Evidence map›Paper›PMID 41676319›Full record

ReviewQuantitative biology (Beijing, China)2026

Large language models for bioinformatics.

Wei Ruan, Yanjun Lyu, Jing Zhang, Jiazhang Cai, Peng Shu, Yang Ge, Yao Lu, Shang Gao, Yue Wang, Peilong Wang and 45 more

Abstract readReview
PubMed Full text at PMC Publisher
In one paragraph

Review in Quantitative biology (Beijing, China), 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.

0numbers the graph read from it
0cells of the map it votes in
8citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

8 citing papers in PubMed.

  1. Review
  2. Review
  3. Article
  4. Review
  5. Large language models for bioinformatics.Quantitative biology (Beijing, China) · 2026
    Review
  6. Article
  7. Article
  8. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

55 authors.

Wei RuanSchool of Computing University of Georgia Athens Georgia USA.
Yanjun LyuDepartment of Computer Science and Engineering University of Texas at Arlington Arlington Texas USA.
Jing ZhangDepartment of Computer Science and Engineering University of Texas at Arlington Arlington Texas USA.
Jiazhang CaiDepartment of Statistics University of Georgia Athens Georgia USA.
Peng ShuSchool of Computing University of Georgia Athens Georgia USA.
Yang GeDepartment of Epidemiology and Biostatistics University of Georgia Athens Georgia USA.
Yao LuDepartment of Epidemiology and Biostatistics University of Georgia Athens Georgia USA.
Shang GaoDepartment of Biostatistics UNC Chapel Hill Chapel Hill North Carolina USA.
Yue WangSchool of Computing University of Georgia Athens Georgia USA.
Peilong WangDepartment of Radiation Oncology Mayo Clinic Phoenix Arizona USA.
Lin ZhaoSchool of Computing University of Georgia Athens Georgia USA.
Tao WangDepartment of Statistics University of Georgia Athens Georgia USA.
Yufang LiuDepartment of Statistics University of Georgia Athens Georgia USA.
Luyang FangDepartment of Statistics University of Georgia Athens Georgia USA.
Ziyu LiuDepartment of Statistics University of Georgia Athens Georgia USA.
Zhengliang LiuSchool of Computing University of Georgia Athens Georgia USA.
Yiwei LiSchool of Computing University of Georgia Athens Georgia USA.
Zihao WuSchool of Computing University of Georgia Athens Georgia USA.
Junhao ChenSchool of Computing University of Georgia Athens Georgia USA.
Hanqi JiangSchool of Computing University of Georgia Athens Georgia USA.
Yi PanSchool of Computing University of Georgia Athens Georgia USA.
Zhenyuan YangSchool of Computing University of Georgia Athens Georgia USA.
Jingyuan ChenDepartment of Radiation Oncology Mayo Clinic Phoenix Arizona USA.
Shizhe LiangInstitute of Plant Breeding, Genetics & Genomics University of Georgia Athens Georgia USA.
Wei ZhangSchool of Computer and Cyber Sciences Augusta University Augusta Georgia USA.
Terry MaSchool of Computer Science Carnegie Mellon University Pittsburgh Pennsylvania USA.
Yuan DouCollege of Engineering University of Georgia Athens Georgia USA.
Jianli ZhangCollege of Engineering University of Georgia Athens Georgia USA.
Xinyu GongCollege of Engineering University of Georgia Athens Georgia USA.
Qi GanCollege of Engineering University of Georgia Athens Georgia USA.
Yusong ZouCollege of Engineering University of Georgia Athens Georgia USA.
Zebang ChenCollege of Engineering University of Georgia Athens Georgia USA.
Yuanxin QianCollege of Engineering University of Georgia Athens Georgia USA.
Shuo YuCollege of Engineering University of Georgia Athens Georgia USA.
Jin LuSchool of Computing University of Georgia Athens Georgia USA.
Kenan SongCollege of Engineering University of Georgia Athens Georgia USA.
Xianqiao WangCollege of Engineering University of Georgia Athens Georgia USA.
Andrea SikoraDepartment of Biomedical Informatics University of Colorado Boulder Colorado USA.
Gang LiDepartment of Radiology University of North Carolina at Chapel Hill Chapel Hill North Carolina USA.
Xiang LiDepartment of Radiology Massachusetts General Hospital Harvard Medical School Boston Massachusetts USA.
Quanzheng LiDepartment of Radiology Massachusetts General Hospital Harvard Medical School Boston Massachusetts USA.
Yingfeng WangDepartment of Computer Science and Engineering University of Tennessee at Chattanooga Chattanooga Tennessee USA.
Lu ZhangDepartment of Computer Science Indiana University Indianapolis Indianapolis Indiana USA.
Yohannes AbateDepartment of Physics and Astronomy University of Georgia Athens Georgia USA.
Lifang HeDepartment of Computer Science and Engineering Lehigh University Bethlehem Pennsylvania USA.
Wenxuan ZhongDepartment of Statistics University of Georgia Athens Georgia USA.
Rongjie LiuDepartment of Statistics University of Georgia Athens Georgia USA.
Chao HuangDepartment of Epidemiology and Biostatistics University of Georgia Athens Georgia USA.
Wei LiuDepartment of Radiation Oncology Mayo Clinic Phoenix Arizona USA.
Ye ShenDepartment of Epidemiology and Biostatistics University of Georgia Athens Georgia USA.
Ping MaDepartment of Statistics University of Georgia Athens Georgia USA.
Hongtu ZhuDepartment of Biostatistics UNC Chapel Hill Chapel Hill North Carolina USA.
Yajun YanCollege of Engineering University of Georgia Athens Georgia USA.
Dajiang ZhuDepartment of Computer Science and Engineering University of Texas at Arlington Arlington Texas USA.
Tianming LiuSchool of Computing University of Georgia Athens Georgia USA.

Funding

Collaborative Research: DMS/NIGMS 2: Novel machine-learning framework for AFMscanner in DNA-protein interaction detectionR01GM152814 · NIGMS · UNIVERSITY OF GEORGIA · PI Wenxuan Zhong · 2023 to 2026
$1.2M
NIGMS NIH HHS R01 GM152814
6 · The paper itself

Abstract

With the rapid advancements in large language model technology and the emergence of bioinformatics-specific language models (BioLMs), there is a growing need for a comprehensive analysis of the current landscape, computational characteristics, and diverse applications. This survey aims to address this need by providing a thorough review of BioLMs, focusing on their evolution, classification, and distinguishing features, alongside a detailed examination of training methodologies, datasets, and evaluation frameworks. We explore the wide-ranging applications of BioLMs in critical areas such as disease diagnosis, drug discovery, and vaccine development, highlighting their impact and transformative potential in bioinformatics. We identify key challenges and limitations inherent in BioLMs, including data privacy and security concerns, interpretability issues, biases in training data and model outputs, and domain adaptation complexities. Finally, we highlight emerging trends and future directions, offering valuable insights to guide researchers and clinicians toward advancing BioLMs for increasingly sophisticated biological and clinical applications.

Indexed as

bioinformatics‐specific language modelsbiological systemsbiomedical AIlarge language modelslife active factors

Identifiers

PMID41676319
PMCPMC12806030

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.