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Hire Dr. Rudra P.

United States

USD 40 /hr

Expert in bulk/single cell RNA-seq, Molecular modeling and simulation , virtual drug design, and Machine learning.

Profile Summary

1. Expert in Big Data Engineering (Hadoop, Hive, SQL, Spark, Scala, AWS). 2. Analyze microarrays, next-generation sequencing (NGS) bulk and single-cell RNA seq, RT-qPCR, metabolites, lipidomic, and Hi-C data. 3. Experience in single-cell data pre-processing and mapping pipeline using cellranger and analysis pipeline using Seurat (most preferred), Scanpy, Monocle, Harmony, DubletFinder, Scrublet, and other cell annotation packages (Garnett, CHETAH). 4.Experience in using various mapping tools like Bowtie2, BWA, STAR, Kallisto, etc. and differential analysis tools like Limma-voom, Deseq2, edgeR. Choosing the best one for given condition. 5. More than five years of training in molecular modeling, molecular dynamic simulations (Modeller, Rosetta, All-atom and Coarse-grained in NAMD/GROMACS platform), force-field generation for designed molecules, free energy estimation, molecular docking, and virtual screening (Vina/Auto-dock (rigid/flexible)). Expertise in developing analysis script in TCL and Python for simulation trajectories. Expert in visualizing and rendering trajectories in VMD. 6.Highly experienced in running computational jobs in Unix/Linux-based clusters (SLURMs) and stand-alone servers. Experienced in creating virtual computing environments using the Anaconda platform. 7. Good knowledge of statistical tools using Python (scipy, scikit-learn) and R packages. Experience of using scripting languages like bash, awk, tcl, perl in day-to-day computational pipelines. 8. Expertise in scientific draft writing, producing presentable/publishable high-quality figures using ggplot2, matplotlib and seaborn packages.

Subject Matter Expertise

• ★ Big Data Analytics
• ★ Deep Learning
• ★ Bioinformatics
• ☆ Biophysics
• ☆ Data Analysis
• ☆ Machine Learning

Services

• Writing
• Research
• Data & AI

Writing Technical Writing

Research User Research

Data & AI Predictive Modeling, Statistical Analysis, Algorithm Design-Non ML, Data Visualization, Data Processing

Work Experience

Data Engineer

The University of Arizona

January 2022 - Present

PHD Student

Florida International University

2015 - Present

Postodoctoral researcher

Johns Hopkins University

January 2021 - January 2022

Education

Ph.D. (Physics)

FIU

August 2015 - November 2020

Certifications

• Deep Learning

  deeplearning.ai

  https://www.coursera.org/account/accomplishments/specialization/certificate/PGPWLR324HSN

  June 2020 - Present

Publications

JOURNAL ARTICLE

Rudramani Pokhrel, Prem Chapagain, Jessica Siltberg-Liberles(2020). Potential RNA-dependent RNA polymerase inhibitors as prospective therapeutics against SARS-CoV-2 . Journal of Medical Microbiology. Microbiology Society

Kristen A. Johnson, Rudramani Pokhrel, Melissa R. Budicini, Bernard S. Gerstman, Prem P. Chapagain, Robert V. Stahelin(2020). A Conserved Tryptophan in the Ebola Virus Matrix Protein C-Terminal Domain Is Required for Efficient Virus-Like Particle Formation . Pathogens. 9. (5). p. 402. {MDPI} {AG}

Kristen Johnson, Rudramani Pokhrel, Melissa Budicini, Bernard S. Gerstman, Prem Chapagain, Robert Stahelin (2020). A Conserved Tryptophan in the Ebola Virus Matrix Protein C-Terminal Domain Is Required for Efficient Virus-Like Particle Formation . Pathogens.

Rudramani Pokhrel, Nisha Bhattarai, Prabin Baral, Bernard S. Gerstman, Jae H. Park, Martin Handfield, Prem P. Chapagain(2019). Molecular mechanisms of pore formation and membrane disruption by the antimicrobial lantibiotic peptide Mutacin 1140 . Physical Chemistry Chemical Physics. Royal Society of Chemistry ({RSC})

Rudramani Pokhrel, Elumalai Pavadai, Bernard S. Gerstman, Prem P. Chapagain(2019). Membrane pore formation and ion selectivity of the Ebola virus delta peptide . Physical Chemistry Chemical Physics. Royal Society of Chemistry ({RSC})

Pokhrel,Rudramani and Sompornpisut,Pornthep and Chapagain,Prem and Olson,Brian and Gerstman,Bernard and Pandey,R. B. (2018). Domain rearrangement and denaturation in Ebola virus protein VP40 . AIP Advances. 8. (12). p. 125129.

Pokhrel, Rudramani and Gerstman, Bernard S. and Hutcheson, Joshua D. and Chapagain, Prem P.(2018). In Silico Investigations of Calcium Phosphate Mineralization in Extracellular Vesicles . The Journal of Physical Chemistry B. 122. (14). p. 3782-3789.

Jeevan B. GC and Rudramani Pokhrel and Nisha Bhattarai and Kristen A. Johnson and Bernard S. Gerstman and Robert V. Stahelin and Prem P. Chapagain(2017). Graphene-VP40 interactions and potential disruption of the Ebola virus matrix filaments . Biochemical and Biophysical Research Communications. 493. (1). p. 176 - 181.