analysis of C. briggsae transcriptome. Genome Research, 2012, 22(8)1567-1580. Chu JSC, Tarailo-Graovac M, Zhang D, Wang J, Uyar B, Tu D, Trinh J, Baillie DL, and Chen N. Fine tuning of RFX/DAF-19-regulated target gene expression through binding to multiple sites in Caenorhabditis elegans. Nucleic Acids Research , 2012, 40(1):53-64. Frech C and Chen N. Genome comparison of human and non-human malaria parasites reveals parasites-specific genes potentially linked to human disease. PLoS Computational Biology, 2011.