Publications

Generative latent diffusion language modeling yields anti-infective synthetic peptides

Cell Biomaterials, 2025

Marcelo D. T. Torres , Leo Tianlai Chen , Fangping Wan , Pranam Chatterjee , Cesar de la Fuente-Nunez

Deep learning reveals antibiotics in the archaeal proteome

Nature Microbiology, 2025

Marcelo D. T. Torres* , Fangping Wan* , Cesar de la Fuente

Covering Multiple Objectives with a Small Set of Solutions Using Bayesian Optimization

NeurIPS, 2025

Natalie Maus , Kyurae Kim , Yimeng Zeng , Haydn Thomas Jones , Fangping Wan , Marcelo D. T. Torres , Cesar de la Fuente-Nunez , Jacob R. Gardner.

Predicting and generating antibiotics against future pathogens with ApexOracle

NeurIPS 2025 2nd Workshop FM4LS, 2025 (Journal version in preparation)

Tianang Leng* , Fangping Wan* , Marcelo D. T. Torres , Cesar de la Fuente-Nunez

Large Scale Multi-Task Bayesian Optimization with Large Language Models

in submission

Yimeng Zeng , Natalie Maus , Haydn Thomas Jones , Jeffrey Tao , Fangping Wan , Marcelo D. T. Torres , Cesar de la Fuente-Nunez , Ryan Marcus , Osbert Bastani , Jacob R. Gardner

Antiviral discovery using sparse datasets by integrating experiments, molecular simulations, and machine learning

Cell Reports Physical Science, 2025

Angela Cesaro* , Fangping Wan* , Haoyuan Shi* , Kaiyang Wang , C Mark Maupin , Matt L Barker , Jiqian Liu , Stephen J Fox , Jingjie Yeo , Cesar de la Fuente-Nunez

Tutorial: guidelines for the use of machine learning methods to mine genomes and proteomes for antibiotic discovery

Nature Protocols, 2025

Fangping Wan* , Marcelo D. T. Torres* , Changge Guan , Cesar de la Fuente-Nunez

Improving functional protein generation via foundation model-derived latent space likelihood optimization

in submission

Changge Guan* , Fangping Wan* , Marcelo D. T. Torres , Cesar de la Fuente-Nunez

Design of multimodal antibiotics against intracellular infections using deep learning

in submission

Angela Cesaro , Fangping Wan , Marcelo D. T. Torres , Cesar de la Fuente-Nunez

A generative artificial intelligence approach for antibiotic optimization

in submission

Marcelo D. T. Torres* , Yimeng Zeng* , Fangping Wan* , Natalie Maus , Jacob R. Gardner , Cesar de la Fuente-Nunez

Analyzing Large-Scale Single-Cell RNA-Seq Data Using Coreset

IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2024

Khalid Usman , Fangping Wan , Dan Zhao , Jian Peng , Jianyang Zeng

Deep-learning-enabled antibiotic discovery through molecular de-extinction

Nature Biomedical Engineering, 2024

Fangping Wan* , Marcelo D. T. Torres* , Jacqueline Peng , Cesar de la Fuente

Machine Learning for Antimicrobial Peptide Identification and Design

Nature Reviews Bioengineering, 2024

Fangping Wan* , Felix Wong* , James J. Collins , Cesar de la Fuente

Deep learning tools to accelerate antibiotic discovery

Expert Opinion on Drug Discovery, 2023

Angela Cesaro , Mojtaba Bagheri , Marcelo D. T. Torres , Fangping Wan , Cesar de la Fuente-Nunez

Improving molecular property prediction through a task similarity enhanced transfer learning strategy

Iscience, 2022

Han Li , Xinyi Zhao , Shuya Li , Fangping Wan , Dan Zhao , Jianyang Zeng

Deep generative models for peptide design

Digital Discovery, 2022

Fangping Wan* , Daphne Kontogiorgos-Heintz* , Cesar de la Fuente-Nunez

A community challenge for a pancancer drug mechanism of action inference from perturbational profile data

Cell Reports Medicine, 2022

Eugene F Douglass Jr. , Robert J Allaway , Bence Szalai , Wenyu Wang , Tingzhong Tian , Adria Fernandez-Torras , Ron Realubit , Charles Karan , Shuyu Zheng , Alberto Pessia , Ziaurrehman Tanoli , Mohieddin Jafari , Fangping Wan , Shuya Li , Yuanpeng Xiong , Miquel Duran-Frigola , Martino Bertoni , Pau Badia-i-Mompel , Lidia Mateo , Oriol Guitart-Pla , Verena Chung , Jing Tang , Jianyang Zeng , Patrick Aloy , Julio Saez-Rodriguez , Justin Guinney , Daniela S Gerhard , Andrea Califano

A deep-learning framework for multi-level peptide-protein interaction prediction

Nature communications, 2021

Yipin Lei , Shuya Li , Ziyi Liu , Fangping Wan , Tingzhong Tian , Shao Li , Dan Zhao , Jianyang Zeng

Crowdsourcing assessment of maternal blood multi-omics for predicting gestational age and preterm birth

Cell Reports Medicine, 2021

Adi L. Tarca , Bálint Ármin Pataki , Roberto Romero , Marina Sirota , Yuanfang Guan , Rintu Kutum , Nardhy Gomez-Lopez , Bogdan Done , Gaurav Bhatti , Thomas Yu , Gaia Andreoletti , Tinnakorn Chaiworapongsa , The DREAM Preterm Birth Prediction Challenge Consortium , Sonia S. Hassan , Chaur-Dong Hsu , Nima Aghaeepour , Gustavo Stolovitzky , Istvan Csabai , James C. Costello

Crowdsourced mapping of unexplored target space of kinase inhibitors

Nature Communications, 2021

Anna Cichonska , Balaguru Ravikumar , Robert J Allaway , Sungjoon Park , Fangping Wan , Olexandr Isayev , Shuya Li , Michael J Mason , Andrew Lamb , Minji Jeon , Sunkyu Kim , Mariya Popova , Jianyang Zeng , Kristen Dang , Gregory Koytiger , Jaewoo Kang , Carrow I Wells , Timothy M Willson , Tudor I Oprea , Avner Schlessinger , David H Drewry , Gustavo A Stolovitzky , Krister Wennerberg , Justin Guinney , Tero Aittokallio

An integrative drug repositioning framework discovered a potential therapeutic agent targeting COVID-19

Signal Transduction and Targeted Therapy, 2021

Yiyue Ge* , Tingzhong Tian* , Sulin Huang* , Fangping Wan* , Jingxin Li , Shuya Li , Hui Yang , Lixiang Hong , Nian Wu , Enming Yuan , Lili Cheng , Yipin Lei , Hantao Shu , Xiaolong Feng , Ziyuan Jiang , Ying Chi , Xiling Guo , Lunbiao Cui , Liang Xiao , Zeng Li , Chunhao Yang , Zehong Miao , Haidong Tang , Ligong Chen , Hainian Zeng , Dan Zhao , Fengcai Zhu , Xiaokun Shen , Jianyang Zeng

NeoDTI: neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions

Bioinformatics, 2019

Fangping Wan , Lixiang Hong , An Xiao , Tao Jiang , Jianyang Zeng

Publications

Generative latent diffusion language modeling yields anti-infective synthetic peptides

Deep learning reveals antibiotics in the archaeal proteome

Covering Multiple Objectives with a Small Set of Solutions Using Bayesian Optimization

Predicting and generating antibiotics against future pathogens with ApexOracle

Large Scale Multi-Task Bayesian Optimization with Large Language Models

Antiviral discovery using sparse datasets by integrating experiments, molecular simulations, and machine learning

Tutorial: guidelines for the use of machine learning methods to mine genomes and proteomes for antibiotic discovery

Improving functional protein generation via foundation model-derived latent space likelihood optimization

Design of multimodal antibiotics against intracellular infections using deep learning

A generative artificial intelligence approach for antibiotic optimization

Analyzing Large-Scale Single-Cell RNA-Seq Data Using Coreset

Deep-learning-enabled antibiotic discovery through molecular de-extinction

Machine Learning for Antimicrobial Peptide Identification and Design

Deep learning tools to accelerate antibiotic discovery

Improving molecular property prediction through a task similarity enhanced transfer learning strategy

Deep generative models for peptide design

A community challenge for a pancancer drug mechanism of action inference from perturbational profile data

A deep-learning framework for multi-level peptide-protein interaction prediction

Crowdsourcing assessment of maternal blood multi-omics for predicting gestational age and preterm birth

Crowdsourced mapping of unexplored target space of kinase inhibitors

An integrative drug repositioning framework discovered a potential therapeutic agent targeting COVID-19

A novel machine learning based framework for modeling transcription elongation

MoTSE: an interpretable task similarity estimator for small molecular property prediction tasks

A novel machine learning framework for automated biomedical relation extraction from large-scale literature repositories

Secure multiparty computation for privacy-preserving drug discovery

MONN: A Multi-objective Neural Network for Predicting Compound-Protein Interactions and Anities

EXP2SL: A Machine Learning Framework for Cell-Line-Specific Synthetic Lethality Prediction

ACME: pan-specific peptide-MHC class I binding prediction through attention-based deep neural networks

DeepCPI: A Deep Learning-based Framework for Large-scale in silico Drug Screening

NeoDTI: neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions