Social Media Ideas for Bioinformatics Workflow

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rna-seqblog.com /3 weeks ago

scFlowReport brings multiple single-cell RNA sequencing analyses into one workflow

RNA sequencing analysis with scFlowReport integrates differential expression, pathway enrichment, regulatory networks and cell communication into a reproducible workflow for compar...

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journals.plos.org /2 weeks ago

Omics data discovery agents: Agent-supported retrieval, reanalysis, and synthesis of published omics data

by Alexandre Hutton, Jesse G. Meyer The biomedical literature contains a vast collection of omics studies, yet most published data remain functionally inaccessible for computation...

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rna-seqblog.com /1 month ago

An end-to-end computational framework for “Record-seq” transcriptional recording data

A new framework adapts RNA sequencing analysis for Record-seq, improving spacer extraction, transcription-unit quantification, normalization, differential expression, and modeling...

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rna-seqblog.com /6 days ago

RNAmel simplifies RNA sequencing data analysis with a reproducible, integrated platform

RNAmel integrates RNA sequencing data analysis, gene expression profiling, pathway enrichment and visualization into a reproducible platform that simplifies...

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journals.plos.org /1 month ago

PanDelos-plus: A parallel algorithm for computing sequence homology in pangenomic analysis

by Simone Colli, Emiliano Maresi, Vincenzo Bonnici The identification of homologous gene families across multiple genomes is a central task in bacterial pangenomics traditionally...

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r-bloggers.com /1 month ago

Research Workflows

I’m teaching MPTC again this semester and have been developing a few workflow slides. Here’s a popular one. The Scientific Process. Now if you’ll excuse me there’s a ma...

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journals.plos.org /1 month ago

Sequence-free landscape inference for directed evolution

by Sebastian Towers, Jessica James, Harrison Steel, Idris Kempf Directed evolution is a method for engineering biological systems or components, such as proteins, wherein desired...

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rna-seqblog.com /1 week ago

Bulk RNA-seq Analysis: A Complete Beginner’s Guide

Bulk RNA sequencing helps researchers identify gene expression patterns associated with differences in drug response, supporting biomarker discovery and personalized medicine while...

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journals.plos.org /1 month ago

Twelve quick tips for designing AI-driven HPC workflows

by Jamie J. Alnasir

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journals.plos.org /6 days ago

Computational deconvolution of drug sensitivity via single-cell–to–bulk transcriptome mapping

by Alexandre Coudray, Romain Forey, Benjamin Bejar Haro, Filipe Martins, Joana Carlevaro-Fita, Shaoline Sheppard, Sandra Eloise Offner, Gioele La Manno, Guillaume Obozinski, Didier...

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rna-seqblog.com /3 days ago

Ribosome profiling reveals shared patterns in ribosome diversity and collisions

Researchers analyzed ribosomal RNA sequencing fragments to identify shared patterns of ribosome heterogeneity and collisions, improving computational detection of changes in protei...

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journals.plos.org /1 month ago

Model Context Protocol: The unexpected catalyst of a bioinformatics interoperability revolution

by Nathan C. Sheffield

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rna-seqblog.com /2 weeks ago

DeCoRE – a computational method to resolve RNA structural heterogeneity from RNA structure probing data by direct RNA se...

Direct RNA sequencing with DeCoRE reveals alternative RNA structures and folding dynamics at single-nucleotide resolution, providing a detailed view of transcript-level structural....

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genengnews.com /1 week ago

Multiomics in 2026 and Beyond

Multiomics analysis combines data from two or more omics layers—such as genomics, transcriptomics, proteomics, and epigenomics. However, published criticisms of multiomics approach...

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journals.plos.org /1 week ago

Process bigraphs and the architecture of compositional systems biology

by Eran Agmon, Ryan K. Spangler Building multiscale biological models requires the integration of independently developed submodels, which means moving shared variables between th...

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journals.plos.org /1 week ago

From prompts to genomes: A constraint-first framework for AI-driven sequence design across life and viruses

by Adhityo Wicaksono, Arli Aditya Parikesit A constraint-first framework for future ‘prompt-to-genome’ AI across Bacteria, Archaea, Eukaryota, and viruses is proposed. Genome-scal...

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rna-seqblog.com /1 month ago

Benchmarking RNA sequencing for more accurate alternative splicing analysis

RNA sequencing benchmarking across 42 laboratories identifies data quality, sequencing depth, and bioinformatics choices that improve alternative splicing and isoform analysis...

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journals.plos.org /1 month ago

Ten quick tips for spatial transcriptomics analysis

by Nagomi Kurogi, Koki Shimbara, Tatsuya Koreeda, Koki Tsuyuzaki Spatial transcriptomics (ST) enables genome-wide gene expression profiling while retaining spatial context within...

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rna-seqblog.com /1 month ago

ExoShorkie – predicting RNA-seq coverage of exogenous genomes in yeast by transfer learning

ExoShorkie uses RNA sequencing data and transfer learning to predict expression from exogenous DNA, supporting more accurate gene-regulation models and synthetic biology...

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rna-seqblog.com /1 month ago

Lexogen Expands NGS Services with GCLP-Compliant Workflows

Lexogen’s GCLP-compliant RNA sequencing workflows support clinical research with controlled sample handling, documented processing, data integrity, bioinformatics, reporting, and t...

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rna-seqblog.com /1 month ago

A real-data approach to evaluating RNA transcript analysis methods

RNA sequencing data provide a real-world framework for comparing differential transcript usage methods across bulk, single-cell, spatial, long-read, and short-read transcriptomics....

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marktechpost.com /1 month ago

From In-Silico to Wet-Lab: Evaluating AI Protein Design Performance

In this tutorial, we analyze Anthropic’s 1,440 AI-designed protein binder dataset to benchmark 10 leading structure predictors. Discover how target identity, expression titers, and...

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journals.plos.org /2 weeks ago

DyME: An MD-based engine exploiting HTP mutagenesis for protein engineering and recognition mimicry

by Pedro M. Guillem-Gloria, Gloria Ruiz-Gómez, M. Teresa Pisabarro Protein recognition mimicry is of great interest in the field of molecular bioengineering and rational design, w...

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genengnews.com /2 days ago

Takara Bio USA, SPT Labtech Team Up to Automate NGS Library Prep Workflows

The partners are targeting NGS core labs with a combined offering that automates next-generation sequencing library prep workflows using kits from Takara Bio and SPT Labtech’s fire...

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