Website: https://sites.google.com/site/neelsoumya/
University of Cambridge, UK (2022–Present)
University of Cambridge, UK (2019–2022)
University of Oxford, UK (2016–2018)
CSIRO, Australia (2015–2016)
Harvard Medical School & Broad Institute of Harvard and MIT, USA (2014–2015)
Max Planck Institute for Molecular Physiology, Germany (2013–2014)
Los Alamos National Laboratories, USA (2009–2012)
University of New Mexico, USA (2007–2013)
Cognizant Technology Solutions Ltd., India (2004–2007)
Automation Engineers, India (2003–2004)
My teaching materials and practical guides are used by students and colleagues and are publicly available: https://sites.google.com/site/neelsoumya/teaching An example course I developed is available here: https://cambiotraining.github.io/ml-unsupervised/
Note: In Computer Science, conferences are peer‑reviewed.
I have over 10 years experience in modelling and computational mathematics in different fields of computational biology ranging from immunology and virology to cell biology and metagenomics. I am committed to building a research program that computational biology to different biological systems of clinical and public health significance. I have applied biostatistical techniques to three different disease systems: West Nile virus infection, cancer biology and inflammatory bowel disease. I have published more than 10 papers in journals and peer-reviewed conferences. One of my publications is in the journal Angewandte Chemie (impact factor = 13.7).
\item Ability to work unsupervised and under own initiative is required.
I am able to work unsupervised and on my own initiative.
\item Experience in teaching and/or supporting junior staff is desirable.
I have some experience teaching and mentoring junior staff and students.
\item At least one first/author research article published, in press or accepted for publication in a major peer-reviewed journal is required.
I have multiple first author publications in journals like the Royal Society Interface. I have the ability to publish high quality papers in leading journals \cite{Banerjee2018d,Banerjee2017g,Banerjee2016,Liu2014a,Mallick2019,Graessl2017,Banerjee2020d,Aschenbrenner2020}. I have published more than 10 papers in journals and peer-reviewed conferences. Some of my publications are in journals like \textit{Nature Communications} (impact factor = 11.8), \textit{Gut} (impact factor = 19.8) and \textit{Angewandte Chemie} (impact factor = 13.7).
Some of my most relevant publications are listed below:
Hydroxychloroquine: balancing the needs of LMICs during the COVID-19 pandemic, Soumya Banerjee, \textit{Lancet Rheumatology}, 2(7):385-386, 2020
Aschenbrenner D, Quaranta M, Banerjee S, et al. (2020) Deconvolution of monocyte responses in inflammatory bowel disease reveals an IL-1 cytokine network that regulates IL-23 in genetic and acquired IL-10 resistance (in press) \textit{Gut} (impact factor = 19.8)
Influence of correlated antigen presentation on T cell negative selection in the thymus, Soumya Banerjee, SJ Chapman, \textit{Journal of the Royal Society Interface}, 15(148), 20180311, 2018 (impact Factor = 4.3)
Modelling the effects of phylogeny and body size on within-host pathogen replication and immune response, S. Banerjee, A. Perelson, M. Moses, \textit{Journal of the Royal Society Interface}, 14(136), 20170479, 2017
Estimating biologically relevant parameters under uncertainty for experimental within-host murine West Nile virus infection, S. Banerjee, J. Guedj, R. Ribeiro, M. Moses and A. Perelson, \textit{Journal of the Royal Society Interface}, 13(117), 20160130, 2016
An excitable Rho GTPase signaling network generates dynamic subcellular contraction patterns, M. Graessl, J. Koch, A. Calderon, S. Banerjee, T. Mazel, N. Schulze, J. Jungkurth, A. Koseska, L. Dehmelt, P. Nalbant, \textit{Journal of Cell Biology}, 216(12), 4271-4285, 2017 (impact Factor = 9.7)
A bioorthogonal small-molecule switch system for controlling protein function in cells, P. Liu, A. Calderon, G. Konstantinidis, J. Hou, S. Voss, X. Chen, F. Li, S. Banerjee, J. et al., \textit{Angewandte Chemie}, 53(38), 10049-10055, 2014 (impact factor = 13.7)
Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences, H. Mallick, E. Franzosa, L. McIver, S. Banerjee, A. Sirota-Madi, A. Kostic, C. Clish, H. Vlamakis, R. Xavier, C. Huttenhower, \textit{Nature Communications}, 10(1):3136, 2019 (impact factor = 12.1)
Optogenetic tuning reveals Rho amplification-dependent dynamics of a cell contraction signal network, D. Kamps, J. Koch, V. Juma, E. Campillo, M. Graessl, S. Banerjee, T. Mazel, X. Chen, Y. Wu, S. Portet, A. Madzvamuse, P. Nalbant, L. Dehmelt, \textit{Cell Reports}, 33(9):108467, 2020 (Cell Press publishing group, Impact Factor = 8.1)
%A relevant paper in the field of Computational Medicine (in press in the \textit{Gut) is also listed below \cite{Aschenbrenner2019} % %Aschenbrenner D, Quaranta M, Banerjee S, Ilott N, Jansen J, et al. (2019) Systems-level analysis of monocyte responses in inflammatory bowel disease identifies IL-10 and IL-1 cytokine networks that regulate IL-23. bioRxiv:719492 (under review)
\item Mandatory skills are;
I have experience in stochastic processes. I also have experience in multi-scale simulations using genomic and single-cell sequencing data. These multi-scale simulations were coupled to large amounts of genomic data and were validated experimentally.
\item Additionally, substantial research experience is valued in the following;
I have experience in multi-scale simulations using genomic and single-cell sequencing data. I also have extensive experience in working with genomic datasets.
I also have a lot of experience programming in python (especially building stochastic simulators).
I am also very proficient in latex.
I have mentored PhD students.
\item Ability to manage own workload in an independent way and to deal appropriately with competing priorities.
In my PhD and post-doc, I have initiated two research projects. I have the ability to work independently and deal with competing priorities.
\item A PhD (or equivalent) in a relevant subject such as mathematical, physical or biological sciences
I have completed my PhD in Computer Science from the University of New Mexico, USA.
\item Fellowship of the Higher Education Academy (A/C/I) and professional body membership such as Member of the British Computer Society
I do not have these affiliations. However I am an active member and part of the organizing committee of Artificial Immune Systems.
\item Experience of teaching in Higher Education
I have experience of teaching in Higher Education especially at the Undergraduate and Postgraduate level.
\item Communication and interpersonal skills required.
I have a high-level of inter-personal and communication skills. I have excellent written and verbal communication skills as evidenced by my publications and 5 invited talks and 5 contributed talks.
\item Ability to teach effectively and communicate with audiences and staff working with different technical and education backgrounds required.
I have a high-level of inter-personal and communication skills. I also work extensively with my collaborators in the experimental sciences. I enjoy communicating mathematical ideas, models and statistical results to non-statisticians including biologists and clinicians. I have experience working with domain experts from different fields and communicating results to diverse stakeholders. I have extensive experience working with experimentalists and have wet-lab experience. I am also very passionate about making computational and statistical tools accessible to biologists. To this end I have conducted lectures that demystify computational techniques for experimentalists.
\item Broad experience in curriculum development for health and/or information technologies
I have experience developing curricula for health and information technologies.
\item Demonstrate evidence of the development of innovative teaching techniques that are designed to create interest, understanding and enthusiasm among students; encouraging them to engage in the highest levels of scholarship and achievement.
I am able to develop innovative teaching techniques that will engage students in the classrooms and lead them to the highest levels of academic and professional achievement.
\item The ability to relate to a diverse cohort of students, including prospective, enrolled and graduated students, with the capacity to conceive, initiate and run activities relevant to each of these different student groups.
I have the ability to teach and relate to diverse group of students. I can conceive and implement lessons and activities that can cater to the individual learning needs of the students.
\item A record of achievement in developing curricula and resources that is research led and led to improved student outcomes.
I design student projects that are currently relevant problems in industry. This makes students more employable after graduation.
I have a record of developing curricula that is driven by current industry-standard research that can lead to better employment and learning outcomes for students.
\item Ability to work productively and cordially as part of a team.
I am able to work effectively in teams. I worked in and managed teams while working in industry.
\item An ability to innovate, including the development of new modules
I am able to innovate in teaching in the classroom and contribute to development of new modules
I have the ability to produce high quality curricula and program materials.
I use technology to engage students. These include graphical user interfaces and interactive environments. These tools complement my hands-on teaching style. I encourage my students to play around with computer programs and user interfaces to build interactive prototypes to solve problems in complex systems.
I am very passionate about teaching. I have also co-designed teaching resources with educators to make my teaching broadly accessible to classrooms \cite{Banerjee2019a}.
I also make my teaching resources freely available for use by others \cite{Banerjee2019a}.
A sample of my teaching material is available online
https://osf.io/25gnz/
https://sites.google.com/site/neelsoumya/teaching
I am very passionate about using educational tools for outreach. I regularly review teaching material for a non-profit organization called SIMIODE. My contributions as a reviewer of peer-reviewed course material have been acknowledged. I have also co-designed teaching resources with educators to make my teaching broadly accessible to classrooms \cite{Banerjee2019a}.
A sample of my teaching material is available online
https://www.simiode.org/resources/3206
https://osf.io/25gnz/
\item An excellent understanding of underlying theory and current, industrial practice in software and/or data engineering
I have an excellent understanding of the theory and industrial practice in software engineering, data engineering and data science.
I have worked in industry (in the financial services sector) for Fortune 500 clients.
I also have experience engaging with industry and other diverse stakeholders. I interact with pharmaceutical companies and other industry partners.
I have knowledge of practical issues related to software and data science in industry. I would like to teach students about practices that are relevant in industry.
I would like to design curricula that is driven by current industry relevant problems and practices. This will lead to better employment and learning outcomes for students.
\item An aptitude for teaching, and the skills and judgement needed to teach advanced concepts and techniques to working professionals with a range of experiences and expectations.
I have an aptitude for teaching. I have the skills needed to teach advanced concepts and practical techniques to working professionals.
I have worked in industry and I would like to teach about practical skills that are relevant to professionals.
\item A genuine enthusiasm for teaching and learning, and the ability to work effectively as part of a team of academic and administrative staff responsible for delivery
I am very passionate about teaching, especially skills that can be used in industry. The skills are related to designing and implementing production systems in data science and software.
I have the ability to work in a team of staff responsible for delivery.
\item Experience of software, data, or security engineering in a production context
I have experience working in industry and have designed and implemented software systems running in production on critical financial data.
I also have experience engaging with industry and other diverse stakeholders. I have interacted with pharmaceutical companies and supply chain management companies. I would like to design student projects that are currently relevant to problems faced by industry.
\item An ability to develop a portfolio of external income generation
I have the ability to generate external income by applying for grants from government agencies and industry.
\item A track record of securing research funding grant
I have the ability to raise research funds through grant applications. I have submitted grant applications as a co-principal investigator to GCRF (Global Challenges Research Fund).
I have the ability to independently plan and manage research projects. I have experience making research budgets.
\item Strong industry and community engagement experience. Proven ability to communicate effectively with academic staff, researchers, students, government and health industry professionals
I have experience engaging with industry and other diverse stakeholders. I interact with pharmaceutical companies and other industry partners.
\item A flexible approach to work and the ability to engage with colleagues and scientists from different backgrounds and fields are required.
I believe collaboration is key to progressing science. I collaborate and interact extensively with my colleagues. I work with my colleagues in biostatistics and mathematics to develop new statistical techniques to analyse biological data. I also work extensively with my collaborators in the experimental sciences, especially immunologists, virologists and cell biologists to apply mathematical techniques to their problems.
\item Time management skills required.
I am very adept at managing my time.
\item Well organized with good time management skills
I am very well organized with good time management skills and can effectively prioritise multiple tasks.
\item Post holder may be required to attend courses or relevant international meetings to enable continuous professional development and remain up to date with current developments in the field.
I am able to and willing to attend courses and relevant meetings to develop myself professionally.
\item Flexible approach to work associated with requirements for research involving interdisciplinary techniques is essential, which will require ability to adapt the working schedule to varying hours at a short notice (e.g. late work).
I am able to work in a flexible and adaptive manner to ensure that deliverables and deadlines are met.
\item Evidence of ability to work collaboratively across disciplines.
I believe collaboration is key to progressing science. I collaborate and interact extensively with my colleagues. I work with my colleagues in biostatistics and mathematics to develop new statistical techniques to analyse biological data. I also work extensively with my collaborators in the experimental sciences, especially immunologists, virologists and cell biologists to apply mathematical techniques to their problems.
\item Willingness to continually update knowledge in the specialist area and engage in continuous professional development.
I am willing to continuously update my knowledge in specialist areas and engage in continuous professional development.
\item Strong programming skills, preferably in Python or Java.
I have strong programming skills in Python, R and MATLAB. I am ranked within the top 200 worldwide on MATLAB Central (an online repository for Matlab code contributed by users all over the world). Prior to graduate school, I was a software engineer working in the financial services sector for Fortune 500 clients. Because of this experience, I write well-documented and rigorously tested code.
Examples of my code and open source projects are available at
https://bitbucket.org/neelsoumya/public_open_source_datascience
https://sites.google.com/site/neelsoumya/software