- Mikaela Koutrouli, Katerina C. Nastou, Pau Piera LĂndez, Robbin Bouwmeester, Simon Rasmussen, Lennart Martens, Lars Juhl Jensen. FAVA: high-quality functional association networks inferred from scRNA-seq and proteomics data. Bioinformatics, 40(2), February 2024.
- Kuan Xie, Yuying Hou, Xionghui Zhou. Deep centroid: a general deep cascade classifier for biomedical omics data classification. Bioinformatics, 40(2), February 2024.
- Yash Patel, Arpi Beshlikyan, Madison Jordan, Gina Kim, Aaron Holmes, Takafumi N. Yamaguchi, Paul C. Boutros. PipeVal: light-weight extensible tool for file validation. Bioinformatics, 40(2), February 2024.
- Jeffrey K. Ng, Tychele Turner. de novo variant calling for highly accurate short-read and long-read sequencing data. Bioinformatics, 40(1), January 2024.
- David Koslicki, Stephen White, Chunyu Ma, Alexei Novikov. YACHT: an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample. Bioinformatics, 40(2), February 2024.
- Qiao Jin 0001, Yifan Yang, Qingyu Chen 0001, Zhiyong Lu. GeneGPT: augmenting large language models with domain tools for improved access to biomedical information. Bioinformatics, 40(2), February 2024.
- Carson M. Andorf, Olivia C. Haley, Rita K. Hayford, John L. Portwood II, Stephen Harding, Shatabdi Sen, Ethalinda K. S. Cannon, Jack M. Gardiner, Hye Seon Kim, Margaret Woodhouse. PanEffect: a pan-genome visualization tool for variant effects in maize. Bioinformatics, 40(2), February 2024.
- Anna Sintsova, Hans-Joachim Ruscheweyh, Christopher M. Field, Lilith Feer, Bidong D. Nguyen, Benjamin Daniel, Wolf-Dietrich Hardt, Julia A. Vorholt, Shinichi Sunagawa. mBARq: a versatile and user-friendly framework for the analysis of DNA barcodes from transposon insertion libraries, knockout mutants, and isogenic strain populations. Bioinformatics, 40(2), February 2024.
- Huangqingbo Sun, Jiayi Li, Robert F. Murphy. Expanding the coverage of spatial proteomics: a machine learning approach. Bioinformatics, 40(2), February 2024.
- Lorenzo Pantolini, Gabriel Studer, Joana Pereira, Janani Durairaj, Gerardo Tauriello, Torsten Schwede. Embedding-based alignment: combining protein language models with dynamic programming alignment to detect structural similarities in the twilight-zone. Bioinformatics, 40(1), January 2024.