Publications
J. Lindsay
Book Chapters:
O. Glebova and Y. Temate-Tiagueu and A. Caciula and S. Al Seesi and A. Artyomenko and S. Mangul and J. Lindsay and I.I. Mandoiu and A. Zelikovsky, Transcriptome Quantification and Differential Expression from NGS Data, In I.I. Mandoiu and A. Zelikovsky, Computational Methods for Next Generation Sequencing Data Analysis, John Wiley & Sons, pp. 301-327, 2016, publisher url, bibtex
I. Mandric and J. Lindsay and I.I. Mandoiu and A. Zelikovsky, Scaffolding Algorithms, In I.I. Mandoiu and A. Zelikovsky, Computational Methods for Next Generation Sequencing Data Analysis, John Wiley & Sons, pp. 105-131, 2016, publisher url, bibtex
Journal Articles:
E. Hemphill and J. Lindsay and C. Lee and I.I. Mandoiu and C.E. Nelson, Feature selection and classifier performance on diverse biological datasets, BMC Bioinformatics 15(Suppl 13):S4, 2014, pdf preprint, publisher url, bibtex
J. Lindsay and H. Salooti and I.I. Mandoiu and A. Zelikovsky, ILP-based maximum likelihood genome scaff olding, BMC Bioinformatics 15(Suppl 9):S9, 2014, pdf preprint, publisher url, bibtex
H. Yu and J. Lindsay and Z.-P. Feng and S. Frankenberg and Y. Hu and D. Carone and G. Shaw and A.J. Pask and R.J. O'Neill and A.T. Papenfuss and M.B. Renfree, Evolution of coding and non-coding genes in HOX clusters of a marsupial, BMC Genomics 13:251, 2012, publisher url, bibtex
M.B. Renfree, A.T. Papenfuss, J.E. Deakin, J. Lindsay, ..., I.I. Mandoiu, et al., Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development, Genome Biology 12:R81, 2011, publisher url, bibtex
T.N. Heider and J. Lindsay and C. Wang and R.J. O'Neill and A.J. Pask, Enhancing genome assemblies by integrating non-sequence based data, BMC Proceedings 5(Suppl 2):S7, 2011, publisher url, bibtex
Conference Articles:
J. Lindsay and H. Salooti and A. Zelikovsky and I.I. Mandoiu, Scalable Genome Scaffolding using Integer Linear Programming, Proc. ACM Conference on Bioinformatics, Computational Biology and Biomedicine, pp. 377-383, 2012, pdf preprint, publisher url, ppt, bibtex
Ph.D. Thesis:
J. Lindsay, Scalable Optimization Algorithms for High-throughput Genomic Data, University of Connecticut, Storrs, CT, May, 2015, pdf preprint, url, bibtex