• Hi!
    I'm Sandeep

    A postdoctoral researcher, working on understanding pattern formation in biological systems.

  • I am
    a researcher

    working on discovering patterns in biological systems.

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What I do?

What I do?

I am currently working on identifying the signaling context and mechanics regulating the shape, size and population dynamics of intestine epithelium (IE) and formation of tumor in IE. Understanding how IE generate and regain its shape/size and population composition (i.e., proportion of different types of cells) is the focus of my current project. To achieve my research objectives, I combine methods from computational statistical mechanics with intestine organoid-based experimental framework. This integrative approach allows me to study the physico-chemical regulation of IE in single unified framework and also help me in handling with issues associated with pure experimental approach (e.g., involvement of multiple length/time scale) and pure computational approach (e.g., model/parameter identification and model calibration).

For my research background and detailed timeline, check by blog morphotonomics

.

Discovering patterns from data.

self-organization in biological systems.

Computational Modeling.

Mechanisms of cancer development.

My documents

CV PhD Thesis
My expertise

Here are some of my expertise

Programming

C/C++, C#, Java, Python, R, HTML, JavaScript, SQL, Latex

Experimental Biology

2D cell culture, 3D organoid culture, IF, Confocal imaging

Data Science

Neural netowork, Machine Learning, Single cell sequencing, time series analysis, multi-dimenstional data analysis

Software development

I worked for Tata Consultancy Services Ltd where I worked on development/testing of online service monitoring services, which were implemented in C#, SQL, XML and related technologies.

Interdisciplinary work

I have worked with Biologists, Civil Engineers, Computer Scientists, Mathematicians etc.

Computational modeling

CC3D, SimBiology

Affiliations

My Affiliations

Postdoc advisor: Dr. Jeff Wrana

Address: 600 University Avenue, Toronto M5G 1X5, ON Canada

Advisor: Dr. Shamik Sen

Address: IIT Bombay, Powai, Mumbai 40076, MH India

Research Topic: Microenvironmental Regulation of Cancer Invasion and Tumor Heterogeneity: Insights from Computational Modeling Research Supervisor: Prof Shamik Sen, Department of Biosciences and Bioengineering, IIT Bombay Research Co-supervisor: Prof Mandar M Inamdar, Department of Civil Engineering, IIT Bombay Research Progress Committe Member #1: Prof Ranjith Padinhateeri, Department of Biosciences and Bioengineering, IIT Bombay Research Progress Committe Member #2: Prof Mithun K Mitra, Physics Department, IIT Bombay Weblink: Sen Lab

Role: System engineer.

Responsibilities: Development of testing related tools/utilities (mainly in C#) for online service monitoring softwares. The project was mainly a Microsoft Project to monitor online Microsoft services (including MSN, Bing, Windows 10 app store etc.).

Major: Computer Engineering

Projects:

  1. Location based reminder using android (LBROID) [Java, Android]
  2. Internet and PC-based appliance control (IPAC) [C, Visual Basic, HTML]
  3. Samvadak: online communication framework [Java]

Major: Computer Engineering

Projects:

  1. Automatic Result Processing [Microsoft Visual Basic, Microsoft Access]
Publications

My publications

Articles
Reviews/book Chapters
Citations
Co-authors
Journal/Book Chapter
  1. Ayyaz A., Kumar S., Sangiorgi B., Ghoshal B., Gosio J., Ouladan S., Fink M., Barutcu S., Trcka D., Shen J., Chan K., Wrana J.L., Gregorieff A., "Single-Cell Transcriptomes of the Regenerating Intestine Reveal a Revival Stem Cell", Nature, May 2019. Link
  2. Das A., Barai A., Monteiro M., Kumar S., Sen S., "Nuclear softening is essential for protease-independent migration", Matrix Biology, Jan 2019. Link
  3. Kumar S., Das A., Sen S., "Multi-compartment cell-based modeling of confined migration: regulation by cell intrinsic and extrinsic factors", Molecular Biology of the Cell - Special Edition on Quantitative Cell Biology, 29(13), Jun 2018, Link
  4. Kumar S.*, Das A.*, Barai A., Sen S., "MMP secretion rate and interinvadopodia spacing collectively govern cancer invasiveness", Biophysical Journal, 114(3), Feb 2018, (Link) (*Contributed equally)
  5. Das A., Monteiro M., Barai A., Kumar S., Sen S., "MMP proteolytic activity regulates cancer invasiveness by modulating integrin", Scientific Reports, Oct 2017, (Link)
  6. Kumar S., Kulkarni R., Sen S., "Cell motility and ECM proteolysis regulate tumor growth and tumor relapse by altering the fraction of cancer stem cells and their spatial scattering", Physical Biology 13(3), 2016 (Link).
  7. Kumar S., Kapoor A., Desai S., Inamdar M. M., Sen S., “Proteolytic and non-proteolytic regulation of collective cell invasion: tuning by ECM density and organization.” Scientific Reports, 2016 (Link).
  8. Kumar S., Sen S.,"Cadherin-Based Cell-Cell Adhesions: Adhesion Structure, Signalling and Computational Modeling", Chapter-8, Intercellular Communication in Cancer (1st Ed), 151 - 168. 2015. ISBN 978-94-017-7380-5 (eBook). DOI 10.1007/978-94-017-7380-5. (Link)
  9. Kumar S., Das A., Sen S.,"Extracellular matrix density promotes drive.google.com/file/d/1LJBFxqGIJjqssN67DKC5OIy1HUMmNtszEMT by weakening cell-cell adhesions", Molecular BioSystems, 2014. doi:10.1039/C3MB70431A. (Link)

Poster/Abstract
  1. Sandeep Kumar*, Shamik Sen, "Influence of ECM geometry on cell cytoplasm, cell polarization and nucleus deformation", EMBL Heidelberg, Germany. 3-6 April 2016. (Poster + Abstract). Poster Link
  2. Sandeep Kumar, "Microenvironmental Regulation of Cancer Invasion", IIT Bombay, India. 5th March 2016. Oral Presentation. (PPT)
  3. Sandeep Kumar*, and Shamik Sen, "In-silico modeling of biological systems: challenges and approaches", Futuristic Approach to Alternatives, IIT Bombay, India 17th Nov 2015. (Poster + Abstract) Poster Link
  4. Sandeep Kumar*, Mandar M Inamdar, Shamik Sen, "Sensing and processing of tumor microenvironment (TME) cues by cancer cell", Conference on Sensing, Information and Decision at the Cellular Level, The Abdus Salam International Centre for Theoretical Physics (ICTP), Italy 14-17th July 2015. (Poster)
  5. Sandeep Kumar*, Mandar M Inamdar, Shamik Sen, "Multiscale modeling of cancer stem cell driven Intratumor Heterogeneity", Joint EMBL-EBI-Wellcome Trust Course: In Silico Systems Biology, European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom, 7-12th June 2015. (Poster). Poster Link
  6. Sandeep Kumar*, Mandar M Inamdar, Shamik Sen, "Understanding the emergence of intratumor heterogeneity using multiscale computational modelling", Cellular Heterogeneity: Role of Variability and Noise in Biological Decision-Making, EMBL Heidelberg, Germany, 15 April - Saturday 18 April 2015. (Poster and Abstract)
  7. Sandeep Kumar*, Shamik Sen, "Understanding cancer through modeling", Science Expo-2015, Nehru Science Centre, Worli, Mumbai, India 4-7th Feb 2015. (Demonstration using simulation videos)
  8. Sandeep Kumar*, Mandar M Inamdar, Shamik Sen, "Microenvironmental regulation of cell migration", Mumbai-Pune Softmatter Meeting, IIT Bombay, Mumbai, Maharashtra, India, 10 Jan 2015. (Poster)
  9. Sandeep Kumar*, Mandar M Inamdar, Shamik Sen, "Probing the role of ECM properties and stromal cells in cancer cell migration", Biophysical Paschim - 7, Advanced Centre for Treatment Research and Education in Cancer (ACTREC), Navi mumbai, Maharashtra, India, 23 Sep 2014. (Poster)


  10. *: presenter
Journals
  • Sandeep Kumar, Archana Gupta, Saiful Islam, Himanshu Bhardwaj, " Appliance Control using IPAC", Journal of Emerging Technologies in Web Intelligence(JETWI, ISSN 1798- 0461), Vol 2, No 3 (2010), 232-238, Aug 2010 doi:10.4304/jetwi.2.3.157-157 (Link)
  • Sandeep Kumar, Deepak Kumar, Rashid Ali, "Factor Analysis using two stages Neural Network Architecture", International Journal of Machine Learning and Computing, Vol. 2, No. 6, 860 - 863, December 2012, (Link)
  • Sandeep Kumar, Md Abdul Qadeer, Sumit Kumar Singh,"Convergence of LBS and AI", International Journal of Machine Learning and Computing, Vol. 2, No. 6, 729 - 732. December 2012 (Link)
  • Sandeep Kumar, Md Abdul Qadeer,, "Applications of AI in Home Automation", IACSIT International Journal of Engineering and Technology, Vol. 4, No. 6, 803 - 807, December 2012 (Link)
  • Sandeep Kumar, Medha Sharma, “BCI: Next Generation for HCI, International Journal of Advanced Research in Computer Science and Software Engineering, March 2012, ISSN 2277 128 X
  • Sandeep Kumar, Medha Sharma, “Convergence of Artificial Intelligence, Emotional Intelligence, Neural Network and Evolutionary Computing, International Journal of Advanced Research in Computer Science and Software Engineering, March 2012, ISSN 2277 128 X

Conferences
  • Sandeep Kumar, Md Abdul Qadeer, "Universal Digital Device Automation and Control", 2nd IEEE International Conference on Computer Science and Information Technology, 2009. ICCSIT 2009. 490 - 494, Issue Date: 8-11 Aug. 2009 Location: Beijing Print ISBN: 978-1-4244-4519-6
  • Sandeep Kumar, Archana Gupta, Saiful Islam, Himanshu Bhardwaj, "Internet and PC Based Appliance Control (IPAC)",The 2nd International Conference on Information and Communication Systems, ICICS 2010, Issue Date: 26-29 Dec 2010 Location: Amman,Jordon Print ISBN:
  • Sandeep Kumar, Archana Gupta, Md Abdul Qadeer,"Location Based Services using Android(LBSOID)",2009 IEEE International Conference on Internet Multimedia Services Architecture and Applications (IMSAA), Issue Date: 9-11 Dec. 2009 Location: Bangalore Print ISBN: 978-1-4244-4792-3
  • Sandeep Kumar, Sandeep Sharma, "Wireless home automation for Physically Handicapped",REES 2011 Issue Date: Sep 2010 Location: Rajasthan Print ISBN:
  • Sandeep Kumar, Md Abdul Qadeer, "Applications of AI in Home Automation", 2011 International Conference on Digital Convergence (ICDC 2011), Issue Date: 26-29 Feb 2011 Location: Chennai, India Print ISBN:
  • Sandeep Kumar, Deepak Kumar, Rashid Ali, "Factor Analysis using two stages Neural Network Architecture", 3rd International Conference on Machine Learning and Computing (ICMLC 2011), Singapore [IEEE] ISBN:978-1-42449252-7
  • Sandeep Kumar, Md Abdul Qadeer, Sumit Kumar Singh, "Convergence of LBS and AI", 2011 3rd International Conference on Machine Learning and Computing (ICMLC 2011), Issue Date: 26-29 Feb 2011 Location: Singapore ISBN:978-1-42449252-7
  • Sandeep Kumar, Archana Gupta, Prof Nesar Ahmad, "Samvadak-A way to Communicate",2011 IEEE 3rd International Conference on Communication Software and Networks (ICCSN), Issue Date: 27-29 May 2011 Location: Xian Print ISBN: 978-1-61284-485-5

Book Chapter
  • Sandeep Kumar, Archana Gupta, Saiful Islam, Himanshu Bhardwaj," Chapter-6 IPAC System for Controlling Devices over Internet", in book "Intelligent Communication Systems", 98 - 116, Ubiquitous Computing and Communication Journal, ISBN978-145639229, Publishing Date: 11/1/2010 (Link)
Awards and Achievements

Awards/Achievements

  • My paper Kumar et al., Physical Biology (2016) chosen as one of 10 highlighted articles published in the journal in 2016)
  • Mathematical Biosciences Institute, Ohio State University, Travel Award, Nov 2016
    To attend “Population Models in the 21st Century”, MBI, Ohio State University, USA
  • Dept. of Sci and Technology, Govt of India, Travel Award, Oct 2016
    To attend “Population Models in the 21st Century”, MBI, Ohio State University, USA
  • EMBO Travel Award, Feb 2016
    To attend “Tumor Microenvironment and Signaling Symposium”, EMBL Heidelberg Germany
  • ICTP Travel Award, Jul 2015
    To attend “Conference on Sensing, Information and Decision at the Cellular Level”, ICTP, Italy
  • Wellcome Trust Travel Award, Jun 2015
    To attend “Joint EMBL-EBI-Wellcome Trust Advance Course on In Silico Systems Biology”, WellcomeTrust, UK
  • EMBO Travel Award, Apr 2015
    To attend “Cell Heterogeneity Role of variability and noise in biological decision making”, EMBL, Germany
  • Travel Grant by ICTS, Dec 2014
    To attend “CTS-PIMS-IISER Pune program - Advances in Mathematical Biology”
  • DST Travel Award, Dec 2010
    To attend “ICMLC 2011, Singapore”
  • DST Travel Award, Dec 2010
    To attend “ICDC 2011, Chennai, India”
  • Best paper award in iCICS 2009, Jordon, Dec 2009
  • First Position in Diploma Engineering, June 2004
Participation

Participation

  1. Population Models in the 21st Century, 14 -18th Nov 2016. Mathematical Biosciences Institute, Ohio State University, Columbus, USA (Poster Presentation)
  2. Conflict and Cooperation in Cellular Populations (CCCP) 2016, 16 – 18 Oct 2016. NCBS, Bangalore, India. (Poster Presentation + 10 minutes Flash Talk)
  3. EMBL|EMBO Symposium on Tumor Microenvironment and Signaling, April 2016, EMBL, Heidelberg, Germany (Poster Presentation + Abstract)
  4. Mumbai-Pune Soft Matter meet, March 2016, IIT Bombay, Mumbai, Maharashtra, India. (Oral Presentation)
  5. Futuristic Approach to Alternatives, Nov 2015, IIT Bombay, Mumbai, Maharashtra, India, (Poster Presentation)
  6. Conference on Sensing, Information and Decision at the Cellular Level, Jul 2015, The AS International Centre for Theoretical Physics, Trieste, Italy (Poster Presentation)
  7. Joint EMBL-EBI-Wellcome Trust Advance Course on In Silico Systems Biology, June 2015, Wellcome Trust Genome Campus, Hinxton, UK (Poster Presentation)
  8. Cellular Heterogeneity : Role of variability and noise in biological decision making, April 2015, EMBL, Heidelberg, Germany (Poster Presentation + Abstract)
  9. Biophysical Paschim - 7, Advanced Centre for Treatment Research and Education in Cancer (ACRTEC), Mumbai, Maharashtra, India, Sep 2014. (Poster Presentation)
  10. ICMLC Feb 2011, Singapore [IEEE, IACSIT] (Oral Presentation)
  11. ICDC Feb 2011, Chennai India [IEEE, IACSIT] (Oral Presentation)
  12. REEES, Sep 2010, Bhilwara, Rajasthan India (Oral Presentation)
  13. IMSAA Dec 2009, Bangalore India [IEEE,IIITB] (Oral Presentation)
  1. ReSCon 2015, IIT Bombay
  2. Rescon 2016, IIT Bombay (Link)
  3. RSAS 2014, IIT Bombay (Link)
  4. AURAA 2013 - 2014, IIT Bombay (Link)
  5. IRSCP 2013 - 2014, IIT Bombay (Link)
  6. Department cordinator Techconect, Techfest 2013, IIT Bombay
  7. ACM Member, 2011 - 2012
  1. Teaching Assistant for the course Biology (BB101) 2013 - 2014, IIT Bombay
Research interests

Research questions

I combine computational and experimental techniques to understand how cell-level small-scale interactions translate into tisssue-level larger scale 'emergent' phenomena and potential role of micro-environment in regulating this multi-scale dynamics. Three broad questions I am interested in are:

How does cellular environment influence cellular dynamics? 2013-2018

Using computational modeling combined with experimental studies, I demonstrated how increase in extracellular matrix (ECM) density (observed during cancer progression) perturbs stability of epithelial tissues and induce epithelial-to-mesenchymal transition (EMT) (Kumar et. al., 2014, Mol BioSys). My study also implicated ECM density in influencing intra-tumor heterogeneity (Kumar et. al., 2016, Phys Biol). Next, cellular potts model (CPM)-based stochastic model was then used to dissect the importance of extracellular matrix (ECM) on cell migration and cancer invasion at the outset of cancer metastasis. Predictions from the model was then validated using MDA-MB-231 and MCF7 cells by assessing their invasiveness under different ECM conditions (Kumar et. al., 2016, Sci Report; Kumar et. al., 2018, Biophys J).

How do individual cells self-organize to form multi-cellular systems? 2017-2018

One of my current research objectives is to identifying the signaling context and mechanics regulating the shape, size and population dynamics of intestine epithelium (IE) and formation of tumor in IE. Understanding how IE generate and regain its shape/size and population composition (i.e., proportion of different types of cells) is the focus of my current project.

How does cellular heterogeneity and cellular interactons evolve during development? 2017-2018

While advancements in single cell technologies have made it possible to quantify mRNA levels of thousands of genes in thousands of cells, understanding and extracting biological information from large amount of data generated remains a challenge. I am currently working on developing stochastic-graph based framework to visualize/analyze single cell RNA-sequencing data.

Get in Touch

Contact

600 University Avenue, Wrana Lab (Lab # 1080), Toronto ON M5G 1X5, Canada