Regeneromics

Regeneromics is a bioinformatics shared resource available to labs of DRC faculty affiliates. It specializes in the genomics of tissue regeneration across many species. Regeneromics is located in Nanaline Duke Room 465, or regeneromics@duke.edu.

Regeneromics is led by Jianhong Ou, PhD and is located in Nanaline Duke, Room 465

Jianhong Ou, PhDJianhong has been at Duke for four years, after serving as the Core Bioinformatician at UMass Medical School. In his 11 years as a Bioinformatician, he has led and assisted over 40 laboratories in a wide range of projects. Jianhong’s areas of greatest interest include data integration and data mining go high-throughput experiments such as microarray, ChIP-chip, ChIP-seq, RNA-seq, MiRNA-seq, iCLIP-seq/HIST-seq, ATAC-seq, and scRNA-seq for transcriptional regulation and post-transcriptional regulation. He develops and applies computational tools (R/Bioconductor package) to analyze and integrate various data sources. Jianhong can bring considerable computational and analytic resources to alleviate the heavy tasks of research projects and assist grant applications and manuscripts. Please bee description below.

 DESCRIPTION OF SERVICES AND HOW THEY WILL BE PROVIDED

The RNI Regeneromics Shared Resource will strive to provide cutting edge data analysis through published and novel pipelines.

The key services are, but not limited to, high-throughput data analysis, data visualization, grant support by data mining from published data, and customized pipeline and tools development.

There are three stages for onboarding projects: initial a project with an estimate of the cost and time of completion, data analysis and communication, and results delivery.  The shared resource will ask affiliated labs using the services to list the resource in the acknowledgements of publications, or authorship based on effort.

The shared resource collaborates with CoreResearch@Duke to provide billing support. This will remove the barrier of payment.

Please email regeneromics@duke.edu consultation or further information.

Contribution to Science

As a collaborator, the shared resource 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 pipelines were build using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It includes docker containers, making installation trivial and results highly reproducible.

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

The full list of Bioconductor/R Packages:

Ou J, Hoye M (2020). ribosomeProfilingQC: Ribosome Profiling Quality Control.

Ou J, (2020). colorBlindness: Safe Color Set for Color Blindness.

Ou J, Yu J, Kelliher M, Castilla L, Lawson N and Zhu LJ (2017). ATACseqQC: ATAC- seq Quality Control.

Ou J, Park SM, Green MR and Zhu LJ (2015). InPAS: Identification of Novel alternative PolyAdenylation Sites (PAS).

Ou J, Nirala N, Acharya U and Zhu LJ (2014). dagLogo: Visualize significant conserved amino acid sequence pattern in groups based on probability theory.

Ou J and Zhu LJ (2014). GeneNetworkBuilder: Build Regulatory Network from ChIP- chip/ChIP-seq and Expression Data.

Ou J, Brodsky M, Wolfe S and Zhu LJ (2014). motifStack: Plot stacked logos for single or multiple DNA, RNA and amino acid sequence.

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, Xiang Y, Diao Y (2021): hicar_tools: pipeline for HiCAR data.

Ou J, Kobayashi Y, Tata A (2018). MintChIP: pipeline for MintChIP.

Publications:

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.

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.

Ou J, Liu H, Yu J, Kelliher MA, Castilla LH, Lawson ND, Zhu LJ. ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data. BMC Genomics. 2018 Mar 1;19(1):169.

Ou J, Wolfe SA, Brodsky MH, Zhu LJ. motifStack for the analysis of transcription factor binding site evolution. Nat Methods. 2018 Jan 3;15(1):8-9.

Contributions to publications (~ April, 2021):

Simone AD, Evanitsky MN, Hayden L, Cox BD, Wang J, Tornini VA, Ou J, Chao A, Poss KD, Talia SD. Control of osteoblast regeneration by a train of Erk activity waves. Nature. 2021 Jan 6.

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.

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):dev191262.

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.

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.

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, Al- man BA. Tracing Tumor Evolution in Sarcoma Reveals Clonal Origin of Advanced Metastasis. Cell Rep. 2019 Sep 10;28(11):2837-2850.e5.

Vertii A, Ou J, Yu J, Yan A, Pages 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.

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 Car- diomyocyte Proliferation and Controls Organ Size and Regeneration in Zebrafish. Dev Cell. 2019 Mar 25; 48(6):853-863.