Supplementary Table 1 : a Search for Papers in the Area of Synthetic Ecology. Topics Searched

Supplementary Table 1: A search for papers in the area of synthetic ecology. Topics searched for included=((("synthetic biology" OR "synthetic bacteri*" OR "synthetic Escherichia" OR "synthetic ecology" OR "synthetic microb*") AND (ecology OR community OR communities OR ecosystem*))). Timespan=All years. Databases=SCI-EXPANDED, SSCI, A&HCI, CPCI-S, CPCI-SSH, BKCI-S, BKCI-SSH, CCR-EXPANDED, IC. 97 results were found, total citations were 1205 (average citations per item=12.42) and h-index=18.

Endin Total Publication Volum Beginnin g Citation Average Title Authors Source Title Date e Issue g Page Page s per Year Spatiotemporal control of gene expression Basu, S; Mehreja, R; Thiberge, S; Chen, PROCEEDINGS OF THE APR 27 101 17 6355 6360 161 16.10 with pulse-generating networks MT; Weiss, R NATIONAL ACADEMY OF 2004 SCIENCES OF THE UNITED STATES OF AMERICA Engineering microbial consortia: a new Brenner, Katie; You, Lingchong; Arnold, TRENDS IN BIOTECHNOLOGY SEP 2008 26 9 483 489 91 15.17 frontier in synthetic biology Frances H. Bacterial quorum sensing: Signals, circuits, Jayaraman, Arul; Wood, Thomas K. ANNUAL REVIEW OF 2008 10 145 167 89 14.83 and implications for biofilms and disease BIOMEDICAL ENGINEERING A synthetic Escherichia coli predator-prey Balagadde, Frederick K.; Song, Hao; MOLECULAR SYSTEMS BIOLOGY APR 2008 4 83 13.83 ecosystem Ozaki, Jun; Collins, Cynthia H.; Barnet, Matthew; Arnold, Frances H.; Quake, Stephen R.; You, Lingchong

Engineered bidirectional communication Brenner, Katie; Karig, David K.; Weiss, PROCEEDINGS OF THE OCT 30 104 44 17300 17304 80 11.43 mediates a consensus in a microbial biofilm Ron; Arnold, Frances H. NATIONAL ACADEMY OF 2007 consortium SCIENCES OF THE UNITED STATES OF AMERICA Synthetic ecosystems based on airborne Weber, Wilfried; Daoud-El Baba, Marie; PROCEEDINGS OF THE JUN 19 104 25 10435 10440 68 9.71 inter- and intrakingdom communication Fussenegger, Martin NATIONAL ACADEMY OF 2007 SCIENCES OF THE UNITED STATES OF AMERICA Synthetic cooperation in engineered yeast Shou, Wenying; Ram, Sri; Vilar, Jose M. G. PROCEEDINGS OF THE FEB 6 2007 104 6 1877 1882 60 8.57 populations NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA More than just bare scaffolds: towards multi- Woolfson, Derek N.; Mahmoud, Zahra N. CHEMICAL SOCIETY REVIEWS 2010 39 9 3464 3479 46 11.50 component and decorated fibrous biomaterials Systems biology approaches to de Lorenzo, Victor CURRENT OPINION IN DEC 2008 19 6 579 589 45 7.50 bioremediation BIOTECHNOLOGY Impact of Pseudomonas fluorescens strain Natsch, A; Keel, C; Hebecker, N; Laasik, E; FEMS MICROBIOLOGY ECOLOGY DEC 1998 27 4 365 380 32 2.00 CHA0 and a derivative with improved Defago, G biocontrol activity on the culturable resident bacterial community on cucumber roots

Models for synthetic biology Kaznessis, Yiannis N. BMC SYSTEMS BIOLOGY NOV 6 1 28 4.00 2007 The Systemic Imprint of Growth and Its Vieira-Silva, Sara; Rocha, Eduardo P. C. PLOS GENETICS JAN 2010 6 1 26 6.50 Uses in Ecological (Meta) Genomics In vitro characterization of the antibacterial Mani, N; Gross, CH; Parsons, JD; ANTIMICROBIAL AGENTS AND APR 2006 50 4 1228 1237 25 3.12 spectrum of novel bacterial type II Hanzelka, B; Muh, U; Mullin, S; Liao, YS; CHEMOTHERAPY topoisomerase inhibitors of the Grillot, AL; Stamos, D; Charifson, PS; aminobenzimidazole class Grossman, TH

Semi-synthetic mammalian gene regulatory Kramer, BP; Fischer, M; Fussenegger, M METABOLIC ENGINEERING JUL 2005 7 4 241 250 25 2.78 networks Engineering of Synthetic Mammalian Gene Weber, Wilfried; Fussenegger, Martin CHEMISTRY & BIOLOGY MAR 27 16 3 287 297 22 4.40 Networks 2009 Social interaction in synthetic and natural Xavier, Joao B. MOLECULAR SYSTEMS BIOLOGY APR 2011 7 21 7.00 microbial communities Bacteria as computers making computers Danchin, Antoine FEMS MICROBIOLOGY REVIEWS JAN 2009 33 1 3 26 20 4.00 Harmonization without consensus: Critical Reichman, Jerome H.; Dreyfuss, Rochelle DUKE LAW JOURNAL OCT 2007 57 1 85 130 19 2.71 reflections on drafting a substantive patent Cooper law treaty Compartmentalized reactions as a case of Stano, Pasquale; Carrara, Paolo; Kuruma, JOURNAL OF MATERIALS 2011 21 47 18887 18902 18 6.00 soft-matter biotechnology: synthesis of Yutetsu; de Souza, Tereza Pereira; Luisi, CHEMISTRY proteins and nucleic acids inside lipid Pier Luigi vesicles Environments that Induce Synthetic Klitgord, Niels; Segre, Daniel PLOS COMPUTATIONAL NOV 2010 6 11 18 4.50 Microbial Ecosystems BIOLOGY Design, construction and characterization of Davis, Joseph H.; Rubin, Adam J.; Sauer, NUCLEIC ACIDS RESEARCH FEB 2011 39 3 1131 1141 15 5.00 a set of insulated bacterial promoters Robert T. Engineering input/output nodes in de las Heras, Aitor; Carreno, Carlos A.; FEMS MICROBIOLOGY REVIEWS SEP 2010 34 5 842 865 15 3.75 prokaryotic regulatory circuits Martinez-Garcia, Esteban; de Lorenzo, Victor Computational approaches to study Babu, M. Madan BIOCHEMICAL SOCIETY AUG 2008 36 758 765 13 2.17 transcriptional regulation TRANSACTIONS An Environment-Sensitive Synthetic Hu, Bo; Du, Jin; Zou, Rui-yang; Yuan, Ying- PLOS ONE MAY 12 5 5 12 3.00 Microbial Ecosystem jin 2010 Ecosystems biology of microbial metabolism Klitgord, Niels; Segre, Daniel CURRENT OPINION IN AUG 2011 22 4 541 546 11 3.67 BIOTECHNOLOGY What are lightness illusions and why do we Corney, David; Lotto, R. Beau PLOS COMPUTATIONAL SEP 2007 3 9 1790 1800 11 1.57 see them? BIOLOGY GPU accelerated biochemical network Zhou, Yanxiang; Liepe, Juliane; Sheng, BIOINFORMATICS MAR 15 27 6 874 876 10 3.33 simulation Xia; Stumpf, Michael P. H.; Barnes, Chris 2011 Self-Organization, Layered Structure, and Brenner, Katie; Arnold, Frances H. PLOS ONE FEB 9 2011 6 2 9 3.00 Aggregation Enhance Persistence of a Synthetic Biofilm Consortium Analysis of a complete DNA-protein affinity Rowe, William; Platt, Mark; Wedge, David JOURNAL OF THE ROYAL MAR 6 7 44 397 408 9 2.25 landscape C.; Day, Philip J.; Kell, Douglas B.; SOCIETY INTERFACE 2010 Knowles, Joshua Communication theory and multicellular Mian, I. S.; Rose, C. INTEGRATIVE BIOLOGY 2011 3 4 350 367 8 2.67 biology A thermodynamically-based model for Istok, J. D.; Park, M.; Michalsen, M.; Spain, JOURNAL OF CONTAMINANT MAR 1 112 1-4 1 14 8 2.00 predicting microbial growth and community A. M.; Krumholz, L. R.; Liu, C.; McKinley, HYDROLOGY 2010 composition coupled to system J.; Long, P.; Roden, E.; Peacock, A. D.; geochemistry: Application to uranium Baldwin, B. bioreduction Synthetic ecology: A model system for Dunham, Maitreya J. PROCEEDINGS OF THE FEB 6 2007 104 6 1741 1742 8 1.14 cooperation NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Microbial linguistics: perspectives and Mitchell, Robert J.; Lee, Sung Kuk; Kim, BMB REPORTS JAN 31 44 1 1 10 7 2.33 applications of microbial cell-to-cell Taesung; Ghim, Cheol-Min 2011 communication Synthetic biology in the analysis and Kaempf, Michael M.; Weber, Wilfried INTEGRATIVE BIOLOGY 2010 2 1 12 24 7 1.75 engineering of signaling processes Designing biological systems: Systems Rollie, Sascha; Mangold, Michael; CHEMICAL ENGINEERING FEB 13 69 1 1 29 6 3.00 Engineering meets Synthetic Biology Sundmacher, Kai SCIENCE 2012 Setting the Stage: The History, Chemistry, Benner, Steven A.; Kim, Hyo-Joong; Yang, COLD SPRING HARBOR JAN 2012 4 1 6 3.00 and Geobiology behind RNA Zunyi PERSPECTIVES IN BIOLOGY A statistical procedure for the analysis of Parente, E; Ricciardi, A JOURNAL OF MICROBIOLOGICAL APR 2002 49 2 121 134 6 0.50 microbial communities based on phenotypic METHODS properties of isolates Programming microbial population dynamics Song, Hao; Payne, Stephen; Tan, BIOTECHNOLOGY JOURNAL JUL 2011 6 7 837 849 5 1.67 by engineered cell-cell communication Cheemeng; You, Lingchong Synthetic biosensing systems Marchisio, Mario Andrea; Rudolf, Fabian INTERNATIONAL JOURNAL OF MAR 2011 43 3 310 319 5 1.67 BIOCHEMISTRY & CELL BIOLOGY Complex function by design using spatially Kim, Hyun Jung; Du, Wenbin; Ismagilov, INTEGRATIVE BIOLOGY 2011 3 2 126 133 5 1.67 pre-structured synthetic microbial Rustem F. communities: degradation of pentachlorophenol in the presence of Hg(II)

Bioenergy for heat and electricity in the UK: Taylor, Gail ENERGY POLICY DEC 2008 36 12 4383 4389 5 0.83 A research atlas and roadmap Synthetic Biology in the Social Context: The Lentzos, Filippa BIOSOCIETIES SEP 2009 4 2-3 303 315 4 0.80 UK Debate to Date Design, implementation and practice of Ham, Timothy S.; Dmytriv, Zinovii; Plahar, NUCLEIC ACIDS RESEARCH OCT 2012 40 18 3 1.50 JBEI-ICE: an open source biological part Hector; Chen, Joanna; Hillson, Nathan J.; registry platform and tools Keasling, Jay D. Pathway engineering via quorum sensing Carter, Karen K.; Valdes, James J.; METABOLIC ENGINEERING MAY 2012 14 3 281 288 3 1.50 and sRNA riboregulators-Interconnected Bentley, William E. networks and controllers Bayesian design strategies for synthetic Barnes, Chris P.; Silk, Daniel; Stumpf, INTERFACE FOCUS DEC 6 1 6 895 908 3 1.00 biology Michael P. H. 2011 Tunable synthetic phenotypic diversification Sekine, Ryoji; Yamamura, Masayuki; PROCEEDINGS OF THE NOV 1 108 44 17969 17973 3 1.00 on Waddington's landscape through Ayukawa, Shotaro; Ishimatsu, Kana; NATIONAL ACADEMY OF 2011 autonomous signaling Akama, Satoru; Takinoue, Masahiro; SCIENCES OF THE UNITED Hagiya, Masami; Kiga, Daisuke STATES OF AMERICA

Using artificial systems to explore the Momeni, Babak; Chen, Chi-Chun; CELLULAR AND MOLECULAR APR 2011 68 8 1353 1368 3 1.00 ecology and evolution of symbioses Hillesland, Kristina L.; Waite, Adam; Shou, LIFE SCIENCES Wenying Tales of Emergence-Synthetic Biology as a Molyneux-Hodgson, Susan; Meyer, Morgan BIOSOCIETIES SEP 2009 4 2-3 129 145 3 0.60 Scientific Community in the Making Evolution, ecology and the engineered Skerker, Jeffrey M.; Lucks, Julius B.; Arkin, GENOME BIOLOGY 2009 10 11 3 0.60 organism: lessons for synthetic biology Adam P. Towards synthetic microbial consortia for Shong, Jasmine; Diaz, Manuel Rafael CURRENT OPINION IN OCT 2012 23 5 798 802 2 1.00 bioprocessing Jimenez; Collins, Cynthia H. BIOTECHNOLOGY