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Computational Biology & Genomics Core

IRP Core: Computational Biology & Genomics Core

Supriyo De, MD, PhD, Chief

The Computational Biology & Genomics Core (CBGC) is involved in interdisciplinary research and institute-wide training by collaborating mainly with the laboratories in the NIA IRP, NIH.

Four interconnected goals of the Computational Biology Core are:1. Data Analysis and Sharing, 2. Data Science Network and Training, 3. Instruments and Computer Resources, 4. Core Research Interests

The goals of the core are to (1) carry out genomic, epigenomic, functional genomic (CRISPR screens), transcriptomic, single-cell data analysis and data sharing using NIH data-sharing guidelines; (2) coordinate the activities of data scientists at NIA IRP by maintaining a Biomedical Data Science Network (BDSN); (3) acquire and maintain novel high-throughput instruments and high-performance computer systems to achieve the mission of the NIA; (4) have a fully functional, aging-centered core research program which fosters collaborations mainly within NIA IRP, NIH.

The Computational Biology & Genomics Core (CBGC) provides advice on experimental design and sample preparation, quality control of samples, data analysis, data sharing, and training. Apart from the primary focus on genomic and transcriptomic research, CBGC is highly interested in applying Artificial Intelligence (AI) for image analysis and novel genomic data analysis algorithms. The core utilizes gene expression microarrays, Illumina and Oxford Nanopore sequencers and 10x Genomics single-cell sample preparation instruments to meet the needs of NIA IRP researchers. Moreover, CBGC maintains several high-performance computer systems and is involved in designing and maintaining NIA IRP cloud computing for use by all interested NIA IRP researchers.

CBGC is involved in fostering wide variety of collaborative research and providing training on diverse data science topics beyond the core research areas by maintaining the Biomedical Data Science Network (BDSN) comprising of all the data scientists in the NIA IRP. The BDSN website (internal to NIA IRP, sign-in required) provides description of the expertise available at NIA IRP, Baltimore and their contact information.  

Core Research Areas

  • Role of microbiome in Aging and age-related diseases (e.g., Alzheimer’s Disease)
  • Detection of DNA and RNA base modifications
  • Applications of Artificial Intelligence in data analysis
  • Functional Genomics (CRISPR) Screens

Publications

Publications by Supriyo De

Selected Recent Publications:

2019

  • Casella G, Munk R, Kim KM, Piao Y, De S, Abdelmohsen K, and Gorospe M. (2019) Transcriptome Signature of Cellular Senescence.  Nucleic Acids Research (in press)
  • Lee JH, Demarest T, Babbar M, Kim E, Okur M, De S, Croteau D, Bohr VA (2019) Cockayne syndrome group B deficiency reduces H3K9me3 chromatin remodeler SETDB1 and exacerbates cellular aging. Nucleic Acids Research (in press)
  • Noh JH, Kim KM, Pandey PR, Hooten NN, Munk R, Kundu G, De S, Martindale JL, Yang X, Evans MK, Abdelmohsen K, Gorospe M (2019) Loss of RNA-binding protein GRSF1 activates mTOR to elicit a proinflammatory transcriptional program. Nucleic Acids Research 47(5):2472-2486.
  • Chatterjee B, Roy P, Sarkar UA, Zhao M, Ratra Y, Singh A, Chawla M, De S, Gomes J, Sen R, Basak S (2019) Immune differentiation regulator p100 tunes NF-κB responses to TNF. Frontiers in immunology 10:997

2018

  • Lee SK, Xue Y, Shen W, Zhang YQ, Joo Y, Ahmad M, Chinen M, Ding Yi, Ku WL, De S, Lehrmann E, Becker KG, Lei EP, Zhao K, Zou S, Sharov A, Wang W (2018) Topoisomerase 3β interacts with RNAi machinery to promote heterochromatin formation and transcriptional silencing in Drosophila Nature Communications 9(1):4946.
  • Zhao M, Joy J, W Zhou, De S, Wood WH, Becker KG, Ji H, Sen R (2018) Transcriptional outcomes and kinetic patterning of gene expression in response to NF-kB activation. PLoS Biology 16(9):e2006347.
  • Dluzen DF*, Hooten NN*, De S, Wood WH, Becker KG, Zonderman AB, Tanaka T, Ferrucci L, Evans MK (2018) Extracellular RNA profiles with human age Aging Cell e12785 (*co-first authors).
  • Qiu X, Kumari G, Gerasimova T, Du H, Labaran L, Singh A, De S, Wood WH 3rd, Becker KG, Zhou W, Ji H, Sen R (2018) Sequential Enhancer Sequestration Dysregulates Recombination Center Formation at the IgH Locus Molecular Cell 70(1):21-33.
  • Kumari G, Gerasimova T, Du H, De S, Wood WH, Becker KG, Sen R (2018) Misregulation of the IgH Locus in Thymocytes Frontiers in immunology 9:2426.