Peng Jiang

Peng Jiang

Computational Biologist

Area:

Phone:

(608) 316-4479

Email:

[javascript protected email address]

My research is focused on developing bioinformatics approaches for analysis of massive genomic and high-throughput sequencing data, and using these approaches to systematically investigate the variation and dynamics of transcriptomic regulation within human populations, in response to environmental stimuli, development, and diseases.

Areas of Expertise

  • Single-cell data analysis
  • Design and application of computational methods for high-throughput transcriptome data analysis, such as microarray, RNA-Seq, SELEX-Seq and CLIP-Seq 
  • Comparative genomics and molecular evolution 
  • Population genomics and genetic variation 
  • Statistical prediction model 
  • Non-coding RNAs (microRNA and siRNA) 
  • Post-transcriptional regulation (such as alternative splicing)

Education

Postdoctoral Fellow in Bioinformatics/Biostatistics, 2008-2012, University of Iowa

Ph.D. State Key Laboratory of Bioelectronics, Department of Biomedical Engineering, 2003-2007, Southeast University, Nanjing, Jiang Su, China

B.S. Biomedical Engineering, 1999-2003, Southeast University, Nanjing, Jiang Su, China

Honors & Affiliations

Editorial Board Member: International Journal of Biometrics and Bioinformatics; Frontiers in Bioinformatics and Computational Biology; European Journal of Bioinformatics

Guest Associate Editor: The special issue ‘Statistical Methods and Software Tools for Biological Big Data’ for the journal Computational and Mathematical Methods in Medicine; The special topic ‘Genetic Variation of Alternative Splicing in Human Populations’ for the journal Frontiers in Bioinformatics and Computational Biology

Selected Publications

  • Jiang P., Hou Z., Bolin JM.,Thomson JA., Stewart R. (Submitted)
  • Jiang P., Thomson JA., Stewart R. Quality Control of Single-cell RNA-seq by SinQC. Bioinformatics 32:16, 2514-2516 (2016)
  • Jiang P.*, Nelson JD*., Leng N., Collins M., Swanson S., Dewey CN., Thomson JA., Stewart R. Analysis of embryonic development in the unsequenced axolotl: waves of transcriptional upheaval and stability. Developmental Biology (2016) (In Press) (* joint first authors)
  • Lin, L.*, Jiang, P.*, Park, J.W.*, Wang, J.*, Lu, Z.X., Lam, M.P., Ping, P. and Xing, Y., (2016). The contribution of Alu exons to the human proteome. Genome biology, 17(1), p.1. (* joint first authors)
  • Schwartz MP., Hou Z., Propson NE., Zhang J., Engstrom CJ., Costa VS., Jiang P., Nguyen BK., Jennifer MB., Daly W., Wang Y., Stewart R., Page CD., Murphy WL., Thomson JA. Human pluripotent stem cell-derived neural constructs for predicting neural toxicity. PNAS 112, no. 40 (2015): 12516-12521.
  • Leng N., Chu LF., Barry C., Li Y., Choi J., Li X., Jiang P., Stewart RM., Thomson JA., Kendziorski C. Oscope identifies oscillatory genes in unsynchronized single-cell RNA-seq experiments. Nature methods 12 (10) (2015): 947-950.
  • Hou Z.*, Jiang P.*, Swanson S., Elwell A., Nguyen B., Bolin J, Stewart R., Thomson, JA. A cost-effective RNA sequencing protocol for large-scale gene expression studies. Scientific reports, 5 (2015).(* joint first authors)
  • Roadmap Epigenomics Consortium (…Jiang P. …), Kundaje, A. et al. Integrative analysis of 111 reference human epigenomes. Nature 518.7539 (2015): 317-330.
  • Hou Z., Meyer S., Propson NE., Nie J., Jiang P., Stewart R., Thomson, JA. Characterization and target identification of a DNA aptamer that labels pluripotent stem cells. Cell research (2015).
  • Jiang P., Meyer S., Hou Z., Nicholas E. Propson, Soh HT., Thomson JA., Stewart R., MPBind: A Meta-Motif Based Statistical Framework and Pipeline to Predict Binding Potential of SELEX-derived Aptamers. (2014), Bioinformatics, 30(18): 2665-2667.
  • Boudreau RL., Jiang P., Gilmore BL., Spengler RM., Tirabassi R., Nelson JA., Ross CA., Xing Y., Davidson BL. (2014) Transcriptome-wide discovery of microRNA binding sites in human brain, Neuron, 81(2):294-305
  • Heinicke LA., Nabet B., Shen S., Jiang P., van Zalen S., Cieply B., Russell JE., Xing Y., Carstens RP. (2013) The RNA Binding Protein RBM38 (RNPC1) Regulates Splicing during Late Erythroid Differentiation. PLoS ONE, 8(10): e78031.
  • Ramachandran S., Karp PH., Osterhaus SR., Jiang P., Wohlford-Lenane C., Lennox KA., Jacobi AM., Praekh K., Rose SD., Behlke MA., Xing Y., Welsh MJ., McCray Jr PB. (2013) Post-transcriptional Regulation of CFTR Expression and Function by MicroRNAs. Am. J. Respir. Cell Mol. Biol., 49(4):544-551
  • Ramachandran S., Karp P., Jiang P., Ostedgaard LS., Walz AE., Fisher JT., Keshavjee S., Lennox KA., Jacobi AM., Rose SD., Behlke MA., Welsh MJ., Xing Y., McCray PB. (2012) A novel microRNA network regulates expression and biosynthesis of CFTR and CFTR-ΔF508. PNAS 109 (46): 18773-18778.
  • Kim J.*, Zhao K.*, Jiang P.*, Lu Z., Wang J., Murray J.C., Xing Y., (2012) Transcriptome landscape of the human placenta. BMC Genomics, 13:115 (* joint first authors)
  • Dittmar KA.*, Jiang P.*, Park JW.*, Amirikian K, Wan J., Shen S., Xing Y., Carstens RP. (2012) Genome-wide determination of a broad ESRP-regulated post-transcriptional network by high throughput sequencing. Molecular and Cellular Biology, 32(8):1468-82   (* joint first authors)
  • Lu ZX.*, Jiang P.*, Cai JJ., Xing Y. (2011) Context-dependent Robustness to 5′ Splice Site Polymorphisms in Human Populations. Human Molecular Genetics, 20:1084-1096 (*joint first authors).
  • Shen S., Lin L., Cai JJ., Jiang P., Kenkel EJ., Stroik MR., Sato S., Davidson BL., Xing Y. (2011) Widespread Establishment and Regulatory Impact of Alu Exons in Human Genes. PNAS 108 (7): 2837-2842.
  • Liu S., Lin L., Jiang P., Wang D., Xing Y. (2011) A comparison of RNA-Seq and high-density exon array for detecting differential gene expression between closely related species. Nucleic Acids Research, 39 (2): 578-588.
  • Lu ZX., Jiang P., Xing Y. (2011). Genetic variation of pre-mRNA alternative splicing in human populations. (Review). Wiley Interdisciplinary Reviews: RNA (WIREs RNA), 3(4):581-92.
  • Warzecha CC., Jiang P., Amirikian, K., Dittmar, KA., Lu, H., Shen, S., Guo, W., Xing Y., Carstens RP. (2010) An ESRP-regulated splicing programme is abrogated during the epithelial-mesenchymal transition. EMBO J, 29:3286-3300.
  • Lin L., Shen S., Jiang P., Sato S., Davidson BL., Xing Y. (2010) Evolution of alternative splicing in primate brain transcriptomes. Human Molecular Genetics, 19:2958-2973.
  • Lin L., Jiang P., Shen S., Sato S., Davidson BL., Xing Y. (2009) Large-scale analysis of exonized mammalian-wide interspersed repeats (MIRs) in primate genomes. Human Molecular Genetics. 18: 2204-2214.
  • Lin L., Liu S., Brockway H., Seok J., Jiang P., Wong WH., Xing Y. (2009) Using high-density exon arrays to profile gene expression in closely related species. Nucleic Acids Research, 12: e90
  • Lin, L., Shen, S., Tye, A., Cai, JJ., Jiang, P., Davidson, BL., Xing, Y. (2008) Diverse splicing patterns of exonized Alu elements in human tissues. PLoS Genetics. 4(10):e1000225.
  • Jiang, P., Wu, H., Wang, W., Ma, W., Sun, X., Lu, Z. (2007) MiPred: Classification of real and pseudo microRNA precursors using random forest prediction model with combined features. Nucleic Acids Res. 35: W339-W344.
  • Jiang, P., Wu, H., Wei, J., Sang, F., Sun, X., Lu, Z. (2007) RF-DYMHC: Detecting the yeast meiotic recombination hotspots and coldspots by random forest model using gapped dinucleotide composition features. Nucleic Acids Res. 35: W47-W51.
  • Jiang, P., Wu, H., Da, Y., Sang, F., Wei, J., Sun, X., Lu, Z. (2007) RFRCDB-siRNA: Improved Design of siRNA by Random Forest Regression Model Coupled with Database Searching. Computer methods and programs in biomedicine. 87 (3): 230-238.
  • Jiang, P., Sun, X., Lu, Z. (2007) Analysis of Synonymous Codon Usage in Aeropyrum pernix K1 and Other Crenarchaeota Microorganisms. Journal of Genetics and Genomics 34 (3), 275-284.
  • Tong, J., Jiang, P., Lu, Z. (2008) RISP: A web-based server for prediction of RNA-binding sites in proteins. Computer Methods and Programs in Biomedicine, 90(2), 148-153.