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Publications

Books

  1. T. Ho and D. S. Lun. Network Coding: An Introduction. Cambridge University Press, Cambridge, 2008. [Review by Olav Geil] [Chinese translation] [Japanese translation]

Book chapters

  1. A. Krishnan, X. Qian, G. Ananyev, D. S. Lun, and G. C. Dismukes. Rewiring of cyanobacterial metabolism for hydrogen production: Synthetic biology approaches and challenges. In W. Zhang and X. Song, editors, Synthetic Biology of Cyanobacteria, pages 171-213. Springer, Singapore, 2018.
  2. F. Zhao, M. Médard, D. Lun, and A. Ozdaglar. Minimum-cost subgraph algorithms for static and dynamic multicasts with network coding. In V. Tarokh, editor, New Directions in Wireless Communications Research, pages 317-349. Springer, Dordrecht, 2009.
  3. D. S. Lun, T. Ho, N. Ratnakar, M. Médard, and R. Koetter. Network coding in wireless networks. In F. H. P. Fitzek and M. Katz, editors, Cooperation in Wireless Networks: Principles and Applications, pages 127-161. Springer, Dordrecht, 2006.

Journal articles

  1. D. S. Lun and C. M. Grgicak. Calculation of the Weight of Evidence for Combined Single-Cell and Extracellular Forensic DNA. IEEE/ACM Trans. Comput. Biol. Bioinform., in press.
  2. M. Podkowik, A. I. Perault, G. Putzel, A. Pountain, J. Kim, A. Dumont, E. Zwack, R. J. Ulrich, T. K. Karagounis, C. Zhou, A. F. Haag, J. Shenderovich, G. A. Wasserman, J. Kwon, J. Chen, A. R. Richardson, J. N. Weiser, C. R. Nowosad, D. S. Lun, D. Parker, A. Pironti, X. Zhao, K. Drlica, I. Yanai, V. J. Torres, and B. Shopsin. Quorum-sensing agr system of Staphylococcus aureus primes gene expression for protection from lethal oxidative stress. eLife, 12:RP89098, April 2024.
  3. C. M. Grgicak, Q. Bhembe, K. Slooten, N. C. Sheth, K. R. Duffy, and D. S. Lun. Single-cell investigative genetics: Single-cell data produces genotype distributions concentrated at the true genotype across all mixture complexities. Forensic Sci. Int. Genet., 69:103000, March 2024.
  4. K. R. Duffy, D. S. Lun, M. M. Mulcahy, L. O’Donnell, N. Sheth, and C. M. Grgicak. Evidentiary evaluation of single cells renders highly informative forensic comparisons across multifarious admixtures. Forensic Sci. Int. Genet., 64:102852, May 2023.
  5. C. M. Grgicak, K. R. Duffy, and D. S. Lun. The a posteriori probability of the number of contributors when conditioned on an assumed contributor. Forensic Sci. Int. Genet., 54:102563, September 2021.
  6. J. Valtl, U. J. Mönich, D. S. Lun, J. Kelley, and C. M. Grgicak. A series of developmental validation tests for number of contributors platforms: Exemplars using NOCIt and a neural network. Forensic Sci. Int. Genet., 54:102556, September 2021.
  7. S. Bhadra-Lobo, M. K. Kim, and D. S. Lun. Assessment of transcriptomic constraint-based methods for central carbon flux inference. PLoS ONE, 15(9):e0238689, September 2020.
  8. C. M. Grgicak, S. Karkar, X. Yearwood-Garcia, L. E. Alfonse, K. R. Duffy, and D. S. Lun. A large-scale validation of NOCIt’s a posteriori probability of the number of contributors and its integration into forensic interpretation pipelines. Forensic Sci. Int. Genet., 47:102296, July 2020.
  9. S. Karkar, L. E. Alfonse, C. M. Grgicak, and D. S. Lun. Statistical modeling of STR capillary electrophoresis signal. BMC Bioinformatics, 20:584, December 2019.
  10. H. Swaminathan, M. O. Qureshi, C. M. Grgicak, K. Duffy, and D. S. Lun. Four model variants within a continuous forensic DNA mixture interpretation framework: Effects on evidential inference and reporting. PLoS ONE, 13(11):e0207599, November 2018.
  11. X. Qian, Y. Zhang, D. S. Lun, and G. C. Dismukes. Rerouting of metabolism into desired cellular products by nutrient stress: Fluxes reveal the selected pathways in cyanobacterial photosynthesis. ACS Synth. Biol., 7(5):1465-1476, May 2018.
  12. S. Norsworthy, D. S. Lun, and C. M. Grgicak. Determining the number of contributors to DNA mixtures in the low-template regime: Exploring the impacts of sampling and detection effects. Leg. Med., 32:1-8, May 2018.
  13. L. Harper, D. Balasubramanian, E. A. Ohneck, W. E. Sause, J. Chapman, B. Mejia-Sosa, T. Lhakhang, A. Heguy, A. Tsirigos, B. Ueberheide, J. M. Boyd, D. S. Lun, and V. J. Torres. Staphylococcus aureus responds to the central metabolite pyruvate to regulate virulence. mBio, 9(1):e02272-17, January 2018.
  14. L. E. Alfonse, A. D. Garrett, D. S. Lun, K. R. Duffy, and C. M. Grgicak. A large-scale dataset of single and mixed-source short tandem repeat profiles to inform human identification strategies: PROVEDIt. Forensic Sci. Int. Genet., 32:62-70, January 2018.
  15. K. C. Peters, H. Swaminathan, J. Sheehan, K. R. Duffy, D. S. Lun, and C. M. Grgicak. Production of high-fidelity electropherograms results in improved and consistent DNA interpretation: Standardizing the forensic validation process. Forensic Sci. Int. Genet., 31:160-170, November 2017.
  16. J. Kim, C. M. Brown, M. K. Kim, E. H. Burrows, S. Bach, D. S. Lun, and P. G. Falkowski. Effect of cell cycle arrest on intermediate metabolism in the marine diatom Phaeodactylum tricornutum. Proc. Natl. Acad. Sci. USA, 114(38):E8007-E8016, October 2017.
  17. J. J. Kelley, S. Maor, M. K. Kim, A. Lane, D. S. Lun. MOST-Visualization: Software for producing automated textbook-style maps of genome-scale metabolic networks. Bioinformatics, 33(16):2596-2597, August 2017.
  18. J. Dinamarca, O. Levitan, G. K. Kumaraswamy, D. S. Lun, and P. G. Falkowski. Overexpression of a diacylglycerol acyltransferase gene in Phaeodactylum tricornutum directs carbon towards lipid biosynthesis. J. Phycology, 53(2):405-414, April 2017.
  19. X. Qian, M. K. Kim, G. K. Kumaraswamy, A. Agarwal, D. S. Lun, and G. C. Dismukes. Flux balance analysis of photoautotrophic metabolism: Uncovering new biological details of subsystems involved in cyanobacterial photosynthesis. BBA – Bioenergetics, 1858(4):276-287, April 2017.
  20. L. E. Alfonse, G. Tejada, H. Swaminathan, D. S. Lun, and C. M. Grgicak. Inferring the number of contributors to complex DNA mixtures using three methods: Exploring the limits of low-template DNA interpretation. J. Forensic Sci., 62(2):308-316, March 2017.
  21. D. Balasubramanian, E. A. Ohneck, J. Chapman, A. Weiss, M. K. Kim, T. Reyes-Robles, J. Zhong, L. N. Shaw, D. S. Lun, B. Ueberheide, B. Shopsin, and V. J. Torres. Staphylococcus aureus coordinates leukocidin expression and pathogenesis by sensing metabolic fluxes via RpiRc. mBio, 7(3):e00818-16, June 2016.
  22. M. K. Kim, A. Lane, J. J. Kelley, and D. S. Lun. E-Flux2 and SPOT: Validated methods for inferring intracellular metabolic flux distributions from transcriptomic data. PLoS ONE, 11(6):e0157101, June 2016.
  23. H. Swaminathan, A. Garg, C. M. Grgicak, M. Medard, and D. S. Lun. CEESIt: A computational tool for the interpretation of STR mixtures. Forensic Sci. Int. Genet., 22:149-160, May 2016.
  24. J. Kim, M. Fabris, G. Baart, M. K. Kim, A. Goossens, W. Vyverman, P. G. Falkowski, and D. S. Lun. Flux balance analysis of primary metabolism in the diatom Phaeodactylum tricornutum. Plant J., 85(1):161-176, January 2016.
  25. H. Swaminathan, C. M. Grgicak, M. Medard, and D. S. Lun. NOCIt: A computational method to infer the number of contributors to DNA samples analyzed by STR genotyping. Forensic Sci. Int. Genet., 16:172-180, May 2015.
  26. J. J. Kelley, A. Lane, X. Li, B. Mutthoju, S. Maor, D. Egen, and D. S. Lun. MOST: A software environment for constraint-based metabolic modeling and strain design. Bioinformatics, 31(4):610-611, February 2015.
  27. O. Levitan, J. Dinamarca, E. Zelzion, D. S. Lun, L. T. Guerra, M. K. Kim, J. Kim, B. A. S. Van Mooy, D. Bhattacharya, and P. G. Falkowski. Remodeling of intermediate metabolism in the diatom Phaeodactylum tricornutum under nitrogen stress. Proc. Natl. Acad. Sci. USA, 112(2):412-417, January 2015.
  28. K. Ip, N. Donoghue, M. K. Kim, and D. S. Lun. Constraint-based modeling of heterologous pathways: Application and experimental demonstration for overproduction of fatty acids in Escherichia coli. Biotechol. Bioeng., 111(10):2056-2066, October 2014.
  29. M. K. Kim and D. S. Lun. Methods for integration of transcriptomic data in genome-scale metabolic models. Comput. Struct. Biotechnol. J., 11(18):59-65, August 2014.
  30. D. Hong, S. Man, J.-C. Birget, and D. S. Lun. A wavelet-based almost sure uniform approximation of fractional Brownian motion with a parallel algorithm. J. Appl. Probab., 51(1):1-18, 2014.
  31. F. Zhao, M. Médard, A. Ozdaglar, and D. S. Lun. Convergence study of decentralized min-cost subgraph algorithms for multicast in coded networks. IEEE Trans. Inform. Theory, 60(1):410-421, January 2014.
  32. K. E. Wiens, H. Swaminathan, R. Copin, D. S. Lun, and J. D. Ernst. Equivalent T cell epitope promiscuity in ecologically diverse human pathogens. PLoS ONE, 8(8):e73124, August 2013.
  33. G. P. Bisson, C. Mehaffy, C. Broeckling, J. Prenni, D. Rifat, D. S. Lun, M. Burgos, D. Weissman, P. C. Karakousis, and K. Dobos. Upregulation of the phthiocerol dimycocerosate biosynthetic pathway by rifampicin-resistant, rpoB-mutant Mycobacterium tuberculosis. J. Bacteriol., 194(23):6441-6452, December 2012.
  34. D. Egen and D. S. Lun. Truncated branch and bound achieves efficient constraint-based genetic design. Bioinformatics, 28(12):1619-1623, June 2012.
  35. A. Brandes, D. S. Lun, K. Ip, J. Zucker, C. Colijn, B. Weiner, and J. E. Galagan. Inferring carbon sources from gene expression profiles using metabolic flux models. PLoS ONE, 7(5):e36947, May 2012.
  36. M. G. Niepielko, K. Ip, J. S. Kanodia, D. S. Lun, and N. Yakoby. Evolution of BMP signaling in Drosophila oogenesis: A receptor-based mechanism. Biophys. J., 102(8):1722-1730, April 2012.
  37. K. Ip, C. Colijn, and D. S. Lun. Analysis of complex metabolic behavior through pathway decomposition. BMC Syst. Biol., 5:91, June 2011.
  38. M. R. Golzarian, R. A. Frick, K. Rajendran, B. Berger, S. Roy, M. Tester, and D. S. Lun. Accurate inference of shoot biomass from high-throughput images of cereal plants. Plant Methods, 7:2, February 2011.
  39. A. Eryilmaz, D. S. Lun, and B. T. Swapna. Control of multi-hop communication networks for inter-session network coding. IEEE Trans. Inform. Theory, 57(2):1092-1110, February 2011.
  40. H. I. M. Boshoff and D. S. Lun. Systems biology approaches to understanding mycobacterial survival mechanisms. Drug Discov. Today: Dis. Mech., 7(1):e75-e82, Spring 2010.
  41. X. Shi, D. S. Lun, M. Médard, R. Kötter, J. C. Meldrim, and A. J. Barry. Joint base-calling of two DNA sequences with factor graphs. IEEE Trans. Inform. Theory, 56(2):724-733, February 2010.
  42. D. S. Lun, A. Sherrid, B. Weiner, D. R. Sherman, and J. E. Galagan. A blind deconvolution approach to high-resolution mapping of transcription factor binding sites from ChIP-Seq data. Genome Biol., 10(12):R142, December 2009.
  43. D. S. Lun, G. Rockwell, N. J. Guido, M. Baym, J. A. Kelner, B. Berger, J. E. Galagan, and G. M. Church. Large-scale identification of genetic design strategies using local search. Mol. Syst. Biol., 5:296, August 2009.
  44. C. Colijn, A. Brandes, J. Zucker, D. S. Lun, B. Weiner, M. R. Farhat, T.-Y. Cheng, D. B. Moody, M. Murray, and J. E. Galagan. Interpreting expression data with metabolic flux models: Predicting Mycobacterium tuberculosis mycolic acid production. PLoS Comput. Biol., 5(8):e1000489, August 2009.
  45. L. D. Jennings, D. S. Lun, M. Médard, and S. Licht. ClpP hydrolyzes a protein substrate processively in the absence of the ClpA ATPase: Mechanistic studies of ATP-independent processive proteolysis. Biochemistry, 47(44):11536-11546, November 2008.
  46. J.-S. Park, U. Lee, S. Y. Oh, M. Gerla, D. S. Lun, W. W. Ro, and J. Park. Delay analysis of car-to-car reliable data delivery strategies based on data mulling with network coding. IEICE Trans. Inf. & Syst., E91-D(10):2524-2527, October 2008.
  47. D. S. Lun, M. Médard, R. Koetter, and M. Effros. On coding for reliable communication over packet networks. Physical Communication, 1(1):3-20, March 2008.
  48. D. S. Lun, L. D. Jennings, R. Koetter, S. Licht, and M. Médard. An information-based computational technique for estimation of chromatographic peak purity. J. Chem. Inf. Model., 47(5):1973-1978, September 2007.
  49. J.-S. Park, M. Gerla, D. S. Lun, Y. Yi, and M. Médard. Codecast: A network-coding based ad hoc multicast protocol. IEEE Wireless Commun. Mag., 13(5):76-81, October 2006.
  50. D. S. Lun, N. Ratnakar, M. Médard, R. Koetter, D. R. Karger, T. Ho, E. Ahmed, and F. Zhao. Minimum-cost multicast over coded packet networks. IEEE Trans. Inform. Theory, 52(6):2608-2623, June 2006.
  51. D. S. Lun, M. Médard, and I. C. Abou-Faycal. On the performance of peaky capacity-achieving signaling on multipath fading channels. IEEE Trans. Commun., 52(6):931-938, June 2004.

Conference papers

  1. S. Karkar, L. E. Alfonse, C. M. Grgicak, and D. S. Lun. Statistical modeling of short-tandem repeat capillary electrophoresis profiles. In Proc. 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2018), pages 869-876, December 2018.
  2. L. E. Alfonse, A. D. Garrett, H. Swaminathan, K. C. Peters, G. Wellner, X. Yearwood-Garcia, L. M. Taranow, J. Sheehan, S. E. Norsworthy, U. Mönich, D. S. Lun, K. R. Duffy, M. Médard, R. W. Cotton, and C. M. Grgicak. The development and release of a collection of computational tools and a large-scale empirical data set for validation: The PROVEDIt initiative. In Proc. 27th International Symposium on Human Identification, September 2016.
  3. H. Swaminathan, C. M. Grgicak, M. Medard, and D. S. Lun. NOCIt–a computational tool to infer the number of contributors to a forensic DNA sample. In Proc. 24th International Symposium on Human Identification, October 2013.
  4. J.-C. Birget, D. S. Lun, A. Wirth, and D. Hong. Identification of binary gene networks. In Proc. 50th Annual Allerton Conference on Communication, Control, and Computing, pages 1467-1474, October 2012.
  5. J.-C. Birget, D. S. Lun, A. Wirth, and D. Hong. A theoretical approach to gene network identification. In Proc. 2012 IEEE Information Theory Workshop (ITW 2012), pages 432-436, September 2012.
  6. D. Traskov, M. Heindlmaier, M. Médard, R. Koetter, and D. S. Lun. Scheduling for network coded multicast: A conflict graph formulation. In Proc. 2008 IEEE Globecom Workshops, pages 1-5, November-December 2008.
  7. X. Shi, D. S. Lun, J. Meldrim, R. Kötter, and M. Médard. Joint base-calling of two DNA sequences with factor graphs. In Proc. 2008 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP 2008), pages 2049-2052, March-April 2008.
  8. F. Zhao, M. Médard, D. Lun, and A. Ozdaglar. Convergence rates of min-cost subgraph algorithms for multicast in coded networks. In Proc. 45th Annual Allerton Conference on Communication, Control, and Computing, September 2007.
  9. F. Zhao, D. S. Lun, M. Médard, and E. Ahmed. Decentralized algorithms for operating coded wireless networks. In Proc. 2007 IEEE Information Theory Workshop (ITW 2007), pages 472-477, September 2007.
  10. D. Traskov, D. S. Lun, R. Koetter, and M. Médard. Network coding in wireless networks with random access. In Proc. 2007 IEEE International Symposium on Information Theory (ISIT 2007), pages 2726-2730, June 2007.
  11. C. Fragouli, D. S. Lun, M. Médard, and P. Pakzad. On feedback for network coding. In Proc. 2007 Conference on Information Sciences and Systems (CISS 2007), pages 248–252, March 2007.
  12. A. Eryilmaz and D. S. Lun. Control for inter-session network coding. In Proc. 2007 Information Theory and Applications Workshop (ITA 2007), January-February 2007.
  13. J.-S. Park, D. S. Lun, F. Soldo, M. Gerla, and M. Médard. Performance of network coding in ad hoc networks. In Proc. IEEE Milcom 2006, pages 1-6, October 2006.
  14. P. Maymounkov, N. J. A. Harvey, and D. S. Lun. Methods for efficient network coding. In Proc. 44th Annual Allerton Conference on Communication, Control, and Computing, September 2006.
  15. J.-S. Park, U. Lee, S. Y. Oh, M. Gerla, and D. S. Lun. Emergency related video streaming in VANET using network coding. In Proc. 3rd International Workshop on Vehicular Ad Hoc Networks (VANET ’06), pages 102-103, September 2006.
  16. D. Traskov, N. Ratnakar, D. S. Lun, R. Koetter, and M. Médard. Network coding for multiple unicasts: An approach based on linear optimization. In Proc. 2006 IEEE International Symposium on Information Theory (ISIT 2006), pages 1758-1762, July 2006.
  17. D. S. Lun, P. Pakzad, C. Fragouli, M. Médard, and R. Koetter. An analysis of finite-memory random linear coding on packet streams. In Proc. 4th International Symposium on Modeling and Optimization in Mobile, Ad Hoc and Wireless Networks (WiOpt ’06), April 2006.
  18. D. S. Lun, M. Médard, and R. Koetter. Network coding for efficient wireless unicast. In Proc. 2006 International Zurich Seminar on Communications (IZS 2006), pages 74-77, February 2006.
  19. D. S. Lun, E. Ahmed, L. R. Brothers, J. A. DeBardelaben, M. Effros, T. Ho, D. Karger, R. Koetter, A. Lee, S. J. MacMullan, M. Médard, and F. Zhao. Network coding for wireless applications. In Proc. SPIE, vol. 5986, page 59860U, October 2005.
  20. D. S. Lun, M. Médard, R. Koetter, and M. Effros. Further results on coding for reliable communication over packet networks. In Proc. 2005 IEEE International Symposium on Information Theory (ISIT 2005), pages 1848-1852, September 2005.
  21. C. Luo, M. Médard, L. Zheng, and D. S. Lun. Multi-tone FSK with feedback. In Proc. 2005 IEEE International Symposium on Information Theory (ISIT 2005), pages 112-116, September 2005.
  22. D. S. Lun, M. Médard, and R. Koetter. Efficient operation of wireless packet networks using network coding. In Proc. International Workshop on Convergent Technologies (IWCT) 2005, June 2005.
  23. S. Deb, M. Effros, T. Ho, D. R. Karger, R. Koetter, D. S. Lun, M. Médard, and N. Ratnakar. Network coding for wireless applications: A brief tutorial. In Proc. International Workshop on Wireless Ad-hoc Networks (IWWAN) 2005, May 2005.
  24. D. S. Lun, M. Médard, and D. R. Karger. On the dynamic multicast problem for coded networks. In Proc. WINMEE, RAWNET and NETCOD 2005 workshops, April 2005.
  25. D. S. Lun, N. Ratnakar, R. Koetter, M. Médard, E. Ahmed, and H. Lee. Achieving minimum cost multicast: A decentralized approach based on network coding. In Proc. IEEE Infocom 2005, volume 3, pages 1607-1617, March 2005. [Errata]
  26. D. S. Lun, M. Médard, T. Ho, and R. Koetter. Network coding with a cost criterion. In Proc. 2004 International Symposium on Information Theory and its Applications (ISITA 2004), October 2004.
  27. D. S. Lun, M. Médard, and M. Effros. On coding for reliable communication over packet networks. In Proc. 42nd Annual Allerton Conference on Communication, Control, and Computing, September-October 2004.
  28. D. S. Lun and M. Médard. On the sufficiency of power control for a class of channels with feedback. In Proc. 2004 IEEE International Symposium on Information Theory (ISIT 2004), page 73, June-July 2004. [Extended version]
  29. D. S. Lun, M. Médard, and I. C. Abou-Faycal. Error exponents for capacity-achieving signaling on wideband Rayleigh fading channels. In Proc. 2002 International Symposium on Information Theory and its Applications (ISITA 2002), October 2002.
  30. D. S. Lun, M. Médard, and I. C. Abou-Faycal. An upper bound on the error probability of capacity-achieving signaling on broadband Rayleigh fading channels. In Proc. 56th IEEE Vehicular Technology Conference (VTC 2002-Fall), volume 1, pages 577-581, September 2002.
  31. D. S. Lun, M. Médard, and I. C. Abou-Faycal. Error exponents for wideband multipath fading channels — a strong coding theorem. In Proc. 2002 Conference on Information Sciences and Systems (CISS 2002), March 2002.