Publications - Dr. Lesley Collins
As with all scientists this is what we should keep up to date...B
I have put in a few links to these papers and chapters and will put more in over time (both papers and links ;-)
Books and Book Chapters
Collins, L.J. Editor of upcoming book “RNA Infrastructure and Networks. Landes Bioscience/Springer, Austin/New York:, To be published 2010.
Collins, L.J. Digging deeper into the spliceosomal RNA infrastructure. In RNA Infrastructure and Networks, edited by L.J. Collins, Landes Bioscience/Springer, Austin/New York 2010, in final preparation.
Collins, L.J. Chen, X.S. and Schönfeld, B. The Epigenetics of Non-coding RNA. In Trygve Tollefsbol, editors: Handbook of Epigenetics,Oxford:Academic Press,2010, pp. 49-61.
Penny, D. and Collins, L.J. Evolutionary genomics leads the way. Evolutionary Genomics and Systems Biology edited by Gustavo Caetano-Anolles, John Wiley & Sons Hoboken, New Jersey USA; 2010:3-16.
Collins 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.
Journal Publications (just the last few years)
Collins, L.J. and Chen, S.X. Ancestral RNA: The RNA biology of the eukaryotic ancestor. (2009) RNA Biology, 6: 495-502.
Collins, L.J. Kurland C.G., Biggs P.J. and Penny D., 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. microRNAs of Giardia lamblia and Trichomonas vaginalis from mass sequencing. (2009) Genome Evolution and Biology, 1:165-175.
Collins, L.J. and Penny D. The RNA-infrastructure of the Eukaryotic Cell. (2009) Trends in Genetics 25:120-128.
Collins, 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: e3106
Trewick S.A., Morgan-Richards M., Collins L.J. Are you my mother? Phylogenetic analysis reveals orphan hybrid stick insect genus is part of a monophyletic New Zealand clade. Molecular Phylogenetics and Evolution. (2008) 48:799-808.
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 44:1342-1354.
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. 35:4619-4628.
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: S13.
Chan Z., Collins L. and Kasabov N., (2007) Bayesian Inference of Sparse Gene Network. Biosystems. 87:299-306.
Kurland, C.G., Collins, L.J. and Penny D. (2006) Genomics and the Irreducible Nature of Eukaryotic Cells. Science. 312: 1011-1014.
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. IEEE Transactions on Circuits and Signals. 30 59-63.
Collins, L.J. and Penny D. (2006) Investigating the Intron Recognition Mechanism in Eukaryotes. Molecular Biology and Evolution. 23:901-910.
Chan Z., Collins L. and Kasabov N., (2006) An efficient greedy K-means algorithm for global gene trajectory clustering. Expert Systems with Applications.30 137-141.
Collins, L.J. and Penny, D. (2005) Complex Spliceosomal Organization Ancestral to Extant Eukaryotes. Molecular Biology and Evolution 22:1-14.
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: 1227-1242.
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.
