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

Professional Service

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

Guest Associate Editor: The special topic ‘Genetic Variation of Alternative Splicing in Human Populations’ for the journal Frontiers in Bioinformatics and Computational Biology

Reviewer for Journals: Nature Communications, Nucleic Acids Research, Bioinformatics, Toxicological Sciences, BMC Genomics, Biomedical Engineering and Computational Biology, International Journal of Biometrics and Bioinformatics, Frontiers in Bioinformatics and Computational Biology, Advances and Applications in Bioinformatics and Chemistry, Biomarker Insights, The Application of Clinical Genetics, Bioinformatics and Biology Insights, Current Biomarker Findings, Genomics, Proteomics & Bioinformatics (GPB)

Selected Publications

#Corresponding author, *Co-first author

  • Jiang, P.#, Chamberlain, C. S., Vanderby, R., Thomson, J. A., Stewart, R. (2020). TimeMeter assesses temporal gene expression similarity and identifies differentially progressing genes. Nucleic Acids Research. (# Corresponding author)
  • Sabin, K.Z., Jiang, P., Gearhart, M.D., Stewart, R. and Echeverri, K. (2019) AP-1(cFos/JunB)/miR-200a regulate the pro-regenerative glial cell response during axolotl spinal cord regeneration. Commun Biol, 2, 91.
  • Chasman, D., Iyer, N., Fotuhi Siahpirani, A., Estevez Silva, M., Lippmann, E., McIntosh, B., Probasco, M.D., Jiang, P., Stewart, R., Thomson, J.A. et al. (2019) Inferring Regulatory Programs Governing Region Specificity of Neuroepithelial Stem Cells during Early Hindbrain and Spinal Cord Development. Cell Syst, 9, 167-186 e112.
  • Vermillion, K.L., Bacher, R., Tannenbaum, A.P., Swanson, S., Jiang, P., Chu, L.F., Stewart, R., Thomson, J.A. and Vereide, D.T. (2018) Spatial patterns of gene expression are unveiled in the chick primitive streak by ordering single-cell transcriptomes. Dev Biol.
  • Phillips, M.J.*, Jiang, P.*, Howden, S., Barney, P., Min, J., York, N.W., Chu, L.F., Capowski, E.E., Cash, A., Jain, S. et al. (2018) A Novel Approach to Single Cell RNA-Sequence Analysis Facilitates In Silico Gene Reporting of Human Pluripotent Stem Cell-Derived Retinal Cell Types. Stem Cells, 36, 313-324. (* Co-first authors)
  • Langer, K.B., Ohlemacher, S.K., Phillips, M.J., Fligor, C.M., Jiang, P., Gamm, D.M. and Meyer, J.S. (2018) Retinal Ganglion Cell Diversity and Subtype Specification from Human Pluripotent Stem Cells. Stem Cell Reports, 10, 1282-1293.
  • Jiang, P., Nelson, J.D., Leng, N., Collins, M., Swanson, S., Dewey, C.N., Thomson, J.A. and Stewart, R. (2017) Analysis of embryonic development in the unsequenced axolotl: Waves of transcriptomic upheaval and stability. Dev Biol, 426, 143-154.
  • Jiang, P.#, Hou, Z.G., Bolin, J.M., Thomson, J.A. and Stewart, R. (2017) RNA-Seq of Human Neural Progenitor Cells Exposed to Lead (Pb) Reveals Transcriptome Dynamics, Splicing Alterations and Disease Risk Associations. Toxicological Sciences, 159, 251-265. (# Corresponding author)
  • Barry, C., Schmitz, M.T., Propson, N.E., Hou, Z., Zhang, J., Nguyen, B.K., Bolin, J.M., Jiang, P., McIntosh, B.E., Probasco, M.D. et al. (2017) Uniform neural tissue models produced on synthetic hydrogels using standard culture techniques. Exp Biol Med (Maywood), 242, 1679-1689.
  • Barry, C., Schmitz, M.T., Jiang, P., Schwartz, M.P., Duffin, B.M., Swanson, S., Bacher, R., Bolin, J.M., Elwell, A.L., Mclntosh, B.E. et al. (2017) Species-specific developmental timing is maintained by pluripotent stem cells ex utero. Developmental Biology, 423, 101-110.
  • 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 Biol, 17, 15. (* Co-first authors)
  • Jiang, P.#, Thomson, J.A. and Stewart, R. (2016) Quality control of single-cell RNA-seq by SinQC. Bioinformatics, 32, 2514-2516. (# Corresponding author)
  • Schwartz, M.P., Hou, Z., Propson, N.E., Zhang, J., Engstrom, C.J., Santos Costa, V., Jiang, P., Nguyen, B.K., Bolin, J.M., Daly, W. et al. (2015) Human pluripotent stem cell-derived neural constructs for predicting neural toxicity. Proc Natl Acad Sci U S A, 112, 12516-12521.
  • Roadmap Epigenomics Consortium (…Jiang P. …), Kundaje A. et al. (2015) Integrative analysis of 111 reference human epigenomes. Nature, 518, 317-330.
  • Leng, N., Chu, L.F., Barry, C., Li, Y., Choi, J., Li, X.M., Jiang, P., Stewart, R.M., Thomson, J.A. and Kendziorski, C. (2015) Oscope identifies oscillatory genes in unsynchronized single-cell RNA-seq experiments. Nature Methods, 12, 947-950.
  • Hou, Z., Meyer, S., Propson, N.E., Nie, J., Jiang, P., Stewart, R. and Thomson, J.A. (2015) Characterization and target identification of a DNA aptamer that labels pluripotent stem cells. Cell Res, 25, 390-393.
  • Hou, Z.*, Jiang, P.*, Swanson, S.A., Elwell, A.L., Nguyen, B.K., Bolin, J.M., Stewart, R. and Thomson, J.A. (2015) A cost-effective RNA sequencing protocol for large-scale gene expression studies. Sci Rep, 5, 9570. (* Co-first authors)
  • Jiang, P., Meyer, S., Hou, Z., Propson, N.E., Soh, H.T., Thomson, J.A. and Stewart, R. (2014) MPBind: a Meta-motif-based statistical framework and pipeline to Predict Binding potential of SELEX-derived aptamers. Bioinformatics, 30, 2665-2667.
  • Boudreau, R.L., Jiang, P., Gilmore, B.L., Spengler, R.M., Tirabassi, R., Nelson, J.A., Ross, C.A., Xing, Y. and Davidson, B.L. (2014) Transcriptome-wide discovery of microRNA binding sites in human brain. Neuron, 81, 294-305.
  • Ramachandran, S., Karp, P.H., Osterhaus, S.R., Jiang, P., Wohlford-Lenane, C., Lennox, K.A., Jacobi, A.M., Praekh, K., Rose, S.D., Behlke, M.A. et al. (2013) Post-Transcriptional Regulation of Cystic Fibrosis Transmembrane Conductance Regulator Expression and Function by MicroRNAs. Am J Resp Cell Mol, 49, 544-551.
  • Heinicke, L.A., Nabet, B., Shen, S., Jiang, P., van Zalen, S., Cieply, B., Russell, J.E., Xing, Y. and Carstens, R.P. (2013) The RNA binding protein RBM38 (RNPC1) regulates splicing during late erythroid differentiation. PLoS One, 8, e78031.
  • Ramachandran, S., Karp, P.H., Jiang, P., Ostedgaard, L.S., Walz, A.E., Fisher, J.T., Keshavjee, S., Lennox, K.A., Jacobi, A.M., Rose, S.D. et al. (2012) A microRNA network regulates expression and biosynthesis of wild-type and DeltaF508 mutant cystic fibrosis transmembrane conductance regulator. Proc Natl Acad Sci U S A, 109, 13362-13367.
  • Lu, Z.X., Jiang, P. and Xing, Y. (2012) Genetic variation of pre-mRNA alternative splicing in human populations. Wiley Interdiscip Rev RNA, 3, 581-592.
  • Kim, J.*, Zhao, K.*, Jiang, P.*, Lu, Z.X., Wang, J., Murray, J.C. and Xing, Y. (2012) Transcriptome landscape of the human placenta. BMC Genomics, 13, 115. (* Co-first authors)
  • Dittmar, K.A.*, Jiang, P*., Park, J.W., Amirikian, K., Wan, J., Shen, S., Xing, Y. and Carstens, R.P. (2012) Genome-wide determination of a broad ESRP-regulated posttranscriptional network by high-throughput sequencing. Mol Cell Biol, 32, 1468-1482. (* Co-first authors)
  • Shen, S., Lin, L., Cai, J.J., Jiang, P., Kenkel, E.J., Stroik, M.R., Sato, S., Davidson, B.L. and Xing, Y. (2011) Widespread establishment and regulatory impact of Alu exons in human genes. Proc Natl Acad Sci U S A, 108, 2837-2842.
  • Lu, Z.X.*, Jiang, P.*, Cai, J.J. and Xing, Y. (2011) Context-dependent robustness to 5′ splice site polymorphisms in human populations. Hum Mol Genet, 20, 1084-1096. (* Co-first authors)
  • Liu, S., Lin, L., Jiang, P., Wang, D. and 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, 578-588.
  • Warzecha, C.C., Jiang, P., Amirikian, K., Dittmar, K.A., Lu, H.Z., Shen, S.H., Guo, W., Xing, Y. and Carstens, R.P. (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, B.L. and Xing, Y. (2010) Evolution of alternative splicing in primate brain transcriptomes. Hum Mol Genet, 19, 2958-2973.
  • Lin, L., Liu, S., Brockway, H., Seok, J., Jiang, P., Wong, W.H. and Xing, Y. (2009) Using high-density exon arrays to profile gene expression in closely related species. Nucleic Acids Res, 37, e90.
  • Lin, L., Jiang, P., Shen, S., Sato, S., Davidson, B.L. and Xing, Y. (2009) Large-scale analysis of exonized mammalian-wide interspersed repeats in primate genomes. Hum Mol Genet, 18, 2204-2214.
  • Tong, J., Jiang, P. and Lu, Z.H. (2008) RISP: a web-based server for prediction of RNA-binding sites in proteins. Comput Methods Programs Biomed, 90, 148-153.
  • Lin, L., Shen, S., Tye, A., Cai, J.J., Jiang, P., Davidson, B.L. and Xing, Y. (2008) Diverse splicing patterns of exonized Alu elements in human tissues. PLoS Genet, 4, e1000225.
  • Jiang, P., Wu, H., Wei, J., Sang, F., Sun, X. and 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, W47-51.
  • Jiang, P., Wu, H., Wang, W., Ma, W., Sun, X. and Lu, Z. (2007) MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features. Nucleic Acids Res, 35, W339-344.
  • Jiang, P., Wu, H., Da, Y., Sang, F., Wei, J., Sun, X. and Lu, Z. (2007) RFRCDB-siRNA: improved design of siRNAs by random forest regression model coupled with database searching. Comput Methods Programs Biomed, 87, 230-238.
  • Jiang, P., Sun, X. and Lu, Z. (2007) Analysis of synonymous codon usage in Aeropyrum pernix K1 and other Crenarchaeota microorganisms. J Genet Genomics, 34, 275-284.