Curriculum vitae

Education

  • Purdue University
    • Ph.D., Computer Science, Jan 2010–Present
      • Advisor: Prof. Ananth Grama
      • Co-Advisor: Prof. Wojciech Szpankowski
      • Specialization:Computational Life Sciences (CLS)
    • M.S., Computer Science, Jan 2010–Dec 2012
      • Extra-curricular courses:
        • Genome Sequencing Algorithms (Co-Op)
        • Basic Principles of Chemical Action on Biological Systems (PHARMA)
        • Introduction to Molecular Biology (BIO)
        • Algorithms In Systems Biology
        • Bioinformatics Algorithms
      • GPA on plan-of-study: 3.97
  • University of Tehran
    • B.S., Computer Science, Seq 2004–Jun 2008
      • Extra-curricular courses:
        • Artificial Neural Networks (Grad)
        • Parallel Algorithms (Grad)
        • Bioinspired Computing (ECE)
        • Dynamical Systems (Math)
  • Allameh Helli High-School
    • High School diploma, Mathematics and Physics, Sep 2000–Jun 2004
      • Affiliated with the National Organization for Development of Exceptional Talents (NODET)

Awards and Honors

  • Travel Fellowship, International Society for Computational Biology (ISCB), May 2016
  • 1st-ranked Student (cumulative GPA), School of Mathematics, Statistics and Computer Science,University of Tehran, Jun 2008
  • Full Grant for Undergraduate Studies, National Elite Foundation, Sep 2004
  • Community Outreach AwardPDF, Tehran, National Youth Organization, Tehran, Iran, Feb 2003
  • National Khwarizmi AwardPDF (Research Proposal: IPX-based framework for cluster computing), Tehran, Iran, Dec 2002

Research Experience

  1. Visiting Student Researcher, Apr 2014–Aug 2014, Andrea Goldsmith, Department of Electrical Engineering, Stanford University, Stanford, CA, USA.
  2. Visiting Graduate Student, Mar 2012–Apr 2012, Shankar Subramaniam, Bioengineering Department, UC San Diego, San Diego, CA USA.
  3. Research Assistant, May 2010–Present, Ananth Grama, Department of Computer Science, Purdue University, West Lafayette, IN USA
  4. Research Assistant, Jan 2010–May 2010, Alex Pothen, Department of Computer Science, Purdue University, West Lafayette, IN USA
  5. Collaborative Researcher, Jan 2008–Apr 2009, Laboratory of Systems Biology and Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.

Leadership

  1. Founder and President, Great Lakes Regional Student Group (RSG), International Society for Computational Biology (ISCB), Feb 2014-Present
  2. Committee Member, Computational Science Leadership Team (CSLT), Computational Science and Engineering (CS&E), Purdue University, Feb 2014-Present.
  3. Member, Outreach and Volunteer Committee, Student Council, International Society for Computational Biology (ISCB), Jan 2013-Aug 2014
  4. Purdue representative, Student Leadership Council (SLC), Center for Science of Information (CSoI), Nov 2011-Present
  5. Elected Member of the Central Committee of FoundersPDF (Science& Technology representative), National Youth Assembly (NyA), Tehran, Iran, Apr 2004–Apr 2005

Publications

Book Chapters

    S. Mohammadi and A. Grama (2011) Biological Network AlignmentPDFDOI. In M. Koyuturk, S. Subramaniam, and A. Grama (eds.), Functional Coherence of Molecular Networks in Bioinformatics, Springer, pages 97–136

Peer-reviewed Articles

  1. S. Mohammadi, V. Ravindra, D. Gleich, and A. Grama (2016) Take ACTION to identify high-resolution cell types and associated transcriptional pathways. PDFDOI. under review (Tech. report available on bioRxiv)
  2. A. Magner, S. Mohammadi (co-first author), and A. G. Grama (2016) Combining Density and Overlap (CoDO): A New Method for Assessing the Significance of Overlap Among Subgraphs. PDFDOI. under review (Tech. report available on arXiv)
  3. S. Mohammadi, S. Kylasa, G. Kollias, and A. Grama (2016) A Context-specific Recommendation System for Predicting Similar PubMed Articles. PDFDOI. ICDMW '16 IEEE International Conference on Data Mining Workshop on Semantics-Enabled Recommender Systems (in press)
  4. S. Mohammadi and A. G. Grama (2016) De novo identification of cell type hierarchywith application to compound marker detection. PDFDOI. BCB ’16: ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB) (under review)
  5. S. Mohammadi, D. Gleich, T. G. Kolda, and A. Grama (2016) Triangular AlignMEnt (TAME): A novel tensor-based approach for global network alignmentPDFDOIIEEE Transactions on Computational Biology and Bioinformatics (TCBB) (in press)
  6. S. Mohammadi, A. Golsmith, and A. Grama (2016) A Comprehensive review on the choice of loss function, regularization, and data preprocessing on the performance of deconvolution methodsPDFDOI. Special Issue of Proceedings of IEEE - Foundations & Applications of Science of Information (in press)
  7. S. Mohammadi and A. Grama (2016) A convex optimization approach for identification of human tissue-specific interactomesPDFDOI. Bioinformatics, 32(12):i243–i252
  8. S. Mohammadi and A. Grama (2015) A novel method to enhance the sensitivity of marker detection using a refined hierarchical prior of tissue similaritiesPDFDOI. Tech. report available on bioRxiv
  9. S. Mohammadi, B. Saberidokht, S. Subramaniam, and A. Grama (2015) Scope and limitations of baker’s yeast as a model organism for studying human tissue-specific pathwaysPDFDOI. BMC Systems Biology, 96(9)
  10. S. Mohammadi, S. Subramaniam, and A. Grama (2013) Inferring the Effective TOR-Dependent Network: A Computational Study in YeastPDFDOI. BMC Systems Biology, 7(1):84
  11. G. Kollias, M. Sathe, S. Mohammadi, and A. Grama (2013) A fast approach to global alignment of protein-protein interaction networksPDFDOI. BMC research notes, 6(1):35
  12. S. Mohammadi, G. Kollias, and A. Grama (2012) Role of Synthetic Genetic Interactions in Understanding Functional Interactions Among PathwaysPDFDOI. In Pacific Symposium on Biocomputing (PSB)
  13. G. Kollias, S. Mohammadi, and A. Grama (2011) Network Similarity Decomposition (NSD): A Fast and Scalable Approach to Network AlignmentPDFDOI. IEEE Transactions on Knowledge and Data Engineering (TKDE), 24(12):2232–2243
  14. Z. R. M. Kashani, H. Ahrabian, E. Elahi, A. Nowzari-Dalini, E. S. Ansari, S. Asadi, S. Mohammadi, F. Schreiber, and A. Masoudi-Nejad (2009) Kavosh: a new algorithm for finding network motifsPDFDOI. BMC bioinformatics, 10(318) (Highly accessed)

Conference Presentations

  1. s. Mohammadi, B. Saberidokht, S. Subramaniam, A. Grama (2014) A Systems Approach to Dissect the tissue-specific architecture of cellular networksPDF. National Academy of Sciences, Washington, DC, USA
  2. S. Mohammadi, B. Saberidokht, and A. Grama (2013) Comparative analysis of yeast interactome versus human tissue-specific networksPDF. Great Lakes Bioinformatics Conference (GLBIO), Pittsburgh, PA, USA
  3. A. Grama and S. Mohammadi (2013) A Systems Study of Aging and Age-Related PathologiesPDF. CSoI Big Data Workshop, Honolulu, HI, USA
  4. S. Mohammadi, S. Subramaniam, and A. Grama (2012) Systematic Identification of TOR Downstream Effectors Using Random-Walks on the Yeast InteractomePDF. RECOMB Conference on Systems Biology and Regulatory Genomics, San Francisco, CA, USA
  5. S. Mohammadi, S. Subramaniam, and A. Grama (2012) Sweet-talking yeast: systematic identification of TOR downstream effectors under dietary restrictionPDF. Network Biology SIG, Intelligent Systems for Molecular Biology (ISMB), Long Beach, CA, USA

Patents

  1. S. Mohammadi (2005) Parallel models for implementing neural networksPDF. IR 30936
  2. S. Mohammadi (2004) A self-adaptive scheduling algorithm for dynamic networksPDF. IR 29574
  3. S. Mohammadi (2004) An IPX-based middleware for cluster computingPDF. IR 29575

Work Experience

  1. Research Associate Intern, Genapsys Inc., Redwood City, CA, USA. May 2014-Aug 2014. Responsibilities:
    • Worked on the noise filtering and base-calling algorithms for the Genapsys sequencing platform
  2. Project Manager, Techanis Company, Tehran, Iran. Oct 2008-Nov 2009, Accomplished project(s):
    • Distributed Obex-based Bluetooth-advertisement system, Tehran Metro System, Tehran, Iran.
    • Automated museum tour guide using an integrated RFID-Bluetooth technology, National Museum of Ancient Iran, Tehran, Iran
  3. Project Manager, Tavanir, Tehran, Iran. Jan 2007–May 2007, Accomplished project(s):
    • Predictive models for electrical consumption, Rafsanjan, Iran

Teaching Experience

  1. Instructor, Allameh Helli High School, Tehran, Iran
    • Directed Research in Computing, Sep 2008–Jun 2009
    • Advanced C/C++ Programming, Sep 2008–Jun 2009
  2. Teaching Assistant, Computer Science Department, University of Tehran, Tehran, Iran
    • Computer Architecture, Feb 2007–Jun 2007
    • Numerical Linear Algebra, Feb 2007–Jun 2007
    • Numerical Analysis, Sep 2006–Feb 2007

Miscellaneous

  • Dream Challenges
    • AstraZeneca-Sanger Drug Combination Prediction DREAM Challenge, Fall 2015

  • Robocup Competitions
    • Robocup @Home Competition, 2007, Atlanta, GA, USA
    • Robocup @Home Competition, 2006, Bremen, Germany
    • Robocup Soccer (Middle-Size) Competition, 2005, Osaka, Japan
    • Robocup Soccer Simulation Competition, 2003, Padova, Italy