Synthetic Biology Group, Professor Timothy Lu

Professor

people_lu1 Timothy Lu
RLE Biography

Timothy Lu is an Associate Professor in the Department of Electrical Engineering and Computer Science and an Associate Member of the Broad Institute of MIT and Harvard. Tim received his undergraduate and M.Eng. degrees from MIT in Electrical Engineering and Computer Science. He obtained an M.D. from Harvard Medical School and Ph.D. from the Harvard-MIT Health Sciences and Technology Medical Engineering and Medical Physics Program. Tim has won the Lemelson-MIT Student Prize, Grand Prize in the National Inventor Hall of Fame’s Collegiate Inventors Competition, and the Leon Reznick Memorial Prize for “outstanding performance in research” from Harvard Medical School. He has also been selected as a Kavli Fellow by the National Academy of Sciences and a Siebel Scholar. Outside of the lab, Tim enjoys playing volleyball and tennis.

Administrative Assistant

IMG_9205_final2 Olga Parkin

Olga is the Lu laboratory administrative assistant in the Department of Biological Engineering.  She has over thirty years of experience at MIT.  She manages the facilities at Technology Square and supports the laboratory personnel with purchasing, accounting procedures, Institute procedures, coordinates events for the Synthetic Biology Center and plays a key role in the daily operations.  She was awarded the Infinite Mile Award for Sustained Excellence, MIT School of Engineering in 2001.    At MIT, she has served as co-convenor of the Working Group for Support Staff Issues twice and has actively participated on many Institute Committees.  As a life time member of the Girl Scouts of USA, she conducts classes in outdoor cooking and is a member of the organizing committee for September fest (an annual event for training leaders and women in a myriad of activities).

Lab Manager

IMG_9215_final2 Ky Lowenhaupt

Ky joined the Lu Lab as Lab Manager in February 2013.  Previously, she was a Research Scientist in the lab of Alexander Rich, where her research concerned protein members of the Z-alpha superfamily. Proteins of the Z-alpha family bind tightly and specifically to the left-handed Z conformation of nucleic acids.  Members of this family play diverse roles in innate immunity, including as sensors for viral DNA and RNA, and as effectors to prevent viral replication in host cells.  There are also viral members of the Z-alpha family; these proteins act as competitive inhibitors of the host Z-alpha proteins, and as transactivators of transcription that prevent the cellular defense against viruses.

Postdoctoral Fellows and Associates

Barbara Jusiak

More information soon!

 Gigi Choi Photo Gigi Choi

Gigi received her PhD in Medical Sciences from Chinese University of Hong Kong. She is currently a post-doctoral associate in the Synthetic Biology Group. She is interested in building higher-order synthetic gene networks and analyzing effects of these networks in mammalian cell system.

DSC02856 Oliver Purcell

Oliver received a BSc. in Molecular Biology and MSc. in Bioinformatics from the University of Manchester, and an MRes and PhD in Complexity Science from the University of Bristol. He is currently a postdoctoral associate in the Lu lab and is interested in building synthetic gene networks with novel properties, and ultimately creating fully synthetic living systems. Outside of the lab he likes to snowboard and Scuba dive.

Slide1 Bijan Zakeri

Bijan is a post-doctoral associate in the Synthetic Biology Group at MIT. He received his HBSc in Biochemistry from McMaster University, where he conducted research in Gene Therapy and developed a new class of oncolytic viruses. Then he earned his MSc in Chemical Biology at McMaster University, where he developed next-generation semi-synthetic antibiotics. Subsequently, he received his PhD in Biochemistry at the University of Oxford as a prestigious Clarendon Scholar and St. Peter’s College Born Scholar. While in Oxford, Bijan specialized in bionanotechnology and invented a versatile new class of peptide tags which bind their target via a spontaneous and irreversible covalent bond (the Isopeptag and SpyTag peptide tagging systems). These ‘Molecular Super-Glues’ were inspired by flesh-eating bacteria and have received much media attention. Bijan’s scientific interests are to use interdisciplinary approaches to develop innovative technologies and therapeutics. For any inquiries and collaborations, Bijan can be contacted at: zakeri@mit.edu.

sele Sebastien Lemire

My name is Sebastien Lemire. I am French borne in Normandy close to Rouen. I have obtained my PhD in microbiology and bacterial physiology from the university of Paris XI Orsay in the laboratory of Lionello Bossi. I was then studying the genetic regulation of Salmonella prophages and their role in the spread of virulence factors. I then moved on to Osaka in the laboratory of Tetsuro Yonesaki to study an uncommon anti-T4 mechanism and its influence on the evolution of the T-even superfamily of phages. I have spent the last 3 years in Denmark where I got in touch with synthetic biology through mentoring of two iGEM teams and started to mix my various scientific experiences into a hopefully great plan to rid humanity of bacterial pathogens through the use of engineered phages. I am married and have a wonderful 4yo son and spend as much time as I can outside hiking, trekking and biking…Although that has not been very frequent over the last years.

Hiroki Hiroki Ando

Hiroki joined the Synthetic Biology Group in July 2012 as a JSPS Postdoctoral Fellow. He is interested in applying synthetic biology techniques to combat bacterial infectious diseases. Hiroki received his PhD in Medical Science from Osaka University in 2007. Prior to MIT, he worked as a Senior Research Fellow in the National Center for Global Health and Medicine, Tokyo. He studied about novel isoniazid resistance mechanisms in Mycobacterium tuberculosis. Outside of the lab, Hiroki likes to snowboarding, carp fishing, and taking a photo of cut-out board (see my photo, taken in Sapporo Beer Garden).

Zhen Zhengtao Deng

Zhengtao Deng is a RLE Translational Fellow/Postdoctoral Associate in the Synthetic Biology Group at MIT. The mission of his research is to engineer nanomaterials for improving human health and sustainability via synthetic biology and synthetic chemistry techniques. In MIT, he works on engineered nanoparticles for treating bacterial infectious disease and for constructing functional “living” materials and devices. Prior to joining MIT, Deng developed robust nanoparticle-DNA conjugates for DNA origami directed self-assembly and nanophotonics. He also explored controlled synthesis of colloidal nanocrystals, such as quantum dots/rods/wires/sheets, as applied to field effect transistors (FETs) and solar cells. For any inquiries and collaborations, he can be contacted at dengz@mit.edu.

Alan Alan Wong

Alan joined the Synthetic Biology Group in September 2012 as a Croucher Postdoctoral Fellow. He received his B.Sc. and M.Phil. degrees in Biochemistry and Molecular Biotechnology from the Chinese University of Hong Kong, and earned his Ph.D. in Biochemistry at the Hong Kong University of Science and Technology. During his studies there, he took molecular and genetic approaches to study signaling mechanisms underlying neurodegenerative disorders, including Parkinson’s disease and polyglutamine diseases, as well as learning and memory. His work was published in international journals including Nature Cell Biology and Nature Neuroscience. Alan was awarded the Butterfield-Croucher Award and Hong Kong Institution of Science Young Scientist Award in Life Science. He was also selected as a Croucher Fellow and a Sir Edward Youde Fellow. He is currently interested in engineering programmable synthetic biology circuits with potential biomedical applications.

 LiorNissim Lior Nissim

Lior joined the group in Oct 2011. His main interest is implementing synthetic biology for therapeutics. He received his B.Sc. Degree (biology) from Tel-Aviv University. In his M.Sc. (Department of Molecular Cell Biology, Weizmann Institute of Science) he studied Fas dependent gain of function of mutant p53. During his Ph.D. (Department of Materials and Interfaces, Weizmann Institute of Science, Rehovot, Israel), he developed a dual-promoter integrator (DPI), a synthetic gene circuit which identifies and target cancer cells according to the integrated activity of two pre-determined promoters. His Ph.D. work was patented by Weizmann Institute of Science. Outside the lab Lior is interested in cooking, surfing and Ninjitsu.

 

  IMG_9701_fina-2 Sara Cleto

Sara joined the lab in September 2012, aiming to apply principles of synthetic biology to the world of small natural products. She became passionate about this topic during her doctoral studies in Roberto Kolter’s lab. Sara received a Ph.D in Chemical and Biological Engineering from the University of Minho (Portugal), in collaboration with Harvard Medical School. Currently, She is working on combinatorial biosynthesis and mutasynthesis of small molecules.Outside the lab, Sara enjoy doing sports, nature and organizing science outreach programs.

 

 

 

2012-10-11  Ramez Ramez Danial

Ramiz Daniel received the B.Sc. degree in electrical engineering from the Technion – Israel Institute of Technology, Haifa, in 2001 and the M.Sc. and Ph.D. in electrical engineering from Tel-Aviv University, Tel-Aviv, Israel 2010. Currently, He is a post-doc in the RLE department and synthetic biology center – MIT,  He is interested in designing analog synthetic biology circuits in living cells

Graduate Students

Eléonore Tham

More information soon!

 2014-01-13 14.23.50 HDR  Isaak Elis Mueller

More information soon!

people_chen1 Allen Chen

Allen graduated with an A.B. in Chemistry and Physics from Harvard and received an M.Phil. in Chemistry from Cambridge. Currently, Allen is an M.D.-Ph.D. student in the Harvard-MIT Health Sciences and Technology Program, and is interested in engineering synthetic biology systems with potential biomedical applications. His non-work pursuits include traveling, basketball, and attempting to do improv comedy.

 IMG_9894_final-2 Fahim Farzadfard

Fahim is a PhD candidate in Microbiology Program at MIT. He earned his Bachelor and MSc degrees in Biotechnology from University of Tehran, Iran. His previous research experiences include study of glucose signaling pathway in yeast, fermentations and microarray data analysis. His research interests range from building new tools for synthetic biology to modeling signaling pathways and regulatory networks. Currently, he is developing a synthetic receptor system in yeast for sensing extracellular synthetic ligands.

people_perli Samuel Perli

Sam is a Ph.D. candidate in the Electrical Engineering and Computer Science department at MIT. Prior to his foray into Synthetic Biology, Sam earned a Bachelors degree in Electrical Engineering from IIT Madras and a Masters degree in Computer Science from MIT. As an undergrad, he won the best paper award at IEEE COMSWARE 2008 and received an Institute Silver Medal from IIT Madras. He is also a Kailath Fellow and a former MIT Presidential Fellow. Sam is currently studying specific mechanisms that give rise to systems-wide properties of biological systems such as robustness and evolvability. He is also working on developing a scalable architecture for designing complex transcriptional networks. Besides research, he enjoys playing the guitar, badminton and cooking.

people_rubens1 Jacob Rubens

Jacob earned his Bachelor of Arts in Molecular Biology and Biochemistry from Washington University in St. Louis. As an undergraduate, Jacob researched the biosynthesis of a unique cyanobacterial photosynthetic pigment and led an undergraduate team in improving photosynthetic microbial biofuel production towards entry into a synthetic biology competition (iGEM). Jacob is a Ph.D. student in the Microbiology program at MIT and receives support from an NSF Graduate Research Fellowship. He is a member of the MIT Society of Energy Fellows and is interested in developing synthetic biology tools for applications in biotechnology and the human microbiome. To contact Jacob: jrubens@mit.edu

 Tomi_000 Tomi Jun

Tomi is an M.D. student in the Harvard- MIT Health Sciences and Technology program. He received his B.A. in Biology from Dartmouth College, where he worked on the molecular biology of iron homeostasis in Arabidopsis. Broadly, he is interested in manipulating biological systems to do useful things in human health. Being from Singapore, he has a particular interest in applications relevant to health in Southeast Asia. He is currently working to develop tools to study host-microbe interactions in the gut.

 RLE_Portraits436 Robert Citorik

Rob completed his undergraduate studies in microbiology at the University of New Hampshire, where he studied toxin production in EHEC. Upon graduating, he decided to continue in the field of pathogenic bacteria as a research assistant in the Infectious Disease department at Massachusetts General Hospital exploring virulence factors in Salmonella and Vibrio cholerae. Three years later, he found himself a PhD candidate in Microbiology at MIT where he is seeking to work somewhere at the interface of synthetic biology and infectious diseases, with particular interests in both antibiotic resistance and enteric pathogens. Outside of academia, Rob enjoys running, hiking, and mixed martial arts, as well as weekend trips back to the clean air of NH where syrup is simply assumed to be pure maple.

LabPic_000 Mark Mimee

Mark is a member of the Microbiology Graduate PhD Program at MIT. He earned his B.Sc. in Microbiology and Immunology from McGill University, where he pursued undergraduate research on characterizing virulence factors in EHEC and EPEC. Mark came to MIT with a strong interest in applying synthetic biology techniques to develop new tools to combat bacterial pathogens and other infectious diseases. Outside of the lab, Mark enjoys cooking and laying down a groove on his double bass.

 IMG_9842_final2 Nathaniel Roquet

Nathaniel received a B.A. in Physics from Princeton University in 2011. Currently he is a Ph.D. student in the Harvard Biophysics Program. He is interested in phage therapy and, more broadly, the medical applications of synthetic biology.  Outside of lab, Nathaniel likes to longboard and play basketball and squash.

Rotation Graduate Students


                                                                                                                                                                                  

Visiting Scientists and Students

DSC00164 Gianluca Selvaggio

Gianluca graduated in 2010 from the University of Bologna, Italy; with specialization in Biomedical Engineering. His master thesis focused on developing algorithm for analysis of fluorescent images to extract single cell data. He has also participated in iGEM working with binary memory of cellular stress in E.coli. Gianluca started his PhD in 2011 at the University of Coimbra, under the MIT Portugal Program. His current project consists of finding the general design principles in the design of cellular defense systems against hydrogen peroxide. Presently he is a part of the Lu lab as a visiting scholar and is involved in the development of hydrogen peroxide sensors in bacterial cell systems.

 

He is also a passionate soccer player and engages in medieval re-enactment events.

 

Lu Lab Pic Kevin Ma

Kevin is currently an undergraduate at Harvard majoring in Chemical and Physical Biology. He is interested broadly in the intersection of global health and synthetic biology. In his free time, he enjoys drawing and running.Contact Kevin at: kevinchenma@college.harvard.edu

Undergraduate and UROP Students

 soleimany  Ava Soleimany

Ava is an MIT undergraduate majoring in Computer Science and Molecular Biology. She is interested in the computational aspects of synthetic biology and its medical applications. Outside of lab, Ava competes on the varsity tennis team, is involved with leadership initiatives on campus, and enjoys running along the Charles.

Alumni

 Chao_000 Chao Zhong

Chao joined the synthetic biology group in Feb 2012. Prior to MIT, he had been working as a postdoc in Professor Rolandi group in MSE at University of Washington, Seattle since summer 2009. Earlier than that, He earned his Ph.D. in BME from Cornell University in Aug 2009. His research interests include bioinspired materials/devices, biomineralization and synthetic biology as a novel toolbox for nanobiomaterials synthesis. He has published work in several prestigious journals like Nature Communications and Advanced Materials et al. His recent work on nanobioprotonic transistor was covered by many media reports including Materials Research Society (MRS), Discovery News, New York Times, MIT Tech Review and IEEE Spectrum. Outside the lab, chao likes travelling, tennis, music and watching movies. Chao can be reached by: zhongc@mit.edu, and more information about him can be found in his personal website.

Chao is now a professor at ShanghaiTech U.

people_cheng Allen Cheng

Allen was an M.D.-Ph.D. student at Harvard Medical School and MIT. He graduated summa cum laude from Harvard with an A.B./A.M. in Chemistry. His research interests lied in biomedical application engineering and platform technology invention. He is co-founder of Hacking Medicine, an MIT organization building the Boston medical entrepreneurship ecosystem. His is always open to discussing collaborations, ventures, or mentorship. Contact: chengal [at] mit.edu

 pilt_pisem Kristjan Eerik Kaseniit

Kristjan was an undergraduate from Estonia, enrolled in the new joint degree program by the EECS and Biology departments. He became fascinated by synthetic biology after hearing about it firsthand at a talk given by iGEM director Randy Rettberg. Outside of academics he enjoys playing the drums and the accordion.

urartu Urartu Ozgur Safak Seker

Urartu Seker received his PhD from Istanbul Technical University in Molecular Biology-Genetics and Biotechnology in December 2009. During his PhD studies he was also a graduate research assistant and visiting graduate student at the University of Washington Genetically Engineered Materials Science and Engineering Center between 2004-2007. After PhD, he worked as a postdoctoral fellow in Bilkent University National Nanotechnology Research Center in Ankara, Turkey until June 2010. He has also worked as a Postdoctoral Fellow in Nanyang Technological University Electrical Engineering and Applied Physics Departments in Singapore in 2011 with Prof. H. Volkan Demir. His research interests while in the Lu Lab covered designing and implementing protein based nano-assemblies by employing tools of molecular biology and biochemistry towards biomedical-biotechnological applications.Current position: Faculty at the Bilkent University (Turkey)

MichelleLu_000 Michelle Lu

Michelle graduated from MIT with a B.S. in Chemical-Biological Engineering. Her interest in synthetic biology research stems from the possibility of applying engineered biological systems to biomedical applications. As an undergraduate at MIT, Michelle was involved in MIT’s Habitat for Humanity, American Institute of Chemical Engineers (AIChE), and Kappa Alpha Theta. She plans to pursue a future career in medicine.

jerry_pic_000 Jerry Wang

Jerry was pursuing his M.Eng in EECS in the Lu Lab.  He earned his B.S. in Electrical Engineering and Computer Science from MIT and was a member of both Tau Beta Pi and Eta Kappa Nu Honor Societies.  Jerry completed his senior thesis with the lab and his current research involves constructing and characterizing specificity and other properties of Transcription Activator-like Effectors.  His research interests lie in engineering biological systems with biomedical applications and disease treatment.  Outside of academia, Jerry enjoys sports, especially football and basketball.

 ApplicationphotoofA.Glieberman_001  Aaron Glieberman

Aaron was a researcher in the Lu lab, where he was also responsible for facilitating the logistics of lab operation.  He earned both an Sc.B. and an Sc.M. in Biomedical Engineering from Brown University.  During his studies there, he participated in the iGEM competition, where his captivation with synthetic biology expanded beyond measure.  The culmination of his work at Brown resulted in the design of a genetic limiter circuit that applies a unique conditional regulation scheme to a gene of interest.  Aaron’s current research centers on understanding the mechanisms of amyloid formation in yeast and the ways in which this process might be harnessed for computational and therapeutic goals.  In the rare occurrence that Aaron is not in lab, he may be found honing his abilities as an outdoorsman, trekking the higher altitudes of New England.  He also engages in long-distance running and teaches CPR classes.

 piro  Piro Siuti

Piro received his PhD from University of Tennessee/Oak Ridge National Laboratory where he worked on Nano-enabled synthetic biology: A cell mimic based sensing platform for exploiting biochemical networks. Piro joined the synthetic biology group in October 2011 and is interested in using single invertase memory modules for building memory and recording events during the lifetime of the cell.

Current position: Research Investigator II at Novartis Institutes for BioMedical Research (Cambridge, MA)

 1 Priscila Pires

Priscila joined the Synthetic Biology Group in September 2012 as a graduate visiting student. She received her M.Sc. in Biomedical Engineering in 2010 from University of Minho, Portugal. Priscila is currently enrolled in the Ph.D. program of Biomedical Engineering from University of Minho and her research interests focus in the use of bacteriophages for the treatment and control of relevant medical biofilms. Outside the lab Priscila enjoys contemporary dance and traveling.Current position: graduate student at University of Minho (Portugal)

Chris Chris Yoon

Chris came to MIT after graduating from Seoul Science High School. He was a silver medalist in the 2007 International Chemistry Olympiad held in Moscow and a member of Korean National Chemistry team. His previous research experiences include research in the Langer Lab at MIT. Outside school, Chris grew up as a kid who loves everything about soccer. He is looking forward to becoming an M.D.-Ph.D after receiving his bachelors degree in Chemical-Biological Engineering.

Michele_000 Michele Becce

Michele was a visiting student at MIT and he is in his M.Sc. in Materials Engineering. He received his B.Sc. in Materials Engineering from Politecnico di Milano (Italy) in 2009 and has studied in TU Delft (The Netherlands) as an UNITECH exchange student in 2010/2011. He also have studied and worked for shorter periods of time in ParisTech (France), ETH Zurich (Switzerland), Trinity College Dublin (Ireland) and Chalmers University (Sweden). In Lu Lab he is working on mechanical characterization of bio-derived materials, mainly in the nanoscale, seeking for potential applications. Besides research, he swims with MIT Masters and enjoys travelling.

webpage_000 Sanna Sillankorva

Sanna is a visiting postdoctoral fellow at the MIT Synthetic Biology group. She received her M.Sc. degree in Environmental Technologies, in 2004, and Ph.D. degree in Biological and Chemical Engineering, in 2008, from the University of Minho, Braga, Portugal. She is a postdoctoral fellow in the Institute of Biotechnology and Bioengineering-Centre of Biological Engineering within the Uminho Biofilm and the Bacteriophage Biotechnology groups. Her research interests are in developing bacteriophage and bacteriophage-based alternatives for the control of clinically relevant biofilms. She enjoys playing volleyball, travelling and hiking.

Current position: research scientist at University of Minho (Portugal)

 MahdiZeraati Mahdi Zeraati

Mahdi graduated with a Doctor of Pharmacy degree from Tabriz University, Iran, where he worked on novel drug delivery systems especially delayed release capsules working based on osmosis. His keen interest in molecular genetics and genetic engineering and their biomedical applications encouraged him to pursue education in this field. Recently Mahdi completed a Master’s program in Biotechnology at Uppsala University, Sweden, and he is now doing a research internship at Synthetic Biology group. During his master thesis, he investigated the kinetic role of two non-coding RNAs in E. coli regulatory networks. Besides research, He enjoys swimming and rowing. Feel free to contact him (mahdiz@mit.edu), if you think he can help you.

Group Pictures

Harpoon Brewery visit – Winter 2013

Screen shot 2014-04-16 at 10.32.40 AM

 

Pre-Celtics game dinner – January 2013

Lab hike – Fall 2012

image-8 Here comes our first group pic, in which Chris and some group members had taken a photo together upon his graduation.
image-7_000 Chris graduated with a S.B. in Chemical-Biological Engineering from MIT in June 2012. Congratulations! And we also wish him good luck for his graduate study in UK