Dashing Growth Curves: a web application for rapid and interactive analysis of microbial growth curves
Recording and analyzing microbial growth is a routine task in the life sciences. Microplate readers that record dozens to hundreds of growth curves simultaneously are increasingly used for this task raising th... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - February 12, 2024 Category: Bioinformatics Authors: Michael A. Reiter and Julia A. Vorholt Tags: Software Source Type: research
Incorporating functional annotation with bilevel continuous shrinkage for polygenic risk prediction
Genetic variants can contribute differently to trait heritability by their functional categories, and recent studies have shown that incorporating functional annotation can improve the predictive performance o... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - February 9, 2024 Category: Bioinformatics Authors: Yongwen Zhuang, Na Yeon Kim, Lars G. Fritsche, Bhramar Mukherjee and Seunggeun Lee Tags: Research Source Type: research
vissE: a versatile tool to identify and visualise higher-order molecular phenotypes from functional enrichment analysis
Functional analysis of high throughput experiments using pathway analysis is now ubiquitous. Though powerful, these methods often produce thousands of redundant results owing to knowledgebase redundancies upst... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - February 8, 2024 Category: Bioinformatics Authors: Dharmesh D. Bhuva, Chin Wee Tan, Ning Liu, Holly J. Whitfield, Nicholas Papachristos, Samuel C. Lee, Malvika Kharbanda, Ahmed Mohamed and Melissa J. Davis Tags: Research Source Type: research
MAC-ErrorReads: machine learning-assisted classifier for filtering erroneous NGS reads
The rapid advancement of next-generation sequencing (NGS) machines in terms of speed and affordability has led to the generation of a massive amount of biological data at the expense of data quality as errors ... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - February 7, 2024 Category: Bioinformatics Authors: Amira Sami, Sara El-Metwally and M. Z. Rashad Tags: Research Source Type: research
Enabling personalised disease diagnosis by combining a patient ’s time-specific gene expression profile with a biomedical knowledge base
Recent developments in the domain of biomedical knowledge bases (KBs) open up new ways to exploit biomedical knowledge that is available in the form of KBs. Significant work has been done in the direction of b... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - February 7, 2024 Category: Bioinformatics Authors: Ghanshyam Verma, Dietrich Rebholz-Schuhmann and Michael G. Madden Tags: Research Source Type: research
Correction: Multiple imputation and direct estimation for qPCR data with non-detects
(Source: BMC Bioinformatics)
Source: BMC Bioinformatics - February 7, 2024 Category: Bioinformatics Authors: Valeriia Sherina, Helene R. McMurray, Winslow Powers, Harmut Land, Tanzy M. T. Love and Matthew N. McCall Tags: Correction Source Type: research
A comparison of embedding aggregation strategies in drug –target interaction prediction
The prediction of interactions between novel drugs and biological targets is a vital step in the early stage of the drug discovery pipeline. Many deep learning approaches have been proposed over the last decad... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - February 6, 2024 Category: Bioinformatics Authors: Dimitrios Iliadis, Bernard De Baets, Tapio Pahikkala and Willem Waegeman Tags: Research Source Type: research
MRMPro: a web-based tool to improve the speed of manual calibration for multiple reaction monitoring data analysis by mass spectrometry
As a gold-standard quantitative technique based on mass spectrometry, multiple reaction monitoring (MRM) has been widely used in proteomics and metabolomics. In the analysis of MRM data, as no peak picking alg... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - February 6, 2024 Category: Bioinformatics Authors: Ruimin Wang, Hengxuan Jiang, Miaoshan Lu, Junjie Tong, Shaowei An, Jinyin Wang and Changbin Yu Tags: Software Source Type: research
Modifying the false discovery rate procedure based on the information theory under arbitrary correlation structure and its performance in high-dimensional genomic data
Controlling the False Discovery Rate (FDR) in Multiple Comparison Procedures (MCPs) has widespread applications in many scientific fields. Previous studies show that the correlation structure between test stat... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - February 5, 2024 Category: Bioinformatics Authors: Sedighe Rastahi, Azadeh Saki and Hamed Tabesh Tags: Research Source Type: research
A new approach to describe the taxonomic structure of microbiome and its application to assess the relationship between microbial niches
Data from microbiomes from multiple niches is often collected, but methods to analyse these often ignore associations between niches. One interesting case is that of the oral microbiome. Its composition is rec... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - February 5, 2024 Category: Bioinformatics Authors: Vincent Y. Pappalardo, Leyla Azarang, Egija Zaura, Bernd W. Brandt and Ren ée X. de Menezes Tags: Research Source Type: research
Colocalization by cross-correlation, a new method of colocalization suited for super-resolution microscopy
A common goal of scientific microscopic imaging is to determine if a spatial correlation exists between two imaged structures. This is generally accomplished by imaging fluorescently labeled structures and mea... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - February 2, 2024 Category: Bioinformatics Authors: Andrew D. McCall Tags: Software Source Type: research
Evaluation of penalized and machine learning methods for asthma disease prediction in the Korean Genome and Epidemiology Study (KoGES)
Genome-wide association studies have successfully identified genetic variants associated with human disease. Various statistical approaches based on penalized and machine learning methods have recently been pr... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - February 2, 2024 Category: Bioinformatics Authors: Yongjun Choi, Junho Cha and Sungkyoung Choi Tags: Research Source Type: research
Multi-label classification with XGBoost for metabolic pathway prediction
Metabolic pathway prediction is one possible approach to address the problem in system biology of reconstructing an organism ’s metabolic network from its genome sequence. Recently there have been developments ... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - February 1, 2024 Category: Bioinformatics Authors: Hyunwhan Joe and Hong-Gee Kim Tags: Research Source Type: research
Cirscan: a shiny application to identify differentially active sponge mechanisms and visualize circRNA –miRNA–mRNA networks
Non-coding RNAs represent a large part of the human transcriptome and have been shown to play an important role in disease such as cancer. However, their biological functions are still incompletely understood.... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - February 1, 2024 Category: Bioinformatics Authors: Rose-Marie Fraboulet, Yanis Si Ahmed, Marc Aubry, Sebastien Corre, Marie-Dominique Galibert and Yuna Blum Tags: Software Source Type: research
ClusTrast: a short read de novo transcript isoform assembler guided by clustered contigs
Transcriptome assembly from RNA-sequencing data in species without a reliable reference genome has to be performed de novo, but studies have shown that de novo methods often have inadequate ability to reconstr... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - February 1, 2024 Category: Bioinformatics Authors: Karl Johan Westrin, Warren W. Kretzschmar and Olof Emanuelsson Tags: Software Source Type: research
