🧰 Now published in Bioinformatics Advances: "Atlantool: A command line tool to retrieve DNA and RNA sequencing reads from BAM files by the read identifier"    Read the full paper here: https://doi.org/10.1093/bioadv/vbaf226  Authors include: @nibor.org, @egiannoulatou.bsky.social

📊 Just out in Bioinformatics Advances: "tBN-CSDI: A time-varying blue noise-based diffusion model for time series imputation" Explore the full study: https://doi.org/10.1093/bioadv/vbaf225

🖥️ Explore the latest from Bioinformatics Advances: "Termal: A fast and interactive terminal-based viewer for multiple sequence alignments" Full article available: https://doi.org/10.1093/bioadv/vbaf208

🧬 Now published in Bioinformatics Advances: "DeepEPI: CNN-Transformer-based model for extracting TF interactions through predicting enhancer–promoter interactions" Read the full paper here: https://doi.org/10.1093/bioadv/vbaf221

🧩 Recently published in Bioinformatics Advances: “Rosace-AA: Enhancing interpretation of deep mutational scanning data with amino acid substitution and position-specific insights”   Full article available: https://doi.org/10.1093/bioadv/vbaf218

🧪 Now published in Bioinformatics Advances: "HeraNorm: An R Shiny application for identifying optimal endogenous controls for miRNA and RNA assays in qPCR and ddPCR"   Read the full paper here: https://doi.org/10.1093/bioadv/vbaf220

🧪 Explore the latest from Bioinformatics Advances: "Core fucose identification in glycoproteomics: An ML approach addressing fucose migration in mass spectrometry" Full article available: https://doi.org/10.1093/bioadv/vbaf186

Bioinformatics Advances is looking for new #AssociateEditors to join the editorial board! Details about the position and instructions on how to apply can be found here: academic.oup.com/bioinformati...

📘 Just out in Bioinformatics Advances: "Competencies for bioinformatics core facility scientists: Extension of the ISCB competency framework for bioinformatics" Explore the full study: https://doi.org/10.1093/bioadv/vbaf206 Authors include: @downingtim.bsky.social

🖼️ Now published in Bioinformatics Advances: "MSA Class Logos: a web server for automated sequence logo generation for user-defined sequence classes based on one multiple sequence alignment"    Read the full paper here: https://doi.org/10.1093/bioadv/vbaf217

🧫 Just out in Bioinformatics Advances: "PACO: a Shiny app for comparing perturbed pathways associated with different phenotypes"    Explore the full study: https://doi.org/10.1093/bioadv/vbaf212

🧫Now published in Bioinformatics Advances: "DRAGoN: a robust pipeline for analyzing DRUG-seq datasets"  Read the full paper here: https://doi.org/10.1093/bioadv/vbaf214

🧪 Explore the latest from Bioinformatics Advances: "PerseuCPP: A machine learning strategy to predict cell-penetrating peptides and their uptake efficiency" Full article available: https://doi.org/10.1093/bioadv/vbaf213 Authors include: @wagnermeirajr and @DrDouglasPires

🔬 Just out in Bioinformatics Advances: "EMICSS: Added-value annotations for EMDB entries"  Explore the full study: https://doi.org/10.1093/bioadv/vbaf203

🧬 Now published in Bioinformatics Advances: "DNPcall: A new pipeline for accurate double nucleotide polymorphism calling" Read the full paper here: https://doi.org/10.1093/bioadv/vbaf209  Authors include: @eugeniadat.bsky.social

🧮 Explore the latest from Bioinformatics Advances: “MADVAR: A lightweight, data-driven tool for automated feature selection in omics data” Full article available:  https://doi.org/10.1093/bioadv/vbaf211

🩸 Just out in Bioinformatics Advances: “bloodAGENT: A versatile tool for blood group typing and genomic variation analysis” Explore the full study: https://doi.org/10.1093/bioadv/vbaf210

🍇 Now published in Bioinformatics Advances: “Exploration of chaos game representation and integrative deep learning approaches for whole-genome sequencing-based grapevine genetic testing” Read the full paper here: https://doi.org/10.1093/bioadv/vbaf193

🦠 Now published in Bioinformatics Advances: “GCompip: A pipeline for estimating the gene abundance in microbial communities” Read the full paper here: https://doi.org/10.1093/bioadv/vbaf207

📂 Now published in Bioinformatics Advances: “IGD: A simple, efficient genotype data format” Read the full paper here: https://doi.org/10.1093/bioadv/vbaf205

🌱 Just out in Bioinformatics Advances: “NFEmbed: Modeling nitrogenase activity via classification and regression with pretrained protein embeddings” Explore the full study: https://doi.org/10.1093/bioadv/vbaf204

🧪 Explore the latest from Bioinformatics Advances: “ResLysEmbed: A ResNet-based framework for succinylated lysine residue prediction using sequence and language model embeddings” Full article available: https://doi.org/10.1093/bioadv/vbaf198

🦠 Now published in Bioinformatics Advances: “An explainable machine learning pipeline for prediction of antimicrobial resistance in Pseudomonas aeruginosa” Read the full paper here: https://doi.org/10.1093/bioadv/vbaf190

🧬 Now published in Bioinformatics Advances: “Multimodal deep learning for predicting protein ubiquitination sites” Find the full paper here: https://doi.org/10.1093/bioadv/vbaf200

📊 Just out in Bioinformatics Advances: “DgeaHeatmap: An R package for transcriptomic analysis and heatmap generation”  Explore the full study: doi.org/10.1093/bioadv/vbaf194

🧬 Now published in Bioinformatics Advances: “Direct inference of haplotypes from sequencing data”     Read the full paper here: doi.org/10.1093/bioadv/vbaf195

🕸️ Now published in Bioinformatics Advances: "MBC PathNet: Integration and visualization of networks connecting functionally related pathways predicted from transcriptomic and proteomic datasets"     Read the full paper here: https://doi.org/10.1093/bioadv/vbaf197

🧠 Discover "A foundation model for learning genetic associations from brain imaging phenotypes" in Bioinformatics Advances!  Read the full paper here: https://doi.org/10.1093/bioadv/vbaf196 Authors include: @bosea.bsky.social

📊 Explore the latest from Bioinformatics Advances: "Revealing tissue architecture through the hypercomplex Fourier analysis of spatial transcriptomics data" Read the full study: https://doi.org/10.1093/bioadv/vbaf191

🔬 Explore the latest from Bioinformatics Advances: "Harmonizing heterogeneous single-cell gene expression data with individual-level covariate information" Full article available: https://doi.org/10.1093/bioadv/vbaf189

🧪 Now published in Bioinformatics Advances: "NGBO: Introducing -omics contextual data to biobanking ontology" Explore the full study: https://doi.org/10.1093/bioadv/vbaf131

💻 Now published in Bioinformatics Advances: “robin2: Accelerating single cell data clustering evaluation”     Full article available: https://doi.org/10.1093/bioadv/vbaf184 Authors include: @luisacutillo.bsky.social

🧫 Just out in Bioinformatics Advances: “Marker genes reveal dynamic features of cell evolving processes” Explore the full study: https://doi.org/10.1093/bioadv/vbaf185

🧬 Explore the latest from Bioinformatics Advances: “Heterogeneous graph neural networks for link prediction in biomedical networks” Read the full paper here: https://doi.org/10.1093/bioadv/vbaf187

🧠 Now published in Bioinformatics Advances: “Struc2mapGAN: Improving synthetic cryo-EM density maps with generative adversarial networks”    Explore the full study: https://doi.org/10.1093/bioadv/vbaf179

🧬 Now published in Bioinformatics Advances: “smartSim: Simulation of splice aware single cell Smart-seq3 data”     Explore the full study: https://doi.org/10.1093/bioadv/vbaf183

🧠 Explore the latest from Bioinformatics Advances: “Estimating protein complex model accuracy using graph transformers and pairwise similarity graphs” Full article available: https://doi.org/10.1093/bioadv/vbaf180

🧬 Now published in Bioinformatics Advances: “In silico design of immunogenic antigen cocktail via affinity maturation guided optimization” Explore the full study: https://doi.org/10.1093/bioadv/vbaf182

⚙️ Just out in Bioinformatics Advances: “SW-Actors: Accelerating the Smith–Waterman Algorithm via Actors” Explore the full study: https://doi.org/10.1093/bioadv/vbaf173

🧬 Explore the latest from Bioinformatics Advances: “Exonize: a tool for finding and classifying exon duplications in annotated genomes” Full article available: https://doi.org/10.1093/bioadv/vbaf177 Authors include: @chriswheat.bsky.social

🦠 Now published in Bioinformatics Advances: “Diffusion model for imputing time-series gut microbiome profiles using phylogenetic information and metadata integration” Read the full paper here: https://doi.org/10.1093/bioadv/vbaf181

🧬Now in Bioinformatics Advances: “Gene-Set Enrichment Analysis and visualization on the web using EnrichmentMap: RNASeq” Read the full paper here: https://doi.org/10.1093/bioadv/vbaf178 Authors include: @garybader.bsky.social

🧠 Explore the latest from Bioinformatics Advances: “Statistical relationships across epigenomes using large-scale hierarchical clustering” Full article available: https://doi.org/10.1093/bioadv/vbaf175

🧬 Now published in Bioinformatics Advances: “Multi-metric locality sensitive hashing enhances alignment accuracy of bisulfite-sequencing reads: BisHash” Explore the full study: https://doi.org/10.1093/bioadv/vbaf144

🧬 Now out in Bioinformatics Advances: “GRPhIN: Graphlet Characterization of Regulatory and Physical Interaction Networks” Explore the full study: https://doi.org/10.1093/bioadv/vbaf176

🧪 Just out in Bioinformatics Advances: “Structure-based metabolite function prediction using graph neural networks”    Explore the full study here: https://doi.org/10.1093/bioadv/vbaf174 Authors include: @alisaadatv.bsky.social, @jannahastings.bsky.social

🗂️ Just out in Bioinformatics Advances: "Review of open-source software for developing heterogeneous data management systems for bioinformatics applications"   Explore the full study: https://doi.org/10.1093/bioadv/vbaf168 Authors include: @tuliodna.bsky.social

🧠 Just out in Bioinformatics Advances: "ScaleSC: A superfast and scalable single cell RNA-seq data analysis pipeline powered by GPU"   Explore the full study: https://doi.org/10.1093/bioadv/vbaf167

🧬 Now published in Bioinformatics Advances: "IsoPrimer: a pipeline for designing isoform-aware primer pairs for comprehensive gene expression quantification"  Explore the full study: https://doi.org/10.1093/bioadv/vbaf171

🧬 Just out in Bioinformatics Advances: "Hybrid representation learning for human m6A modifications with chromosome-level generalizability"   Full article available: https://doi.org/10.1093/bioadv/vbaf170