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Last updated on May, 2018


EDUCATION

Johns Hopkins University School of Medicine, USA; 8/2012 – 1/2018
Ph.D. in Biophysics
Advisor: Prof. Taekjip Ha

Indian Institute of Technology, Kharagpur; 7/2007 – 4/2012
Integrated BS+MS in Chemistry
Advisor: Prof. Swagata Dasgupta

 

RESEARCH EXPERIENCE

Postdoctoral researcher; 3/2018 – present
Department of Biology, University of California, San Diego, USA
Principal investigator: Prof. Elizabeth Villa
• Development and application of cryo-electron microscopy for cellular structural biology.

Ph.D. researcher;  1/2013 – 1/2018
Department of Biophysics, Johns Hopkins University School of Medicine, USA transferred from Center for Biophysics & Quantitative Biology, University of Illinois at Urbana-Champaign, USA
Principal investigator : Prof. Taekjip Ha
• Single molecule imaging and biochemical assays to characterize molecular mechanisms and specificity of DNA targeting by CRISPR-Cas9 and CRISPR-Cpf1 family of RNA-guided endonucleases which are being widely used for various genome engineering applications. Collaborated with Prof. Jennifer A. Doudna ( UC Berkeley) and Prof. Scott Bailey (Johns Hopkins School of Public Health).
• Collaboration with Prof. Venigala B. Rao (CUA) to characterize mechanism of coordination between different subunits of bacteriophage T4 DNA packaging motor using single molecule imaging.
• Design and implementation of data-analysis packages for single molecule studies.

Visiting research assistant; 6/2012 – 8/2012          
Principal investigator : Prof. Robert Best (now at NIH), University of Cambridge, UK
Theoretical Biophysics - Construction of multi-dimensional free energy surfaces of protein folding.

Master thesis student; 8/2011 – 3/2012          
Principal investigator : Prof. Swagata Dasgupta, Indian Institute of Technology, Kharagpur
Computational Biophysics - Modeling of amyloid beta multimers via protein structure prediction (Rosetta).

Visiting research assistant; 5/2011 – 7/2011   
Principal investigator : Prof. Collin M. Stultz, Massachusetts Institute of Technology, USA
• Computational Biophysics – Construction of structural library of intrinsically disordered amyloid beta protein, using molecular dynamics simulations, for creation of its conformational ensembles. 

Visiting research assistant; 11/2010 – 12/2010      
Principal investigator : Prof. Anne S. Ulrich, Karlsruhe Institute of Technology, Germany
• Solid State NMR - Synthesis of membrane active peptides and evaluation of its alignment in lipid bilayer from NMR (Nuclear Magnetic Resonance) signals of 19F labels on the peptides.

Visiting research assistant; 5/2010 – 7/2010          
Principal investigator : Prof. Martin Gruebele, University of Illinois at Urbana-Champaign, USA
• Protein Folding - Expression and purification of FRET probe labeled protein construct for its use in fast relaxation imaging following temperature shocks.

Research intern; 11/2009 – 12/2009
Unilever, Bangalore, India
• Investigation of binding affinity of tea polyphenols with milk caseins.

Research intern; 4/2009 – 7/2009
General Electric, Bangalore, India
• Synthesis of radio labeled indoles & amides with high binding affinity to certain specific receptors found in human nervous system for its use in PET (Positron Emission Tomography) imaging.

 

PUBLICATIONS

•  [9] Digvijay Singh, Yanbo Wang, John Mallon, Olivia Yang, Jingyi Fei, Anustup Poddar, Damon Ceylan, Scott Bailey, Taekjip Ha. "Mechanism of improved specificity of engineered Cas9s revealed by single molecule analysis". Nature Structural and Molecular Biology (2018)Pre-print

•  [8] Digvijay Singh, John Mallon, Anustup Poddar, Yanbo Wang, Ramreddy Tipanna, Olivia Yang, Scott Bailey, Taekjip Ha. "Real-time observation of DNA target interrogation and product release by RNA-guided endonuclease CRISPR-Cpf1". PNAS (2018). Pre-print

•  [7] Digvijay Singh, Taekjip Ha. "Understanding the molecular mechanism of CRISPR toolbox using single-molecule approaches". ACS Chemical Biology (2018). 

•  [6] Boyang Hua, Yanbo Wang, Kyu Young Han, Seongjin Park, Digvijay Singh, Jin H. Kim, Wei Cheng, Taekjip Ha. "Single-molecule centroid localization algorithm improves the accuracy of fluorescence binding assays". Biochemistry (2018)

•  [5] Li Dai, Digvijay Singh, Reza Vafabakhsh, Marthandan Mahalingam, Vishal Kottadiel, Yann Chemla, Taekjip Ha, Venigalla B Rao. "Mechanism of coordination of the bacteriophage T4 DNA packaging motor analyzed by real-time single molecule fluorescence assay". Manuscript in preparation.

•  [4] Digvijay Singh, Samuel H. Sternberg, Jingyi Fei, Jennifer A. Doudna, Taekjip Ha “Real-time observation of DNA recognition and rejection by the RNA-guided endonuclease Cas9”. Nature Communications. (2016). Pre-print

•  [3] Jingyi Fei, Digvijay Singh, Qiucen Zhang, Seongjin Park, Divya Balasubramanian, Ido Golding, Carin K. Vanderpool, Taekjip Ha. “Determination of in vivo target search kinetics of regulatory non-coding RNA”. Science. (2015).

•  [2] Boyang Hua, Kyu Young Han, Ruobo Zhou, Hajin Kim, Xinghua Shi, Sanjaya C. Abeysirigunawarden, Ankur Jain, Digvijay Singh, Vasudha Aggarwal, Sarah A. Woodson, Taekjip Ha. “An improved surface passivation method for single-molecule Studies”. Nature Methods. (2014).

•  [1] A. Dhar, K. Girdhar, D. Singh, S. Ebbinghaus and M. Gruebele, “Different protein stability and folding kinetics in the nucleus, endoplasmic reticulum, and cytoplasm of living cells”. Biophys. J. 101, 421-430 (2011).



 

CONFERENCE PROCEEDINGS

•  Yanbo Wang, Digvijay Singh, John Mallon, Boyang Hua, Scott Bailey, Taekjip Ha. “Simultaneous Real-Time Observation of DNA Unwinding and Nuclease Domain Activation in Cas9-RNA-DNA Complex via Three-Color Single Molecule FRET”. Biophysical Society Meeting (2018).

Digvijay Singh, Yanbo Wang, John Mallon, Samuel H. Sternberg, Olivia Yang, Jingyi Fei, Anustup Poddar, Damon Ceylan, Jennifer A. Doudna, Scott Bailey, Taekjip Ha. "Mechanistic basis of the specificity improving mutations of Engineered Cas9s". NCI RNA Biology (2017).

Digvijay Singh, Yanbo Wang, John Mallon, Samuel H. Sternberg, Olivia Yang, Jingyi Fei, Anustup Poddar, Damon Ceylan, Jennifer A. Doudna, Scott Bailey, Taekjip Ha. "Mechanistic basis of the specificity improving mutations of Engineered Cas9s". Chesapeake Bay Area Single Molecule Meeting (2017).

Digvijay Singh, Samuel H. Sternberg, Jingyi Fei, Jennifer A. Doudna, Taekjip Ha. "Real-time observation of DNA recognition and rejection by the RNA-guided endonuclease Cas9". Bayview Research Symposium (2017).

• Li Dai, Digvijay Singh, Reza Vafabakhsh, Marthandan Mahalingam, Vishal Kottadiel, Yann Chemla, Taekjip Ha, Venigalla B Rao. "Mechanism of coordination of the bacteriophage T4 DNA packaging motor analyzed by real-time single molecule fluorescence assay". Biophysical Society Meeting (2016).

Digvijay Singh, Samuel H. Sternberg, Jingyi Fei, Jennifer A. Doudna, Taekjip Ha. "Real-time observation of DNA recognition and rejection by the RNA-guided endonuclease Cas9". Biophysical Society Meeting (2016).

• Boyang Hua, Ruobo Zhou, Hajin Kim, Xinghua Shi, Ankur Jain, Digvijay Singh, Vasudha Aggarwal, Taekjip Ha. "An improved surface passivation method for single-molecule studies". Biophysical Society Meeting (2014).

• Seongjin Park, Sultan Doǧanay, Jingyi Fei, Digvijay Singh, Taekjip Ha. "Super-resolution imaging of immune response proteins against viral infection". Biophysical Society Meeting (2014).

• Jingyi Fei, Digvijay Singh, Qiucen Zhang, Seongjin Park, Ido Golding, Carin K Vanderpool, Taekjip Ha. "Watching gene regulation by small RNA in bacteria with super-resolution Imaging". Biophysical Society Meeting (2013).

• Jingyi Fei, Seongjin Park, Digvijay Singh, Yanxin Liu, John E. Stone, Klaus Schulten, Kannanganattu V.Prasanth and Taekjip Ha. "Organization of long non-coding RNAs in nuclear bodies revealed by super resolution imaging". EMBO | EMBL Symposia: The Complex Life of mRNA (2012).

 

SELECTED PUBLIC PRESENTATIONS

• Digvijay Singh. "Role of co-factors in Rhodopsin: An action potential story of vision". Wednesday Morning Seminar Series, Biophysics, JHMI (2017). Literature Survey.

• Digvijay Singh. "DNA targeting by CRISPR-Cas at the single molecule level". Student Evening Seminar Series, Biophysics, JHMI (2017).

• Digvijay Singh. "Investigation of DNA binding, nucleolysis and product release specificity of RNA guided endonuclease CRISPR-Cpf1 family reveals important differences from Cas9-RNA". Biophysical Society Meeting (2017).

• Digvijay Singh. "Real-time observation of DNA recognition and rejection by the RNA-guided endonuclease Cas9”. Physics of Living Systems Conference, Arlington, VA (2015) .

• Digvijay Singh. "Real-time observation of DNA recognition and rejection by the RNA-guided endonuclease Cas9”. Biophysical Society Meeting (2015).

• Digvijay Singh. "Real-time observation of DNA recognition and rejection by the RNA-guided endonuclease Cas9”. Center for Physics of Living Cells Symposium, University of Illinois (2015).

 

TEACHING and MENTORING EXPERIENCE

Mentor; Fall 2014-present
• Directly mentored one undergraduate and two graduate students.

Instructor; 2013-2015
Center for the Physics of Living Cells (CPLC) summer schools, University of Illinois at Urbana-Champaign, USA

Teaching assistant; 2014-2015
Advanced Biophysics course (smFRET module), Department of Physics, University of Illinois at Urbana-Champaign, USA.

 

PROFESSIONAL SERVICE

Reviewer for : Proceedings of the National Academy of Sciences, Cellular and Molecular Life Sciences, Springer Books.

 

HONORS, AWARDS and FINALIST POSITIONS

• Lola Ellis Robertson Endowed Scholarship; 2017

• Graduate Travel Award, Department of Biophysics, JHMI; 2017

• Biophysical Society Education Travel Award; 2017

• Finalist of International HHMI fellowship; 2015

• INSPIRE fellowship by Government of India; 2008-12

• Department nominee for the international Weintraub Graduate Student Award; 2018 (results not announced)

 

PROFESSIONAL SOCIETY MEMBERSHIPS

• Biophysical Society

 

MISCELLANEOUS

Summer colloquium; Optical Microscopy & Imaging in the Biomedical sciences-2017
Marine Biological Laboratory, University of Chicago

Consultant; Spring 2015
Illinois Business Consulting


*Some additional details can be found in my LinkedIn profile.