Research

Contributions to Packages and Pipelines

As a collaborator, Regeneromics development tools and pipelines to meet the fast-development requirements of new emerging high-throughput techniques. To help researchers meet the goal of increasing the reproducibility of scientific findings, the tools will be presented as packages or pipelines. The pipelines were build using Nextflow, a workflow tool to run tasks across multiple computer infrastructures in a very portable manner. It includes docker containers, making installation trivial and results highly reproducible.

The list of Bioconductor/R Packages:

  1. Ou J (2024). geomeTriD: A R/Bioconductor package for interactive 3D plot of epigenetic data or single cell data. 
  2. Ou J (2023). hicVennDiagram: Venn Diagram for genomic interaction data. 
  3. Ou J (2023). scRNAseqApp: A single-cell RNAseq Shiny app-package.
  4. Ou J (2022). enhancerHomologSearch: Identification of putative mammalian orthologs to given enhancer.
  5. Ou J (2022). ATACseqTFEA: Transcription Factor Enrichment Analysis for ATAC-seq. 
  6. Ou, J (2021). GenomicInteractionNodes: A R/Bioconductor package to detect the interaction nodes from HiC/HiChIP/HiCAR data.
  7. Ou J, Hoye M (2020). ribosomeProfilingQC: Ribosome Profiling Quality Control.
  8. Ou J, (2020). colorBlindness: Safe Color Set for Color Blindness.
  9. Ou J, Yu J, Kelliher M, Castilla L, Lawson N and Zhu LJ (2017). ATACseqQC: ATAC- seq Quality Control.
  10. Ou J, Park SM, Green MR and Zhu LJ (2015). InPAS: Identification of Novel alternative PolyAdenylation Sites (PAS).
  11. Ou J, Nirala N, Acharya U and Zhu LJ (2014). dagLogo: Visualize significant conserved amino acid sequence pattern in groups based on probability theory.
  12. Ou J and Zhu LJ (2014). GeneNetworkBuilder: Build Regulatory Network from ChIP- chip/ChIP-seq and Expression Data.
  13. Ou J, Brodsky M, Wolfe S and Zhu LJ (2014). motifStack: Plot stacked logos for single or multiple DNA, RNA and amino acid sequence.
  14. Ou J, Wang Y and Zhu LJ (2014). trackViewer: A bioconductor package with minimalist design for drawing elegant tracks or lollipop plot.

Nextflow pipelines:

  • Ou J, Jeff Letourneau,(2022): 16S_pipeline: a bioinformatics best-practice analysis pipeline for 16S rRNA gene sequencing
  • Ou J, (2022): shotgun: a bioinformatics best-practice analysis pipeline for Shotgun Sequencing Pipelines.
  • Ou J, Xiang Y, Diao Y (2021): hicar_tools: pipeline for HiCAR data.
  • Ou J, Kobayashi Y, Tata A (2018). MintChIP: pipeline for MintChIP.

Contributions to publications (December, 2024):

With the help of the bioinformatic analysis, affiliated labs successfully completed multiple research projects and produced many peer-reviewed publications in high impact journals.

  1. Puviindran V, Shimada E, Huang Z, Ma X, Ban GI, Xiang Y, Zhang H, Ou J, Wei X, Nakagawa M, Martin J, Diao Y, Alman BA. Single cell analysis of Idh mutant growth plates identifies cell populations responsible for longitudinal bone growth and enchondroma formation. Sci Rep. 2024 Oct 31;14(1):26208. doi: 10.1038/s41598-024-76539-y. PubMed PMID: 39482341; PubMed Central PMCID: PMC11527983.select
  2. Ban GI, Puviindran V, Xiang Y, Nadesan P, Tang J, Ou J, Guardino N, Nakagawa M, Browne M, Wallace A, Ishikawa K, Shimada E, Martin JT, Diao Y, Kirsch DG, Alman BA. The COMPASS complex maintains the metastatic capacity imparted by a subpopulation of cells in UPS. iScience. 2024 Jul 19;27(7):110187. doi: 10.1016/j.isci.2024.110187. eCollection 2024 Jul 19. PubMed PMID: 38989451; PubMed Central PMCID: PMC11233968.select
  3. Puviindran V, Shimada E, Huang Z, Ma X, Ban GI, Xiang Y, Zhang H, Ou J, Wei X, Nakagawa M, Martin J, Diao Y, Alman BA. Single-cell transcriptomic analyses of mouse idh1 mutant growth plate chondrocytes reveal distinct cell populations responsible for longitudinal growth and enchondroma formation. Res Sq. 2024 Jun 4;. doi: 10.21203/rs.3.rs-4451086/v1. PubMed PMID: 38883785; PubMed Central PMCID: PMC11178001.select
  4. Ando K, Ou J, Thompson JD, Welsby J, Bangru S, Shen J, Wei X, Diao Y, Poss KD. A screen for regeneration-associated silencer regulatory elements in zebrafish. Dev Cell. 2024 Mar 11;59(5):676-691.e5. doi: 10.1016/j.devcel.2024.01.004. Epub 2024 Jan 29. PubMed PMID: 38290519; PubMed Central PMCID: PMC10939760.select
  5. Cigliola V, Shoffner A, Lee N, Ou J, Gonzalez TJ, Hoque J, Becker CJ, Han Y, Shen G, Faw TD, Abd-El-Barr MM, Varghese S, Asokan A, Poss KD. Spinal cord repair is modulated by the neurogenic factor Hb-egf under direction of a regeneration-associated enhancer. Nat Commun. 2023 Aug 11;14(1):4857. doi: 10.1038/s41467-023-40486-5. PubMed PMID: 37567873; PubMed Central PMCID: PMC10421883.select
  6. Sun T, Xu Y, Xiang Y, Ou J, Soderblom EJ, Diao Y. Crosstalk between RNA m(6)A and DNA methylation regulates transposable element chromatin activation and cell fate in human pluripotent stem cells. Nat Genet. 2023 Aug;55(8):1324-1335. doi: 10.1038/s41588-023-01452-5. Epub 2023 Jul 20. PubMed PMID: 37474847; PubMed Central PMCID: PMC10766344.select
  7. Wang ME, Chen J, Lu Y, Bawcom AR, Wu J, Ou J, Asara JM, Armstrong AJ, Wang Q, Li L, Wang Y, Huang J, Chen M. RB1-deficient prostate tumor growth and metastasis are vulnerable to ferroptosis induction via the E2F/ACSL4 axis. J Clin Invest. 2023 May 15;133(10). doi: 10.1172/JCI166647. PubMed PMID: 36928314; PubMed Central PMCID: PMC10178842.select
  8. Yan R, Cigliola V, Oonk KA, Petrover Z, DeLuca S, Wolfson DW, Vekstein A, Mendiola MA, Devlin G, Bishawi M, Gemberling MP, Sinha T, Sargent MA, York AJ, Shakked A, DeBenedittis P, Wendell DC, Ou J, Kang J, Goldman JA, Baht GS, Karra R, Williams AR, Bowles DE, Asokan A, Tzahor E, Gersbach CA, Molkentin JD, Bursac N, Black BL, Poss KD. An enhancer-based gene-therapy strategy for spatiotemporal control of cargoes during tissue repair. Cell Stem Cell. 2023 Jan 5;30(1):96-111.e6. doi: 10.1016/j.stem.2022.11.012. Epub 2022 Dec 13. PubMed PMID: 36516837; PubMed Central PMCID: PMC9830588.select
  9. Yang T, Ou J, Yildirim E. Xist exerts gene-specific silencing during XCI maintenance and impacts lineage-specific cell differentiation and proliferation during hematopoiesis. Nat Commun. 2022 Aug 1;13(1):4464. doi: 10.1038/s41467-022-32273-5. PubMed PMID: 35915095; PubMed Central PMCID: PMC9343370.select
  10. Sun J, Peterson EA, Wang AZ, Ou J, Smith KE, Poss KD, Wang J. hapln1 Defines an Epicardial Cell Subpopulation Required for Cardiomyocyte Expansion During Heart Morphogenesis and Regeneration. Circulation. 2022 Jul 5;146(1):48-63. doi: 10.1161/CIRCULATIONAHA.121.055468. Epub 2022 Jun 2. PubMed PMID: 35652354; PubMed Central PMCID: PMC9308751.select
  11. Hoye ML, Calviello L, Poff AJ, Ejimogu NE, Newman CR, Montgomery MD, Ou J, Floor SN, Silver DL. Aberrant cortical development is driven by impaired cell cycle and translational control in a DDX3X syndrome model. Elife. 2022 Jun 28;11. doi: 10.7554/eLife.78203. PubMed PMID: 35762573; PubMed Central PMCID: PMC9239684.select
  12. Sun F, Ou J, Shoffner AR, Luan Y, Yang H, Song L, Safi A, Cao J, Yue F, Crawford GE, Poss KD. Enhancer selection dictates gene expression responses in remote organs during tissue regeneration. Nat Cell Biol. 2022 May;24(5):685-696. doi: 10.1038/s41556-022-00906-y. Epub 2022 May 5. PubMed PMID: 35513710; PubMed Central PMCID: PMC9107506.select
  13. Wei X, Xiang Y, Peters DT, Marius C, Sun T, Shan R, Ou J, Lin X, Yue F, Li W, Southerland KW, Diao Y. HiCAR is a robust and sensitive method to analyze open-chromatin-associated genome organization. Mol Cell. 2022 Mar 17;82(6):1225-1238.e6. doi: 10.1016/j.molcel.2022.01.023. Epub 2022 Feb 22. PubMed PMID: 35196517; PubMed Central PMCID: PMC8934281.select
  14. Cao Y, Xia Y, Balowski JJ, Ou J, Song L, Safi A, Curtis T, Crawford GE, Poss KD, Cao J. Identification of enhancer regulatory elements that direct epicardial gene expression during zebrafish heart regeneration. Development. 2022 Feb 15;149(4). doi: 10.1242/dev.200133. Epub 2022 Feb 18. PubMed PMID: 35179181; PubMed Central PMCID: PMC8918790.select
  15. Panzarino NJ, Krais JJ, Cong K, Peng M, Mosqueda M, Nayak SU, Bond SM, Calvo JA, Doshi MB, Bere M, Ou J, Deng B, Zhu LJ, Johnson N, Cantor SB. Replication Gaps Underlie BRCA Deficiency and Therapy Response. Cancer Res. 2021 Mar 1;81(5):1388-1397. doi: 10.1158/0008-5472.CAN-20-1602. Epub 2020 Nov 12. PubMed PMID: 33184108; PubMed Central PMCID: PMC8026497.select
  16. De Simone A, Evanitsky MN, Hayden L, Cox BD, Wang J, Tornini VA, Ou J, Chao A, Poss KD, Di Talia S. Control of osteoblast regeneration by a train of Erk activity waves. Nature. 2021 Feb;590(7844):129-133. doi: 10.1038/s41586-020-03085-8. Epub 2021 Jan 6. PubMed PMID: 33408418; PubMed Central PMCID: PMC7864885.select
  17. Ou J, Liu H, Nirala NK, Stukalov A, Acharya U, Green MR, Zhu LJ. dagLogo: An R/Bioconductor package for identifying and visualizing differential amino acid group usage in proteomics data. PLoS One. 2020;15(11):e0242030. doi: 10.1371/journal.pone.0242030. eCollection 2020. PubMed PMID: 33156866; PubMed Central PMCID: PMC7647101.select
  18. Shoffner A, Cigliola V, Lee N, Ou J, Poss KD. Tp53 Suppression Promotes Cardiomyocyte Proliferation during Zebrafish Heart Regeneration. Cell Rep. 2020 Sep 1;32(9):108089. doi: 10.1016/j.celrep.2020.108089. PubMed PMID: 32877671; PubMed Central PMCID: PMC7494019.select
  19. Kobayashi Y, Tata A, Konkimalla A, Katsura H, Lee RF, Ou J, Banovich NE, Kropski JA, Tata PR. Persistence of a regeneration-associated, transitional alveolar epithelial cell state in pulmonary fibrosis. Nat Cell Biol. 2020 Aug;22(8):934-946. doi: 10.1038/s41556-020-0542-8. Epub 2020 Jul 13. PubMed PMID: 32661339; PubMed Central PMCID: PMC7461628.select
  20. Thompson JD, Ou J, Lee N, Shin K, Cigliola V, Song L, Crawford GE, Kang J, Poss KD. Identification and requirements of enhancers that direct gene expression during zebrafish fin regeneration. Development. 2020 Jul 30;147(14). doi: 10.1242/dev.191262. PubMed PMID: 32665240; PubMed Central PMCID: PMC7406312.select
  21. Kadota S, Ou J, Shi Y, Lee JT, Sun J, Yildirim E. Nucleoporin 153 links nuclear pore complex to chromatin architecture by mediating CTCF and cohesin binding. Nat Commun. 2020 May 25;11(1):2606. doi: 10.1038/s41467-020-16394-3. PubMed PMID: 32451376; PubMed Central PMCID: PMC7248104.select
  22. Leech CM, Flynn MJ, Arsenault HE, Ou J, Liu H, Zhu LJ, Benanti JA. The coordinate actions of calcineurin and Hog1 mediate the stress response through multiple nodes of the cell cycle network. PLoS Genet. 2020 Apr;16(4):e1008600. doi: 10.1371/journal.pgen.1008600. eCollection 2020 Apr. PubMed PMID: 32343701; PubMed Central PMCID: PMC7209309.select
  23. Tang YJ, Huang J, Tsushima H, Ban GI, Zhang H, Oristian KM, Puviindran V, Williams N, Ding X, Ou J, Jung SH, Lee CL, Jiao Y, Chen BJ, Kirsch DG, Alman BA. Tracing Tumor Evolution in Sarcoma Reveals Clonal Origin of Advanced Metastasis. Cell Rep. 2019 Sep 10;28(11):2837-2850.e5. doi: 10.1016/j.celrep.2019.08.029. PubMed PMID: 31509746; PubMed Central PMCID: PMC6750751.select
  24. Vertii A, Ou J, Yu J, Yan A, Pagès H, Liu H, Zhu LJ, Kaufman PD. Two contrasting classes of nucleolus-associated domains in mouse fibroblast heterochromatin. Genome Res. 2019 Aug;29(8):1235-1249. doi: 10.1101/gr.247072.118. Epub 2019 Jun 14. PubMed PMID: 31201210; PubMed Central PMCID: PMC6673712.select
  25. Ou J, Zhu LJ. trackViewer: a Bioconductor package for interactive and integrative visualization of multi-omics data. Nat Methods. 2019 Jun;16(6):453-454. doi: 10.1038/s41592-019-0430-y. PubMed PMID: 31133757.select
  26. Ma L, Pak ML, Ou J, Yu J, St Louis P, Shan Y, Hutchinson L, Li S, Brehm MA, Zhu LJ, Green MR. Prosurvival kinase PIM2 is a therapeutic target for eradication of chronic myeloid leukemia stem cells. Proc Natl Acad Sci U S A. 2019 May 21;116(21):10482-10487. doi: 10.1073/pnas.1903550116. Epub 2019 May 8. PubMed PMID: 31068472; PubMed Central PMCID: PMC6535024.select
  27. Han Y, Chen A, Umansky KB, Oonk KA, Choi WY, Dickson AL, Ou J, Cigliola V, Yifa O, Cao J, Tornini VA, Cox BD, Tzahor E, Poss KD. Vitamin D Stimulates Cardiomyocyte Proliferation and Controls Organ Size and Regeneration in Zebrafish. Dev Cell. 2019 Mar 25;48(6):853-863.e5. doi: 10.1016/j.devcel.2019.01.001. Epub 2019 Jan 31. PubMed PMID: 30713073; PubMed Central PMCID: PMC6435404.