Synthetic Biology Group, Professor Timothy Lu

Publication Record

Asterisks* indicate co-first-authorship, underlines indicate corresponding authorship

Articles

– current –

59. M. Mimee, R. Citorik and T.K. Lu, “Engineering the Microbiome for Human Health Applications,” The National Academies Press,[pdf]

58. P. Perez-Pinera, N. Han, S. Cleto, J. Cao, O. Purcell, K. Shah, K. Lee, R. Ram, T. K. Lu, “Synthetic Biology and Microbioreactor Platforms for Programmable Production of Biologics at the Point-of-Care,” Nature Communications, in press.

57. N. Roquet, A. P. Soleimany, A. C. Ferris, S. Aaronson, T. K. Lu, “Synthetic Recombinase-Based State Machines in Living Cells,” Science, in press.

56. J.R. Rubens, G. Selvaggio, T. K. Lu, “Synthetic mixed-signal computation in living cells,” Nature Communications, vol. 7, article 11658, June 3, 2016. [pdf]
http://www.nature.com/ncomms/2016/160603/ncomms11658/full/ncomms11658.html

55. D. P. Pires, S. Cleto, S. Sillankorva, J. Azeredo, T.K. Lu, “Genetically Engineered Phages: A Review of Advances over the Last Decade.” Microbiol Mol Biol Rev, June 1, 2016. [pdf]
http://mmbr.asm.org/content/80/3/523.short?rss=1

54. S. Perli*, C. Cui*, T. K. Lu, “Continuous Genetic Recording with Self-Targeting CRISPR-Cas in Human Cells,” Science in revision, (preprint at bioRxiv, May 20, 2016).
http://biorxiv.org/content/early/2016/05/20/053058.abstract

53. M. Mimee, R. Citorik and T.K. Lu, “Microbiome Therapeutics — Advances and Challenges.” Advanced Drug Delivery Reviews, April 28, 2016. [pdf]
http://www.sciencedirect.com/science/journal/aip/0169409X

52. B. Zakeri, P.A. Carr and T.K. Lu, “Multiplexed Sequence Encoding: A Framework for DNA Communication.” PLOS One, April 6, 2016. [pdf]
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0152774#abstract0

51. T.K. Lu and O. Purcell, “Cells That Compute Come Closer to Reality.” Scientific American, April 1, 2016. [pdf]
http://www.scientificamerican.com/article/cells-that-compute-come-closer-to-reality/

50. K.C. Ma, S.D. Perli and T.K. Lu, “Foundations and Emerging Paradigms for Computing Living Cells.” Journal of Molecular BIology, February 22, 2016. [pdf]
http://www.sciencedirect.com/science/article/pii/S0022283616001340

49. S. Cleto*, J. Jensen*, V. F. Wendisch, T. K. Lu, “Corynebacterium glutamicum metabolic engineering with CRISPR interference (CRISPRi),” ACS Synthetic Biology, February 16, 2016. [pdf]
http://pubs.acs.org/doi/abs/10.1021/acssynbio.5b00216

48. A. SL Wong, G. CG Choi, C.H. Cui, G. Pregemig, P. Milani, M. Adam, S.D. Perli, S.W. Kazer, A. Gailard, M.Hermann, A. Shalek, E. Fraenkel and T.K. Lu, “Multiplexed barcoded CRISPR-Cas9 screening enabled by CombiGEM.” PNAS, February 10, 2016. [pdfhttp://www.pnas.org/content/early/2016/02/09/1517883113.short?rss=1

47. T.K. Lu, S. Chandrasegaran, H. Hodak, “The Era of Synthetic Biology and Genome Engineering: Where No Man Has Gone Before,” Journal of Molecular Biology, January 29, 2016. [pdf]
http://www.sciencedirect.com/science/article/pii/S0022283616000802

46. B. Jusiak*, S. Cleto*, P. Perez-Piñera, and T.K. Lu, “Engineering Synthetic Gene Circuits in Living Cells with CRISPR Technology.” Trends in Biotechnology, January 22, 2016. [pdf]
http://www.sciencedirect.com/science/article/pii/S0167779915002747

-2015-

45. D. P. Pires, S. Sillankorva, A. M. Kropinski, T. K. Lu, J. Azeredo, “Complete Genome Sequence of Pseudomonas aeruginosa Phage vB_PaeM_CEB_DP1,” Genome Announcements, vol. 3, no. 5, pp. 00918-5, September 24, 2015. [pdf]
http://genomea.asm.org/content/3/5/e00918-15.long

44. H. Ando, S. Lemire, D. P. Pires, T.K. Lu, “Engineering Modular Viral Scaffolds for Targeted Bacterial Population Editing,” Cell Systems, September 23, 2015. [pdf]
http://www.cell.com/cell-systems/fulltext/S2405-4712%2815%2900111-8

43. A. SL Wong, G. CG Wong, A.A. Cheng, O. Purcell and T.K. Lu, “Massively parallel high-order combinatorial genetics in human cells,” Nature Biotechnology, August 17, 2015. [pdf]
http://www.nature.com/nbt/journal/v33/n9/full/nbt.3326.html

42. M. Mimee, A.C. Tucker, C. A. Voigt, T.K. Lu, “Programming a Human Commensal Bacterium, Bacteroides thetaiotaomicron, to Sense and Respond to Stimuli in the Murine Gut Microbiota,” Cell Systems, July 29, 2015. [pdf]
http://www.cell.com/abstract/S2405-4712%2815%2900006-X

41. B. Zakeri  and T. K. Lu, “DNA nanotechnology: new adventures for an old warhorse,” Current Opinion in Chemical Biology, vol. 28, pp. 9-14, June 5, 2015. [pdf]

40. A. Y. Chen, C. Zhong,  and T. K. Lu, “Engineering Living Functional Materials,” ACS Synthetic Biology, pp. 8-11, January 16, 2015. [pdf]
http://pubs.acs.org/doi/abs/10.1021/sb500113b

-2014-

39. F. Farzadfard and T. K. Lu, “Genomically encoded analog memory with precise in vivo DNA writing in living cell populations,” Science, 346:1256272 November 14, 2014. [pdf]
http://www.sciencemag.org/content/346/6211/1256272.abstract
Highlighted in Nature NewsScience, Nature Methods,The Scientist, MIT News, New Scientist, GEN, and others.

38. Han, O. Purcell, F. Farzadfard, K. S. Lee, T. K. Lu, and R. J. Ram, “Microfluidics for Control in Synthetic Biology,” Proceedings of the 18th International Conference on Miniaturized Systems for Chemistry and Life Sciences (MicroTAS 2014), pp. 312-314, October 26-30, 2014.

37. L. Yang, A. A.K. Nielsen, J. Fernandez-Rodriguez, C. J. McClune, M. T. Laub, T. K. Lu, C. A. Voigt, “Permanent genetic memory with >1 byte capacity”, Nature Methods, October 26, 2014. [pdf]
http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3147.html

36. B. Jusiak, R. Daniel, F. Farzadfard, L. Nissim, O. Purcell, J. Rubens, and T. K. Lu, “Synthetic Gene Networks”, Encyclopedia of Molecular Cell Biology and Molecular Medicine, October 20, 2014. [pdf]
http://onlinelibrary.wiley.com/doi/10.1002/3527600906.mcb.20120068/abstract

35. H. Ando, R. Citorik, S. Cleto, S. Lemire, M. Mimee, and T. K. Lu, “Synthetic Biology and Therapies for Infectious Diseases”, Novel Antimicrobial Agents and Strategies, pp. 109-180, 2014.
Google Books link

34. C. Zhong, T. Gurry, A. A. Cheng, J. Downey, Z. Deng, C. M. Stultz, and T. K. Lu, “Strong underwater adhesives made by self-assembling multi-protein nanofibres”, Nature Nanotechnology, September 21, 2014. [pdf]
http://www.nature.com/nnano/journal/vaop/ncurrent/full/nnano.2014.199.html
Highlighted in The Scientist, PBS, Microbe Post, and others.

33. R. Citorik*, M. Mimee*, and T. K. Lu, “Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases”, Nature Biotechnology, September 21, 2014. [pdf]
http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.3011.html
Highlighted in Nature Biotechnology News and ViewsNature Reviews Microbiology, SciBXBBC News, Science 2.0Genetic Engineering and Biotechnology Newsand others.

32. A. A. Cheng, H. Ding, and T. K. Lu, “Enhanced killing of antibiotic-resistant bacteria enabled by massively parallel combinatorial genetics”, Proceedings of the National Academy of Sciences, August 11, 2014. [pdf]
http://www.pnas.org/content/early/2014/08/07/1400093111.abstract
Highlighted in SciencePNAS In This Issue, Genetic Engineering and Biotechnology News.

31. R. Citorik*, M. Mimee*, and T. K. Lu, “Bacteriophage-based synthetic biology for the study of infectious diseases”, Current Opinion in Microbiology, Volume 19, Pages 59-69, June 2014. [pdf]
http://dx.doi.org/10.1016/j.mib.2014.05.022

30. L. Nissim*, S. Perli*, A. Fridkin, P. Perez-Pinera, and T. K. Lu, “Multiplexed and Programmable Regulation of Gene Networks with an Integrated RNA and CRISPR/Cas Toolkit in Human Cells”, Molecular Cell, May 15, 2014. [pdf]
http://dx.doi.org/10.1016/j.molcel.2014.04.022
Highlighted in Nature Methods.

MOLCEL_54_4.c1.indd
Cover Article.

Preprint: L. Nissim*, S. Perli*, A. Fridkin, P. Perez-Pinera, and T. K. Lu, “An integrated RNA and CRISPR/Cas toolkit for multiplexed synthetic circuits and endogenous gene regulation in human cells”, bioRxiv, April 23, 2014.
http://biorxiv.org/content/early/2014/04/23/004432

29. P. Siuti*, J. Yazbek*, and T. K. Lu, “Engineering genetic circuits that compute and remember”, Nature Protocols, vol. 9, pp. 1292–1300, May 8, 2014. doi:10.1038/nprot.2014.089. [pdf]
http://www.nature.com/nprot/journal/v9/n6/full/nprot.2014.089.html

28. O. Purcell and T. K. Lu, “Synthetic Analog and Digital Circuits for Cellular Computation and Memory”, Current Opinion in Biotechnology, vol. 29, pp. 146-155, October 2014. [pdf]
http://www.sciencedirect.com/science/article/pii/S0958166914000810

27. A. Y. Chen, Z. Deng, A. Billings, U. Seker, M. Lu, R. Citorik, B. Zakeri, and T. K. Lu, “Synthesis and patterning of tunable multiscale materials with engineered cells”, Nature Materials, March 23, 2014. [pdf]
http://www.nature.com/nmat/journal/vaop/ncurrent/full/nmat3912.html
Highlighted in ScienceNPR Science FridayUSA Today, Wired, BBC, Gizmodo, Discover, LA Times, Christian Science Monitorand others.

Preprint: A. Y. Chen, U. Seker, M. Lu, R. Citorik, and T. K. Lu, “Synthesizing and Patterning Tunable Multiscale Materials with Engineered Biofilms”, bioRxiv, February 14, 2014.
http://biorxiv.org/content/early/2014/02/13/002659

– 2013 –

26. N. Roquet and T. K. Lu, “Digital and analog gene circuits for biotechnology”,  Biotechnology Journal, February 20, 2014. doi: 10.1002/biot.201300258 [pdf]
http://onlinelibrary.wiley.com/doi/10.1002/biot.201300258/full

25. O. Purcell, J. Peccoud, and T. K. Lu, “Rule-based design of synthetic transcription factors in eukaryotes”,  ACS Synthetic Biology, December 12, 2013. [pdf]
http://pubs.acs.org/doi/abs/10.1021/sb400134k

24. F. Farzadfard, S. D. Perli, and T. K. Lu, “Tunable and Multi-Functional Eukaryotic Transcription Factors Based on CRISPR/Cas,” ACS Synthetic Biology, August 26, 2013. [pdf]
http://pubs.acs.org/doi/abs/10.1021/sb400081r

23. A. Khalil, C. Bashor, and T. K. Lu, “Engineering Life,” The Scientist, August 1, 2013. [pdf]
http://www.the-scientist.com/?articles.view/articleNo/36724/title/Engineering-Life/
http://www.the-scientist.com/?articles.view/articleNo/36811/title/Cellular-Engineering-in-Context/
1646-1-L
Cover Article.

22. O. Purcell*, B. Jain*, J. R. Karr, M. W. Covert, and T. K. Lu, “Towards a whole-cell modeling approach for synthetic biology,” Chaos, June 13, 2013. [pdf]
http://dx.doi.org/10.1063/1.4811182

21. R. Danial, J. Rubens, R. Sarpeshkar, and T. K. Lu, “Synthetic Analog Computation in Living Cells,” Nature, May 15, 2013. [pdf]
http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12148.html
Highlighted in Nature, The Scientist, and others.

20.T. K. Lu, J. Bowers, M. S. Koeris,  “Advancing bacteriophage-based microbial diagnostics with synthetic biology,” Trends in Biotechnology, April 19, 2013. [pdf]
http://www.sciencedirect.com/science/article/pii/S0167779913000711
S0167779913X0006X_covhighres
Cover Article.

19. P. Siuti, J. Yazbek, and T. K. Lu, “Synthetic circuits integrating logic and memory in living cells,” Nature Biotechnology, February 10, 2013. [pdf]
http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2510.html
Highlighted in Science, Nature BiotechnologyNature News, Nature Reviews Genetics, ACS Chemical Biology, Wired, BioTechniques, and others.
largecover
Cover Article.

– 2012 –

18. B. Zakeri and T. K. Lu, “Synthetic Biology of Antimicrobial Discovery,” ACS Synthetic Biology, November 19, 2012 (online). [pdf]
http://pubs.acs.org/doi/abs/10.1021/sb300101g
asbcd6_v002i007.indd
Cover Article.

17. A. S. Khalil*, T. K. Lu*, C. J. Bashor*, C. L. Ramirez, N. C. Pysenson, K. Joung, and J. J. Collins, “A Synthetic Biology Framework For Programming Eukaryotic Transcription Functions,” Cell, vol. 150, issue 3, pp. 647-658, August 3, 2012. [pdf]
http://www.sciencedirect.com/science/article/pii/S0092867412007805

16. A. A. Cheng and T. K. Lu, “Synthetic Biology: An Emerging Engineering Discipline,” Annual Review of Biomedical Engineering, May 7, 2012 [epub]. [pdf]
http://www.annualreviews.org/doi/abs/10.1146/annurev-bioeng-071811-150118

15. A. F. Radovic-Moreno, T. K. Lu, V. A. Puscasu, C. J. Yoon, R. Langer, and O. C. Farokhzad, “Surface Charge-Switching Polymeric Nanoparticles for Bacterial Cell Wall-Targeted Delivery of Antibiotics,” ACS Nano, April 3, 2012 [epub]. [pdf]
http://pubs.acs.org/doi/abs/10.1021/nn3008383

– 2011 –

14. K. E. Kaseniit, S. Perli, T. K. Lu, “Designing Extensible Protein-DNA Interactions for Synthetic Biology,” Proceedings of the 2011 IEEE Biomedical Circuits and Systems Conference (BioCAS), pp. 349-352, November 10-12, 2011. [pdf]

13.T. K. Lu and M. Koeris, “The Next Generation of Bacteriophage Therapy,” Current Opinion in Microbiology, vol. 14, no. 5, pp. 524-531, October, 2011. [pdf]
http://www.sciencedirect.com/science/article/pii/S1369527411001123
cover.tif
Cover Article.

– 2010 –

12. T. K. Lu, “Engineering Scalable Biological Systems,” Bioengineered Bugs, vol. 1, no. 6, pp. 1-6, November/December, 2010. [pdf]
http://www.landesbioscience.com/journals/31/article/13086/

– 2009 and before –

11. T. K. Lu, A. S. Khalil, and J. J. Collins, “Next-Generation Synthetic Gene Networks,” Nature Biotechnology, vol. 27, no. 12, pp. 1139-1150, December 7, 2009. [pdf]
http://www.nature.com/nbt/journal/v27/n12/abs/nbt.1591.html

10. A. E. Friedland*, T. K. Lu*, X. Wang, D. Shi, G. M. Church,and J. J. Collins, “Synthetic Gene Networks that Count,” Science, vol. 324, no. 5931, pp. 1199-1202, May 29, 2009. [pdf]
http://www.sciencemag.org/cgi/content/abstract/324/5931/1199

9. T. K. Lu and J. J. Collins, “Engineering Synthetic Bacteriophage to Combat Antibiotic-Resistant Bacteria,” Proceedings of the 35th Annual Northeast Bioengineering Conference, April 3-5, 2009.

8. T. K. Lu and J. J. Collins, “Engineered Bacteriophage Targeting Gene Networks as Adjuvants for Antibiotic Therapy,” Proceedings of the National Academy of Sciences, vol. 106, no. 12, pp. 4629-4634, March 24, 2009. [pdf]
http://www.pnas.org/content/106/12/4629.abstract

7. T. K. Lu and J. J. Collins, “Dispersing Biofilms with Engineered Enzymatic Bacteriophage,” Proceedings of the National Academy of Sciences, vol. 104, no. 27, pp. 11197-11202, July 3, 2007.  [pdf]
http://www.pnas.org/cgi/content/abstract/0704624104v1.  In the top 15 most read articles in July 2007.

6. T. K. Lu, S. Zhak, P. Dallos, and R. Sarpeshkar, “Fast cochlear amplification with slow outer hair cells,” Hearing Research, vol. 214, no. 1-2, pp. 45-67, April 2006. [pdf]
http://dx.doi.org/10.1016/j.heares.2006.01.018

5. T. K. Lu, S. Zhak, P. Dallos, and R. Sarpeshkar, “A Micromechanical Model for Fast Cochlear Amplification with Slow Outer Hair Cells,” Proceedings of the International Symposium on Auditory Mechanisms:  Processes and Models, Portland, OR, pp. 433-441, July 23-28, 2005.

4. R. Sarpeshkar, C. Salthouse, J.-J. Sit, M. Baker, S. Zhak, T. K.-T. Lu, L. Turicchia, and S. Balster, “An Ultra-Low-Power Programmable Analog Bionic Ear Processor,” IEEE Transactions on Biomedical Engineering, vol. 52, no. 4, pp. 711-727, April 2005. [pdf]
http://dx.doi.org/10.1109/TBME.2005.844043

3. M.W. Baker, T. K.-T. Lu, and R. Sarpeshkar, “A Low-Power AGC with Level Independent Phase Margin,” IEEE 2004 American Controls Conference, Boston, MA, vol. 1, pp. 386-389, June 30 – July 2, 2004. [pdf]

2. M.W. Baker, T. K.-T. Lu, C.D. Salthouse, J.-J. Sit, S. Zhak, and R. Sarpeshkar, “A 16-channel Analog VLSI Processor for Bionic Ears and Speech-Recognition Front Ends,” Proceedings of the IEEE Custom Integrated Circuits Conference, San Jose, CA, vol. 23, no. 4, pp. 521-526, September 21-24, 2003.  [pdf]
http://dx.doi.org/10.1109/CICC.2003.1249452

1. T. K.-T. Lu, M. Baker, C. Salthouse, J.-J. Sit, S. Zhak, and R. Sarpeshkar, “A Micropower Analog VLSI Processing Channel for Bionic Ears and Speech-Recognition Front Ends,” Proceedings of the 2003 IEEE International Symposium on Circuits and Systems (ISCAS 2003), Bangkok, Thailand, vol. 5, pp. 41-44, May 25-28, 2003.  [pdf]
http://dx.doi.org/10.1109/ISCAS.2003.1206169

Technical Reports

T. K. Lu, S. Zhak, P. Dallos, and R. Sarpeshkar, “Fast Cochlear Amplification with Slow Outer Hair Cells,” Massachusetts Institute of Technology Microsystems Technology Laboratories Annual Research Report, p. 40, September 2006.

Selected Presentations

“Scalable and Tunable Platforms for Engineering Synthetic Gene Circuits,” 2011 MIT Research and Development Conference, Cambridge, MA, November 15, 2011.

“Synthetic Gene Circuits for Scalable Biological Design,” Fifth Annual Workshop on the Business-Government Interface, Forum on Systems and Synthetic Biology, Braga, Portugal, June 6, 2011.

“Synthetic Biology: Engineering and Reengineering Life,” 10 Conference, Leavenworth, WA, May 20, 2011.

“Debugging Superbugs with Engineered Phages,” The Mathematics of Microbes: Biophysical Details of the
Evolving Cell, London, United Kingdom, April 29, 2011.

“Debugging Biofilms and Superbugs,” Invited Talk, Institute of Medicine Board on Global Health, Forum on
Microbial Threats, Washington, DC , March 15, 2011.

“Next-Generation Antimicrobial Agents for Combating Antibiotic-Resistant Bacteria,” 27th Army Science
Conference, Orlando, FL, November 30, 2010.

“Synthetic Biological Memory and Counter Circuits,” Kavli Frontiers of Science, Irvine, CA, November 13, 2009.

“Engineered Bacteriophage to Combat Bacterial Biofilms and Antibiotic-Resistant Bacteria,” Invited Talk, Covidien, New Haven, CT, May 28, 2009.

“Engineered Gene Circuits for Medicine,” Invited Talk, National Chiao-Tung University, Hsinchu, Taiwan, April 10, 2009.

“Engineered Gene Circuits for Medicine,” Special Seminar, Massachusetts Institute of Technology, Cambridge, MA, March 30, 2009.

“Engineered Bacteriophage to Combat Bacterial Biofilms and Antibiotic-Resistant Bacteria,” Invited Talk, Frontiers in Synthetic Biology: Engineering Genes, Genomes & Cells for Drug Discovery, Boston, MA, December 1-2, 2008.

“Dispersing Biofilms with Engineered Enzymatic Bacteriophage,” Harvard-MIT Health Sciences and Technology Forum, Cambridge, MA, March 8, 2007.

“Engineered Phage for Enhanced Biofilm Removal,” Harvard-MIT Health Sciences and Technology Forum, Cambridge, MA, March 23, 2006.

Peer-Reviewed Abstracts

R. Krishnan, T. K. Lu, K. L. Allendoerfer, J. J. Collins, and S. Lindquist, “Molecular insights into the assembly of a bacterial amyloid,” American Chemical Society National Meeting and Exposition, August 16-20, 2009.

E. Perez, T. K. Lu, J. J. Collins, and R. M. Donlan, “Control of Escherichia coli Biofilm Formation on Urinary Catheters Using a Genetically Engineered Bacteriophage,” American Society for Microbiology General Meeting, May 20, 2009.