Advancing admixture graph estimation via maximum likelihood network orientation.

APAtizer: a tool for alternative polyadenylation analysis of RNA-Seq data.

Spatial mutual nearest neighbors for spatial transcriptomics data.

ReAlign-P: A vertical iterative realignment method for protein multiple sequence alignment.

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022.

RPS 2.0: an updated database of RNAs involved in liquid–liquid phase separation

RM2Target: a comprehensive database for targets of writers, erasers and readers of RNA modifications

3DSNP 2.0: update and expansion of the noncoding genomic variant annotation database

Supervised analysis of alternative polyadenylation from single-cell and spatial transcriptomics data with spvAPA.

HiCDiff: single-cell Hi-C data denoising with diffusion models.

CACIMAR: cross-species analysis of cell identities, markers, regulations, and interactions using single-cell RNA sequencing data.

Spatiotemporal constrained RNA-protein heterogeneous network for protein complex identification.

Soft graph clustering for single-cell RNA sequencing data.

Searchlight: automated bulk RNA-seq exploration and visualisation using dynamically generated R scripts

CHIPIN: ChIP-seq inter-sample normalization based on signal invariance across transcriptionally constant genes

NOREC4DNA: using near-optimal rateless erasure codes for DNA storage

COLOR: A Compositional Linear Operation-Based Representation of Protein Sequences for Identification of Monomer Contributions to Properties.

Unraveling Disease-Associated PIWI-Interacting RNAs with a Contrastive Learning Methods.

TransABseq: A Two-Stage Approach for Predicting Antigen-Antibody Binding Affinity Changes upon Mutation Based on Protein Sequences.

Creating Coarse-Grained Systems with COBY: Toward Higher Accuracy of Complex Biological Systems.

Direct profiling of non-adenosines in poly(A) tails of endogenous and therapeutic mRNAs with Ninetails.

scPriorGraph: constructing biosemantic cell-cell graphs with prior gene set selection for cell type identification from scRNA-seq data.

Mining alternative splicing patterns in scRNA-seq data using scASfind.

SonicParanoid2: fast, accurate, and comprehensive orthology inference with machine learning and language models.

Splam: a deep-learning-based splice site predictor that improves spliced alignments.

A robust tool for the prediction of multiple lipid modification sites

MUNDO: protein function prediction embedded in a multispecies world.

cblaster: a remote search tool for rapid identification and visualization of homologous gene clusters.

Secondary structure assignment of proteins in the absence of sequence information.

Cutevariant: a standalone GUI-based desktop application to explore genetic variations from an annotated VCF file.

EnzymeML is a free and open standard based XML markup interchange format for enzyme kinetics.

Sequence-based modeling of single-cell ATAC-seq using convolutional neural networks.

Omnipose is a general image segmentation tool that builds on Cellpose in a number of ways described in our paper. It works for both 2D and 3D images and on any imaging modality or cell shape, so long as you train it on representative images.

Light-directed in situ barcoding of biomolecules in fixed cells and tissues for spatially indexed sequencing.