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\begin{cv}{\huge \it \bfseries Rohit Farmer}
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\hfill \url{rohit.farmer@gmail.com},  \url{https://rohitfarmer.com}, \url{+1 (314)-255-6763}, \url{Bethesda, } \url{MD, USA}

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\begin{cvlist}{Research Summary}
	\item I have eight years of post-Ph.D. interdisciplinary research experience, applying computational methods at the intersection of biology, chemistry, and medicine. In my current position at CHI, NIH, I am building tools for high-dimensional analysis of flow/mass cytometry and SomaScan data and establishing an analysis pipeline for spatial transcriptomics. In the past, I have worked on applying deep learning to large-scale molecular data to understand drug bioactivation and toxicity. I have also worked with protein structure/complex prediction, modeling protein-protein interactions, molecular dynamics simulations, virtual screening, and sequence analysis. \end{cvlist}
}

\begin{cvlist}{Research \& Teaching Experience}
        \item[2019-\emph{now}] Computational Biologist \hfill Medical Science \& Computing, USA\\ \hspace*{\fill}On site at the National Institutes of Health (NIH)\\ \hspace*{\fill} NIH Center for Human Immunology, Inflammation, and Autoimmunity (CHI)
	\item[2018-2019] Postdoctoral Research Associate \hfill Washington University in St. Louis, USA\\  \hspace*{\fill} Department of Pathology and Immunology
	\item[2016-2018] Associate Editor \hfill The Allahabad Journal of Science and Technology \\  \hspace*{\fill} (Formerly The Allahabad Farmer)
        \item[2015-2018] Assistant Professor \hfill Sam Higginbottom University of Agri., Tech. and Sci. (SHUATS), India\\  \hspace*{\fill} Department of Computational Biology and Bioinformatics (CBBI)
        \item[2008-2011] Assistant Professor \hfill Sam Higginbottom Institute of Agri., Tech. and Sci. (SHIATS), India\\  \hspace*{\fill} Department of Computational Biology and Bioinformatics (CBBI)
\end{cvlist}

\begin{cvlist}{Administrative Experience}
	\item[2015-2016] International Training Associate \hfill SHUATS, India \\  \hspace*{\fill} Directorate of International Education and Training
\end{cvlist}

\begin{cvlist}{Teaching Assignments}
	\item[2008] Molecular Genetics (UG, MBGE-441) \hfill SHUATS, India 
	\item[2009-2011] Biomolecular Modelling (UG, BI-605)  \hfill SHUATS, India
	\item[2012-2014] \emph{Assisted in teaching} Physical Biochemistry (UG, Bio143) \hfill University of Birmingham, UK
	\item[2015-2017] Concepts of Bioinformatics (UG, CBBI-502) \hfill SHUATS, India 
	\item[2015-2017] Structural Bioinformatics (UG, CBBI-601)  \hfill SHUATS, India 
	\item[2015-2017] Fundamentals of Bioinformatics and Information Technology (PG, CBBI-701) \hfill SHUATS, India
	\item[2015-2017] Computer Aided Drug Designing (PG, CBBI-803) \hfill SHUATS, India
\end{cvlist}

\begin{cvlist}{Education}
	\item[2011-2015] Doctor of Philosophy (Ph.D.) \hfill University of Birmingham, UK \\ Biosciences
	\item[2008-2010] Master of Technology (M.Tech.) \hfill Sam Higginbottom Institute of Agri., Tech. and Sci. (SHIATS), India  \\ Bioinformatics \emph{CGPA 9.35/10; Silver Medal}
	\item[2004-2008] Bachelor of Technology (B.Tech.) \hfill Allahabad Agricultural Institute, India  \\ Biotechnology \emph{CGPA 8.41/10}
\end{cvlist}

\begin{cvlist}{Certifications \& Licenses}
    \item[2021] Amateur Radio Technician Class - KC3SNU \hfill Federal Communications Commission, USA
    \item[2019] Deep Learning with Python and Keras \hfill Udemy
    \item[2019] Python for Data Science and Machine Learning Bootcamp \hfill Udemy
    \item[2017] Algorithms for DNA Sequencing \hfill Johns Hopkins University, Coursera
	\item[2017] Python for Genomic Data Science \hfill Johns Hopkins University, Coursera
\end{cvlist}

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\begin{cvlist}{Awards \& Achievements}
	\item[2014] Travel grant, $28^{th}$ Annual Symposium of The Protein Society, USA \hfill Biochemical Society
	\item[2013] Travel grant, $15^{th}$ EMBL PhD Symposium, Germany \hfill EMBL
	\item[2013] Travel grant, ISMB/ECCB'13, Germany \hfill National Science Foundation
	\item[2013] George Parks travel grant,  Molecular Perspectives On Protein-Protein Interactions, Poland \hfill University of \\ \hspace*{\fill} Birmingham
	\item[2012] Travel grant, ECCB'12, Switzerland \hfill Swiss Foundation for Excellence and \\ \hspace*{\fill} Talent in Biomedical Research
	\item[2011-2014] PhD scholarship \hfill The Darwin Trust of Edinburgh
	\item[2010] Silver medal in M.Tech. Bioinformatics \hfill SHIATS
\end{cvlist}

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\begin{cvlist}{Scientific Skills}
	\item[\textbf{Computational Biology:}] Flow/mass cytometry, SomaScan and spatial transcriptomics data analysis, molecular structure prediction, molecular docking, molecular dynamics simulation, bioinformatics
	\item[\textbf{Experimental Biology:}] PCR, Gibson assembly, restriction digestion, plasmid transformation, microbiology techniques, HPLC
    \item[\textbf{Data Science \& Machine Learning:}] Data wrangling \& visualization, feature engineering, dimensionality reduction, supervised \& unsupervised learning, linear \& mixed-effects modeling, deep-learning $ \sim $ Tidyverse, Lme4, NumPy, Pandas, SciPy, Matplotlib, Seaborn, Plotly, Scikit Learn, Keras, TensorFlow
	\item[\textbf{Operating Systems:}] Linux, Mac OS X, MS Windows
	\item[\textbf{Computer Languages:}] R, Python, Perl, C++, \LaTeX, HTML, CSS, Java Script
	\item[\textbf{Database:}] SQLite, Neo4J
	\item[\textbf{HPC:}] SLURM, PBS
	\item[\textbf{Containers \& VMs:}] Docker, Singularity, Oracle Virtual Box
	\item[\textbf{VCS:}] Git, Mercurial
\end{cvlist}

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\begin{cvlist}{Transferable Skills Training}
	\item[2018] Mentorship Training Program \hfill Washington University in Saint Louis, USA
	\item[2018] Mentoring Undergraduate Research \hfill Washington University in Saint Louis, USA
	\item[2012] Leading Academics, Leadership development program \hfill University of Birmingham, UK
	\item[2012] One day course on Poster Presentations: Planning the Content \hfill University of Birmingham, UK
	\item[2012] Talent Pool, Training program on entrepreneurship \hfill University of Birmingham, UK
	\item[2012] One day course on Speed Reading \hfill University of Birmingham, UK
	\item[2011] One day course on Time Management \hfill University of Birmingham, UK
\end{cvlist}

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\begin{cvlist}{Conferences Attnded \& Organised}
    \item[2022] CSHL Biological Data Science, Virtual \hfill Poster Presentation 
    \item[2021] CSHL Systems Immunology, Virtual \hfill Poster Presentation 
    \item[2020] CSHL Biological Data Science, Virtual \hfill Poster Presentation 
    \item[2019] Symposium on Personal Control of Genomic Data for Research, USA \hfill Participant 
    \item[2019] FOCIS 2019, USA \hfill Participant
    \item[2015] National Conference on Bioinformatics Panorama in Agriculture and Health, India \hfill Sponsor Liaison
	\item[2014] $1^{st}$ RSG-UK Student Symposium on Computational Biology and Life Sciences, UK \hfill Secretary
	\item[2014] Synthetic Biology of Antibiotic Production II, Spain \hfill Short Talk
	\item[2014] The $28^{th}$ Annual Symposium of the Protein Society, USA, \hfill Poster Presentation
	\item[2013] $15^{th}$ EMBL PhD Symposium, Germany \hfill Short Talk
	\item[2013] ISMB/ECCB'13, Germany \hfill Poster Presentation
	\item[2013] Molecular Perspectives On Protein-Protein Interactions, Poland \hfill Poster Presentation
	\item[2012] $11^{th}$ European Conference on Computational Biology, Switzerland \hfill Poster Presentation
	\item[2012] $3^{rd}$ BEAR Postgraduate Conference on Research Computing, UK \hfill Secretary and Sponsor Liaison
	\item[2010] The Eighth Asia Pacific Bioinformatics Conference, India \hfill Poster Presentation
	\item[2009] National Workshop on Functional Genomics and Proteomics, India \hfill Participant
	\item[2009] International Conference on Open Source for Computer Aided Drug Discovery, India \hfill Poster Presentation
\end{cvlist}

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\begin{cvlist}{Professional Memberships}
	\item[2013-2014] The Protein Society
	\item[2012-2015] International Society for Computational Biology (ISCB)
	\item[2012-2015] Biochemical Society
\end{cvlist}

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\begin{cvlist}{Extra Curricular Positions Held}
	\item[2013-2014] Co-Founder and Secretary, Regional Student Group, UK \hfill Student Council, ISCB
	\item[2011-2012] Secretary, Bharat Parivar, Guild of Students \hfill University of Birmingham
	\item[2009-2010] Vice president for Society of Biotechnology \hfill SHIATS
\end{cvlist}

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\begin{cvlist}{Community Involvement}
        \item[2019] Reviewed 1 research article for MEEGID - Infection, Genetics and Evolution.
        \item[2020] Reviewed 1 research article for Biophysical Journal.
        \item[2020-2023] Reviewed 8 research articles for the Journal of Biomolecular Structure \& Dynamics.
        \item[2021-2022] Reviewed 7 research articles for ACS Omega.
        \item[2021] Reviewed 1 research article for Textile Research Journal.
        \item[2022] Contributed curated datasets for data science education and advancement at \url{https://www.kaggle.com/rohitfarmer}.
        \item[2022-\emph{now}] Built and maintained \url{https://www.dataalltheway.com}, a tutorial website with concepts, methods, and example code on data science, statistics, and machine learning.
\end{cvlist}

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\begin{cvlist}{Software Developed}
	\item {\begin{itemize}
			\item{\bf HDStIM}: High Dimensional Stimulation Immune Mapping \url{https://niaid.github.io/HDStIM/}
                \end{itemize}}
\end{cvlist}

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\begin{cvlist}{Publications}
\item {\begin{itemize}\item{\bf Rohit Farmer}. Modelling polyketide synthases and related macromolecular complexes. \emph{PhD Thesis. University of Birmingham,} 2015. \url{https://etheses.bham.ac.uk/id/eprint/5909/} \end{itemize}}

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\item {\textbf{Book Chapter}}
\item {\begin{itemize}\item{\bf Farmer R.}\footnote{Corresponding Author}, Thomas C. M., and Winn P. J. Modelling Polyketide Synthases and Similar Macromolecular Complexes. \emph{In: Wadhwa G., Shanmughavel P., Singh A., Bellare J. (eds) Current trends in Bioinformatics: An Insight. Springer, Singapore,} 2018, 121-144. \url{https://doi.org/10.1007/978-981-10-7483-7_7} \end{itemize}}

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\item {\textbf{Submitted Peer Reviewed Article(s)}}
\item {\begin{itemize}
	\item  2022 - \textbf{Farmer R.}, Apps R., and Tsang J. S. Multiparameter stimulation mapping of signaling states in single pediatric immune cells reveals heightened tonic activation during puberty.

	\item  2022 -  Apps R., Biancotto A., Candia J., Kotliarov Y., Perl S., Cheung F., \textbf{Farmer R.}, Mule M. P., Chen J., Martins A. J., Shi R., Zhou H., Bansal N., Schum P., Olnes M. J., Milanez-Almeida P., Han K. L., Sellers B. A., Cortese M., Hagan T., Rouphael N., Pulendran B., King L., Manischewitz J., Khurana S., Golding H., Most R. G. van der, Dickler H. B., Germain R. N., Schwartzberg P. L., and Tsang J. S. High dimensional dynamic response pattern discovery reveals acute and persistent impacts of H5N1 vaccination with and without adjuvant. 
\end{itemize}}

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\item {\bf Published Peer Reviewed Articles}
\item {\textit{Google Scholar: h-index 11, i10-index 12,} \url{http://bit.ly/rf_cite}}
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\nocitejournal{Flynn2021}
\nocitejournal{Farmer2019}
\nocitejournal{Konda2018}
\nocitejournal{Dhusia2018}
\nocitejournal{Lodhi2015}
\nocitejournal{Lodhi2014}
\nocitejournal{Khanim2014}
\nocitejournal{Kumar2013}
\nocitejournal{Haines2013}
\nocitejournal{Singh2013}
\nocitejournal{Paital2013}
\nocitejournal{Kumari2012}
\nocitejournal{Lodhi2012}
\nocitejournal{Gautam2012}
\nocitejournal{Fazil2012}
\nocitejournal{Paital2011}
\nocitejournal{singh2011prediction}
\nocitejournal{Jeyakumar2011}
\nocitejournal{yadav2011hsv}
\nocitejournal{yadav2011tlr}
\nocitejournal{gautam2010drug}
\nocitejournal{Farmer2010}
\item{\bibliographyjournal{citations} }

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\item {\textbf{Preprints}}
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\item Mul{\`e}, M. P.,  Martins, A. J., Cheung, F., \textbf{Farmer, R.}, Sellers, B., Quiel, J. A., Jain, A., Kotliarov, Y., Bansal, N., Chen, J., Schwartzberg, P. L., Tsang, J. S. Multiscale integration of human and single-cell variations reveals unadjuvanted vaccine high responders are naturally adjuvanted. \emph{medRxiv}, 2023.03.20.23287474; doi: \url{https://doi.org/10.1101/2023.03.20.23287474}
\item \textbf{Farmer R.}, Apps R., Quiel J., Sellers B. A., Cheung F., Chen J., Mukherjee A., McGuire P. J., and Tsang J. S. Multiparameter stimulation mapping of signaling states in single pediatric immune cells reveals heightened tonic activation during puberty. \emph{bioRxiv}, 2022.11.14.516371; doi: \url{https://doi.org/10.1101/2022.11.14.516371} 
\item Rahman F., \textbf{Farmer, R.}, Das S., Vayani F. and Hassan M. Highlights of the $1^{st}$ Student Symposium of the ISCB RSG UK. \emph{F1000Research}, 4:154, 2015. \url{https://doi.org/10.12688/f1000research.6616.1} 
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