Malvika Sharan


Through Open Science and equitable community practices, research and data science skills should become accessible, adoptable and beneficial for a wider community.

Openness and best practices mean different things in different contexts. These many facets should not be taken as restriction or distraction, but as scientific freedom. You can learn, unlearn, challenge, dismantle and rebuild research infrastructure that prioritises reproducible, ethical and collaborative research for collective benefit.


Scroll down to browse my CV


 

Skills and Competencies

 

o   Exhibited Open Science community leadership and management skills in various capacities. Developed and implemented strategies at an organisational and global scale for Open Science development, project sustainability and community building. (1) I lead The Turing Way, a community-led guide to data science at The Alan Turing Institute. (2) I am a co-founder and co-director of Open Life Science training and mentoring programme (non-profit organisation).  In both projects, I take strategic roles in scoping, development, management, and decision-making. These programmes have together engaged over 600 international researchers to collaborate, develop resources, and integrate open practices in their projects in countries across the Global South and North.

o   Conducted interdisciplinary bioinformatics research as a master’s and PhD researcher in Germany with published open access resources. A background in computational biology with experience developing and maintaining Open Source Python Projects. I also wrote project reports, technical documentation, scientific papers, learning resources, community guides and blog posts, most of which are published under open licenses.

o   Contributed to the EU level efforts to develop and implement computational skills and capacity building through high-profile collaborations, 1:1 consulting and technical support at European Molecular Biology Laboratory (intergovernmental organisation) and ELIXIR Germany (Europe's leading life science organisations for infrastructure and capacity building). I delivered training and outreach programs, and co-authored Open Source Software recommendations for the ELIXIR training platform (2016-2020).

o   Recognised as an expert in community building and open research with several community awards and recognitions. Participated in Open Access and Open Source policy development at organisation levels through team lead for the Open Research Community Building team at The Alan Turing Institute, The Carpentries Code of Conduct Committee chair (2018-), Open Bioinformatics Foundation board member (2019-), Code of Science and Society event fund committee member (2020-), Society of Research Software Engineering trustee (2022-), MetaDocencia Advisory committee (2021-) and EMBL Staff Association (2017-2019).

o   Established collaborations with multiple stakeholders at The Alan Turing Institute. I work closely with the members of the Academic Engagement, National Skills and Strategy team and Research Engineering Group in training and capacity building projects, two of which are funded under the EPSRC’s £10m awards. I am leading the development of Introduction to Data Science for Biomedical Scientists, a Turing-Crick Partnership Project funded under the AI for Science and Government programme. I am a member of Facilitating responsible participation in the data science Interest Group.

o   Designed proposals and received funding to support research, training, and project development at The Alan Turing Institute (>£130,000, in 2020 and 2021), at European Molecular Biology Laboratory - EMBL (£126,000, in 2018 and 2019) and in the Open Life Science project awarded to the team (£577,000, in 2020 and 2021 from Wellcome Trust and Chan Zuckerberg Initiative).

o   Actively promoted and trained researchers in Open Source, Open Access, Open Data, FAIR principles, and participatory research. I delivered six keynotes and plenary/invited talks at international conferences at >40 events. I organised and taught in more than 40 training courses/workshops on a wide range of topics that help scientists develop their skills to make their research open, reproducible, and digitally accessible.

 

Professional Experience

 

September-2019 – Present

Senior Researcher - Open Research, Tools, Practices and Systems and the AI for Science and Government programme (EPSRC funded), The Alan Turing Institute, London, UK.

I lead The Turing Way,  a community-led open science project on data science. I strategically lead its diverse community of >325 contributors who collaborate to share research practices, guidance and recommendations as chapters across five guides of The Turing Way handbook.

 

I lead a team of community managers under the theme Open Research Community Building that aims to establish cross-community collaborations and promote open research in data science across different research programmes.

 

September-2019 – Present

Co-founder, Board of Directors - Open Life Science, a non-profit organisation that offers open science training and mentoring programme, UK.

This program offers an international platform for researchers to learn and apply open science principles in their work to create, lead and sustain relevant projects in their communities.

 

July-2016 – January-2020

Community and Outreach Coordinator - European Molecular Biology Laboratory (EMBL), Bio-IT Project, Heidelberg, Germany.

Bio-IT open source project supports and fosters a community of researchers from six EMBL sites. My role was to lead organisation-wide initiatives to facilitate knowledge exchange, skill-building and networking around bioinformatics and open practices.

 

Deputy Training Coordinator - German Network for Bioinformatics Infrastructure (de.NBI) | ELIXIR-Germany. I represented EMBL at the national level in de.NBI/ELIXIR-Germany. As a deputy training coordinator, I contributed to the development of ELIXIR’s training platform (ELIXIR coordinates bioinformatics infrastructure for researchers Europe-wide).

 

Educational Background

 

May-2012 – June-2016

Ph.D. in Computational Biology, Institute of Molecular Infection Biology, Graduate School of Life Science, University of Würzburg, Würzburg, Germany.

Thesis title: Bio-computational identification and characterisation of RNA-binding proteins in bacteria. Published 10 articles and an Open Source Python Package: https://github.com/malvikasharan/APRICOT.

 

October-2009 – February-2012

M.Sc. in Life Science Informatics, Bonn-Aachen International Center for Information Technology (B-IT), University of Bonn, Bonn, Germany.

Research carried out at the Max Planck Institute for Biology of Aging (MPI-BA), Cologne.

 

July-2005 – June-2008

B.Sc. in Biotechnology, People’s Education Society Institute of Applied Science, Bangalore University, Bangalore, India.

 

Selected Grants & Recognitions

 

o   Internal funding calls at The Alan Turing institute from EPSRC’s additional award for ‘Turing 2.0’, three successful proposals for AI for Science and Government funding and the Turing Online Training grant (total funding £128,000).

o   The Wellcome Trust Open Research fund (£99,999) and Chan Zuckerberg Initiative grant ($575,000) were awarded to Open Life Science to carry out community research, develop open source software training modules and strategic planning for project sustainability (2022-2023).

o   Three short-term grants awarded to the Open Life Science team: Turing Online Training Grant, Code for Science and Society 2021 and The EOSC-Life Training Grant 2020 (total funding £37,000)

o   Community Champions Award - 2022 by JISC (Joint Information Systems Committee, UK)

o   The Turing Way was shortlisted for awards by OpenUK and Open Publishing, and was highly commended by HiddenRef (2021)

o   CogX 2020 Recognising Leadership - Award Co-Winner. Tech Community Leaders Award.

o   Software Sustainability Institute Fellow (2019-) to lead open source efforts for exploring and developing training strategies effective for the low-income research environment.

o   Mozilla Open Leaders 7 and Open Leaders X (2019) training on open source movement-building and mentorship on project development, web literacy and digital inclusion.

o   Open Bioinformatics Foundation Fellowship (2019) to lead discussions and events around policy and practices to enhance diversity in the Open Source and bioinformatics communities.

o   The Carpentries Community Service Award (2018) for setting standards for CarpentryCon and community conferences as a chair of the committee and leading training courses internationally.

o   4 EMBO grants to organise international conferences on protein bioinformatics and systems biology in Austria (2018) and India (2019), and practical courses in Italy (2018) and India (2019).

o   Grants by Fáilte Ireland & University College Dublin for computational events in Ireland (2018)

o   Recipient of Scientific Python (SciPy) Computing Diversity scholarships (2017 and 2018). Chair of SciPy mini symposium on biosciences/bioinformatics (2017-2021).

o   Recipient of the best scientific talk award for the PhD research at ‘Critical Assessment of Functional Annotation’ Special Interest Group at ISMB-ECCB 2015 in Dublin.

 

Community Involvements

 

o   Society of Research Software Engineering Trustee (2022)

o   MetaDocencia Advisory Committee Member (2021-)

o   Code for Science & Society Event Fund Committee member (2020-)

o   Google Season of Docs project host and lead mentor (2020-)

o   Open Bioinformatics Foundation (OBF) Board Member and chair of Event Fellowship (2019-)

o   The Carpentries instructor trainer, mentor, content curator & Code of Conduct Committee (2015-)

o   EMBL Open Science and Open Access event series Chair (2017-2019)

o   Organised and facilitated more than 35 coding and data-handling workshops teaching Python, command line, version control, GitHub project design and literate programming (2016-2020).

o   Organiser and instructor at Computing Skills for Reproducible Research training series (2016-2020)

o   Instructor for a module on using APIs in Python at the Postgraduate Certificate course in Biocuration by the University of Cambridge and EMBL-EBI, Hinxton, UK (2019).

o   Trainer at ‘train-the-trainer’ workshops in Argentina, Germany, Greece, India, South Africa, Sweden, United Kingdom and online for teaching computation skills (2018-2020).

o   Organiser of public events Technical Sessions with Bio-IT & de.NBier, Heidelberg (2017-2018)

o   Co-organiser of Heidelberg Unseminars in Bioinformatics (2016-2019)

o   Co-founder of Würzburg Unseminars in Bioinformatics and Systems Biology (2015)

o   Designed and taught programming course for beginners at Open Source Software writing for researchers by FOSTER, Helmholtz Centre Potsdam, Germany (2015).

o   Speaker of the Doctoral Researchers Council at The University of Würzburg, represented the interests of ECRs at FOSTER-UNESCO Open Science for Doctoral Schools, France (2015)

 

Invited and Selected Talks:

 

o   Keynote at the first Open Science Concordia conference in Montreal 2022 “Open science for enabling reproducible, ethical and collaborative research”.

o   Keynote at the Open Science fair 2021 “Can we reimagine FAIR for Open Science communities”

o   Plenary talk at inaugural Society for Open, Reliable, and Transparent Ecology and Evolutionary Biology conference “The Turing Way Guide to Reproducible, Ethical and Collaborative Research” (2021)

o   Invited talk at FOSS-Backstage “Building a culture of collaboration in open science communities” (2021)

o   Panellist at Declaration of Research Assessment (DORA) event “Assessing Contributions to Research reproducibility and Open Science” (EuroScience Open Forum 2020 and DORA webinar 2021)

o   Guest Lecture and Demo at MIT Experiential Ethics Virtual Field Trip “The Turing Way Guide to Ethical Research” (2020)

o   Keynotes lecture at 'Open Science in Practice' at Eurotech Summer School, Switzerland (2019).

o   Keynote ‘Inclusiveness in Open Science’ at OpenCon, Bern, Switzerland (2018)

 

Chair/co-organiser of international conferences:

 

o   Bioinformatics Open Source Conference hosted by Open Bioinformatics Foundation (online - 2021)

o   The impact of the COVID-19 crisis on women in science at EMBL (online - 2020)

o   4 EMBO conferences and training events in Europe and Asia (2018 & 2019)

o   3 The Carpentries conferences (Dublin - 2018, Manchester - 2019, and online - 2020)

 

Selected Research Articles

 

A complete list of 20+ publications can be found here: https://tinyurl.com/MalvikaSharanPublications

o   Treasure, A. M., Hall, S. M., Lesko, I., Moore, D., Sharan, M., van Zaanen, M., Yehudi, Y., van der Walt, A. (2022). Ten simple rules for establishing a mentorship programme. PLOS Computational Biology, 18(5), e1010015. https://doi.org/10.1371/journal.pcbi.1010015 

o   Yehudi, Y., Whitney, K. S., & Sharan, M. (2020). Enhancing the inclusivity and accessibility of your online calls. OSF Preprints. https://doi.org/10.31219/osf.io/k3bfn

o   Wibberg, D., et. al. (multi-author paper) (2019). The de.NBI/ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR. F1000Research, 8. https://doi.org/10.12688/f1000research.20244.2

o   Sharan, M., Förstner, K. U., Eulalio, A., & Vogel, J. (2017). APRICOT: an integrated computational pipeline for the sequence-based identification and characterization of RNA-binding proteins. Nucleic Acids Res., 45(11), e96–e96. https://doi.org/10.1093/nar/gkx137

o   Tawk, C., Sharan, M., Eulalio, A., & Vogel, J. (2017). A systematic analysis of the RNA-targeting potential of secreted bacterial effector proteins - Scientific Reports, 7(9328), 1–14. https://doi.org/10.1038/s41598-017-09527-0

o   Chowdhury, S. R., Reimer, A., Sharan, M., Kozjak-Pavlovic, V., Eulalio, A., Prusty, B. K., ...Rudel, T. (2017). Chlamydia preserves the mitochondrial network necessary for replication via microRNA-dependent inhibition of fission. J. Cell Biology., 216(4), 1071–1089. https://doi.org/10.1083/jcb.201608063

o   Michaux, C., Holmqvist, E., Vasicek, E., Sharan, M., Barquist, L., Westermann, A. J., ...Vogel, J. (2017). RNA target profiles direct the discovery of virulence functions for the cold-shock proteins CspC and CspE. PNAS, 114(26), 6824–6829. https://doi.org/10.1073/pnas.1620772114

o   García-Betancur, J.-C., Goñi-Moreno, A., Horger, T., Schott, M., Sharan, ...Lopez, D. (2017). Cell differentiation defines acute and chronic infection cell types in Staphylococcus aureus. eLife. https://doi.org/10.7554/eLife.28023

o   Maudet, C., Mano, M., Sunkavalli, U., Sharan, M., Giacca, M., Förstner, K. U., & Eulalio, A. (2014). Functional high-throughput screening identifies the miR-15 microRNA family as cellular restriction factors for Salmonella infection - Nature Communications. 5(4718), 1–13. https://doi.org/10.1038/ncomms5718