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% $Id: bioinfo.bib 286 2016-01-15 18:50:25Z jtk $
% $Date: 2016-01-15 18:50:25 +0000 (Fri, 15 Jan 2016) $
% $Author: jtk $
@string{pnas = {Proceedings of the National Academy of Sciences, USA}}
@article{ ISI:000245413900027,
Author = {Walter, Achim and Scharr, Hanno and Gilmer, Frank and Zierer, Rainer and
Nagel, Kerstin A. and Ernst, Michaela and Wiese, Anika and Virnich,
Olivia and Christ, Maja M. and Uhlig, Beate and Juenger, Sybille and
Schurr, Uli},
Title = {{Dynamics of seedling growth acclimation towards altered light conditions
can be quantified via GROWSCREEN: a setup and procedure designed for
rapid optical phenotyping of different plant species}},
Journal = {{NEW PHYTOLOGIST}},
Year = {{2007}},
Volume = {{174}},
Number = {{2}},
Pages = {{447-455}},
DOI = {{10.1111/j.1469-8137.2007.02002.x}},
ISSN = {{0028-646X}},
ResearcherID-Numbers = {{Wiese-Klinkenberg, Anika/C-8196-2009
Walter, Achim/N-8392-2013
Scharr, Hanno/D-9051-2015}},
ORCID-Numbers = {{Scharr, Hanno/0000-0002-8555-6416}},
Unique-ID = {{ISI:000245413900027}},
}
@article{ZAITOUN2015797,
title = "International Conference on Communications, management, and Information technology (ICCMIT'2015) Survey on Image Segmentation Techniques",
journal = "Procedia Computer Science",
volume = "65",
number = "",
pages = "797 - 806",
year = "2015",
note = "",
issn = "1877-0509",
doi = "http://dx.doi.org/10.1016/j.procs.2015.09.027",
url = "http://www.sciencedirect.com/science/article/pii/S1877050915028574",
author = "Vaclav Snasel and Marcelo Alancar and Dorota Jeloneck and Abdel Badeeh Salem and Luigi Valanderau and Yacoub Saleh and Senthil Kumar and Evgenia Theodoutou and Nida M. Zaitoun and Musbah J. Aqel",
keywords = "Image processing",
keywords = "Image segmentation",
keywords = "Image engineering",
keywords = "Image analysis",
keywords = "Image understanding.",
abstract = "Due to the advent of computer technology image-processing techniques have become increasingly important in a wide variety of applications. Image segmentation is a classic subject in the field of image processing and also is a hotspot and focus of image processing techniques. Several general-purpose algorithms and techniques have been developed for image segmentation. Since there is no general solution to the image segmentation problem, these techniques often have to be combined with domain knowledge in order to effectively solve an image segmentation problem for a problem domain. This paper presents a comparative study of the basic Block-Based image segmentation techniques."
}
@article{Udupa200675,
title = "A framework for evaluating image segmentation algorithms ",
journal = "Computerized Medical Imaging and Graphics ",
volume = "30",
number = "2",
pages = "75 - 87",
year = "2006",
note = "",
issn = "0895-6111",
doi = "http://dx.doi.org/10.1016/j.compmedimag.2005.12.001",
url = "http://www.sciencedirect.com/science/article/pii/S089561110500114X",
author = "Jayaram K. Udupa and Vicki R. LeBlanc and Ying Zhuge and Celina Imielinska and Hilary Schmidt and Leanne M. Currie and Bruce E. Hirsch and James Woodburn",
keywords = "Image segmentation",
keywords = "Evaluation of segmentation",
keywords = "Image analysis",
keywords = "Segmentation efficacy ",
abstract = "The purpose of this paper is to describe a framework for evaluating image segmentation algorithms. Image segmentation consists of object recognition and delineation. For evaluating segmentation methods, three factors—precision (reliability), accuracy (validity), and efficiency (viability)—need to be considered for both recognition and delineation. To assess precision, we need to choose a figure of merit, repeat segmentation considering all sources of variation, and determine variations in figure of merit via statistical analysis. It is impossible usually to establish true segmentation. Hence, to assess accuracy, we need to choose a surrogate of true segmentation and proceed as for precision. In determining accuracy, it may be important to consider different ‘landmark’ areas of the structure to be segmented depending on the application. To assess efficiency, both the computational and the user time required for algorithm training and for algorithm execution should be measured and analyzed. Precision, accuracy, and efficiency factors have an influence on one another. It is difficult to improve one factor without affecting others. Segmentation methods must be compared based on all three factors, as illustrated in an example wherein two methods are compared in a particular application domain. The weight given to each factor depends on application. "
}
@article{Rathnayaka2011226,
title = "Effects of \{CT\} image segmentation methods on the accuracy of long bone 3D reconstructions ",
journal = "Medical Engineering \& Physics ",
volume = "33",
number = "2",
pages = "226 - 233",
year = "2011",
note = "",
issn = "1350-4533",
doi = "http://dx.doi.org/10.1016/j.medengphy.2010.10.002",
url = "http://www.sciencedirect.com/science/article/pii/S1350453310002225",
author = "Kanchana Rathnayaka and Tony Sahama and Michael A. Schuetz and Beat Schmutz",
keywords = "Computed tomography",
keywords = "Image segmentation",
keywords = "Canny edge detection",
keywords = "Thresholding",
keywords = "Bone models",
keywords = "MicroCT",
keywords = "Femur",
keywords = "Mechanical digitiser "
}
@article{fpls.2014.00770,
AUTHOR={Junker, Astrid and Muraya, Moses Mahugu and Weigelt-Fischer, Kathleen and Arana-Ceballos, Fernando and Klukas, Christian and Melchinger, Albrecht E and Meyer, Rhonda C and Riewe, David and Altmann, Thomas},
TITLE={Optimizing experimental procedures for quantitative evaluation of crop plant performance in high throughput phenotyping systems},
JOURNAL={Frontiers in Plant Science},
VOLUME={5},
YEAR={2015},
NUMBER={770},
URL={http://www.frontiersin.org/crop_science_and_horticulture/10.3389/fpls.2014.00770/abstract},
DOI={10.3389/fpls.2014.00770},
ISSN={1664-462X},
}
@article{Fawcett:2006:IRA:1159473.1159475,
author = {Fawcett, Tom},
title = {An Introduction to ROC Analysis},
journal = {Pattern Recogn. Lett.},
issue_date = {June 2006},
volume = {27},
number = {8},
month = jun,
year = {2006},
issn = {0167-8655},
pages = {861--874},
numpages = {14},
url = {http://dx.doi.org/10.1016/j.patrec.2005.10.010},
doi = {10.1016/j.patrec.2005.10.010},
acmid = {1159475},
publisher = {Elsevier Science Inc.},
address = {New York, NY, USA},
keywords = {Classifier evaluation, Evaluation metrics, ROC analysis},
}
@book{MATLAB:2010,
year = {2010},
author = {MATLAB},
title = {version 7.10.0 (R2010a)},
publisher = {The MathWorks Inc.},
address = {Natick, Massachusetts}
}
@article{10.1371/journal.pgen.1000551,
author = {Kover, Paula X. AND Valdar, William AND Trakalo, Joseph AND Scarcelli, Nora AND Ehrenreich, Ian M. AND Purugganan, Michael D. AND Durrant, Caroline AND Mott, Richard},
journal = {PLoS Genet},
publisher = {Public Library of Science},
title = {A Multiparent Advanced Generation Inter-Cross to Fine-Map Quantitative Traits in <italic>Arabidopsis thaliana</italic>},
year = {2009},
month = {07},
volume = {5},
url = {http://dx.doi.org/10.1371%2Fjournal.pgen.1000551},
pages = {1-15},
abstract = {<title>Author Summary</title>
<p>Most traits of economic and evolutionary interest vary quantitatively and have multiple genes affecting their expression. Dissecting the genetic basis of such traits is crucial for the improvement of crops and management of diseases. Here, we develop a new resource to identify genes underlying such quantitative traits in <italic>Arabidopsis thaliana</italic>, a genetic model organism in plants. We show that using a large population of inbred lines derived from intercrossing 19 parents, we can localize the genes underlying quantitative traits better than with existing methods. Using these lines, we were able to replicate the identification of previously known genes that affect developmental traits in <italic>A. thaliana</italic> and identify some new ones. This paper also presents all the necessary biological and computational material necessary for the scientific community to use these lines in their own research. Our results suggest that the use of lines derived from a multiparent advanced generation inter-cross (MAGIC lines) should be very useful in other organisms.</p>
},
number = {7},
doi = {10.1371/journal.pgen.1000551}
}
@article{Mott07112000,
author = {Mott, Richard and Talbot, Christopher J. and Turri, Maria G. and Collins, Allan C. and Flint, Jonathan},
title = {A method for fine mapping quantitative trait loci in outbred animal stocks},
volume = {97},
number = {23},
pages = {12649-12654},
year = {2000},
doi = {10.1073/pnas.230304397},
abstract ={High-resolution mapping of quantitative trait loci (QTL) in
animals has proved to be difficult because the large effect sizes
detected in crosses between inbred strains are often caused by numerous
linked QTLs, each of small effect. In a study of fearfulness in mice,
we have shown it is possible to fine map small-effect QTLs in a
genetically heterogeneous stock (HS). This strategy is a powerful
general method of fine mapping QTLs, provided QTLs detected in crosses
between inbred strains that formed the HS can be reliably detected in
the HS. We show here that single-marker association analysis identifies
only two of five QTLs expected to be segregating in the HS and
apparently limits the strategy's usefulness for fine mapping. We solve
this problem with a multipoint analysis that assigns the probability
that an allele descends from each progenitor in the HS. The analysis
does not use pedigrees but instead requires information about the HS
founder haplotypes. With this method we mapped all three previously
undetected loci [chromosome (Chr.) 1 logP 4.9, Chr. 10 logP 6.0, Chr.
15 logP 4.0]. We show that the reason for the failure of single-marker
association to detect QTLs is its inability to distinguish opposing
phenotypic effects when they occur on the same marker allele. We have
developed a robust method of fine mapping QTLs in genetically
heterogeneous animals and suggest it is now cost effective to undertake
genomewide high-resolution analysis of complex traits in parallel on
the same set of mice.},
URL = {http://www.pnas.org/content/97/23/12649.abstract},
eprint = {http://www.pnas.org/content/97/23/12649.full.pdf},
journal = {Proceedings of the National Academy of Sciences}
}
@article{PBI:PBI232,
author = {Gregersen, Per L. and Holm, Preben Bach},
title = {Transcriptome analysis of senescence in the flag leaf of wheat (Triticum aestivum L.)},
journal = {Plant Biotechnology Journal},
volume = {5},
number = {1},
publisher = {Blackwell Publishing Ltd},
issn = {1467-7652},
url = {http://dx.doi.org/10.1111/j.1467-7652.2006.00232.x},
doi = {10.1111/j.1467-7652.2006.00232.x},
pages = {192--206},
keywords = {leaf senescence, microarrays, nutrient remobilization, transcriptome, Triticum aestivum},
year = {2007},
}
@article{PLB:PLB114,
author = {Gregersen, P. L. and Holm, P. B. and Krupinska, K.},
title = {Leaf senescence and nutrient remobilisation in barley and wheat},
journal = {Plant Biology},
volume = {10},
publisher = {Blackwell Publishing Ltd},
issn = {1438-8677},
url = {http://dx.doi.org/10.1111/j.1438-8677.2008.00114.x},
doi = {10.1111/j.1438-8677.2008.00114.x},
pages = {37--49},
keywords = {Cereals, leaf senescence, nitrogen remobilisation, protein degradation},
year = {2008},
}
@Article{plants4030449,
AUTHOR = {Häffner, Eva and Konietzki, Sandra and Diederichsen, Elke},
TITLE = {Keeping Control: The Role of Senescence and Development in Plant Pathogenesis and Defense},
JOURNAL = {Plants},
VOLUME = {4},
YEAR = {2015},
NUMBER = {3},
PAGES = {449},
URL = {http://www.mdpi.com/2223-7747/4/3/449},
ISSN = {2223-7747},
ABSTRACT = {Many plant pathogens show interactions with host development. Pathogens may modify plant development according to their nutritional demands. Conversely, plant development influences pathogen growth. Biotrophic pathogens often delay senescence to keep host cells alive, and resistance is achieved by senescence-like processes in the host. Necrotrophic pathogens promote senescence in the host, and preventing early senescence is a resistance strategy of plants. For hemibiotrophic pathogens both patterns may apply. Most signaling pathways are involved in both developmental and defense reactions. Increasing knowledge about the molecular components allows to distinguish signaling branches, cross-talk and regulatory nodes that may influence the outcome of an infection. In this review, recent reports on major molecular players and their role in senescence and in pathogen response are reviewed. Examples of pathosystems with strong developmental implications illustrate the molecular basis of selected control strategies. A study of gene expression in the interaction between the hemibiotrophic vascular pathogen Verticillium longisporum and its cruciferous hosts shows processes that are fine-tuned to counteract early senescence and to achieve resistance. The complexity of the processes involved reflects the complex genetic control of quantitative disease resistance, and understanding the relationship between disease, development and resistance will support resistance breeding.},
DOI = {10.3390/plants4030449}
}
@Article{Singh2009,
author="Singh, P. K.
and Singh, R. P.
and Duveiller, E.
and Mergoum, M.
and Adhikari, T. B.
and Elias, E. M.",
title="Genetics of wheat--Pyrenophora tritici-repentis interactions",
journal="Euphytica",
year="2009",
volume="171",
number="1",
pages="1--13",
abstract="Tan spot, caused by an ascomycete fungus Pyrenophora tritici-repentis, is one of the most devastating foliar diseases of wheat. This fungus induces two distinct symptoms, tan necrosis and extensive chlorosis, on susceptible wheat cultivars. Besides causing average yield losses of 5--10\%, tan spot also causes significant losses in grain quality by grain shriveling, red smudge, and black point. Conservation agriculture in combination with wheat monoculture involving cultivation of susceptible cultivars has resulted in frequent onset of tan spot epidemics worldwide. Development of new resistant wheat cultivars, in conjunction with crop rotation, will provide an effective, economical, and environmentally safe means of controlling tan spot. Presently, eight races of P. tritici-repentis have been identified worldwide based on the ability to induce necrosis and chlorosis symptoms on a set of differential wheat cultivars. P. tritici-repentis is a homothallic fungus having both sexual and asexual reproduction resulting in high genetic diversity worldwide. Both quantitative and qualitative mode of inheritance for resistance to tan spot of wheat has been reported. The tan spot fungus produces multiple host-specific toxins and host resistance is highly correlated to insensitivity to toxins. Genetic studies have further confirmed that wheat--P. tritici-repentis follows the toxin model of gene-for-gene hypothesis although other mechanism of host--pathogen interaction may exist and exploitation of all resistance phenomenon is to be adopted to develop durable resistant cultivars.",
issn="1573-5060",
doi="10.1007/s10681-009-0074-6",
url="http://dx.doi.org/10.1007/s10681-009-0074-6"
}
@article{Distelfeld27012014,
author = {Distelfeld, Assaf and Avni, Raz and Fischer, Andreas M.},
title = {Senescence, nutrient remobilization, and yield in wheat and barley},
year = {2014},
doi = {10.1093/jxb/ert477},
abstract ={Cereals including wheat and barley are of primary importance to ensure food security for the 21st century. A combination of lab- and field-based approaches has led to a considerably improved understanding of the importance of organ and particularly of whole-plant (monocarpic) senescence for wheat and barley yield and quality. A delicate balance between senescence timing, grain nutrient content, nutrient-use efficiency, and yield needs to be considered to (further) improve cereal varieties for a given environment and end use. The recent characterization of the Gpc-1 (NAM-1) genes in wheat and barley demonstrates the interdependence of these traits. Lines or varieties with functional Gpc-1 genes demonstrate earlier senescence and enhanced grain protein and micronutrient content but, depending on the environment, somewhat reduced yields. A major effort is needed to dissect regulatory networks centred on additional wheat and barley transcription factors and signalling pathways influencing the senescence process. Similarly, while important molecular details of nutrient (particularly nitrogen) remobilization from senescing organs to developing grains have been identified, important knowledge gaps remain. The genes coding for the major proteases involved in senescence-associated plastidial protein degradation are largely unknown. Membrane transport proteins involved in the different transport steps occurring between senescing organ (such as leaf mesophyll) cells and protein bodies in the endosperm of developing grains remain to be identified or further characterized. Existing data suggest that an improved understanding of all these steps will reveal additional, important targets for continued cereal improvement.},
URL = {http://jxb.oxfordjournals.org/content/early/2014/01/24/jxb.ert477.abstract},
eprint = {http://jxb.oxfordjournals.org/content/early/2014/01/24/jxb.ert477.full.pdf+html},
journal = {Journal of Experimental Botany}
}
@article{Mackay01092014,
author = {Mackay, Ian J. and Bansept-Basler, Pauline and Barber, Toby and Bentley, Alison R. and Cockram, James and Gosman, Nick and Greenland, Andy J. and Horsnell, Richard and Howells, Rhian and O’Sullivan, Donal M. and Rose, Gemma A. and Howell, Phil J.},
title = {An Eight-Parent Multiparent Advanced Generation Inter-Cross Population for Winter-Sown Wheat: Creation, Properties, and Validation},
volume = {4},
number = {9},
pages = {1603-1610},
year = {2014},
doi = {10.1534/g3.114.012963},
abstract ={MAGIC populations represent one of a new generation of crop genetic mapping resources combining high genetic recombination and diversity. We describe the creation and validation of an eight-parent MAGIC population consisting of 1091 F7 lines of winter-sown wheat (Triticum aestivum L.). Analyses based on genotypes from a 90,000-single nucleotide polymorphism (SNP) array find the population to be well-suited as a platform for fine-mapping quantitative trait loci (QTL) and gene isolation. Patterns of linkage disequilibrium (LD) show the population to be highly recombined; genetic marker diversity among the founders was 74\% of that captured in a larger set of 64 wheat varieties, and 54\% of SNPs segregating among the 64 lines also segregated among the eight founder lines. In contrast, a commonly used reference bi-parental population had only 54\% of the diversity of the 64 varieties with 27\% of SNPs segregating. We demonstrate the potential of this MAGIC resource by identifying a highly diagnostic marker for the morphological character "awn presence/absence" and independently validate it in an association-mapping panel. These analyses show this large, diverse, and highly recombined MAGIC population to be a powerful resource for the genetic dissection of target traits in wheat, and it is well-placed to efficiently exploit ongoing advances in phenomics and genomics. Genetic marker and trait data, together with instructions for access to seed, are available at http://www.niab.com/MAGIC/.},
URL = {http://www.g3journal.org/content/4/9/1603.abstract},
eprint = {http://www.g3journal.org/content/4/9/1603.full.pdf+html},
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