---
title: "Bioinformatics 2024 — papers — Elamur Research"
description: "Bioinformatics 2024 — papers: 1 paper in the Elamur Research library, with our summaries, ranked by citations."
canonical: "https://research.elamur.ai/free/en/venues/bioinformatics/2024/"
---
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# 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.

[**788** works that year](#all) · [**1** work in our library](https://md.research.elamur.ai/free/en/venues/bioinformatics/2024/#works) · [**164** citations of these works](https://md.research.elamur.ai/free/en/venues/bioinformatics/2024/#works)

## 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 ↗](https://doi.org/10.1093/bioinformatics/btae416)**Kyle Swanson, Parker Walther, Jeremy Leitz et al.*372 citations*
2. **[RCSB protein Data Bank: exploring protein 3D similarities via comprehensive structural alignments ↗](https://doi.org/10.1093/bioinformatics/btae370)**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 information](https://md.research.elamur.ai/free/en/papers/jin-2023-genegpt-augmenting-large-language-models/)**Qiao Jin, Yifan Yang, Qingyu Chen et al.*174 citations · our summary*
4. **[Biomedical knowledge graph-optimized prompt generation for large language models ↗](https://doi.org/10.1093/bioinformatics/btae560)**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 models](https://md.research.elamur.ai/free/en/papers/jeong-2024-improving-medical-reasoning-through-retrieval/)**Minbyul 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 ↗](https://doi.org/10.1093/bioinformatics/btae038)**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 ↗](https://doi.org/10.1093/bioinformatics/btae029)**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 ↗](https://doi.org/10.1093/bioinformatics/btae104)**John Harry Caufield, Harshad Hegde, Vincent Emonet et al.*120 citations*
9. **[DAVID Ortholog: an integrative tool to enhance functional analysis through orthologs ↗](https://doi.org/10.1093/bioinformatics/btae615)**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 ↗](https://doi.org/10.1093/bioinformatics/btae353)**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 ↗](https://doi.org/10.1093/bioinformatics/btae416)**Kyle Swanson, Parker Walther, Jeremy Leitz et al.*372 citations*
2. **[RCSB protein Data Bank: exploring protein 3D similarities via comprehensive structural alignments ↗](https://doi.org/10.1093/bioinformatics/btae370)**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 information](https://md.research.elamur.ai/free/en/papers/jin-2023-genegpt-augmenting-large-language-models/)**Qiao Jin, Yifan Yang, Qingyu Chen et al.*174 citations · our summary*
4. **[Biomedical knowledge graph-optimized prompt generation for large language models ↗](https://doi.org/10.1093/bioinformatics/btae560)**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 models](https://md.research.elamur.ai/free/en/papers/jeong-2024-improving-medical-reasoning-through-retrieval/)**Minbyul 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 ↗](https://doi.org/10.1093/bioinformatics/btae038)**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 ↗](https://doi.org/10.1093/bioinformatics/btae029)**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 ↗](https://doi.org/10.1093/bioinformatics/btae104)**John Harry Caufield, Harshad Hegde, Vincent Emonet et al.*120 citations*
9. **[DAVID Ortholog: an integrative tool to enhance functional analysis through orthologs ↗](https://doi.org/10.1093/bioinformatics/btae615)**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 ↗](https://doi.org/10.1093/bioinformatics/btae353)**Nicholas Matsumoto, Jay Moran, Hyun‐Jun Choi et al.*108 citations*
11. **[selscan 2.0: scanning for sweeps in unphased data ↗](https://doi.org/10.1093/bioinformatics/btae006)**Zachary A. Szpiech*106 citations*
12. **[Parsnp 2.0: scalable core-genome alignment for massive microbial datasets ↗](https://doi.org/10.1093/bioinformatics/btae311)**Bryce L. Kille, Michael Nute, Victor Huang et al.*105 citations*
13. **[Advancing entity recognition in biomedicine via instruction tuning of large language models ↗](https://doi.org/10.1093/bioinformatics/btae163)**Vipina K. Keloth, Yan Hu, Qianqian Xie et al.*104 citations*
14. **[Bin2cell reconstructs cells from high resolution Visium HD data ↗](https://doi.org/10.1093/bioinformatics/btae546)**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 ↗](https://doi.org/10.1093/bioinformatics/btae586)**Claudio Mirabello, Björn Wallner*95 citations*
16. **[DeepAVP-TPPred: identification of antiviral peptides using transformed image-based localized descriptors and binary tree growth algorithm ↗](https://doi.org/10.1093/bioinformatics/btae305)**Matee Ullah, Shahid Akbar, Ali Raza et al.*74 citations*
17. **[Predicting the subcellular location of prokaryotic proteins with DeepLocPro ↗](https://doi.org/10.1093/bioinformatics/btae677)**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 ↗](https://doi.org/10.1093/bioinformatics/btae175)**Martin Hölzer*72 citations*
19. **[Addressing the antibody germline bias and its effect on language models for improved antibody design ↗](https://doi.org/10.1093/bioinformatics/btae618)**Tobias Hegelund Olsen, Iain H. Moal, Charlotte Mary Deane*67 citations*
20. **[lefser: implementation of metagenomic biomarker discovery tool, LEfSe, in R ↗](https://doi.org/10.1093/bioinformatics/btae707)**Asya Khleborodova, Samuel David Gamboa-Tuz, Marcel Ramos et al.*66 citations*
21. **[TemStaPro: protein thermostability prediction using sequence representations from protein language models ↗](https://doi.org/10.1093/bioinformatics/btae157)**Ieva Pudžiuvelytė, Kliment Olechnovič, Eglė Godliauskaitė et al.*65 citations*
22. **[DTI-LM: language model powered drug–target interaction prediction ↗](https://doi.org/10.1093/bioinformatics/btae533)**Khandakar Tanvir Ahmed, Md. Istiaq Ansari, Wei Zhang*62 citations*
23. **[ModDotPlot—rapid and interactive visualization of tandem repeats ↗](https://doi.org/10.1093/bioinformatics/btae493)**Alexander P. Sweeten, Michael C. Schatz, Adam M. Phillippy*62 citations*
24. **[iNGNN-DTI: prediction of drug–target interaction with interpretable nested graph neural network and pretrained molecule models ↗](https://doi.org/10.1093/bioinformatics/btae135)**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 ↗](https://doi.org/10.1093/bioinformatics/btae084)**Jun Xue, Bingyi Wang, Hongchao Ji et al.*56 citations*

[See all 788 papers in Bioinformatics 2024 — papers →](https://md.research.elamur.ai/free/en/venues/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 Models](https://md.research.elamur.ai/free/en/papers/jeong-2024-improving-medical-reasoning-through-retrieval/) [Bioinformatics](https://md.research.elamur.ai/free/en/venues/bioinformatics/)**Minbyul 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)](https://md.research.elamur.ai/free/en/topics/reasoning/) · [Information retrieval & search (1)](https://md.research.elamur.ai/free/en/topics/information-retrieval/)

## Fields

[Arts and Humanities (1)](https://md.research.elamur.ai/free/en/shelves/arts-and-humanities/) · [Computer Science (1)](https://md.research.elamur.ai/free/en/shelves/computer-science/) · [Medicine (1)](https://md.research.elamur.ai/free/en/shelves/medicine/)

## Top authors

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

[🧑‍🔬**Jaewoo Kang**1 work here · 164 citations](https://md.research.elamur.ai/free/en/authors/jaewoo-kang/) · [🧑‍🔬**Jiwoong Sohn**1 work here · 164 citations](https://md.research.elamur.ai/free/en/authors/jiwoong-sohn/) · [🧑‍🔬**Minbyul Jeong**1 work here · 164 citations](https://md.research.elamur.ai/free/en/authors/minbyul-jeong/) · [🧑‍🔬**Mujeen Sung**1 work here · 164 citations](https://md.research.elamur.ai/free/en/authors/mujeen-sung/)

## Top institutions

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

[🎓**Korea University** Seoul · South Korea 1 work here](https://md.research.elamur.ai/free/en/universities/korea-university/) · [🎓**Kyung Hee University** Seoul · South Korea 1 work here](https://md.research.elamur.ai/free/en/universities/kyung-hee-university/)

works and citations from OpenAlex and our library.

- [← previous Bioinformatics 2023](https://md.research.elamur.ai/free/en/venues/bioinformatics/2023/)
- [↑ back to Bioinformatics](https://md.research.elamur.ai/free/en/venues/bioinformatics/)