📰 Bioinformatics 2024 — papers

The works of Bioinformatics published in 2024 that our library holds (publisher: Oxford University Press): 1 work, listed below with the most cited first; each has a page with our summary, its key points and its references.

Most cited papers

By their OpenAlex citations; a paper with our summary links to its page here, the others to the original.

1. ADMET-AI: a machine learning ADMET platform for evaluation of large-scale chemical libraries ↗Kyle Swanson, Parker Walther, Jeremy Leitz et al.372 citations
2. RCSB protein Data Bank: exploring protein 3D similarities via comprehensive structural alignments ↗Sebastian Bittrich, Joan Segura, José M. Duarte et al.211 citations
3. GeneGPT: augmenting large language models with domain tools for improved access to biomedical informationQiao Jin, Yifan Yang, Qingyu Chen et al.174 citations · our summary
4. Biomedical knowledge graph-optimized prompt generation for large language models ↗Karthik Soman, Peter W. Rose, John H Morris et al.136 citations
5. Improving medical reasoning through retrieval and self-reflection with retrieval-augmented large language modelsMinbyul Jeong, Jiwoong Sohn, Mujeen Sung et al.131 citations · our summary
6. BCFtools/liftover: an accurate and comprehensive tool to convert genetic variants across genome assemblies ↗Giulio Genovese, Nicole B. Rockweiler, Bryan R. Gorman et al.120 citations
7. Conumee 2.0: enhanced copy-number variation analysis from DNA methylation arrays for humans and mice ↗Bjarne Daenekas, Eilís Pérez, Fabio Boniolo et al.120 citations
8. Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning ↗John Harry Caufield, Harshad Hegde, Vincent Emonet et al.120 citations
9. DAVID Ortholog: an integrative tool to enhance functional analysis through orthologs ↗Brad T. Sherman, Ganesh Prabhakar Panzade, Tomozumi Imamichi et al.110 citations
10. KRAGEN: a knowledge graph-enhanced RAG framework for biomedical problem solving using large language models ↗Nicholas Matsumoto, Jay Moran, Hyun‐Jun Choi et al.108 citations

All works of the year (788)

The most cited first; 1 with our summary link to their page here, the others to the original.

1. ADMET-AI: a machine learning ADMET platform for evaluation of large-scale chemical libraries ↗Kyle Swanson, Parker Walther, Jeremy Leitz et al.372 citations
2. RCSB protein Data Bank: exploring protein 3D similarities via comprehensive structural alignments ↗Sebastian Bittrich, Joan Segura, José M. Duarte et al.211 citations
3. GeneGPT: augmenting large language models with domain tools for improved access to biomedical informationQiao Jin, Yifan Yang, Qingyu Chen et al.174 citations · our summary
4. Biomedical knowledge graph-optimized prompt generation for large language models ↗Karthik Soman, Peter W. Rose, John H Morris et al.136 citations
5. Improving medical reasoning through retrieval and self-reflection with retrieval-augmented large language modelsMinbyul Jeong, Jiwoong Sohn, Mujeen Sung et al.131 citations · our summary
6. BCFtools/liftover: an accurate and comprehensive tool to convert genetic variants across genome assemblies ↗Giulio Genovese, Nicole B. Rockweiler, Bryan R. Gorman et al.120 citations
7. Conumee 2.0: enhanced copy-number variation analysis from DNA methylation arrays for humans and mice ↗Bjarne Daenekas, Eilís Pérez, Fabio Boniolo et al.120 citations
8. Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning ↗John Harry Caufield, Harshad Hegde, Vincent Emonet et al.120 citations
9. DAVID Ortholog: an integrative tool to enhance functional analysis through orthologs ↗Brad T. Sherman, Ganesh Prabhakar Panzade, Tomozumi Imamichi et al.110 citations
10. KRAGEN: a knowledge graph-enhanced RAG framework for biomedical problem solving using large language models ↗Nicholas Matsumoto, Jay Moran, Hyun‐Jun Choi et al.108 citations
11. selscan 2.0: scanning for sweeps in unphased data ↗Zachary A. Szpiech106 citations
12. Parsnp 2.0: scalable core-genome alignment for massive microbial datasets ↗Bryce L. Kille, Michael Nute, Victor Huang et al.105 citations
13. Advancing entity recognition in biomedicine via instruction tuning of large language models ↗Vipina K. Keloth, Yan Hu, Qianqian Xie et al.104 citations
14. Bin2cell reconstructs cells from high resolution Visium HD data ↗Krzysztof Polański, Raquel Bartolomé-Casado, Ioannis Sarropoulos et al.100 citations
15. DockQ v2: improved automatic quality measure for protein multimers, nucleic acids, and small molecules ↗Claudio Mirabello, Björn Wallner95 citations
16. DeepAVP-TPPred: identification of antiviral peptides using transformed image-based localized descriptors and binary tree growth algorithm ↗Matee Ullah, Shahid Akbar, Ali Raza et al.74 citations
17. Predicting the subcellular location of prokaryotic proteins with DeepLocPro ↗Jaime Moreno, Henrik Nielsen, Ole Winther et al.74 citations
18. POCP-nf: an automatic Nextflow pipeline for calculating the percentage of conserved proteins in bacterial taxonomy ↗Martin Hölzer72 citations
19. Addressing the antibody germline bias and its effect on language models for improved antibody design ↗Tobias Hegelund Olsen, Iain H. Moal, Charlotte Mary Deane67 citations
20. lefser: implementation of metagenomic biomarker discovery tool, LEfSe, in R ↗Asya Khleborodova, Samuel David Gamboa-Tuz, Marcel Ramos et al.66 citations
21. TemStaPro: protein thermostability prediction using sequence representations from protein language models ↗Ieva Pudžiuvelytė, Kliment Olechnovič, Eglė Godliauskaitė et al.65 citations
22. DTI-LM: language model powered drug–target interaction prediction ↗Khandakar Tanvir Ahmed, Md. Istiaq Ansari, Wei Zhang62 citations
23. ModDotPlot—rapid and interactive visualization of tandem repeats ↗Alexander P. Sweeten, Michael C. Schatz, Adam M. Phillippy62 citations
24. iNGNN-DTI: prediction of drug–target interaction with interpretable nested graph neural network and pretrained molecule models ↗Yan Sun, Yan Yi Li, Carson Kai-Sang Leung et al.59 citations
25. RT-Transformer: retention time prediction for metabolite annotation to assist in metabolite identification ↗Jun Xue, Bingyi Wang, Hongchao Ji et al.56 citations

See all 788 papers in Bioinformatics 2024 — papers →

📄 Works with our summary in our library (1)

The most cited first (OpenAlex citations plus our library's).

1. Improving Medical Reasoning through Retrieval and Self-Reflection with Retrieval-Augmented Large Language ModelsBioinformaticsMinbyul Jeong, Jiwoong Sohn, Mujeen Sung, et al.2024 · 164 citations

🧭 Top topics

Topics of its works in our library, with the number of works on each.

🧮Reasoning (1)🔍Information retrieval & search (1)

📚 Fields

🎭Arts and Humanities (1)🖥️Computer Science (1)🩺Medicine (1)

🧑‍🔬 Top authors

Authors with a page who published here most often: their works here, and the citations of those works.

🏛️ Top institutions

Institutions on the bylines of its works here, by the number of works.

🎓Korea UniversitySeoul · South Korea1 work here🎓Kyung Hee UniversitySeoul · South Korea1 work here

works and citations from OpenAlex and our library.

↑ back to top

This page in Markdown → https://md.research.elamur.ai/free/en/venues/bioinformatics/2024/