Telling stories with just four letters

My vision

I am a 5th year Ph.D. candidate specializing in computational biology, single-cell sequencing analysis to investigate the evolution of the primate brain.

My vision is to push the envelope forward in translational research using multiple bioinformatic datatypes – omics, imaging and proteomics. I leverage a strong molecular and cellular biological foundation and several years of programming experience, data analysis and communication skills to effectively liaise between the dry and wet labs to deliver impactful results.

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Programming Languages and Environments

C, C++, Shell, R, Python, Arduino, HTML, Javascript, SQL

HPC, Google Colab, AWS, CUDA, slurm, snakemake, nextflow, RStudio, MATLAB, Jupyter notebook, COMSOL

Computational Biology tools and skills

Various omic data analysis – DNASeq, RNASeq, ATACSeq, WGBSeq.

DESeq2, edgeR, biopython, Seurat, scanpy, STAR, CellChat, CellBender, Geneious, data sharing across public repositories.

Data Analysis skills

Modelling and simulation, Hypothesis testing, Statistical modeling, Convex optimization, linear and non-linear dimensionality reduction, deep neural network design and training, Gradient descent, Finite Element Methods, Numerical methods, Computational Fluid Dynamics

Laboratory Skills

PCR and primer design, DNA and RNA extration, Next Generation Sequencing (NGS) sample preparation (bulk), Genomic integration via recombination, plasmid design and subcloning, BSL2 cell culture and maintenance,

My publications

Hasnain, A., Balakrishnan, S., Joshy, D. M., Smith, J., Haase, S. B., & Yeung, E. (2023). Learning perturbation-inducible cell states from observability analysis of transcriptome dynamics. Nature Communications, 14(1), 3148.

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Hasnain, A., Balakrishnan, S., Joshy, D.M., Haase, S.B., Smith, J. and Yeung, E., 2022. Learning transcriptome dynamics for discovery of optimal genetic reporters of novel compounds. bioRxiv, pp.2022-05.

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Parada, C., Banavar, S.P., Khalilian, P., Rigaud, S., Michaut, A., Liu, Y., Joshy, D.M., Campàs, O. and Gros, J., 2022. Mechanical feedback defines organizing centers to drive digit emergence. Developmental Cell, 57(7), pp.854-866.

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Balakrishnan, S., Hasnain, A., Boddupalli, N., Joshy, D.M., Egbert, R.G. and Yeung, E., 2020, July. Prediction of fitness in bacteria with causal jump dynamic mode decomposition. In 2020 American Control Conference (ACC) (pp. 3749-3756). IEEE.

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Joshy, Dennis Manjaly. Continuum Simulations of Multi-Cellular Tumor Spheroids Using Two-phase Flow Models. University of California, Santa Barbara, 2019.

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Feel free to reach out, I’d love to hear from you.

dennis.joshy@gmail.com