sequence-to-function modeling

Exploring the Design Space of 310-helical Bundles using Non-canonical Amino Acids

This paper explores sequence constraints for de novo 310-helical bundles by mutating key residues in a designed peptide and assessing stability and functionality.

Human-specific CCG-repeat insertion in the RBFOX1 promoter implicated in autism and speech enhances EGR1-responsive activity

A human-specific CCG insertion in the RBFOX1 promoter boosts EGR1-driven reporter activity in HEK293T cells, as does an autism-linked CCG-gaining duplication in PTCHD1.

Coevolutionary mining of prokaryotic non-coding elements with a genome language model

Minerva extracts RNA base-pairing, protein-contact and repeat maps from a genome language model without alignments, flagging unannotated structured loci and a phage ncRNA array reverse-transcribed into short cDNAs.

Multi-attribute characterisation of mRNA via MazF endoribonuclease and LC-MS workflows

The paper presents two LC-MS workflows using MazF endoribonuclease to characterise mRNA sequence identity, 5' capping efficiency, and poly(A) tail length and heterogeneity.

Lossless compression of protein databases for efficient and accurate metagenomic sequence classification with Centrifuger

The paper introduces a lossless compression algorithm for protein databases, improving memory efficiency and classification accuracy in Centrifuger for metagenomic analysis.

A foundation model learns the sequence and functional grammar of fully human heavy-chain-only antibodies

The paper develops a foundation model trained on fully human heavy-chain-only antibodies, showing it captures sequence and functional constraints distinct from conventional antibody models.

OligoSeq: Rapid nanopore-sequencing of single-stranded oligonucleotides

OligoSeq enables accurate sequencing of single-stranded oligonucleotides using nanopore technology, offering a cost-effective alternative for quality control in oligonucleotide synthesis.

A multi-tissue epigenomic atlas links the sheep non-coding genome to domestication and complex traits

SheepEpimap combines 516 histone CUT&Tag, ATAC-seq and RNA-seq datasets from 43 sheep tissues to annotate 2.93 million cis-regulatory elements and 145,407 allele-specific variants for trait interpretation.

Multiplexed sequence-resolved screening of transient DNA hybridization for programmable nanotechnology

The paper introduces SPARXS-Hyb, a method for multiplexed screening of DNA hybridization kinetics, identifying sequences with improved performance in DNA-PAINT.

Functional pocketomes and complete allosteric maps of five protein kinases

Energy-model maps of five human kinases show conserved distance-dependent decay of inhibitory allostery, but distal allosteric pockets and activating sites diverge between kinases.

BioReason-Pro: Advancing Protein Function Prediction with Multimodal Biological Reasoning

A reasoning LLM combining ESM3 embeddings with GO-GPT term predictions produces protein function annotations that experts rated tie-or-better than UniProt in 79% of cases (SFT model).

Replaying germinal center evolution on a quantified affinity landscape

Across 119 monoclonal germinal centers, B cell affinity rises reliably despite divergent phylogenies. Selection is noisy but persistent; mutability limits exploration. A DMS-based landscape shows saturating fitness and survivorship biases.

Deep Proteoform Sequencing with Top-Down Direct Mass Technology

This paper introduces a top-down mass spectrometry workflow with DMTm technology and a new software platform to achieve deeper proteoform sequencing and improved sequence coverage.

Functional Profiling of Thousands of Sequence-Diverse Protease Homologs with GROQ-seq

The paper uses GROQ-seq to profile function across a diverse protease library, showing robust activity across sequence divergence.

PARAS: high-accuracy machine-learning of substrate specificities in nonribosomal peptide synthetases

Random forest predictors PARAS and PARASECT, trained on 3,653 curated adenylation domains, outperform earlier NRPS substrate predictors and correctly assigned L-Trp to an unusual tryptopeptin synthetase domain.

DefensePredictor: A Machine Learning Model to Discover Novel Prokaryotic Immune Systems

DefensePredictor combines ESM2 protein language model embeddings with genomic context features in a gradient boosting classifier to identify prokaryotic anti-phage defense genes, validating 45 previously unknown Escherichia coli systems.

AistSeq: An In-House Tn5-Based Plasmid Sequencing Platform Using A Compact Benchtop Sequencer

This paper describes an in-house Tn5-based plasmid sequencing platform called AistSeq using a compact benchtop sequencer, demonstrating a streamlined workflow for plasmid sequence verification.

HyDrop v2: Scalable atlas construction for training sequence-to-function models

The paper introduces HyDrop v2, a microfluidic system for generating large scATAC-seq atlases, and shows its data is comparable to commercial platforms for training sequence-to-function models.

NW-flex: flexible-block sequence alignment for short tandem repeats

NW-flex improves STR read alignment by allowing flexible block contraction while maintaining alignment optimality and using minimal computational overhead.

Split inteins for generating combinatorial non-ribosomal peptide libraries

This paper introduces split inteins to enable modular NRPS engineering, generating 324 hybrid NRPS and over 200 novel peptides through combinatorial transformation.

GPU-accelerated homology search with MMseqs2

The paper introduces GPU-accelerated homology search with MMseqs2, achieving faster sequence similarity detection than CPU methods and improving structure prediction speeds.

A novel NGS-compatible Enzymatic Strategy Enables Carryover Contamination Removal and Enhances Sequencing Performance.

This paper introduces a novel enzymatic strategy using 7-deaza-dGTP and Fpg to remove carryover contamination and improve sequencing performance in NGS.

Missense3D-PTMdb an interactive web resource to explore and visualize genetic variants and post-translational modifications sites (PTMs) using AlphaFold 3D models

Missense3D-PTMdb maps missense variants and PTM sites to AlphaFold 3D models to explore their structural and functional impacts.

Exploiting uniqueness: seed-chain-extend alignment on elastic founder graphs

This paper introduces a seed-chain-extend alignment workflow using elastic founder graphs to improve sequence-to-graph alignment accuracy and efficiency in pangenomics.

Nicking Loop™: An infinite amplification of single-stranded circular DNA

The paper introduces Nicking Loop, a method for converting DNA into circular single-stranded DNA for NGS, showing improved reproducibility, sensitivity, and compatibility with sequencing platforms.

Solution structure of the Z0 domain from transcription repressor BCL11A sheds light on the sequence properties of protein-binding zinc-fingers

The paper determines the solution structure of the Z0 domain of BCL11A and identifies sequence patterns distinguishing DNA-binding from non-binding zinc-fingers.

Characterization of Soybean Vein Necrosis Virus (SVNV) Proteins: Sequence Analysis of Field Strains and Comparison of Localization Patterns in Differing Cell Types

This study characterizes SVNV proteins through sequence analysis of field strains and compares their localization in plant and insect cells.

Prediction of protein biophysical traits from limited data: a case study on nanobody thermostability through NanoMelt

NanoMelt, a ridge-stacked ensemble of regressors on four diverse sequence embeddings, predicts nanobody melting temperature from 640 curated sequences, reaching Spearman 0.832 under nested cross-validation.

Leveraging ancestral sequence reconstruction for protein representation learning

This paper introduces LASE, a method using ancestral sequence reconstruction to train protein language models with higher accuracy and faster computation than large models.

A Rapid, Cost-Effective Method for High-Yield DNA Purification from PCR Products and Agarose Gels.

The paper develops a cost-effective in-house DNA purification protocol for PCR products and agarose gels, showing improved clarity and purity compared to commercial kits.