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Dr David Roberts
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Natural History Museum
Cromwell Road
London
SW7 5BD

Biography

Education

1972   B.Sc. Microbiology, Queen Elizabeth College, University of London.

1982   Ph.D, The Volume Distribution of Tetrahymena elliotti: its measurement and application to growth parameter estimation, University of Surrey

Employment history

1989  Head of Protista & Mathematics Division, NHM

1987  Principle Scientific Officer (UG7), Protozoa Section, BMNH

1982  Senior Scientific Officer, Protozoa Section, BMNH

1976  Higher Scientific Officer, Protozoa Section, BMNH

1972  Scientific Officer, Protozoa Section, BMNH

Professional Roles

Awards

2003     IEEE InfoViz competition:  2nd place “Comparison of multiple taxonomic hierarchies using TaxoNote”

Grants

2006     EU project “Toward the European Distributed Institute of Taxonomy” (12.5 M Euros)

2005     Marie Curie grant: The Application of Protistan Diversity and Community Analysis, an integrated approach to Water Quality Assessment (Dr Jun Gong to visit the NHM for 2007-8) (160K Euros)

2003     The Gen Foundation: The discovery of unseen biodiversity through the extraction and examination of environmental DNA from lakes and soils. (£500)

2003     Daiwa Foundation Small Grant: The discovery of unseen biodiversity through the extraction and examination of environmental DNA from lakes and soils. (£1,500 awarded)

1998     A language for link types in taxonomic databases.  Application to BBSRC for PhD studentship.  Awarded

1998       Developing a user-friendly key to uk coastal planktonic ciliates.  Application to NERC.  (associated applicant) Amount sought £67k.  Awarded

External collaborations

2005 – present    Member of EDIT Network Steering Group

2002 – present    Consultant to Japan Marine Science and Technology Centre (JAMSTEC),  Frontier Research Programme for Extremeophiles

1998 – 2001        Consultant to Japan Marine Science and Technology Centre (JAMSTEC),  Frontier Research Programme Deep-sea Environment

1996 – 1997        Consultant to Japan Marine Science and Technology Centre (JAMSTEC),  DeepStar programme

1994 – 2001        Visiting Professor, University of Tsukuba

1995 – 2000        Publications Officer, Society for General Microbiology

Research

Biodiversity informatics.

The classical approach to taxonomy, of individual scientists producing scholarly monographs every 5 or 10 years, is no longer tenable.  It is necessary to increase the efficiency with which we use taxonomic effort and to put the results onto the web for dissemination.  I have been managing the Scratchpad project as part of the EU project  EDIT , which is basically a data-publishing platform that is available to anyone working in natural history.  Put simply, we give you a web site, you fill it with stuff.

Biological Wastewater-Treatment Processes.

Ciliated protozoa (ciliates) are an important component of the microbial community in aerobic biological wastewater-treatment plants with about 175 species reported. They commonly number 50 million cells per litre in the mixed liquor of the activated-sludge process where their major role is the removal of dispersed bacteria by predation. It has long been known that ciliates can be used as reliable indicators of effluent quality in biological aerobic sewage-treatment processes. The advantage of using ciliates as bioindicators is that of speed, with an accurate prediction of effluent quality being available within an hour or two of sampling. Ciliates are rarely used on site in this way, however, mainly because of the difficulty that non-specialists have in identifying them. This project has produced a multimedia, user-friendly guide that can be used by specialists and non-specialists alike for both training and routine monitoring and it can be downloaded from <http://ciliateguide.myspecies.info>.

 

Diversity of the Protista.

No mechanism yet exists to list all the microbial organisms present in a tiny sample from an ecosystem. Molecular techniques now permit the extraction of DNA and RNA from a sample which will inevitably contain material from many different individuals. Some individuals might be rare in the sample but important to the ecosystem function. Others might be dormant, but lend the ecosystem a measure of flexibility against changing circumstances. This project is evaluating method of untangling the wealth of information present in these nucleic acid sample, including assessing the efficiency of recovery, the means to count how many distinct species are present and finally to name them.

 

Eukaryotes from extreme environments.

Life exists almost everywhere on the Earth. Archaea and bacteria are well known from many of the more extreme environments, but our knowledge of the extent of eukaryotic life is far more limited. Eukaryotes seem to be everywhere except for very hot sites, but why should this be so? What adaptations have been evolved to cope with these stressful situations. http://www.nhm.ac.uk/zoology/extreme.html

Publications

 

Vincent S. Smith, Daphne Duin, David Self, Irina Brake, and Dave Roberts. (2010) Motivating Online Publication of Scholarly Research Through Social Networking Tools. International reports on socio-informatics: Workshop Proceedings of 9th International Conference on the Design of Cooperative Systems 7(1): 329-339.http://www.iisi.de/fileadmin/IISI/upload/IRSI/IRSIV7I1.pdf

Penev, Lyubomir, David Roberts, Vincent Smith, Donat Agosti, and Terry Erwin. (2010) Taxonomy shifts up a gear: New publishing tools to accelerate biodiversity research. ZooKeys 50: i-iv. http://pensoftonline.net/zookeys/index.php/journal/article/view/543.

Penev, Lyubomir, Donat Agosti, Teodor Georgiev, Terry Catapano, Jeremy Miller, Vladimir Blagoderov, David Roberts, et al. “Semantic tagging of and semantic enhancements to systematics papers: ZooKeys working examples.” ZooKeys 50, no. 0 (6, 2010). http://pensoftonline.net/zookeys/index.php/journal/article/view/538.

Blagoderov, Vladimir, Irina Brake, Teodor Georgiev, Lyubomir Penev, David Roberts, Simon Ryrcroft, Ben Scott, Donat Agosti, Terrence Catapano, and Vincent S. Smith. “Streamlining taxonomic publication: a working example with Scratchpads and ZooKeys.” ZooKeys 50, no. 0 (6, 2010). http://pensoftonline.net/zookeys/index.php/journal/article/view/539.

Willis, A., King, D., Morse, D., Dil, A., Lyal, C., Roberts, D. (2010) From XML to XML: The Why and How of Making the Biodiversity Literature Accessible to Researchers In Proceedings of the Seventh conference on International Language Resources and Evaluation (LREC'10). Edited by Nicoletta Calzolari (Conference Chair), Khalid Choukri, Bente Maegaard, Joseph Mariani, Jan Odjik, Stelios Piperidis, Mike Rosner, Daniel Tapias. European Language Resources Association (ELRA). 1237-1244.

Warren, A., Salvado, H., Curds, C. R., Roberts, D. M. & Seviour, R. J. (2010). Protozoa in activated-sludge processes. In The Microbial Ecology of Activated Sludge. Edited by Robert J. Seviour & Per H Nielsen: IWA Publishing. 127-139.

Smith, Vincent S., Rycroft, Simon D.,Harman, Kehan T., Scott, Benand Roberts, David (2009) Scratchpads: a data-publishing framework to build, share and manage information on the diversity of life. BMC Bioinformatics, 10(Suppl 14):S6 doi:10.1186/1471-2105-10-S14-S6

Gong, J., Stoeck, T., Yi, Z., Miao, M., Zhang, Q., Roberts, D. M., Warren, A. & Song, W. (2009).Small Subunit rRNA Phylogenies Show that the Class Nassophorea is Not Monophyletic (Phylum Ciliophora). J euk Microbiol., 56, 339-347.

Yi, Z., Chen, Z., Warren, A., Roberts, D. M., al-Rasheid, K., Gao, S., Shao, C., & Song, W. (2008) Molecular phylogeny of Pseudokeronopsis (Protozoa, Ciliophora, Urostylida), with reconsideration of three closely related species at inter- and intra-specific levels inferred from the small subunit ribosomal RNA gene and the ITS1-5.8S-ITS2 region sequences. Journal of Zoology, 275, 268-275.

Yi, Z., Song, W., Warren, A., Roberts, D. M., Al-Rasheid, K. A. S., Chen, Z., Shao, C., Al-Farraj, S. A. & Hu, X. (2008). A molecular phylogenetic investigation of Pseudoamphisiella and Parabirojimia (Protozoa, Ciliophora), two genera with ambiguous systematic positions. European Journal of Protistology 44, 45-53.

Yi, Z., Song, W., Shao, C., Warren, A., Al-Rasheid, K. A. S., Roberts, D. M.,Miao M., Al-Quraishy, S.A. & Chen, Z. (2008). Phylogeny of some systematically uncertain urostyloids -Apokeronopsis, Metaurostylopsis, Thigmokeronopsis (Ciliophora, Stichotrichia) estimated with small subunit rRNA gene sequence information: Discrepancies and agreements with morphological data. European Journal of Protistology, 44, 254-262.

Mayo, S. J., Allkin, R., Baker, W. & other authors (2008). Alpha e-taxonomy: responses from systematics community to the biodiversity crisis. Kew Bulletin, 63, 1-16.

Gong, J., Gao, S., Roberts, D. M., Al-Rasheid, K. A. S. & Song, W. (2008). Trichopodiella faurei n. sp. (Ciliophora, Phyllopharyngea, Cyrtophoria): morphology, SSU rRNA and group I intron phylogenies. J euk Microbiol., 55, 492-500.

⁠Yi, Z., Song, W., Shao, C., Warren, A., Al-Rasheid, K. A. S., Roberts, D. M., et al. (2008). Phylogeny of some systematically uncertain urostyloids -Apokeronopsis, Metaurostylopsis, Thigmokeronopsis (Ciliophora, Stichotrichia) estimated with small subunit rRNA gene sequence information: Discrepancies and agreements with morphological data. European Journal of Protistology, 44(4), 254-62

Li, L., Song, W., Warren, A., Al-Rasheid, K. A. S., Roberts, D., Yi, Z. Al Farraj, S.A. & Hu, X. (2008). Morphology and morphogenesis of a new marine hypotrichous ciliate, Apokeronopsis bergeri nov. spec. from the Yellow Sea, China (Ciliophora, Hypotrichida). European Journal Protistology. 44, 208-219

Xu, D., Song, W., Warren, A., Roberts, D. & Hu, X. (2007). Redescriptions of two marine planktonic ciliates from China, Parastrombidium faurei (Kahl, 1932) Maeda, 1986 and Strombidium capitatum (Leegaard, 1915) Kahl, 1932 (Ciliophora, Oligotrichea). European Journal of Protistology 43, 27-35.

Gong, J., Song, W., Warren, A., Lin, X. & Roberts, D. M. (2007). Microscopical observations on four marine Dysteria species (Ciliophora, Cyrtophorida). European Journal of Protistology 43, 147-161.

Gong, J., Choi, J. K., Roberts, D. M., Kim, S. Y. & Min, G. S. (2007). Morphological Descriptions of New and Little Known Benthic Ciliates from Ganghwa Tidal Flat, Korea. Journal of Eukaryotic Microbioogy 54, 306-316.

Gong, J., Choi, J.-K., Kim, S.-Y., Roberts, D. M., Min, G.-S. & Kim, S.-J. (2007). Taxonomic redescriptions of two ciliates, Protogastrostyla pulchra n. G., N. Comb. and Hemigastrostyla enigmatica (Ciliophora: Spirotrichea, Stichotrichia), with phylogenetic analyses based on 18s and 28s rRNA gene sequences. Journal of Eukaryotic Microbioogy 54, 468-478.

Ytow, N., Morse, D. R. & Roberts, D. M. (2006). Rough set approximation as Formal Concept. Journal of Advanced Computational Intelligence and Intelligent Informatics 10, 606-611.

Tillier, S. & Roberts, D. (2006). Taxonomy on the fly in a European web project. Nature, Lond 440, 24.

Song, W., Warren, A., Roberts, D., Wilbert, N., Li, L., Sun, P., Hu, X. & Ma, H. (2006). Comparison and redefinition of four marine, coloured Pseudokeronopsis spp. (Ciliophora, Hypotrichida), with emphasis on their living morphology. Acta Protozool 45, 271-287.

Sneath, P. & Roberts, D. (2006). The world in miniature: sealed ecosystems. Microbiology Today 33, 64-67.

Ma, H., Song, W., Warren, A., Roberts, D., Gong, J. & al-Rasheid, K. A. S. (2006). Redescription of the marine scuticociliate Glauconema trihymene Thompson, 1966 (Protozoa; Ciliophora): life cycle and stomatogenesis. Zootaxa 1296, 1-17.

Benjamin, E. L., Collins, M. W. & Roberts, D. M. (2006). An inquiry into the morphology of Ciliate Protozoa using an engineering design approach. In Design and Nature III: Comparing design in Nature with Science and Engineering, pp. 23-34. Edited by C. A. Brebbia.

Song, W., Warren, A., Roberts, D., Shang, H., Ma, H., Wilbert, N., Miao, M. & Yi, Z. (2005). Re-evaluation of the phylogenetic position of the genus Dexiotrichides (Protozoa, Ciliophora Scuticociliatida) inferred from stomatogenetic and molecular information for Dexiotrichides pangi. Progress in Natural Science 15, 700-707.

Curds, C. R., Novarino, G., Warren, A. & Roberts, D. M. (2005). Comments on the neotypification of protists, especially ciliates (Protozoa, Ciliophora). Bulletin of Zoological Nomenclature 62, 26-28.

Ikeda, S., Roberts, D. M., Watanabe, K. N. & Ytow, N. (2004). Microbial community analyses using a simple, rapid detection of DNA fingerprints using fluorescence scanner. Journal of Bioscience and Bioengineering 98, 500-503.

Morse, D. R., Ytow, N., Roberts, D. M. & Sato, A. (2003).Comparison of multiple taxonomic hierarchies using TaxoNote: IEEE Symposium on Information Visualisation.

Cordero Peters, R., Ytow, N. & Roberts, D. M. (2003).Analysis of bias in environmental nucleic acid extraction. In 4th European Congress of Protistology and 10th European Conference on Ciliate Biology. San Benedetto del Tronto (AP) Italy.

Kajihara, H. & Roberts, D. M. (2002).TaxoNote. Kuala Lumpur.

Curds, C. R., Roberts, D. M., Salvado, H. & Warren, A. (2002). Ciliated protozoa in aerobic wastewater treatment processes: Their identification and use as bioindicators. In Design, Operation and Control of the Activated Sludge Process, pp. 31-33. Edited by N. J. Horan: Aqua Enviro Technology Transfer.

Ytow, N., Morse, D. R. & Roberts, D. M. (2001). Nomencurator: a nomenclatural history model to handle multiple taxonomic views. Biol J Linn Soc 73, 81-98.

Roberts, D. M. & Novarino, G. (1999). Its all a question of image. Microbiology Today 26, 51-53.

England, R., Hobbs, G., Bainton, N. & Roberts, D. M. (1999).Microbial Signalling and Communication. In Society for General Microbiology Symposium. Edited by D. M. Roberts. Cambridge: Society for General Microbiology.

Roberts, D. M. (1998). Meeting report: the difference of being small: what it means to be a microbe. Protist 149, 197-200.

Roberts, D. M. (1998). Eukaryotic Cells Under Extreme Conditions. In Origin, Evolution And Versatility Of Microorganisms, pp. 163-173. Edited by J. Seckbach. The Netherlands: Kluwer.

Roberts, D. M. (1997).The role of the deep sea environments in understanding evolution. In UK-Japan seminar on deep-sea microbiology (UK-Japan collaboration program). RIKEN Institute, Wako-shi, Saitama.

Roberts, D. M. (1997). The Naming Game. Biological Sciences Review 9, 31-35.

Roberts, D. M., Sharp, P. M., Alderson, G. & Collins, M. (1996).Evolution of Microbial Life. In Society for General Microbiology Symposium. Edited by D. M. Roberts. Cambridge: Society for General Microbiology.

Roberts, D. M. (1996).A quiet revolution. In The Friends of the NHM Newsletter.

Roberts, D. M. (1996).Explaining taxonomy to kids. In Society for General Microbiology Quarterly, pp. 7-8.

Roberts, D. M. (1996). Deep-Sea Microbiology: UK-Japan Collaboration and the Role of the British Council. London: British Council.

Hirt, R. P., Dyal, P. L., Roberts, D. M. & Embley, T. M. (1996).Development of rRNA based methods for the investigation of ciliate communities. London: The Natural History Museum.

Yang, Z. & Roberts, D. M. (1995). On the use of nucleic acid sequences to infer early branchings in the tree of life. Molecular Biology & Evolution 12, 451-458.

Roberts, D. M. & McGarva, D. (1995). Society publishing in the electronic age. SGM Quarterly 22, 20-21.

Roberts, D. M. (1995).Survival strategies of eukaryotes in extreme environments. In Life in extreme environments, pp. 50-66. Toyama: Toyama University of International Study.

Roberts, D. M. (1995). The naming of names for biotechnology. The Biochemist 17, 25-29.

McGarva, D. & Roberts, D. M. (1995). From paper to pixels: electronic publishing and the microbiologist. Learned Publishing 8, 225-227.

Hirt, R. P., Dyal, P. L., Wilkinson, M., Finlay, B. J., Roberts, D. M. & Embley, T. M. (1995). Phylogenetic relationships among karyorelictids and heterotrichs inferred from small subunit rRNA sequences: resolution at the base of the ciliate tree. Molec Phylog Evol 4, 77-87.

Dyal, P. L., Hope, S., Roberts, D. M. & Embley, T. M. (1995). Use of the Pcr and Fluorescent-Probes to Recover Ssu Ribosomal- Rna Gene-Sequences from Single Cells of the Ciliate Protozoan Spathidium. Molecular Ecology 4, 499-503.

Dyal, P. L., Hope, S., Roberts, D. M. & Embley, T. M. (1995). Use Of the Pcr and Fluorescent-Probes to Recover Ssu Ribosomal-Rna Gene-Sequences From Single Cells Of the Ciliate Protozoan Spathidium. Molecular Ecology 4, 499-503.

Novarino, G. & Roberts, D. M. (1994). The use of digital film as an aid for studying live protists. Binary: Computing In Microbiology 6, 197-203.

Roberts, D. M. & Furlong, J. (1988). The detection of motion. Binary: Computing in Microbiology 1, 53-55.

Roberts, D. M. & Furlong, J. (1988). New lamps for old. Binary 14, 21-24.

Roberts, D. M. & Causton, H. (1988). Silver nitrate impregnation of ciliated Protozoa. Arch Protistenk 135, 299-318.

Roberts, D. M. (1988). The automatic generation of file names. Binary: Computing in Microbiology 1, 15-17.

Roberts, D. M. (1988). MS-DOS and data recovery. Binary 15, 14-18.

Roberts, D. M. & Warren, A. (1987). An Inexpensive Apparatus For Automatic Continuous Dehydration. Stain Technology 62, 211-215.

Roberts, D. M. (1987). Interfacing microcomputers to the Coulter counter. Binary 12, 25-29.

Roberts, D. M. (1987). 3-Dimensional analysis of morphological information. Journal Of Applied Bacteriology 63, R 2-R 2 (Abstract).

Roberts, D. M. & Paterson, A. J. C. (1985). The use of image analysis as an aid to microbial identification. Binary 5, 13.

Roberts, D. M. (1984). Low cost digitisation. Binary 3, 21-22.

Roberts, D. M. (1984). Scientific word processing on an Apple. Binary 2, 33-35.

Roberts, D. M., Warren, A. & Curds, C. R. (1983). Morphometric Analysis Of Outline Shape Applied to the Peritrich Genus Vorticella. Syst Zool 32, 377-388.

Roberts, D. M. (1983). Apple graphics tablet software modification. Laboratory Microcomputer 2, 15-18.

Curds, C. R., Gates, M. A. & Roberts, D. M. (1983). British and other freshwater ciliated protozoa. Cambridge: Cambridge University Press for Linnean Society of London and Estuarine and Brackish-water Sciences.

Warren, A. & Roberts, D. M. (1982). Does Vorticella have vital statistics? A mathematical analysis of shape with taxonomic implications. J Protozool 29, 641-642 (Abstract).

Roberts, D. M. (1982). Cell Death In Cultures Of Tetrahymena elliotti. J Protozool 29, 318-319 (Abstract).

Roberts, D. M. (1980). Aspects of cell size measurement in Tetrahymena elliotti. J Gen Microbiol 120, 211-218.

Curds, C. R., Roberts, D. M. & Wu, C.-H. (1978). The use of continuous cultures and electronic sizing devices to study the growth of two species of ciliated protozoa. In Techniques for the study of mixed populations The Society for Applied Bacteriology Technical Series No 11,, pp. 165-177. Edited by D. W. Lovelock & R. Davies. London: Academic Press.

Roberts, D. M. (1977). Aspects of cell size measurement in Tetrahymena pyriformis. J Protozool 24, 47A-48A (Abstract).

Curds, C. R. & Roberts, D. M. (1975). Preliminary notes on the continuous culture of two species of Tetrahymena. J Protozool 22, 50A (Abstract).