Bioinformatics

Machine Learning for Bioinformatics/Computational Biology

Application of machine/deep learning to single cell RNA sequence (scRNAseq), Assay for Transposase-Accessible Chromatin using sequence (ATAC-seq), etc. Analysis of high throughput sequencing genomics data (ChIP-Seq, DNase-Seq, and/or ATAC-Seq). Deep learning, explainable AI for computational biology problems - quality control (QC), clustering, denoising, imputation, trajectory inference, immunogenicity prediction, RNA binding protein prediction, transcription factor binding prediction, Gene regulatory network (GRN) inference, antimicrobial resistance prediction, CyTOF, flow and mass cytometry. Analysis of multiplexed imaging, mass spectrometry imaging (MSI), CODEX imaging, spatial transcriptomics in tandem with single-cell genomics data and in general multi-omics, and multimodal analysis. Exploration of latent structures in single cell data, finding common embeddings/integration for mutimodal biological data. Automated cell population discovery, exploration of latent structures in single cell data, finding common embeddings/integration for mutimodal biological data.

Project pages:

1. Imaging-based:  Clustering, Spatial Transcriptomics

2. Single-cell: DeepImmuno, CellDrift, scTriangulate, MaxATAC

3. Metagenomics: MGS2AMR

Selected publications:

• J. Zhang, Q. Wu, C. B. Johnson, G. Pham, J. M. Kinder, A. Olsson, A. Slaughter, M. May, B. Weinhaus, A. D'Alessandro, J. D. Engel, J. X. Jiang, J. M. Kofron, L. F. Huang, V. B. S. Prasath, S. S. Way, N. Salomonis, H. L. Grimes, D. Lucas. In situ mapping identifies distinct vascular niches for myelopoiesis. Nature, 590, 457-462, February 2021. doi:10.1038/s41586-021-03201-2 [Clustering]

• G. Li, B. Iyer, V. B. S. Prasath, Y. Ni, N. Salomonis. DeepImmuno: Deep learning-empowered prediction and generation of immunogenic peptides for T-cell immunity. Briefings in Bioinformatics, 22(6), November 2021. doi:10.1093/bib/bbab160. Code, online app. [DeepImmuno] (ScienceBlog, Featured-Research @ CCHMC 2022)

• K. Jin, D. Schnell, G. Li, N. Salomonis, S. Prasath, R. Szczesniak, B. J. Aronow. CellDrift: Inferring perturbation responses in temporally-sampled single cell data. Briefings in Bioinformatics, 23(5), September 2022. doi:10.1093/bib/bbac324. Code [CellDrift]

• G. Li, B. Song, H. Singh, V. B. S. Prasath, H. L. Grimes, N. Salomonis. Decision level integration of unimodal and multimodal single cell data with scTriangulate. Nature Communications, 14, 406, January 2023. doi:10.1038/s41467-023-36016-y  Biorxiv version doi:10.1101/2021.10.16.464640 [scTriangulate]

• T. A Cazares, F. W. Rizvi, B. Iyer, X. Chen, M. Kotliar, J. A. Wayman, A. Bejjani, O. Donmez, B. Wronowski, S. Parameswaran, L. C. Kottyan, A. Barski, M. T. Weirauch, V. B. S. Prasath, E. R. Miraldi. maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks. PLOS Computational Biology, 19(1), e1010863, January 2023. doi:10.1371/journal.pcbi.1010863. Code [maxATAC]

• N. Gaddis, J. Fortriede, M. Guo, E. E. Bardes, M. Kouril, S. Tabar, K. Burns, M. E. Ardini-Poleske, S. Loos, D. Schnell, K. Jin, B. Iyer, Y. Du, B.-X. Huo, A. Bhattacharjee, J. Korte, R. Munshi, V. Smith, A. Herbst, J. A. Kitzmiller, G. C. Clair, J. Carson, J. Adkins, E. E. Morrisey, G. S. Pryhuber, R. Misra, J. A. Whitsett, X. Sun, T. Heathorn, B. Paten, V. B. S. Prasath, Y. Xu, T. Tickle, B. J. Aronow, N. Salomonis. LungMAP portal ecosystem: Systems-level exploration of the lung. American Journal of Respiratory Cell and Molecular Biology. doi:10.1165/rcmb.2022-0165OC.

• P.-J. Van Camp, V. B. S. Prasath, D. B. Haslam, A. Porollo. MGS2AMR: A gene-centric mining of metagenomic sequencing data for pathogens and their antimicrobial resistance profile. Submitted, February 2023. [MGS2AMR]