T. Qiu, S. Bhatia, ``Error-guided Search for Part Assignment in Genetic Circuits,'' AI for Synthetic Biology, Mar 2021. (pdf)
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.)
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)
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.)
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.
)
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.)
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)
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.)
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)
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.)
D. Densmore and S. Bhatia `` Bio-design automation: software + biology +
robots'' (Invited) Trends in
Biotechnology, November, 2013.
(journal link)
(info)
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.)
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.)
*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.)
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.)
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)
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)
also in RECOMB, March 2011, Vancouver, Canada.
(pdf)
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)
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)
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)
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)
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.
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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
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.
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.
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)
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.
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)
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)
talk at the International Workshop on Bio-Design Automation, San
Diego, CA, June 2011.
talk at the Annual Conference of the Institute of Biological Engineering, Atlanta, GA, March 2011.
poster at Synthetic Biology 5.0, BioBricks Foundation, Palo Alto CA, June 2011.
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)
S. Bhatia, USENIX FAST '08 Conference session summaries, USENIX ``login;'' Magazine , June 2008
(
pdf
)
S. Bhatia, ``Look Up and Scream: Analytical Difficulties Resolved!,'' Journal of Recreational Mathematics, vol. 34, no. 1,
2005-2006, pp. 12-23. (pdf)
S. Bhatia, ``Design of DBA Algorithms for EPONs,''
(poster) in Proc. of IEEE INFOCOM 2006 Student's Workshop, Barcelona, Spain, April 2006
(pdf.gz)
A
sequence that counts matchings of size k edges in the K_{2n}.
(special case: A062346)
in the Online Encyclopedia of Integer Sequences.
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
S. Bhatia, et al.,``Combinatorial genetic design,''
(under review), 2017.
S. Bhatia and R. Bartoš, ``Notes on dynamic bandwidth allocation
algorithms for EPONs,''
(email me for details)