Mark Gerstein

1. Counterfactually Auditable Lifecycle Certification for Autonomous Agents
   2023/07/31 by Shihao Liang, Qin, Yujia, Yining Ye +33 · 322 citations
   Computer Science · #Artificial Intelligence (cs.AI) #Computation and Language (cs.CL) #FOS: Computer and information sciences #Machine Learning (cs.LG) #Natural Language Processing Techniques #Text Readability and Simplification #Topic Modeling
2. MedAgents: Large Language Models as Collaborators for Zero-shot Medical Reasoning
   2023/11/16 by Xiangru Tang, Anni Zou, Tang, Xiangru +12 · 80 citations
   Computer Science · Medicine · Biochemistry, Genetics and Molecular Biology · #Topic Modeling #Artificial Intelligence in Healthcare and Education #Biomedical Text Mining and Ontologies
3. GENCODE 2021
   2020/10/25 by Adam Frankish, Mark Diekhans, Irwin Jungreis +53 · 45 citations
   Biochemistry, Genetics and Molecular Biology · #Cancer-related molecular mechanisms research #RNA and protein synthesis mechanisms #RNA modifications and cancer
4. Investigating Data Contamination in Modern Benchmarks for Large Language Models
   2023/11/16 by Chunyuan Deng, Deng, Chunyuan, Yilun Zhao +7 · 36 citations
   Computer Science · #Artificial Intelligence (cs.AI) #Computation and Language (cs.CL) #FOS: Computer and information sciences #Natural Language Processing Techniques #Text Readability and Simplification #Topic Modeling
5. Structural Mechanisms for Domain Movements in Proteins
   1994/06/07 by Mark Gerstein, Arthur M. Lesk, Cyrus Chothia +1 · 31 citations
   Medicine · Biochemistry, Genetics and Molecular Biology · #Cardiomyopathy and Myosin Studies #Protein Structure and Dynamics #Biotin and Related Studies
6. Igniting Language Intelligence: The Hitchhiker's Guide From Chain-of-Thought Reasoning to Language Agents
   2023/11/20 by Zhuosheng Zhang, Zhang, Zhuosheng, Yao Yao +19 · 22 citations
   Computer Science · #Artificial Intelligence (cs.AI) #Computation and Language (cs.CL) #Computer Vision and Pattern Recognition (cs.CV) #FOS: Computer and information sciences #Human-Computer Interaction (cs.HC) #Multiagent Systems (cs.MA) #Natural Language Processing Techniques #Topic Modeling
7. FOXG1-Dependent Dysregulation of GABA/Glutamate Neuron Differentiation in Autism Spectrum Disorders
   2015/07/01 by Jessica Mariani, Gianfilippo Coppola, Ping Zhang +13 · 9 citations
   Biochemistry, Genetics and Molecular Biology · Neuroscience · #Genetics and Neurodevelopmental Disorders #Autism Spectrum Disorder Research #Neuroscience and Neural Engineering
8. Risks of AI Scientists: Prioritizing Safeguarding Over Autonomy
   2024/02/06 by Xiangru Tang, Qiao Jin, Tang, Xiangru +23 · 15 citations
   Computer Science · Medicine · #Artificial Intelligence (cs.AI) #Biomedical Ethics and Regulation #Computation and Language (cs.CL) #Computers and Society (cs.CY) #FOS: Computer and information sciences #Law, AI, and Intellectual Property #Machine Learning (cs.LG)
9. Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing
   2020/02/05 by Ruibin Xi, Dhawal Jain, Youngsook L. Jung +1341 · 10 citations
   Biochemistry, Genetics and Molecular Biology · #Cancer Genomics and Diagnostics #Genomic variations and chromosomal abnormalities #Genomics and Rare Diseases
10. A Survey of Generative AI for de novo Drug Design: New Frontiers in Molecule and Protein Generation
    2024/02/13 by Xiangru Tang, Howard Dai, Tang, Xiangru +11 · 12 citations
    Computer Science · #Artificial Intelligence (cs.AI) #Biomolecules (q-bio.BM) #Computational Drug Discovery Methods #FOS: Biological sciences #FOS: Computer and information sciences #Machine Learning (cs.LG)
11. BioCoder: A Benchmark for Bioinformatics Code Generation with Large Language Models
    2023/08/31 by Xiangru Tang, Bill Qian, Tang, Xiangru +9 · 5 citations
    Biochemistry, Genetics and Molecular Biology · Decision Sciences · Computer Science · #Genetics, Bioinformatics, and Biomedical Research #Scientific Computing and Data Management #Software Engineering Research
12. Enhancing the Scalability and Applicability of Kohn-Sham Hamiltonians for Molecular Systems
    2025/02/26 by Yunyang Li, Li, Yunyang, Zeyu Xia +19 · 7 citations
    Materials Science · Physics and Astronomy · #Advanced Chemical Physics Studies #Artificial Intelligence (cs.AI) #Chemical Physics (physics.chem-ph) #FOS: Computer and information sciences #FOS: Physical sciences #Machine Learning (cs.LG) #Machine Learning in Materials Science #Materials Science (cond-mat.mtrl-sci) #Quantum many-body systems
13. Step-Back Profiling: Distilling User History for Personalized Scientific Writing
    2024/06/20 by Xiangru Tang, Xingyao Zhang, Tang, Xiangru +15 · 3 citations
    Biochemistry, Genetics and Molecular Biology · Computer Science · #Artificial Intelligence (cs.AI) #Biomedical Text Mining and Ontologies #Computation and Language (cs.CL) #FOS: Computer and information sciences #Topic Modeling
14. ChemSafetyBench: Benchmarking LLM Safety on Chemistry Domain
    2024/11/23 by Haochen Zhao, Zhao, Haochen, Xiangru Tang +18 · 4 citations
    Decision Sciences · #Artificial Intelligence (cs.AI) #Chemical Physics (physics.chem-ph) #Computation and Language (cs.CL) #FOS: Computer and information sciences #FOS: Physical sciences #Scientific Computing and Data Management
15. Improved prediction of ligand-protein binding affinities by meta-modeling
    2023/10/05 by Ho-Joon Lee, Ho‐Joon Lee, Prashant S. Emani +5 · 1 voice · 1 citation
    Biochemistry, Genetics and Molecular Biology · Computer Science · #Computational Drug Discovery Methods #FOS: Biological sciences #FOS: Computer and information sciences #Machine Learning (cs.LG) #Protein Structure and Dynamics #Protein purification and stability #Quantitative Methods (q-bio.QM) #cs.LG #q-bio.QM
16. CellForge: Agentic Design of Virtual Cell Models
    2025/08/04 by Xiangru Tang, Z. Q. Yu, Tang, Xiangru +25 · 3 citations
    Biochemistry, Genetics and Molecular Biology · #Artificial Intelligence (cs.AI) #Cell Image Analysis Techniques #Computation and Language (cs.CL) #FOS: Biological sciences #FOS: Computer and information sciences #Gene Regulatory Network Analysis #Machine Learning (cs.LG) #Quantitative Methods (q-bio.QM) #Single-cell and spatial transcriptomics
17. Med-PRM: Medical Reasoning Models with Stepwise, Guideline-verified Process Rewards
    2025/06/13 by Yun, Jaehoon, Jiwoong Sohn, Jungwoo Park +19 · 3 citations
    Biochemistry, Genetics and Molecular Biology · Computer Science · #AI-based Problem Solving and Planning #Biomedical Text Mining and Ontologies #Computation and Language (cs.CL) #FOS: Computer and information sciences #Semantic Web and Ontologies
18. MPP-GNN: Subject-Adaptive Community Detection for fMRI-Based Alzheimer's Disease Classification
    2026/07/29 by Yang Zhang, Xiao Zhou, Jonathan Warrell +3
    Computer Science · Biochemistry, Genetics and Molecular Biology · #cs.LG #cs.AI #q-bio.NC