@article {49735,
	title = {Quantitative 4D analyses of epithelial folding during Drosophila gastrulation.},
	journal = {Development},
	volume = {141},
	year = {2014},
	month = {2014 Jul},
	pages = {2895-900},
	abstract = {<p>Understanding the cellular and mechanical processes that underlie the shape changes of individual cells and their collective behaviors in a tissue during dynamic and complex morphogenetic events is currently one of the major frontiers in developmental biology. The advent of high-speed time-lapse microscopy and its use in monitoring the cellular events in fluorescently labeled developing organisms demonstrate tremendous promise in establishing detailed descriptions of these events and could potentially provide a foundation for subsequent hypothesis-driven research strategies. However, obtaining quantitative measurements of dynamic shapes and behaviors of cells and tissues in a rapidly developing metazoan embryo using time-lapse 3D microscopy remains technically challenging, with the main hurdle being the shortage of robust imaging processing and analysis tools. We have developed EDGE4D, a software tool for segmenting and tracking membrane-labeled cells using multi-photon microscopy data. Our results demonstrate that EDGE4D enables quantification of the dynamics of cell shape changes, cell interfaces and neighbor relations at single-cell resolution during a complex epithelial folding event in the early Drosophila embryo. We expect this tool to be broadly useful for the analysis of epithelial cell geometries and movements in a wide variety of developmental contexts.</p>},
	keywords = {Animals, Body Patterning, Cell Shape, Cell Tracking, Drosophila melanogaster, Epithelial Cells, Epithelium, Gastrulation, Image Processing, Computer-Assisted, software},
	issn = {1477-9129},
	doi = {10.1242/dev.107730},
	author = {Khan, Zia and Wang, Yu-Chiun and Wieschaus, Eric F and Kaschube, Matthias}
}
@article {38455,
	title = {Quantitative PCR for Detection of Shigella Improves Ascertainment of Shigella Burden in Children with Moderate-to-Severe Diarrhea in Low-Income Countries},
	journal = {Journal of Clinical MicrobiologyJournal of Clinical Microbiology},
	volume = {51},
	year = {2013},
	publisher = {American Society for Microbiology},
	isbn = {0095-1137},
	author = {Lindsay, Brianna and Ochieng, John B. and Ikumapayi, Usman N. and Toure, Aliou and Ahmed, Dilruba and Li, Shan and Panchalingam, Sandra and Levine, Myron M. and Kotloff, Karen and Rasko, David A.}
}
@article {49547,
	title = {Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS},
	journal = {Molecular Systems Biology},
	volume = {8},
	year = {2012},
	month = {Feb-08-2013},
	doi = {10.1038/msb.2012.34},
	url = {http://msb.embopress.org/cgi/doi/10.1038/msb.2012.34},
	author = {Khan, Zia and Bloom, Joshua S and Amini, Sasan and Singh, Mona and Perlman, David H and Caudy, Amy A and Kruglyak, Leonid}
}
@article {49548,
	title = {Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS.},
	volume = {8},
	year = {2012},
	month = {2012},
	pages = {602},
	abstract = {<p>Understanding the genetic basis of gene regulatory variation is a key goal of evolutionary and medical genetics. Regulatory variation can act in an allele-specific manner (cis-acting) or it can affect both alleles of a gene (trans-acting). Differential allele-specific expression (ASE), in which the expression of one allele differs from another in a diploid, implies the presence of cis-acting regulatory variation. While microarrays and high-throughput sequencing have enabled genome-wide measurements of transcriptional ASE, methods for measurement of protein ASE (pASE) have lagged far behind. We describe a flexible, accurate, and scalable strategy for measurement of pASE by liquid chromatography-coupled mass spectrometry (LC-MS). We apply this approach to a hybrid between the yeast species Saccharomyces cerevisiae and Saccharomyces bayanus. Our results provide the first analysis of the relative contribution of cis-acting and trans-acting regulatory differences to protein expression divergence between yeast species.</p>},
	keywords = {Alleles, Chromatography, Liquid, Fungal Proteins, Gene Expression Profiling, Gene Expression Regulation, Fungal, HUMANS, Mass Spectrometry, proteomics, Regression Analysis, Saccharomyces, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Species Specificity},
	issn = {1744-4292},
	doi = {10.1038/msb.2012.34},
	author = {Khan, Zia and Bloom, Joshua S and Amini, Sasan and Singh, Mona and Perlman, David H and Caudy, Amy A and Kruglyak, Leonid}
}
