Peer reviewed publications

(For citations click here. Below, this color highlights journal names.)
  1. S. Bhatia, M. Smanski, D. Densmore, and C Voigt, ``Constrained combinatorial genetic design,''
    ACS Synbio (submitted), May 2017.
    (This manuscript is first to introduce idea of synbio design spaces as directed graphs.
    I proposed the idea (ca. 2012) and wrote the code. The tool is available at synbiotools.
    Differs from Eugene in its expressive power (and amenability imo) and is an ideative precursor to Knox.)

  2. B Weinberg, NTH Pham, LD Caraballo, T Lozanoski, A Engel, S. Bhatia, and W Wong
    ``Large-scale design of robust genetic circuits with multiple inputs and outputs for mammalian cells,''
    Nature Biotechnology, 2017.
    (journal link) (WIRED) (Science Magazine)

  3. S. Bhatia, C. LaBoda, V. Yanez, T. Haddock-Angelli, and D. Densmore,
    ``Permutation Machines,'' ACS Synthetic Biology, Special Issue on Programming Biology, 2016.
    (journal link)
    (I proposed the idea and conceived some of the algorithms. Craig and I developed the algorithms,
    and implemented the software, and wrote the technical paper. Vanessa and Traci advised us on
    and wrote about the biology and attemped to build these machines in the lab.)

  4. R. J. Silva, S. Bhatia, and D. Densmore,
    ``A reconfigurable continuous-flow fluidic routing fabric using a modular, scalable primitive,''
    Lab on a Chip, 2016. (journal link)
    (I proposed the idea of a transposer and a microfluidic routing fabric, and algorithms for connections and routing.
    Ryan designed and developed the #hackerfluidics workflow, built the prototypes, and implemented the algorithms. )

  5. M. Quintin, N. Ma, S. Ahmed, S. Bhatia, A. Lewis, F. Isaacs, and D. Densmore,
    ``Merlin: Computer-Aided Oligonucleotide Design for Large Scale
    Genome Engineering with MAGE,'' ACS Synthetic Biology, 2016. (journal link)
    (I first designed the algorithmic approach for Merlin with Samir and Doug.)

  6. J. Quinn, R. S. Cox III, A. Adler, J. Beal, S. Bhatia, Y. Cai, et al.
    "SBOL Visual: A Graphical Language for Genetic Designs"
    PLoS Biology, 2015. (journal link)

  7. P. Vaidyanathan, B. Der, S. Bhatia, N. Roehner, R. Silva, C. Voigt, D. Densmore
    ``A framework for Genetic Logic Synthesis,''
    Proceedings of the IEEE, (12 pages) 99, 2015. (journal link)
    (I wrote the complexity section and helped position this as a framework paper.)

  8. Smanski MJ, Bhatia S, Park YJ, Zhao D,
    Giannoukos G, Ciulla D, Busby M, Calderon J,
    Nicol R, Gordon DB, Densmore D, Voigt CA,
    `` Functional optimization of gene clusters by combinatorial design and assembly''
    Nature Biotechnology, 32, 1241-1249, 2014. (journal link) (info) (press)

  9. E. Oberortner, S. Bhatia, E. Lindgren, and D. Densmore,
    ``Rule-based design of synthetic biological systems,''
    ACM Journal of Emerging Technologies in Computing Systems,
    Special Issue on Computational Synthetic Biology, 11:3, Dec. 2014. (journal link)
    (I developed and wrote the proof and helped with the formal writing.)

  10. D. Densmore and S. Bhatia `` Bio-design automation: software + biology + robots''
    (Invited) Trends in Biotechnology, November, 2013. (journal link) (info)

  11. S. Bhatia and D. Densmore, ``Pigeon: a design visualizer for synthetic biology,''
    (Technical Note) ACS Synthetic Biology, April, 2013. (journal link) (info)
    (I concieved and developed the software and wrote the paper.)

  12. O. Shaer*, C. Valdes, S. Liu, K. Lu, K. Chang, W. Xu,
    T. Haddock, S. Bhatia, D. Densmore, R. Kincaid,
    ``Designing Reality-based Interfaces for Experiential Bio-design,''
    Personal and Ubiquitous Computing , 18(6), pp. 1515-1532, 2014. (pdf)
    (*This is a collaboration with Wellesley College's HCI lab and Agilent.)

  13. *J. Beal, R. Weiss, D. Densmore, A. Adler, E. Appleton, J. Babb, S. Bhatia,
    N. Davidsohn, T. Haddock, J. Loyall, R. Schantz, V. Vasilev, and F. Yaman,
    ``An End-to-End Workflow for Engineering of Biological Networks from High-Level Specifications,''
    ACS Synthetic Biology, July, 2012. (journal link) (info)
    (*Author list is in alphabetical order, except for Principal Investigators Beal, Weiss, and Densmore.)
    (I proved the complexity and helped develop the algorithms and software for matchmaker and robot automation.)

  14. F. Yaman, S. Bhatia, A. Adler, D. Densmore, and J. Beal
    ``Automated Selection of Synthetic Biology Parts for Genetic Regulatory Networks,''
    ACS Synthetic Biology, July, 2012. (journal link) (info)
    (I proved the complexity and helped develop the algorithms for matchmaker.)

  15. B. Yordanov, E. Appleton, R. Ganguly, E. Gol, S. Carr, S. Bhatia, T. Haddock, C. Belta, D. Densmore,
    ``Experimentally driven verification of synthetic biological circuits,''
    Design and Test in Europe, Dresden, Germany, March 2012. (pdf)




  16. S. Bhatia, Y. Kil, B. Ueberheide, B. Chait, L. Tayo, L. Cruz, B. Lu, J. Yates III, and M. Bern,
    ``Constrained De Novo Sequencing of Conotoxins,''
    ACS Journal of Proteome Research, 11 (8), pp 4191-4200, June, 2012. (journal link)





  17. K. Ma, R. Bartoš, S. Bhatia, and R. Nair, ``Mobile video delivery with HTTP,''
    in the IEEE Communications Magazine, 49:4, pp. 166--175, Apr 2011. (pdf)

  18. K. Ma, R. Bartoš, S. Bhatia, ``A survey of schemes for Internet-based video delivery,''
    in the Elsevier Journal of Network and Computer Applications, 2011. (pdf)

  19. S. Bhatia, E. Varki, and A. Merchant, ``Sequential prefetch cache sizing for maximal hit rate,''
    in Proc. of the 18th Annual Meeting of the IEEE International Symposium on Modeling, Analysis, and
    Simulation of Computer and Telecommunications Systems (MASCOTS)
    , Aug. 2010. (pdf)

  20. M. Charpentier, R. Bartoš, and S. Bhatia, ``When Opportunity Proceeds from Autonomy:
    A Tour-Based Architecture for Disconnected Mobile Sensors,'' Third International IEEE
    WoWMoM Workshop on Autonomic and Opportunistic Communications (AOC 2009)
    ,
    Kos, Greece, June 2009. (pdf)

  21. K. Ma, R. Bartoš, and S. Bhatia, ``Scalability of HTTP Pacing with Intelligent Bursting,''
    poster accepted for presentation at the IEEE International Conference on Multimedia and Expo
    (ICME 2009)
    , Mexico, June 2009.

  22. S. Bhatia and R. Bartoš, ``Self-similar functions and population protocols: a characterization and a comparison,''
    10th International Conference on Distributed Computing and Networking (ICDCN 2009), Hyderabad, India, January 2009. (pdf)

  23. M. Charpentier, R. Bartoš, and S. Bhatia, ``A mechanism to structure mission-aware interaction in mobile sensor networks,''
    10th International Conference on Distributed Computing and Networking (ICDCN 2009), Hyderabad, India, January 2009. (pdf)

  24. M. Li, E. Varki, S. Bhatia, and A. Merchant,``TaP: Table-based Prefetching for Storage Caches,'' in
    Proc. of USENIX FAST 2008, Feb. 2008, San Jose, CA (pdf)

  25. S. Bhatia, R. Bartoš and K. Ma, ``Throughput-Delay Tradeoff in Small and Sparse Mobile Ad hoc Networks,''
    (poster) in Proc. of ACM/SIGMOBILE MobiHoc 2007, Montreal, Canada, Sep. 2007 (pdf.gz)

    A modified version was subsequently also published in ACM SIGMOBILE Mobile Computing and Communications
    Review (MC2R)
    , vol. 12, no. 2, Apr. 2008. (pdf.gz)

  26. S. Bhatia and R. Bartoš, ``IPACT with Smallest Available Report First: A New DBA Algorithm for EPON,'' in
    Proc. of IEEE ICC 2007, Glasgow, Scotland, June 24-28, 2007 (pdf.gz)

  27. S. Bhatia, D. Garbuzov and R. Bartoš, ``Analysis of the Gated IPACT Scheme for EPONs,'' in
    Proc. of IEEE ICC 2006, Istanbul, Turkey, June 11-15, 2006 (pdf)

  28. S. Bhatia and R. Bartoš, ``Closed-form expression for the collision probability in the IEEE Ethernet Passive Optical Network
    registration scheme,'' Journal of Optical Networking, 5, 1-14 (2005), (journal link)
    A shorter version was first published in the Proc. of IEEE GLOBECOM 2005, St. Louis, MO, November 2005 (pdf)

  29. S. Bhatia, R. Bartoš and C. Godsay, ``Empirical Evaluation of Upstream Throughput in a DOCSIS Access Network,'' in
    Proc. of the IEEE Conference on Multimedia Services Access Networks, Orlando, FL, June 2005 (pdf.gz)

  30. S. Bhatia and R. Bartoš, ``Performance of the IEEE 802.3 EPON Registration Scheme Under High Load,''
    Proc. of SPIE: Optics East - Performance, Quality of Service, and Control of Next-Generation Communication Networks Conference,
    Philadelphia, PA, October 2004 (pdf)

  31. R. Bartoš and S. Bhatia, ``Fast Restoration Signaling in Optical Networks,'' in Proc. of the Special Session on Optical Networks and Communications of
    the Fourteenth International Conference on Parallel and Distributed Computing and Systems (PDCS)
    ,
    Cambridge, MA, (S. G. Akl and T. Gonzalez, eds.), pp. 845-850, November 2002 (pdf.gz)

  32. A. Gandhi, E. Varki, S. Bhatia, ``Reader-Writer Locks for Network Attached Storage and Storage Area Networks,''
    Proc. of 17th International Conference on Computers and Their Applications, ISBN 1-880843-42-0, San Francisco, CA, April 2002 (pdf.gz)
[I gratefully acknowledge the support of Cisco Systems (2005 and 2006) and the UNH IOL (<2005).]

Other peer-reviewed contributions

  1. Jacqueline Quinn, Swapnil Bhatia, Robert Sidney Cox, Cesar Rodriguez, Larisa Soldatova,
    Jacob Beal, Kevin Clancy and Drew Endy.
    ``Synthetic Biology Open Language Visual: An Open-Source Graphical Notation for Synthetic Biology,''
    talk at the 5th International Workshop on Bio-Design Automation, London, England, July 2013.

  2. Michal Galdzicki, Ernst Oberortner, Mathew Pocock, Jacqueline Quinn, Mandy Wilson,
    Evan Appleton, Bryan Bartley, Jacob Beal, Swapnil Bhatia, Robert Cox, Raik Grunberg,
    Goskel Misirli, Hector Plahar, Nicholas Roehner, Larisa Soldotova, Guy-Bart Stan,
    Douglas Densmore, Chris Myers, Herbert Sauro and Anil Wipat.
    ``Recent Advances in the Synthetic Biology Open Language,''
    talk at the 5th International Workshop on Bio-Design Automation, London, England, July 2013.

  3. V. Vasilev, C. Liu, T. Haddock, S. Bhatia, A. Adler, F. Yaman,
    J. Beal, J. Babb, R. Weiss and D. Densmore,
    ``A Software Stack for Specification and Robotic Execution of Protocols for Synthetic Biological Engineering,''
    talk at the International Workshop on Bio-Design Automation, June 2011. (pdf)

  4. R. Ghamari, B. Stanton, T. Haddock, S. Bhatia, K. Clancy, T. Peterson,
    C. Voigt and D. Densmore, ``Applying Hardware Description Languages to Genetic Circuit Design,''
    poster at the International Workshop on Bio-Design Automation, June 2011.

  5. J. Beal, R. Weiss, D. Densmore, A. Adler, J. Babb, S. Bhatia,
    N. Davidsohn, T. Haddock, F. Yaman, R. Schantz and J. Loyall,
    ``TASBE: A Tool-Chain to Accelerate Synthetic Biological Engineering,''
    talk at the International Workshop on Bio-Design Automation, June 2011. (pdf)

  6. A. Adler, J. Beal, S. Bhatia, N. Davidsohn, D. Densmore, T. Haddock, J. Loyall, R. Schantz, R. Weiss,
    and F. Yaman, ``Towards automated selection of parts for genetic regulatory networks,'' (pdf)



  7. M. Li, S. Bhatia, and E. Varki, ``The case for a new sequential prefetching scheme'' (abstract),
    in Proc. of USENIX FAST 2010 Work-in-progress session, Feb. 2010, San Jose, CA. (link)

  8. S. Bhatia, USENIX FAST '08 Conference session summaries,
    USENIX ``login;'' Magazine , June 2008 ( pdf )

  9. S. Bhatia, ``Look Up and Scream: Analytical Difficulties Resolved!,''
    Journal of Recreational Mathematics, vol. 34, no. 1, 2005-2006, pp. 12-23. (pdf)

  10. S. Bhatia, ``Design of DBA Algorithms for EPONs,'' (poster) in
    Proc. of IEEE INFOCOM 2006 Student's Workshop, Barcelona, Spain, April 2006 (pdf.gz)

  11. A sequence that counts matchings of size k edges in the K_{2n}. (special case: A062346)
    in the Online Encyclopedia of Integer Sequences.
  12. (my favorite movie)

Other contributions

  1. J. Quinn, J. Beal, S. Bhatia, P. Cai, J, Chen, K. Clancy, N. Hillson, M. Galdzicki,
    A. Maheshwari, Umesh P., M. Pocock, C. Rodriguez, G. Stan, D. Endy,
    ``BBF RFC 93: Synthetic Biology Open Language Visual (SBOL Visual) Version 1.0.0,''
    BioBricks Foundation RFC, 2013. (pdf)

Manuscripts

  1. S. Bhatia, et al.,``Combinatorial genetic design,'' (under review), 2017.

  2. S. Bhatia and R. Bartoš, ``Notes on dynamic bandwidth allocation algorithms for EPONs,''
    (email me for details)
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