NovelSNPer: A Fast Tool for the Identification and Characterization of Novel SNPs and InDels [0.03%]
新颖的新型 SNP 和 InDels 的识别和表征的快速工具
Jens Aßmus,Armin O Schmitt,Ralf H Bortfeldt et al.
Jens Aßmus et al.
Typically, next-generation resequencing projects produce large lists of variants. NovelSNPer is a software tool that permits fast and efficient processing of such output lists. In a first step, NovelSNPer determines if a variant represents ...
Prediction of enzyme mutant activity using computational mutagenesis and incremental transduction [0.03%]
基于计算诱变和增量传递的酶突变体活性预测模型
Nada Basit,Harry Wechsler
Nada Basit
Wet laboratory mutagenesis to determine enzyme activity changes is expensive and time consuming. This paper expands on standard one-shot learning by proposing an incremental transductive method (T2bRF) for the prediction of enzyme mutant ac...
A growth curve model with fractional polynomials for analysing incomplete time-course data in microarray gene expression studies [0.03%]
基于微阵列基因表达研究中不完整时间过程数据的增长曲线模型及分数多项式分析方法研究
Qihua Tan,Mads Thomassen,Jacob V B Hjelmborg et al.
Qihua Tan et al.
Identifying the various gene expression response patterns is a challenging issue in expression microarray time-course experiments. Due to heterogeneity in the regulatory reaction among thousands of genes tested, it is impossible to manually...
Jonas Winkler,Giuliano Armano,J Nikolaj Dybowski et al.
Jonas Winkler et al.
Computational design of novel proteins with well-defined functions is an ongoing topic in computational biology. In this work, we generated and optimized a new synthetic fusion protein using an evolutionary approach. The optimization was gu...
Nickolaas Maria van Rodijnen,Math Pieters,Sjack Hoop et al.
Nickolaas Maria van Rodijnen et al.
Propidium Iodide is a fluorochrome that is used to measure the DNA content of individual cells, taken from solid tissues, with a flow cytometer. Compensation for spectral cross-over of this fluorochrome still leads to compensation results t...
Genome evolution [0.03%]
基因组进化
Izabela Makałowska,Igor B Rogozin,Wojciech Makałowski
Izabela Makałowska
Rhydon Jackson,Debra Knisley,Cecilia McIntosh et al.
Rhydon Jackson et al.
MACHINE LEARNING WAS APPLIED TO A CHALLENGING AND BIOLOGICALLY SIGNIFICANT PROTEIN CLASSIFICATION PROBLEM: the prediction of avonoid UGT acceptor regioselectivity from primary sequence. Novel indices characterizing graphical models of resid...
Sheenal Srivastava,Yumi Patton,David W Fisher et al.
Sheenal Srivastava et al.
Peptides fold on a time scale that is much smaller than the time required for synthesis, whence all proteins potentially fold cotranslationally to some degree (followed by additional folding events after release from the ribosome). In this ...
ModEnzA: Accurate Identification of Metabolic Enzymes Using Function Specific Profile HMMs with Optimised Discrimination Threshold and Modified Emission Probabilities [0.03%]
基于优化的判别阈值和改进的概率谱式隐马尔可夫模型的代谢酶鉴定方法
Dhwani K Desai,Soumyadeep Nandi,Prashant K Srivastava et al.
Dhwani K Desai et al.
Various enzyme identification protocols involving homology transfer by sequence-sequence or profile-sequence comparisons have been devised which utilise Swiss-Prot sequences associated with EC numbers as the training set. A profile HMM cons...
Vladimir A Likić,Malcolm J McConville,Trevor Lithgow et al.
Vladimir A Likić et al.
Biochemical systems biology augments more traditional disciplines, such as genomics, biochemistry and molecular biology, by championing (i) mathematical and computational modeling; (ii) the application of traditional engineering practices i...