journal
https://read.qxmd.com/read/38490256/admix-kit-an-integrated-toolkit-and-pipeline-for-genetic-analyses-of-admixed-populations
#21
JOURNAL ARTICLE
Kangcheng Hou, Stephanie Gogarten, Joohyun Kim, Xing Hua, Julie-Alexia Dias, Quan Sun, Ying Wang, Taotao Tan, Elizabeth G Atkinson, Alicia Martin, Jonathan Shortt, Jibril Hirbo, Yun Li, Bogdan Pasaniuc, Haoyu Zhang
SUMMARY: Admixed populations, with their unique and diverse genetic backgrounds, are often underrepresented in genetic studies. This oversight not only limits our understanding but also exacerbates existing health disparities. One major barrier has been the lack of efficient tools tailored for the special challenges of genetic study of admixed populations. Here, we present admix-kit, an integrated toolkit and pipeline for genetic analyses of admixed populations. Admix-kit implements a suite of methods to facilitate genotype and phenotype simulation, association testing, genetic architecture inference, and polygenic scoring in admixed populations...
March 15, 2024: Bioinformatics
https://read.qxmd.com/read/38490248/icellnet-v2-a-versatile-method-for-cell-cell-communication-analysis-from-human-transcriptomic-data
#22
JOURNAL ARTICLE
Lucile Massenet-Regad, Vassili Soumelis
SUMMARY: Several methods have been developed in the past years to infer cell-cell communication networks from transcriptomic data based on ligand and receptor expression. Among them, ICELLNET is one of the few approaches to consider the multiple subunits of ligands and receptors complexes to infer and quantify cell communication. In here, we present a major update of ICELLNET. As compared to its original implementation, we 1) drastically expanded the ICELLNET ligand-receptor database from 380 to 1669 biologically curated interactions, 2) integrated important families of communication molecules involved in immune crosstalk, cell adhesion, and Wnt pathway, 3) optimized ICELLNET framework for single-cell RNA sequencing data analyses, 4) provided new visualizations of cell-cell communication results to facilitate prioritization and biological interpretation...
March 15, 2024: Bioinformatics
https://read.qxmd.com/read/38485700/vizapa-visualizing-dynamics-of-alternative-polyadenylation-from-bulk-and-single-cell-data
#23
JOURNAL ARTICLE
Xingyu Bi, Wenbin Ye, Xin Cheng, Ning Yang, Xiaohui Wu
MOTIVATION: Alternative polyadenylation (APA) is a widespread post-transcriptional regulatory mechanism across all eukaryotes. With the accumulation of genome-wide APA sites, especially those with single-cell resolution, it is imperative to develop easy-to-use visualization tools to guide APA analysis. RESULTS: We developed an R package called vizAPA for visualizing APA dynamics from bulk and single-cell data. vizAPA implements unified data structures for APA data and genome annotations...
March 14, 2024: Bioinformatics
https://read.qxmd.com/read/38485699/lambda3-homology-search-for-protein-nucleotide-and-bisulfite-converted-sequences
#24
JOURNAL ARTICLE
Hannes Hauswedell, Sara Hetzel, Simon G Gottlieb, Helene Kretzmer, Alexander Meissner, Knut Reinert
MOTIVATION: Local alignments of query sequences in large databases represent a core part of metagenomic studies and facilitate homology search. Following the development of NCBI Blast, many applications aimed to provide faster and equally sensitive local alignment frameworks. Most applications focus on protein alignments, while only few also facilitate DNA-based searches. None of the established programs allow searching DNA sequences from bisulfite sequencing experiments commonly used for DNA methylation profiling, for which specific alignment strategies need to be implemented...
March 14, 2024: Bioinformatics
https://read.qxmd.com/read/38485697/longmixr-a-tool-for-robust-clustering-of-high-dimensional-cross-sectional-and-longitudinal-variables-of-mixed-data-types
#25
JOURNAL ARTICLE
Jonas Hagenberg, Monika Budde, Teodora Pandeva, Ivan Kondofersky, Sabrina K Schaupp, Fabian J Theis, Thomas G Schulze, Nikola S Müller, Urs Heilbronner, Richa Batra, Janine Knauer-Arloth
SUMMARY: Accurate clustering of mixed data, encompassing binary, categorical, and continuous variables, is vital for effective patient stratification in clinical questionnaire analysis. To address this need, we present longmixr, a comprehensive R package providing a robust framework for clustering mixed longitudinal data using finite mixture modeling techniques. By incorporating consensus clustering, longmixr ensures reliable and stable clustering results. Moreover, the package includes a detailed vignette that facilitates cluster exploration and visualization...
March 14, 2024: Bioinformatics
https://read.qxmd.com/read/38485690/arch-improving-the-performance-of-clonal-hematopoiesis-variant-calling-and-interpretation
#26
JOURNAL ARTICLE
Irenaeus C C Chan, Alex Panchot, Evelyn Schmidt, Samantha McNulty, Brian J Wiley, Jie Liu, Kimberly Turner, Lea Moukarzel, Wendy S W Wong, Duc Tran, J Scott Beeler, Armel Landry Batchi-Bouyou, Mitchell J Machiela, Danielle M Karyadi, Benjamin J Krajacich, Junhua Zhao, Semyon Kruglyak, Bryan Lajoie, Shawn Levy, Minal Patel, Philip W Kantoff, Christopher E Mason, Daniel C Link, Todd E Druley, Konrad H Stopsack, Kelly L Bolton
MOTIVATION: The acquisition of somatic mutations in hematopoietic stem and progenitor stem cells (HSPCs) with resultant clonal expansion, termed clonal hematopoiesis (CH), is associated with increased risk of hematologic malignancies and other adverse outcomes. CH is generally present at low allelic fractions, but clonal expansion and acquisition of additional mutations leads to hematologic cancers in a small proportion of individuals. With high depth and high sensitivity sequencing, CH can be detected in most adults and its clonal trajectory mapped over time...
March 14, 2024: Bioinformatics
https://read.qxmd.com/read/38483285/mindg-a-drug-target-interaction-prediction-method-based-on-an-integrated-learning-algorithm
#27
JOURNAL ARTICLE
Hailong Yang, Yue Chen, Yun Zuo, Zhaohong Deng, Xiaoyong Pan, Hong-Bin Shen, Kup-Sze Choi, Dong-Jun Yu
MOTIVATION: Drug target interaction (DTI) prediction refers to the prediction of whether a given drug molecule will bind to a specific target and thus exert a targeted therapeutic effect. Although intelligent computational approaches for drug target prediction have received much attention and made many advances, they are still a challenging task that requires further research. The main challenges are manifested as follows: (1) Most graph neural network-based methods only consider the information of the first-order neighboring nodes (drug and target) in the graph, without learning deeper and richer structural features from the higher-order neighboring nodes...
March 14, 2024: Bioinformatics
https://read.qxmd.com/read/38478395/scpathoquant-a-tool-for-efficient-alignment-and-quantification-of-pathogen-sequence-reads-from-10x-single-cell-sequencing-data-sets
#28
JOURNAL ARTICLE
Leanne S Whitmore, Jennifer Tisoncik-Go, Michael Gale
MOTIVATION: Currently there is a lack of efficient computational pipelines/tools for conducting simultaneous genome mapping of pathogen-derived and host reads from single cell RNA sequencing (scRNAseq) output from pathogen-infected cells. Contemporary options include processes involving multiple steps and/or running multiple computational tools, increasing user operations time. RESULTS: To address the need for new tools to directly map and quantify pathogen and host sequence reads from within an infected cell from scRNAseq data sets in a single operation, we have built a python package, called scPathoQuant...
March 13, 2024: Bioinformatics
https://read.qxmd.com/read/38478393/digger-directed-annotation-of-immunoglobulin-and-t-cell-receptor-v-d-and-j-gene-sequences-and-assemblies
#29
JOURNAL ARTICLE
William D Lees, Swati Saha, Gur Yaari, Corey T Watson
SUMMARY: Knowledge of immunoglobulin and T cell receptor encoding genes is derived from high-quality genomic sequencing. High throughput sequencing is delivering large volumes of data, and precise, high-throughput approaches to annotation are needed. Digger is an automated tool that identifies coding and regulatory regions of these genes, with results comparable to those obtained by current expert curational methods. AVAILABILITY AND IMPLEMENTATION: Digger is published under open source licence at https://github...
March 13, 2024: Bioinformatics
https://read.qxmd.com/read/38478392/icarust-a-real-time-simulator-for-oxford-nanopore-adaptive-sampling
#30
JOURNAL ARTICLE
Rory Munro, Satrio Wibowo, Alexander Payne, Matthew Loose
MOTIVATION: Oxford Nanopore Technologies (ONT) sequencers enable real-time generation of sequence data, which allows for concurrent analysis during a run. Adaptive sampling leverages this real-time capability in extremis, rejecting or accepting reads for sequencing based on assessment of the sequence from the start of each read. This functionality is provided by ONT's software, MinKNOW (Oxford Nanopore Techologies). Designing and developing software to take advantage of adaptive sampling can be costly in terms of sequencing consumables, using precious samples and preparing sequencing libraries...
March 13, 2024: Bioinformatics
https://read.qxmd.com/read/38460192/molecular-mechanisms-reconstruction-from-single-cell-multi-omics-data-with-hummus
#31
JOURNAL ARTICLE
Remi Trimbour, Ina Maria Deutschmann, Laura Cantini
MOTIVATION: The molecular identity of a cell results from a complex interplay between heterogeneous molecular layers. Recent advances in single-cell sequencing technologies have opened the possibility to measure such molecular layers of regulation. RESULTS: Here, we present HuMMuS, a new method for inferring regulatory mechanisms from single-cell multi-omics data. Differently from the state-of-the-art, HuMMuS captures cooperation between biological macromolecules and can easily include additional layers of molecular regulation...
March 9, 2024: Bioinformatics
https://read.qxmd.com/read/38452348/aacflow-an-end-to-end-model-based-on-attention-augmented-convolutional-neural-network-and-flow-attention-mechanism-for-identification-of-anticancer-peptides
#32
JOURNAL ARTICLE
Shengli Zhang, Ya Zhao, Yunyun Liang
MOTIVATION: Anticancer peptides (ACPs) have natural cationic properties and can act on the anionic cell membrane of cancer cells to kill cancer cells. Therefore, ACPs have become a potential anticancer drug with good research value and prospect. RESULTS: In this paper, we propose AACFlow, an end-to-end model for identification of ACPs based on deep learning. End-to-end models have more room to automatically adjust according to the data, making the overall fit better and reducing error propagation...
March 7, 2024: Bioinformatics
https://read.qxmd.com/read/38452346/shu-visualization-of-high-dimensional-biological-pathways
#33
JOURNAL ARTICLE
Jorge Carrasco Muriel, Nicholas Cowie, Shannara Taylor Parkins, Marjan Mansouvar, Teddy Groves, Lars Keld Nielsen
SUMMARY: Shu is a visualization tool that integrates diverse data types into a metabolic map, with a focus on supporting multiple conditions and visualizing distributions. The goal is to provide a unified platform for handling the growing volume of multi-omics data, leveraging the metabolic maps developed by the metabolic modeling community. Additionally, shu offers a streamlined python API, based on the Grammar of Graphics, for easy integration with data pipelines. AVAILABILITY AND IMPLEMENTATION: Freely available at https://github...
March 7, 2024: Bioinformatics
https://read.qxmd.com/read/38449285/ingnn-dti-prediction-of-drug-target-interaction-with-interpretable-nested-graph-neural-network-and-pretrained-molecule-models
#34
JOURNAL ARTICLE
Yan Sun, Yan Yi Li, Carson K Leung, Pingzhao Hu
MOTIVATION: Drug-target interaction (DTI) prediction aims to identify interactions between drugs and protein targets. Deep learning can automatically learn discriminative features from drug and protein target representations for DTI prediction, but challenges remain, making it an open question. Existing approaches encode drugs and targets into features using deep learning models, but they often lack explanations for underlying interactions. Moreover, limited labeled DTIs in the chemical space can hinder model generalization...
March 7, 2024: Bioinformatics
https://read.qxmd.com/read/38449297/rapid-generation-of-high-quality-structure-figures-for-publication-with-pymol-pub
#35
JOURNAL ARTICLE
Yuting Chen, Haoling Zhang, Wen Wang, Yue Shen, Zhi Ping
MOTIVATION: The advancement of structural biology has increased the requirements for researchers to quickly and efficiently visualize molecular structures in silico. Meanwhile, it is also time-consuming for structural biologists to create publication-standard figures, as no useful tools can directly generate figures from structure data. Although manual editing can ensure that figures meet the standards required for publication, it requires a deep understanding of software operations and/or program call commands...
March 6, 2024: Bioinformatics
https://read.qxmd.com/read/38449296/graph-theoretical-prediction-of-biological-modules-in-quaternary-structures-of-large-protein-complexes
#36
JOURNAL ARTICLE
Florian J Gisdon, Mariella Zunker, Jan Niclas Wolf, Kai Prüfer, Jörg Ackermann, Christoph Welsch, Ina Koch
MOTIVATION: The functional complexity of biochemical processes is strongly related to the interplay of proteins and their assembly into protein complexes. In recent years, the discovery and characterization of protein complexes have substantially progressed through advances in cryo-electron microscopy, proteomics, and computational structure prediction. This development results in a strong need for computational approaches to analyse the data of large protein complexes for structural and functional characterization...
March 6, 2024: Bioinformatics
https://read.qxmd.com/read/38449295/abflex-designing-antibody-complementarity-determining-regions-with-flexible-cdr-definition
#37
JOURNAL ARTICLE
Woosung Jeon, Dongsup Kim
MOTIVATION: Antibodies are proteins that the immune system produces in response to foreign pathogens. Designing antibodies that specifically bind to antigens is a key step in developing antibody therapeutics. The complementarity determining regions (CDRs) of the antibody are mainly responsible for binding to the target antigen, and therefore must be designed to recognize the antigen. RESULTS: We develop an antibody design model, AbFlex, that exhibits state-of-the-art performance in terms of structure prediction accuracy and amino acid recovery rate...
March 6, 2024: Bioinformatics
https://read.qxmd.com/read/38449289/epivar-browser-advanced-exploration-of-epigenomics-data-under-controlled-access
#38
JOURNAL ARTICLE
David R Lougheed, Hanshi Liu, Katherine A Aracena, Romain Grégoire, Alain Pacis, Tomi Pastinen, Luis B Barreiro, Yann Joly, David Bujold, Guillaume Bourque
MOTIVATION: Human epigenomic data has been generated by large consortia for thousands of cell types to be used as a reference map of normal and disease chromatin states. Since epigenetic data contains potentially identifiable information, similarly to genetic data, most raw files generated by these consortia are stored in controlled-access databases. It is important to protect identifiable information, but this should not hinder secure sharing of these valuable datasets. RESULTS: Guided by the Framework for responsible sharing of genomic and health-related data from the Global Alliance for Genomics and Health (GA4GH), we have developed an approach and a tool to facilitate the exploration of epigenomics datasets' aggregate results, while filtering out identifiable information...
March 6, 2024: Bioinformatics
https://read.qxmd.com/read/38449288/identifying-tad-like-domains-on-single-cell-hi-c-data-by-graph-embedding-and-changepoint-detection
#39
JOURNAL ARTICLE
Erhu Liu, Hongqiang Lyu, Yuan Liu, Laiyi Fu, Xiaoliang Cheng, Xiaoran Yin
MOTIVATION: Topologically associating domains (TADs) are fundamental building blocks of three-dimensional genome. TAD-like domains in single cells are regarded as the underlying genesis of TADs discovered in bulk cells. Understanding the organization of TAD-like domains helps to get deeper insights into their regulatory functions. Unfortunately, it remains a challenge to identify TAD-like domains on single-cell Hi-C data due to its ultra-sparsity. RESULTS: We propose scKTLD, an in silico tool for the identification of TAD-like domains on single-cell Hi-C data...
March 6, 2024: Bioinformatics
https://read.qxmd.com/read/38445722/tutorial-on-survival-modeling-with-applications-to-omics-data
#40
JOURNAL ARTICLE
Zhi Zhao, John Zobolas, Manuela Zucknick, Tero Aittokallio
MOTIVATION: Identification of genomic, molecular and clinical markers prognostic of patient survival is important for developing personalized disease prevention, diagnostic and treatment approaches. Modern omics technologies have made it possible to investigate the prognostic impact of markers at multiple molecular levels, including genomics, epigenomics, transcriptomics, proteomics and metabolomics, and how these potential risk factors complement clinical characterization of patient outcomes for survival prognosis...
March 5, 2024: Bioinformatics
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