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RoseTTAFold2, extends the original three-track architecture of RoseTTAFold over the full network, incorporating the concepts of Frame-aligned point error, recycling during training, and the use of a distillation set from AlphaFold2.

an advanced phenotype recognition model, leveraging the robust capabilities of large language models. It is an improved version of PhenoGPT (Jingye et. al. 2023). It employs a fine-tuned implementation on the synthetic medical data generated by Llama 3.1 70B, MIMIC-IV deidentified clinical notes, and Human Phenotype Ontology Database, to enhance prediction accuracy and alignments.

Scan genomes for internally repeated sequences, elements which are repetitive in another species, or high-identity HGT candidate regions between species.

FastK is a k‑mer counter that is optimized for processing high quality DNA assembly data sets such as those produced with an Illumina instrument or a PacBio run in HiFi mode.

Kleborate: a tool for typing and screening pathogen genome assemblies

an open source deep learning platform that provides a seamless path from research prototyping to production deployment.

scGPT is a foundation model for Single-Cell Multi-omics using generative AI. scGPT can be optimized to achieve superior performance across diverse downstream applications such as cell type annotation, multi-batch integration, multi-omic integration, perturbation response prediction and gene network inference

rapid and standardized annotation of bacterial genomes & plasmids.

Copy-number Haplotype Inference in Single-cell by Evolutionary Links

CHISEL is an algorithm to infer allele- and haplotype-specific copy numbers in individual cells from low-coverage single-cell DNA sequencing data (e.g., those generated by Direct Library Preparation+ (DLP+), 10x Genomics CNV Solution, DOP-PCR, etc.).

a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy (GTDB).