We provide a complete thermodynamic solution of a 1D hopping model in the presence of a random potential by obtaining the density of states. Since the partition function is related to the density of states by a Laplace transform, the density of states determines completely the thermodynamic behavior of the system. We have also shown that the transfer matrix technique, or the so-called dynamic programming, used to obtain the density of states in the 1D hopping model may be generalized to tackle a long-standing problem in statistical significance assessment for one of the most important proteomic tasks - peptide sequencing using tandem mass spectrometry data.
Dynamical System Modeling to Simulate Donor T Cell Response to Whole Exome Sequencing-Derived Recipient Peptides: Understanding Randomness in Clinical Outcomes Following Stem Cell Transplantation
Improving the Results of De novo Peptide Identification via Tandem Mass Spectrometry Using a Genetic Programming-based Scoring Function for Re-ranking Peptide-Spectrum Matches
In Silico Derivation of HLA-Specific Alloreactivity Potential from Whole Exome Sequencing of Stem Cell Transplant Donors and Recipients: Understanding the Quantitative Immuno-biology of Allogeneic Transplantation
RAId_aPS: MS/MS analysis with multiple scoring functions and spectrum-specific statistics
由于缺乏通用的统计标准，阻碍了对来自各种搜索方法的肽鉴定结果进行统计学上有意义的比较/组合。提供一个E值校准协议，我们之前证明了将任何方法报告的得分或启发式E值转换为教科书定义的E值的可行性，该E值可以作为通用的统计标准。该方案虽然稳健，但可能会丢失光谱特定统计数据，并且在实验设置发生变化时可能需要新的校准。为了缓解这些问题，我们开发了一种新的MS/MS搜索工具RAId_aPS，该工具能够为加性评分函数提供光谱特定的E值。给定从RAId评分、K评分、Hyperscore和XCorr中选择的评分函数，RAId_aPS使用动态编程生成所有可能肽的相应评分直方图。使用这些评分直方图来分配E值，使得无需校准的协议能够为每个评分函数进行准确的显著性分配。RAId_aPS具有四种不同的模式：（i）计算给定分子量范围的可能肽的总数，（ii）生成给定MS/MS谱和评分函数的评分直方图，（iii）重新分配给定MS/MS谱和所选评分函数的候选肽列表的E值，以及（iv）使用所选评分函数执行数据库搜索。在模式（iii）和（iv）中，RAId_aPS还能够使用频谱特定统计来组合来自不同评分函数的结果。网站链接是http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/raid_aps/index.html。Linux、Windows和Mac OS X的相关二进制文件可从同一页面获…
A Weighted U Statistic for Genetic Association Analyses of Sequencing Data
Michigan State University（密歇根州立大学）；University of North Texas Health Science Center（北德克萨斯大学健康科学中心）；University of Arkansas for Medical Sciences（阿肯色大学医学科学大学）；University of Michigan（密歇根大学）；Mayo Clinic（梅奥诊所）
