The Experts below are selected from a list of 400140 Experts worldwide ranked by ideXlab platform
Jeffrey P Townsend - One of the best experts on this subject based on the ideXlab platform.
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PhyDesign: an online application for profiling phylogenetic Informativeness
BMC Evolutionary Biology, 2011Co-Authors: Francesc López-giráldez, Jeffrey P TownsendAbstract:Background The rapid increase in number of sequenced genomes for species across of the tree of life is revealing a diverse suite of orthologous genes that could potentially be employed to inform molecular phylogenetic studies that encompass broader taxonomic sampling. Optimal usage of this diversity of loci requires user-friendly tools to facilitate widespread cost-effective locus prioritization for phylogenetic sampling. The Townsend (2007) phylogenetic Informativeness provides a unique empirical metric for guiding marker selection. However, no software or automated methodology to evaluate sequence alignments and estimate the phylogenetic Informativeness metric has been available. Results Here, we present PhyDesign, a platform-independent online application that implements the Townsend (2007) phylogenetic Informativeness analysis, providing a quantitative prediction of the utility of loci to solve specific phylogenetic questions. An easy-to-use interface facilitates uploading of alignments and ultrametric trees to calculate and depict profiles of Informativeness over specified time ranges, and provides rankings of locus prioritization for epochs of interest. Conclusions By providing these profiles, PhyDesign facilitates locus prioritization increasing the efficiency of sequencing for phylogenetic purposes compared to traditional studies with more laborious and low capacity screening methods, as well as increasing the accuracy of phylogenetic studies. Together with a manual and sample files, the application is freely accessible at http://phydesign.townsend.yale.edu .
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The Phylogenetic Informativeness of Nucleotide and Amino Acid Sequences for Reconstructing the Vertebrate Tree
Journal of Molecular Evolution, 2008Co-Authors: Jeffrey P Townsend, Francesc López-giráldez, Robert FriedmanAbstract:To aid in future efforts to accurately reconstruct the vertebrate tree, a quantitative measure of phylogenetic Informativeness was applied to nucleotide and amino acid sequences for a set of 11 genes. We identified orthologues and assembled published fossil-calibrated divergence times between taxa that had been sequenced for each gene. Rates of molecular evolution for each site were estimated to characterize the molecular evolutionary pattern of genes and to calculate the phylogenetic Informativeness. The fast-evolving gene albumin yielded the highest Informativeness over the period from 60 million years ago to 500 million years ago. In contrast, calmodulin yielded the lowest Informativeness, presumably because functional constraint minimized substitutions in the amino acid sequence. The gene c-myc showed an intermediate level of Informativeness. The nucleotide sequence of cytochrome b showed extremely high utility for recent epochs, but low utility for times before 100 million years ago. We ranked nine other genes for their utility during the epochs of the divergence of the muroid rodents, early placental mammals, early vertebrates, and early metazoa, yielding results consistent with, but more precise than, previous studies. Interestingly, DNA sequence always exceeded amino acid sequence in Informativeness over all time scales, yet support values were at best moderately higher. For epochs not subject to strong phylogenetic conflict due to convergence, we advocate gleaning the additional power of the threefold increase in number of characters that is present for DNA sequences over resorting to the less noisy but less informative amino acid sequences.
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Profiling Phylogenetic Informativeness
Systematic biology, 2007Co-Authors: Jeffrey P TownsendAbstract:The resolution of four controversial topics in phylogenetic experimental design hinges upon the Informativeness of characters about the historical relationships among taxa. These controversies regard the power of different classes of phylogenetic character, the relative utility of increased taxonomic versus character sampling, the differentiation between lack of phylogenetic signal and a historical rapid radiation, and the design of taxonomically broad phylogenetic studies optimized by taxonomically sparse genome-scale data. Quantification of the Informativeness of characters for resolution of phylogenetic hypotheses during specified historical epochs is key to the resolution of these controversies. Here, such a measure of phylogenetic Informativeness is formulated. The optimal rate of evolution of a character to resolve a dated four-taxon polytomy is derived. By scaling the asymptotic Informativeness of a character evolving at a nonoptimal rate by the derived asymptotic optimum, and by normalizing so that net phylogenetic Informativeness is equivalent for all rates when integrated across all of history, an Informativeness profile across history is derived. Calculation of the Informativeness per base pair allows estimation of the cost-effectiveness of character sampling. Calculation of the Informativeness per million years allows comparison across historical radiations of the utility of a gene for the inference of rapid adaptive radiation. The theory is applied to profile the phylogenetic Informativeness of the genes BRCA1, RAG1, GHR, and c-myc from a muroid rodent sequence data set. Bounded integrations of the phylogenetic profile of these genes over four epochs comprising the diversifications of the muroid rodents, the mammals, the lobe-limbed vertebrates, and the early metazoans demonstrate the differential power of these genes to resolve the branching order among ancestral lineages. This measure of phylogenetic Informativeness yields a new kind of information for evaluation of phylogenetic experiments. It conveys the utility of the addition of characters a phylogenetic study and it provides a basis for deciding whether appropriate phylogenetic power has been applied to a polytomy that is proposed to be a rapid radiation. Moreover, it provides a quantitative measure of the capacity of a gene to resolve soft polytomies.
Ganapathi S Narayanamoorthy - One of the best experts on this subject based on the ideXlab platform.
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did the sec impact banks loan loss reserve policies and their Informativeness
Journal of Accounting and Economics, 2013Co-Authors: Paul J Beck, Ganapathi S NarayanamoorthyAbstract:Abstract During the late 1990s, the SEC alleged that banks were overstating loan loss allowances to establish cookie jar reserves. Their intervention in bank accounting culminated in 2001 with new guidance (SAB 102) designed to improve financial reporting quality. We show that banks' allowance estimation changed in response to the SEC's intervention. While allowance Informativeness (as proxied by the ability to explain future losses) improved for Strong Banks, Informativeness declined for Weak Banks whose incentives are to understate allowances. Our results help to explain why some (Weak) banks delayed loss recognition during the recent financial crisis.
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did the sec impact banks loan loss reserve policies and their Informativeness
2012Co-Authors: Paul J Beck, Ganapathi S NarayanamoorthyAbstract:During the late 1990’s, the SEC alleged that banks were overstating their loan loss allowances to establish cookie jar reserves and issued new guidance on allowance estimation designed to improve financial reporting quality. We show that banks’ estimation methods changed in response to the guidance and the changes significantly affected the Informativeness of the allowances as proxied by their ability to explain future losses. While the SEC’s guidance has improved the Informativeness of allowances for strong banks, it has had the opposite effect on Weak Banks whose incentives are to understate allowances. Our results help to explain why some (Weak) banks delayed loss recognition during the recent financial crisis.
Ewa Sletten - One of the best experts on this subject based on the ideXlab platform.
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voluntary disclosure incentives and earnings Informativeness
The Accounting Review, 2012Co-Authors: Sugata Roychowdhury, Ewa SlettenAbstract:ABSTRACT: We propose that the value of the earnings reporting process as an information source lies in limiting delays in the release of bad news, either by inducing managers to disclose it voluntarily or by directly releasing the negative news that managers have incentives to withhold. We compare earnings Informativeness in bad-news and good-news quarters. Using returns to measure news, we find, consistent with our prediction, that earnings Informativeness relative to other sources is higher in bad-news quarters than in good-news quarters. Further, cross-sectional tests indicate that earnings differential Informativeness in bad-news quarters is more pronounced when managers do not voluntarily disclose the news, information asymmetry is stronger, and managers are net sellers of stock. JEL Classifications: G3; M4; M40; M41; M48. Data Availability: Data are available from Compustat, CRSP, First Call, I/B/E/S, ISSM, TAQ, and Thompson Financial.
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voluntary disclosure incentives and earnings Informativeness
2012Co-Authors: Sugata Roychowdhury, Ewa SlettenAbstract:We propose that the value of the earnings reporting process as an information source lies in limiting delays in the release of bad news either by inducing managers to disclose it voluntarily, or by directly releasing the negative news that managers have incentives to withhold. We compare earnings’ Informativeness in bad-news and good-news quarters. Using returns to measure news, we find, consistent with our prediction, that earnings’ Informativeness relative to other sources is higher in bad-news quarters than in good-news quarters. Further, cross-sectional tests indicate that earnings’ differential Informativeness in bad-news quarters is more pronounced when managers do not voluntarily disclose the news, information asymmetry is stronger, and managers are net sellers of stock.
Paul J Beck - One of the best experts on this subject based on the ideXlab platform.
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did the sec impact banks loan loss reserve policies and their Informativeness
Journal of Accounting and Economics, 2013Co-Authors: Paul J Beck, Ganapathi S NarayanamoorthyAbstract:Abstract During the late 1990s, the SEC alleged that banks were overstating loan loss allowances to establish cookie jar reserves. Their intervention in bank accounting culminated in 2001 with new guidance (SAB 102) designed to improve financial reporting quality. We show that banks' allowance estimation changed in response to the SEC's intervention. While allowance Informativeness (as proxied by the ability to explain future losses) improved for Strong Banks, Informativeness declined for Weak Banks whose incentives are to understate allowances. Our results help to explain why some (Weak) banks delayed loss recognition during the recent financial crisis.
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did the sec impact banks loan loss reserve policies and their Informativeness
2012Co-Authors: Paul J Beck, Ganapathi S NarayanamoorthyAbstract:During the late 1990’s, the SEC alleged that banks were overstating their loan loss allowances to establish cookie jar reserves and issued new guidance on allowance estimation designed to improve financial reporting quality. We show that banks’ estimation methods changed in response to the guidance and the changes significantly affected the Informativeness of the allowances as proxied by their ability to explain future losses. While the SEC’s guidance has improved the Informativeness of allowances for strong banks, it has had the opposite effect on Weak Banks whose incentives are to understate allowances. Our results help to explain why some (Weak) banks delayed loss recognition during the recent financial crisis.
Francesc López-giráldez - One of the best experts on this subject based on the ideXlab platform.
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PhyDesign: an online application for profiling phylogenetic Informativeness
BMC Evolutionary Biology, 2011Co-Authors: Francesc López-giráldez, Jeffrey P TownsendAbstract:Background The rapid increase in number of sequenced genomes for species across of the tree of life is revealing a diverse suite of orthologous genes that could potentially be employed to inform molecular phylogenetic studies that encompass broader taxonomic sampling. Optimal usage of this diversity of loci requires user-friendly tools to facilitate widespread cost-effective locus prioritization for phylogenetic sampling. The Townsend (2007) phylogenetic Informativeness provides a unique empirical metric for guiding marker selection. However, no software or automated methodology to evaluate sequence alignments and estimate the phylogenetic Informativeness metric has been available. Results Here, we present PhyDesign, a platform-independent online application that implements the Townsend (2007) phylogenetic Informativeness analysis, providing a quantitative prediction of the utility of loci to solve specific phylogenetic questions. An easy-to-use interface facilitates uploading of alignments and ultrametric trees to calculate and depict profiles of Informativeness over specified time ranges, and provides rankings of locus prioritization for epochs of interest. Conclusions By providing these profiles, PhyDesign facilitates locus prioritization increasing the efficiency of sequencing for phylogenetic purposes compared to traditional studies with more laborious and low capacity screening methods, as well as increasing the accuracy of phylogenetic studies. Together with a manual and sample files, the application is freely accessible at http://phydesign.townsend.yale.edu .
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The Phylogenetic Informativeness of Nucleotide and Amino Acid Sequences for Reconstructing the Vertebrate Tree
Journal of Molecular Evolution, 2008Co-Authors: Jeffrey P Townsend, Francesc López-giráldez, Robert FriedmanAbstract:To aid in future efforts to accurately reconstruct the vertebrate tree, a quantitative measure of phylogenetic Informativeness was applied to nucleotide and amino acid sequences for a set of 11 genes. We identified orthologues and assembled published fossil-calibrated divergence times between taxa that had been sequenced for each gene. Rates of molecular evolution for each site were estimated to characterize the molecular evolutionary pattern of genes and to calculate the phylogenetic Informativeness. The fast-evolving gene albumin yielded the highest Informativeness over the period from 60 million years ago to 500 million years ago. In contrast, calmodulin yielded the lowest Informativeness, presumably because functional constraint minimized substitutions in the amino acid sequence. The gene c-myc showed an intermediate level of Informativeness. The nucleotide sequence of cytochrome b showed extremely high utility for recent epochs, but low utility for times before 100 million years ago. We ranked nine other genes for their utility during the epochs of the divergence of the muroid rodents, early placental mammals, early vertebrates, and early metazoa, yielding results consistent with, but more precise than, previous studies. Interestingly, DNA sequence always exceeded amino acid sequence in Informativeness over all time scales, yet support values were at best moderately higher. For epochs not subject to strong phylogenetic conflict due to convergence, we advocate gleaning the additional power of the threefold increase in number of characters that is present for DNA sequences over resorting to the less noisy but less informative amino acid sequences.
