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Search Results: 1 - 10 of 231384 matches for " Brian R Haas "
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Premotor biomarkers for Parkinson's disease - a promising direction of research
Brian R Haas, Tessandra H Stewart, Jing Zhang
Translational Neurodegeneration , 2012, DOI: 10.1186/2047-9158-1-11
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
Brian J Haas, Steven L Salzberg, Wei Zhu, Mihaela Pertea, Jonathan E Allen, Joshua Orvis, Owen White, C Robin Buell, Jennifer R Wortman
Genome Biology , 2008, DOI: 10.1186/gb-2008-9-1-r7
Abstract: Accurate and comprehensive gene discovery in eukaryotic genome sequences requires multiple independent and complementary analysis methods including, at the very least, the application of ab initio gene prediction software and sequence alignment tools. The problem is technically challenging, and despite many years of research no single method has yet been able to solve it, although numerous tools have been developed to target specialized and diverse variations on the gene finding problem (for review [1,2]). Conventional gene finding software employs probabilistic techniques such as hidden Markov models (HMMs). These models are employed to find the most likely partitioning of a nucleotide sequence into introns, exons, and intergenic states according to a prior set of probabilities for the states in the model. Such gene finding programs, including GENSCAN [3], GlimmerHMM [4], Fgenesh [5], and GeneMark.hmm [6], are effective at identifying individual exons and regions that correspond to protein-coding genes, but nevertheless they are far from perfect at correctly predicting complete gene structures, differing from correct gene structures in exon content or position [7-10].The correct gene structures, or individual components including introns and exons, are often apparent from spliced alignments of homologous transcript or protein sequences. Many software tools are available that perform these alignment tasks. Tools used to align expressed sequence tags (ESTs) and full-length cDNAs (FL-cDNAs) to genomic sequence include EST_GENOME [11], AAT [12], sim4 [13], geneseqer [14], BLAT [15], and GMAP [16], among numerous others. The list of programs that perform spliced alignments of protein sequences to DNA are much fewer, including the multifunctional AAT, exonerate [17], and PMAP (derived from GMAP). An extension of spliced protein alignment that includes a probabilistic model of eukaryotic gene structure is implemented in GeneWise [18], a popular homology-based gene predict
'Next-generation' sequencing becomes 'now-generation'
Daniel E Neafsey, Brian J Haas
Genome Biology , 2011, DOI: 10.1186/gb-2011-12-3-303
Abstract: In the last Genome Biology report on this annual conference, Manolis Kellis noted in 2004 that sequencing had reached a mature state, in which the research community 'took for granted that we can sequence, assemble, and align complete genomes' (Genome Biol 2004, 5:324). The technological innovations of the next few years, which shifted sequencing from the Sanger-style long reads used to complete the first human genome to short 'next-generation' reads, required a second wave of innovation to prepare samples for sequencing and deal with the new format of the resulting data. Finally, as attendees of the Advances in Genome Biology & Technology conference learned in February, the field can once again begin to take for granted our ability to effectively produce and process the copious sequencing data that contemporary sequencing technologies more affordably provide. The maturation of these technologies creates interesting new analytical applications for sequencing.Many presenters highlighted innovative approaches to simplify sequencing library preparation, expand the range of samples eligible for sequencing, or limit sequencing to specific genomic regions. In describing the Wellcome Trust Sanger Centre's sequencing pipeline, Harold Swerdlow (Sanger Centre, Hinxton, UK) detailed the degree to which amplification-free Illumina library construction reduces the effect of GC composition on sequencing coverage. Andi Gnirke (Broad Institute, Cambridge, USA) described approaches by which base composition coverage bias can be minimized during the amplification phase of Illumina library construction, for instances where circumstances do not permit amplification-free libraries.Hybrid selection has become a widely adopted means by which to selectively sequence just the exonic portion of the human genome, or other specific regions of interest. By designing oligonucleotides complementary to targeted regions and then hybridizing those oligonucleotides with genomic DNA on a chip or in so
Probabilistic downscaling of precipitation data in a subtropical mountain area: a two-step approach
R. Haas ,K. Born
Nonlinear Processes in Geophysics (NPG) , 2011,
Abstract: In this study, a two-step probabilistic downscaling approach is introduced and evaluated. The method is exemplarily applied on precipitation observations in the subtropical mountain environment of the High Atlas in Morocco. The challenge is to deal with a complex terrain, heavily skewed precipitation distributions and a sparse amount of data, both spatial and temporal. In the first step of the approach, a transfer function between distributions of large-scale predictors and of local observations is derived. The aim is to forecast cumulative distribution functions with parameters from known data. In order to interpolate between sites, the second step applies multiple linear regression on distribution parameters of observed data using local topographic information. By combining both steps, a prediction at every point of the investigation area is achieved. Both steps and their combination are assessed by cross-validation and by splitting the available dataset into a trainings- and a validation-subset. Due to the estimated quantiles and probabilities of zero daily precipitation, this approach is found to be adequate for application even in areas with difficult topographic circumstances and low data availability.
Premetazoan genome evolution and the regulation of cell differentiation in the choanoflagellate Salpingoeca rosetta
Stephen R Fairclough, Zehua Chen, Eric Kramer, Qiandong Zeng, Sarah Young, Hugh M Robertson, Emina Begovic, Daniel J Richter, Carsten Russ, M Jody Westbrook, Gerard Manning, B Franz Lang, Brian Haas, Chad Nusbaum, Nicole King
Genome Biology , 2013, DOI: 10.1186/gb-2013-14-2-r15
Abstract: A comparison of the 55 Mb S. rosetta genome with genomes from diverse opisthokonts suggests that the origin of metazoans was preceded by a period of dynamic gene gain and loss. The S. rosetta genome encodes homologs of cell adhesion, neuropeptide, and glycosphingolipid metabolism genes previously found only in metazoans and expands the repertoire of genes inferred to have been present in the progenitors of metazoans and choanoflagellates. Transcriptome analysis revealed that all four S. rosetta septins are upregulated in colonies relative to single cells, suggesting that these conserved cytokinesis proteins may regulate incomplete cytokinesis during colony development. Furthermore, genes shared exclusively by metazoans and choanoflagellates were disproportionately upregulated in colonies and the single cells from which they develop.The S. rosetta genome sequence helps to refine the catalog of metazoan-specific genes while also extending the evolutionary history of certain gene families that are central to metazoan biology. Transcriptome data suggest that conserved cytokinesis genes, including septins, may contribute to S. rosetta colony formation and indicate that the initiation of colony development may preferentially draw upon genes shared with metazoans, while later stages of colony maturation are likely regulated by genes unique to S. rosetta.
Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release
Brian J Haas, Jennifer R Wortman, Catherine M Ronning, Linda I Hannick, Roger K Smith, Rama Maiti, Agnes P Chan, Chunhui Yu, Maryam Farzad, Dongying Wu, Owen White, Christopher D Town
BMC Biology , 2005, DOI: 10.1186/1741-7007-3-7
Abstract: Over the course of three years, TIGR has completed its effort to standardize the structural and functional annotation of the Arabidopsis genome. Using both manual and automated methods, Arabidopsis gene structures were refined and gene products were renamed and assigned to Gene Ontology categories. We present an overview of the methods employed, tools developed, and protocols followed, summarizing the contents of each data release with special emphasis on our final annotation release (version 5).Over the entire period, several thousand new genes and pseudogenes were added to the annotation. Approximately one third of the originally annotated gene models were significantly refined yielding improved gene structure annotations, and every protein-coding gene was manually inspected and classified using Gene Ontology terms.Arabidopsis thaliana has long been considered the foremost model organism in plant biology. It is favored for its short generation time, plentiful seeds, conveniently small stature, and ease of genetic transformation using Agrobacterium tumefaciens. Its comparatively small genome size, estimated at 140 million base pairs, and low repetitive sequence content drove the choice of Arabidopsis as a target for complete genome sequencing in the early nineties. Ten years later, the genome sequence was completed [1], providing a valuable resource for furthering the understanding of Arabidopsis biology and providing a reference sequence from which results in Arabidopsis could be extended to other plants.Since its publication, the Arabidopsis genome has been mined for clues to numerous important metabolic pathways and biological processes, many of which are documented in peer-reviewed publications including the Arabidopsis Book [2]. Additionally, the Arabidopsis genome has been used extensively as a tool for comparative genomics, both for genome-wide comparisons and to study specific processes among a wide range of plant species, including the gametophytic transcr
Effects of aqueous complexation on reductive precipitation of uranium by Shewanella putrefaciens
Johnson R Haas, Abraham Northup
Geochemical Transactions , 2004, DOI: 10.1186/1467-4866-5-41
Abstract: Uranium (U) is a prominent environmental radiocontaminant at a local to regional scale throughout much of the developed world. Most historic releases of U into natural aquatic systems have occurred through the agencies of U mining, ore processing, isotopic separation, and waste disposal related to the production of fission weapons, and the operation of commercial nuclear reactors. Other major sources of environmental U dispersal include coal combustion, releasing U through fly ash or stack emissions, and the military use of 235U-depleted U(IV) oxide in kinetic penetrators.Under oxic conditions the stable form of uranium is U(VI), which is highly soluble and in aqueous solution tends to adsorb onto available mineral and organic surfaces.[1-11] Uranium(VI) adsorption onto sedimentary minerals may retard its propagation through aquifers, however dispersal could be facilitated by adsorption onto transportable organic matter, such as bacteria.[12,13] Transport in the aqueous phase is also facilitated by the tendency of U(VI) to stably complex with a wide range of inorganic and organic ligands.[14,15]Reduction of soluble U(VI) to relatively insoluble U(IV) may serve as one potential method, under anoxic conditions, of removing uranium from the aqueous phase, or of sequestering uranium adsorbed onto organic or mineral surfaces. Uranium(IV) is sparingly soluble, and will tend to precipitate forming amorphous UO2(s). Abiotic methods exploiting U(VI) reduction as a means of U removal from groundwater have been approached, including permeable groundwater barriers incorporating zero-valent iron or sodium dithionite as reducing agents.[16-18] These methods seek to isolate U from the biotic environment through chemical reductive precipitation, and could presumably offer a more permanent remedial solution than sedimentary U(VI) adsorption, which would be vulnerable to reversibility via shifts in groundwater pH (e.g., industrial acidification) or ionic strength (e.g., salt water in
Continuum Monte Carlo Simulation at Constant Pressure of Stiff Chain Molecules at Surfaces
R. Hilfer,F. M. Haas
Physics , 1996,
Abstract: Continuum Monte-Carlo simulations at constant pressure are performed on short chain molecules at surfaces. The rodlike chains, consisting of seven effective monomers, are attached at one end to a flat twodimensional substrate. It is found that the model exhibits phases similar to the liquid condensed and liquid expanded phases of Langmuir monolayers. The model is investigated here for a wide range of pressures and temperatures using a special form of constant pressure simulation compatible with the symmetry breaking during tilting transitions in the liquid condensed phases. At low pressures the chains undergo a tilting transition exhibiting tilt directions towards nearest and also next nearest neighbours depending on temperature. At elevated temperatures and low pressure the film enters a fluidlike phase similar to whose surface area per molecule is in rough quantitative agreement with that of the liquid expanded phase observed in experiment.
Variations in Integrated Galactic Initial Mass Functions due to Sampling Method and Cluster Mass Function
M. R. Haas,P. Anders
Physics , 2010, DOI: 10.1051/0004-6361/200912967
Abstract: [abridged] Stars are thought to be formed predominantly in clusters. The clusters are formed following a cluster initial mass function (CMF) similar to the stellar initial mass function (IMF). Both the IMF and the CMF favour low-mass objects. The numerous low-mass clusters will lack high mass stars. If the integrated galactic initial mass function originates from stars formed in clusters, the IGIMF could be steeper than the IMF. We investigate how well constrained this steepening is and how it depends on the choice of sampling method and CMF. We compare analytic sampling to several implementations of random sampling of the IMF, and different CMFs. We implement different IGIMFs into GALEV to obtain colours and metallicities for galaxies. Choosing different ways of sampling the IMF results in different IGIMFs. Depending on the lower cluster mass limit and the slope of the cluster mass function, the steepening varies between very strong and negligible. We find the size of the effect is continuous as a function of the power-law slope of the CMF, if the CMF extends to masses smaller than the maximum stellarmass. The number of O-stars detected by GAIA might help in judging on the importance of the IGIMF effect. The impact of different IGIMFs on integrated galaxy photometry is small, within the intrinsic scatter of observed galaxies. Observations of gas fractions and metallicities could rule out at least the most extreme sampling methods. As we still do not understand the details of star formation, one sampling method cannot be favoured over another. Also, the CMF at very low cluster masses is not well constrained observationally. These uncertainties need to be taken into account when using an IGIMF, with severe implications for galaxy evolution models and interpretations of galaxy observations.
Galactic consequences of clustered star formation
M. R. Haas,P. Anders
Physics , 2009, DOI: 10.1017/S1743921309991566
Abstract: If all stars form in clusters and both the stars and the clusters follow a power law distribution which favours the creation of low mass objects, then the numerous low mass clusters will be deficient in high mass stars. Therefore, the mass function of stars, integrated over the whole galaxy (the Integrated Galactic Initial Mass Function, IGIMF) will be steeper at the high mass end than the underlying IMF of the stars. We show how the steepness of the IGIMF depends on the sampling method and on the assumptions made for the star cluster mass function. We also investigate the O-star content, integrated photometry and chemical enrichment of galaxies that result from several IGIMFs, as compared to more standard IMFs.
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