Frontiers in bioinformatics最新文献_第8页

New alignment method for remote protein sequences by the direct use of pairwise sequence correlations and substitutions. 通过直接使用成对序列相关性和取代的远程蛋白质序列的新比对方法。

Frontiers in bioinformatics Pub Date : 2023-10-12 eCollection Date: 2023-01-01 DOI: 10.3389/fbinf.2023.1227193

Kejue Jia, Mesih Kilinc, Robert L Jernigan

{"title":"New alignment method for remote protein sequences by the direct use of pairwise sequence correlations and substitutions.","authors":"Kejue Jia, Mesih Kilinc, Robert L Jernigan","doi":"10.3389/fbinf.2023.1227193","DOIUrl":"10.3389/fbinf.2023.1227193","url":null,"abstract":"Understanding protein sequences and how they relate to the functions of proteins is extremely important. One of the most basic operations in bioinformatics is sequence alignment and usually the first things learned from these are which positions are the most conserved and often these are critical parts of the structure, such as enzyme active site residues. In addition, the contact pairs in a protein usually correspond closely to the correlations between residue positions in the multiple sequence alignment, and these usually change in a systematic and coordinated way, if one position changes then the other member of the pair also changes to compensate. In the present work, these correlated pairs are taken as anchor points for a new type of sequence alignment. The main advantage of the method here is its combining the remote homolog detection from our method PROST with pairwise sequence substitutions in the rigorous method from Kleinjung et al. We show a few examples of some resulting sequence alignments, and how they can lead to improvements in alignments for function, even for a disordered protein.","PeriodicalId":73066,"journal":{"name":"Frontiers in bioinformatics","volume":"3 ","pages":"1227193"},"PeriodicalIF":0.0,"publicationDate":"2023-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10602800/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71415730","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

VariantSurvival: a tool to identify genotype-treatment response. VariantSurvival：一种识别基因型治疗反应的工具。

Frontiers in bioinformatics Pub Date : 2023-10-11 eCollection Date: 2023-01-01 DOI: 10.3389/fbinf.2023.1277923

Thomas Krannich, Marina Herrera Sarrias, Hiba Ben Aribi, Moustafa Shokrof, Alfredo Iacoangeli, Ammar Al-Chalabi, Fritz J Sedlazeck, Ben Busby, Ahmad Al Khleifat

{"title":"VariantSurvival: a tool to identify genotype-treatment response.","authors":"Thomas Krannich, Marina Herrera Sarrias, Hiba Ben Aribi, Moustafa Shokrof, Alfredo Iacoangeli, Ammar Al-Chalabi, Fritz J Sedlazeck, Ben Busby, Ahmad Al Khleifat","doi":"10.3389/fbinf.2023.1277923","DOIUrl":"10.3389/fbinf.2023.1277923","url":null,"abstract":"Motivation: For a number of neurological diseases, such as Alzheimer's disease, amyotrophic lateral sclerosis, and many others, certain genes are known to be involved in the disease mechanism. A common question is whether a structural variant in any such gene may be related to drug response in clinical trials and how this relationship can contribute to the lifecycle of drug development. Results: To this end, we introduce VariantSurvival, a tool that identifies changes in survival relative to structural variants within target genes. VariantSurvival matches annotated structural variants with genes that are clinically relevant to neurological diseases. A Cox regression model determines the change in survival between the placebo and clinical trial groups with respect to the number of structural variants in the drug target genes. We demonstrate the functionality of our approach with the exemplary case of the SETX gene. VariantSurvival has a user-friendly and lightweight graphical user interface built on the shiny web application package.","PeriodicalId":73066,"journal":{"name":"Frontiers in bioinformatics","volume":"3 ","pages":"1277923"},"PeriodicalIF":0.0,"publicationDate":"2023-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10598652/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54232718","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

DeepRaccess: high-speed RNA accessibility prediction using deep learning. DeepRaccess：使用深度学习进行高速RNA可及性预测。

Frontiers in bioinformatics Pub Date : 2023-10-10 eCollection Date: 2023-01-01 DOI: 10.3389/fbinf.2023.1275787

Kaisei Hara, Natsuki Iwano, Tsukasa Fukunaga, Michiaki Hamada

{"title":"DeepRaccess: high-speed RNA accessibility prediction using deep learning.","authors":"Kaisei Hara, Natsuki Iwano, Tsukasa Fukunaga, Michiaki Hamada","doi":"10.3389/fbinf.2023.1275787","DOIUrl":"10.3389/fbinf.2023.1275787","url":null,"abstract":"RNA accessibility is a useful RNA secondary structural feature for predicting RNA-RNA interactions and translation efficiency in prokaryotes. However, conventional accessibility calculation tools, such as Raccess, are computationally expensive and require considerable computational time to perform transcriptome-scale analysis. In this study, we developed DeepRaccess, which predicts RNA accessibility based on deep learning methods. DeepRaccess was trained to take artificial RNA sequences as input and to predict the accessibility of these sequences as calculated by Raccess. Simulation and empirical dataset analyses showed that the accessibility predicted by DeepRaccess was highly correlated with the accessibility calculated by Raccess. In addition, we confirmed that DeepRaccess could predict protein abundance in E.coli with moderate accuracy from the sequences around the start codon. We also demonstrated that DeepRaccess achieved tens to hundreds of times software speed-up in a GPU environment. The source codes and the trained models of DeepRaccess are freely available at https://github.com/hmdlab/DeepRaccess.","PeriodicalId":73066,"journal":{"name":"Frontiers in bioinformatics","volume":"3 ","pages":"1275787"},"PeriodicalIF":0.0,"publicationDate":"2023-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10597636/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"50163995","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Artificial intelligence in imaging flow cytometry. 成像流式细胞术中的人工智能。

Frontiers in bioinformatics Pub Date : 2023-10-09 eCollection Date: 2023-01-01 DOI: 10.3389/fbinf.2023.1229052

Paolo Pozzi, Alessia Candeo, Petra Paiè, Francesca Bragheri, Andrea Bassi

引用次数: 0

NeighborNet: improved algorithms and implementation. NeighborNet：改进的算法和实现。

Frontiers in bioinformatics Pub Date : 2023-09-20 eCollection Date: 2023-01-01 DOI: 10.3389/fbinf.2023.1178600

David Bryant, Daniel H Huson

引用次数: 0

VariBench, new variation benchmark categories and data sets. VariBeach，新的变体基准类别和数据集。

IF 2.8

Frontiers in bioinformatics Pub Date : 2023-09-19 eCollection Date: 2023-01-01 DOI: 10.3389/fbinf.2023.1248732

Niloofar Shirvanizadeh, Mauno Vihinen

引用次数: 0

Corrigendum: A review on deep learning applications in highly multiplexed tissue imaging data analysis. 更正：深度学习在高度复用组织成像数据分析中的应用综述。

Frontiers in bioinformatics Pub Date : 2023-09-13 eCollection Date: 2023-01-01 DOI: 10.3389/fbinf.2023.1287407

Mohammed Zidane, Ahmad Makky, Matthias Bruhns, Alexander Rochwarger, Sepideh Babaei, Manfred Claassen, Christian M Schürch

引用次数: 0

Editorial: Recent advances in peptide informatics: challenges and opportunities. 社论：肽信息学的最新进展：挑战与机遇。

Frontiers in bioinformatics Pub Date : 2023-09-12 eCollection Date: 2023-01-01 DOI: 10.3389/fbinf.2023.1271932

Rahul Kumar, Kumardeep Chaudhary, Sandeep Kumar Dhanda

引用次数: 0

The origin of eukaryotes and rise in complexity were synchronous with the rise in oxygen. 真核生物的起源和复杂性的增加与氧气的增加是同步的。

IF 2.8

Frontiers in bioinformatics Pub Date : 2023-09-01 eCollection Date: 2023-01-01 DOI: 10.3389/fbinf.2023.1233281

Jack M Craig, Sudhir Kumar, S Blair Hedges

{"title":"The origin of eukaryotes and rise in complexity were synchronous with the rise in oxygen.","authors":"Jack M Craig, Sudhir Kumar, S Blair Hedges","doi":"10.3389/fbinf.2023.1233281","DOIUrl":"10.3389/fbinf.2023.1233281","url":null,"abstract":"The origin of eukaryotes was among the most important events in the history of life, spawning a new evolutionary lineage that led to all complex multicellular organisms. However, the timing of this event, crucial for understanding its environmental context, has been difficult to establish. The fossil and biomarker records are sparse and molecular clocks have thus far not reached a consensus, with dates spanning 2.1-0.91 billion years ago (Ga) for critical nodes. Notably, molecular time estimates for the last common ancestor of eukaryotes are typically hundreds of millions of years younger than the Great Oxidation Event (GOE, 2.43-2.22 Ga), leading researchers to question the presumptive link between eukaryotes and oxygen. We obtained a new time estimate for the origin of eukaryotes using genetic data of both archaeal and bacterial origin, the latter rarely used in past studies. We also avoided potential calibration biases that may have affected earlier studies. We obtained a conservative interval of 2.2-1.5 Ga, with an even narrower core interval of 2.0-1.8 Ga, for the origin of eukaryotes, a period closely aligned with the rise in oxygen. We further reconstructed the history of biological complexity across the tree of life using three universal measures: cell types, genes, and genome size. We found that the rise in complexity was temporally consistent with and followed a pattern similar to the rise in oxygen. This suggests a causal relationship stemming from the increased energy needs of complex life fulfilled by oxygen.","PeriodicalId":73066,"journal":{"name":"Frontiers in bioinformatics","volume":"3 ","pages":"1233281"},"PeriodicalIF":2.8,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10505794/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41142624","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Orthogonal outlier detection and dimension estimation for improved MDS embedding of biological datasets. 用于改进生物数据集 MDS 嵌入的正交离群点检测和维度估计。

IF 2.8

Frontiers in bioinformatics Pub Date : 2023-08-10 eCollection Date: 2023-01-01 DOI: 10.3389/fbinf.2023.1211819

Wanxin Li, Jules Mirone, Ashok Prasad, Nina Miolane, Carine Legrand, Khanh Dao Duc

引用次数: 0