Jiang Lab - Publications

Publications (# Corresponding author, * Co-first author)

2025

1. Zhang Z, Keyser C, Li Y, Rosolia BJ, Porch MW, Zhang W, Su B, Jiang P., Zukin RS, Yan J. Autophagy controls the hippocampal postsynaptic organization and affects cognition in a mouse model of Fragile X syndrome. Mol Psychiatry. 2025 Sep 10. doi:10.1038/s41380-025-03207-6.

2. Peng, Y., Toh, H., Clegg, D. and Jiang, P.#, (2025) AI-Enhanced Fluorescein Angiography Detection of Diabetes-Induced Silent Retinal Capillary Dropout and RNA-Seq Identification of Pre-Symptomatic Biomarkers. Biomedicines, 13(8), p.1926. (#Corresponding author)

3. Bagheri A, Kim J, Jiang P.# Distinct nuclear and cytoplasmic transcriptomic signatures reveal-transcription alone is insufficient to determine glucose-induced transcriptomic dynamics. Biomedical Informatics. 2025;1(2):0006. doi:10.55092/bi20250004. (#Corresponding author)

4. Roy A, Bzdak VA, Sinha M, Komar AA, Jiang, P.#, Mazumder B#. Myeloid-specific deficiency of ribosomal protein L13a alters macrophage polarity and diversity during differentiation from bone marrow. J Leukoc Biol. 2025;117(7). PMID: 40631353. (#Co-Corresponding author)

5. Prabahar, A., Chamberlain, C.S., Vanderby, R., Murphy, W.L., Dangelo, W., Mangesh, K., Brown, B., Mazumder, B., Badylak, S. and Jiang, P.#, 2025. Transcriptomic landscape around wound bed defines regenerative versus non-regenerative outcomes in mouse digit amputation. PLOS Computational Biology, 21(4), p.e1012997. (#Corresponding author)

2024

1. Bohara S, Bagheri A, Ertugral EG, Radzikh I, Sandlers Y, Jiang P#, Kothapalli CR#. Integrative analysis of gene expression, protein abundance, and metabolomic profiling elucidates complex relationships in chronic hyperglycemia-induced changes in human aortic smooth muscle cells. J Biol Eng. 2024;18(1):61. PMID: 39473010; PMCID: PMC11523773. (#Co-Corresponding author)

2. Chamberlain, C.S., Prabahar, A., Kink, J.A., Mueller, E., Li, Y., Yopp, S., Capitini, C.M., Hematti, P., Murphy, W.L., Vanderby, R. and Jiang, P. #, 2024. Modulating the mesenchymal stromal cell microenvironment alters exosome RNA content and ligament healing capacity. Stem Cells, p.sxae028. (#Corresponding author)

3. Astafev, A.A., Mezhnina, V., Poe, A., Jiang, P#. and Kondratov, R.V.#, 2024. Sexual Dimorphism of Circadian Liver Transcriptome. iScience. (#Co-Corresponding author)

4. Prabahar, A., Zamora, R., Barclay, D., Yin, J., Ramamoorthy, M., Bagheri, A., Johnson, S.A., Badylak, S., Vodovotz, Y. and Jiang, P. #, 2024. Unraveling the complex relationship between mRNA and protein abundances: a machine learning-based approach for imputing protein levels from RNA-seq data. NAR Genomics and Bioinformatics, 6(1), p.lqae019. (# Corresponding author)

5. Bukhman YV, Morin PA, Meyer S, Chu LF, Jacobsen JK, Antosiewicz-Bourget J, Mamott D, Gonzales M, Argus C, Bolin J, Berres ME, Fedrigo O, Steill J, Swanson SA, Jiang P., Rhie A, Formenti G, Phillippy AM, Harris RS, Wood JMD, Howe K, Kirilenko BM, Munegowda C, Hiller M, Jain A, Kihara D, Johnston JS, Ionkov A, Raja K, Toh H, Lang A, Wolf M, Jarvis ED, Thomson JA, Chaisson MJP, Stewart R. A high-quality blue whale genome, segmental duplications, and historical demography. Mol Biol Evol. 2024 Feb 20;41(3):msae036.

2023

1. Anderson BJ, Curtis AM, Jen A, Thomson JA, Clegg DO, Jiang P, Coon JJ, Overmyer KA, Toh H. Plasma metabolomics supports non-fasted sampling for metabolic profiling across a spectrum of glucose tolerance in the Nile rat model for type 2 diabetes. Lab Anim (NY). 2023 Nov;52(11):269-277.

2. Toh H, Smolentsev A, Sadjadi R, Clegg D, Yan J, Stewart R, Thomson JA, Jiang P.# Transcriptomic clock predicts vascular changes of prodromal diabetic retinopathy. Scientific Reports. 2023 Aug 10;13(1):12968. (#Corresponding author)

3. Toh H, Bagheri A, Dewey C, Stewart R, Yan L, Clegg D, Thomson JA, Jiang P.# A Nile rat transcriptomic landscape across 22 organs by ultra-deep sequencing and comparative RNA-seq pipeline (CRSP). Comput Biol Chem. 2023 Feb;102:107795. doi: 10.1016/j.compbiolchem.2022.107795. Epub 2022 Nov 23. PMID: 36436489. (#Corresponding author)

4. Teague J, Socia D, An G, Badylak S, Johnson S, Jiang P, Vodovotz Y, Cockrell RC. Artificial Intelligence Optical Biopsy for Evaluating the Functional State of Wounds. Journal of Surgical Research. 2023 Nov 1;291:683-90.

2022

1. Bagheri A, Astafev A, Al-Hashimy T, Jiang P.# Tracing Translational Footprint by Ribo-Seq: Principle, Workflow, and Applications to Understand the Mechanism of Human Diseases. Cells. 2022 Sep 23;11(19):2966. doi: 10.3390/cells11192966. PMID: 36230928; PMCID: PMC9562884. (#Corresponding author)

2. Sinha S, Sparks HD, Labit E, Robbins HN, Gowing K, Jaffer A, Kutluberk E, Arora R, Raredon MSB, Cao L, Swanson S, Jiang P, Hee O, Pope H, Workentine M, Todkar K, Sharma N, Bharadia S, Chockalingam K, de Almeida LGN, Adam M, Niklason L, Potter SS, Seifert AW, Dufour A, Gabriel V, Rosin NL, Stewart R, Muench G, McCorkell R, Matyas J, Biernaskie J. Fibroblast inflammatory priming determines regenerative versus fibrotic skin repair in reindeer. Cell. 2022 Dec 8;185(25):4717-4736.e25. doi: 10.1016/j.cell.2022.11.004. PMID: 36493752; PMCID: PMC9888357.

3. Rolnick KI, Choe JA, Leiferman EM, Kondratko-Mittnacht J, Clements AEB, Baer GS, Jiang P, Vanderby R, Chamberlain CS. Periostin modulates extracellular matrix behavior in tendons. Matrix Biol Plus. 2022 Nov 9;16:100124. doi: 10.1016/j.mbplus.2022.100124. PMID: 36405342; PMCID: PMC9673102.

4. Turner NJ, Quijano LM, Hussey GS, Jiang P, Badylak SF. Matrix Bound Nanovesicles Have Tissue-Specific Characteristics That Suggest a Regulatory Role. Tissue Eng Part A. 2022 Nov;28(21-22):879-892. doi: 10.1089/ten.TEA.2022.0091. Epub 2022 Oct 3. PMID: 35946072.

5. Toh H, Yang C, Formenti G, Raja K, Yan L, Tracey A, Chow W, Howe K, Bergeron LA, Zhang G, Haase B, Mountcastle J, Fedrigo O, Fogg J, Kirilenko B, Munegowda C, Hiller M, Jain A, Kihara D, Rhie A, Phillippy AM, Swanson SA, Jiang P, Clegg DO, Jarvis ED, Thomson JA, Stewart R, Chaisson MJP, Bukhman YV. A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes. BMC Biol. 2022 Nov 8;20(1):245. doi: 10.1186/s12915-022-01427-8. PMID: 36344967; PMCID: PMC9641963.

6. Crum RJ, Johnson SA, Jiang P, Jui JH, Zamora R, Cortes D, Kulkarni M, Prabahar A, Bolin J, Gann E, Elster E, Schobel SA, Larie D, Cockrell C, An G, Brown B, Hauskrecht M, Vodovotz Y, Badylak SF. Transcriptomic, Proteomic, and Morphologic Characterization of Healing in Volumetric Muscle Loss. Tissue Eng Part A. 2022 Dec;28(23-24):941-957. doi: 10.1089/ten.TEA.2022.0113. Epub 2022 Oct 11. PubMed PMID: 36039923.

7. Schumaker G, Becker A, An G, Badylak S, Johnson S, Jiang P, Vodovotz Y, Cockrell RC. Optical Biopsy Using a Neural Network to Predict Gene Expression From Photos of Wounds. J Surg Res. 2022 Feb;270:547-554. PMID: 34826690.

8. M. Cramer, W. D’Angelo, M. Dewey, A. Manuel, S. Mullett, S. Wendell, D. Napierala, P. Jiang, S. Badylak. Extracellular vesicles present in bone, blood and extracellular matrix have distinctive characteristics and biologic roles. Journal of Immunology and Regenerative Medicine. Volume 18, 2022,100066, ISSN 2468-4988.

Before 2021

1. Toh, H., Thomson, J.A., Jiang, P.# Maternal high-Fiber diet protects offspring against type 2 diabetes. Nutrients 2021, 13, 94. (# Corresponding author)

2. 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)

3. Wang, F., Qi, Z., Yao, Y., Yu, G., Feng, T., Zhao, T., Xue, H.H., Zhao, Y., Jiang, P., Bao, L. and Yu, S., 2020. Exploring the stage-specific roles of Tcf-1 in T cell development and malignancy at single-cell resolution. Cellular & Molecular Immunology, pp.1-16.

4. 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.

5. 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.

6. 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.

7. 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)

8. 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.

9. 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.

10. 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)

11. 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.

12. 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.

13. 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)

14. Jiang, P.#, Thomson, J.A. and Stewart, R. (2016) Quality control of single-cell RNA-seq by SinQC. Bioinformatics, 32, 2514-2516. (# Corresponding author)

15. 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.

16. Roadmap Epigenomics Consortium (…Jiang P. …), Kundaje A. et al. (2015) Integrative analysis of 111 reference human epigenomes. Nature, 518, 317-330.

17. 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.

18. 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.

19. 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)

20. 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.

21. 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.

22. 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.

23. 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.

24. 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.

25. 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.

26. 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)

27. 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)

28. 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.

29. 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)

30. 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.

31. 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.

32. 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.

33. 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.

34. 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.

35. 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.

36. 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.

37. 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.

38. 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.

39. 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.

40. 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.