BMC Bioinformatics

CO-AMPPRED FOR IN SILICO-AIDED PREDICTIONS OF ANTIMICROBIAL PEPTIDES BY INTEGRATING COMPOSITION-BASED FEATURES

Antimicrobial peptides are oligopeptides that act as crucial components of innate immunity, naturally occur in all multicellular organisms,...

COPLA, A TAXONOMIC CLASSIFIER OF PLASMIDS

Plasmids are mobile genetic elements, key in the dissemination of antibiotic resistance, virulence determinants and other adaptive...

MATISSE: A MATLAB-BASED ANALYSIS TOOLBOX FOR IN SITU SEQUENCING EXPRESSION MAPS

A range of spatially resolved transcriptomic methods has recently emerged as a way to spatially characterize the molecular and cellular...

MUREN: A ROBUST AND MULTI-REFERENCE APPROACH OF RNA-SEQ TRANSCRIPT NORMALIZATION

Normalization of RNA-seq data aims at identifying biological expression differentiation between samples by removing the effects of...

MINING A STROKE KNOWLEDGE GRAPH FROM LITERATURE

Stroke has an acute onset and a high mortality rate, making it one of the most fatal diseases worldwide. Its underlying biology and...

TAXALLNOMY: AN EXTENSION OF NCBI TAXONOMY THAT PRODUCES A HIERARCHICALLY COMPLETE TAXONOMIC TREE

NCBI Taxonomy is the main taxonomic source for several bioinformatics tools and databases since all organisms with sequence accessions...

UNCOVERING THE EFFECTS OF HETEROGENEITY AND PARAMETER SENSITIVITY ON WITHIN-HOST DYNAMICS OF DISEASE: MALARIA AS A CASE STUDY

The fidelity and reliability of disease model predictions depend on accurate and precise descriptions of processes and determination...

A NEURAL NETWORK-BASED METHOD FOR POLYPHARMACY SIDE EFFECTS PREDICTION

Polypharmacy is a type of treatment that involves the concurrent use of multiple medications. Drugs may interact when they are used...

GAT-LI: A GRAPH ATTENTION NETWORK BASED LEARNING AND INTERPRETING METHOD FOR FUNCTIONAL BRAIN NETWORK CLASSIFICATION

Autism spectrum disorders imply a spectrum of symptoms rather than a single phenotype. ASD could affect brain connectivity at different...

FEATURE SELECTION FOR RNA CLEAVAGE EFFICIENCY AT SPECIFIC SITES USING THE LASSO REGRESSION MODEL IN ARABIDOPSIS THALIANA

RNA degradation is important for the regulation of gene expression. Despite the identification of proteins and sequences related to...

CORRECTION TO: SPEAQEASY: A SCALABLE PIPELINE FOR EXPRESSION ANALYSIS AND QUANTIFICATION FOR R/BIOCONDUCTOR‑POWERED RNA‑SEQ ANALYSES

NEODL: A NOVEL NEOANTIGEN INTRINSIC FEATURE-BASED DEEP LEARNING MODEL IDENTIFIES IDH WILD-TYPE GLIOBLASTOMAS WITH THE LONGEST SURVIVAL

Neoantigen based personalized immune therapies achieve promising results in melanoma and lung cancer, but few neoantigen based models...

PDBECIF: AN OPEN-SOURCE MMCIF/CIF PARSING AND PROCESSING PACKAGE

Biomacromolecular structural data outgrew the legacy Protein Data Bank format which the scientific community relied on for decades,...

PRE-CAPTURE MULTIPLEXING PROVIDES ADDITIONAL POWER TO DETECT COPY NUMBER VARIATION IN EXOME SEQUENCING

As exome sequencing integrates into clinical practice, we should make every effort to utilize all information generated. Copy-number...

ACCURATE PLANT PATHOGEN EFFECTOR PROTEIN CLASSIFICATION AB INITIO WITH DEEPREDEFF: AN ENSEMBLE OF CONVOLUTIONAL NEURAL NETWORKS

Plant pathogens cause billions of dollars of crop loss every year and are a major threat to global food security. Effector proteins...

HAVOC, A BIOINFORMATIC PIPELINE FOR REFERENCE-BASED CONSENSUS ASSEMBLY AND LINEAGE ASSIGNMENT FOR SARS-COV-2 SEQUENCES

SARS-CoV-2 related research has increased in importance worldwide since December 2019. Several new variants of SARS-CoV-2 have emerged...

MSCFS: INFERRING CIRCRNA FUNCTIONAL SIMILARITY BASED ON MULTIPLE DATA SOURCES

More and more evidence shows that circRNA plays an important role in various biological processes and human health. Therefore, inferring...

SPLICE-Q: A PYTHON TOOL FOR GENOME-WIDE QUANTIFICATION OF SPLICING EFFICIENCY

Introns are generally removed from primary transcripts to form mature RNA molecules in a post-transcriptional process called splicing....

MITOTOX: A COMPREHENSIVE MITOCHONDRIAL TOXICITY DATABASE

Mitochondria play essential roles in regulating cellular functions. Some drug treatments and molecular interventions have been reported...

PUBLISHER CORRECTION TO: TRANCRIPTOMERECONSTRUCTOR: DATA‑DRIVEN ANNOTATION OF COMPLEX TRANSCRIPTOMES