The diversity in the applications of partial least squares: an overview

Advances in technology make it happen to have massive amount of information in the form of multiple variables per object. The use of multivariate approaches for modeling the real‐life phenomena is natural in such situation. There are numerous multivariate approaches in the literature, and its a challenge to stay updated on the possibilities. Partial least squares (PLSs) are one of the many modeling approaches for high‐throughput data, and its use in different fields to address the variety of problems has been increased in recent years. We therefore present an overview of PLS's applications. The objective of this paper is to give a comprehensive overview on the advances in PLS algorithm together with its applications for regression, classification, variable selection, and survival analysis problems covering genomics, chemometrics, neuroinformatics, process control, computer vision, econometric, environmental studies, and so on. We have mainly presented different PLS approaches and their applications, so that the reader can easily get an understanding of possibility to use PLS for their own field. For further reading, literature references together with software availability are provided. Copyright © 2015 John Wiley & Sons, Ltd.     

Virtual Gene Concept and a Corresponding Pragmatic Research Program in Genetical Data Science

Mendel proposed an experimentally verifiable paradigm of particle-based heredity that has been influential for over 150 years. The historical arguments have been reflected in the near past as Mendel’s concept has been diversified by new types of omics data. As an effect of the accumulation of omics data, a virtual gene concept forms, giving rise to genetical data science. The concept integrates genetical, functional, and molecular features of the Mendelian paradigm. I argue that the virtual gene concept should be deployed pragmatically. Indeed, the concept has already inspired a practical research program related to systems genetics. The program includes questions about functionality of structural and categorical gene variants, about regulation of gene expression, and about roles of epigenetic modifications. The methodology of the program includes bioinformatics, machine learning, and deep learning. Education, funding, careers, standards, benchmarks, and tools to monitor research progress should be provided to support the research program.     

材料的高通量制备与表征技术

 经过40 年的发展,材料高通量制备与表征技术已取得了较大的进展,并被证明可有效地加速材料研发-应用进程,因此被列为材料基因组计划的三大技术要素之一。本文简要回顾材料高通量实验技术的发展历程,阐述高通量实验在材料基因组技术中的地位与作用,系统介绍一系列有代表性的高通量制备与表征技术,并指出一些高通量实验方法的应用局限。对未来面临的挑战与发展趋势进行了分析展望,重点介绍基于同步辐射、散裂中子源等大科学装置以及基于材料非均匀性本质的原位统计映射表征解析等发展新一代材料原位实时高通量制备、表征与分析技术的新思路,以期为中国材料基因组技术的跨越式发展提供参考。     

全长cDNA文库构建方法及应用研究

构建全长cDNA文库是获得大量基因全序列信息的有效途径,也是进行功能基因组研究的一条经济、快速的途径,它克服了常规cDNA文库的缺点,极大地推进了功能基因组的研究,尤其是对于那些因基因组庞大而未能进行全基因组序列测定的生物来说更为重要．全长cDNA文库的研究在不断发展,几种文库构建方法已经建立,并得到了较为广泛的应用．本文重点阐述了全长cDNA文库的构建方法,对各种方法进行了分析和比较;同时对全长cDNA文库的应用也作了介绍．     

Chaining algorithms for multiple genome comparison

Given n fragments from k>2 genomes, Myers and Miller showed how to find an optimal global chain of colinear non-overlapping fragments in O(nlog^kn) time and O(nlog^k−1n) space. For gap costs in the L₁-metric, we reduce the time complexity of their algorithm by a factor and the space complexity by a factor logn. For the sum-of-pairs gap cost, our algorithm improves the time complexity of their algorithm by a factor . A variant of our algorithm finds all significant local chains of colinear non-overlapping fragments. These chaining algorithms can be used in a variety of problems in comparative genomics: the computation of global alignments of complete genomes, the identification of regions of similarity (candidate regions of conserved synteny), the detection of genome rearrangements, and exon prediction.     

Mumford dendrograms and discrete p-adic symmetries

In this article, we present an effective encoding of dendrograms by embedding them into the Bruhat-Tits trees associated to p-adic number fields. As an application, we show how strings over a finite alphabet can be encoded in cyclotomic extensions of ℚ _p and discuss p-adic DNA encoding. The application leads to fast p-adic agglomerative hierarchic algorithms similar to the ones recently used e.g. by A. Khrennikov and others. From the viewpoint of p-adic geometry, to encode a dendrogram X in a p-adic field K means to fix a set S of K-rational punctures on the p-adic projective line ℙ₁. To ℙ₁ \ S is associated in a natural way a subtree inside the Bruhat-Tits tree which recovers X, a method first used by F. Kato in 1999 in the classification of discrete subgroups of PGL₂(K). Next, we show how the p-adic moduli space of ℙ¹ with n punctures can be applied to the study of time series of dendrograms and those symmetries arising from hyperbolic actions on ℙ¹. In this way, we can associate to certain classes of dynamical systems a Mumford curve, i.e. a p-adic algebraic curve with totally degenerate reduction modulo p. Finally, we indicate some of our results in the study of general discrete actions on ℙ¹, and their relation to p-adic Hurwitz spaces. The text was submitted by the author in English.     

A reagent-based strategy for the design of large combinatorial libraries: A preliminary experimental validation

Combinatorial library design can be carried out at either the reagent or the product level. Various reports in the literature have come to conflicting conclusions in favor of one over the other. In this paper a reagent-based screening library design strategy is presented. The method relies on analysis of scaffolds and building blocks separately to define the overall diversity in a compound file. The primary diversity selection by properties relevant for molecular recognition and by redundancy is followed by the application of filters for molecular properties known to be relevant for drug-likeness. Filter properties are rapidly estimated at the product level using a fragmental estimation approach. Initial experimental data suggest that high diversity in vast screening libraries can be achieved by carefully applied reagent level analysis. A potential role of diverse screening libraries in chemical genomics (pharmacological knockouts) is also discussed.     

蜡状芽孢杆菌ATCC 10987基因组蛋白质编码基因的重新注释与分析

蜡状芽胞杆菌ATCC 10987对于细菌比较基因组学的研究有重要意义.但其染色体中基因的数目被RefSeq注释为5 603个,这个注释是有疑问的.本文采用Zcurve和Glimmer程序联合打分的方法来识别其蛋白质编码基因.为保证预测结果的可靠性,对联合判别附加预测的基因使用了BLAST方法进行数据库同源性搜索.结果,蜡状芽胞杆菌ATCC 10987基因组中的蛋白质编码基因的数目被重新确定为5 180个.这个数目明显低于原始注释的数目,并且一些指标表明新的注释更为可信.这些相对正确的基因集合为该细菌亲缘物种的深入研究提供了基础.     

Genotyping--from genomic DNA to genotype in a single tube

Nucleotide variations in the human genome, such as single-nucleotide polymorphisms, have been researched more intensively since it became apparent that these deviations are linked to various diseases and also several side effects of drugs. The investigation of genomic DNA in the laboratory requires routine methods that are time-, labour-, and cost-effective. These criteria are fulfilled by so-called closed-tube methods, which are applied directly to isolated genomic DNA without any preamplification.