to establish the validity of the technique. It also enumerates 21 recommendations for specific im... more to establish the validity of the technique. It also enumerates 21 recommendations for specific improvements that should be undertaken to improve the methodology, including such basic steps as the development of a consensus on the interpretation of test results and efforts to establish "best practices" for interpretation.
Analysis of 37 short repetitive elements (SINES) in rabbit DNA that are known as C repeats has re... more Analysis of 37 short repetitive elements (SINES) in rabbit DNA that are known as C repeats has revealed three that contribute functional polyadenylation signals to genes into which they have been inserted. Similar roles have been attributed to particular individual SINES in rodents and primates before, suggesting that these roles may be common to SINES in all mammalian orders. Although
C repeats constitute the predominant family of short interspersed repeats (SINES) in the rabbit g... more C repeats constitute the predominant family of short interspersed repeats (SINES) in the rabbit genome. Determination of the nucleotide sequence 5' to rabbit (- globin genes reveals clusters of C repeats, and analysis of these and other sequenced regions of rabbit chromosomes shows that the C repeats have a strong tendency to insert within or in close proximity to other
The rates and patterns of molecular evolution in many eukaryotic organisms have been shown to be ... more The rates and patterns of molecular evolution in many eukaryotic organisms have been shown to be influenced by the compartmentalization of their genomes into fractions of distinct base composition and mutational properties. We have examined the Drosophila genome to explore relationships between the nucleotide content of large chromosomal segments and the base composition and rate of evolution of genes within
Bioinformatics: Where Biology meets Computer Science
IEEE Potentials
Computational methods are becoming an increasingly important aspect of the evaluation and analysi... more Computational methods are becoming an increasingly important aspect of the evaluation and analysis of experimental data in molecular biology. The use of computational methods towards solving problems in biology is known as bioinformatics. The field of bioinformatics is constantly redefining itself as methods for collecting biological data are developed and refined. While the future directions of the field are impossible to predict, one conclusion seems to be evident: computational techniques have changed the way in which biologists collect and analyze experimental data. Computation will continue to be a prominent component of biochemistry and molecular biology research for the foreseeable future. While early studies developed the techniques necessary to sequence entire genomes, scientists are now investigating the interacting mechanisms that control the expression of genes. Ambitious new efforts are underway to identify the complex biological pathways of interaction between genes, t...
Computational methods are becoming an increasingly important aspect of the evaluation and analysi... more Computational methods are becoming an increasingly important aspect of the evaluation and analysis of experimental data in molecular biology. The use of computational methods towards solving problems in biology is known as bioinformatics. The field of bioinformatics is constantly redefining itself as methods for collecting biological data are developed and refined. While the future directions of the field are impossible to predict, one conclusion seems to be evident: computational techniques have changed the way in which biologists collect and analyze experimental data. Computation will continue to be a prominent component of biochemistry and molecular biology research for the foreseeable future. While early studies developed the techniques necessary to sequence entire genomes, scientists are now investigating the interacting mechanisms that control the expression of genes. Ambitious new efforts are underway to identify the complex biological pathways of interaction between genes, t...
Although forensic DNA testing is well established, experts sometimes disagree about the interpret... more Although forensic DNA testing is well established, experts sometimes disagree about the interpretation and statistical characterization of test results. This article will describe the key controversies and will explain what lawyers need to know to recognize controversial types of DNA evidence. The focus is on low-template or low-copy number (LCN) DNA testing.
Proceedings of the National Academy of Sciences, 1992
Highly polymorphic segments of the human genome containing variable numbers of tandem repeats (VN... more Highly polymorphic segments of the human genome containing variable numbers of tandem repeats (VNTRs) have been widely used to establish DNA profiles of individuals for use in forensics. Methods of estimating the probability of occurrence of matching DNA profiles between two randomly selected individuals have been subject to extensive debate regarding the possibility of signicant substructure occurring within the major races. We have sampl two Caucasian subpopulations, Finns and Italians, at four commonly used VNTR loci to determine the extent to which the subgroups differ from each other and from a mixed Caucasian database. The data were also analyzed for the occurrence of linkage disequilibrium among the loci. The allele frequency distributions of some loci were found to differ sgificantly among the subpopulations in a manner consistent with population substructure. Major differences were also found in the Abbreviations: VNTR, variable number of tandem repeats; HWE, Hardy-Weinberg equilibrium.
Parsimony approach to test the Evolving Master Gene hypothesis for human Alu repeats
Sixth IEEE Symposium on BioInformatics and BioEngineering (BIBE'06), 2006
The Alu family of Short interspersed repeats (SINEs) account for a significant portion of the &am... more The Alu family of Short interspersed repeats (SINEs) account for a significant portion of the "junk DNA" within the mammalian genome. Thousands of copies of Alu subfamilies are scattered essentially randomly through the human genome. The relative abundance of these repeats provides a rich fossil record of primate and human history. Since Alus have no known functionality, a great deal
Bioinformatics is a new and rapidly evolving discipline that has emerged from the fields of exper... more Bioinformatics is a new and rapidly evolving discipline that has emerged from the fields of experimental molecular biology and biochemistry, and from the the artificial intelligence, database, and algorithms disciplines of computer science. Largely because of the inherently interdisciplinary nature of bioinformatics research, academia has been slow to respond to strong industry and government demands for trained scientists to develop and apply novel bioinformatics techniques to the rapidly-growing, freely-available repositories of genetic and proteomic data. While some institutions are responding to this demand by establishing graduate programs in bioinformatics, the entrance barriers for these programs are high, largely due to the significant amount of prerequisite knowledge in the disparate fields of biochemistry and computer science required to author sophisticated new approaches to the analysis of bioinformatics data. We present a proposal for an undergraduate-level bioinformatics curriculum in computer science that lowers these barriers.
A Comparision of Codon Usage Trends in Prokaryotes
2009 Ohio Collaborative Conference on Bioinformatics, 2009
ABSTRACT Codon usage bias is an effective measure of the differences among organisms at a genomic... more ABSTRACT Codon usage bias is an effective measure of the differences among organisms at a genomic level. These genomic differences also reflect some differences in the organisms’ lifestyles and physiology. Here we demonstrate that prokaryotic obligate intracellular parasites and symbionts have a codon usage pattern that differs significantly from that of exclusively free-living prokaryotes. This result is valuable in that it suggests that the habitat of an organism may directly influence that organism’s use of synonymous codons, which in turn demonstrates evidence of an evolutionary mechanism that operates at a finer molecular level than that of amino acids and proteins.
Freshwater mussels (Bivalvia:Unionidae) are among the most imperiled organisms in North America. ... more Freshwater mussels (Bivalvia:Unionidae) are among the most imperiled organisms in North America. Information on the spatial scale of reproduction and population connectivity will better enable mussel conservation programs to sustain long-term population viability, particularly restocking and recovery programs. Here we used genetic methods to characterize population structure, dispersal potential, and reproductive strategies in the freshwater mussel Lampsilis cardium from Twin Creek and Big Darby Creek (Ohio, USA). We genotyped adults and individual glochidia at 12 microsatellite loci to assess local population structure relative to within-population patterns of relatedness and parentage. Local populations within watersheds were weakly structured, and within-population estimates of relatedness identified probable full-and half-siblings several kilometers apart. Parent-offspring comparisons provided evidence of multiple paternity in single broods and identified the likely father of 3 glochidia from 1 female's brood 16.2 km upstream of the mother, indicating that long-distance transport of spermatozoa can promote population connectivity within watersheds. Given that lampsilines and other unionoids exhibit similar reproductive strategies, it is possible that other species are capable of long-distance fertilization. If so, fertilization in populations of many freshwater mussels might not be limited by local density of breeding adults. Therefore, the prospects for recovery of imperiled freshwater mussels might be better than what is now expected.
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