Saket Choudhary

Saket Choudhary

It's all about doing it right!











  • Syed, Parvez, Shabarni Gupta, Saket Choudhary, Narendra Goud Pandala, Apurva Atak, Annie Richharia, Heng Zhu et al. Autoantibody Profiling of Glioma Serum Samples to Identify Biomarkers Using Human Proteome Arrays Scientific reports 5 (2015). Link
  • Yachdav, Guy, Tatyana Goldberg, Sebastian Wilzbach, David Dao, Iris Shih, Saket Choudhary, Steve Crouch et al. Anatomy of BioJS, an open source community for the life sciences. eLife 4 (2015): e07009. Link
  • Choudhary, Saket, and Santosh B. Noronha. GalDrive: Pipeline for comparative identification of driver mutations using the Galaxy framework. bioRxiv (2014): 010538. Link
  • Choudhary, Saket, Vishnu Raj, K. Sanmugasundaram, Gyan Singh Patel, and Kannan Moudgalya. Scilab on Cloud and Textbook Companion Project: A Web 2.0 Service for Open Source Education. In 2013 International Conference on Cloud Computing and Big Data. Link
  • Gatkine, Pradip, Swati Gatkine, Sushanth Poojary, Saket Choudhary, and Santosh Noronha. Development of piezo-electric sensor based noninvasive low cost Arterial Pulse Analyzer. In Biomedical Engineering International Conference (BMEiCON), 2013 6th, pp. 1-4. IEEE, 2013. Link
  • Dilip Save, Yogesh, R. Rakhi, N. D. Shambhulingayya, Amit Srivastava, Manas Ranjan Das, Saket Choudhary, and Kannan M. Moudgalya. Oscad: An open source EDA tool for circuit design, simulation, analysis and PCB design. In Electronics, Circuits, and Systems (ICECS), 2013 IEEE 20th International Conference on, pp. 851-854. IEEE, 2013. Link
  • Research Experience

    Tools for Motif Conservation Analysis, PhD Project
    Guide: Prof. Anton Valouev Dept. of Preventive Medicine, Keck School of Medicine, USC

    Motif analysis of ChIP-Seq datasets often reports multiple motifs. However, determining the quality of a reported motif is hard. Motifs predicted by motif discovery tools can often not be the ‘true motifs’ and can have significant p-value(or E-values) for even ‘false motifs’. We hypothesized that, a ‘true motif’ should exhibit high evolutionary conservation scores. MoCA makes use of the PhyloP and Gerp scores to assess the conservation profile of the motif bases and compares it with flanking bases and by searching for motifs in random genomic regions. We performed analysis on various ENCODE Chip-Seq datasets and found that the ‘true motifs’, validated experimentally do exhibit high conservation scores.

    MoCA is available as a web service at

    Pattern Recognition in Clinical Data, Masters Thesis
    Guide: Prof. Santosh Noronha Dept. of Chemical Engineering, IIT Bombay

    Awarded Outstanding Thesis Award

    Cancer is a disease known to be affected by mutations. These mutations however may not all be significant. Distinguishing driver mutations from passengers is a non-trivial problem. The current methods are either focused on functional pathway analysis or machine learning. We developed a Galaxy based toolbox to run multiple such prediction tools at once, thus removing the need to convert data formats, in a reproducible manner. The end results were displayed as a heatmap, to give an insight into those mutations which are predicted to be drivers, by all the tools, thus possibly reducing the set of mutations to the ‘real’ drivers.

    In a separate project, we analysed proteomics data from Glioblastoma patienes. We use Correspondence Analysis and recursive feature elimination to predict a smaller set of marker genes that can be used to differentiate marker genes of Glioblastoma.

    The Galaxy tools are hosted on Testtoolshed here

    [Publication] Autoantibody Profiling of Glioma Serum Samples to Identify Biomarkers Using Human Proteome Arrays

    [Thesis] Pattern Recognition in Clinical Data

    [Defense Presentation]

    [Preprint] GalDrive: Pipeline for comparative identification of driver mutations using the Galaxy framework

    Automated Mining of Reaction Patterns
    Guide: Dr. Syed Asad Rahman

    EC-BLAST is a novel tool to compare enzymes and map reactions. I used Machine Learning(clustering) based approaches to point out misclassified enzymes in the established classification system. I also developed a RESTful web-service to allow automated job submissions that would allow the users to keep track of all submitted jobs and retrieve results on demand.

    Next Generation Sequencing, Supervised Learning Project
    Guide: Prof. Santosh Noronha Dept. of Chemical Engineering, IIT Bombay

    This project was in collaboration with Advanced Centre for Treatment, Research and Education in Cancer (ACTREC). Surveyed literature on Next Generation Sequencing techniques and developed automated pipelines using Python to analyze whole genome data of cancer tumors. As part of the project I contributed open source modules for BWA and samtools for Biopython, a Python based open source library for bioinformatics.

    Scilab On Cloud
    Guide: Prof. Kannan Moudagalya

    Scilab is an open source software for numerical computation and is primarily command line/GUI based. We developed a back end that allowed running Scilab through browser much like the modern day IPython notebooks.

    Presented at IEEE Conference Cloud Computing and Big Data (CloudCom-Asia), 2013


    Google Summer of Code | BioJS

    Student Contract Developer
    June, 2014 - Aug, 2014

  • Worked with BioJavascript, an open source library of javascript components to represent biological data
  • Developed Human Genetic Variation Viewer, a d3.js based component to visualise genetic variations in humans
  • Demo:
  • Screencast: Youtube

  • My blog for GSoC 2014 sits here

    My other contributions to BioJS codebase: Commits

    Google Summer of Code-Penn State University | Galaxy Project

    Student Contract Developer
    July, 2013 - Sep,2013

  • Worked with Galaxy Project, an open source web-based platform for data intensive biomedical research
  • Implemented 'nested workflows' that allows users to run a workflow inside a workflow, obviating the need of replicating steps, available at Pull request 370
  • Added 'edit on the go' functionality to edit default parameters before runtime available at Pull Request 301

  • I still contribute to the Galaxy codebase: Commits

    My blog for GSoC 2013 sits here

    Google Summer of Code-Rice University | Connexions Project

    Student Contract Developer
    July, 2012 - Sep, 2012

  • Developed a Python module to aid conversion of slideshows to online published notebooks using SlideShare API
  • Implemented the functionality to add user defined quiz as an additional achievement
  • Complete source code available at OERPub Slideimporter

  • Screencast: Youtube
  • My Blog for GSoC 2012 sits here.


    Software Engineering Intern
    New Delhi, India
    May, 2011 - Jul, 2011

    Slideshare is an online platform to view and upload presentations

  • Deployed a Ruby on Rails module to allow administrators to delete/suspend defunct users and slideshows using filters
  • Tool is being used currently at SlideShare internally for management of users and slideshows

  • A presentation describing my experiences that almost went viral is here :-)

    iDiscoveri Education

    Content Developer
    Dec 2011
    New Delhi, India

  • Developed innovative & interactive lessons for teaching Mathematics in engaging ways
  • Awarded 'Best Intern Award' based on outstanding performance
  • Education

    Indian Institute of Technology

    Bachelor and Master of Technology, Chemical Engineering

    CGPA = 8.47 on a scale of 10

    Awarded URA01 and URA03, URA= Undergraduate Research Award


  • Provost Fellowship, USC
  • 2014-
  • Gandhian Young Technological Innovation Award for designing a low cost spectrophotometer for testing water impurity by Indian Institute of Management Ahemdabad
  • 2013
  • Institute Organizational Color for excellence in Organizational activities as a Web Manager for the UG Academic Council
  • 2013
  • Institute Technical Special Mention for contributing actively to technical activities
  • 2012
  • Undergraduate Research Award for developing 'Scilab on Cloud'
  • 2012
  • Institute Technical Special Mention for improving studnt participation in technical activities, while working as a core team member of the Student Technical Body
  • 2011
  • Institute Technical Special Mention for contributing to Institute's Technical activities as a freshman
  • 2010
  • Kishor Vaignyanik Protsahan Yojana(KVPY) Fellowship by Indian Institute of Science, granted to 125 students in India
  • 2007
  • Homi Bhabha Young Scientists' Gold Medal by Bombay's Science Teacher Association
  • 2005


  • Top 250 in Indian National Physics Olympiad (INPhO)
  • 2009
  • Amongst Top 6 and Top 30 to appear for Indian National Mathematics Olympiad(INMO) for two consecutive years from Mumbai
  • 2007,08
  • Top 300 in Indian National Astronomy Olympiad (INAO)
  • 2009


    Image Analysis of Tuberculosis samples

    Supervised Learning Project, Collaborator: Hinduja Hospital, Mumbai
    Jan, 2013 - Apr, 2013

  • Implemented image processing algorithms for to automatically identify true positives in TB sputum images
  • Developed a wxPython based GUI and OpenCV based image processor
  • Undergraduate Research Award

    Guide: Prof. Kannan Moudagalya, Chemical Engineering Departmen, IIT Bombay

  • Implemented a Python based solution for porting Scilab on Cloud, thus developing a solution for running Scilab codes on the browser
  • Awarded Undergraduate Research Award
  • Presented at IEEE Cloudcom-asia conference
  • Pratham, Student Satellite Programme

    Part of India's First Student's Satellite Team, IIT Bombay

  • Pratham is an interdisciplinary programme aiming to build a cubesat,to measure the Total Electron Count in the atmosphere
  • Implemented ADC submodule on ATMEGA32, performed hardware testing
  • IIT Bombay Grading System on SMS

    Course Project
    Oct, 2011- Dec, 2011

  • Developed a Python/Flask(microframework) based app to automatically scrape the IITB webpages
  • Used the TxtWeb SMS API to receive queries on SMS and send back the fetched grades from the IITB servers, received 500+ SMS requests
  • Deployed a GMail based chat bot to perform similar operations, received more than 1000 chat requests
  • Positions

    Web Manager, UG Academic Council, IIT Bombay

    July, 2012 - April, 2013

  • Initiated a number of web portals for improving the accessibility of academic resources to the students
  • Implemented Online Notice Board System via Institute's Gymkhana website
  • Awarded Institute Organizational Color
  • Institute Internship Coordinator, Practical Training Cell, IIT Bombay

    July, 2011 - April, 2012

  • Initiated Industry & University Interaction for internships
  • Number of internships registered a 40 percent growth
  • TechniC (Now STAB) Core Group Member

    July, 2010 - April, 2011

  • Organised technical events inside the institute along with nine other members
  • Mentored students for various technical competitions