@article {38364,
	title = {A mammalian promoter model links cis elements to genetic networks},
	journal = {Biochemical and Biophysical Research CommunicationsBiochemical and Biophysical Research Communications},
	volume = {347},
	year = {2006},
	type = {16/j.bbrc.2006.06.062},
	abstract = {An accurate identification of gene promoters remains an important challenge. Computational approaches for this problem rely on promoter sequence attributes that are believed to be critical for transcription initiation. Here we report a probabilistic model that captures two important properties of promoters, not used by previous methods, viz., the location preference and co-occurrence of promoter elements. Additionally, we found that many of the position-specific DNA elements are strongly linked with the function of the gene product. For instance, a highly conserved motif CCTTT at -1 position is strongly associated with protein synthesis, cellular and tissue development. Our comparative analysis of promoter classes reveals that the promoters devoid of CpG islands are more conserved and have fewer alternative transcription start sites. The discovered links between promoter elements and gene function allows us to infer genetic networks from promoter elements. The web server for the PSPA promoter predictor is available at http://cagr.pcbi.upenn.edu/PSPA.},
	keywords = {conservation, Core promoter prediction, CpG island, Genetic networks, Position-specific motif, Propensity, Transcription factor binding site (TFBS)},
	isbn = {0006-291X},
	author = {Wang, Junwen and Sridhar Hannenhalli}
}
@article {38283,
	title = {Genetic consequences of ecological reserve design guidelines: An empirical investigation},
	journal = {Conserv GenetConserv Genet},
	volume = {4},
	year = {2003},
	abstract = {We assessed the genetic diversity consequences of applying ecological reserve design guidelines to four federally-listed globally-rare plant species. Consequences were measured using two metrics: proportion of all alleles and of common alleles included in reserves. Common alleles were defined as those alleles having a frequency of greater than or equal to0.05 in at least one population. Four conservation professionals applied ecological reserve guidelines to choose specific populations of each species for inclusion in reserves of size 1 to N - 1, where N is the total number of populations of each species. Information regarding genetic diversity was not used in selecting populations. The resulting reserve designs were compared to random designs, and the agreement among experts was assessed using Kendall{\textquoteright}s coefficient of concordance. Application of ecological reserve design guidelines proved mostly ineffective in capturing more genetic diversity than is captured selecting populations randomly. Meeting established targets for genetic diversity, such as one advocated by the Center for Plant Conservation, required larger numbers of populations than are suggested to be sufficient. Relative performance of expert designs differed among species and was dependent on whether the proportion of all alleles or of common alleles was used as a measure of diversity. Furthermore there was no significant concordance among experts in order in which populations were incorporated into reserves as experts differed in priority they placed on individual guidelines.},
	keywords = {albens, Astragulus, Bernardino, conservation, design, diversity, Erigeron, Eriogonum, genetic, Genetics, goodmaniana, Mountains, ovalifolium, Oxytheca, parishii, plant, reserve, San, var., vineum},
	author = {Neel, M. C. and Michael P. Cummings}
}
