Yingshu Li,My T Thai,Zhen Liu et al.
Yingshu Li et al.
The interactions between bait proteins and prey proteins are often critical in many biological processes, such as the formation of macromolecular complexes and the transduction of signals in biological pathways. Thus, identifying all protei...
Temporal gene expression classification with regularised neural network [0.03%]
基于正则化神经网络的时序基因表达分类方法
Yulan Liang,Arpad Kelemen
Yulan Liang
This paper proposes regularised neural networks for characterisation of the multiple heterogeneous temporal dynamic patterns of gene expressions. Regularisation is developed to deal with noisy, high dimensional time course data and overfitt...
Biomolecular autonomous solution of the Hamiltonian path problem via hairpin formation [0.03%]
通过发夹形成法解决生物分子自主Hamilton路径问题
Israel M Martinez-Perez,Gong Zhang,Zoya Ignatova et al.
Israel M Martinez-Perez et al.
The Hamiltonian path problem is one of the famous hard combinatorial problems. We provide the first molecular-scale autonomous solution of the decision Hamiltonian path problem. It is based on the formation of secondary structures of DNA mo...
Optimal group testing algorithms with interval queries and their application to splice site detection [0.03%]
带有区间查询的最优组测试算法及其在拼接位点检测中的应用
Ferdinando Cicalese,Peter Damaschke,Ugo Vaccaro
Ferdinando Cicalese
Given an ordered set of n items and an unknown subset P of up to p positive elements, we want to identify P by asking the least number of queries 'does Q intersect P?' where Q must consist of consecutive elements. This Interval Group Testin...
Xiaolin Wu,Sorina Dumitrescu,Pravesh Biyani et al.
Xiaolin Wu et al.
We consider the problem of automated classification of human chromosomes or karyotyping and study discrete optimisation algorithms to solve the problem as one of joint maximum likelihood classification. We demonstrate that the auction algor...
Cellular function prediction and biological pathway discovery in Arabidopsis thaliana using microarray data [0.03%]
基于基因芯片数据的拟南芥细胞功能预测及生物通路发现
Trupti Joshi,Yu Chen,Nickolai N Alexandrov et al.
Trupti Joshi et al.
Determination of protein function and biological pathway is one of the most challenging problems in the post-genomic era. To address this challenge, we have developed a new integrated probabilistic method for cellular function prediction us...
Robert E Langlois,Alice Diec,Ognjen Perisic et al.
Robert E Langlois et al.
Because of the relatively large gap of knowledge between number of protein sequences and protein structures, the ability to construct a computational model predicting structure from sequence information has become an important area of resea...
Corpus based learning of stochastic, context-free grammars combined with Hidden Markov Models for tRNA modelling [0.03%]
基于语料库的随机上下文无关文法的学习与隐马尔可夫模型结合用于tRNA建模
Juan Miguel Garcia-Gomez,Jose Miguel Benedi,Javier Vicente et al.
Juan Miguel Garcia-Gomez et al.
In this paper, a new method for modelling tRNA secondary structures is presented. This method is based on the combination of stochastic context-free grammars (SCFG) and Hidden Markov Models (HMM). HMM are used to capture the local relations...
A bottom-up clustering algorithm to detect ncRNA molecules with a common secondary structure [0.03%]
一种自底向上聚类算法检测具有共同二级结构的ncRNA分子
Yair Horesh,Ron Unger
Yair Horesh
Recently, there has been much interest in exploring the universe of non-protein coding RNA molecules that operate in the cell. We suggested an approach using a simple two-dimensional representation of RNA molecules that can identify common ...
A software system for gene sequence database construction based on fast approximate string matching [0.03%]
一个基于快速串匹配的基因序列数据库生成系统
Zheng Liu,James Borneman,Tao Jiang
Zheng Liu
We propose a web-based software system for sequence acquisition and database construction. An example application of this system is to construct a ribosomal RNA gene (rDNA) sequence database to facilitate the study of microbial communities....