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@article{DBLP:journals/csur/ZhangYZTMHWGWLZ25,
author = {Zhuosheng Zhang and
Yao Yao and
Aston Zhang and
Xiangru Tang and
Xinbei Ma and
Zhiwei He and
Yiming Wang and
Mark Gerstein and
Rui Wang and
Gongshen Liu and
Hai Zhao},
title = {Igniting Language Intelligence: The Hitchhiker's Guide from Chain-of-Thought
Reasoning to Language Agents},
journal = {{ACM} Comput. Surv.},
volume = {57},
number = {8},
pages = {206:1--206:39},
year = {2025},
url = {https://doi.org/10.1145/3719341},
doi = {10.1145/3719341},
timestamp = {Sun, 06 Jul 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/csur/ZhangYZTMHWGWLZ25.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbi/NiKG25,
author = {Eric Ni and
Elizabeth Knight and
Mark Gerstein},
title = {Scalable and efficient on-chain data management in blockchain for
large biomedical data},
journal = {J. Biomed. Informatics},
volume = {165},
pages = {104818},
year = {2025},
url = {https://doi.org/10.1016/j.jbi.2025.104818},
doi = {10.1016/J.JBI.2025.104818},
timestamp = {Sat, 31 May 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jbi/NiKG25.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iclr/LiXHWHYLWZLSG25,
author = {Yunyang Li and
Zaishuo Xia and
Lin Huang and
Xinran Wei and
Samuel Harshe and
Han Yang and
Erpai Luo and
Zun Wang and
Jia Zhang and
Chang Liu and
Bin Shao and
Mark Gerstein},
title = {Enhancing the Scalability and Applicability of Kohn-Sham Hamiltonians
for Molecular Systems},
booktitle = {The Thirteenth International Conference on Learning Representations,
{ICLR} 2025, Singapore, April 24-28, 2025},
publisher = {OpenReview.net},
year = {2025},
url = {https://openreview.net/forum?id=twEvvkQqPS},
timestamp = {Thu, 15 May 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/iclr/LiXHWHYLWZLSG25.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iclr/TangHYSYOZL00CG25,
author = {Xiangru Tang and
Tianyu Hu and
Muyang Ye and
Yanjun Shao and
Xunjian Yin and
Siru Ouyang and
Wangchunshu Zhou and
Pan Lu and
Zhuosheng Zhang and
Yilun Zhao and
Arman Cohan and
Mark Gerstein},
title = {ChemAgent: Self-updating Memories in Large Language Models Improves
Chemical Reasoning},
booktitle = {The Thirteenth International Conference on Learning Representations,
{ICLR} 2025, Singapore, April 24-28, 2025},
publisher = {OpenReview.net},
year = {2025},
url = {https://openreview.net/forum?id=kuhIqeVg0e},
timestamp = {Thu, 15 May 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/iclr/TangHYSYOZL00CG25.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2501-06590,
author = {Xiangru Tang and
Tianyu Hu and
Muyang Ye and
Yanjun Shao and
Xunjian Yin and
Siru Ouyang and
Wangchunshu Zhou and
Pan Lu and
Zhuosheng Zhang and
Yilun Zhao and
Arman Cohan and
Mark Gerstein},
title = {ChemAgent: Self-updating Library in Large Language Models Improves
Chemical Reasoning},
journal = {CoRR},
volume = {abs/2501.06590},
year = {2025},
url = {https://doi.org/10.48550/arXiv.2501.06590},
doi = {10.48550/ARXIV.2501.06590},
eprinttype = {arXiv},
eprint = {2501.06590},
timestamp = {Thu, 01 May 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2501-06590.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2501-19216,
author = {Yunyang Li and
Lin Huang and
Zhihao Ding and
Chu Wang and
Xinran Wei and
Han Yang and
Zun Wang and
Chang Liu and
Yu Shi and
Peiran Jin and
Jia Zhang and
Mark Gerstein and
Tao Qin},
title = {E2Former: {A} Linear-time Efficient and Equivariant Transformer for
Scalable Molecular Modeling},
journal = {CoRR},
volume = {abs/2501.19216},
year = {2025},
url = {https://doi.org/10.48550/arXiv.2501.19216},
doi = {10.48550/ARXIV.2501.19216},
eprinttype = {arXiv},
eprint = {2501.19216},
timestamp = {Fri, 28 Feb 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2501-19216.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2502-19227,
author = {Yunyang Li and
Zaishuo Xia and
Lin Huang and
Xinran Wei and
Han Yang and
Sam Harshe and
Zun Wang and
Chang Liu and
Jia Zhang and
Bin Shao and
Mark B. Gerstein},
title = {Enhancing the Scalability and Applicability of Kohn-Sham Hamiltonians
for Molecular Systems},
journal = {CoRR},
volume = {abs/2502.19227},
year = {2025},
url = {https://doi.org/10.48550/arXiv.2502.19227},
doi = {10.48550/ARXIV.2502.19227},
eprinttype = {arXiv},
eprint = {2502.19227},
timestamp = {Mon, 07 Apr 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2502-19227.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2503-07459,
author = {Xiangru Tang and
Daniel Shao and
Jiwoong Sohn and
Jiapeng Chen and
Jiayi Zhang and
Jinyu Xiang and
Fang Wu and
Yilun Zhao and
Chenglin Wu and
Wenqi Shi and
Arman Cohan and
Mark Gerstein},
title = {MedAgentsBench: Benchmarking Thinking Models and Agent Frameworks
for Complex Medical Reasoning},
journal = {CoRR},
volume = {abs/2503.07459},
year = {2025},
url = {https://doi.org/10.48550/arXiv.2503.07459},
doi = {10.48550/ARXIV.2503.07459},
eprinttype = {arXiv},
eprint = {2503.07459},
timestamp = {Sun, 13 Apr 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2503-07459.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2505-04638,
author = {Tianyu Liu and
Simeng Han and
Xiao Luo and
Hanchen Wang and
Pan Lu and
Biqing Zhu and
Yuge Wang and
Keyi Li and
Jiapeng Chen and
Rihao Qu and
Yufeng Liu and
Xinyue Cui and
Aviv Yaish and
Yuhang Chen and
Minsheng Hao and
Chuhan Li and
Kexing Li and
Arman Cohan and
Hua Xu and
Mark Gerstein and
James Zou and
Hongyu Zhao},
title = {Towards Artificial Intelligence Research Assistant for Expert-Involved
Learning},
journal = {CoRR},
volume = {abs/2505.04638},
year = {2025},
url = {https://doi.org/10.48550/arXiv.2505.04638},
doi = {10.48550/ARXIV.2505.04638},
eprinttype = {arXiv},
eprint = {2505.04638},
timestamp = {Thu, 26 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2505-04638.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2506-11474,
author = {Jaehoon Yun and
Jiwoong Sohn and
Jungwoo Park and
Hyunjae Kim and
Xiangru Tang and
Yanjun Shao and
Yonghoe Koo and
Minhyeok Ko and
Qingyu Chen and
Mark Gerstein and
Michael Moor and
Jaewoo Kang},
title = {Med-PRM: Medical Reasoning Models with Stepwise, Guideline-verified
Process Rewards},
journal = {CoRR},
volume = {abs/2506.11474},
year = {2025},
url = {https://doi.org/10.48550/arXiv.2506.11474},
doi = {10.48550/ARXIV.2506.11474},
eprinttype = {arXiv},
eprint = {2506.11474},
timestamp = {Thu, 10 Jul 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2506-11474.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2507-11660,
author = {Jo{\~{a}}o F. Rocha and
Ke Xu and
Xingzhi Sun and
Ananya Krishna and
Dhananjay Bhaskar and
Blanche Mongeon and
Morgan Craig and
Mark Gerstein and
Smita Krishnaswamy},
title = {{STAGED:} {A} Multi-Agent Neural Network for Learning Cellular Interaction
Dynamics},
journal = {CoRR},
volume = {abs/2507.11660},
year = {2025},
url = {https://doi.org/10.48550/arXiv.2507.11660},
doi = {10.48550/ARXIV.2507.11660},
eprinttype = {arXiv},
eprint = {2507.11660},
timestamp = {Mon, 18 Aug 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2507-11660.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/TangDKWLLG24,
author = {Xiangru Tang and
Howard Dai and
Elizabeth Knight and
Fang Wu and
Yunyang Li and
Tianxiao Li and
Mark Gerstein},
title = {A survey of generative {AI} for \emph{de novo} drug design: new frontiers
in molecule and protein generation},
journal = {Briefings Bioinform.},
volume = {25},
number = {4},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae338},
doi = {10.1093/BIB/BBAE338},
timestamp = {Fri, 02 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/TangDKWLLG24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/DuanXSHLYGLGZ24,
author = {Ziheng Duan and
Siwei Xu and
Shushrruth Sai Srinivasan and
Ahyeon Hwang and
Cheyu Lee and
Feng Yue and
Mark Gerstein and
Yu Luan and
Matthew J. Girgenti and
Jing Zhang},
title = {scENCORE: leveraging single-cell epigenetic data to predict chromatin
conformation using graph embedding},
journal = {Briefings Bioinform.},
volume = {25},
number = {Supplement 1},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae096},
doi = {10.1093/BIB/BBAE096},
timestamp = {Sun, 10 Aug 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/DuanXSHLYGLGZ24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TangQGCCG24,
author = {Xiangru Tang and
Bill Qian and
Rick Gao and
Jiakang Chen and
Xinyun Chen and
Mark B. Gerstein},
title = {BioCoder: a benchmark for bioinformatics code generation with large
language models},
journal = {Bioinform.},
volume = {40},
number = {Supplement{\_}1},
pages = {i266--i276},
year = {2024},
url = {https://doi.org/10.1093/bioinformatics/btae230},
doi = {10.1093/BIOINFORMATICS/BTAE230},
timestamp = {Mon, 03 Mar 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/TangQGCCG24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TangTTG24,
author = {Xiangru Tang and
Andrew Tran and
Jeffrey Tan and
Mark B. Gerstein},
title = {\emph{MolLM}: a unified language model for integrating biomedical
text with 2D and 3D molecular representations},
journal = {Bioinform.},
volume = {40},
number = {Supplement{\_}1},
pages = {i357--i368},
year = {2024},
url = {https://doi.org/10.1093/bioinformatics/btae260},
doi = {10.1093/BIOINFORMATICS/BTAE260},
timestamp = {Mon, 03 Mar 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/TangTTG24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SongCWKGMW24,
author = {Tianci Song and
Eric Cosatto and
Gaoyuan Wang and
Rui Kuang and
Mark Gerstein and
Martin Renqiang Min and
Jonathan Warrell},
title = {Predicting spatially resolved gene expression via tissue morphology
using adaptive spatial GNNs},
journal = {Bioinform.},
volume = {40},
number = {Supplement{\_}2},
pages = {ii111--ii119},
year = {2024},
url = {https://doi.org/10.1093/bioinformatics/btae383},
doi = {10.1093/BIOINFORMATICS/BTAE383},
timestamp = {Mon, 03 Mar 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SongCWKGMW24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/LeeEG24,
author = {Ho{-}Joon Lee and
Prashant S. Emani and
Mark B. Gerstein},
title = {Improved Prediction of Ligand-Protein Binding Affinities by Meta-modeling},
journal = {J. Chem. Inf. Model.},
volume = {64},
number = {23},
pages = {8684--8704},
year = {2024},
url = {https://doi.org/10.1021/acs.jcim.4c01116},
doi = {10.1021/ACS.JCIM.4C01116},
timestamp = {Wed, 08 Jan 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/LeeEG24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/natmi/ZhangWJLGPROS24,
author = {Yumeng Zhang and
Zhikang Wang and
Yunzhe Jiang and
Dene R. Littler and
Mark Gerstein and
Anthony W. Purcell and
Jamie Rossjohn and
Hong{-}Yu Ou and
Jiangning Song},
title = {Epitope-anchored contrastive transfer learning for paired {CD8+} {T}
cell receptor-antigen recognition},
journal = {Nat. Mac. Intell.},
volume = {6},
number = {11},
pages = {1344--1358},
year = {2024},
url = {https://doi.org/10.1038/s42256-024-00913-8},
doi = {10.1038/S42256-024-00913-8},
timestamp = {Fri, 09 May 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/natmi/ZhangWJLGPROS24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/acl/TangZ0L0ZCG24,
author = {Xiangru Tang and
Anni Zou and
Zhuosheng Zhang and
Ziming Li and
Yilun Zhao and
Xingyao Zhang and
Arman Cohan and
Mark Gerstein},
editor = {Lun{-}Wei Ku and
Andre Martins and
Vivek Srikumar},
title = {MedAgents: Large Language Models as Collaborators for Zero-shot Medical
Reasoning},
booktitle = {Findings of the Association for Computational Linguistics, {ACL} 2024,
Bangkok, Thailand and virtual meeting, August 11-16, 2024},
pages = {599--621},
publisher = {Association for Computational Linguistics},
year = {2024},
url = {https://doi.org/10.18653/v1/2024.findings-acl.33},
doi = {10.18653/V1/2024.FINDINGS-ACL.33},
timestamp = {Thu, 01 May 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/acl/TangZ0L0ZCG24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iclr/QinLYZYLLCTQZHT24,
author = {Yujia Qin and
Shihao Liang and
Yining Ye and
Kunlun Zhu and
Lan Yan and
Yaxi Lu and
Yankai Lin and
Xin Cong and
Xiangru Tang and
Bill Qian and
Sihan Zhao and
Lauren Hong and
Runchu Tian and
Ruobing Xie and
Jie Zhou and
Mark Gerstein and
Dahai Li and
Zhiyuan Liu and
Maosong Sun},
title = {ToolLLM: Facilitating Large Language Models to Master 16000+ Real-world
APIs},
booktitle = {The Twelfth International Conference on Learning Representations,
{ICLR} 2024, Vienna, Austria, May 7-11, 2024},
publisher = {OpenReview.net},
year = {2024},
url = {https://openreview.net/forum?id=dHng2O0Jjr},
timestamp = {Mon, 29 Jul 2024 16:19:40 +0200},
biburl = {https://dblp.org/rec/conf/iclr/QinLYZYLLCTQZHT24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/naacl/TangZPZZCG24,
author = {Xiangru Tang and
Yiming Zong and
Jason Phang and
Yilun Zhao and
Wangchunshu Zhou and
Arman Cohan and
Mark Gerstein},
editor = {Kevin Duh and
Helena G{\'{o}}mez{-}Adorno and
Steven Bethard},
title = {Struc-Bench: Are Large Language Models Good at Generating Complex
Structured Tabular Data?},
booktitle = {Proceedings of the 2024 Conference of the North American Chapter of
the Association for Computational Linguistics: Human Language Technologies:
Short Papers, {NAACL} 2024, Mexico City, Mexico, June 16-21, 2024},
pages = {12--34},
publisher = {Association for Computational Linguistics},
year = {2024},
url = {https://doi.org/10.18653/v1/2024.naacl-short.2},
doi = {10.18653/V1/2024.NAACL-SHORT.2},
timestamp = {Sat, 31 May 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/naacl/TangZPZZCG24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/naacl/Deng0TGC24,
author = {Chunyuan Deng and
Yilun Zhao and
Xiangru Tang and
Mark Gerstein and
Arman Cohan},
editor = {Kevin Duh and
Helena G{\'{o}}mez{-}Adorno and
Steven Bethard},
title = {Investigating Data Contamination in Modern Benchmarks for Large Language
Models},
booktitle = {Proceedings of the 2024 Conference of the North American Chapter of
the Association for Computational Linguistics: Human Language Technologies
(Volume 1: Long Papers), {NAACL} 2024, Mexico City, Mexico, June 16-21,
2024},
pages = {8706--8719},
publisher = {Association for Computational Linguistics},
year = {2024},
url = {https://doi.org/10.18653/v1/2024.naacl-long.482},
doi = {10.18653/V1/2024.NAACL-LONG.482},
timestamp = {Thu, 29 Aug 2024 17:13:57 +0200},
biburl = {https://dblp.org/rec/conf/naacl/Deng0TGC24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2402-04247,
author = {Xiangru Tang and
Qiao Jin and
Kunlun Zhu and
Tongxin Yuan and
Yichi Zhang and
Wangchunshu Zhou and
Meng Qu and
Yilun Zhao and
Jian Tang and
Zhuosheng Zhang and
Arman Cohan and
Zhiyong Lu and
Mark Gerstein},
title = {Prioritizing Safeguarding Over Autonomy: Risks of {LLM} Agents for
Science},
journal = {CoRR},
volume = {abs/2402.04247},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2402.04247},
doi = {10.48550/ARXIV.2402.04247},
eprinttype = {arXiv},
eprint = {2402.04247},
timestamp = {Thu, 01 May 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2402-04247.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2402-08703,
author = {Xiangru Tang and
Howard Dai and
Elizabeth Knight and
Fang Wu and
Yunyang Li and
Tianxiao Li and
Mark Gerstein},
title = {A Survey of Generative {AI} for De Novo Drug Design: New Frontiers
in Molecule and Protein Generation},
journal = {CoRR},
volume = {abs/2402.08703},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2402.08703},
doi = {10.48550/ARXIV.2402.08703},
eprinttype = {arXiv},
eprint = {2402.08703},
timestamp = {Fri, 16 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2402-08703.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2404-04285,
author = {Chunyuan Deng and
Xiangru Tang and
Yilun Zhao and
Hanming Wang and
Haoran Wang and
Wangchunshu Zhou and
Arman Cohan and
Mark Gerstein},
title = {{MIMIR:} {A} Streamlined Platform for Personalized Agent Tuning in
Domain Expertise},
journal = {CoRR},
volume = {abs/2404.04285},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2404.04285},
doi = {10.48550/ARXIV.2404.04285},
eprinttype = {arXiv},
eprint = {2404.04285},
timestamp = {Wed, 15 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2404-04285.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2406-14275,
author = {Xiangru Tang and
Xingyao Zhang and
Yanjun Shao and
Jie Wu and
Yilun Zhao and
Arman Cohan and
Ming Gong and
Dongmei Zhang and
Mark Gerstein},
title = {Step-Back Profiling: Distilling User History for Personalized Scientific
Writing},
journal = {CoRR},
volume = {abs/2406.14275},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2406.14275},
doi = {10.48550/ARXIV.2406.14275},
eprinttype = {arXiv},
eprint = {2406.14275},
timestamp = {Mon, 23 Dec 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2406-14275.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2411-16736,
author = {Haochen Zhao and
Xiangru Tang and
Ziran Yang and
Xiao Han and
Xuanzhi Feng and
Yueqing Fan and
Senhao Cheng and
Di Jin and
Yilun Zhao and
Arman Cohan and
Mark Gerstein},
title = {ChemSafetyBench: Benchmarking {LLM} Safety on Chemistry Domain},
journal = {CoRR},
volume = {abs/2411.16736},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2411.16736},
doi = {10.48550/ARXIV.2411.16736},
eprinttype = {arXiv},
eprint = {2411.16736},
timestamp = {Fri, 03 Jan 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2411-16736.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LauECYLMWGL23,
author = {Bayo Lau and
Prashant S. Emani and
Jackson Chapman and
Lijing Yao and
Tarsus Lam and
Paul Merrill and
Jonathan Warrell and
Mark B. Gerstein and
Hugo Y. K. Lam},
title = {Insights from incorporating quantum computing into drug design workflows},
journal = {Bioinform.},
volume = {39},
number = {1},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btac789},
doi = {10.1093/BIOINFORMATICS/BTAC789},
timestamp = {Tue, 05 Aug 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LauECYLMWGL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChenZGECJGNCM23,
author = {Ziqi Chen and
Baoyi Zhang and
Hongyu Guo and
Prashant S. Emani and
Trevor Clancy and
Chongming Jiang and
Mark Gerstein and
Xia Ning and
Chao Cheng and
Martin Renqiang Min},
title = {Binding peptide generation for {MHC} Class {I} proteins with deep
reinforcement learning},
journal = {Bioinform.},
volume = {39},
number = {2},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad055},
doi = {10.1093/BIOINFORMATICS/BTAD055},
timestamp = {Mon, 03 Mar 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChenZGECJGNCM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/FrankishSDJLMSWABBBBBBRCCDDDFGGGHHH23,
author = {Adam Frankish and
Silvia Carbonell Sala and
Mark Diekhans and
Irwin Jungreis and
Jane E. Loveland and
Jonathan M. Mudge and
Cristina Sisu and
James C. Wright and
Carme Arnan and
If Barnes and
Abhimanyu Banerjee and
Ruth Bennett and
Andrew E. Berry and
Alexandra Bignell and
Carles Boix and
Ferriol Calvet Riera and
Daniel Cerd{\'{a}}n{-}V{\'{e}}lez and
Fiona Cunningham and
Claire Davidson and
Sarah M. Donaldson and
Cagatay Dursun and
Reham Fatima and
Stefano Giorgetti and
Carlos Garc{\'{\i}}a{-}Gir{\'{o}}n and
Jose M. Gonzalez and
Matthew Hardy and
Peter W. Harrison and
Thibaut Hourlier and
Zoe Hollis and
Toby Hunt and
Benjamin James and
Yunzhe Jiang and
Rory Johnson and
Mike P. Kay and
Julien Lagarde and
Fergal J. Martin and
Laura Mart{\'{\i}}nez G{\'{o}}mez and
Surag Nair and
Pengyu Ni and
Fernando Pozo and
Vivek Ramalingam and
Magali Ruffier and
Bianca M. Schmitt and
Jacob M. Schreiber and
Emily Steed and
Marie{-}Marthe Suner and
Dulika Sumathipala and
Irina Sycheva and
Barbara Uszczynska{-}Ratajczak and
Elizabeth Wass and
Yucheng T. Yang and
Andrew D. Yates and
Zahoor Zafrulla and
Jyoti Choudhary and
Mark Gerstein and
Roderic Guig{\'{o}} and
Tim J. P. Hubbard and
Manolis Kellis and
Anshul Kundaje and
Benedict Paten and
Michael L. Tress and
Paul Flicek},
title = {{GENCODE:} reference annotation for the human and mouse genomes in
2023},
journal = {Nucleic Acids Res.},
volume = {51},
number = {{D1}},
pages = {942--949},
year = {2023},
url = {https://doi.org/10.1093/nar/gkac1071},
doi = {10.1093/NAR/GKAC1071},
timestamp = {Fri, 04 Jul 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/FrankishSDJLMSWABBBBBBRCCDDDFGGGHHH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/ZhouALLZMAKBBCFGKLMPRSSWNSL23,
author = {Hufeng Zhou and
Theodore Arapoglou and
Xihao Li and
Zilin Li and
Xiuwen Zheng and
Jill Moore and
Abhijith Asok and
Sushant Kumar and
Elizabeth E. Blue and
Steven Buyske and
Nancy J. Cox and
Adam Felsenfeld and
Mark Gerstein and
Eimear Kenny and
Bingshan Li and
Tara Cox Matise and
Anthony Philippakis and
Heidi L. Rehm and
Heidi J. Sofia and
Grace Snyder and
Zhiping Weng and
Benjamin M. Neale and
Shamil R. Sunyaev and
Xihong Lin},
title = {{FAVOR:} functional annotation of variants online resource and annotator
for variation across the human genome},
journal = {Nucleic Acids Res.},
volume = {51},
number = {{D1}},
pages = {1300--1311},
year = {2023},
url = {https://doi.org/10.1093/nar/gkac966},
doi = {10.1093/NAR/GKAC966},
timestamp = {Tue, 29 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/ZhouALLZMAKBBCFGKLMPRSSWNSL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/LouYLZCYG23,
author = {Shaoke Lou and
Mingjun Yang and
Tianxiao Li and
Weihao Zhao and
Hannah Cevasco and
Yucheng T. Yang and
Mark Gerstein},
title = {Constructing a full, multiple-layer interactome for SARS-CoV-2 in
the context of lung disease: Linking the virus with human genes and
microbes},
journal = {PLoS Comput. Biol.},
volume = {19},
number = {7},
year = {2023},
url = {https://doi.org/10.1371/journal.pcbi.1011222},
doi = {10.1371/JOURNAL.PCBI.1011222},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/LouYLZCYG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/acl-clinicalnlp/TangCG23,
author = {Xiangru Tang and
Arman Cohan and
Mark Gerstein},
editor = {Tristan Naumann and
Asma Ben Abacha and
Steven Bethard and
Kirk Roberts and
Anna Rumshisky},
title = {Aligning Factual Consistency for Clinical Studies Summarization through
Reinforcement Learning},
booktitle = {Proceedings of the 5th Clinical Natural Language Processing Workshop,
ClinicalNLP@ACL 2023, Toronto, Canada, July 14, 2023},
pages = {48--58},
publisher = {Association for Computational Linguistics},
year = {2023},
url = {https://doi.org/10.18653/v1/2023.clinicalnlp-1.7},
doi = {10.18653/V1/2023.CLINICALNLP-1.7},
timestamp = {Thu, 10 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/acl-clinicalnlp/TangCG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/acl-clinicalnlp/TangTTG23,
author = {Xiangru Tang and
Andrew Tran and
Jeffrey Tan and
Mark Gerstein},
editor = {Tristan Naumann and
Asma Ben Abacha and
Steven Bethard and
Kirk Roberts and
Anna Rumshisky},
title = {GersteinLab at MEDIQA-Chat 2023: Clinical Note Summarization from
Doctor-Patient Conversations through Fine-tuning and In-context Learning},
booktitle = {Proceedings of the 5th Clinical Natural Language Processing Workshop,
ClinicalNLP@ACL 2023, Toronto, Canada, July 14, 2023},
pages = {546--554},
publisher = {Association for Computational Linguistics},
year = {2023},
url = {https://doi.org/10.18653/v1/2023.clinicalnlp-1.58},
doi = {10.18653/V1/2023.CLINICALNLP-1.58},
timestamp = {Thu, 10 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/acl-clinicalnlp/TangTTG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/nips/LiGGGM23,
author = {Tianxiao Li and
Hongyu Guo and
Filippo Grazioli and
Mark Gerstein and
Martin Renqiang Min},
editor = {Alice Oh and
Tristan Naumann and
Amir Globerson and
Kate Saenko and
Moritz Hardt and
Sergey Levine},
title = {Disentangled Wasserstein Autoencoder for T-Cell Receptor Engineering},
booktitle = {Advances in Neural Information Processing Systems 36: Annual Conference
on Neural Information Processing Systems 2023, NeurIPS 2023, New Orleans,
LA, USA, December 10 - 16, 2023},
year = {2023},
url = {http://papers.nips.cc/paper\_files/paper/2023/hash/e95da8078ec8389533c802e368da5298-Abstract-Conference.html},
timestamp = {Fri, 01 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/nips/LiGGGM23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2305-05001,
author = {Xiangru Tang and
Andrew Tran and
Jeffrey Tan and
Mark Gerstein},
title = {GersteinLab at MEDIQA-Chat 2023: Clinical Note Summarization from
Doctor-Patient Conversations through Fine-tuning and In-context Learning},
journal = {CoRR},
volume = {abs/2305.05001},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2305.05001},
doi = {10.48550/ARXIV.2305.05001},
eprinttype = {arXiv},
eprint = {2305.05001},
timestamp = {Fri, 12 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2305-05001.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2307-16789,
author = {Yujia Qin and
Shihao Liang and
Yining Ye and
Kunlun Zhu and
Lan Yan and
Yaxi Lu and
Yankai Lin and
Xin Cong and
Xiangru Tang and
Bill Qian and
Sihan Zhao and
Runchu Tian and
Ruobing Xie and
Jie Zhou and
Mark Gerstein and
Dahai Li and
Zhiyuan Liu and
Maosong Sun},
title = {ToolLLM: Facilitating Large Language Models to Master 16000+ Real-world
APIs},
journal = {CoRR},
volume = {abs/2307.16789},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2307.16789},
doi = {10.48550/ARXIV.2307.16789},
eprinttype = {arXiv},
eprint = {2307.16789},
timestamp = {Tue, 07 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2307-16789.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2308-16458,
author = {Xiangru Tang and
Bill Qian and
Rick Gao and
Jiakang Chen and
Xinyun Chen and
Mark Gerstein},
title = {BioCoder: {A} Benchmark for Bioinformatics Code Generation with Contextual
Pragmatic Knowledge},
journal = {CoRR},
volume = {abs/2308.16458},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2308.16458},
doi = {10.48550/ARXIV.2308.16458},
eprinttype = {arXiv},
eprint = {2308.16458},
timestamp = {Mon, 04 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2308-16458.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2309-08963,
author = {Xiangru Tang and
Yiming Zong and
Jason Phang and
Yilun Zhao and
Wangchunshu Zhou and
Arman Cohan and
Mark Gerstein},
title = {Struc-Bench: Are Large Language Models Really Good at Generating Complex
Structured Data?},
journal = {CoRR},
volume = {abs/2309.08963},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2309.08963},
doi = {10.48550/ARXIV.2309.08963},
eprinttype = {arXiv},
eprint = {2309.08963},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2309-08963.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2310-03946,
author = {Ho{-}Joon Lee and
Prashant S. Emani and
Mark B. Gerstein},
title = {Improved prediction of ligand-protein binding affinities by meta-modeling},
journal = {CoRR},
volume = {abs/2310.03946},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2310.03946},
doi = {10.48550/ARXIV.2310.03946},
eprinttype = {arXiv},
eprint = {2310.03946},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2310-03946.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2311-09783,
author = {Chunyuan Deng and
Yilun Zhao and
Xiangru Tang and
Mark Gerstein and
Arman Cohan},
title = {Investigating Data Contamination in Modern Benchmarks for Large Language
Models},
journal = {CoRR},
volume = {abs/2311.09783},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2311.09783},
doi = {10.48550/ARXIV.2311.09783},
eprinttype = {arXiv},
eprint = {2311.09783},
timestamp = {Tue, 21 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2311-09783.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2311-09835,
author = {Yuliang Liu and
Xiangru Tang and
Zefan Cai and
Junjie Lu and
Yichi Zhang and
Yanjun Shao and
Zexuan Deng and
Helan Hu and
Zengxian Yang and
Kaikai An and
Ruijun Huang and
Shuzheng Si and
Sheng Chen and
Haozhe Zhao and
Zhengliang Li and
Liang Chen and
Yiming Zong and
Yan Wang and
Tianyu Liu and
Zhiwei Jiang and
Baobao Chang and
Yujia Qin and
Wangchunshu Zhou and
Yilun Zhao and
Arman Cohan and
Mark Gerstein},
title = {ML-Bench: Large Language Models Leverage Open-source Libraries for
Machine Learning Tasks},
journal = {CoRR},
volume = {abs/2311.09835},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2311.09835},
doi = {10.48550/ARXIV.2311.09835},
eprinttype = {arXiv},
eprint = {2311.09835},
timestamp = {Tue, 19 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2311-09835.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2311-10537,
author = {Xiangru Tang and
Anni Zou and
Zhuosheng Zhang and
Yilun Zhao and
Xingyao Zhang and
Arman Cohan and
Mark Gerstein},
title = {MedAgents: Large Language Models as Collaborators for Zero-shot Medical
Reasoning},
journal = {CoRR},
volume = {abs/2311.10537},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2311.10537},
doi = {10.48550/ARXIV.2311.10537},
eprinttype = {arXiv},
eprint = {2311.10537},
timestamp = {Thu, 01 May 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2311-10537.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2311-11797,
author = {Zhuosheng Zhang and
Yao Yao and
Aston Zhang and
Xiangru Tang and
Xinbei Ma and
Zhiwei He and
Yiming Wang and
Mark Gerstein and
Rui Wang and
Gongshen Liu and
Hai Zhao},
title = {Igniting Language Intelligence: The Hitchhiker's Guide From Chain-of-Thought
Reasoning to Language Agents},
journal = {CoRR},
volume = {abs/2311.11797},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2311.11797},
doi = {10.48550/ARXIV.2311.11797},
eprinttype = {arXiv},
eprint = {2311.11797},
timestamp = {Wed, 11 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2311-11797.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/LeeCDXGXGZ22,
author = {Cheyu Lee and
Yuhang Chen and
Ziheng Duan and
Min Xu and
Matthew J. Girgenti and
Ke Xu and
Mark Gerstein and
Jing Zhang},
title = {Venus: An efficient virus infection detection and fusion site discovery
method using single-cell and bulk RNA-seq data},
journal = {PLoS Comput. Biol.},
volume = {18},
number = {10},
pages = {1010636},
year = {2022},
url = {https://doi.org/10.1371/journal.pcbi.1010636},
doi = {10.1371/JOURNAL.PCBI.1010636},
timestamp = {Sat, 15 Mar 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ploscb/LeeCDXGXGZ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/embc/KhannaSGG22,
author = {Amol Khanna and
Vincent Schaffer and
Gamze G{\"{u}}rsoy and
Mark Gerstein},
title = {Privacy-preserving Model Training for Disease Prediction Using Federated
Learning with Differential Privacy},
booktitle = {44th Annual International Conference of the {IEEE} Engineering in
Medicine {\&} Biology Society, {EMBC} 2022, Glasgow, Scotland,
United Kingdom, July 11-15, 2022},
pages = {1358--1361},
publisher = {{IEEE}},
year = {2022},
url = {https://doi.org/10.1109/EMBC48229.2022.9871742},
doi = {10.1109/EMBC48229.2022.9871742},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/embc/KhannaSGG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2203-15972,
author = {Jonathan Warrell and
Mark Gerstein},
title = {Higher-Order Generalization Bounds: Learning Deep Probabilistic Programs
via PAC-Bayes Objectives},
journal = {CoRR},
volume = {abs/2203.15972},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2203.15972},
doi = {10.48550/ARXIV.2203.15972},
eprinttype = {arXiv},
eprint = {2203.15972},
timestamp = {Mon, 04 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2203-15972.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2204-05496,
author = {Esha Sarkar and
Eduardo Chielle and
Gamze G{\"{u}}rsoy and
Leo Chen and
Mark Gerstein and
Michail Maniatakos},
title = {Scalable privacy-preserving cancer type prediction with homomorphic
encryption},
journal = {CoRR},
volume = {abs/2204.05496},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2204.05496},
doi = {10.48550/ARXIV.2204.05496},
eprinttype = {arXiv},
eprint = {2204.05496},
timestamp = {Tue, 19 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2204-05496.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/access/SarkarCGMGM21,
author = {Esha Sarkar and
Eduardo Chielle and
Gamze G{\"{u}}rsoy and
Oleg Mazonka and
Mark Gerstein and
Michail Maniatakos},
title = {Fast and Scalable Private Genotype Imputation Using Machine Learning
and Partially Homomorphic Encryption},
journal = {{IEEE} Access},
volume = {9},
pages = {93097--93110},
year = {2021},
url = {https://doi.org/10.1109/ACCESS.2021.3093005},
doi = {10.1109/ACCESS.2021.3093005},
timestamp = {Tue, 16 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/access/SarkarCGMGM21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GursoyBNG21,
author = {Gamze G{\"{u}}rsoy and
Charlotte M. Brannon and
Fabio C. P. Navarro and
Mark Gerstein},
title = {{FANCY:} fast estimation of privacy risk in functional genomics data},
journal = {Bioinform.},
volume = {36},
number = {21},
pages = {5145--5150},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btaa661},
doi = {10.1093/BIOINFORMATICS/BTAA661},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GursoyBNG21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LouLLG21,
author = {Shaoke Lou and
Tianxiao Li and
Jason Liu and
Mark Gerstein},
title = {Gene Tracer: a smart, interactive, voice-controlled Alexa skill For
gene information retrieval and browsing, mutation annotation and network
visualization},
journal = {Bioinform.},
volume = {37},
number = {18},
pages = {2998--3000},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab107},
doi = {10.1093/BIOINFORMATICS/BTAB107},
timestamp = {Mon, 29 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LouLLG21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChenZLDLMXG21,
author = {Zhanlin Chen and
Jing Zhang and
Jason Liu and
Yi Dai and
Donghoon Lee and
Martin Renqiang Min and
Min Xu and
Mark Gerstein},
title = {{DECODE:} a Deep-learning framework for Condensing enhancers and refining
boundaries with large-scale functional assays},
journal = {Bioinform.},
volume = {37},
number = {Supplement},
pages = {280--288},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab283},
doi = {10.1093/BIOINFORMATICS/BTAB283},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChenZLDLMXG21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/FrankishDJLLMSW21,
author = {Adam Frankish and
Mark Diekhans and
Irwin Jungreis and
Julien Lagarde and
Jane E. Loveland and
Jonathan M. Mudge and
Cristina Sisu and
James C. Wright and
Joel Armstrong and
If Barnes and
Andrew E. Berry and
Alexandra Bignell and
Carles Boix and
Silvia Carbonell Sala and
Fiona Cunningham and
Tom{\'{a}}s Di Domenico and
Sarah M. Donaldson and
Ian T. Fiddes and
Carlos Garc{\'{\i}}a{-}Gir{\'{o}}n and
Jose M. Gonzalez and
Tiago Grego and
Matthew Hardy and
Thibaut Hourlier and
Kevin L. Howe and
Toby Hunt and
Osagie G. Izuogu and
Rory Johnson and
Fergal J. Martin and
Laura Mart{\'{\i}}nez and
Shamika Mohanan and
Paul Muir and
Fabio C. P. Navarro and
Anne Parker and
Baikang Pei and
Fernando Pozo and
Ferriol Calvet Riera and
Magali Ruffier and
Bianca M. Schmitt and
Eloise Stapleton and
Marie{-}Marthe Suner and
Irina Sycheva and
Barbara Uszczynska{-}Ratajczak and
Maxim Y. Wolf and
Jinrui Xu and
Yucheng T. Yang and
Andrew D. Yates and
Daniel R. Zerbino and
Yan Zhang and
Jyoti Choudhary and
Mark Gerstein and
Roderic Guig{\'{o}} and
Tim J. P. Hubbard and
Manolis Kellis and
Benedict Paten and
Michael L. Tress and
Paul Flicek},
title = {{GENCODE} 2021},
journal = {Nucleic Acids Res.},
volume = {49},
number = {Database-Issue},
pages = {D916--D923},
year = {2021},
url = {https://doi.org/10.1093/nar/gkaa1087},
doi = {10.1093/NAR/GKAA1087},
timestamp = {Fri, 04 Jul 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/FrankishDJLLMSW21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/LiuSAHAZLLZPGSN21,
author = {Jason Liu and
Daniel J. Spakowicz and
Garrett I. Ash and
Rebecca Hoyd and
Rohan Ahluwalia and
Andrew Zhang and
Shaoke Lou and
Donghoon Lee and
Jing Zhang and
Carolyn Presley and
Ann Greene and
Matthew Stults{-}Kolehmainen and
Laura M. Nally and
Julien S. Baker and
Lisa M. Fucito and
Stuart A. Weinzimer and
Andrew V. Papachristos and
Mark Gerstein},
title = {Bayesian structural time series for biomedical sensor data: {A} flexible
modeling framework for evaluating interventions},
journal = {PLoS Comput. Biol.},
volume = {17},
number = {8},
year = {2021},
url = {https://doi.org/10.1371/journal.pcbi.1009303},
doi = {10.1371/JOURNAL.PCBI.1009303},
timestamp = {Mon, 29 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/LiuSAHAZLLZPGSN21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2103-11802,
author = {Zhanlin Chen and
Philip Tuckman and
Jeremy Goldwasser and
Jing Zhang and
Mark Gerstein},
title = {Forest Fire Clustering: Cluster-oriented Label Propagation Clustering
and Monte Carlo Verification Inspired by Forest Fire Dynamics},
journal = {CoRR},
volume = {abs/2103.11802},
year = {2021},
url = {https://arxiv.org/abs/2103.11802},
eprinttype = {arXiv},
eprint = {2103.11802},
timestamp = {Tue, 18 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2103-11802.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HoCGCWGY20,
author = {Edwin Yu{-}Kiu Ho and
Qin Cao and
Mengting Gu and
Ricky Wai{-}Lun Chan and
Qiong Wu and
Mark Gerstein and
Kevin Y. Yip},
title = {Shaping the nebulous enhancer in the era of high-throughput assays
and genome editing},
journal = {Briefings Bioinform.},
volume = {21},
number = {3},
pages = {836--850},
year = {2020},
url = {https://doi.org/10.1093/bib/bbz030},
doi = {10.1093/BIB/BBZ030},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/HoCGCWGY20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LouLKZLLG20,
author = {Shaoke Lou and
Tianxiao Li and
Xiangmeng Kong and
Jing Zhang and
Jason Liu and
Donghoon Lee and
Mark Gerstein},
title = {TopicNet: a framework for measuring transcriptional regulatory network
change},
journal = {Bioinform.},
volume = {36},
number = {Supplement-1},
pages = {i474--i481},
year = {2020},
url = {https://doi.org/10.1093/bioinformatics/btaa403},
doi = {10.1093/BIOINFORMATICS/BTAA403},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LouLKZLLG20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/YePGY20,
author = {Cheng Ye and
Alberto Paccanaro and
Mark Gerstein and
Koon{-}Kiu Yan},
title = {The corrected gene proximity map for analyzing the 3D genome organization
using Hi-C data},
journal = {{BMC} Bioinform.},
volume = {21},
number = {1},
pages = {222},
year = {2020},
url = {https://doi.org/10.1186/s12859-020-03545-y},
doi = {10.1186/S12859-020-03545-Y},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/YePGY20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MeyersonLNG20,
author = {William Meyerson and
John Leisman and
Fabio C. P. Navarro and
Mark Gerstein},
title = {Origins and characterization of variants shared between databases
of somatic and germline human mutations},
journal = {{BMC} Bioinform.},
volume = {21},
number = {1},
pages = {227},
year = {2020},
url = {https://doi.org/10.1186/s12859-020-3508-8},
doi = {10.1186/S12859-020-3508-8},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/MeyersonLNG20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhangLLLCGG20,
author = {Jing Zhang and
Jason Liu and
Donghoon Lee and
Shaoke Lou and
Zhanlin Chen and
Gamze G{\"{u}}rsoy and
Mark Gerstein},
title = {DiNeR: a Differential graphical model for analysis of co-regulation
Network Rewiring},
journal = {{BMC} Bioinform.},
volume = {21},
number = {1},
pages = {281},
year = {2020},
url = {https://doi.org/10.1186/s12859-020-03605-3},
doi = {10.1186/S12859-020-03605-3},
timestamp = {Mon, 29 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhangLLLCGG20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LouLSYCG20,
author = {Shaoke Lou and
Tianxiao Li and
Daniel Spakowicz and
Xiting Yan and
Geoffrey Lowell Chupp and
Mark Gerstein},
title = {Latent-space embedding of expression data identifies gene signatures
from sputum samples of asthmatic patients},
journal = {{BMC} Bioinform.},
volume = {21},
number = {1},
pages = {457},
year = {2020},
url = {https://doi.org/10.1186/s12859-020-03785-y},
doi = {10.1186/S12859-020-03785-Y},
timestamp = {Fri, 25 Dec 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/LouLSYCG20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhangLMYLLG20,
author = {Jing Zhang and
Jason Liu and
Patrick D. McGillivray and
Caroline Yi and
Lucas Lochovsky and
Donghoon Lee and
Mark Gerstein},
title = {NIMBus: a negative binomial regression based Integrative Method for
mutation Burden Analysis},
journal = {{BMC} Bioinform.},
volume = {21},
number = {1},
pages = {474},
year = {2020},
url = {https://doi.org/10.1186/s12859-020-03758-1},
doi = {10.1186/S12859-020-03758-1},
timestamp = {Mon, 29 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhangLMYLLG20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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author = {Esther Rheinbay and
Morten Muhlig Nielsen and
Federico Abascal and
Jeremiah Wala and
Ofer Shapira and
Grace Tiao and
Henrik Hornsh{\o}j and
Julian M. Hess and
Randi Istrup Juul and
Ziao Lin and
Lars Feuerbach and
Radhakrishnan Sabarinathan and
Tobias Madsen and
Jaegil Kim and
Loris Mularoni and
Shimin Shuai and
Andr{\'{e}}s Lanz{\'{o}}s and
Carl Herrmann and
Yosef E. Maruvka and
Ciyue Shen and
Samirkumar B. Amin and
Pratiti Bandopadhayay and
Johanna Bertl and
Keith A. Boroevich and
John Busanovich and
Joana Carlevaro{-}Fita and
Dimple Chakravarty and
Calvin Wing Yiu Chan and
David Craft and
Priyanka Dhingra and
Klev Diamanti and
Nuno A. Fonseca and
Abel Gonzalez{-}Perez and
Qianyun Guo and
Mark P. Hamilton and
Nicholas J. Haradhvala and
Chen Hong and
Keren Isaev and
Todd A. Johnson and
Malene Juul and
Andr{\'{e}} Kahles and
Abdullah Kahraman and
Youngwook Kim and
Jan Komorowski and
Kiran Kumar and
Sushant Kumar and
Donghoon Lee and
Kjong{-}Van Lehmann and
Yilong Li and
Eric Minwei Liu and
Lucas Lochovsky and
Keunchil Park and
Oriol Pich and
Nicola D. Roberts and
Gordon Saksena and
Steven E. Schumacher and
Nikos Sidiropoulos and
Lina Sieverling and
Nasa Sinnott{-}Armstrong and
Chip Stewart and
David Tamborero and
Jose M. C. Tubio and
Husen M. Umer and
Liis Uusk{\"{u}}la{-}Reimand and
Claes Wadelius and
Lina Wadi and
Xiaotong Yao and
Cheng{-}Zhong Zhang and
Jing Zhang and
James E. Haber and
Asger Hobolth and
Marcin Imielinski and
Manolis Kellis and
Michael S. Lawrence and
Christian von Mering and
Hidewaki Nakagawa and
Benjamin J. Raphael and
Mark A. Rubin and
Chris Sander and
Lincoln D. Stein and
Joshua M. Stuart and
Tatsuhiko Tsunoda and
David A. Wheeler and
Rory Johnson and
J{\"{u}}ri Reimand and
Mark Gerstein and
Ekta Khurana and
Peter J. Campbell and
N{\'{u}}ria L{\'{o}}pez{-}Bigas and
Gary D. Bader and
Jonathan Barenboim and
Rameen Beroukhim and
S{\o}ren Brunak and
Ken Chen and
Jung Kyoon Choi and
Jordi Deu{-}Pons and
J. Lynn Fink and
Joan Frigola and
Carlo Gambacorti Passerini and
Dale W. Garsed and
Gad Getz and
Ivo Glynne Gut and
David Haan and
Arif Ozgun Harmanci and
Mohamed Helmy and
Ermin Hodzic and
Jos{\'{e}} M. G. Izarzugaza and
Jong K. Kim and
Jan O. Korbel and
Erik Larsson and
Shantao Li and
Xiaotong Li and
Shaoke Lou and
Kathleen Marchal and
I{\~{n}}igo Martincorena and
Alexander Mart{\'{\i}}nez{-}Fundichely and
Patrick D. McGillivray and
William Meyerson and
Ferran Mui{\~{n}}os and
Marta Paczkowska and
Kiejung Park and
Jakob Skou Pedersen and
Tirso Pons and
Sergio Pulido{-}Tamayo and
Iker Reyes{-}Salazar and
Matthew A. Reyna and
Carlota Rubio{-}Perez and
S{\"{u}}leyman Cenk Sahinalp and
Leonidas Salichos and
Mark Shackleton and
Raunak Shrestha and
Alfonso Valencia and
Miguel Vazquez and
Lieven P. C. Verbeke and
Jiayin Wang and
Jonathan Warrell and
Sebastian M. Waszak and
Joachim Weischenfeldt and
Guanming Wu and
Jun Yu and
Xuanping Zhang and
Yan Zhang and
Zhongming Zhao and
Lihua Zou and
Kadir C. Akdemir and
Eva G. Alvarez and
Adrian Baez{-}Ortega and
Paul C. Boutros and
David D. L. Bowtell and
Benedikt Brors and
Kathleen H. Burns and
Kin Chan and
Isidro Cort{\'{e}}s{-}Ciriano and
Ana Dueso{-}Barroso and
Andrew J. Dunford and
Paul A. Edwards and
Xavier Estivill and
Dariush Etemadmoghadam and
Milana Frenkel{-}Morgenstern and
Dmitry A. Gordenin and
Barbara Hutter and
David T. W. Jones and
Young Seok Ju and
Marat D. Kazanov and
Leszek J. Klimczak and
Youngil Koh and
Eunjung Alice Lee and
Jake June{-}Koo Lee and
Andy G. Lynch and
Geoff MacIntyre and
Florian Markowetz and
Matthew Meyerson and
Satoru Miyano and
Fabio C. P. Navarro and
Stephan Ossowski and
Peter J. Park and
John V. Pearson and
Montserrat Puiggr{\`{o}}s and
Karsten Rippe and
Steven A. Roberts and
Bernardo Rodriguez{-}Martin and
Ralph Scully and
David Torrents and
Izar Villasante and
Nicola Waddell and
Jeremiah A. Wala and
Lixing Yang and
Sung{-}Soo Yoon and
Jorge Zamora},
title = {Analyses of non-coding somatic drivers in 2,658 cancer whole genomes},
journal = {Nat.},
volume = {578},
number = {7793},
pages = {102--111},
year = {2020},
url = {https://doi.org/10.1038/s41586-020-1965-x},
doi = {10.1038/S41586-020-1965-X},
timestamp = {Thu, 11 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nature/RheinbayNAWSTHH20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/LeeZLG20,
author = {Donghoon Lee and
Jing Zhang and
Jason Liu and
Mark Gerstein},
title = {Epigenome-based splicing prediction using a recurrent neural network},
journal = {PLoS Comput. Biol.},
volume = {16},
number = {6},
year = {2020},
url = {https://doi.org/10.1371/journal.pcbi.1008006},
doi = {10.1371/JOURNAL.PCBI.1008006},
timestamp = {Mon, 29 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/LeeZLG20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/LiYCG20,
author = {Bian Li and
Yucheng T. Yang and
John A. Capra and
Mark B. Gerstein},
title = {Predicting changes in protein thermodynamic stability upon point mutation
with deep 3D convolutional neural networks},
journal = {PLoS Comput. Biol.},
volume = {16},
number = {11},
year = {2020},
url = {https://doi.org/10.1371/journal.pcbi.1008291},
doi = {10.1371/JOURNAL.PCBI.1008291},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/LiYCG20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/FrankishDFJJLMS19,
author = {Adam Frankish and
Mark Diekhans and
Anne{-}Maud Ferreira and
Rory Johnson and
Irwin Jungreis and
Jane E. Loveland and
Jonathan M. Mudge and
Cristina Sisu and
James C. Wright and
Joel Armstrong and
If Barnes and
Andrew E. Berry and
Alexandra Bignell and
Silvia Carbonell Sala and
Jacqueline Chrast and
Fiona Cunningham and
Tom{\'{a}}s Di Domenico and
Sarah M. Donaldson and
Ian T. Fiddes and
Carlos Garc{\'{\i}}a{-}Gir{\'{o}}n and
Jose M. Gonzalez and
Tiago Grego and
Matthew Hardy and
Thibaut Hourlier and
Toby Hunt and
Osagie G. Izuogu and
Julien Lagarde and
Fergal J. Martin and
Laura Mart{\'{\i}}nez and
Shamika Mohanan and
Paul Muir and
Fabio C. P. Navarro and
Anne Parker and
Baikang Pei and
Fernando Pozo and
Magali Ruffier and
Bianca M. Schmitt and
Eloise Stapleton and
Marie{-}Marthe Suner and
Irina Sycheva and
Barbara Uszczynska{-}Ratajczak and
Jinrui Xu and
Andrew D. Yates and
Daniel R. Zerbino and
Yan Zhang and
Bronwen L. Aken and
Jyoti Choudhary and
Mark Gerstein and
Roderic Guig{\'{o}} and
Tim J. P. Hubbard and
Manolis Kellis and
Benedict Paten and
Alexandre Reymond and
Michael L. Tress and
Paul Flicek},
title = {{GENCODE} reference annotation for the human and mouse genomes},
journal = {Nucleic Acids Res.},
volume = {47},
number = {Database-Issue},
pages = {D766--D773},
year = {2019},
url = {https://doi.org/10.1093/nar/gky955},
doi = {10.1093/NAR/GKY955},
timestamp = {Fri, 04 Jul 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/FrankishDFJJLMS19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/NavarroHBCZZLG19,
author = {Fabio C. P. Navarro and
Jacob Hoops and
Lauren Bellfy and
Eliza Cerveira and
Qihui Zhu and
Chengsheng Zhang and
Charles Lee and
Mark B. Gerstein},
title = {TeXP: Deconvolving the effects of pervasive and autonomous transcription
of transposable elements},
journal = {PLoS Comput. Biol.},
volume = {15},
number = {8},
year = {2019},
url = {https://doi.org/10.1371/journal.pcbi.1007293},
doi = {10.1371/JOURNAL.PCBI.1007293},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/NavarroHBCZZLG19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Kaczor-Urbanowicz18,
author = {Karolina Elzbieta Kaczor{-}Urbanowicz and
Yong Kim and
Feng Li and
Timur Galeev and
Robert R. Kitchen and
Mark Gerstein and
Kikuye Koyano and
Sung{-}Hee Jeong and
Xiaoyan Wang and
David Elashoff and
So Young Kang and
Su Mi Kim and
Kyoung Kim and
Sung Kim and
David Chia and
Xinshu Xiao and
Joel S. Rozowsky and
David T. W. Wong},
title = {Novel approaches for bioinformatic analysis of salivary {RNA} sequencing
data for development},
journal = {Bioinform.},
volume = {34},
number = {1},
pages = {1--8},
year = {2018},
url = {https://doi.org/10.1093/bioinformatics/btx504},
doi = {10.1093/BIOINFORMATICS/BTX504},
timestamp = {Sat, 05 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/Kaczor-Urbanowicz18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LochovskyZG18,
author = {Lucas Lochovsky and
Jing Zhang and
Mark Gerstein},
title = {{MOAT:} efficient detection of highly mutated regions with the Mutations
Overburdening Annotations Tool},
journal = {Bioinform.},
volume = {34},
number = {6},
pages = {1031--1033},
year = {2018},
url = {https://doi.org/10.1093/bioinformatics/btx700},
doi = {10.1093/BIOINFORMATICS/BTX700},
timestamp = {Tue, 18 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LochovskyZG18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/AlvesLWG18,
author = {Pedro Alves and
Shuang Liu and
Daifeng Wang and
Mark Gerstein},
title = {Multiple-Swarm Ensembles: Improving the Predictive Power and Robustness
of Predictive Models and Its Use in Computational Biology},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {15},
number = {3},
pages = {926--933},
year = {2018},
url = {https://doi.org/10.1109/TCBB.2017.2691329},
doi = {10.1109/TCBB.2017.2691329},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/AlvesLWG18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1812-00172,
author = {Jonathan Warrell and
Hussein Mohsen and
Mark Gerstein},
title = {Rank Projection Trees for Multilevel Neural Network Interpretation},
journal = {CoRR},
volume = {abs/1812.00172},
year = {2018},
url = {http://arxiv.org/abs/1812.00172},
eprinttype = {arXiv},
eprint = {1812.00172},
timestamp = {Tue, 01 Jan 2019 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-1812-00172.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YanYYNG17,
author = {Koon{-}Kiu Yan and
Galip G{\"{u}}rkan Yardimci and
Chengfei Yan and
William S. Noble and
Mark Gerstein},
title = {HiC-spector: a matrix library for spectral and reproducibility analysis
of Hi-C contact maps},
journal = {Bioinform.},
volume = {33},
number = {14},
pages = {2199--2201},
year = {2017},
url = {https://doi.org/10.1093/bioinformatics/btx152},
doi = {10.1093/BIOINFORMATICS/BTX152},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/YanYYNG17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/ZhangLAG17,
author = {Yan Zhang and
Shantao Li and
Alexej Abyzov and
Mark B. Gerstein},
title = {Landscape and variation of novel retroduplications in 26 human populations},
journal = {PLoS Comput. Biol.},
volume = {13},
number = {6},
year = {2017},
url = {https://doi.org/10.1371/journal.pcbi.1005567},
doi = {10.1371/JOURNAL.PCBI.1005567},
timestamp = {Thu, 04 Jul 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/ZhangLAG17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/YanLG17,
author = {Koon{-}Kiu Yan and
Shaoke Lou and
Mark Gerstein},
title = {MrTADFinder: {A} network modularity based approach to identify topologically
associating domains in multiple resolutions},
journal = {PLoS Comput. Biol.},
volume = {13},
number = {7},
year = {2017},
url = {https://doi.org/10.1371/journal.pcbi.1005647},
doi = {10.1371/JOURNAL.PCBI.1005647},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/YanLG17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biomedsem/CheungKRSRSAGGA16,
author = {Kei{-}Hoi Cheung and
Shivakumar Keerthikumar and
Paola Roncaglia and
Sai Lakshmi Subramanian and
Matthew E. Roth and
Monisha Samuel and
Sushma Anand and
Lahiru Gangoda and
Stephen Gould and
Roger Alexander and
David Galas and
Mark B. Gerstein and
Andrew F. Hill and
Robert R. Kitchen and
Jan L{\"{o}}tvall and
Tushar Patel},
title = {Extending gene ontology in the context of extracellular {RNA} and
vesicle communication},
journal = {J. Biomed. Semant.},
volume = {7},
pages = {19},
year = {2016},
url = {https://doi.org/10.1186/s13326-016-0061-5},
doi = {10.1186/S13326-016-0061-5},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biomedsem/CheungKRSRSAGGA16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/WangHMG16,
author = {Daifeng Wang and
Fei He and
Sergei Maslov and
Mark Gerstein},
title = {{DREISS:} Using State-Space Models to Infer the Dynamics of Gene Expression
Driven by External and Internal Regulatory Networks},
journal = {PLoS Comput. Biol.},
volume = {12},
number = {10},
year = {2016},
url = {https://doi.org/10.1371/journal.pcbi.1005146},
doi = {10.1371/JOURNAL.PCBI.1005146},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/WangHMG16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MuMLAGAWL15,
author = {John C. Mu and
Marghoob Mohiyuddin and
Jian Li and
Narges Bani Asadi and
Mark B. Gerstein and
Alexej Abyzov and
Wing H. Wong and
Hugo Y. K. Lam},
title = {VarSim: a high-fidelity simulation and validation framework for high-throughput
genome sequencing with cancer applications},
journal = {Bioinform.},
volume = {31},
number = {9},
pages = {1469--1471},
year = {2015},
url = {https://doi.org/10.1093/bioinformatics/btu828},
doi = {10.1093/BIOINFORMATICS/BTU828},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MuMLAGAWL15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MohiyuddinMLAGA15,
author = {Marghoob Mohiyuddin and
John C. Mu and
Jian Li and
Narges Bani Asadi and
Mark B. Gerstein and
Alexej Abyzov and
Wing H. Wong and
Hugo Y. K. Lam},
title = {MetaSV: an accurate and integrative structural-variant caller for
next generation sequencing},
journal = {Bioinform.},
volume = {31},
number = {16},
pages = {2741--2744},
year = {2015},
url = {https://doi.org/10.1093/bioinformatics/btv204},
doi = {10.1093/BIOINFORMATICS/BTV204},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MohiyuddinMLAGA15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KuksaMDG15,
author = {Pavel P. Kuksa and
Martin Renqiang Min and
Rishabh Dugar and
Mark Gerstein},
title = {High-order neural networks and kernel methods for peptide-MHC binding
prediction},
journal = {Bioinform.},
volume = {31},
number = {22},
pages = {3600--3607},
year = {2015},
url = {https://doi.org/10.1093/bioinformatics/btv371},
doi = {10.1093/BIOINFORMATICS/BTV371},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KuksaMDG15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/WangYSCRMG15,
author = {Daifeng Wang and
Koon{-}Kiu Yan and
Cristina Sisu and
Chao Cheng and
Joel S. Rozowsky and
William Meyerson and
Mark B. Gerstein},
title = {Loregic: {A} Method to Characterize the Cooperative Logic of Regulatory
Factors},
journal = {PLoS Comput. Biol.},
volume = {11},
number = {4},
year = {2015},
url = {https://doi.org/10.1371/journal.pcbi.1004132},
doi = {10.1371/JOURNAL.PCBI.1004132},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ploscb/WangYSCRMG15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nature/BoyleABCCCGHJJK14,
author = {Alan P. Boyle and
Carlos L. Araya and
Cathleen Brdlik and
Philip Cayting and
Chao Cheng and
Yong Cheng and
Kathryn Gardner and
LaDeana W. Hillier and
Judith Janette and
Lixia Jiang and
Dionna Kasper and
Trupti Kawli and
Pouya Kheradpour and
Anshul Kundaje and
Jingyi Jessica Li and
Lijia Ma and
Wei Niu and
E. Jay Rehm and
Joel S. Rozowsky and
Matthew Slattery and
Rebecca Spokony and
Robert Terrell and
Dionne Vafeados and
Daifeng Wang and
Peter Weisdepp and
Yi{-}Chieh Wu and
Dan Xie and
Koon{-}Kiu Yan and
Elise A. Feingold and
Peter J. Good and
Michael J. Pazin and
Haiyan Huang and
Peter J. Bickel and
Steven E. Brenner and
Valerie Reinke and
Robert H. Waterston and
Mark Gerstein and
Kevin P. White and
Manolis Kellis and
Michael Snyder},
title = {Comparative analysis of regulatory information and circuits across
distant species Open},
journal = {Nat.},
volume = {512},
number = {7515},
pages = {453--456},
year = {2014},
url = {https://doi.org/10.1038/nature13668},
doi = {10.1038/NATURE13668},
timestamp = {Sat, 31 May 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nature/BoyleABCCCGHJJK14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/aistats/MinNCG14,
author = {Martin Renqiang Min and
Xia Ning and
Chao Cheng and
Mark Gerstein},
title = {Interpretable Sparse High-Order Boltzmann Machines},
booktitle = {Proceedings of the Seventeenth International Conference on Artificial
Intelligence and Statistics, {AISTATS} 2014, Reykjavik, Iceland, April
22-25, 2014},
series = {{JMLR} Workshop and Conference Proceedings},
volume = {33},
pages = {614--622},
publisher = {JMLR.org},
year = {2014},
url = {http://proceedings.mlr.press/v33/min14.html},
timestamp = {Wed, 29 May 2019 08:41:44 +0200},
biburl = {https://dblp.org/rec/conf/aistats/MinNCG14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/ChengFSG13,
author = {Chao Cheng and
Yao Fu and
Linsheng Shen and
Mark Gerstein},
title = {Identification of yeast cell cycle regulated genes based on genomic
features},
journal = {{BMC} Syst. Biol.},
volume = {7},
pages = {70},
year = {2013},
url = {https://doi.org/10.1186/1752-0509-7-70},
doi = {10.1186/1752-0509-7-70},
timestamp = {Tue, 05 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcsb/ChengFSG13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/KhuranaFCG13,
author = {Ekta Khurana and
Yao Fu and
Jieming Chen and
Mark Gerstein},
title = {Interpretation of Genomic Variants Using a Unified Biological Network
Approach},
journal = {PLoS Comput. Biol.},
volume = {9},
number = {3},
year = {2013},
url = {https://doi.org/10.1371/journal.pcbi.1002886},
doi = {10.1371/JOURNAL.PCBI.1002886},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/KhuranaFCG13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bcb/WangPFKHWMG13,
author = {Daifeng Wang and
Eric Pan and
Gang Fang and
Sunita Kumari and
Fei He and
Doreen Ware and
Sergei Maslov and
Mark Gerstein},
editor = {Jing Gao},
title = {Comparative network analysis of gene co-expression networks reveals
the conserved and species-specific functions of cell-wall related
genes between Arabidopsis and Poplar},
booktitle = {{ACM} Conference on Bioinformatics, Computational Biology and Biomedical
Informatics. {ACM-BCB} 2013, Washington, DC, USA, September 22-25,
2013},
pages = {689},
publisher = {{ACM}},
year = {2013},
url = {https://doi.org/10.1145/2506583.2506690},
doi = {10.1145/2506583.2506690},
timestamp = {Tue, 06 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/bcb/WangPFKHWMG13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HabeggerBCKSHRCSG12,
author = {Lukas Habegger and
Suganthi Balasubramanian and
David Z. Chen and
Ekta Khurana and
Andrea Sboner and
Arif Ozgun Harmanci and
Joel S. Rozowsky and
Declan Clarke and
Michael Snyder and
Mark Gerstein},
title = {{VAT:} a computational framework to functionally annotate variants
in personal genomes within a cloud-computing environment},
journal = {Bioinform.},
volume = {28},
number = {17},
pages = {2267--2269},
year = {2012},
url = {https://doi.org/10.1093/bioinformatics/bts368},
doi = {10.1093/BIOINFORMATICS/BTS368},
timestamp = {Mon, 02 Jan 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HabeggerBCKSHRCSG12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HabeggerSGRASG11,
author = {Lukas Habegger and
Andrea Sboner and
Tara A. Gianoulis and
Joel S. Rozowsky and
Ashish Agarwal and
Michael Snyder and
Mark Gerstein},
title = {RSEQtools: a modular framework to analyze RNA-Seq data using compact,
anonymized data summaries},
journal = {Bioinform.},
volume = {27},
number = {2},
pages = {281--283},
year = {2011},
url = {https://doi.org/10.1093/bioinformatics/btq643},
doi = {10.1093/BIOINFORMATICS/BTQ643},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HabeggerSGRASG11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AbyzovG11,
author = {Alexej Abyzov and
Mark Gerstein},
title = {{AGE:} defining breakpoints of genomic structural variants at single-nucleotide
resolution, through optimal alignments with gap excision},
journal = {Bioinform.},
volume = {27},
number = {5},
pages = {595--603},
year = {2011},
url = {https://doi.org/10.1093/bioinformatics/btq713},
doi = {10.1093/BIOINFORMATICS/BTQ713},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/AbyzovG11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JeeRYLBZZFWWG11,
author = {Justin Jee and
Joel S. Rozowsky and
Kevin Y. Yip and
Lucas Lochovsky and
Robert D. Bjornson and
Guoneng Zhong and
Zhengdong D. Zhang and
Yutao Fu and
Jie Wang and
Zhiping Weng and
Mark Gerstein},
title = {{ACT:} aggregation and correlation toolbox for analyses of genome
tracks},
journal = {Bioinform.},
volume = {27},
number = {8},
pages = {1152--1154},
year = {2011},
url = {https://doi.org/10.1093/bioinformatics/btr092},
doi = {10.1093/BIOINFORMATICS/BTR092},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/JeeRYLBZZFWWG11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChengMG11,
author = {Chao Cheng and
Renqiang Min and
Mark Gerstein},
title = {{TIP:} {A} probabilistic method for identifying transcription factor
target genes from ChIP-seq binding profiles},
journal = {Bioinform.},
volume = {27},
number = {23},
pages = {3221--3227},
year = {2011},
url = {https://doi.org/10.1093/bioinformatics/btr552},
doi = {10.1093/BIOINFORMATICS/BTR552},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChengMG11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KarpikovRG11,
author = {Alexander Karpikov and
Joel S. Rozowsky and
Mark Gerstein},
title = {Tiling array data analysis: a multiscale approach using wavelets},
journal = {{BMC} Bioinform.},
volume = {12},
pages = {57},
year = {2011},
url = {https://doi.org/10.1186/1471-2105-12-57},
doi = {10.1186/1471-2105-12-57},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/KarpikovRG11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/FloresG11,
author = {Samuel Flores and
Mark B. Gerstein},
title = {Predicting protein ligand binding motions with the Conformation Explorer},
journal = {{BMC} Bioinform.},
volume = {12},
pages = {417},
year = {2011},
url = {https://doi.org/10.1186/1471-2105-12-417},
doi = {10.1186/1471-2105-12-417},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/FloresG11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/ShouBLYKSG11,
author = {Chong Shou and
Nitin Bhardwaj and
Hugo Y. K. Lam and
Koon{-}Kiu Yan and
Philip M. Kim and
Michael Snyder and
Mark B. Gerstein},
title = {Measuring the Evolutionary Rewiring of Biological Networks},
journal = {PLoS Comput. Biol.},
volume = {7},
number = {1},
year = {2011},
url = {https://doi.org/10.1371/journal.pcbi.1001050},
doi = {10.1371/JOURNAL.PCBI.1001050},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ploscb/ShouBLYKSG11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/ChengYHQBRLNAKSG11,
author = {Chao Cheng and
Koon{-}Kiu Yan and
Woochang Hwang and
Jiang Qian and
Nitin Bhardwaj and
Joel S. Rozowsky and
Zhi John Lu and
Wei Niu and
Pedro Alves and
Masaomi Kato and
Michael Snyder and
Mark Gerstein},
title = {Construction and Analysis of an Integrated Regulatory Network Derived
from High-Throughput Sequencing Data},
journal = {PLoS Comput. Biol.},
volume = {7},
number = {11},
year = {2011},
url = {https://doi.org/10.1371/journal.pcbi.1002190},
doi = {10.1371/JOURNAL.PCBI.1002190},
timestamp = {Mon, 03 Mar 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ploscb/ChengYHQBRLNAKSG11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/GreenbaumSMG11,
author = {Dov Greenbaum and
Andrea Sboner and
Xinmeng Jasmine Mu and
Mark Gerstein},
title = {Genomics and Privacy: Implications of the New Reality of Closed Data
for the Field},
journal = {PLoS Comput. Biol.},
volume = {7},
number = {12},
year = {2011},
url = {https://doi.org/10.1371/journal.pcbi.1002278},
doi = {10.1371/JOURNAL.PCBI.1002278},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/GreenbaumSMG11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HolfordKCG10,
author = {Matthew Holford and
Ekta Khurana and
Kei{-}Hoi Cheung and
Mark Gerstein},
title = {Using semantic web rules to reason on an ontology of pseudogenes},
journal = {Bioinform.},
volume = {26},
number = {12},
pages = {71--78},
year = {2010},
url = {https://doi.org/10.1093/bioinformatics/btq173},
doi = {10.1093/BIOINFORMATICS/BTQ173},
timestamp = {Tue, 01 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HolfordKCG10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BhardwajGL10,
author = {Nitin Bhardwaj and
Mark Gerstein and
Hui Lu},
title = {Genome-wide sequence-based prediction of peripheral proteins using
a novel semi-supervised learning technique},
journal = {{BMC} Bioinform.},
volume = {11},
number = {{S-1}},
pages = {6},
year = {2010},
url = {https://doi.org/10.1186/1471-2105-11-S1-S6},
doi = {10.1186/1471-2105-11-S1-S6},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/BhardwajGL10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LamKMTSTSG10,
author = {Hugo Y. K. Lam and
Philip M. Kim and
Janine Mok and
Raffi Tonikian and
Sachdev S. Sidhu and
Benjamin E. Turk and
Michael Snyder and
Mark B. Gerstein},
title = {{MOTIPS:} Automated Motif Analysis for Predicting Targets of Modular
Protein Domains},
journal = {{BMC} Bioinform.},
volume = {11},
pages = {243},
year = {2010},
url = {https://doi.org/10.1186/1471-2105-11-243},
doi = {10.1186/1471-2105-11-243},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/LamKMTSTSG10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhangG10a,
author = {Zhengdong D. Zhang and
Mark B. Gerstein},
title = {Detection of copy number variation from array intensity and sequencing
read depth using a stepwise Bayesian model},
journal = {{BMC} Bioinform.},
volume = {11},
pages = {539},
year = {2010},
url = {https://doi.org/10.1186/1471-2105-11-539},
doi = {10.1186/1471-2105-11-539},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhangG10a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/VossG10,
author = {Neil Voss and
Mark Gerstein},
title = {3V: cavity, channel and cleft volume calculator and extractor},
journal = {Nucleic Acids Res.},
volume = {38},
number = {Web-Server-Issue},
pages = {555--562},
year = {2010},
url = {https://doi.org/10.1093/nar/gkq395},
doi = {10.1093/NAR/GKQ395},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/VossG10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/FangBRG10,
author = {Gang Fang and
Nitin Bhardwaj and
Rebecca Robilotto and
Mark B. Gerstein},
title = {Getting Started in Gene Orthology and Functional Analysis},
journal = {PLoS Comput. Biol.},
volume = {6},
number = {3},
year = {2010},
url = {https://doi.org/10.1371/journal.pcbi.1000703},
doi = {10.1371/JOURNAL.PCBI.1000703},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/FangBRG10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/LeeYHFZWLHCLGWXL10,
author = {Younghee Lee and
Xinan Yang and
Yong Huang and
Hanli Fan and
Qingbei Zhang and
Youngfei Wu and
Jianrong Li and
Rifat Hasina and
Chao Cheng and
Mark W. Lingen and
Mark B. Gerstein and
Ralph R. Weichselbaum and
H. Rosie Xing and
Yves A. Lussier},
title = {Network Modeling Identifies Molecular Functions Targeted by miR-204
to Suppress Head and Neck Tumor Metastasis},
journal = {PLoS Comput. Biol.},
volume = {6},
number = {4},
year = {2010},
url = {https://doi.org/10.1371/journal.pcbi.1000730},
doi = {10.1371/JOURNAL.PCBI.1000730},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/LeeYHFZWLHCLGWXL10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/BhardwajCAYLG10,
author = {Nitin Bhardwaj and
Matthew B. Carson and
Alexej Abyzov and
Koon{-}Kiu Yan and
Hui Lu and
Mark B. Gerstein},
title = {Analysis of Combinatorial Regulation: Scaling of Partnerships between
Regulators with the Number of Governed Targets},
journal = {PLoS Comput. Biol.},
volume = {6},
number = {5},
year = {2010},
url = {https://doi.org/10.1371/journal.pcbi.1000755},
doi = {10.1371/JOURNAL.PCBI.1000755},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/BhardwajCAYLG10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bcb/Gerstein10,
author = {Mark Gerstein},
editor = {Aidong Zhang and
Mark Borodovsky and
Gultekin {\"{O}}zsoyoglu and
Armin R. Mikler},
title = {Analysis of molecular networks},
booktitle = {Proceedings of the First {ACM} International Conference on Bioinformatics
and Computational Biology, {BCB} 2010, Niagara Falls, NY, USA, August
2-4, 2010},
pages = {1},
publisher = {{ACM}},
year = {2010},
url = {https://doi.org/10.1145/1854776.1854778},
doi = {10.1145/1854776.1854778},
timestamp = {Tue, 06 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/bcb/Gerstein10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gensips/BhardwajG10,
author = {Nitin Bhardwaj and
Mark Gerstein},
title = {Dynamic and static analysis of transcriptional regulatory networks
in a hierarchical context},
booktitle = {2010 {IEEE} International Workshop on Genomic Signal Processing and
Statistics, GENSiPS 2010, Cold Spring Harbor, NY, USA, November 10-12,
2010},
pages = {1},
publisher = {{IEEE}},
year = {2010},
url = {https://doi.org/10.1109/GENSIPS.2010.5719671},
doi = {10.1109/GENSIPS.2010.5719671},
timestamp = {Wed, 16 Oct 2019 14:14:54 +0200},
biburl = {https://dblp.org/rec/conf/gensips/BhardwajG10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gensips/YanG10,
author = {Koon{-}Kiu Yan and
Mark Gerstein},
title = {Hierarchical analysis of regulatory networks and cross-disciplinary
comparison with the Linux call graph},
booktitle = {2010 {IEEE} International Workshop on Genomic Signal Processing and
Statistics, GENSiPS 2010, Cold Spring Harbor, NY, USA, November 10-12,
2010},
pages = {1},
publisher = {{IEEE}},
year = {2010},
url = {https://doi.org/10.1109/GENSIPS.2010.5719687},
doi = {10.1109/GENSIPS.2010.5719687},
timestamp = {Thu, 25 May 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/gensips/YanG10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isbra/Gerstein10,
author = {Mark B. Gerstein},
editor = {Mark Borodovsky and
Johann Peter Gogarten and
Teresa M. Przytycka and
Sanguthevar Rajasekaran},
title = {Human Genome Annotation},
booktitle = {Bioinformatics Research and Applications, 6th International Symposium,
{ISBRA} 2010, Storrs, CT, USA, May 23-26, 2010. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {6053},
pages = {50--51},
publisher = {Springer},
year = {2010},
url = {https://doi.org/10.1007/978-3-642-13078-6\_7},
doi = {10.1007/978-3-642-13078-6\_7},
timestamp = {Tue, 14 May 2019 10:00:51 +0200},
biburl = {https://dblp.org/rec/conf/isbra/Gerstein10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YipG09,
author = {Kevin Y. Yip and
Mark Gerstein},
title = {Training set expansion: an approach to improving the reconstruction
of biological networks from limited and uneven reliable interactions},
journal = {Bioinform.},
volume = {25},
number = {2},
pages = {243--250},
year = {2009},
url = {https://doi.org/10.1093/bioinformatics/btn602},
doi = {10.1093/BIOINFORMATICS/BTN602},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/YipG09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/YipKMG09,
author = {Kevin Y. Yip and
Philip M. Kim and
Drew McDermott and
Mark Gerstein},
title = {Multi-level learning: improving the prediction of protein, domain
and residue interactions by allowing information flow between levels},
journal = {{BMC} Bioinform.},
volume = {10},
year = {2009},
url = {https://doi.org/10.1186/1471-2105-10-241},
doi = {10.1186/1471-2105-10-241},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/YipKMG09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/LamKFCCCG09,
author = {Hugo Y. K. Lam and
Ekta Khurana and
Gang Fang and
Philip Cayting and
Nicholas Carriero and
Kei{-}Hoi Cheung and
Mark B. Gerstein},
title = {Pseudofam: the pseudogene families database},
journal = {Nucleic Acids Res.},
volume = {37},
number = {Database-Issue},
pages = {738--743},
year = {2009},
url = {https://doi.org/10.1093/nar/gkn758},
doi = {10.1093/NAR/GKN758},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/LamKFCCCG09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/XiaFG09,
author = {Yu Xia and
Eric A. Franzosa and
Mark B. Gerstein},
title = {Integrated Assessment of Genomic Correlates of Protein Evolutionary
Rate},
journal = {PLoS Comput. Biol.},
volume = {5},
number = {6},
year = {2009},
url = {https://doi.org/10.1371/journal.pcbi.1000413},
doi = {10.1371/JOURNAL.PCBI.1000413},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ploscb/XiaFG09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/DuBZKSG09,
author = {Jiang Du and
Robert D. Bjornson and
Zhengdong D. Zhang and
Yong Kong and
Michael Snyder and
Mark B. Gerstein},
title = {Integrating Sequencing Technologies in Personal Genomics: Optimal
Low Cost Reconstruction of Structural Variants},
journal = {PLoS Comput. Biol.},
volume = {5},
number = {7},
year = {2009},
url = {https://doi.org/10.1371/journal.pcbi.1000432},
doi = {10.1371/JOURNAL.PCBI.1000432},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ploscb/DuBZKSG09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/GuoZGZ09,
author = {Xingyi Guo and
Zhaolei Zhang and
Mark B. Gerstein and
Deyou Zheng},
title = {Small RNAs Originated from Pseudogenes: \emph{cis}- or \emph{trans}-Acting?},
journal = {PLoS Comput. Biol.},
volume = {5},
number = {7},
year = {2009},
url = {https://doi.org/10.1371/journal.pcbi.1000449},
doi = {10.1371/JOURNAL.PCBI.1000449},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/GuoZGZ09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/RzhetskySG09,
author = {Andrey Rzhetsky and
Michael R. Seringhaus and
Mark B. Gerstein},
title = {Getting Started in Text Mining: Part Two},
journal = {PLoS Comput. Biol.},
volume = {5},
number = {7},
year = {2009},
url = {https://doi.org/10.1371/journal.pcbi.1000411},
doi = {10.1371/JOURNAL.PCBI.1000411},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/RzhetskySG09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YipPKEMG08,
author = {Kevin Y. Yip and
Prianka Patel and
Philip M. Kim and
Donald M. Engelman and
Drew McDermott and
Mark Gerstein},
title = {An integrated system for studying residue coevolution in proteins},
journal = {Bioinform.},
volume = {24},
number = {2},
pages = {290--292},
year = {2008},
url = {https://doi.org/10.1093/bioinformatics/btm584},
doi = {10.1093/BIOINFORMATICS/BTM584},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/YipPKEMG08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/BourneFG08,
author = {Philip E. Bourne and
J. Lynn Fink and
Mark Gerstein},
title = {Open Access: Taking Full Advantage of the Content},
journal = {PLoS Comput. Biol.},
volume = {4},
number = {3},
year = {2008},
url = {https://doi.org/10.1371/journal.pcbi.1000037},
doi = {10.1371/JOURNAL.PCBI.1000037},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/BourneFG08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/ZhangRSCG08,
author = {Zhengdong D. Zhang and
Joel S. Rozowsky and
Michael Snyder and
Joseph T. Chang and
Mark Gerstein},
title = {Modeling ChIP Sequencing In Silico with Applications},
journal = {PLoS Comput. Biol.},
volume = {4},
number = {8},
year = {2008},
url = {https://doi.org/10.1371/journal.pcbi.1000158},
doi = {10.1371/JOURNAL.PCBI.1000158},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ploscb/ZhangRSCG08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RoyceRG07,
author = {Thomas E. Royce and
Joel S. Rozowsky and
Mark Gerstein},
title = {Assessing the need for sequence-based normalization in tiling microarray
experiments},
journal = {Bioinform.},
volume = {23},
number = {8},
pages = {988--997},
year = {2007},
url = {https://doi.org/10.1093/bioinformatics/btm052},
doi = {10.1093/BIOINFORMATICS/BTM052},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/RoyceRG07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YipYKSG07,
author = {Kevin Y. Yip and
Haiyuan Yu and
Philip M. Kim and
Martin H. Schultz and
Mark Gerstein},
title = {The tYNA platform for comparative interactomics: a web tool for managing,
comparing and mining multiple networks},
journal = {Bioinform.},
volume = {23},
number = {8},
pages = {1048},
year = {2007},
url = {https://doi.org/10.1093/bioinformatics/btm099},
doi = {10.1093/BIOINFORMATICS/BTM099},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/YipYKSG07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YuJSG07,
author = {Haiyuan Yu and
Ronald Jansen and
Gustavo Stolovitzky and
Mark Gerstein},
title = {Total ancestry measure: quantifying the similarity in tree-like classification,
with genomic applications},
journal = {Bioinform.},
volume = {23},
number = {16},
pages = {2163--2173},
year = {2007},
url = {https://doi.org/10.1093/bioinformatics/btm291},
doi = {10.1093/BIOINFORMATICS/BTM291},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/YuJSG07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SmithCKSG07,
author = {Andrew K. Smith and
Kei{-}Hoi Cheung and
Michael Krauthammer and
Martin H. Schultz and
Mark Gerstein},
title = {Leveraging the structure of the Semantic Web to enhance information
retrieval for proteomics},
journal = {Bioinform.},
volume = {23},
number = {22},
pages = {3073--3079},
year = {2007},
url = {https://doi.org/10.1093/bioinformatics/btm452},
doi = {10.1093/BIOINFORMATICS/BTM452},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SmithCKSG07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/FloresG07,
author = {Samuel Flores and
Mark Gerstein},
title = {FlexOracle: predicting flexible hinges by identification of stable
domains},
journal = {{BMC} Bioinform.},
volume = {8},
year = {2007},
url = {https://doi.org/10.1186/1471-2105-8-215},
doi = {10.1186/1471-2105-8-215},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/FloresG07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/FloresLYCG07,
author = {Samuel Flores and
Long J. Lu and
Julie Yang and
Nicholas Carriero and
Mark Gerstein},
title = {Hinge Atlas: relating protein sequence to sites of structural flexibility},
journal = {{BMC} Bioinform.},
volume = {8},
year = {2007},
url = {https://doi.org/10.1186/1471-2105-8-167},
doi = {10.1186/1471-2105-8-167},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/FloresLYCG07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/RoyceCG07,
author = {Thomas E. Royce and
Nicholas Carriero and
Mark B. Gerstein},
title = {An efficient pseudomedian filter for tiling microrrays},
journal = {{BMC} Bioinform.},
volume = {8},
year = {2007},
url = {https://doi.org/10.1186/1471-2105-8-186},
doi = {10.1186/1471-2105-8-186},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/RoyceCG07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SeringhausG07,
author = {Michael R. Seringhaus and
Mark B. Gerstein},
title = {Publishing perishing? Towards tomorrow's information architecture},
journal = {{BMC} Bioinform.},
volume = {8},
year = {2007},
url = {https://doi.org/10.1186/1471-2105-8-17},
doi = {10.1186/1471-2105-8-17},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/SeringhausG07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SmithCYSG07,
author = {Andrew K. Smith and
Kei{-}Hoi Cheung and
Kevin Y. Yip and
Martin H. Schultz and
Mark Gerstein},
title = {LinkHub: a Semantic Web system that facilitates cross-database queries
and information retrieval in proteomics},
journal = {{BMC} Bioinform.},
volume = {8},
number = {{S-3}},
year = {2007},
url = {https://doi.org/10.1186/1471-2105-8-S3-S5},
doi = {10.1186/1471-2105-8-S3-S5},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/SmithCYSG07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/YuBG07,
author = {Eric Z. Yu and
Anne E. Counterman Burba and
Mark Gerstein},
title = {{PARE:} {A} tool for comparing protein abundance and mRNA expression
data},
journal = {{BMC} Bioinform.},
volume = {8},
year = {2007},
url = {https://doi.org/10.1186/1471-2105-8-309},
doi = {10.1186/1471-2105-8-309},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/YuBG07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbi/GersteinGCM07,
author = {Mark Gerstein and
Dov Greenbaum and
Kei{-}Hoi Cheung and
Perry L. Miller},
title = {An interdepartmental Ph.D. program in computational biology and bioinformatics:
The Yale perspective},
journal = {J. Biomed. Informatics},
volume = {40},
number = {1},
pages = {73--79},
year = {2007},
url = {https://doi.org/10.1016/j.jbi.2006.02.008},
doi = {10.1016/J.JBI.2006.02.008},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jbi/GersteinGCM07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/KarroYZZCCHG07,
author = {John E. Karro and
Yangpan Yan and
Deyou Zheng and
Zhaolei Zhang and
Nicholas Carriero and
Philip Cayting and
Paul M. Harrison and
Mark Gerstein},
title = {Pseudogene.org: a comprehensive database and comparison platform for
pseudogene annotation},
journal = {Nucleic Acids Res.},
volume = {35},
number = {Database-Issue},
pages = {55--60},
year = {2007},
url = {https://doi.org/10.1093/nar/gkl851},
doi = {10.1093/NAR/GKL851},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/KarroYZZCCHG07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/GersteinD07,
author = {Mark Gerstein and
Shawn M. Douglas},
title = {RNAi Development},
journal = {PLoS Comput. Biol.},
volume = {3},
number = {4},
year = {2007},
url = {https://doi.org/10.1371/journal.pcbi.0030080},
doi = {10.1371/JOURNAL.PCBI.0030080},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/GersteinD07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/YuKSTG07,
author = {Haiyuan Yu and
Philip M. Kim and
Emmett Sprecher and
Valery Trifonov and
Mark Gerstein},
title = {The Importance of Bottlenecks in Protein Networks: Correlation with
Gene Essentiality and Expression Dynamics},
journal = {PLoS Comput. Biol.},
volume = {3},
number = {4},
year = {2007},
url = {https://doi.org/10.1371/journal.pcbi.0030059},
doi = {10.1371/JOURNAL.PCBI.0030059},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/YuKSTG07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YuPTG06,
author = {Haiyuan Yu and
Alberto Paccanaro and
Valery Trifonov and
Mark Gerstein},
title = {Predicting interactions in protein networks by completing defective
cliques},
journal = {Bioinform.},
volume = {22},
number = {7},
pages = {823--829},
year = {2006},
url = {https://doi.org/10.1093/bioinformatics/btl014},
doi = {10.1093/BIOINFORMATICS/BTL014},
timestamp = {Tue, 01 Apr 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/YuPTG06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhangCZKHG06,
author = {Zhaolei Zhang and
Nicholas Carriero and
Deyou Zheng and
John E. Karro and
Paul M. Harrison and
Mark Gerstein},
title = {PseudoPipe: an automated pseudogene identification pipeline},
journal = {Bioinform.},
volume = {22},
number = {12},
pages = {1437--1439},
year = {2006},
url = {https://doi.org/10.1093/bioinformatics/btl116},
doi = {10.1093/BIOINFORMATICS/BTL116},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhangCZKHG06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BurbaLYG06,
author = {Anne E. Counterman Burba and
Ursula Lehnert and
Eric Z. Yu and
Mark Gerstein},
title = {Helix Interaction Tool {(HIT):} a web-based tool for analysis of helix-helix
interactions in proteins},
journal = {Bioinform.},
volume = {22},
number = {22},
pages = {2735--2738},
year = {2006},
url = {https://doi.org/10.1093/bioinformatics/btl274},
doi = {10.1093/BIOINFORMATICS/BTL274},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/BurbaLYG06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/YipYKSG06,
author = {Kevin Y. Yip and
Haiyuan Yu and
Philip M. Kim and
Martin H. Schultz and
Mark Gerstein},
title = {The tYNA platform for comparative interactomics: a web tool for managing,
comparing and mining multiple networks},
journal = {Bioinform.},
volume = {22},
number = {23},
pages = {2968--2970},
year = {2006},
url = {https://doi.org/10.1093/bioinformatics/btl488},
doi = {10.1093/BIOINFORMATICS/BTL488},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/YipYKSG06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DuRKZRSSG06,
author = {Jiang Du and
Joel S. Rozowsky and
Jan O. Korbel and
Zhengdong D. Zhang and
Thomas E. Royce and
Martin H. Schultz and
Michael Snyder and
Mark Gerstein},
title = {A supervised hidden markov model framework for efficiently segmenting
tiling array data in transcriptional and chIP-chip experiments: systematically
incorporating validated biological knowledge},
journal = {Bioinform.},
volume = {22},
number = {24},
pages = {3016--3024},
year = {2006},
url = {https://doi.org/10.1093/bioinformatics/btl515},
doi = {10.1093/BIOINFORMATICS/BTL515},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/DuRKZRSSG06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/FloresEMHKLWYTG06,
author = {Samuel Flores and
Nathaniel Echols and
Duncan Milburn and
Brandon Hespenheide and
Kevin Keating and
Jason Lu and
Stephen Wells and
Eric Z. Yu and
Michael Thorpe and
Mark Gerstein},
title = {The Database of Macromolecular Motions: new features added at the
decade mark},
journal = {Nucleic Acids Res.},
volume = {34},
number = {Database-Issue},
pages = {296--301},
year = {2006},
url = {https://doi.org/10.1093/nar/gkj046},
doi = {10.1093/NAR/GKJ046},
timestamp = {Thu, 27 May 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/FloresEMHKLWYTG06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/LiuLSGGL06,
author = {Yang Liu and
Jianrong Li and
Lee T. Sam and
Chern{-}Sing Goh and
Mark Gerstein and
Yves A. Lussier},
title = {An Integrative Genomic Approach to Uncover Molecular Mechanisms of
Prokaryotic Traits},
journal = {PLoS Comput. Biol.},
volume = {2},
number = {11},
year = {2006},
url = {https://doi.org/10.1371/journal.pcbi.0020159},
doi = {10.1371/JOURNAL.PCBI.0020159},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/LiuLSGGL06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ciss/SaywardYNEUBRWG06,
author = {Frederick G. Sayward and
Jin Yang and
Kenneth Nelson and
Ghia Euskirchen and
Alexander E. Urban and
Paul Bertone and
John Rinn and
Sherman Weissman and
Mark Gerstein and
Michael Snyder and
Perry L. Miller},
title = {Design Issues in Implementing a Portable Sample Tracking and Analysis
Research Support {(STARS)} System for {PCR} Based Microarray Research},
booktitle = {40th Annual Conference on Information Sciences and Systems, {CISS}
2006, Princeton, NJ, USA, 22-24 March 2006},
pages = {1578--1598},
publisher = {{IEEE}},
year = {2006},
url = {https://doi.org/10.1109/CISS.2006.286390},
doi = {10.1109/CISS.2006.286390},
timestamp = {Fri, 08 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ciss/SaywardYNEUBRWG06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jamia/CarrieroOCMGZWRCZWWS05,
author = {Nicholas Carriero and
Michael V. Osier and
Kei{-}Hoi Cheung and
Perry L. Miller and
Mark Gerstein and
Hongyu Zhao and
Baolin Wu and
Scott Rifkin and
Joseph T. Chang and
Heping Zhang and
Kevin P. White and
Kenneth R. Williams and
Martin H. Schultz},
title = {Case Report: {A} High Productivity/Low Maintenance Approach to High-performance
Computation for Biomedicine: Four Case Studies},
journal = {J. Am. Medical Informatics Assoc.},
volume = {12},
number = {1},
pages = {90--98},
year = {2005},
url = {https://doi.org/10.1197/jamia.M1571},
doi = {10.1197/JAMIA.M1571},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jamia/CarrieroOCMGZWRCZWWS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/GreenbaumSG05,
author = {Dov Greenbaum and
Andrew K. Smith and
Mark Gerstein},
title = {Editorial},
journal = {Nucleic Acids Res.},
volume = {33},
number = {Database-Issue},
pages = {3--4},
year = {2005},
url = {https://doi.org/10.1093/nar/gki134},
doi = {10.1093/NAR/GKI134},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/GreenbaumSG05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ijcnn/PaccanaroTYG05,
author = {Alberto Paccanaro and
Valery Trifonov and
Haiyuan Yu and
Mark Gerstein},
title = {Inferring protein-protein interactions using interaction network topologies},
booktitle = {{IEEE} International Joint Conference on Neural Networks, {IJCNN}
2005, Montreal, QC, Canada, July 31 - August 4, 2005},
pages = {161--166},
publisher = {{IEEE}},
year = {2005},
url = {https://doi.org/10.1109/IJCNN.2005.1555823},
doi = {10.1109/IJCNN.2005.1555823},
timestamp = {Tue, 21 Jan 2025 17:15:28 +0100},
biburl = {https://dblp.org/rec/conf/ijcnn/PaccanaroTYG05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/CheungYSdMG05,
author = {Kei{-}Hoi Cheung and
Kevin Y. Yip and
Andrew K. Smith and
Remko de Knikker and
Andy Masiar and
Mark Gerstein},
title = {YeastHub: a semantic web use case for integrating data in the life
sciences domain},
booktitle = {Proceedings Thirteenth International Conference on Intelligent Systems
for Molecular Biology 2005, Detroit, MI, USA, 25-29 June 2005},
pages = {85--96},
year = {2005},
url = {https://doi.org/10.1093/bioinformatics/bti1026},
doi = {10.1093/BIOINFORMATICS/BTI1026},
timestamp = {Wed, 25 Sep 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ismb/CheungYSdMG05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wob/RozowskyBRWSG05,
author = {Joel S. Rozowsky and
Paul Bertone and
Thomas E. Royce and
Sherman Weissman and
Michael Snyder and
Mark Gerstein},
editor = {Jo{\~{a}}o C. Setubal and
Sergio Verjovski{-}Almeida},
title = {Analysis of Genomic Tiling Microarrays for Transcript Mapping and
the Identification of Transcription Factor Binding Sites},
booktitle = {Advances in Bioinformatics and Computational Biology, Brazilian Symposium
on Bioinformatics, {BSB} 2005, Sao Leopoldo, Brazil, July 27-29, 2005,
Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3594},
pages = {28--29},
publisher = {Springer},
year = {2005},
url = {https://doi.org/10.1007/11532323\_4},
doi = {10.1007/11532323\_4},
timestamp = {Tue, 07 May 2024 20:12:02 +0200},
biburl = {https://dblp.org/rec/conf/wob/RozowskyBRWSG05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@incollection{DBLP:books/wi/05/LuXYRLSG05,
author = {Long J. Lu and
Yu Xia and
Haiyuan Yu and
Alexander Rives and
Haoxin Lu and
Falk Schubert and
Mark Gerstein},
editor = {Francisco Azuaje and
Joaqu{\'{\i}}n Dopazo},
title = {Protein Interaction Prediction by Integrating Genomic Features and
Protein Interaction Network Analysis},
booktitle = {Data Analysis and Visualization in Genomics and Proteomics},
pages = {61--81},
publisher = {Wiley},
year = {2005},
url = {https://doi.org/10.1002/0470094419.ch5},
doi = {10.1002/0470094419.CH5},
timestamp = {Tue, 08 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/books/wi/05/LuXYRLSG05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AlexandrovG04,
author = {Vadim Alexandrov and
Mark Gerstein},
title = {Using 3D Hidden Markov Models that explicitly represent spatial coordinates
to model and compare protein structures},
journal = {{BMC} Bioinform.},
volume = {5},
pages = {2},
year = {2004},
url = {https://doi.org/10.1186/1471-2105-5-2},
doi = {10.1186/1471-2105-5-2},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/AlexandrovG04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LinWJGZ04,
author = {Nan Lin and
Baolin Wu and
Ronald Jansen and
Mark Gerstein and
Hongyu Zhao},
title = {Information assessment on predicting protein-protein interactions},
journal = {{BMC} Bioinform.},
volume = {5},
pages = {154},
year = {2004},
url = {https://doi.org/10.1186/1471-2105-5-154},
doi = {10.1186/1471-2105-5-154},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/LinWJGZ04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/BermanBDGKS04,
author = {Piotr Berman and
Paul Bertone and
Bhaskar DasGupta and
Mark Gerstein and
Ming{-}Yang Kao and
Michael Snyder},
title = {Fast Optimal Genome Tiling with Applications to Microarray Design
and Homology Search},
journal = {J. Comput. Biol.},
volume = {11},
number = {4},
pages = {766--785},
year = {2004},
url = {https://doi.org/10.1089/cmb.2004.11.766},
doi = {10.1089/CMB.2004.11.766},
timestamp = {Mon, 15 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/BermanBDGKS04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/metmbs/CheungPSSDG04,
author = {Kei{-}Hoi Cheung and
Deyun Pan and
Andrew K. Smith and
Michael R. Seringhaus and
Shawn M. Douglas and
Mark Gerstein},
editor = {Faramarz Valafar and
Homayoun Valafar},
title = {A XML-Based Approach to Integrating Heterogeneous Yeast Genome Data},
booktitle = {Proceedings of the International Conference on Mathematics and Engineering
Techniques in Medicine and Biological Scienes, {METMBS} '04, June
21-24, 2004, Las Vegas, Nevada, {USA}},
pages = {236--242},
publisher = {{CSREA} Press},
year = {2004},
timestamp = {Thu, 23 Jun 2016 15:53:27 +0200},
biburl = {https://dblp.org/rec/conf/metmbs/CheungPSSDG04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/QianLLYG03,
author = {Jiang Qian and
C. Jimmy Lin and
Nicholas M. Luscombe and
Haiyuan Yu and
Mark Gerstein},
title = {Prediction of regulatory networks: genome-wide identification of transcription
factor targets from gene expression data},
journal = {Bioinform.},
volume = {19},
number = {15},
pages = {1917--1926},
year = {2003},
url = {https://doi.org/10.1093/bioinformatics/btg347},
doi = {10.1093/BIOINFORMATICS/BTG347},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/QianLLYG03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/EcholsMG03,
author = {Nathaniel Echols and
Duncan Milburn and
Mark Gerstein},
title = {MolMovDB: analysis and visualization of conformational change and
structural flexibility},
journal = {Nucleic Acids Res.},
volume = {31},
number = {1},
pages = {478--482},
year = {2003},
url = {https://doi.org/10.1093/nar/gkg104},
doi = {10.1093/NAR/GKG104},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/EcholsMG03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/LuscombeRBEHCSG03,
author = {Nicholas M. Luscombe and
Thomas E. Royce and
Paul Bertone and
Nathaniel Echols and
Christine E. Horak and
Joseph T. Chang and
Michael Snyder and
Mark Gerstein},
title = {ExpressYourself: a modular platform for processing and visualizing
microarray data},
journal = {Nucleic Acids Res.},
volume = {31},
number = {13},
pages = {3477--3482},
year = {2003},
url = {https://doi.org/10.1093/nar/gkg628},
doi = {10.1093/NAR/GKG628},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/LuscombeRBEHCSG03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gcb/Gerstein03,
author = {Mark Gerstein},
title = {Computational Proteomics: Genome-scale Analysis of Protein Structure,
Function, {\&} Evolution(Invited Talk)},
booktitle = {Proceedings of the German Conference on Bioinformatics, {GCB} 2003,
October 12-14, 2003, Neuherberg/Garching near Munich, Germany},
pages = {53},
year = {2003},
timestamp = {Tue, 15 Mar 2005 13:11:15 +0100},
biburl = {https://dblp.org/rec/conf/gcb/Gerstein03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GreenbaumJG02,
author = {Dov Greenbaum and
Ronald Jansen and
Mark Gerstein},
title = {Analysis of mRNA expression and protein abundance data: an approach
for the comparison of the enrichment of features in the cellular population
of proteins and transcripts},
journal = {Bioinform.},
volume = {18},
number = {4},
pages = {585--596},
year = {2002},
url = {https://doi.org/10.1093/bioinformatics/18.4.585},
doi = {10.1093/BIOINFORMATICS/18.4.585},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GreenbaumJG02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TsaiG02,
author = {Jerry Tsai and
Mark Gerstein},
title = {Calculations of protein volumes: sensitivity analysis and parameter
database},
journal = {Bioinform.},
volume = {18},
number = {7},
pages = {985--995},
year = {2002},
url = {https://doi.org/10.1093/bioinformatics/18.7.985},
doi = {10.1093/BIOINFORMATICS/18.7.985},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/TsaiG02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/pieee/LanJG02,
author = {Ning Lan and
Ronald Jansen and
Mark Gerstein},
title = {Toward a systematic definition of protein function that scales to
the genome level: defining function in terms of interactions},
journal = {Proc. {IEEE}},
volume = {90},
number = {12},
pages = {1848--1858},
year = {2002},
url = {https://doi.org/10.1109/JPROC.2002.805302},
doi = {10.1109/JPROC.2002.805302},
timestamp = {Tue, 17 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/pieee/LanJG02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/amia/CheungWHGRNMSLLZLASMW02,
author = {Kei{-}Hoi Cheung and
Kevin P. White and
Janet Hager and
Mark Gerstein and
Valerie Reinke and
Kenneth Nelson and
Peter Masiar and
Ranjana Srivastava and
Yuli Li and
Ju Li and
Hongyu Zhao and
Jinming Li and
David B. Allison and
Michael Snyder and
Perry L. Miller and
Kenneth R. Williams},
title = {{YMD:} a microarray database for large-scale gene expression analysis},
booktitle = {{AMIA} 2002, American Medical Informatics Association Annual Symposium,
San Antonio, TX, USA, November 9-13, 2002},
publisher = {{AMIA}},
year = {2002},
url = {https://knowledge.amia.org/amia-55142-a2002a-1.610020/t-001-1.612667/f-001-1.612668/a-028-1.613169/a-029-1.613164},
timestamp = {Wed, 17 Apr 2024 11:48:33 +0200},
biburl = {https://dblp.org/rec/conf/amia/CheungWHGRNMSLLZLASMW02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/BermanBDGKS02,
author = {Piotr Berman and
Paul Bertone and
Bhaskar DasGupta and
Mark Gerstein and
Ming{-}Yang Kao and
Michael Snyder},
editor = {Roderic Guig{\'{o}} and
Dan Gusfield},
title = {Fast Optimal Genome Tiling with Applications to Microarray Design
and Homology Search},
booktitle = {Algorithms in Bioinformatics, Second International Workshop, {WABI}
2002, Rome, Italy, September 17-21, 2002, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {2452},
pages = {419--433},
publisher = {Springer},
year = {2002},
url = {https://doi.org/10.1007/3-540-45784-4\_32},
doi = {10.1007/3-540-45784-4\_32},
timestamp = {Mon, 15 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/wabi/BermanBDGKS02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/TsaiVG01,
author = {Jerry Tsai and
Neil Voss and
Mark Gerstein},
title = {Determining the minimum number of types necessary to represent the
sizes of protein atoms},
journal = {Bioinform.},
volume = {17},
number = {10},
pages = {949--956},
year = {2001},
url = {https://doi.org/10.1093/bioinformatics/17.10.949},
doi = {10.1093/BIOINFORMATICS/17.10.949},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/TsaiVG01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/BertoneKLZCYEAMG01,
author = {Paul Bertone and
Yuval Kluger and
Ning Lan and
Deyou Zheng and
Dinesh Christendat and
Adelinda Yee and
Aled M. Edwards and
Cheryl H. Arrowsmith and
Gaetano T. Montelione and
Mark Gerstein},
title = {{SPINE:} an integrated tracking database and data mining approach
for identifying feasible targets in high-throughput structural proteomics},
journal = {Nucleic Acids Res.},
volume = {29},
number = {13},
pages = {2884--2898},
year = {2001},
url = {https://doi.org/10.1093/nar/29.13.2884},
doi = {10.1093/NAR/29.13.2884},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/BertoneKLZCYEAMG01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibe/CheungLKSGM01,
author = {Kei{-}Hoi Cheung and
Yang Liu and
Anuj Kumar and
Michael Snyder and
Mark Gerstein and
Perry L. Miller},
editor = {Nikolaos G. Bourbakis},
title = {An {XML} Application For Genomic Data Interoperation},
booktitle = {2nd {IEEE} International Symposium on Bioinformatics and Bioengineering,
Bethesda, Maryland, USA, November 4-5, 2001, Proceedings},
pages = {97--103},
publisher = {{IEEE} Computer Society},
year = {2001},
url = {https://doi.org/10.1109/BIBE.2001.974417},
doi = {10.1109/BIBE.2001.974417},
timestamp = {Thu, 01 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bibe/CheungLKSGM01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Gerstein98,
author = {Mark Gerstein},
title = {Measurement of the effectiveness of transitive sequence comparison,
through a third 'intermediate' sequence},
journal = {Bioinform.},
volume = {14},
number = {8},
pages = {707--714},
year = {1998},
url = {http://bioinformatics.oxfordjournals.org/content/14/8/707.abstract},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/Gerstein98.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gcb/Gerstein98,
author = {Mark Gerstein},
title = {[Invited Lecture] {A} Structural Census of Genomes: Comparing Bacterial,
Eukaryotic, and Archaea Genomes in Terms of Protein Structure},
booktitle = {Proceedings of the German Conference on Bioinformatics, {GCB} 1998,
University of Cologne, Germany, October 1998},
publisher = {Oxford University Press},
year = {1998},
timestamp = {Fri, 02 Aug 2019 15:48:14 +0200},
biburl = {https://dblp.org/rec/conf/gcb/Gerstein98.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/GersteinL96,
author = {Mark Gerstein and
Michael Levitt},
editor = {David J. States and
Pankaj Agarwal and
Terry Gaasterland and
Lawrence Hunter and
Randall Smith},
title = {Using Iterative Dynamic Programming to Obtain Accurate Pairwise and
Multiple Alignments of Protein Structures},
booktitle = {Proceedings of the Fourth International Conference on Intelligent
Systems for Molecular Biology, St. Louis, MO, USA, June 12-15 1996},
pages = {59--67},
publisher = {{AAAI}},
year = {1996},
url = {http://www.aaai.org/Library/ISMB/1996/ismb96-007.php},
timestamp = {Fri, 11 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ismb/GersteinL96.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GersteinA95,
author = {Mark Gerstein and
Russ B. Altman},
title = {Using a measure of structural variation to define a core for the globins},
journal = {Comput. Appl. Biosci.},
volume = {11},
number = {6},
pages = {633--644},
year = {1995},
url = {https://doi.org/10.1093/bioinformatics/11.6.633},
doi = {10.1093/BIOINFORMATICS/11.6.633},
timestamp = {Tue, 01 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GersteinA95.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/AltmanG94,
author = {Russ B. Altman and
Mark Gerstein},
editor = {Russ B. Altman and
Douglas L. Brutlag and
Peter D. Karp and
Richard H. Lathrop and
David B. Searls},
title = {Finding an Average Core Structure: Application to the Globins},
booktitle = {Proceedings of the Second International Conference on Intelligent
Systems for Molecular Biology, August 14-17, 1994, Stanford University,
Stanford, California, {USA}},
pages = {19--27},
publisher = {{AAAI}},
year = {1994},
url = {http://www.aaai.org/Library/ISMB/1994/ismb94-003.php},
timestamp = {Thu, 13 Dec 2012 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ismb/AltmanG94.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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