Nexentis Subsidiary MitoCareX Bio Advances SLC Transporter Drug Discovery with Broad Analysis and International AI Initiative

MitoCareX Bio completes comprehensive SLC transport protein analysis to support discovery of small molecules for hard-to-treat cancers and inflammatory metabolic diseases and enters an AI-driven small ...

Optimizing RNA design with AI and an Ising machine: Encoding matters

RNA has emerged as one of the most promising molecules in modern medicine, enabling advances from mRNA vaccines and gene ...
IEEE

Current Trends and Ongoing Progress in the Computational Alignment of Biological Sequences

Abstract: The computational techniques for nucleic acid and protein sequence comparison reduce the extensive burden of molecular biologists. The sequence alignment is one of the main research areas in ...
GitHub

pggb: the PanGenome Graph Builder

pggb builds pangenome variation graphs from a set of input sequences. A pangenome variation graph is a kind of generic multiple sequence alignment. It lets us understand any kind of sequence variation ...
Frontiers

Advances in post-processing methods for multiple sequence alignment

The reliability of multiple sequence alignment (MSA) results directly determines the credibility of the conclusions drawn from biological research. However, MSA is inherently an NP-hard problem, ...
IEEE

BLASTP-ACC: Parallel Architecture and Hardware Accelerator Design for BLAST-Based Protein Sequence Alignment

Abstract: In this study, we design a hardware accelerator for a widely used sequence alignment algorithm, the basic local alignment search tool for proteins (BLASTP). The architecture of the proposed ...
GitHub

Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis

This script works with Python 3, it takes as input a VCF file and will use the SNP genotypes to create a matrix for phylogenetic analysis in the PHYLIP (relaxed version), FASTA, NEXUS, or binary NEXUS ...
eLife

Sensitive remote homology search by local alignment of small positional embeddings from protein language models

This important study addresses the problem of detecting weak similarity between protein sequences, a procedure commonly used to infer homology or assign putative functions to uncharacterized proteins.
acm.org

Maximum Flow Through a Network: A Storied Problem and a Groundbreaking Solution

In 2022, a team of computer scientists presented a groundbreaking algorithm for the maximum flow problem: How does one transport the most supplies from a source node to a sink node in a network while ...
acm.org

Theoretical Analysis of Edit Distance Algorithms

Edit distance—a classical problem in computer science—has received ongoing attention from both practitioners and theoreticians. Given two strings A and B, the edit distance is the minimum number of ...
C&EN

Machine Learning Guided Design of High-Affinity ACE2 Decoys for SARS-CoV-2 Neutralization

Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61081, United States Department of Bioengineering, University of Illinois ...