Lesley Collins
ExperienceFrom April 2010 (Previous Research Positions) 2004-2007 Postdoctoral Fellow, Allan Wilson Centre 2001-2004 Doctoral Student, Massey University (Technical capacity) 1989-1991 Science Technician, Biotechnology Division (later Grasslands), DSIR BackgroundA strong background in molecular biology has meant a clear understanding of how statistical informatics applies to the analysis of genomic and evolutionary data. Many years in the commercial scientific arena (DSIR and Dairy Research Institute) provided experience in animal and associated microbiota group projects. A change in career to follow a more analytical path began with a PhD in bioinformatics researching eukaryotic evolution through the use of large genomic datasets. Skills further gained in large dataset analysis with the rise of high throughput sequencing (aka Next Generation Sequencing). Instrumental in the set up of Illumina (Solexa) sequencing at the Allan Wilson Centre Genome Service and currently holds a position as a research consultant. This consultancy includes the assessment of projects prior to sequencing due to newness of this technology. In 2010, closer ties to the Institute of Fundamental Sciences at Massey University will allow an expanding research, in the areas of mass sequencing statistics, as well as an individual project on the evolutionary analysis of RNA networks. Active collaborations include Dr. Robin McDiarmid, Plant and Food (plant viral RNA) and Prof. Nigel French (Giardia mass sequencing and SNP analysis). As a genome analysis specialist, there is also informal contact with animal and plant genome operations. Current Research InterestsEvolution of RNA-based networks in eukayotes: RNA-based metabolism including RNA regulation (RNAi and epigenetics) and RNA processing (e.g. splicing) underpin the action of proteins in the eukaryotic cell. This underlying network is known as the ‘RNA-Infrastructure’. After developing this concept my research is concentrating on how to use databases and tools constructed primarily for proteins to investigate the evolution of these RNA-protein networks. Published information from model organisms (e.g. human and yeast) is used as well as transcription and small RNA data from non-model and deeply branched eukaryotes such as Giardia lamblia and Trichomonas vaginalis.
Achievements and AffiliationsEditor of upcoming book “RNA Infrastructure: RNA processing and regulatory networks (Publishers Landes Bioscience and Springer) Editorial board of Trends in Evolutionary Biology Invited lecturer at the 2009 Winter School in Mathematical and Computational Biology, University of Queensland, Brisbane Australia. Keynote speaker, Sydney Bioinformatics Research Symposium, Sydney, Australia Co-organiser and major informatics presenter at the national Next Generation Sequencing Workshop, Te Manawa, Palmerston North 2009 and Solexa Sequencing Workshop 2008. Invited presenter, American Genetic Association Annual Symposium: Mechanisms of Genome Evolution, Indiana University, Bloomington IN, USA. 2007. 2006 Queenstown Molecular Biology Meeting (QMB) Promising Researcher Award The Walter M. Fitch Prize (Society for Molecular Biology and Evolution) awarded at MBE’05 International Conference 2005 New Zealand Representative at the SMBE Tri-Nations Young Investigators Workshop (NZ, Japan, USA) 2005. Reviewer for the European Science Foundation (ESF) and member of the ESF pool of reviewers (2004 – present) PublicationsPlease note that pdfs accessed via this site are for personal use only and copyright rests with the publisher. 2010Collins, L.J. Chen, X.S. and Schönfeld, B. The Epigenetics of Non-coding RNA (Chapter in the ‘Handbook of Epigenetics’) edited by T.Tollefsbol, Elsevier. In Press Penny, D. and Collins, L.J. Evolutionary genomics leads the way. Book chapter introduction for Evolutionary Genomics and Systems Biology, John Wiley & Sons. In Press. X.S. Chen, Penny D, Biggs P.J. and Collins L.J. Deep sequencing reveals medium length non-coding RNAs from early-branching protozoan parasites. In final preparation. 2009Collins, L.J. and Chen, S.X. (2009). Ancestral RNA: The RNA biology of the eukaryotic ancestor. RNA Biology, 6: 495-502. Collins, L.J. Kurland C.G., Biggs P.J. and Penny D. (2009). The modern RNA-based world of Eukaryotes. (2009) Journal of Heredity, 100:597-604. Chen, X.S., Collins L.J., Biggs P.J. and Penny D. (2009). microRNAs of Giardia lamblia and Trichomonas vaginalis from mass sequencing. Genome Evolution and Biology, 1(1):165-175. Collins, L.J. and Penny D. (2009). The RNA-infrastructure of the Eukaryotic Cell. Trends in Genetics 25:120-128. PDF 2008Collins, L.J., Biggs P.J., Voelckel, C. and Joly, S. (2008). An approach to transcriptome analysis of non-model organisms using short-read sequences. Genome Informatics 21:3-14. Chen, X.S., White W.T.J., Collins L.J. and Penny D. (2008). Computational Identification of Four Spliceosomal snRNAs from the Deep-Branching Eukaryote Giardia intestinalis. PLoS ONE 3(8): e3106. doi:10.1371/journal.pone.003106. Trewick S.A., Morgan-Richards M., Collins L.J. (2008). Are you my mother? Phylogenetic analysis reveals orphan hybrid stick insect genus is part of a monophyletic New Zealand clade. Molecular Phylogenetics and Evolution. 48:799-808. Collins, L.J. and Schoenfield B. (2008). Next Generation Sequencing in New Zealand. New Zealand BioScience 17(1):12-15). 2007Collins LJ. and Lockhart P.J., Evolutionary properties of sequences and ancestral state reconstruction. In: Ancestral Sequence Reconstruction. Edited by Liberles DA. Oxford, New York: Oxford University Press; 2007: 95-102. Zhang S.G., Schwelin A., Jin H.P, Collins L.J, and Bradshaw R.E. (2007). A fragmented aflatoxin-like gene cluster in the forest pathogen Dothistroma septosporum. Fungal Genetics and Biology 44(12):1342-1354. Chen X.S., Rozhdestvensky, T.S., Collins, L.J., Schmitz, J. and Penny, D. (2007) Combined experimental and computational approach to identify non-protein-coding RNAs in the deep-branching eukaryote Giardia intestinalis. Nucleic Acids Research. 35(14):4619-4628. PDF Kurland C.G., Collins L.J. and Penny D. (2007) Response to letter in Science 316:542 – 543. Woodhams M.D, Stadler P.F., Penny D., and Collins L.J.. (2007). RNase MRP and the RNA processing cascade in the eukaryotic ancestor. BMC Evolutionary Biology 7: Suppl 1, S13. 2006Kurland, C.G., Collins, L.J. and Penny D. (2006). Genomics and the Irreducible Nature of Eukaryotic Cells. Science. 312 (5776): 1011-1014. PDF Collins, L.J. and Penny D. (2006). Investigating the Intron Recognition Mechanism in Eukaryotes. Molecular Biology and Evolution. 23 (5):901-910. PDF Chan, Z.S.H., Kasabov, N. and Collins L. (2006). A two-stage methodology for gene regulatory network extraction from time-course gene expression data, presented at IEEE Workshop on Biomedical Applications of Circuits and Systems, Singapore, Dec 2004. IEEE Transactions on Circuits and Signals. 30(1) 59-63. Online: doi:10.1016/j.eswa.2005.09.049) Chan Z., Collins L. and Kasabov N, (2006). An efficient greedy K-means algorithm for global gene trajectory clustering. Expert Systems with Applications. 30 (1) 137-141. 2005Collins, L.J. and Penny, D. (2005). Complex Spliceosomal Organization Ancestral to Extant Eukaryotes. Molecular Biology and Evolution 22(4):1-14. PDF Chan, Z. H. Kasabov, N and Collins L. (2005). A Hybrid Genetic Algorithm and Expectation Maximization Method for Global Gene Trajectory Clustering. Journal of Bioinformatics and Computational Biology. 3 (5): 1227-1242. 2004 and priorCollins, L.J. (2004). PhD Thesis “Lost in the RNA World: Non-coding RNA and the Spliceosome in the Eukaryotic Ancestor.” Massey University, Palmerston North, New Zealand. Collins, L.J. and Penny D. (2004). Lost in the RNA World – The Genomics of ncRNA. NZ BioScience. February: 38-40. Collins, L.J., Macke T. and Penny D. (2004). Searching for ncRNAs in eukaryotic genomes: Maximizing biological input with RNAmotif. Journal of Integrative Bioinformatics 1: 61-77. PDF Collins, L.J., Poole, A. M. and Penny D. (2003). Using Ancestral Sequences to Uncover Potential Gene Homologs. Applied Bioinformatics 2 (3 Suppl): S85-S95. Collins, L. J., Moulton V. and Penny D. (2000). Use of RNA secondary structure for studying the evolution of RNase P and RNase MRP.” Journal of Molecular Evolution 51(3): 194-204. PDF Collins, L., Moulton, V. and Penny D. (1999). RNA secondary structure as an identification tool in the identification of putative pRNA sequences in the chloroplast of green plant species. Mid Sweden University Department of Mathematics Reports No 3, ISSN 1400-4798.
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Senior Research Fellow
Evolution of Eukaryotic Signature Proteins (with PhD student Jian Han): Eukaryotic Signature Proteins are by definition, proteins present in ‘all’ eukaryotes but not prokaryotes, implying conserved and possibly ancestral functions throughout eukaryotes. Because parasites are often subject to genome reduction, we expect these proteins to be present in parasites only if their presence is still evolutionary constrained. This project has collated current datasets of ESPs evolutionarily comparing ESPs between host (human) and eukaryotic parasites (Giardia lamblia, Trichomonas vaginalis and Plasmodium falciparum). This project is funded by a Health Research Council of New Zealand Emerging Researcher Grant.