Similarity-assisted variational autoencoder for nonlinear dimension reduction with application to single-cell RNA sequencing data
Deep generative models naturally become nonlinear dimension reduction tools to visualize large-scale datasets such as single-cell RNA sequencing datasets for revealing latent grouping patterns or identifying o... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - November 14, 2023 Category: Bioinformatics Authors: Gwangwoo Kim and Hyonho Chun Tags: Research Source Type: research

Protein language models can capture protein quaternary state
Determining a protein ’s quaternary state, i.e. the number of monomers in a functional unit, is a critical step in protein characterization. Many proteins form multimers for their activity, and over 50% are estima... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - November 14, 2023 Category: Bioinformatics Authors: Orly Avraham, Tomer Tsaban, Ziv Ben-Aharon, Linoy Tsaban and Ora Schueler-Furman Tags: Research Source Type: research

Mdwgan-gp: data augmentation for gene expression data based on multiple discriminator WGAN-GP
Although gene expression data play significant roles in biological and medical studies, their applications are hampered due to the difficulty and high expenses of gathering them through biological experiments.... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - November 13, 2023 Category: Bioinformatics Authors: Rongyuan Li, Jingli Wu, Gaoshi Li, Jiafei Liu, Junbo Xuan and Qi Zhu Tags: Research Source Type: research

Optimizing diabetes classification with a machine learning-based framework
Diabetes is a metabolic disorder usually caused by insufficient secretion of insulin from the pancreas or insensitivity of cells to insulin, resulting in long-term elevated blood sugar levels in patients. Pati... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - November 13, 2023 Category: Bioinformatics Authors: Xin Feng, Yihuai Cai and Ruihao Xin Tags: Research Source Type: research

A novel two-way rebalancing strategy for identifying carbonylation sites
As an irreversible post-translational modification, protein carbonylation is closely related to many diseases and aging. Protein carbonylation prediction for related patients is significant, which can help cli... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - November 13, 2023 Category: Bioinformatics Authors: Linjun Chen, Xiao-Yuan Jing, Yaru Hao, Wei Liu, Xiaoke Zhu and Wei Han Tags: Research Source Type: research

DG-Affinity: predicting antigen –antibody affinity with language models from sequences
Antibody-mediated immune responses play a crucial role in the immune defense of human body. The evolution of bioengineering has led the progress of antibody-derived drugs, showing promising efficacy in cancer ... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - November 13, 2023 Category: Bioinformatics Authors: Ye Yuan, Qushuo Chen, Jun Mao, Guipeng Li and Xiaoyong Pan Tags: Research Source Type: research

Statistical modeling to quantify the uncertainty of FoldX-predicted protein folding and binding stability
Computational methods of predicting protein stability changes upon missense mutations are invaluable tools in high-throughput studies involving a large number of protein variants. However, they are limited by ... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - November 12, 2023 Category: Bioinformatics Authors: Yesol Sapozhnikov, Jagdish Suresh Patel, F. Marty Ytreberg and Craig R. Miller Tags: Research Source Type: research

Role of environmental specificity in CASP results
Recently, significant progress has been made in the field of protein structure prediction by the application of artificial intelligence techniques, as shown by the results of the CASP13 and CASP14 (Critical As... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - November 11, 2023 Category: Bioinformatics Authors: Irena Roterman, Katarzyna Stapor and Leszek Konieczny Tags: Research Source Type: research

Comparative Study of Single-stranded Oligonucleotides Secondary Structure Prediction Tools
Single-stranded nucleic acids (ssNAs) have important biological roles and a high biotechnological potential linked to their ability to bind to numerous molecular targets. This depends on the different spatial ... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - November 8, 2023 Category: Bioinformatics Authors: Thomas Binet, S éverine Padiolleau-Lefèvre, Stéphane Octave, Bérangère Avalle and Irene Maffucci Tags: Research Source Type: research

A model-based clustering via mixture of hierarchical models with covariate adjustment for detecting differentially expressed genes from paired design
The causes of many complex human diseases are still largely unknown. Genetics plays an important role in uncovering the molecular mechanisms of complex human diseases. A key step to characterize the genetics o... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - November 8, 2023 Category: Bioinformatics Authors: Yixin Zhang, Wei Liu and Weiliang Qiu Tags: Research Source Type: research

ILIAD: a suite of automated Snakemake workflows for processing genomic data for downstream applications
Processing raw genomic data for downstream applications such as imputation, association studies, and modeling requires numerous third-party bioinformatics software tools. It is highly time-consuming and resour... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - November 8, 2023 Category: Bioinformatics Authors: Noah Herrick and Susan Walsh Tags: Software Source Type: research

Fast alignment of mass spectra in large proteomics datasets, capturing dissimilarities arising from multiple complex modifications of peptides
In proteomics, the interpretation of mass spectra representing peptides carrying multiple complex modifications remains challenging, as it is difficult to strike a balance between reasonable execution time, a ... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - November 8, 2023 Category: Bioinformatics Authors: Gr égoire Prunier, Mehdi Cherkaoui, Albane Lysiak, Olivier Langella, Mélisande Blein-Nicolas, Virginie Lollier, Emile Benoist, Géraldine Jean, Guillaume Fertin, Hélène Rogniaux and Dominique Tessier Tags: Software Source Type: research

ScLSTM: single-cell type detection by siamese recurrent network and hierarchical clustering
Categorizing cells into distinct types can shed light on biological tissue functions and interactions, and uncover specific mechanisms under pathological conditions. Since gene expression throughout a populati... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - November 7, 2023 Category: Bioinformatics Authors: Hanjing Jiang, Yabing Huang, Qianpeng Li and Boyuan Feng Tags: Research Source Type: research

Ab initio protein structure prediction: the necessary presence of external force field as it is delivered by Hsp40 chaperone
The aqueous environment directs the protein folding process towards the generation of micelle-type structures, which results in the exposure of hydrophilic residues on the surface (polarity) and the concentrat... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - November 7, 2023 Category: Bioinformatics Authors: Irena Roterman, Katarzyna Stapor and Leszek Konieczny Tags: Research Source Type: research

Hybrid deep learning approach to improve classification of low-volume high-dimensional data
The performance of machine learning classification methods relies heavily on the choice of features. In many domains, feature generation can be labor-intensive and require domain knowledge, and feature selecti... (Source: BMC Bioinformatics)
Source: BMC Bioinformatics - November 7, 2023 Category: Bioinformatics Authors: Pegah Mavaie, Lawrence Holder and Michael K. Skinner Tags: Research Source Type: research