Bioinformatics advances最新文献

{"title":"VCAb: a web-tool for structure-guided exploration of antibodies.","authors":"Dongjun Guo, Joseph Chi-Fung Ng, Deborah K Dunn-Walters, Franca Fraternali","doi":"10.1093/bioadv/vbae137","DOIUrl":"https://doi.org/10.1093/bioadv/vbae137","url":null,"abstract":"<p><strong>Motivation: </strong>Effective responses against immune challenges require antibodies of different isotypes performing specific effector functions. Structural information on these isotypes is essential to engineer antibodies with desired physico-chemical features of their antigen-binding properties, and optimal developability as potential therapeutics. <i>In silico</i> mutational scanning profiles on antibody structures would further pinpoint candidate mutations for enhancing antibody stability and function. Current antibody structure databases lack consistent annotations of isotypes and structural coverage of 3D antibody structures, as well as computed deep mutation profiles.</p><p><strong>Results: </strong>The <i>V</i> and <i>C</i> region bearing <i>a</i>nti<i>b</i>ody (VCAb) web-tool is established to clarify these annotations and provides an accessible resource to facilitate antibody engineering and design. VCAb currently provides data on 7,166 experimentally determined antibody structures including both V and C regions from different species. Additionally, VCAb provides annotations of species and isotypes with numbering schemes applied. These information can be interactively queried or downloaded in batch.</p><p><strong>Availability and implementation: </strong>VCAb is implemented as a R shiny application to enable interactive data interrogation. The online application is freely accessible https://fraternalilab.cs.ucl.ac.uk/VCAb/. The source code to generate the database and the online application is available open-source at https://github.com/Fraternalilab/VCAb.</p>","PeriodicalId":72368,"journal":{"name":"Bioinformatics advances","volume":"4 1","pages":"vbae137"},"PeriodicalIF":2.4,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11471263/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142482214","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}

{"title":"DECOMICS, a shiny application for unsupervised cell type deconvolution and biological interpretation of bulk omic data.","authors":"Slim Karkar, Ashwini Sharma, Carl Herrmann, Yuna Blum, Magali Richard","doi":"10.1093/bioadv/vbae136","DOIUrl":"https://doi.org/10.1093/bioadv/vbae136","url":null,"abstract":"<p><strong>Summary: </strong>Unsupervised deconvolution algorithms are often used to estimate cell composition from bulk tissue samples. However, applying cell-type deconvolution and interpreting the results remain a challenge, even more without prior training in bioinformatics. Here, we propose a tool for estimating and identifying cell type composition from bulk transcriptomes or methylomes. DECOMICS is a shiny-web application dedicated to unsupervised deconvolution approaches of bulk omic data. It provides (i) a variety of existing algorithms to perform deconvolution on the gene expression or methylation-level matrix, (ii) an enrichment analysis module to aid biological interpretation of the deconvolved components, based on enrichment analysis, and (iii) some visualization tools. Input data can be downloaded in csv format and preprocessed in the web application (normalization, transformation, and feature selection). The results of the deconvolution, enrichment, and visualization processes can be downloaded.</p><p><strong>Availability and implementation: </strong>DECOMICS is an R-shiny web application that can be launched (i) directly from a local R session using the R package available here: https://gitlab.in2p3.fr/Magali.Richard/decomics (either by installing it locally or via a virtual machine and a Docker image that we provide); or (ii) in the Biosphere-IFB Clouds Federation for Life Science, a multi-cloud environment scalable for high-performance computing: https://biosphere.france-bioinformatique.fr/catalogue/appliance/193/.</p>","PeriodicalId":72368,"journal":{"name":"Bioinformatics advances","volume":"4 1","pages":"vbae136"},"PeriodicalIF":2.4,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11479579/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142482210","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}

{"title":"Investigation of protein family relationships with deep learning.","authors":"Irina Ponamareva, Antonina Andreeva, Maxwell L Bileschi, Lucy Colwell, Alex Bateman","doi":"10.1093/bioadv/vbae132","DOIUrl":"https://doi.org/10.1093/bioadv/vbae132","url":null,"abstract":"<p><strong>Motivation: </strong>In this article, we propose a method for finding similarities between Pfam families based on the pre-trained neural network ProtENN2. We use the model ProtENN2 per-residue embeddings to produce new high-dimensional per-family embeddings and develop an approach for calculating inter-family similarity scores based on these embeddings, and evaluate its predictions using structure comparison.</p><p><strong>Results: </strong>We apply our method to Pfam annotation by refining clan membership for Pfam families, suggesting both new members of existing clans and potential new clans for future Pfam releases. We investigate some of the failure modes of our approach, which suggests directions for future improvements. Our method is relatively simple with few parameters and could be applied to other protein family classification models. Overall, our work suggests potential benefits of employing deep learning for improving our understanding of protein family relationships and functions of previously uncharacterized families.</p><p><strong>Availability and implementation: </strong>github.com/iponamareva/ProtCNNSim, 10.5281/zenodo.10091909.</p>","PeriodicalId":72368,"journal":{"name":"Bioinformatics advances","volume":"4 1","pages":"vbae132"},"PeriodicalIF":2.4,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11467057/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142482211","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}

{"title":"EmbedGEM: a framework to evaluate the utility of embeddings for genetic discovery.","authors":"Sumit Mukherjee, Zachary R McCaw, Jingwen Pei, Anna Merkoulovitch, Tom Soare, Raghav Tandon, David Amar, Hari Somineni, Christoph Klein, Santhosh Satapati, David Lloyd, Christopher Probert, Daphne Koller, Colm O'Dushlaine, Theofanis Karaletsos","doi":"10.1093/bioadv/vbae135","DOIUrl":"10.1093/bioadv/vbae135","url":null,"abstract":"<p><strong>Summary: </strong>Machine learning-derived embeddings are a compressed representation of high content data modalities. Embeddings can capture detailed information about disease states and have been qualitatively shown to be useful in genetic discovery. Despite their promise, embeddings have a major limitation: it is unclear if genetic variants associated with embeddings are relevant to the disease or trait of interest. In this work, we describe EmbedGEM (<b>Embed</b>ding <b>G</b>enetic <b>E</b>valuation <b>M</b>ethods), a framework to systematically evaluate the utility of embeddings in genetic discovery. EmbedGEM focuses on comparing embeddings along two axes: heritability and disease relevance. As measures of heritability, we consider the number of genome-wide significant associations and the mean <math> <mrow> <mrow> <msup><mrow><mo>χ</mo></mrow> <mn>2</mn></msup> </mrow> </mrow> </math> statistic at significant loci. For disease relevance, we compute polygenic risk scores for each embedding principal component, then evaluate their association with high-confidence disease or trait labels in a held-out evaluation patient set. While our development of EmbedGEM is motivated by embeddings, the approach is generally applicable to multivariate traits and can readily be extended to accommodate additional metrics along the evaluation axes. We demonstrate EmbedGEM's utility by evaluating embeddings and multivariate traits in two separate datasets: (i) a synthetic dataset simulated to demonstrate the ability of the framework to correctly rank traits based on their heritability and disease relevance and (ii) a real data from the UK Biobank, including metabolic and liver-related traits. Importantly, we show that greater disease relevance does not automatically follow from greater heritability.</p><p><strong>Availability and implementation: </strong>https://github.com/insitro/EmbedGEM.</p>","PeriodicalId":72368,"journal":{"name":"Bioinformatics advances","volume":"4 1","pages":"vbae135"},"PeriodicalIF":2.4,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11632179/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142815225","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}

{"title":"Batch-effect correction in single-cell RNA sequencing data using JIVE.","authors":"Joseph Hastings, Donghyung Lee, Michael J O'Connell","doi":"10.1093/bioadv/vbae134","DOIUrl":"10.1093/bioadv/vbae134","url":null,"abstract":"<p><strong>Motivation: </strong>In single-cell RNA sequencing analysis, addressing batch effects-technical artifacts stemming from factors such as varying sequencing technologies, equipment, and capture times-is crucial. These factors can cause unwanted variation and obfuscate the underlying biological signal of interest. The joint and individual variation explained (JIVE) method can be used to extract shared biological patterns from multi-source sequencing data while adjusting for individual non-biological variations (i.e. batch effect). However, its current implementation is originally designed for bulk sequencing data, making it computationally infeasible for large-scale single-cell sequencing datasets.</p><p><strong>Results: </strong>In this study, we enhance JIVE for large-scale single-cell data by boosting its computational efficiency. Additionally, we introduce a novel application of JIVE for batch-effect correction on multiple single-cell sequencing datasets. Our enhanced method aims to decompose single-cell sequencing datasets into a joint structure capturing the true biological variability and individual structures, which capture technical variability within each batch. This joint structure is then suitable for use in downstream analyses. We benchmarked the results against four popular tools, Seurat v5, Harmony, LIGER, and Combat-seq, which were developed for this purpose. JIVE performed best in terms of preserving cell-type effects and in scenarios in which the batch sizes are balanced.</p><p><strong>Availability and implementation: </strong>The JIVE implementation used for this analysis can be found at https://github.com/oconnell-statistics-lab/scJIVE.</p>","PeriodicalId":72368,"journal":{"name":"Bioinformatics advances","volume":"4 1","pages":"vbae134"},"PeriodicalIF":2.4,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11461915/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142395682","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}

{"title":"Evaluating GPT and BERT models for protein-protein interaction identification in biomedical text.","authors":"Hasin Rehana, Nur Bengisu Çam, Mert Basmaci, Jie Zheng, Christianah Jemiyo, Yongqun He, Arzucan Özgür, Junguk Hur","doi":"10.1093/bioadv/vbae133","DOIUrl":"https://doi.org/10.1093/bioadv/vbae133","url":null,"abstract":"<p><strong>Motivation: </strong>Detecting protein-protein interactions (PPIs) is crucial for understanding genetic mechanisms, disease pathogenesis, and drug design. As biomedical literature continues to grow rapidly, there is an increasing need for automated and accurate extraction of these interactions to facilitate scientific discovery. Pretrained language models, such as generative pretrained transformers and bidirectional encoder representations from transformers, have shown promising results in natural language processing tasks.</p><p><strong>Results: </strong>We evaluated the performance of PPI identification using multiple transformer-based models across three manually curated gold-standard corpora: Learning Language in Logic with 164 interactions in 77 sentences, Human Protein Reference Database with 163 interactions in 145 sentences, and Interaction Extraction Performance Assessment with 335 interactions in 486 sentences. Models based on bidirectional encoder representations achieved the best overall performance, with BioBERT achieving the highest recall of 91.95% and F1 score of 86.84% on the Learning Language in Logic dataset. Despite not being explicitly trained for biomedical texts, GPT-4 showed commendable performance, comparable to the bidirectional encoder models. Specifically, GPT-4 achieved the highest precision of 88.37%, a recall of 85.14%, and an F1 score of 86.49% on the same dataset. These results suggest that GPT-4 can effectively detect protein interactions from text, offering valuable applications in mining biomedical literature.</p><p><strong>Availability and implementation: </strong>The source code and datasets used in this study are available at https://github.com/hurlab/PPI-GPT-BERT.</p>","PeriodicalId":72368,"journal":{"name":"Bioinformatics advances","volume":"4 1","pages":"vbae133"},"PeriodicalIF":2.4,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11419952/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142333636","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}

{"title":"AlphaCRV: a pipeline for identifying accurate binder topologies in mass-modeling with AlphaFold.","authors":"Francisco J Guzmán-Vega, Stefan T Arold","doi":"10.1093/bioadv/vbae131","DOIUrl":"https://doi.org/10.1093/bioadv/vbae131","url":null,"abstract":"<p><strong>Motivation: </strong>The speed and accuracy of deep learning-based structure prediction algorithms make it now possible to perform in silico \"pull-downs\" to identify protein-protein interactions on a proteome-wide scale. However, on such a large scale, existing scoring algorithms are often insufficient to discriminate biologically relevant interactions from false positives.</p><p><strong>Results: </strong>Here, we introduce AlphaCRV, a Python package that helps identify correct interactors in a one-against-many AlphaFold screen by clustering, ranking, and visualizing conserved binding topologies, based on protein sequence and fold.</p><p><strong>Availability and implementation: </strong>AlphaCRV is a Python package for Linux, freely available at https://github.com/strubelab/AlphaCRV.</p>","PeriodicalId":72368,"journal":{"name":"Bioinformatics advances","volume":"4 1","pages":"vbae131"},"PeriodicalIF":2.4,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11405088/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142302315","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}

{"title":"SPIDER: constructing cell-type-specific protein-protein interaction networks.","authors":"Yael Kupershmidt, Simon Kasif, Roded Sharan","doi":"10.1093/bioadv/vbae130","DOIUrl":"https://doi.org/10.1093/bioadv/vbae130","url":null,"abstract":"<p><strong>Motivation: </strong>Protein-protein interactions (PPIs) play essential roles in the buildup of cellular machinery and provide the skeleton for cellular signaling. However, these biochemical roles are context dependent and interactions may change across cell type, time, and space. In contrast, PPI detection assays are run in a single condition that may not even be an endogenous condition of the organism, resulting in static networks that do not reflect full cellular complexity. Thus, there is a need for computational methods to predict cell-type-specific interactions.</p><p><strong>Results: </strong>Here we present SPIDER (Supervised Protein Interaction DEtectoR), a graph attention-based model for predicting cell-type-specific PPI networks. In contrast to previous attempts at this problem, which were unsupervised in nature, our model's training is guided by experimentally measured cell-type-specific networks, enhancing its performance. We evaluate our method using experimental data of cell-type-specific networks from both humans and mice, and show that it outperforms current approaches by a large margin. We further demonstrate the ability of our method to generalize the predictions to datasets of tissues lacking prior PPI experimental data. We leverage the networks predicted by the model to facilitate the identification of tissue-specific disease genes.</p><p><strong>Availability and implementation: </strong>Our code and data are available at https://github.com/Kuper994/SPIDER.</p>","PeriodicalId":72368,"journal":{"name":"Bioinformatics advances","volume":"4 1","pages":"vbae130"},"PeriodicalIF":2.4,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11438548/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142333637","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}

{"title":"synphage: a pipeline for phage genome synteny graphics focused on gene conservation.","authors":"Virginie Grosboillot, Anna Dragoš","doi":"10.1093/bioadv/vbae126","DOIUrl":"10.1093/bioadv/vbae126","url":null,"abstract":"<p><strong>Motivation: </strong>Visualization and comparison of genome maps of bacteriophages can be very effective, but none of the tools available on the market allow visualization of gene conservation between multiple sequences at a glance. In addition, most bioinformatic tools running locally are command line only, making them hard to setup, debug, and monitor.</p><p><strong>Results: </strong>To address these motivations, we developed synphage, an easy-to-use and intuitive tool to generate synteny diagrams from GenBank files. This software has a user-friendly interface and uses metadata to monitor the progress and success of the data transformation process. The output plot features colour-coded genes according to their degree of conservation among the group of displayed sequences. The strength of synphage lies also in its modularity and the ability to generate multiple plots with different configurations without having to re-process all the data. In conclusion, synphage reduces the bioinformatic workload of users and allows them to focus on analysis, the most impactful area of their work.</p><p><strong>Availability and implementation: </strong>The synphage tool is implemented in the Python language and is available from the GitHub repository at https://github.com/vestalisvirginis/synphage. This software is released under an Apache-2.0 licence. A PyPI synphage package is available at https://pypi.org/project/synphage/ and a containerized version is available at https://hub.docker.com/r/vestalisvirginis/synphage. Contributions to the software are welcome whether it is reporting a bug or proposing new features and the contribution guidelines are available at https://github.com/vestalisvirginis/synphage/blob/main/CONTRIBUTING.md.</p>","PeriodicalId":72368,"journal":{"name":"Bioinformatics advances","volume":"4 1","pages":"vbae126"},"PeriodicalIF":2.4,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11368388/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142121160","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}

{"title":"ginmappeR: an unified approach for integrating gene and protein identifiers across biological sequence databases.","authors":"Fernando Sola, Daniel Ayala, Marina Pulido, Rafael Ayala, Lorena López-Cerero, Inma Hernández, David Ruiz","doi":"10.1093/bioadv/vbae129","DOIUrl":"https://doi.org/10.1093/bioadv/vbae129","url":null,"abstract":"<p><strong>Summary: </strong>The proliferation of biological sequence data, due to developments in molecular biology techniques, has led to the creation of numerous open access databases on gene and protein sequencing. However, the lack of direct equivalence between identifiers across these databases difficults data integration. To address this challenge, we introduce <i>ginmappeR</i>, an integrated R package facilitating the translation of gene and protein identifiers between databases. By providing a unified interface, <i>ginmappeR</i> streamlines the integration of diverse data sources into biological workflows, so it enhances efficiency and user experience.</p><p><strong>Availability and implementation: </strong>from Bioconductor: https://bioconductor.org/packages/ginmappeR.</p>","PeriodicalId":72368,"journal":{"name":"Bioinformatics advances","volume":"4 1","pages":"vbae129"},"PeriodicalIF":2.4,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11387618/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142302316","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}