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Peter Koo

Peter Koo

Associate Professor
Cancer Center Member

Ph.D., Yale University, 2015

[email protected] | 516-367-5520

 

Deep learning has the potential to make a significant impact in basic biology and cancer, but a major challenge is understanding the reasons behind their predictions. My research develops methods to interpret this powerful class of black box models, with a goal of elucidating data-driven insights into the underlying mechanisms of sequence-function relationships.

Deep learning is being applied rapidly in many areas of genomics, demonstrating improved performance over previous methods on benchmark datasets. Despite the promise of deep learning, it remains unclear whether improved predictions will translate to new biological discoveries because of their low interpretability, which has earned them a reputation as a black box. Understanding the reasons underlying a deep learning model鈥檚 prediction may reveal new biological insights not captured by previous methods. Our group develops methods to interpret high-performing deep learning models to distill knowledge that they learn from big, noisy, biological sequence data. Our goal is to elucidate biological mechanisms that underlie sequence-function relationships for gene regulation and protein (dys)function. Recently, we have teamed up with other members of the CSHL Cancer Center to investigate the sequence basis of epigenomic differences across healthy and cancer cells.

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All Publications

14 Jul 2025 | Genome Biology | 26(1)
Tang, Ziqi;  Somia, Nirali;  Yu, Yiyang;  Koo, Peter;  

8 Jul 2025 | bioRxiv
Luthra, Ishika;  Priyadarshi, Satyam;  Guo, Rui;  Mahieu, Lukas;  Kempynck, Niklas;  Dooley, Damion;  Penzar, Dmitry;  Vorontsov, Ilya;  Sheng, Yilun;  Tu, Xinming;  Klie, Adam;  Drusinsky, Shiron;  Floren, Alexander;  Armand, Ethan;  Alasoo, Kaur;  Seelig, Georg;  Tewhey, Ryan;  Koo, Peter;  Agarwal, Vikram;  Gosai, Sager;  Pinello, Luca;  White, Michael;  Lal, Avantika;  Zeitlinger, Julia;  Pollard, Katherine;  Libbrecht, Maxwell;  Carter, Hannah;  Mostafavi, Sara;  Kulakovskiy, Ivan;  Hsiao, Will;  Aerts, Stein;  Zhou, Jian;  de Boer, Carl;  

5 May 2025 | Cold Spring Harbor Perspectives in Biology | :a041877
Koo, Peter;  Dallago, Christian;  Nambiar, Ananthan;  Yang, Kevin;  

2 May 2025 | Science Advances | 11(18):eadt5111
Thompson, Mike;  Martín, Mariano;  Olmo, Trinidad;  Rajesh, Chandana;  Koo, Peter;  Bolognesi, Benedetta;  Lehner, Ben;  

8 Feb 2025 | Nucleic Acids Research (NAR) | 53(4)
Liu, Lingjie;  Zhao, Yixin;  Hassett, Rebecca;  Toneyan, Shushan;  Koo, Peter;  Siepel, Adam;  

8 Feb 2025 | Nucleic Acids Research (NAR) | 53(4)
Liu, Lingjie;  Zhao, Yixin;  Hassett, Rebecca;  Toneyan, Shushan;  Koo, Peter;  Siepel, Adam;  

10 Jan 2025
Kaczmarzyk, Jakub;  Sharma, Rishul;  Koo, Peter;  Saltz, Joel;  

15 Nov 2024 | bioRxiv
Zhou, Jessica;  Rizzo, Kaeli;  Tang, Ziqi;  Koo, Peter;  

11 Oct 2024 | Nature Biotechnology
Rafi, Abdul;  Nogina, Daria;  Penzar, Dmitry;  Lee, Dohoon;  Lee, Danyeong;  Kim, Nayeon;  Kim, Sangyeup;  Kim, Dohyeon;  Shin, Yeojin;  Kwak, Il-Youp;  Meshcheryakov, Georgy;  Lando, Andrey;  Zinkevich, Arsenii;  Kim, Byeong-Chan;  Lee, Juhyun;  Kang, Taein;  Vaishnav, Eeshit;  Yadollahpour, Payman;  Random Promoter DREAM Challenge Consortium;  Kim, Sun;  Albrecht, Jake;  Regev, Aviv;  Gong, Wuming;  Kulakovskiy, Ivan;  Meyer, Pablo;  de Boer, Carl;  

10 Oct 2024 | Cell Genomics | :100672
Zhou, Jessica;  Guruvayurappan, Karthik;  Toneyan, Shushan;  Chen, Hsiuyi;  Chen, Aaron;  Koo, Peter;  McVicker, Graham;