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journals.plos.org /4 weeks ago

A spectral framework for measuring diversity in multiple sequence alignments

by Vaitea Opuu Machine learning (ML) methods for proteins and RNAs rely on multiple sequence alignments (MSAs) and related datasets such as experimental mutagenesis libraries, yet...

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rna-seqblog.com /1 month ago

Ultrafast and reference-free sequence discovery in single-cell data

Malva enables ultrafast, reference-free searches across massive single-cell RNA sequencing datasets for mutations, splice junctions, pathogens, transcripts, and other sequence-leve...

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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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journals.plos.org /1 month ago

Direct microhaplotype genotyping for GT-seq (Genotyping-in-Thousands by Sequencing) using a diploid abundance model

by Nathan R. Campbell, Amanda R. Campbell, Shannon K. Blair, Amanda J. Finger GT-seq (Genotyping-in-Thousands by Sequencing) is widely used for high-throughput amplicon genotyping...

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rna-seqblog.com /2 weeks ago

Tracing 700 million years of cell evolution

RNA sequencing combined with AI helps Unify compare cell types across distant species by identifying shared biological functions even when individual genes no longer directly...

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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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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 /1 month ago

Detection and sequencing of Ap2N-capped RNAs in human cells

RNA sequencing identifies newly characterized Ap2N caps on human RNAs, including tRNA-derived fragments, revealing additional complexity in RNA processing and responses to oxidativ...

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journals.plos.org /1 month ago

From sequences to strategies: Early detection of new SARS-CoV-2 variants via genetic distance to reduce hospitalizations

by Marika D’Avanzo, Aung Pone Myint, Giacomo Cacciapaglia, Stefan Hohenegger, Francesco Conventi, Marta Nunes The COVID-19 pandemic highlighted the critical need for robust method...

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rna-seqblog.com /1 week ago

RiboBA improves detection of hidden protein-coding regions using ribosome profiling

RiboBA improves ribosome profiling and RNA sequencing analysis by correcting experimental biases, enabling more accurate identification of hidden protein-coding regions and transla...

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journals.plos.org /2 weeks ago

DeCTCF: Decoding CTCF binding sequences by leveraging predicted epigenomic features

by Lu Chai, Jie Gao, Tinghe Guo, Teer Ba, Zihan Li, Junjie Liu, Yong Wang, Lirong Zhang CTCF is a key architectural protein with diverse roles in genome organization and gene regu...

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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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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 /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 /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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phys.org /1 month ago

Uniting sequence and structure to map the protein universe across billions of years of evolution

An international team of researchers, including those at the Earth-Life Science Institute (ELSI) at the Institute of Science Tokyo, has developed a protein language model that brin...

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bioengineer.org /2 weeks ago

AI Reads Protein Sequences to Find Domain Boundaries Without Any Structural Data

A new machine learning framework called Seq2DomML predicts residue-level protein domain boundaries in bacterial proteins directly from sequence, outperforming established annotatio...

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marktechpost.com /1 month ago

Google DeepMind Releases AlphaGenome Atlas With Precomputed Molecular Effect Predictions and AVI Scores for 9 Billion Hu...

DeepMind's AlphaGenome Atlas maps every single-letter change in the human genome with 1 impact score per variant. The post Google DeepMind Releases AlphaGenome Atlas With Precomput...

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journals.plos.org /1 week ago

DipSkmer: Reference-free population genomics with diploid genome skims

by Eduardo Charvel, Homère J. Alves Monteiro, Siavash Mirarab, Vineet Bafna Ecologists and conservation biologists rely on genetic diversity as a key essential biodiversity variab...

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journals.plos.org /1 month ago

Balanced DNA interpolation improves learning of genetic distance-informed embeddings in plants

by Lara M. Kösters, Kevin Karbstein, Ladislav Hodač, Laura Albreht, Elvira Sahuquillo Balbuena, Daniel Botello, Olivier Hardy, Phebian Odufuwa, Eva Pardo Otero, Aireen Phang, Manue...

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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 /3 weeks ago

Fast structural search for classification of gut bacterial mucin O-glycan degrading enzymes

by Mert Erden, Tyler Schult, Karin Yanagi, Jugal Kishore Sahoo, David L. Kaplan, Lenore J. Cowen, Kyongbum Lee The Enzyme Commission (EC) numbering scheme provides a hierarchical...

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rna-seqblog.com /4 weeks ago

Single-cell TimeLapse-seq reveals MTA is an essential retrotransposon

Very early in development, an embryo must begin using its own genome instead of relying only on RNA and proteins inherited from the egg. This transition is known as zygotic genome...

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rna-seqblog.com /4 weeks ago

RNA variant imaging for cancer diagnosis

RNA Variant Imaging is attracting attention because it addresses a persistent blind spot in cancer diagnostics: many clinically relevant RNA isoforms, splice events, and fusion tra...

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