BMC Bioinformatics

GENTLE: A NOVEL BIOINFORMATICS TOOL FOR GENERATING FEATURES AND BUILDING CLASSIFIERS FROM T CELL REPERTOIRE CANCER DATA

In the global effort to discover biomarkers for cancer prognosis, prediction tools have become essential resources. TCR repertoires...

ION-PUMPING MICROBIAL RHODOPSIN PROTEIN CLASSIFICATION BY MACHINE LEARNING APPROACH

Rhodopsin is a seven-transmembrane protein covalently linked with retinal chromophore that absorbs photons for energy conversion and...

DETECTING GENOMIC DELETIONS FROM HIGH-THROUGHPUT SEQUENCE DATA WITH UNSUPERVISED LEARNING

DEEPSELECTNET: DEEP NEURAL NETWORK BASED SELECTIVE SEQUENCING FOR OXFORD NANOPORE SEQUENCING

Nanopore sequencing allows selective sequencing, the ability to programmatically reject unwanted reads in a sample. Selective sequencing...

GDAPHEN, R PIPELINE TO IDENTIFY THE MOST IMPORTANT QUALITATIVE AND QUANTITATIVE PREDICTOR VARIABLES FROM PHENOTYPIC DATA

In individuals or animals suffering from genetic or acquired diseases, it is important to identify which clinical or phenotypic variables...

SINGLE-CELL SPATIAL EXPLORER: EASY EXPLORATION OF SPATIAL AND MULTIMODAL TRANSCRIPTOMICS

The development of single-cell technologies yields large datasets of information as diverse and multimodal as transcriptomes, immunophenotypes,...

EFFECTIVE MATRIX DESIGNS FOR COVID-19 GROUP TESTING

Grouping samples with low prevalence of positives into pools and testing these pools can achieve considerable savings in testing resources...

NF-CORE/CIRCRNA: A PORTABLE WORKFLOW FOR THE QUANTIFICATION, MIRNA TARGET PREDICTION AND DIFFERENTIAL EXPRESSION ANALYSIS OF CIRCULAR RNAS

Circular RNAs are a class of covalenty closed non-coding RNAs that have garnered increased attention from the research community due...

IDENTIFICATION OF PROGNOSTIC AND PREDICTIVE BIOMARKERS IN HIGH-DIMENSIONAL DATA WITH PPLASSO

In clinical trials, identification of prognostic and predictive biomarkers has became essential to precision medicine. Prognostic biomarkers...

ACCOMMODATING MULTIPLE POTENTIAL NORMALIZATIONS IN MICROBIOME ASSOCIATIONS STUDIES

Microbial communities are known to be closely related to many diseases, such as obesity and HIV, and it is of interest to identify...

SVHOUND: DETECTION OF REGIONS THAT HARBOR YET UNDETECTED STRUCTURAL VARIATION

Recent population studies are ever growing in number of samples to investigate the diversity of a population or species. These studies...

BADASS: BACTERIOCIN-DIVERSITY ASSESSMENT SOFTWARE

Bacteriocins are defined as thermolabile peptides produced by bacteria with biological activity against taxonomically related species....

MULTISCALE-CNN-4MCPRED: A MULTI-SCALE CNN AND ADAPTIVE EMBEDDING-BASED METHOD FOR MOUSE GENOME DNA N4-METHYLCYTOSINE PREDICTION

N4-methylcytosine is an important epigenetic mechanism, which regulates many cellular processes such as cell differentiation and gene...

PDA-PRGCN: IDENTIFICATION OF PIWI-INTERACTING RNA-DISEASE ASSOCIATIONS THROUGH SUBGRAPH PROJECTION AND RESIDUAL SCALING-BASED FEATURE AUGMENTATION

Emerging evidences show that Piwi-interacting RNAs play a pivotal role in numerous complex human diseases. Identifying potential piRNA-disease...

GENOMIC AND IMMUNOGENOMIC ANALYSIS OF THREE PROGNOSTIC SIGNATURE GENES IN LUAD

Searching for immunotherapy-related markers is an important research content to screen for target populations suitable for immunotherapy....

A SIGNATURE OF IMMUNE-RELATED GENES CORRELATING WITH CLINICAL PROGNOSIS AND IMMUNE MICROENVIRONMENT IN SEPSIS

Immune-related genes remain poorly understood in their function in the onset and progression of sepsis.

IDENTIFICATION OF BIOMARKERS PREDICTIVE OF METASTASIS DEVELOPMENT IN EARLY-STAGE COLORECTAL CANCER USING NETWORK-BASED REGULARIZATION

Colorectal cancer is the third most common cancer and the second most deathly worldwide. It is a very heterogeneous disease that can...

IDENTIFYING CANCER DRIVER GENES BASED ON MULTI-VIEW HETEROGENEOUS GRAPH CONVOLUTIONAL NETWORK AND SELF-ATTENTION MECHANISM

Correctly identifying the driver genes that promote cell growth can significantly assist drug design, cancer diagnosis and treatment....

XCORE: AN R PACKAGE FOR INFERENCE OF GENE EXPRESSION REGULATORS

Elucidating the Transcription Factors that drive the gene expression changes in a given experiment is a common question asked by researchers....

CORRECTION: A LIGHTWEIGHT CLASSIFICATION OF ADAPTOR PROTEINS USING TRANSFORMER NETWORKS