Database Content
| Author | Title | Category | Type | Description | Year Published | Publication | Date/Time | |
| Handelsman, J. | Metagenomics: application of genomics to uncultured microorganisms | Metagenomics | Overview | A helpful overview of metagenomics by one of its key figures | 2004 | Microbiology and Molecular Biology Reviews, 68: 669-685 | 5 July 06 | |
| Riesenfeld, C.S., Schloss, P.D., & Handelsman, J. | Metagenomics: genomic analysis of microbial communities | Metagenomics | Overview | Detailed and clear overview of the aims and achievements of metagenomics | 2004 | Annual Review of Genetics, 38: 525-552 | 5 July 06 | |
| Schloss, P.D., & Handelsman, J. | Biotechnological prospects from metagenomics | Metagenomics | Applications | Overview with a focus on potential applications of metagenomics | 2003 | Current Opinion in Biotechnology, 14: 303-310 | 5 July 06 | |
| Breitbart, M., Felts, B., Kelley, S., et al. | Diversity and population structure of a near[shore marine-sediment viral community | Metagenomics | Research | Viral metagenomics, and its indications of enormous untapped biodiversity | 2004 | Proceedings of the Royal Society London B, 271: 565-574 | 5 July 06 | |
| Breitbart, M., Hewson, I., Felts, B., et al. | Metagenomic analyses of an uncultured viral community from human feces | Metagenomics | Research | Partial shotgun sequencing of a viral metagenome from human faeces, of which most sequence is not previously known | 2003 | Journal of Bacteriology, 185: 6220-6223 | 5 July 06 | |
| Breitbart, M., Salomon, P., Andresen, B., et al. | Genomic analysis of uncultured marine virus communities | Metagenomics | Research | Viral metagenomics, indicating vast amounts of uncharacterized diversity and the potential of existing methods to sequence the entire metagenome | 2002 | PNAS, 99: 14250-14255 | 5 July 06 | |
| Streit, W.R., & Schmitz, R.A. | Metagenomics - the key to the uncultured microbes | Metagenomics | Overview | Overview of metagenomics, especially technical issues and biases | 2004 | Current Opinion in Microbiology, 7, 492-498 | 5 July 06 | |
| Daniel, R. | The soil metagenome - a rich resource for the discovery of novel natural products | Metagenomics | Applications | Discusses how soil metagenomics could lead to the discovery of new commercially valuable antibiotics and biocatalysts | 2004 | Current Opinion in Biotechnology, 15: 199-204 | 5 July 06 | |
| DeLong, E.F. | Towards microbial systems science: integrating microbial perspectives from genomes to biomes | Metagenomics | Overview | Far-reaching overview of metagenomics, taking it to a systems-level understanding of 'metaorganisms' | 2002 | Environmental Microbiology, 4: 9-10 | 5 July 06 | |
| DeLong, E.F. | Reconstructing the wild types | Metagenomics | Overview | Overview of metagenomics, commenting on Tyson et al's study of an acid mine drainage community | 2004 | Nature, 428: 25-26 | 5 July 06 | |
| Tyson, G.W., Chapman, J., Hugenholz, P., et al. | Community structure and metabolism through reconstruction of microbial genomes from the environment | Metagenomics | Research | Metagenomic analysis of the microorganisms in acidic mining waste. The study reveals a simple community, of which two genomes could be reconstructed from the shotgun sequence of the environmental library | 2004 | Nature, 428: 37-43 | 5 July 06 | |
| DeLong, E.F. | Microbial population genomics and ecology: the road ahead | Metagenomics | Overview | Overview of metagenomics and its future directions | 2002 | Environmental Microbiology, 6: 875-878 | 5 July 06 | |
| DeLong, E.F. | Microbial community genomics in the ocean | Metagenomics | Overview | Extended overview of metagenomics to date; discussion of analysis problems in Venter's findings; anticipations of metagenomics' value for evolutionary and ecological analyses | 2005 | Nature Reviews Microbiology, 3: 459-469 | 5 July 06 | |
| Falkowski, P.G., & de Vargas, C. | Shotgun sequencing in the sea: a blast from the past | Metagenomics | Overview | Discussion of Venter's findings and analysis | 2004 | Science, 304: 58-60 | 5 July 06 | |
| Handelsman, J., Rondon, M.R., Brady, S.F., et al. | Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products | Metagenomics | Research | First use of the word 'metagenome' in relation to sequence and screening analysis of soil sample | 1998 | Chemistry and Biology, 5: R245-R249 | 5 July 06 | |
| Rodríguez-Valera, F. | Environmental genomics: the big picture | Metagenomics | Overview | Overview of metagenomics and its implications for evolutionary and ecological studies | 2004 | FEMS Microbiology Letters, 231: 153-158 | 5 July 06 | |
| Rodríguez-Valera, F. | Approaches to prokaryotic diversity: a population genetics approach | Metagenomics | Overview | Outlines metagenomics and what it means for understandings of microbial diversity | 2002 | Environmental Microbiology, 4: 628-633 | 5 July 06 | |
| Schloss, P.D., & Handelsman, J. | Metagenomics for studying unculturable microorganisms: cutting the Gordian knot | Metagenomics | Overview | Outline of metagenomics and some key studies | 2005 | Genome Biology, 6: 229+ | 5 July 06 | |
| Venter, J.C., Remington, K., Heidelberg, J.F., et al. | Environmental genome shotgun sequencing of the Sargasso Sea | Metagenomics | Research | Key research finding, showing potential for shotgun sequencing of complex communities; numerous discoveries | 2004 | Science, 304: 66-74 | 5 July 06 | |
| Ward, N. | New directions and interactions in metagenomics research | Metagenomics | Overview | Comprehensive overview of different strands of metagenomics research, plus issues and future developments | 2006 | FEMS Microbiology Letters, 55: 331-338 | 5 July 06 | |
| Tringe, S.G., & Rubin, E.M. | Metagenomics: DNA sequencing of environmental samples | Metagenomics | Overview | Detailed overview of metagenomic methods, research achievements, future potential and current problems | 2005 | Nature Reviews Genetics, 6: 805-814 | 5 July 06 | |
| Steele, H.L., & Streit, W.R | Metagenomics: advances in ecology and biotechnology | Metagenomics | Applications | Overview of potential applications for metagenomics, as well as more general findings | 2005 | FEMS Microbiology Letters, 247: 105-111 | 5 July 06 | |
| Edwards, R.A., & Rohwer, F. | Viral metagenomics | Metagenomics | Overview | Overview of viral metagenomics, its potential for phylogeny and population genetics, plus computational challenges | 2005 | Nature Reviews Microbiology, 3: 504-510 | 5 July 06 | |
| Galperin, M.Y. | Metagenomics: from acid mine to shining sea | Metagenomics | Overview | Review of shotgun sequence metagenomic studies (Venter et al.'s and Tyson et al.'s) | 2004 | Environmental Microbiology, 6: 543-545 | 5 July 06 | |
| Cowan, D., Meyer, Q., Stafford, W., et al. | Metagenomic gene discovery: past, present and future | Metagenomics | Overview | Discussion of metagenomics' achievements and potential, especially for gene discovery | 2005 | Trends in Biotechnology, 23: 321-329 | 5 July 06 | |
| Holmes, A.J., Gillings, M.R., Nield, B.S., et al. | The gene cassette metagenome is a basic resource for bacterial genome evolution | Metagenomics | Overview | Discussion of metagenomics in relation to the evolutionary resource of gene cassettes | 2003 | Environmental Microbiology, 5: 383-394 | 5 July 06 | |
| Wilmes, P., & Bond, P.L. | Metaproteomics: studying functional gene expression in microbial ecosystems | Metagenomics | Overview | Overview of the existing studies, challenges and potential of metaproteomics. | 2006 | Trends in Microbiology, 14: 92-97 | 29 July 06 | |
| Noonan, J.P., Hofreiter, M., Smith, D., et al. | Genomic sequencing of Pleistocene cave bears | Metagenomics | Overview | Palaeogenomics. Ancient Pleistocene cave bear DNA study using metagenomic techniques | 2005 | Science, 309: 597-599 | 29 July 06 | |
| Poinar, H.N., Schwartz, C., Qi, J., et al. | Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA | Metagenomics | Overview | Palaeogenomics. Ancient mammoth DNA study using metagenomic techniques | 2006 | Science, 311: 392-394 | 29 July 06 | |
| Allen, E.E., & Banfield, J.F. | Community genomics in microbial ecology and evolution | Metagenomics | Overview | Systems-oriented overview of metagenomics, with a particular focus on acid mine drainage community, plus development of metatranscriptomics and metaproteomics | 2005 | Nature Reviews Microbiology, 3: 489-498 | 5 July 06 | |
| Béjà,, O. | To BAC or not to BAC: marine ecogenomics | Metagenomics | Overview | Overview of metagenomic techniques, particularly large-insert BACs and fosmids versus small-insert shotgun libraries | 2004 | Current Opinion in Biotechnology, 15: 187-190 | 5 July 06 | |
| Béjà, O., Suzuki, M.T., Koonin, E.V., et al. | Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage | Metagenomics | Research | Disovery of proteorhodopsin genes in bacteria from analysis of a marine microbial metagenome. Several subsequent papers by Béjà's group extend the functional, phylogenetic and biogeographic analysis of proteorhodopsin and bacterial phototrophy | 2000 | Environmental Microbiology, 2: 516-529 | 5 July 06 | |
| Tringe, S.G., von Mering, C., Kobayashi, A., et al. | Comparative metagenomics of microbial communities | Metagenomics | Research | Comparative analysis of shotgun metagenomic data from farm soil, whale skeletons on the ocean floor, acid mine drainage and Sargasso Sea. Notable for taking a 'gene-centric' approach, concerned with functional fingerprinting rather than individual genome | 2005 | Science, 308: 554-557 | 5 July 06 | |
| Michael, C.A., Gillings, M.R., Holmes, A.J., et al. | Mobile gene cassettes: a fundamental resource for bacterial evolution | Metagenomics | Overview | Overview of gene cassette metagenome studies and their implications for evolutionary understanding | 2004 | The American Naturalist, 164: 1-12 | 5 July 06 | |
| Xu, J. | Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances | Metagenomics | Overview | Overview of metagenomics in the context of microbial ecology and genomics | 2006 | Molecular Ecology, 15: 1713-1731 | 5 July 06 | |
| Ram, R.J., VerBerkmoes, N.C., Thelen, M.P., et al. | Community proteomics of a natural microbial biofilm | Metagenomics | Overview | Metaproteomics. Early application of proteomic techniques to an acid mine drainage community. Validates functional predictions, discovers many novel proteins, and locates crucial metabolic process | 2005 | Science, 308: 1915-1920 | 29 July 06 | |
| Schulze, W.X., Gleixner, G., Kaiser, K., et al. | A proteomic fingerprint of dissolved organic carbon and soil particles | Metagenomics | Overview | Metaproteomics. Application of mass spectrometry proteomic analysis to the metaproteome of forest and lake soil communities. 'Fingerprints' the seasonal variation of protein activity in such communities and indicates their taxonomic composition | 2005 | Oecologia, 142: 335-343 | 29 July 06 | |
| Sebat, J.L., Colwell, F.S., & Crawford, R.L. | Metagenomic profiling: microarray analysis of an environmental genomic library | Metagenomics | Overview | Metatranscriptomics. Early application of microarray technology to a metagenome derived from a biofilm community in an aquifer. Profiles clones to identify important gene functions | 2003 | Applied and Environmental Microbiology, 69: 4927-4934 | 29 July 06 | |
| Wu, L., Thompson, D.K., Guangshan, L., et al. | Development and evaluation of functional gene arrays for detection of selected genes in the environment | Metagenomics | Overview | Metatranscriptomics. Early application of microarray technology to environmental DNA from sediment and soil. Provides 'proof of principle' that microarray analysis can be extended to complex environmental samples | 2001 | Applied and Environmental Microbiology, 67: 5780-5790 | 29 July 06 | |
| Chen, K., & Pachter, L. | Bioinformatics for whole-genome shotgun sequencing of microbial communities | Metagenomics | Overview | Introduces shotgun metagenomics to the bioinformatics community, discusses assembly and coverage issues for shotgunned metagenomes, and encourages involvement of computational biologists | 2005 | PLoS Computational Biology, 1: e24 | 5 July 06 | |
| Ordovas, J.M., & Mooser, V. | Metagenomics: the role of the microbiome in cardiovascular disease | Metagenomics | Applications | Discusses relationship of human microbiome (especially the gut microbiome) to health and the promise of metagenomics for providing deeper understandings of human physiology and disease | 2006 | Current Opinion in Lipidology, 17: 157-161 | 5 July 06 | |
| Hallam, S.J., Putnam, N., Preston, C.M., et al. | Reverse methanogenesis: testing the hypothesis with environmental genomics | Metagenomics | Research | Uses environmental DNA libraries to find genes underpinning methane consumption in archaeal communities in deep-sea sediments | 2004 | Science, 305: 1457-1462 | 5 July 06 | |
| Zhang, T., Breitbart, M., Lee, W.H., et al. | RNA viral community in human feces: prevalence of plant pathogenic viruses | Metagenomics | Research | Metagenomic analysis of viral DNA in human faeces. Discovers large number of live pathogenic plant viruses (rather than the expected human or animal viruses) and discusses complex symbioses between human gut microbes | 2006 | PLoS Biology, 4: e3 | 5 July 06 | |
| Li, X., & Qin, L. | Metagenomics-based drug discovery and marine microbial diversity | Metagenomics | Applications | Overviews metagenomic techniques and findings in relation to drug-discovery potential | 2005 | Trends in Biotechnology, 23: 349-543 | 5 July 06 | |
| Manichanh, C., Rigottier-Gois, L., Bonnaud, E., et al. | Reduced diversity of faecel microbiota in Crohn's disease revealed by a metagenomic approach | Metagenomics | Research | Uses a metagenomic approach to investigate microbial diversity in the human intestine. Finds that reduced complexity of the intestinal community is correlated with Crohn's disease | 2006 | Gut, 55: 205-211 | 5 July 06 | |
| Courtois, S., Cappellano, C.M., Ball, M., et al. | Recombinant environmental libraries provide access to microbial diversity for drug discovery from natural products | Metagenomics | Applications | Analyses environmental DNA libraries for novel natural products with the aim of developing metagenomics as an effective tool for drug discovery | 2003 | Applied and Environmental Microbiology, 69: 49-55 | 5 July 06 | |
| Schmeisser, C., Stöckigt, C., Raasch, C., et al. | Metagenome survey of biofilms in drinking-water networks | Metagenomics | Research | Analyses environmental DNA from biofilms in drinking-water valves to gain insight into community structure and metabolic potential | 2003 | Applied and Environmental Microbiology, 69: 7298-7309 | 5 July 06 | |
| Diaz-Torres, M.L., McNab, R., Spratt, D.A., et al. | Novel tetracycline resistance determinant from the oral metagenome | Metagenomics | Research | Functional analysis of human oral cavity metagenome for enzymatic activity that inactivates the antibiotic tetracycline | 2003 | Antimicrobial Agents and Chemotherapy, 47: 1430-1432 | 5 July 06 | |
| Wellington, E.M.H., Berry, A., & Krsek, M. | Resolving functional diversity in relation to microbial community structure in soil: exploiting genomics and stable isotype probing | Metagenomics | Overview | Overview of methods and techniques, as well as limitations of metagenomic analysis, especially in relation to functional metagenomics | 2003 | Current Opinion in Microbiology, 6: 295-301 | 5 July 06 | |
| Rondon, M.R., August, P.R., Betterman, A.D., et al. | Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms | Metagenomics | Research | Provides early evidence that genomic techniques can be applied to even the most complex microbial communities in soils | 2000 | Applied and Environmental Microbiology, 66: 2541-2547 | 5 July 06 | |
| Robinson, G.E., Grozinger, C.M., & Whitfield, C.W. | Sociogenomics: social life in molecular terms | Sociogenomics | Overview | Definitive overview of sociogenomics, which is outlined in relation to social and eusocial animals, the genes involved in solitary behaviour, and the social regulation of gene expression | 2005 | Nature Reviews Genetics, 6: 257-270 | 25 February 07 | |
| Robinson, G.E | Sociogenomics takes flight | Sociogenomics | Overview | Brief outline of sociogenomics in relation to a study of gene expression in ants. | 2002 | Science, 297: 204-205 | 25 February 07 | |
| Robinson, G.E., Fahrbach, S.E., & Winston, M.L | Insect societies and the molecular biology of social behavior | Sociogenomics | Overview | Early manifesto of sociogenomics, focused on honeybees and fire ants. | 1997 | BioEssays, 19: 1099-1108 | 25 February 07 | |
| Fitzpatrick, M.J., Ben-Shahar, Y., Smid, H.M., et al. | Candidate genes for behavioural ecology | Sociogenomics | Overview | Addresses sociogenomics in the context of behavioural ecology and advocates cross-species comparative studies of candidate genes. | 2005 | Trends in Ecology and Evolution, 20: 96-104 | 25 February 07 | |
| Robinson, G.E., & Ben-Shahar, Y. | Social behavior and comparative genomics: new genes or new gene regulation? | Sociogenomics | Overview | Well illustrated discussion of whether the evolution of social behaviour depends on the evolution of new genes with new functions or the novel regulation of genes. | 2002 | Genes, Brain and Behavior, 1: 197-203 | 25 February 07 | |
| Robinson, G.E. | Integrative animal behavior and sociogenomics | Sociogenomics | Overview | Outlines sociogenomics in relation to behavioural ecology and behavioural neuroscience; sets out a general research agenda for the future | 1999 | Trends in Ecology and Evolution, 14: 202-205 | 25 February 07 | |
| Robinson, G.E. | From society to genes with the honey bee | Sociogenomics | Overview | Discusses social behaviour in honeybees and how it can be understood through molecular genetics and, ultimately, sociogenomics. | 1998 | American Scientist, 86: 456-462 | 25 February 07 | |
| Scharf, M.E., Wu-Scharf, D., Pittendrigh, B.R., & Bennett, G.W. | Caste- and development-associated gene expression in a lower termite | Sociogenomics | Research | Macroarray analysis of gene expression in termite castes and intermediate developmental stages. Suggests further work to be done, involving other intermediary developmental stages and endosymbionts. | 2003 | Genome Biology, 4: R62 | 25 February 07 | |
| Sinha, S., Ling, X., Whitfield, C.W., Zhai, C., & Robinson, G.E. | Genome scan for cis-regulatory DNA motifs associated with social behavior in honey bees | Sociogenomics | Research | Describes research that connects cis regulation and social regulation of brain gene expression in honeybees; finds important similarities and differences between transcriptional networks in Drosophila and honeybees. | 2006 | PNAS, 103: 16352-16357 | 25 February 07 | |
| Krieger, M.J.B., & Ross, K.G. | Molecular evolutionary analyses of the odorant-binding protein gene Gp-9 in fire ants and other Solenopsis species | Sociogenomics | Research | Evolutionary analysis of the gene involved in single-queen and multiple-queen colonies in fire ants. | 2005 | Molecular Biology and Evolution, 22: 2090-2103 | 25 February 07 | |
| Pereboom, J.J.M., Jordan, W.C., Sumner, S., et al. | Differential gene expression in queen-worker caste determination in bumble-bees | Sociogenomics | Research | Anaysis of gene expression data in bumble bees to understand caste differentiation. Finds the crucial factor in the differentation of workers and queens is the timing of gene expression, not the involvement of different genes. | 2005 | Proceedings of the Royal Society B, 272: 1145-1152 | 25 February 07 | |
| Drapeau, M.D., Albert, S., Kucharski, R., et al. | Evolution of the Yellow/Major Royal Jelly protein family and the emergence of social behavior in honey bees | Sociogenomics | Research | Analysis of honey bee genome data to describe the molecular evolution of important protein families, which are then examined for gene expression patterns characteristic of developmental stages, castes and sexes. Concludes that these proteins played a key | 2006 | Genome Research, 16: 1385-1394 | 25 February 07 | |
| Ben-Shahar, Y. | The foraging gene, behavioral plasticity, and honeybee division of labor | Sociogenomics | Overview | Review of research concerned with the foraging gene and the mechanisms of transitions in the division of labour in honeybees. | 2005 | Journal of Comparative Physiology, 191: 987-994 | 25 February 07 | |
| Miura, T. | Developmental regulation of caste-specific characters in social-insect polyphenism | Sociogenomics | Overview | Examines gene expression studies of caste differentiation and body plan alteration in ants and termites. Links molecular and social evolution with a discussion of the interaction between ontogeny and environment. | 2005 | Evolution and Development, 7: 122-129 | 25 February 07 | |
| Evans, J.D., & Wheeler, D.E. | Gene expression and the evolution of insect polyphenisms | Sociogenomics | Overview | Helpful review of gene expression studies of insect social caste differentiation. | 2001 | BioEssays, 23: 62-68 | 25 February 07 | |
| Miura, T. | Morphogenesis and gene expression in the soldier-cast differentiation of termites | Sociogenomics | Overview | Description of caste-differentiation mechanisms in termites, as well as appropriate molecular methods of investigation. | 2001 | Insectes Sociaux, 48: 216-223 | 25 February 07 | |
| Nedelcu, A.M., & Michod, R.E. | The evolutionary origin of an altruistic gene | Sociogenomics | Research | Traces a social gene for reproductive altruism in multicellular algae (Volvox carteri) back to a solitary ancestor, then draws parallels with caste differentiation regulatory networks in social insects. | 2006 | Molecular Biology and Evolution, 23: 1460-1464 | 25 February 07 | |
| Scharf, M.E., Wu-Scharf, D., Zhou, X., et al. | Gene expression profiles among immature and adult reproductive castes of the termite Reticulitermes flavipes | Sociogenomics | Research | Describes use of macroarrays to examine caste-biased gene expression in termites. | 2005 | Insect Molecular Biology, 14: 31-44 | 25 February 07 | |
| Zhou, X., Oi, F.M., & Scharf, M.E. | Social exploitation of hexamerin: RNAi reveals a major caste-regulatory factor in termites. | Sociogenomics | Research | Describes use of RNAi gene silencing to identify regulatory mechanisms of caste differentiation in termites (specifically the supression of the differentiation of workers to soldiers). | 2006 | PNAS, 103: 4499-4504 | 25 February 07 | |
| Whitfield, C.W., Ben-Shahar, Y., Brillet, C., et al. | Genomic dissection of behavioral maturation in the honey bee | Sociogenomics | Research | Analysis of bee brain microarray data to understand age-related socially regulated shifts in honey bee work behaviour. | 2006 | PNAS, 103: 16068-16075 | 25 February 07 | |
| Linksvayer, T.A., & Wade, M.J. | The evolutionary origin and elaboration of sociality in the aculeate Hymenoptera: maternal effects, sib-social effects, and heterochrony | Sociogenomics | Overview | Investigates the evolution and development of sociality via 'indirect genetic effects' (genes expressed by social partners) in Hymenoptera. | 2005 | Quarterly Review of Biology, 80: 317-336 | 25 February 07 | |
| Miura, T. | Proximate mechanisms and evolution of caste polyphenism in social insects: from sociality to genes | Sociogenomics | Overview | Review of work on regulatory mechanisms of social behaviour and the evolution of social behaviour, particularly in relation to termites and the molecular bases of caste differentiation. | 2004 | Ecological Research, 19: 141-148 | 25 February 07 | |
| Evans, J.D., & Wheeler, D.E. | Differential gene expression between developing queens and workers in the honey bee, Apis mellifera | Sociogenomics | Research | Early demonstration that the regulation of gene expression rather than genetic polymorphism is the mechanism of caste differentiation in honey bees. | 1999 | PNAS, 96: 5575-5580 | 26 February 07 | |
| Whitfield, C.W., Cziko, A.-M., and Robinson, G.E. | Gene expression profiles in the brain predict behavior in individual honey bees | Sociogenomics | Research | Microarray study of gene expression in honey bee brains. Demonstrates high neural and behavioural plasticity in bees. | 2003 | Science, 302: 296-299 | 26 February 07 | |
| Sumner, S., Pereboom, J.J., & Jordan, W.C. | Differential gene expression and phenotypic plasticity in behavioral castes of the primitively eusocial wasp, Polistes canadensis | Sociogenomics | Research | Comparative analysis of caste-associated genes in wasps and other 'advanced' eusocial insects. Finds four independent origins of eusociality and nine evolutionarily important genes. | 2006 | Proceedings. Biological Science, 273: 19-26 | 26 February 07 | |
| Csete, M.E., & Doyle, J.C. | Reverse engineering of biological complexity | Systems Biology | Overview | Outlines and advocates a reverse engineering approach for understanding systems. Draws parallels between technological systems and biological systems. Uses the Lego analogy to demonstrate the importance of protocols (assembly rules) over modularity. | 2002 | Science, 295: 1664-1669 | 26 February 07 | |
| Kitano, H. | Computational systems biology | Systems Biology | Overview | Famous systems biology manifesto that outlines how computational biology when integrated with experimental biology can produce systems biology. Suggests practical innovations in pharmaceutical applications. | 2002 | Nature, 420: 206-210 | 26 February 07 | |
| Attur, M.G., Dave, M.N., Tsunoyama, K., et al. | 'A system biology' approach to bioinformatics and functional genomics in complex human diseases: arthritis | Systems Biology | Overview | Discusses how systems biology can develop out of genomics and what it can offer the investigation of human disease. | 2002 | Current Issues in Molecular Biology | 26 February 07 | |
| Aggarwal, K., & Lee, K.H. | Functional genomics and proteomics as a foundation for systems biology | Systems Biology | Overview | Sets out a general rationale and goals for systems biology, with an emphasis on how models can be used with omic data. | 2003 | Briefings in Functional Genomics and Proteomics, 2: 175-184 | 26 February 07 | |
| Ge, H., Walhout, A.J.M., & Vidal, M. | Integrating 'omic' information: a bridge between genomics and systems biology | Systems Biology | Overview | Discusses how to move from omic datasets to integrated systems biology. | 2003 | Trends in Genetics | 26 February 07 | |
| Alon, U. | Biological networks: The tinkerer as an engineer | Systems Biology | Overview | Advocates an engineering approach for understanding biological systems. Sets out three principles (modularity, robustness, recurring circuit elements). Argues that the aim of systems biology is to understand laws of nature that unite evolved and designed | 2003 | Science, 301: 1866-1867 | 26 February 07 | |
| Kitano, H. | Looking beyond the details: a rise in system-oriented approaches in genetics and molecular biology | Systems Biology | Overview | Outlines systems biology; rejects von Bertalanffy's general systems theory as a candidate for any 'serious scientific discipline'. Emphasizes the investigation of system states rather than system components. Sets out phases of systems biologic research an | 2002 | Current Genetics, 41: 1-10 | 26 February 07 | |
| Brent, R. | A partnership between biology and engineering | Systems Biology | Overview | Discusses the relationship between synthetic and systems biology. Bemoans the vagueness of systems biology definitions, and argues that a systems biology 'that is more than a collection of slogans' will have to align itself with the engineering capacities | 2004 | Nature Biotechnology, 22: 1211-1214 | 26 February 07 | |
| Huang, S. | Back to the biology in systems biology: what can we learn from biomolecular networks? | Systems Biology | Overview | Outlines two trends in network analysis: localists and globalists. Outlines ways in which to study networks in order to understand global dynamics and system-level properties. | 2004 | Briefings in Functional Genomics and Proteomics, 2: 279-297 | 26 February 07 | |
| Fox Keller, E. | The century beyond the gene | Systems Biology | Overview | Useful view-at-a-distance of systems biology. Argues against laws/rules or a universal conceptual framework as the first aim of systems biology, and proposes instead a 'dynamic relational epistemology' that can form the basis for new methods, concepts and | 2005 | Journal of Biosciences, 30: 101-108 | 26 February 07 | |
| Kitano, H. | Biological robustness | Systems Biology | Overview | Focuses on the systems property of robustness: how it works, mechanisms that bring it about, how to understand it. Relates robustness to evolvability, and then to the disease system of cancer. Concludes with a manifesto to develop a theory of robustness. | 2004 | Nature Reviews Genetics, 5: 826-837 | 26 February 07 | |
| Borodina, I., & Nielsen, J. | From genomes to in silico cells via metabolic networks | Systems Biology | Overview | Discusses the importance of genome-scale metabolic modelling for systems biology. | 2005 | Current Opinion in Biotechnology, 16: 350-355 | 27 February 07 | |
| Sorger, P.K. | A reductionist's systems biology | Systems Biology | Overview | Outlines system biology; sceptical towards engineering approaches using circuit analogies. Advocates chemical reaction engineering and the eventual fusion of cybernetic and reaction-based perspectives. | 2005 | Current Opinion in Cell Biology, 17: 9-11 | 27 February 07 | |
| Davidson, E.H., Rast, J.P., Oliveri, P., et al. | A genomic regulatory network for development | Systems Biology | Research | Demonstration of the feasibility of a systems biology approach through the provision of a 'first stage' model of gene regulation in sea urchin development. | 2002 | Science, 295: 1669-1678 | 27 February 07 | |
| Lazebnik, Y. | Can a biologist fix a radio? - Or, what I learned while studying apoptosis | Systems Biology | Overview | Often cited reflection on how a biologist might approach a radio and fail to understand or fix it. Advocates an engineering approach to systems understanding. | 2002 | Cancer Cell, 2: 179-182 | 27 February 07 | |
| Ideker, T., & Lauffenburger, D. | Building with a scaffold: emerging strategies for high- to low-level cellular modeling | Systems Biology | Overview | Very helpful overview of levels of modelling strategies available (and being developed) for understanding system networks. | 2003 | Trends in Biotechnology, 21: 255-262 | 27 February 07 | |
| Kell, D.B., Brown, M., Davey, H.M., et al. | Metabolic footprinting and systems biology: the medium is the message | Systems Biology | Overview | Outlines the potential contributions of metabolomics, specifically metabolomic footprinting (measurements of metabolites excreted by a cell in particular conditions), to systems biology | 2005 | Nature Reviews Microbiology, 3: 557-565 | 27 February 07 | |
| Bothwell, J.H.F. | The long past of systems biology | Systems Biology | Overview | Sceptical discussion of systems biology, especially re its revolutionariness. | 2006 | New Phytologist, 170: 6-10 | 27 February 07 | |
| Ideker, T., Winslow, L.R., and Lauffenburger, A.D. | Bioengineering and systems biology | Systems Biology | Overview | Discusses how systems biology involves a bioengineering approach. | 2006 | Annals of Biomedical Engineering, 34: 1226-1233 | 27 February 07 | |
| Hood, L., heath, J.R., Phelps, M.E., & Lin, B. | Systems biology and new technologies enable predictive and preventive medicine | Systems Biology | Overview | Outlines how systems biology will transform health science and result in personalized and preventive medicine. | 2004 | Science, 306: 640-643 | 27 February 07 | |
| Weston, A.D., and Hood, L. | Systems biology, proteomics, and the future of health care: toward predictive, preventative, and personalized medicine | Systems Biology | Overview | Another outline of how systems biology achievements presage a transformation in approaches to health. Focuses on the contribution proteomics will make. | 2004 | Journal of Proteome Research, 3: 179-196 | 27 February 07 | |
| Pennisi, E. | Tracing life's circuitry | Systems Biology | Overview | A useful overview from a science journalist of systems biology aims, players and challenges. | 2003 | Science, 302: 1646-1649 | 27 February 07 | |
| Kitano, H. | Systems biology: a brief overview | Systems Biology | Overview | Another much cited systems biology manifesto from a founder of the field. It emphasizes the study of the structure and dynamics of systems functions, rather than the parts. | 2002 | Science, 295: 1662-1664 | 27 February 07 | |
| Ehrenberg, M., Elf, J., Aurell, E., et al. | Systems biology is taking off | Systems Biology | Overview | Sketch of important aspects of systems biology and its challenges. | 2003 | Genome Research, 13: 2377-2380 | 27 February 07 | |
| Kirschner, M.W. | The meaning of systems biology | Systems Biology | Overview | Very brief outline of what systems biology could be. | 2005 | Cell, 121: 503-504 | 27 February 07 | |
| Apic, G., Ignatovic, T., Boyer, S., & Russell, R.B. | Illuminating drug discovery with biological pathways | Systems Biology | Applications | Discusses failure of drug discovery in genomics and how systems biology might advance the success of drug trials. | 2005 | FEBS Letters 579: 1872-1877 | 27 February 07 | |
| Werner, E. | Genome semantics, in silico multicellular systems and the Central Dogma | Systems Biology | Overview | Introduces the idea of 'genome semantics' as understanding the genome in its multicellular context. Advocates an 'escape from the constraints of the Central Dogma' via in silico models. | 2005 | FEBS Letters, 579: 1779-1782 | 27 February 07 | |
| Uetz, P., and Finley Jr., R.L. | From protein networks to biological systems | Systems Biology | Overview | Discusses protein interaction networks and how these will contribute to systems biology. | 2005 | FEBS Letters 579: 1821-1827 | 27 February 07 | |
| Schlitt, T., & Brazma, A. | Modelling gene networks at different organizational levels | Systems Biology | Overview | Helpful categorization of modelling strategies for gene networks, and the issues involved in bringing these up to the genome scale. | 2005 | FEBS Letters 579: 1859-1866 | 27 February 07 | |
| Hasty, J., McMillen, D., Isaacs, F., & Collins, J.J. | Computational studies of gene regulatory networks: in numero molecular biology | Systems Biology | Overview | Discussion of how genetic networks can be understood through a combination of experimental work on natural systems and tests of engineered networks. This paper also fits into the synthetic biology literature. | 2001 | Nature Reviews Genetics, 2: 268-279 | 27 February 07 | |
| Bork, P. | Is there biological research beyond systems biology? A comparative analysis of terms | Systems Biology | Overview | Editorial discussing proliferation of systems biology papers in relation to genomics and other omics (shows sharp rise in synthetic biology too). Argues that systems biology was inevitable given the technology and data available. | 2005 | Molecular Systems Biology | 27 February 07 | |
| Levesque, M.P., & Benfey, P.N. | Systems biology | Systems Biology | Overview | Very short but interesting division of systems biology into two camps: panomicists (bottom up) and dynamicists (top down). | 2004 | Current Biology, 14: R179-R180 | 27 February 07 | |
| Ideker, T., Galitski, T., & Hood, L. | A new approach to decoding life: systems biology | Systems Biology | Overview | Classic early paper that outlines systems biology's aims and approaches. Describes 'proof of principle' examples of successful systems biology. | 2001 | Annual Review of Genomics and Human Genetics, 2: 343-372 | 27 February 07 | |
| Barabasi, A.-L., & Oltvai, Z.N. | Network biology: understanding the cell's functional organization | Systems Biology | Overview | Discusses how network tools and theory make a vital contribution to systems biology. Emphasizes teh scale-free nature of networks in cells and universal laws that govern them. | 2004 | Nature Reviews Genetics, 5: 101-113 | 24 April 07 | |
| Hood, L., and Perlmutter, R.M. | The impact of systems approaches on biological problems in drug discovery | Systems Biology | Applications | Outline of how systems biology can contribute to stalled drug discovery. | 2004 | Nature Biotechnology, 22: 1215-1217 | 27 February 07 | |
| Arita, M., Robert, M., & Tomita, M. | All systems go: launching cell simulation fueled by integrated experimental biology data | Systems Biology | Overview | Outlines the role of computer simulations in systems biology. | 2005 | Current Opinion in Biotechnology, 16: 344-349 | 27 February 07 | |
| Snoep, J.L. | The Silicon Cell initiative: working towards a detailed kinetic description at the cellular level | Systems Biology | Overview | Discusses the Silicon Cell project as a repository of kinetic models of enzyme systems. | 2005 | Current Opinion in Biotechnology, 16: 336-343 | 27 February 07 | |
| Cornish-Bowden, A. | Putting the systems back into systems biology | Systems Biology | Overview | Criticizes much current systems biology for being no more than old reductionist approaches writ large. Outlines what 'genuinely systemic thinking' would involve and gives it an historical basis. | 2006 | Perspectives in Biology and Medicine, 49: 475-489 | 28 February 07 | |
| Bruggeman, F.J., & Westerhoff, H.V. | The nature of systems biology | Systems Biology | Overview | A very interesting general discussion of systems biology from the perspective of two philosophically oriented practising systems biologists. | 2006 | Trends in Microbiology, 15: 45-50 | 28 February 07 | |
| Trewavas, A. | A brief history of systems biology | Systems Biology | Overview | A rather unusual but thought-provoking history of systems biology from the point of view of a well-known plant scientist. | 2006 | Plant Cell, 18: 2420-2430 | 28 February 07 | |
| Barrett, C.L., Kim, T.Y., Kim, H.U., et al. | Systems biology as a foundation for genome-scale synthetic biology | Systems Biology | Overview | Argues that systems biology is the basis for one sort of synthetic biology, and outlines the flow of benefits from the former to the latter. | 2006 | Current Opinion in Biotechnology, 17: 488-492 | 28 February 07 | |
| Mesarovic, M.D., Sreenath, S.N., & Keene, J.D. | Search for organising principles: understanding in systems biology | Systems Biology | Overview | Useful for history and definitions of systems biology. Calls for organising principles to be developed, not only models. Gets a bit technical in some parts but the general argument is in ordinary language. | 2004 | Systems Biology, 1: 19-27 | 28 February 07 | |
| Koonin, E.V., and Wolf, Y.I. | Evolutionary systems biology: links between gene function and evolution | Systems Biology | Overview | Outlines elements of an evolutionary systems biology and argues that systems biology has to be understood within the general framework of evolutionary biology. | 2006 | Current Opinion in Biotechnology, 17: 481-487 | 28 February 07 | |
| Sako, Y. | Imaging single molecules in living cells for systems biology | Systems Biology | Overview | Discusses the importance of single molecule imaging (SMI) for systems biology, especially for the quantitative analysis SMI provides. | 2006 | Molecular Systems Biology, doi: 10.1038/msb4100100 | 28 February 07 | |
| Hood, L., & Galas, D. | The digital code of DNA | Systems Biology | Overview | Argues that DNA is the digital core of information (within an informational hierarchy) for organisms and that systems biology is an informational science that allows the 'grand unification of the biological sciences'. | 2003 | Nature, 421: 444-448 | 28 February 07 | |
| Kell, D.B. | Metabolomics and systems biology: making sense of the soup | Systems Biology | Overview | Very useful outline of metabolomics and how it contributes to systems biology. | 2004 | Current Opinion in Microbiology, 7: 296-307 | 28 February 07 | |
| Noble, D. | Modeling the heart - from genes to cells to the whole organ | Systems Biology | Overview | An outline of 'systems physiology' or what a systems biology focused on organs, such as the heart, would entail. | 2002 | Science, 295: 1678-1682 | 28 February 07 | |
| Oltvai, Z.N., & Barabasi, A.-L. | Life's complexity pyramid | Systems Biology | Overview | A popular diagrammatic outline of systems biology in which the science's objects and methods are ranked according to complexity. The pyramid peaks in universal organizing principles. | 2002 | Science, 298: 763-764 | 28 February 07 | |
| Hood, L. | Systems biology: integrating technology, biology and computation | Systems Biology | Overview | Another outline, from one of systems biology's founders, of systems biology as an informational science. Hood argues that systems-biologic medicine will transform understanding and treatment of ageing. | 2003 | Mechanisms of Ageing and Development, 124: 9-16 | 28 February 07 | |
| Toscano, W.A., Oehlke, K.P. | Systems biology: new approaches to old environmental health problems | Systems Biology | Applications | Sees systems biology as the natural approach to environmental health and outlines how it would work. | 2005 | International Journal of Environmental Research and Public Health, 2: 4-9 | 28 February 07 | |
| Hohmann, S. | The Yeast Systems Biology Network: mating communities | Systems Biology | Overview | An outline of yeast systems biology and the groups involved; also discusses why yeast is the ideal system for whole cell analysis. | 2005 | Current Opinion in Biotechnology, 16: 356-360 | 28 February 07 | |
| Philippi, S., & Kohler, J. | Addressing the problems with life-science databases for traditional uses and systems biology | Systems Biology | Overview | Discusses database obstacles that obstruct progress in systems biology. | 2006 | Nature Reviews Genetics, 7: 482-488 | 28 February 07 | |
| Oliver, S.G. | From genomes to systems: the path with yeast | Systems Biology | Overview | Outlines yeast systems biology with a focus on metabolic control analysis. | 2006 | Philosophical Transactions of the Royal Society B, 361: 477-482 | 28 February 07 | |
| Selinger, D.W., Wright, M.A., & Church, G.M. | On the complete determination of biological systems | Systems Biology | Overview | Defines 'model', and argues that biological systems can be completely determined by an appropriate model. | 2003 | Trends in Biotechnology, 21: 251-254 | 28 February 07 | |
| Kell, D.B. | Metabolomics, modelling and machine learning in systems biology - towards an understanding of the languages of cells | Systems Biology | Overview | Detailed outline of potential contributing approaches to systems biology, with an emphasis on the different phases of hypothesis-dependent and hypothesis-generating research. | 2006 | FEBS Journal, 273: 873-894 | 28 February 07 | |
| Forst, C.V. | Host-pathogen systems biology | Systems Biology | Overview | Marries host-pathogen systems with systems-biologic approaches. | 2006 | Drug Discovery Today, 11: 220-227 | 28 February 07 | |
| Ahn, A.C., Tewari, M., Poon, C.-S., & Phillips, R.S. | The limits of reductionism in medicine: could systems biology offer an alternative? | Systems Biology | Applications | Discusses how the constraints of reductionism in medicine could be overcome with a systems-biologic approach. | 2006 | PLoS Medicine | 28 February 07 | |
| Auffray, C., Imbeaud, S., Roux-Rouquie, M., & Hood, L. | From functional genomics to systems biology: concepts and practices | Systems Biology | Overview | Outlines systems biology's approaches and aims, and illustrates them with galactose utilization in yeast and sea urchin development networks (frequently used examples in these first few years of systems biology). | 2003 | Comptes Rendus Biology, 326: 879-892 | 28 February 07 | |
| Letelier, J.-C., Soto-Andrade, J., Abarzua, F.G., et al. | Organizational invariance and metabolic closure: analysis in terms of (M,R) systems | Systems Biology | Overview | Clarifies and extends Robert Rosen's (M,R) system idea. Rosen is frequently mentioned as a predecessor of systems biology, but his ideas are rarely put to work. | 2006 | Journal of Theoretical Biology, 238: 949-961 | 28 February 07 | |
| Wolkenhauer, O., & Mesarovic, M. | Feedback dynamics and cell function: why systems biology is called Systems Biology | Systems Biology | Overview | Argues that systems biology should not be engineering applied to biology, but a more profound integration of systems and control theory to molecular and cellular data. Advocates mathematical modelling and simulation to do so. | 2005 | Molecular BioSystems, 1: 14-16 | 28 February 07 | |
| Cornish-Bowden, A., Cardenas, M.L., Letelier, J.-C., et al. | Understanding the parts in terms of the whole | Systems Biology | Overview | A non-technical and insightful account of how Robert Rosen's work is useful for systems biology. | 2004 | Biology of the Cell, 96: 713-717 | 28 February 07 | |
| Burja, A.M., Dhamwichukorn, S., & Wright, P.C. | Cyanobacterial postgenomic research and systems biology | Systems Biology | Overview | Outline of how microbial genomics is leading to a systems-biologic approach, and why cyanobacteria would be a good focus for systems biology. | 2003 | Trends in Biotechnology, 21: 504-511 | 28 February 07 | |
| Ishii, N., Robert, M., Nakayama, Y., et al. | Toward large-scale modeling of the microbial cell for computer simulation | Systems Biology | Overview | Helpful outline of the different types of models of microorganisms available, and the issues involved in constructing a complete model of a microbial cell. | 2004 | Journal of Biotechnology, 113: 281-294 | 28 February 07 | |
| Minorsky, P.V. | Achieving the in silico plant. Systems biology and the future of plant biological research | Systems Biology | Overview | Outlines systems biology and the integration of approaches and data needed for plant systems biology. [PubMed author citation misattributed] | 2003 | Plant Physiology, 132: 404-409 | 28 February 07 | |
| Hammer, G.L., Sinclair, T.R., Chapman, S.C., and van Oosterom, E. | On systems thinking, systems biology, and the in silico plant | Systems Biology | Overview | Argues that plant systems biology needs a more top-down approach than the bottom-up one usually advocated. | 2004 | Plant Physiology, 134: 909-911 | 28 February 07 | |
| Cassman, M., Arkin, A., Doyle, F., et al. | WTEC Panel Report on Assessment of International Research and Development in Systems Biology | Systems Biology | Overview | This is a report that discusses systems biology from a wide range of perspectives and provides lots of data about systems biology and centres around the world. | 2005 | WTEC Evaluation Centre, Baltimore, MD: www.wtec.org/sysbio/ | 28 February 07 | |
| Stark, J., Callard, R., & Hubank, M. | From the top down: towards a predictive biology of signalling networks | Systems Biology | Overview | Discussion of top-down modelling approaches especially in relation to reconstructing functional networks from microarray data. | 2003 | Trends in Biotechnology, 21: 290-293 | 1 March 07 | |
| Stelling, J. | Mathematical models in systems biology | Systems Biology | Overview | Very clear overview of major modelling approaches in (microbial) systems biology. | 2004 | Current Opinion in Microbiology, 7: 513-518 | 1 March 07 | |
| Thiel, K. | Systems Biology, Incorporated? | Systems Biology | Overview | Early overview of systems biology companies: their commercial products and marketing strategies. | 2006 | Nature Biotechnology, 24: 1055-1057 | 1 March 07 | |
| Nicholson, J.K. | Global systems biology, personalized medicine and molecular epidemiology | Systems Biology | Overview | Outlines the medical implications of systems biology. Provides a helpful glossary of metabolite-related terminology. | 2006 | Molecular systems Biology, doi: 10.1038/msb4100095 | 1 March 07 | |
| Medina, M. | Genomes, phylogeny, and evolutionary systems biology | Systems Biology | Overview | Outlines 'evolutionary systems biology' as more extensive comparative genomics plus the comparison of biological networks of different levels. | 2005 | PNAS, 102 (Suppl. 1): 6630-6635 | 1 March 07 | |
| Westerhoff, H.V., & Palsson, B.O. | The evolution of molecular biology into systems biology | Systems Biology | Overview | Traces two historical roots of contemporary systems biology: molecular biology and non-equilibrium thermodynamics. Recommends looking back at some of the earlier literature, rather than reinventing it. | 2004 | Nature Biotechnology, 22: 1249-1252 | 1 March 07 | |
| Nicholson, J.K., Holmes, E., Lindon, J.C., & Wilson, I.D. | The challenges of modeling mammalian biocomplexity | Systems Biology | Overview | Very stimulating discussion of systems biology in relation to single cells, multicellular organisms, and 'superorganisms'. Focuses on mammalian-microbe interactions in the gut. | 2004 | Nature Biotechnology, 22: 1268-1274 | 1 March 07 | |
| Strange, K. | The end of 'naive reductionism': rise of systems biology or renaissance of physiology? | Systems Biology | Overview | Discusses the common goals of systems biology and physiology, but their different trajectories (systems biology = waxing; physiology = waning). Makes a case for 'big picture' systems-biologic physiology. | 2005 | Perspectives in Cell Physiology, 288: C968-C974 | 1 March 07 | |
| Mustacchi, R., Hohmann, S., & Nielsen, J. | Yeast systems biology to unravel the network of life | Systems Biology | Overview | More on yeast systems biology, prefaced by a discussion of how systems biology will impact on the general public. | 2006 | Yeast, 23: 227-238 | 1 March 07 | |
| Kitano, H., & Oda, K. | Self-extending symbiosis: a mechanism for increasing robustness through evolution | Systems Biology | Overview | A very interesting discussion of the evolutionary achievement of system robustness through the extension of 'self' via symbiosis with 'foreign' entities. Focuses on the immune system and its enhancement through the maintenance of prokaryote symbioses. See | 2006 | Biological Theory, 1: 61-66 | 1 March 07 | |
| Kitano, H. | Cancer as a robust system: implications for anticancer therapy | Systems Biology | Overview | Explores the property of robustness in systems of cancer cells, and the implications of such systems-based analysis for treatment. | 2004 | Nature Reviews Cancer, 4: 227-235 | 1 March 07 | |
| Auffray, C., Imbeaud, S., Roux-Rouquie, M., & Hood, L. | Self-organized living systems: conjunction of a stable organization with chaotic fluctuations in biological space-time | Systems Biology | Overview | Argues the 'analytical reductionist framework' is insufficient to understand living systems. Explores self-organization through the 'biosystemic paradigm' of systems biology. | 2003 | Philosophical Transactions of the Royal Society A, 361: 1125-1139 | 1 March 07 | |
| Keller, E.F. | Revisiting 'scale-free' networks | Systems Biology | Overview | Sceptical discussion of the significance of power-law distributions or scale-free networks; downplays the existence of general laws in biology. | 2005 | BioEssays, 27: 1060-1068 | 1 March 07 | |
| Henry, C.M. | Systems biology | Systems Biology | Overview | Jargon-free journalistic outline of systems biology. Covers academic science as well as commercial research. | 2003 | Chemical and Engineering News, 81: 45-55 | 1 March 07 | |
| Greenbaum, D., Luscombe, N.M., Jansen, R., et al. | Interrelating different types of genomic data, from proteome to secretome: 'oming in on the function | Systems Biology | Overview | Helpful discussion of integrating all levels of 'omic data (all omics carefully defined), along with experimental and computational approaches. Never mentions systems biology. | 2001 | Genome Research, 11: 1463-1468 | 1 March 07 | |
| van der Greef, J., Stroobant, P., & van der Heijden, R. | The role of analytical sciences in medical systems biology | Systems Biology | Overview | Outlines 'medical systems biology' and the challenges it faces in making progress. | 2004 | Current Opinion in Chemical Biology, 8: 559-565 | 1 March 07 | |
| Glaser, P., & Boone, C. | Beyond the genome: from genomics to systems biology | Systems Biology | Overview | Editorial overview of a special issue that tackles the transition from genomics to systems biology in several areas of microbiology. | 2004 | Current Opinion in Microbiology, 7: 489-491 | 1 March 07 | |
| Tadmor, B., & Tidor, B. | Interdisciplinary research and education at the biology-engineering-computer science interface: a perspective | Systems Biology | Overview | Discusses the interdisciplinarity essential to systems biology and how to achieve it. | 2005 | Drug Discovery Today, 10: 1183-1189 | 1 March 07 | |
| Heath, J.R., Phelps, M.E., & Hood, L. | NanoSystems biology | Systems Biology | Overview | Discusses systems biology in relation to nanotechnologies, microfluidics and molecular imaging techniques. Outlines how these techniques need to develop to serve systems biology, and what their diagnostic and therapeutic benefits could be within a systems | 2003 | Molecular Imaging and Biology, 5: 312-325 | 24 April 07 | |
| Wolkenhauer, O. | Systems biology: the reincarnation of systems theory applied in biology? | Systems Biology | Overview | Provides a historical outline of earlier systems biology attempts with a particular emphasis on Robert Rosen's relational biology, which is reworked for contemporary systems biology. | 2001 | Briefings in Bioinformatics, 2: 258-270 | 1 March 07 | |
| Norris, V., Cabin, A., & Zemirline, A. | Hypercomplexity | Systems Biology | Overview | Uses E. coli as the exemplar of a cellular system through which to define and employ new terminology to understand system processes: hypercomplexity, hyperstructures, competitive coherence. | 2005 | Acta Biotheoretica, 53: 313-330 | 1 March 07 | |
| Boogerd, F.C., Bruggeman, F.J., Richardson, R.C., et al. | Emergence and its place in nature: a case study of biochemical networks | Systems Biology | Overview | A philosophically oriented discussion of the system properties of biochemical networks. Integrates Broad's concept of emergence with mechanistic explanation. | 2005 | Synthese, 145: 131-164 | 1 March 07 | |
| Bruggeman, F.J., Westerhoff, H.V., & Boogerd, F.C. | BioComplexity: a pluralist research strategy is necessary for a mechanistic explanation of the 'live' state | Systems Biology | Overview | Advocacy of a pluralist research programme to understand complex living systems. Discusses reductionist and emergentist approaches. | 2002 | Philosophical Psychology, 15: 411-440 | 1 March 07 | |
| Noble, D. | The future: putting Humpty-Dumpty together again | Systems Biology | Overview | Discussion of top-down, bottom-up, and middle-out approaches in relation to systems-biologic modelling. | 2003 | Biochemical Society Transactions, 31: 156-158 | 1 March 07 | |
| Kell, D.B., & Oliver, S.G. | Here is the evidence, now what is the hypothesis? The complementary roles of inductive and hypothesis-driven science in the post-genomic era | Systems Biology | Overview | Interesting discussion of reductionism, induction and the role of hypotheses in relation to systems biology. | 2003 | BioEssays, 26: 99-105 | 1 March 07 | |
| Endy, D., & Brent, R. | Modelling cellular behaviour | Systems Biology | Overview | Optimistic non-technical account of progress in the modelling of cellular networks. | 2001 | Nature, 409: 391-395 | 1 March 07 | |
| Bray, D. | Molecular networks: the top-down view | Systems Biology | Overview | Clear outline of molecular network modelling; argues analysis is necessary at multiple levels. | 2003 | Science, 301: 1864-1865 | 1 March 07 | |
| Neves, S.R., & Iyengar, R. | Modeling of signaling networks | Systems Biology | Overview | Discusses issues of modelling in relation to biochemical networks and their system-level behaviours. Outlines emergent properties of such networks: hypersensitivity, flexible bistability, rhythmic behaviour. | 2002 | BioEssays, 24: 1110-1117 | 1 March 07 | |
| Ideker, T., Thorsson, V., Ranish, J.A., et al. | Integrated genomic and proteomic analyses of a systematically perturbed metabolic network | Systems Biology | Research | A 'proof of principle' paper that establishes systems biology as an effective approach. Uses microarrays and mass spectrometry to analyse mRNA and protein levels when genes in galactose utilization pathways of yeast were systematically perturbed. | 2001 | Science, 292: 929-934 | 1 March 07 | |
| Wiss, J.N., Qu, Z., & Garfinkel, A. | Understanding biological complexity: lessons from the past | Systems Biology | Overview | Locates systems biology in the Hodgkin-Huxley model of nerve excitation and Turing's work on biological morphogenesis (both early 1950s). Argues that an integration of these two very different modelling approaches is needed for advances in biological unde | 2003 | FASEB Journal, 17: 1-6 | 1 March 07 | |
| Kohl, P., Noble, D., Winslow, R.L., & Hunter, P.J. | Computational modelling of biological systems: tools and visions | Systems Biology | Overview | Outlines the development of in silico organs which can be integrated into a comprehensive in silico model of the organism, the physiome. Takes cardiac computer models as a starting point and concludes with an outline of applications and social benefits. | 2000 | Philosophical Transactions of the Royal Society A, 358: 579-610 | 1 March 07 | |
| Brazma, A., Krestyaninova, M., & Sarkans, U. | Standards for systems biology | Systems Biology | Overview | Discusses database standardization and its issues in relation to systems biology. | 2006 | Nature Reviews Genetics, 7: 593-605 | 1 March 07 | |
| Collins, F.S., Gren, E.D., Guttmacher, A.E., et al. | A vision for the future of genomics research: a blueprint for the genomic era | Genomics | Overview | Outlines all the achievements of genomics to date and broadly anticipates its future (including social benefits and ethical issues). | 2003 | Nature, 422: 835-847 | 1 March 07 | |
| Snyder, M., & Gerstein, M. | Defining genes in the genomic era | Genomics | Overview | Claims 'genome' is easily defined but not 'gene'. Finds five criteria of a gene, but their application is messy. Believes more functional annotation may help. | 2003 | Science, 300: 258-260 | 1 March 07 | |
| Lander, E.S., & Weinberg, R.A. | Journey to the center of biology | Genomics | Overview | Argues that genomics has revolutionized studies of heredity, and caused reductionism to yield to holism. Concludes that this shift will bring about an entirely new kind of biology in the 21st century. | 2000 | Science, 287: 1777-1282 | 1 March 07 | |
| Gilbert, W. | Towards a paradigm shift in biology | Genomics | Overview | Brief argument that genomics has transformed traditional biology and opened up a new paradigm of biological inquiry. | 1991 | Nature, 349: 99 | 1 March 07 | |
| Pennisi, E. | Searching for the genome's second code | Genomics | Overview | A journalist's outline of the 'second' human genome project, for the regulatory code. | 2004 | Science, 306: 632-635 | 1 March 07 | |
| Clayton, E.W. | Through the lens of the sequence | Genomics | Overview | Overview of ethical, legal and social issues associated with the Human Genome Project. | 2001 | Genome Research, 11: 659-664 | 2 March 07 | |
| Binnewies, T.T., Motro, Y., Hallin, P.F., et al. | Ten years of bacterial genome sequencing: comparative-genomics-based discoveries | Genomics | Overview | Detailed overview of prokaryote genomics and the many discoveries it has made. Concludes with a discussion of applications and intellectual property rights. | 2006 | Functional &Integrative Genomics, 6: 165-185 | 2 March 07 | |
| Abby, S., & Daubin, V. | Comparative genomics and the evolution of prokaryotes | Genomics | Overview | Discusses the many achievements and problems of evolutionary microbial genomics. | 2007 | Trends in Microbiology, doi: 10.1016/j.tim.2007.01.007 | 2 March 07 | |
| Goodfellow, P. | A celebration and a farewell | Genomics | Overview | Very brief but interesting reflections on the relationship between genetics and genomics, and model organisms. | 1997 | Nature Genetics, 16: 209-210 | 2 March 07 | |
| Hopkins, M.M., Mahdi, S., Patel, P., and Thomas, S.M. | DNA patenting: the end of an era? | Genomics | Overview | Describes and predicts the end of the surge in DNA patent applications that arose from genomics. | 2007 | Nature Biotechnology, 25: 185-187 | 2 March 07 | |
| Boore, J.L. | The use of genome-level characters for phylogenetic reconstruction | Genomics | Overview | Uses genome-level characters (e.g.: gene arrangements) instead of genome sequence to construct phylogenies. Sets out the advantages of doing so from the perspective of problematic phylogenies. | 2006 | Trends in Ecology and Evolution, 21: 439-446 | 2 March 07 | |
| Noonan, J.P., Coop, G., Kudaravalli, S., et al. | Sequencing and analysis of Neanderthal genomic DNA | Metagenomics | Research | Uses a metagenomic technique to sequence Neanderthal DNA (the interest is not the metagenome but the single Neanderthal genome, so this is really an ordinary genomics paper). Uses pyrosequencing for the highthroughput technology. | 2006 | Science, 314: 1113-1118 | 2 March 07 | |
| Green, R.E., Krause, J., Ptak, S.E., et al. | Analysis of one million base pairs of Neanderthal DNA | Genomics | Research | First results of a Neanderthal genome sequencing project, directly sequencing uncontaminated DNA (cf the metagenomic Neanderthal DNA project). Compares Neanderthal sequence with modern human and chimpanzee sequence. Estimates the draft sequence will be co | 2006 | Nature, 444: 330-336 | 2 March 07 | |
| Pennisi, E. | The dawn of stone age genomics | Genomics | Overview | Journalist overview of background to and issues of Neanderthal genome project. | 2006 | Science, 314: 1068-1071 | 2 March 07 | |
| Church, G.M. | The personal genome project | Genomics | Overview | Brief outline of what personal genomics means (including ELSI issues). | 2005 | Molecular Systems Biology, doi: 10.1038/msb4100040 | 24 April 07 | |
| Eyre-Walker, A. | The genomic rate of adaptive evolution | Genomics | Overview | Uses genomic data to evaluate the rate of adaptive evolution in various species: high in microbes, almost non-existent in humans. | 2006 | Trends in Ecology and Evolution, 21: 569-575 | 2 March 07 | |
| Garrigan, D., & Hammer, M.F. | Reconstructing human origins in the genomic era | Genomics | Overview | Comprehensive discussion of the use of different kinds of data to recontruct population history; outlines revised models of human evolution produced by genomic data. | 2006 | Nature Reviews Genetics, 7: 669-680 | 2 March 07 | |
| Weatherall, D.J. | Genomics and global health: time for a reappraisal | Genomics | Overview | Outline of how genomics could be put to use to bring about health benefits in developing countries. | 2003 | Science, 302: 597-599 | 2 March 07 | |
| Rubin, G.M., Yandell, M.D., Wortman, J.R., et al. | Comparative genomics of the eukaryotes | Genomics | Research | Developmental, evolutionary and cellular comparison of nematode, yeast and fruitfly genomes and proteomes. | 2000 | Science, 287: 2204-2215 | 2 March 07 | |
| Mattick, J.S. | The functional genomics of noncoding RNA | Genomics | Overview | Concise introduction to the analysis of important functions of non-coding RNA. | 2005 | Science, 309: 1527-1528 | 2 March 07 | |
| Mattick, J.S. | RNA regulation: a new genetics? | Genomics | Overview | Longer outline of the functional genomics of non-coding RNA, and the radical evolutionary interpretation that can be made of it. | 2004 | Nature Reviews Genetics, 5: 316-323 | 2 March 07 | |
| Brookfield, J.F.Y. | The ecology of the genome - mobile DNA elements and their hosts | Genomics | Overview | Draws parallels between genomes and ecological communities to analyse mobile DNA and its histories. | 2005 | Nature Reviews Genetics, 6: 128-136 | 2 March 07 | |
| Vij, S., Gupta, V., Kumar, D., et al. | Decoding the rice genome | Genomics | Overview | Very useful outline of rice genomics: history, achievements, future potential. | 2006 | BioEssays, 28: 421-432 | 2 March 07 | |
| Luikart, G., England, P.R., Tallmon, D., et al. | The power and promise of population genomics: from genotyping to genome typing | Genomics | Overview | Defines and elaborates on population genomics and the biological knowledge it promises. | 2003 | Nature Reviews Genetics, 4: 981-994 | 2 March 07 | |
| Bell, J. | Predicting disease using genomics | Genomics | Applications | Outlines the potential human health applications of genomics. | 2004 | Nature, 429: 453-456 | 2 March 07 | |
| Noble, D. | Will genomics revolutionize pharmaceutical R&D? | Genomics | Applications | Discusses genomics in relation to drug discovery and outlines what else is needed besides genomic data to revolutionize pharmaceutical research. | 2003 | Trends in Biotechnology, 21: 333-337 | 2 March 07 | |
| Murray, A.W. | Whither genomics? | Genomics | Overview | Discusses the future of genomics and how it should evolve. | 2000 | Genome Biology, 1: comment003.1-006.6 | 2 March 07 | |
| MckBird, D., Opperman, C.H., Jones, S.J.M., & Baillie, D.L. | The Caenorhabditis elegans genome: a guide in the post genomic age | Genomics | Overview | Outlines the importance of the C. elegans genome sequence to biology generally; defines genomics. | 1999 | Annual Review of Phytopathology, 37: 247-265 | 2 March 07 | |
| Jeffroy, O., Brinkmann, H., Delsuc, F., & Philippe, H. | Phylogenomics: the beginning of incongruence? | Genomics | Overview | Outlines the problems of using phylogenomic data (i.e.: multiple genes) for constructing phylogenetic trees. | 2006 | Trends in Genetics, 22: 225-231 | 2 March 07 | |
| Rokas, A. | Genomics and the tree of life | Genomics | Overview | Very brief but precise account of the issues generated in phylogeny by genomic data. | 2006 | Science, 313: 1897-1898 | 2 March 07 | |
| Petsko, G.A. | The Rosetta stone | Genomics | Overview | Decodes some of the metaphors used in the production of genomics. | 2001 | Genome Biology, 2: comment1007.1-1007.2 | 2 March 07 | |
| Botstein, D., and Cherry, J.M. | Molecular linguistics: extracting information form gene and protein sequences | Genomics | Overview | Uses linguistic and the Rosetta stone metaphor to characterize the state of play in sequencing efforts. Argues for the unification of biology, previously fractured along model organism lines. | 1997 | PNAS, 94: 5506-5507 | 2 March 07 | |
| Hughes, T.R., Robinson, M.D., Mitsakakis, N., & Johston, M. | The promise of functional genomics: completing the encyclopaedia of a cell | Genomics | Overview | Acknowledges that information about yeast genes has not led easily to knowledge of function, but sees a positive relationship between large-scale sequencing efforts and small-scale functional work. | 2004 | Current Opinion in Microbiology, 7: 546-554 | 2 March 07 | |
| Rocha, E.P.C. | Order and disorder in bacterial genomes | Genomics | Overview | Outlines how bacterial genomics has revised notions of genome stability. | 2004 | Current Opinion in Microbiology, 7: 519-527 | 2 March 07 | |
| Eisenberg, D., Marcotte, E.M., Xenarios, I., & Yeates, T.O. | Protein function in the post-genomic era | Genomics | Overview | Revises early understandings of functional genomics to a more sophisticated, complex form of inquiry. | 2000 | Nature, 405: 823-826 | 2 March 07 | |
| Parker, H.G., & Ostrander, E.A. | Canine genomics and genetics: running with the pack | Genomics | Overview | Draws out some of the knowledge gained from the canine genome sequence. | 2005 | PLoS Genetics, 1 (5): e58 | 2 March 07 | |
| International Rice Genome Sequencing Project | The map-based sequence of the rice genome | Genomics | Research | One of the rice genome sequence papers. | 2005 | Nature, 436: 793-800 | 2 March 07 | |
| Southern, E. | Tools for genomics | Genomics | Overview | Outline of the range of techniques used in early genomics, written by the creator of the Southern blotting method. | 2005 | Nature Medicine, 11: 1029-1034 | 2 March 07 | |
| Venter, J.C., Levy, S., Stockwell, T., et al. | Massive parallelism, randomness and genomic advances | Genomics | Overview | Technological overview of genomics, with a focus on the most dramatic innovations. | 2003 | Nature Genetics, Supplement: 33: 219-227 | 2 March 07 | |
| Shendure, J., Mitra, R.D., Varma, C., & Church, G.M. | Advanced sequencing technologies: methods and goals | Genomics | Overview | Excellent overview of sequencing methods. | 2004 | Nature Reviews Genetics, 5: 335-344 | 2 March 07 | |
| Collins, F.S., Morgan, M., & Patrinos, A. | The Human Genome Project: lessons from large-scale biology | Genomics | Overview | Perspective on human genomics from three scientists involved in the HGP. Focuses on the project's general implications for managing large-scale biological inquiry. | 2003 | Science, 300: 286-290 | 2 March 07 | |
| Wolfe, K.H., & Li, W.-H. | Molecular evolution meets the genomics revolution | Genomics | Overview | Discusses numerous ways in which genomics has revolutionized the molecular understanding of evolution. | 2003 | Nature Genetics, Supplement: 33: 255-265 | 2 March 07 | |
| Lander, E.S. | The new genomics: global views of biology | Genomics | Overview | A glimpse into the future of genomics by one of the key players in the HGP. He outlines ten goals for the next phase of genomics. | 1996 | Science, 274: 536-539 | 2 March 07 | |
| Roberts, L. | Controversial from the start | Genomics | Overview | Science journalist's overview of the history of the human genome sequencing projects, with a focus on the controversies they have generated. | 2001 | Science, 291: 1182-1188 | 2 March 07 | |
| Pennisi, E. | The human genome | Genomics | Overview | Science journalist's account of the significance of the first draft of the human genome. | 2001 | Science, 291: 1177-1180 | 2 March 07 | |
| Lewin, R. | Proposal to sequence the human genome stirs debate | Genomics | Overview | Report of the Cold Spring Harbor Symposium where the merits of sequencing the human genome were debated. | 1986 | Science, 232: 1598-1600 | 2 March 07 | |
| McKusick, V.A. | Genomics: structural and functional studies of genomes | Genomics | Overview | Sketches out the progress made in genomics since 1987, in regard to structural, functional and comparative analyses. Predicts future developments. | 1997 | Genomics, 45: 244-249 | 2 March 07 | |
| Lederberg, J., & McCray, A.T. | 'Ome sweet 'omics: a genealogical treasury of words | Genomics | Overview | Provides an etymology of 'omic' and genomics, and lists a large number of omic or -ome terms. | 2001 | The Scientist, 15 (7): 8 | 2 March 07 | |
| McKusick, V.A., & Ruddle, F.H. | A new discipline, a new name, a new journal | Genomics | Overview | Establishes the origins of the term 'genomics', defines the field, and outlines the scope of the new journal 'Genomics'. | 1987 | Genomics, 1: 1-2 | 2 March 07 | |
| Kuska, B. | Beer, Bethesda, and biology: how 'genomics' came into being | Genomics | Overview | Interview wih Thomas Roderick about the circumstances in which he coined the word 'genomics'. | 1998 | Journal of the National Cancer Institute, 90: 93 | 2 March 07 | |
| Orphanides, g., and Reinberg, D. | A unified theory of gene expression | Genomics | Overview | Proposes a comprehensive approach to gene expression as the next step in understanding the biological meaning of genomes. | 2002 | Cell, 108: 439-451 | 2 March 07 | |
| Li, J., Brumeister, M. | Genetical genomics: combining genetics with gene expression analysis | Genomics | Overview | Combines genetic and genomic approaches via microarray analysis. | 2005 | Human Molecular Genetics, 14: R163-R169 | 2 March 07 | |
| Lindpaintner, K. | The impact of pharmacogenetics and pharmacogenomics on drug discovery | Genomics | Applications | Outlines pharmacogenomics and genetics and the obstacles they face in improving drug therapy. | 2002 | Nature Reviews Drug Discovery, 1: 463-468 | 2 March 07 | |
| Waterston, R.H., Lander, E.S., & Sulston, J.E. | On the sequencing of the human genome | Genomics | Overview | Strongly criticizes Celera whole-genome shotgun sequencing method. | 2002 | PNAS, 99: 3712-3216 | 2 March 07 | |
| Weber, J.L., & Myers, E.W. | Human whole-genome shotgun sequencing | Genomics | Overview | Defends WGS against its critics. | 1997 | Genome Research, 7: 401-409 | 2 March 07 | |
| Istrail, S., Sutton, G.G., Florea, L., et al. | Whole-genome shotgun assembly and comparison of human genome assemblies | Genomics | Overview | Compares Celera and HGP genome assembly methods and finds each has different advantages. | 2004 | PNAS, 101: 1916-1921 | 2 March 07 | |
| Ureta-Vidal, A., Ettwiller, L., & Birney, E. | Comparative genomics: genome-wide analysis in metazoan eukaryotes | Genomics | Overview | Reviews progress in comparative metazoan genomics and predicts future advances. | 2003 | Nature Reviews Genetics, 4: 251-262 | 2 March 07 | |
| Avise, J.C. | Evolving genomic metaphors: a new look at the language of DNA | Genomics | Overview | Discusses the metaphors used in genomics. | 2001 | Science, 294: 86-87 | 2 March 07 | |
| Benson, D.A., Boguski, M.S., Lipman, D.J., et al. | GenBank | Genomics | Overview | Overview of how the genome sequence database, GenBank, works. Updated every year in the same journal. | 1999 | Nucleic Acids Research, 27: 12-17 | 2 March 07 | |
| Lee, K.H. | Proteomics: a technology-driven and technology-limited discovery science | Genomics | Overview | Outlines proteomics methods and problems. | 2001 | Trends in Biotechnology, 19: 217-222 | 2 March 07 | |
| Collins, F.S., & McKusick, V.A. | Implications of the Human Genome Project for medical science | Genomics | Overview | Sketches out the potential medical applications of human genomics and concludes with a discussion of the issues in the new research environment created by genomics. | 2001 | JAMA, 285: 540-544 | 2 March 07 | |
| Thomas, J.W., & Touchman, J.W. | Vertebrate genome sequencing: building a backbone for comparative genomics | Genomics | Overview | Outlines the current state of vertebrate genomics and argues for expansion of the genome sequence database. | 2002 | Trends in Genetics, 18: 104-108 | 2 March 07 | |
| Green, P. | Against a whole-genome shotgun | Genomics | Overview | Longer discussion of the problems of WGS. | 1997 | Genome Research, 7: 410-417 | 2 March 07 | |
| Green, P. | Whole-genome dissasembly | Genomics | Overview | Downplays the advantages of WGS method of sequencing. | 2002 | PNAS, 99: 4143-4144 | 2 March 07 | |
| Myers, E.W., Sutton,G.G., Smith, H.O., et al. | On the sequencing and assembly of the human genome | Genomics | Overview | Criticizes HGP criticisms of Celera sequencing strategies. | 2002 | PNAS, 99: 4145-4146 | 2 March 07 | |
| Stein, L. | Genome annotation: from sequence to biology | Genomics | Overview | Overviews aims, tools and 'sociology' of genome annotation. | 2001 | Nature Reviews Genetics, 2: 493-503 | 2 March 07 | |
| Patterson, S.D., & Aebersold, R.H. | Proteomics: the first decade and beyond | Genomics | Overview | Outlines the history, aims, methods and future of proteomics. | 2003 | Nature Genetics, 33: Supplement: 311-323 | 2 March 07 | |
| Cinkosky, M.J., Fickett, J.W., Gilna, P., & Burks, C. | Electronic data publishing and GenBank | Genomics | Overview | Early evaluation of electronic data publishing in genomics. | 1991 | Science, 252: 1273-1277 | 2 March 07 | |
| Steinmetz, L.M., & Davis, R.W. | Maximizing the potential of functional genomics | Genomics | Overview | Outlines technological innovations and how they are bringing about progress in functional genomics. | 2004 | Nature Reviews Genetics, 5: 190-201 | 2 March 07 | |
| Li, S., Cutler, G., Liu, J.J., et al. | A comparative analysis of HGSC and Celera human genome assemblies and gene sets | Genomics | Overview | Compares HGP and Celera sequencing methods and their resultant datasets. | 2003 | Bioinformatics, 19: 1597-1605 | 2 March 07 | |
| Kondrashov, A.S. | Comparative genomics and evolutionary biology | Genomics | Overview | Outlines the impact of comparative genomics on evolutionary biology in relation to seven fundamental issues. | 1999 | Current Opinion in Genetics and Development, 9: 624-629 | 2 March 07 | |
| The Chimpanzee Sequencing and Analysis Consortium | Initial sequence of the chimpanzee genome and comparison with the human genome | Genomics | Research | As the title says. | 2005 | Nature, 437: 69-87 | 2 March 07 | |
| Foerstner, K.U., von Mering, C., Hooper, S.D., & Bork, P. | Environments shape the nucleotide composition of genomes | Genomics | Overview | Discusses the implications of findings that nucleotide composition of microbial genomes is affected by environmental conditions. | 2005 | EMBO Reports, 6: 1208-1213 | 2 March 07 | |
| Li, W.-H., & Saunders, M.A. | The chimpanzee and us | Genomics | Overview | Overview of the chimpanzee genome sequencing project and its evolutionary implications. | 2005 | Nature, 437: 50-51 | 2 March 07 | |
| Dennis, C. | Chimpanzee genome: branching out | Genomics | Overview | Outline of the implications of the chimpanzee genome sequence. | 2005 | Nature, 437: 17-19 | 2 March 07 | |
| Gregory, T.R. | Synergy between sequence and size in large-scale genomics | Genomics | Overview | Discusses the insights into genome size and the C-value enigma afforded by genomics. | 2005 | Nature Reviews Genetics, 6: 699-708 | 2 March 07 | |
| Gregory, T.R. | Genome size and developmental complexity | Genomics | Overview | Analyses genome size and its relationship to developmental complexity. | 2002 | Genetica, 115: 131-146 | 2 March 07 | |
| Brent, R. | Genomic biology | Genomics | Overview | Extensive outline of genomics, its epistemological strategies, bodies of knowledge and future transformations. | 2000 | Cell, 100: 169-183 | 24 April 07 | |
| Brown, P.O., & Botstein, D. | Exploring the new world of the genome with DNA microarrays | Genomics | Overview | Outlines how to understand genome function via microarrays and transcriptomics. | 1999 | Nature Genetics, 21: Supplement: 33-37 | 2 March 07 | |
| Jorde, L.B., Watkins, W.S., & Bamshad, M.J. | Population genomics: a bridge from evolutionary history to genomic medicine | Genomics | Overview | Links evolved genetic variation in human populations with specific disease states. | 2001 | Human Molecular Genetics, 10: 2199-2207 | 2 March 07 | |
| Waters, M.D., & Fostel, J.M. | Toxicogenomics and systems toxicology: aims and prospects | Genomics | Overview | Outlines toxicogenomics as the investigation of genes and toxic environments in disease causation. Anticipates systems toxicology as the way forward. | 2004 | Nature Reviews Genetics, 5: 936-948 | 2 March 07 | |
| Lander, E.S., Linton, L.M., Birren, B., et al. | Initial sequencing and analysis of the human genome | Genomics | Research | Draft sequence of the human genome along with some preliminary analysis. | 2001 | Nature, 409: 860-921 | 3 March 07 | |
| Venter, J.C., Adams, M.D., Myers, E.W., et al. | The sequence of the human genome | Genomics | Research | The 'other' draft human genome sequence (Celera's). As well as providing initial analysis, the paper outlines assembly differences from the public project. | 2001 | Science, 291:1304-1351 | 3 March 07 | |
| Ball, C.A., & Cherry, J.M. | Genome comparisons highlight similarity and diversity within the eukaryotic kingdoms | Genomics | Overview | Compares the four released eukaryotic genomes: Saccharomyces, Arabidopsis, Caenorhabditis and Drosophila. Finds many similarities in evolutionary processes shaping genome content. | 2001 | Current Opinion in Chemical Biology, 5: 86-89 | 3 March 07 | |
| Emes, R.D., Goodstadt, L., Winter, E.E., & Ponting, C.P. | Comparison of the genomes of human and mouse lays the foundation of genome zoology | Genomics | Overview | Compares mouse and human genome sequences and their evolutionary implications; reflects on broader animal genomics. | 2003 | Human Molecular Genetics, 12:701-709 | 3 March 07 | |
| Cronk, Q.C. | Plant evolution and development in a post-genomic context | Genomics | Overview | Discusses limitations of comparisons between currently available plant genome sequences; forecasts better genome comparisons in the near future. | 2001 | Nature Reviews Genetics, 2:607-619 | 3 March 07 | |
| Grutzner, F., & Graves, J.A. | A platypus' eye view of the mammalian genome | Genomics | Overview | Compares platypus and mammalian genome analyses and makes organizational and evolutionary observations. | 2004 | Current Opinion in Genetics and Development, 14:642-649 | 3 March 07 | |
| Fraser-Liggett, C.M. | Insights on biology and evolution from microbial genome sequencing. | Genomics | Overview | Outlines the astonishing advances made in microbiology due to genomic technology and genome analysis. | 2005 | Genome Research, 15):1603-1610 | 3 March 07 | |
| Heckel, D.G. | Genomics in pure and applied entomology | Genomics | Overview | Outlines benefits of insect genomics and anticipates a future science with model insects beyond Drosophila. | 2002 | Annual Review of Entomology, 48:235-60 | 3 March 07 | |
| Hoffman, S.L., Subramanian, G.M., Collins, F.H., & Venter, J.C. | Plasmodium, human and Anopheles genomics and malaria | Genomics | Overview | Outlines the scientific and therapeutic benefits of comparative genomic analyses of the malaria parasiste, mosquito and human. | 2002 | Nature, 415:702-709 | 3 March 07 | |
| Burdett, H., & van den Heuvel, M. | Fruits and flies: a genomics perspective of an invertebrate model organism | Genomics | Overview | Outlines ongoing centrality of Drosophila to invertebrate genomics. | 2004 | Briefings in Functional Genomics & Proteomics, 3:257-266 | 3 March 07 | |
| Womack, J.E. | Advances in livestock genomics: opening the barn door | Genomics | Overview | Outlines current state of farm animal genomics and its anticipated future. | 2005 | Genome Research, 5:1699-1705 | 3 March 07 | |
| Fadiel, A., Anidi, I., & Eichenbaum, K.D. | Farm animal genomics and informatics: an update | Genomics | Overview | Overviews farm animal genomics to date, and suggests multiple ways in which such data can be put to use. | 2005 | Nucleic Acids Research, 33: 6308-6318 | 3 March 07 | |
| Wolfe, K.H. | Comparative genomics and genome evolution in yeasts | Genomics | Overview | Outlines the multiple yeast genome sequences available, and the comparative evolutionary understandings their analysis leads to. | 2006 | Philosophical Transactions of the Royal Society B, 361:403-12 | 3 March 07 | |
| Galagan, J.E., Henn, M.R., Ma, L.J., et al. | Genomics of the fungal kingdom: insights into eukaryotic biology | Genomics | Overview | Overviews all the fungal genomes available and the mass of biological insights fungal genomics has provided - for fungi biology and eukaryotic biology and evolution generally. | 2005 | Genome Research, 15:1620-1631 | 3 March 07 | |
| Kellam, P. | Post-genomic virology: the impact of bioinformatics, microarrays and proteomics on investigating host and pathogen interactions | Genomics | Overview | A basic overview of viral genomics. | 2001 | Reviews in Medical Virology, 11: 313-329 | 3 March 07 | |
| Hendrix, R.W. | Bacteriophage genomics | Genomics | Overview | Overview of phage genomics and the evolutionary findings generated so far. | 2003 | Current Opinion in Microbiology, 6: 506-511 | 3 March 07 | |
| Canchaya, C., Proux, C., Fournous, G., et al. | Prophage genomics | Genomics | Overview | Discusses the myriad prophage sequences in sequenced bacterial genomes (as well as plants and animals) and their biological, evolutionary and bioinformatic implications. | 2003 | Microbiology and Molecular Biology Reviews, 67: 238-276 | 3 March 07 | |
| Roest Crollius H., & Weissenbach, J. | Fish genomics and biology | Genomics | Overview | Outlines the present and future of fish genomics; makes biological and evolutionary comparisons with mammalian genomes, development and evolution. | 2005 | Genome Research, 15: 1675-1682 | 3 March 07 | |
| Doolittle, W.F. | Lateral genomics | Genomics | Overview | Outlines how genomic data has revealed extensive lateral gene transfer between prokaryotes; discusses the consequences for tree patterns in phylogeny. | 1999 | Trends in Cell Biology, 9: M5-M8 | 4 March 07 | |
| Benner, S.A., & Sismour, A.M. | Synthetic biology | Synthetic Biology | Overview | Excellent overview of the main classes of synthetic biology, preceded by a brief outline of the field's historical roots. Discusses the aims of synthetic biology as well as its risks. | 2005 | Nature Reviews Genetics, 6: 533-543 | 12 March 07 | |
| Endy, D. | Foundations for engineering biology | Synthetic Biology | Overview | Succinct outline of synthetic biology's background, participants, aims and central ideas (standardization, decoupling, abstraction). Risks also receive a brief mention. | 2005 | Nature, 438: 449-453 | 12 March 07 | |
| Brent, R. | A partnership between biology and engineering | Synthetic Biology | Overview | Connects synthetic biology to systems biology and outlines their mutually beneficial relationship. Argues for more precise definitions of both and provides them. | 2004 | Nature Biotechnology, 22: 1211-1214 | 12 March 07 | |
| Andrianantoandro, E., Basu, S., Karig, D.K., and Weiss, R. | Synthetic biology: new engineering rules for an emerging discipline | Synthetic Biology | Overview | Detailed outline of what synthetic biology involves and what it needs to develop at a range of biological levels (devices, modules, single cells, multicellular systems). Illustrations of various points are provided with descriptions and analyses of some k | 2006 | Molecular Systems Biology, doi: 10.1038/msb4100073 | 12 March 07 | |
| Stahler, P., Beier, M., Gao, X., & Hoheisel, J.D. | Another side of genomics: synthetic biology as a means for the exploitation of whole-genome sequence information | Synthetic Biology | Overview | Discusses synthetic biology as the necessary outcome of genome sequencing. Provides a definition and history then focuses on advances in DNA synthesis. | 2006 | Journal of Biotechnology, 124: 206-212 | 12 March 07 | |
| Ball, P. | Synthetic biology for nanotechnology | Synthetic Biology | Overview | Outlines synthetic biology past and present and how its modification of biological structures could help develop nanotechnologies. Describes several synthetic biology successes; mentions risks and social perception problems. | 2005 | Nanotechnology, 16: R1-R8 | 12 March 07 | |
| Heinemann, M., & Panke, S. | Synthetic biology: putting engineering into biology | Synthetic Biology | Overview | Discusses what the integration of an engineering perspective implies for biological research. Outlines a variety of achievements and emphasizes the necessary differences between design and fabrication. | 2006 | Bioinformatics, 22: 2790-2799 | 12 March 07 | |
| McDaniel, R., & Weiss, R. | Advances in synthetic biology: on the path from prototypes to applications | Synthetic Biology | Overview | Outlines the central aims and entities of synthetic biology as well as achievements. | 2005 | Current Opinion in Biotechnology, 16: 476-483 | 12 March 07 | |
| Barrett, C.L., Kim, T.Y., Kim, H.U., et al. | Systems biology as a foundation for genome-scale synthetic biology | Synthetic Biology | Overview | Discusses the relationship between systems and synthetic biology and how achievements in one will provide positive feedback for the other. | 2006 | Current Opinion in Biotechnology, 17: 1-5 | 12 March 07 | |
| Hasty, J., McMillen, D., & Collins, J.J. | Nature, 420: 224-230 | Synthetic Biology | Overview | Outlines the design elements involved in gene circuits and the biological equivalents of several electronic engineering techniques. | 2002 | Engineered gene circuits | 12 March 07 | |
| Luisi, P.L., Ferri, F., & Stano, P. | Approaches to semi-synthetic minimal cells: a review | Synthetic Biology | Overview | Discusses miminal cell research and the approaches currently deployed. Outlines future challenges and neglected aspects of cellular synthesis. | 2006 | Naturwissenschaften, 93: 1-13 | 12 March 07 | |
| Wall, M.E., Hlavacek, W.S., & Savageau, M.A. | Design of gene circuits: lessons from bacteria | Synthetic Biology | Overview | Describes the development of gene circuit synthesis and the biological insight it produces. | 2004 | Nature Reviews Genetics, 5: 34-42 | 12 March 07 | |
| Yokobayashi, Y., Weiss, R., & Arnold, F.H. | Directed evolution of a gene circuit | Synthetic Biology | Research | Important research demonstrating the success of rational evolutionary design of gene circuits and how this overcomes some of the problems of unpredicted behaviour in synthetic circuits. | 2002 | PNAS, 99: 16587-16591 | 12 March 07 | |
| Benner, S.A. | Act natural | Synthetic Biology | Overview | Very brief but illuminating precis of synthetic biology: aims, historical background, strategies, applications and general insights. | 2003 | Nature, 421: 118 | 12 March 07 | |
| Sprinzak, D., and Elowitz, M.B. | Reconstruction of genetic circuits | Synthetic Biology | Overview | Advocates the use of synthetic gene circuits as physical models used to explore the relationshipe between genetic structure and function. | 2005 | Nature, 438: 443-448 | 12 March 07 | |
| Martin, V.J.J, Pitera, D.J., Withers, S.T., et al. | Engineering a mevalonate pathway in Escherichia coli for production of terpenoids | Synthetic Biology | Research | Often mentioned as a demonstration of the feasibility of synthetic biology, this paper describes the synthetic production of an antimalarial product in a laboratory bacterium. | 2003 | Nature Biotechnology, 21: 796-802 | 12 March 07 | |
| Elowitz, M.B., & Leibler, S. | A synthetic oscillatory network of transcriptional regulators | Synthetic Biology | Research | Also described as a key exemplar of early synthetic biology, this paper outlines the design and construction of an oscillating network called the repressilator, which produces green fluorescent protein to mark its oscillations. | 2000 | Nature, 403: 335-338 | 12 March 07 | |
| Cello, J., Paul, A.V., & Wimmer, E. | Chemical synthesis of poliovirus cDNA: generation of infectious virus in the absence of natural template | Synthetic Biology | Research | Famous exemplar describing the synthesis of a poliovirus entirely from scratch (using known sequence as the only instruction). | 2002 | Science, 297: 1016-1018 | 12 March 07 | |
| Chan, L.Y., Kosuri, S., & Endy, D. | Refactoring bacteriophage T7 | Synthetic Biology | Research | 'Improved' design of a bacteriophage, in which internal elements were refactored but external functions maintained. Suggests that natural biological systems are amenable to human design and intervention - hence the paper is another key exemplar for fledgl | 2005 | Molecular Systems Biology, doi: 10.1038/msb4100025 | 12 March 07 | |
| Gardner, T.S., Cantor, C.R., & Collins, J.J. | Construction of a genetic toggle switch in Escherichia coli | Synthetic Biology | Research | An early exemplar of successful synthetic biology. The paper outlines the construction of a genetic toggle switch and a model for understanding its bistability. Discusses the switch's applications as a cellular memory unit. | 2000 | Nature, 403: 339-342 | 12 March 07 | |
| NEST (New & Emerging Science and Technology), European Commission | Synthetic biology: applying engineering to biology | Synthetic Biology | Overview | Good non-technical overview of synthetic biology, from definitions, scope and aims to activities and applications. Available at http://www.univ-poitiers.fr/recherche/documents/pcrdt7/syntheticbiology.pdf | 2005 | European Commission Directorate General for Research | 12 March 07 | |
| Isaacs, F.J., Dwyer, D.J., & Collins, J.J. | RNA synthetic biology | Synthetic Biology | Overview | Outlines synthetic biology in relation to synthetic RNA components. | 2006 | Nature Biotechnology, 24: 545-554 | 12 March 07 | |
| Blake, W.J., & Isaacs, F.J. | Synthetic biology evolves | Synthetic Biology | Overview | Outlines some early achievements of synthetic biology and how the next step involves in silico design of the evolution of components, followed by in vitro directed evolution. | 2004 | Trends in Biotechnology, 22: 321-324 | 12 March 07 | |
| Ball, P. | Starting from scratch | Synthetic Biology | Overview | Journalist's coverage of synthetic biology's aims and achievements, as well as anticipated risks and measures taken to deal with them. | 2004 | Nature, 431: 624-626 | 12 March 07 | |
| Check, E. | Synthetic biologists face up to security issues | Synthetic Biology | Overview | Outlines scientists' perceptions of the risks of synthetic biology and the steps they are considering for self-regulation. | 2005 | Nature, 436, 894-895 | 12 March 07 | |
| Forster, A.C., & Church, G.M. | Towards synthesis of a minimal cell | Synthetic Biology | Overview | Discusses minimal cell synthesis, including the components needed and the biological knowledge that would be generated. | 2006 | Molecular Systems Biology, doi: 10.1038/msb4100090 | 12 March 07 | |
| Pennisi, E. | Synthetic biology makes small genomes | Synthetic Biology | Overview | Journalist's overview of the research aimed at the synthetic construction of bacterial genomes. | 2005 | Science, 310: 769-770 | 12 March 07 | |
| Campbell, A.M. | Meeting report: synthetic biology jamboree for undergraduates | Synthetic Biology | Overview | Reports on the now famous and highly prestigious synthetic biology competition, focusing on two of the biological machines created by participants. | 2005 | Cell Biology Education | 12 March 07 | |
| Levskaya, A., Chevalier, A.A., Tabor, J.J., et al. | Synthetic biology: engineering Escherichia coli to see light | Synthetic Biology | Research | This paper outlines the creation of a novel genetic circuit with an image-processing function. The system consists of a synthetic sensor kinase that allows a lawn of bacteria to function as a biological film and produce a two-dimensional image. The variou | 2005 | Nature, 438: 441-442 | 12 March 07 | |
| Parsek, M.R., & Greenberg, E.P. | Sociomicrobiology: the connections between quorum sensing and biofilms | Sociomicrobiology | Overview | Discusses sociomicrobiology in relation to the key behaviours of quorum sensing and living in biofilms. Defines sociomicrobiology as 'investigations of any group behaviours of microbes'. | 2005 | Trends in Microbiology, 13: 27-33 | 25 March 07 | |
| West, S.A., Griffin, A.S., Gardner, A., & Diggle, S.P. | Social evolution theory for microorganisms | Sociomicrobiology | Overview | Discusses a wide range of social behaviours of multicellular microbial communities, then considers them from an evolutionary perspective. The paper makes comparisons between microbial communities and social animal groups and introduce the various complica | 2006 | Nature Reviews Microbiology, 4: 597-607 | 25 March 07 | |
| Andrews, J.H. | Bacteria as modular organisms | Sociomicrobiology | Overview | This paper argues that instead of understanding bacteria as clonal lineages, biologists should approach them as successively complex modules that are analogous to macroorganisms. A unified perspective of modularity, argues the author, will enable a better | 1998 | Annual Review of Microbiology, 52: 105-126 | 25 March 07 | |
| Caldwell, D.E., Atuku, E., Wilkie, D.C., et al. | Germ theory vs. community theory in understanding and controlling the proliferation of biofilms | Sociomicrobiology | Overview | Outlines why germ theory and pure culture are insufficient to understand microbial behaviour, and how to approach community-level behaviour. | 1997 | Advances in Dental Research, 11: 4-13 | 25 March 07 | |
| Kolenbrander, P.E | Oral microbial communities: biofilms, interactions, and genetic systems | Sociomicrobiology | Overview | Discusses oral microbial communities (in dental plaque) from the perspectives of composition and activities (with a special focus on genetic exchange as communication). | 2000 | Annual Review of Microbiology, 54: 413-437 | 25 March 07 | |
| Crespi, B.J. | The evolution of social behaviour in microorganisms | Sociomicrobiology | Overview | Reviews a range of social behaviours in microorganismal groups, compares them to social and eusocial animals, and discusses the implications for evolutionary theory and biology in general. | 2001 | Trends in Ecology and Evolution, 16: 178-183 | 25 March 07 | |
| Shapiro, J.A. | Thinking about bacterial populations as multicellular organisms | Sociomicrobiology | Overview | A classic paper that outlines many of the most basic findings of and ideas about sociomicrobiology. Builds on and extends the author's earlier (1988) introduction of the concept of bacteria as multicellular organisms. | 1998 | Annual Review of Microbiology, 52: 81-104 | 25 March 07 | |
| Davey, M.E., & O'Toole, G.A. | Microbial biofilms: from ecology to molecular genetics | Sociomicrobiology | Overview | Argues that the perception of bacteria as unicellular is an artefact of the pure culture approach and that more environmentally oriented approaches allow microbiologists to investigate the interdependent, closely aggregated lifestyle of biofilms. The pape | 2000 | Microbiology and Molecular Biology Reviews, 64: 847-867 | 25 March 07 | |
| Kaiser, D. | Building a multicellular organism | Sociomicrobiology | Overview | Discusses uncontested examples of bacaterial multicellularity from its early origins at the beginning of life on Earth in cyanobacterial filaments. Outlines the advantages and costs of such multicellular innovations. | 2001 | Annual Review of Genetics, 35: 103-123 | 25 March 07 | |
| Keller, L., & Surette, M.D. | Communication in bacteria: an ecological and evolutionary perspective | Metagenomics | Overview | Argues that quorum sensing, typically interpreted as communication enabling cooperative behaviour in microbial communities, may be simply a response to chemical cues and manipulations. It may therefore be as much if not more involved in conflict than coop | 2006 | Nature Reviews Microbiology, 4: 249-258 | 25 March 07 | |
| Waters, C.M., & Bassler, B.L. | Quorum sensing: cell-to-cell communication in bacteria | Sociomicrobiology | Overview | Outlines the architecture of quorum sensing and the cooperative behaviours such communication enables in populations, mixed-species communities (including eukaryote hosts and their unicellular guests). | 2005 | Annual Review of Cell and Developmental Biology, 21: 319-346 | 25 March 07 | |
| Taga, M.E., & Bassler, B.L. | Chemical communication among bacteria | Sociomicrobiology | Overview | Clear outline of the various quorum sensing systems and the varieties of interspecies communications they enable. The paper also outlines anti-quorum sensing strategies. | 2003 | PNAS, 100, Suppl 2: 14549-54 | 25 March 07 | |
| Stoodley, P., Sauer, K., Davies, D.G., & Costerton, J.W. | Biofilms as complex differentiated communities | Sociomicrobiology | Overview | Detailed overview of biofilms and how they develop (as multicellular organisms). | 2002 | Annual Review of Microbiology, 56: 187-209 | 25 March 07 | |
| O'Toole, G., Kaplan, H.B., & Kolter, R. | Biofilm formation as microbial development | Sociomicrobiology | Overview | Discusses biofilms as complex, highly regulated communities that are ideal model systems for understanding microbial development. | 2000 | Annual Review of Microbiology, 54: 49-79 | 25 March 07 | |
| Keim, C.N., Martins, J.L., Abreu, F., et al. | Multicellular life of magnetotactic prokaryotes | Sociomicrobiology | Research | Presents data on magnetotactic bacteria that exist as multicellular organisms and have no unicellular stage. It reproduces by dividing into two daughter cells that are replicates of the dividing multicellular unit. | 2004 | FEMS Microbiology Letters, 240: 203-208 | 25 March 07 | |
| Engelberg-Kulka, H., Amitai, S., Kolodkin-Gal, I., & Hazan, R. | Bacterial programmed cell death and multicellular behavior in bacteria | Sociomicrobiology | Overview | Discusses programmed cell death in bacterial populations and their similiarities and differences to traditionally conceived multicellular organisms. | 2006 | PLoS Genetics, 2: e135 | 25 March 07 | |
| Armitage, J.P. | Bacterial tactic responses | Sociomicrobiology | Overview | Discusses sensory and movement strategies in bacterial populations | 1999 | Advances in Microbial Physiology, 41:229-89 | 25 March 07 | |
| Graumann, P.L. | Different genetic programmes within identical bacteria under identical conditions: the phenomenon of bistability greatly modifies our view on bacterial populations | Sociomicrobiology | Overview | Discusses some of the implications of findings of bistability or differentiated gene expression that enables different behavioural or developmental behaviours in bacterial populations. | 2006 | Molecular Microbiology, 61: 560-563 | 25 March 07 | |
| Dubnau, D., & Losick, R. | Bistability in bacteria | Sociomicrobiology | Overview | Discusses bistability or non-uniform gene expression in bacterial populations. The papers outlines a wide variety of biological advantages enabled by such phenotypic differentiation. | 2006 | Molecular Microbiology, 61: 564-72. | 25 March 07 | |
| Caldwell, D.E., & Costerton, J.W. | Are bacterial biofilms constrained to Darwin's concept of evolution through natural selection? | Sociomicrobiology | Overview | Considers microbial communities as units of activity, ecology, reproduction and evolution (analogous to organisms), and discusses the theoretical advantages of doing so. | 1996 | Microbiologia, 12: 347-358 | 25 March 07 | |
| Noonan, J.P., Coop, G., Kudaravalli, S. | Sequencing and analysis of Neanderthal genomic DNA | Metagenomics | Research | Uses a metagenomic technique to sequence Neanderthal DNA (the interest is not the metagenome but the single Neanderthal genome, so this is really an ordinary genomics paper). Uses pyrosequencing for the highthroughput technology. | 2006 | Science, 314: 1113-1118 | 4 February 08 | |
| Keller, L., & Surette, M.D. | Communication in bacteria: an ecological and evolutionary perspective | Metagenomics | Overview | Argues that quorum sensing, typically interpreted as communication enabling cooperative behaviour in microbial communities, may be simply a response to chemical cues and manipulations. It may therefore be as much if not more involved in conflict than cooperation. | 2006 | Nature Reviews Microbiology, 4: 249-258 | 4 February 08 | |
| Dubnau, D., & Losick, R. | Bistability in bacteria | Sociomicrobiology | Overview | Discusses bistability or non-uniform gene expression in bacterial populations. The papers outlines a wide variety of biological advantages enabled by such phenotypic differentiation. | 2006 | Molecular Microbiology, 61: 564-72. | 25 March 07 | |
| Caldwell, D.E., & Costerton, J.W | Are bacterial biofilms constrained to Darwin's concept of evolution through natural selection? | Sociomicrobiology | Overview | Considers microbial communities as units of activity, ecology, reproduction and evolution (analogous to organisms), and discusses the theoretical advantages of doing so. | 1996 | Microbiologia, 12: 347-358 | 25 March 07 | |
| Stahler, P., Beier, M., Gao, X., & Hoheisel, J.D. | Another side of genomics: synthetic biology as a means for the exploitation of whole-genome sequence information | Synthetic Biology | Overview | Discusses synthetic biology as the necessary outcome of genome sequencing. Provides a definition and history then focuses on advances in DNA synthesis. | 2006 | Journal of Biotechnology, 124: 206-212 | 12 March 07 | |
| Ball, P. | Synthetic biology for nanotechnology | Synthetic Biology | Overview | Outlines synthetic biology past and present and how its modification of biological structures could help develop nanotechnologies. Describes several synthetic biology successes; mentions risks and social perception problems. | 2005 | Nanotechnology, 16: R1-R8 | 12 March 07 | |
| Heinemann, M., & Panke, S. | Synthetic biology: putting engineering into biology | Synthetic Biology | Overview | Discusses what the integration of an engineering perspective implies for biological research. Outlines a variety of achievements and emphasizes the necessary differences between design and fabrication. | 2006 | Bioinformatics, 22: 2790-2799 | 12 March 06 | |
| McDaniel, R., & Weiss, R. | Advances in synthetic biology: on the path from prototypes to applications | Synthetic Biology | Overview | Outlines the central aims and entities of synthetic biology as well as achievements. | 2005 | Current Opinion in Biotechnology, 16: 476-483 | 12 March 07 | |
| Barrett, C.L., Kim, T.Y., Kim, H.U., et al. | Systems biology as a foundation for genome-scale synthetic biology | Synthetic Biology | Overview | Discusses the relationship between systems and synthetic biology and how achievements in one will provide positive feedback for the other. | 2006 | Current Opinion in Biotechnology, 17: 1-5 | 12 March 07 | |
| Hasty, J., McMillen, D., & Collins, J.J. | Engineered gene circuits | Synthetic Biology | Overview | Outlines the design elements involved in gene circuits and the biological equivalents of several electronic engineering techniques. | 2002 | Nature, 420: 224-230 | 12 March 07 | |
| Luisi, P.L., Ferri, F., & Stano, P. | Approaches to semi-synthetic minimal cells: a review | Synthetic Biology | Overview | Discusses miminal cell research and the approaches currently deployed. Outlines future challenges and neglected aspects of cellular synthesis. | 2006 | Naturwissenschaften, 93: 1-13 | 12 March 06 | |
| Wall, M.E., Hlavacek, W.S., & Savageau, M.A. | Design of gene circuits: lessons from bacteria | Synthetic Biology | Overview | Describes the development of gene circuit synthesis and the biological insight it produces. | 2004 | Nature Reviews Genetics, 5: 34-42 | 12 March 07 | |
| Benner, S.A. | Act natural | Synthetic Biology | Overview | Very brief but illuminating precis of synthetic biology: aims, historical background, strategies, applications and general insights. | 2003 | Nature, 421: 118 | 12 March 07 | |
| Yokobayashi, Y., Weiss, R., & Arnold, F.H. | Directed evolution of a gene circuit | Synthetic Biology | Research | Important research demonstrating the success of rational evolutionary design of gene circuits and how this overcomes some of the problems of unpredicted behaviour in synthetic circuits. | 2002 | PNAS, 99: 16587-16591 | 12 March 07 | |
| Sprinzak, D., and Elowitz, M.B. | Reconstruction of genetic circuits | Synthetic Biology | Overview | Advocates the use of synthetic gene circuits as physical models used to explore the relationshipe between genetic structure and function. | 2005 | Nature, 438: 443-448 | 12 March 07 | |
| Martin, V.J.J, Pitera, D.J., Withers, S.T., et al. | Engineering a mevalonate pathway in Escherichia coli for production of terpenoids | Synthetic Biology | Research | Often mentioned as a demonstration of the feasibility of synthetic biology, this paper describes the synthetic production of an antimalarial product in a laboratory bacterium. | 2003 | Nature Biotechnology, 21: 796-802 | 12 March 07 | |
| Elowitz, M.B., & Leibler, S. | A synthetic oscillatory network of transcriptional regulators | Synthetic Biology | Research | Also described as a key exemplar of early synthetic biology, this paper outlines the design and construction of an oscillating network called the repressilator, which produces green fluorescent protein to mark its oscillations. | 2000 | Nature, 403: 335-338 | 12 March 07 | |
| Cello, J., Paul, A.V., & Wimmer, E. | Chemical synthesis of poliovirus cDNA: generation of infectious virus in the absence of natural template | Synthetic Biology | Research | Famous exemplar describing the synthesis of a poliovirus entirely from scratch (using known sequence as the only instruction). | 2002 | Science, 297: 1016-1018 | 12 March 07 | |
| Chan, L.Y., Kosuri, S., & Endy, D. | Refactoring bacteriophage T7 | Synthetic Biology | Research | 'Improved' design of a bacteriophage, in which internal elements were refactored but external functions maintained. Suggests that natural biological systems are amenable to human design and intervention - hence the paper is another key exemplar for fledgling synthetic biology. | 2005 | Molecular Systems Biology, doi: 10.1038/msb4100025 | 12 March 07 | |
| Gardner, T.S., Cantor, C.R., & Collins, J.J. | Construction of a genetic toggle switch in Escherichia coli | Synthetic Biology | Research | An early exemplar of successful synthetic biology. The paper outlines the construction of a genetic toggle switch and a model for understanding its bistability. Discusses the switch's applications as a cellular memory unit. | 2000 | Nature, 403: 339-342 | 12 March 07 | |
| NEST (New & Emerging Science and Technology), European Commission | Synthetic biology: applying engineering to biology | Synthetic Biology | Overview | Good non-technical overview of synthetic biology, from definitions, scope and aims to activities and applications. Available at http://www.univ-poitiers.fr/recherche/documents/pcrdt7/syntheticbiology.pdf | 2005 | European Commission Directorate General for Research | 12 March 07 | |
| Isaacs, F.J., Dwyer, D.J., & Collins, J.J. | RNA synthetic biology | Synthetic Biology | Overview | Outlines synthetic biology in relation to synthetic RNA components. | 2006 | Nature Biotechnology, 24: 545-554 | 12 March 07 | |
| Blake, W.J., & Isaacs, F.J. | Synthetic biology evolves | Synthetic Biology | Overview | Outlines some early achievements of synthetic biology and how the next step involves in silico design of the evolution of components, followed by in vitro directed evolution. | 2004 | Trends in Biotechnology, 22: 321-324 | 12 March 07 | |
| Ball, P. | Starting from scratch | Synthetic Biology | Overview | Journalist's coverage of synthetic biology's aims and achievements, as well as anticipated risks and measures taken to deal with them. | 2004 | Nature, 431: 624-626 | 12 March 07 | |
| Check, E. | Synthetic biologists face up to security issues | Synthetic Biology | Overview | Outlines scientists' perceptions of the risks of synthetic biology and the steps they are considering for self-regulation. | 2005 | Nature, 436, 894-895 | 12 March 07 | |
| Forster, A.C., & Church, G.M. | Towards synthesis of a minimal cell | Synthetic Biology | Overview | Discusses minimal cell synthesis, including the components needed and the biological knowledge that would be generated. | 2006 | Molecular Systems Biology, doi: 10.1038/msb4100090 | 12 March 07 | |
| Pennisi, E. | Synthetic biology makes small genomes | Synthetic Biology | Overview | Journalist's overview of the research aimed at the synthetic construction of bacterial genomes. | 2005 | Science, 310: 769-770 | 12 March 07 | |
| Campbell, A.M. | Meeting report: synthetic biology jamboree for undergraduates | Synthetic Biology | Overview | Reports on the now famous and highly prestigious synthetic biology competition, focusing on two of the biological machines created by participants. | 2005 | Cell Biology Education | 12 March 07 | |
| Levskaya, A., Chevalier, A.A., Tabor, J.J., et al. | Synthetic biology: engineering Escherichia coli to see light | Synthetic Biology | Research | This paper outlines the creation of a novel genetic circuit with an image-processing function. The system consists of a synthetic sensor kinase that allows a lawn of bacteria to function as a biological film and produce a two-dimensional image. The various biological and application implications are briefly discussed. | 2005 | Nature, 438: 441-442 | 12 March 07 | |
| Parsek, M.R., & Greenberg, E.P. | Sociomicrobiology: the connections between quorum sensing and biofilms | Sociomicrobiology | Overview | Sociomicrobiology: the connections between quorum sensing and biofilms | 2005 | Trends in Microbiology, 13: 27-33 | 12 March 07 | |
| West, S.A., Griffin, A.S., Gardner, A., & Diggle, S.P. | Social evolution theory for microorganisms | Sociomicrobiology | Overview | Discusses a wide range of social behaviours of multicellular microbial communities, then considers them from an evolutionary perspective. The paper makes comparisons between microbial communities and social animal groups and introduce the various complications of such comparisons. | 2006 | Nature Reviews Microbiology, 4: 597-607 | 12 March 07 | |
| Andrews, J.H. | Bacteria as modular organisms | Sociomicrobiology | Overview | This paper argues that instead of understanding bacteria as clonal lineages, biologists should approach them as successively complex modules that are analogous to macroorganisms. A unified perspective of modularity, argues the author, will enable a better evolutionary and developmental understanding. | 1998 | Annual Review of Microbiology, 52: 105-126 | 12 March 07 | |
| Caldwell, D.E., Atuku, E., Wilkie, D.C., et al. | Germ theory vs. community theory in understanding and controlling the proliferation of biofilms | Sociomicrobiology | Overview | Outlines why germ theory and pure culture are insufficient to understand microbial behaviour, and how to approach community-level behaviour. | 1997 | Advances in Dental Research, 11: 4-13 | 12 March 07 | |
| Kolenbrander, P.E | Oral microbial communities: biofilms, interactions, and genetic systems | Sociomicrobiology | Overview | Discusses oral microbial communities (in dental plaque) from the perspectives of composition and activities (with a special focus on genetic exchange as communication). | 2000 | Annual Review of Microbiology, 54: 413-437 | 12 March 07 | |
| Crespi, B.J. | The evolution of social behaviour in microorganisms | Sociomicrobiology | Overview | Reviews a range of social behaviours in microorganismal groups, compares them to social and eusocial animals, and discusses the implications for evolutionary theory and biology in general. | 2001 | Trends in Ecology and Evolution, 16: 178-183 | 12 March 07 | |
| Shapiro, J.A. | Thinking about bacterial populations as multicellular organisms | Sociomicrobiology | Overview | A classic paper that outlines many of the most basic findings of and ideas about sociomicrobiology. Builds on and extends the author's earlier (1988) introduction of the concept of bacteria as multicellular organisms. | 1998 | Annual Review of Microbiology, 52: 81-104 | 12 March 07 | |
| Davey, M.E., & O'Toole, G.A. | Microbial biofilms: from ecology to molecular genetics | Sociomicrobiology | Overview | Argues that the perception of bacteria as unicellular is an artefact of the pure culture approach and that more environmentally oriented approaches allow microbiologists to investigate the interdependent, closely aggregated lifestyle of biofilms. The paper goes on to outline many aspects of biofilm research. | 2000 | Microbiology and Molecular Biology Reviews, 64: 847-867 | 12 March 07 | |
| Kaiser, D. | Building a multicellular organism | Sociomicrobiology | Overview | Discusses uncontested examples of bacaterial multicellularity from its early origins at the beginning of life on Earth in cyanobacterial filaments. Outlines the advantages and costs of such multicellular innovations. | 2001 | Annual Review of Genetics, 35: 103-123 | 12 March 07 | |
| Waters, C.M., & Bassler, B.L. | Quorum sensing: cell-to-cell communication in bacteria | Sociomicrobiology | Overview | Outlines the architecture of quorum sensing and the cooperative behaviours such communication enables in populations, mixed-species communities (including eukaryote hosts and their unicellular guests). | 2005 | Annual Review of Cell and Developmental Biology, 21: 319-346 | 12 March 07 | |
| Taga, M.E., & Bassler, B.L. | Chemical communication among bacteria | Sociomicrobiology | Overview | Clear outline of the various quorum sensing systems and the varieties of interspecies communications they enable. The paper also outlines anti-quorum sensing strategies. | 2003 | PNAS, 100, Suppl 2: 14549-54 | 12 March 07 | |
| Stoodley, P., Sauer, K., Davies, D.G., & Costerton, J.W. | Biofilms as complex differentiated communities | Sociomicrobiology | Overview | Detailed overview of biofilms and how they develop (as multicellular organisms). | 2002 | Annual Review of Microbiology, 56: 187-209 | 12 March 07 | |
| O'Toole, G., Kaplan, H.B., & Kolter, R. | Biofilm formation as microbial development | Sociomicrobiology | Overview | Discusses biofilms as complex, highly regulated communities that are ideal model systems for understanding microbial development. | 2000 | Annual Review of Microbiology, 54: 49-79 | 12 March 07 | |
| Keim, C.N., Martins, J.L., Abreu, F., et al. | Multicellular life of magnetotactic prokaryotes | Sociomicrobiology | Research | Presents data on magnetotactic bacteria that exist as multicellular organisms and have no unicellular stage. It reproduces by dividing into two daughter cells that are replicates of the dividing multicellular unit. | 2004 | FEMS Microbiology Letters, 240: 203-208 | 12 March 07 | |
| Engelberg-Kulka, H., Amitai, S., Kolodkin-Gal, I., & Hazan, R. | Bacterial programmed cell death and multicellular behavior in bacteria | Sociomicrobiology | Overview | Discusses programmed cell death in bacterial populations and their similiarities and differences to traditionally conceived multicellular organisms. | 2006 | PLoS Genetics, 2: e135 | 12 March 07 | |
| Armitage, J.P. | Bacterial tactic responses | Sociomicrobiology | Overview | Discusses sensory and movement strategies in bacterial populations | 1999 | Advances in Microbial Physiology, 41:229-89 | 12 March 07 | |
| Graumann, P.L. | Different genetic programmes within identical bacteria under identical conditions: the phenomenon of bistability greatly modifies our view on bacterial populations | Sociomicrobiology | Overview | Discusses some of the implications of findings of bistability or differentiated gene expression that enables different behavioural or developmental behaviours in bacterial populations. | 2006 | Molecular Microbiology, 61: 560-563 | 12 March 07 |
