Academic Articles & Research Papers

DNA methylation patterns of circadian and ultradian genes are altered in the peripheral blood of patients with hidradenitis suppurativa

BackgroundHidradenitis suppurativa (HS) is a chronic inflammatory skin condition that affects hair follicles in areas with apocrine sweat glands, such as the underarms, groin, and buttocks. The pathogenesis of HS is not fully understood, bu...

Draft genome sequences of two hypermucoviscous carbapenem-resistant ST25 Klebsiella pneumoniae strains causing respiratory and systemic infections

ABSTRACT: Objectives: The emergence and spread of hypermucoviscous KPC-2-producing Klebsiella pneumoniae strains belonging to the sequence type 25 (ST25) clone was reported recently in Northwest Argentina as a leading cause of nosocomial in...

Construction of the cancer patients’ database based on the US National Health and Nutrition Examination Survey (NHANES) datasets for cancer epidemiology research

Abstract Background The US National Health and Nutrition Examination Survey (NHANES) dataset does not include a specific question or laboratory test to confirm a history of cancer diagnosis. However, if straightforward variables for cancer ...

Transcriptome and DNA Methylome Analysis in a Mouse Model of Diet-Induced Obesity Predicts Increased Risk of Colorectal Cancer

Colorectal cancer (CRC) tends to occur at older age; however, CRC incidence rates have been rising sharply among young age groups. The increasing prevalence of obesity is recognized as a major risk, yet the mechanistic underpinnings remain ...

Cofilin-1, LIMK1 and SSH1 are differentially expressed in locally advanced colorectal cancer and according to consensus molecular subtypes

Abstract Background Colorectal cancer (CRC) is among the deadliest cancers, wherein early dissemination of tumor cells, and consequently, metastasis formation, are the main causes of mortality and poor prognosis. Cofilin-1 (CFL-1) and its m...

Efficacious role of silica nanoparticles in improving growth and yield of wheat under drought stress through stress-gene upregulation

Climate change is now evident and severe water shortage due to unpredictable raining season along with extended summers is expected to hamper crop production across the globe. Application of nanoparticle based formulations is one of the mos...

BioDecryptors, a Bioinformatics Escape Game for Undergraduate and Postgraduate Learners in Clinical Microbiology: Prospective Before-and-After Study.

Survey of Natural Language Processing Techniques in Bioinformatics

Informatics methods, such as text mining and natural language processing, are always involved in bioinformatics research. In this study, we discuss text mining and natural language processing methods in bioinformatics from two perspectives....

MedScan, a natural language processing engine for MEDLINE abstracts

MOTIVATION: The importance of extracting biomedical information from scientific publications is well recognized. A number of information extraction systems for the biomedical domain have been reported, but none of them have become widely us...

Attentive interpretable tabular learning (TabNet) for miRNA expression classification in cervical cancer and Alzheimer's disease.

Applications of Natural Language Processing in Biodiversity Science

Centuries of biological knowledge are contained in the massive body of scientific literature, written for human-readability but too big for any one person to consume. Large-scale mining of information from the literature is necessary if bio...

Identifying multi-omics spatial domains via masked autoencoder and diffusion-based latent regularization with SpaMEDM.

Machine learning for RNA–small molecule interactions: methodologies, evaluation, and future directions.

Caps Captioning: A Modern Image Captioning Approach Based on Improved Capsule Network

In image captioning models, the main challenge in describing an image is identifying all the objects by precisely considering the relationships between the objects and producing various captions. Over the past few years, many methods have b...

Natural Language Processing for EHR-Based Computational Phenotyping

This article reviews recent advances in applying natural language processing (NLP) to Electronic Health Records (EHRs) for computational phenotyping. NLP-based computational phenotyping has numerous applications including diagnosis categori...

Biomedical Natural Language Processing

Biomedical Natural Language Processing is a comprehensive tour through the classic and current work in the field. It discusses all subjects from both a rule-based and a machine learning approach, and also describes each subject from the per...

Collectively encoding protein properties enriches protein language models

Abstract Pre-trained natural language processing models on a large natural language corpus can naturally transfer learned knowledge to protein domains by fine-tuning specific in-domain tasks. However, few studies focused on enriching such p...

TransCat: a hybrid CNN-transformer network with KAN for medical image segmentation

Medical image segmentation is a fundamental task in computer vision and plays an important role in clinical diagnosis and treatment planning. Existing methods are mainly built on either convolutional neural networks (CNNs) or Transformer-ba...

From Foundations to Frontiers: Best Papers in Bioinformatics and Translational Informatics 2024.

The long non-coding RNA LINC00152 is essential for cell cycle progression through mitosis in HeLa cells

Abstract In recent years, long non-coding RNA (lncRNA) research has identified essential roles of these transcripts in virtually all physiological cellular processes including tumorigenesis, but their functions and molecular mechanisms are ...