Zhenyu Xuan

Research Assistant Professor
Bioinformatics Shared Resource, Manager
Cold Spring Harbor Laboratory
1 Bungtown Road, NY 11724
email: xuan@cshl.edu
phone: (516) 367-5009
fax: (516) 367-8461

I am a Research Assistant Professor at Cold Spring Harbor Laboratory working on both non-coding RNA function study and computational genomics. I was Research Investigator from 2005-2008. From 2000 to 2005, I worked with Dr. Michael Zhang as his postdoc on gene prediction and mammalian transcriptional regulation. I finished my doctoral dissertation in 2000 supervised by Professor Runsheng Chen. In 1995, I obtained my Bachelor degree of theoretical physics from Department of Intensive Instruction in Nanjing University in China.

CV (in PDF format).

Research Interests

- Genomics of transcriptional regulation and regulatory sequence analysis
- Non-coding RNA function study
- High-throughput genome sequencing data analysis
- Database construction

Bioinformatics Software and Resources

- CSHLmpd: mammalian promoter database in CSHL
- TRED: Database of transcriptionary regulatory elements
- Rmap: Tool for accurately mapping short reads


Wang X, Xuan Z*, Zhao X, Li Y and Zhang MQ. (2008) High-resolution Human Core-promoter prediction with CoreBoost_HM. Genome Res. (In press) (Equally contributed first author with W.X.). [PDF]

Smith AD, Xuan Z*, Zhang MQ (2008) Using quality scores and longer reads improves accuracy of Solexa read mapping. BMC Bioinformatics 9:128. (Equally contributed first author with S.A.). [PDF]

Hodges E, Xuan Z*, Balija V, Karmer M, Molla MN, Smith SW, Middle CM, Rodesch MJ, Albert TJ, Hannon GJ, McCombie WR (2007) Genome-wide in-situ exon capture for selective resequencing. Nat. Genet. (in press) (Equally contributed first author with H.E.). [PDF]

Kim YC, Jung YC, Xuan Z*, Dong H, Zhang MQ, Wang SM. (2006) Pan-genome isolation of low abundance transcripts using SAGE tag. FEBS Lett. 580, 6721-9 (Equally contributed first author). [PDF]

Xuan Z, Zhao F, Wang J, Chen G, Zhang MQ (2005) Improving Promoter Prediction by Incorporating Sequence Conservation. Genome Biology 6, R72. [PDF]

Xuan Z, Zhang MQ (2005) From Worm to Human: Bioinformatics Approaches to Identify FOXO Target Genes. Mech Ageing Dev 126, 209-215. [PDF]

Xuan Z, Wang J, Zhang MQ (2003) Computational comparison of two mouse draft genomes and the human goldenpath. Genome Biology 4, R1. [PDF]

Carmell MA, Xuan Z*, Zhang MQ and Hannon G (2002) Argonaute proteins: tentacles that reach into RNAi, stem cell maintenance and tumorigenesis. Gene & Dev. 16, 2733-2742 (Equally contributed first author) [PDF]

Xuan Z, McCombie R, Zhang MQ (2002) GFScan: a gene family search tool at genomic DNA level. Genome Res. 12, 1142-1149. [PDF]

Xuan Z, Chen R (2000) A new method for protein domain recognition. Eur. Biophys. J. 29, 7-16.

Zhan L, Rosenberg A, Bergami KC, Yu M, Xuan Z, Jaffe AB, Allred C, Muthuswamy SK. (2008) Deregulation of scribble promotes mammary tumorigenesis and reveals a role for cell polarity in carcinoma. Cell. 135:865-78. [PDF]

Chen J, Kim YC, Jung YC, Xuan Z, Dworkin G, Zhang Y, Zhang MQ, Wang SM. (2008) Scanning the human genome at kilobase resolution. Genome Res. 18:751-762. [PDF]

Murchison EP, Kheradpour P, Sachidanandam R, Smith C, Hodges E, Xuan Z, Kellis M, GrĂ¼ zner F, Stark A, Hannon GJ. (2008) Conservation of small RNA pathways in p latypus. Genome Res. 18(6):995-1004. [PDF]

Wu Q, Kim YC, Lu J, Xuan Z, Chen J, Zheng Y, Zhou T, Zhang MQ, Wu CI, Wang SM. (2008) Poly A- transcripts expressed in HeLa cells. PLoS ONE. 3(7):e2803. [PDF]

Karginov FV, Conaco C, Xuan Z, Schmidt BH, Parker JS, Mandel G, Hannon GJ. (2007) A biochemical approach to identifying microRNA targets. Proc Natl Acad Sci U S A. 104:19291-6. [PDF]

He L, He X, Lim LP, de Stanchina E, Xuan Z, Liang Y, Xue W, Zender L, Magnus J, Ridzon D, Jackson AL, Linsley PS, Chen C, Lowe SW, Cleary MA, Hannon GJ (2007) A microRNA component of the p53 tumour suppressor network. Nature 447, 1130-4. [PDF]

Murchison EP, Stein P, Xuan Z, Pan H, Zhang MQ, Schultz RM, and Hannon GJ (2007) Critical roles for Dicer in the female germline. Gene & Dev. 21, 682-93. [PDF]

Zhao X, Xuan Z, Zhang MQ. (2007) Boosting with stumps for predicting transcription start sites. Genome Biol. 8, R17 [PDF]

Jiang C, Xuan Z, Zhao F, Zhang MQ. (2007) TRED: a transcriptional regulatory element database, new entries and other development. Nucleic Acids Res. 35(Database issue):D137-40. [PDF]

Wang X, Bandyopadhyay S, Xuan Z, Zhao X, Zhang MQ, Zhang X. (2007) Prediction of Transcription Start Sites Based on Feature Selection Using AMOSA. Comput. Syst. Bioinformatics Conf. 6:183-93. [PDF]

Das R, Dimitrova N, Xuan Z, Rollins RA, Haghighi FG, Edwards JR, Ju J, Bestor TH and Zhang MQ, (2006) Computational prediction of DNA methylation landscape in the human genome. Proc. Natl. Acad. Sci. USA. 103, 10713-10716 [PDF]

Smith AD, Sumazin P, Xuan Z, Zhang MQ (2006) DNA motifs in human and mouse proximal promoters predict tissue-specific expression. Proc. Natl. Acad. Sci. USA. 103, 6275-6280. [PDF]

Zhang C, Xuan Z, Mandel G, Zhang MQ (2006) A Clustering Property of Highly-degenerate Transcription Factor Binding Sites in the Mammalian Genome. Nucl. Acid. Res. 34, 238-2246 [PDF]

Prasanth KV, Prasanth SG, Xuan Z, Sachidandam R, Hearn S, Frier SM, Bennett CF, Zhang MQ and Spector DL (2005) Regulating Gene Expression Through RNA Nuclear Retention. Cell 123, 249-63. [PDF]

Zhao F, Xuan Z, Liu L, Zhang MQ (2005) TRED: A Transcription Regulatory Element Database and a Platform for in silico Gene Regulation Studies. Nucl. Acid. Res. 33, D103-107. [PDF]

Sujit Dike, Vivekanand S. Balija, Lidia U. Nascimento, Xuan Z, Jacqueline Ou, Theresa Zutavern, Lance E. Palmer, Greg Hannon, Michael Q. Zhang and W. Richard McCombie (2004) The Mouse Genome: Experimental Examination of Gene Predictions and Transcriptional Start Sites. Genome Res. 14, 2424-2429. [PDF]

Lo WS, Lau CF, Xuan Z, Chan CF, Feng GY, He L, Cao ZC, Liu H, Luan QM, Xue H (2004) Association of SNPs and haplotypes in GABAA receptor beta2 gene with schizophrenia. Mol Psychiatry. 9, 603-8. [PDF]

Bao Q, Tian Y, Li W, Xu Z, Xuan Z, Hu S, Dong W, Yang J, Chen Y, Xue Y, Xu Y, Lai X, Huang L, Dong X, Ma Y, Ling L, Tan H, Chen R, Wang J, Yu J, Yang H (2002) A complete sequence of the T. tengcongensis genome. Genome Res. 12, 689-700. [PDF]

Li W, Fang W, Ling L, Wang J, Xuan Z, Chen R (2002) Phylogeny Based on Whole Genome as inferred from Complete Information Set Analysis. J. Biological Physics. 28, 439-447.

International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature 409, 860-921

Xu H, Huang K, Qu X, Gao Z, Liu Q, Chen R, and Xuan Z (2001) Identification of selenocysteine insertion sequence (SECIS) element in eukaryotic selenoproteins by RNA Draw program. Chinese Science Bulletin 46, 1159-60.

Yang C, Ling L, Xuan Z, Chen R (1999) EST contig assembly by computer. Progress in Natural Science 9, 812-817.

Shen L, Xuan Z, Chen R (1999) The molecular modeling and electron density calculation of PrPC and PrPSC. ACTA Biophysica SINICA 15, 766-774.