@article{cheng_blackburn_lin_goshe_williamson_2009, title={Absolute Protein Quantification by LC/MSE for Global Analysis of Salicylic Acid-induced Plant Protein Secretion Responses}, volume={8}, ISSN={["1535-3907"]}, DOI={10.1021/pr800649s}, abstractNote={The plant cell wall is a dynamic cellular compartment consisting of a complex matrix of components that can change dramatically in response to environmental stresses. During pathogen attack, for instance, a wide spectrum of proteins that participate in various sequential processes involved in plant defense is secreted into the cell wall. In this study, a mass spectrometry, data-independent acquisition approach known as LC/MS (E) was used to assess temporal changes in the cell wall proteome in response to different levels of an endogenous inducer of plant disease defense responses, salicylic acid (SA). LC/MS (E) was used as a label-free method that enabled simultaneous protein identification and absolute femtomole quantification of each protein secreted into the extracellular matrix. A total of 74 secreted proteins were identified, 63 of which showed increased specific secretion in response to SA. A majority of this induced secretion occurred within 2 h of treatment, indicating that many proteins are involved in the early stages of plant defenses. We also identified a number of apparently nonclassically secreted proteins, suggesting that, as in many nonplant systems, Golgi/ER-independent mechanisms exist for plant protein secretion. These results provide new insight into plant apoplastic defense mechanisms and demonstrate that LC/MS (E) is a powerful tool for obtaining both relative and absolute proteome-scale quantification that can be applied to complex, time- and dose-dependent experimental designs.}, number={1}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Cheng, Fang-yi and Blackburn, Kevin and Lin, Yu-min and Goshe, Michael B. and Williamson, John D.}, year={2009}, month={Jan}, pages={82–93} }
 @article{lin_fang_thorne_2007, title={A tabu search algorithm for maximum parsimony phylogeny inference}, volume={176}, ISSN={["1872-6860"]}, DOI={10.1016/j.ejor.2005.10.031}, abstractNote={Phylogeny reconstruction is too complex a combinatorial problem for an exhaustive search, because the number of possible solutions increases exponentially with the number of taxa involved. In this paper, we adopt the parsimony principle and design a tabu search algorithm for finding a most parsimonious phylogeny tree. A special array structure is employed to represent the topology of trees and to generate the neighboring trees. We test the proposed tabu search algorithm on randomly selected data sets obtained from nuclear ribosomal DNA sequence data. The experiments show that our algorithm explores fewer trees to reach the optimal one than the commonly used program “dnapenny” (branch-and-bound based) while it generates much more accurate results than the default options of the program “dnapars” (heuristic search based). The percentage of search space needed to find the best solution for our algorithm decreased rapidly as the number of taxa increased. For a 20-taxon phylogeny problem, it needs on average to examine only 3.92 × 10−15% of the sample space.}, number={3}, journal={EUROPEAN JOURNAL OF OPERATIONAL RESEARCH}, author={Lin, Yu-Min and Fang, Shu-Cherng and Thorne, Jeffrey L.}, year={2007}, month={Feb}, pages={1908–1917} }