BaCelLo: a balanced subcellular localization predictor. - Andrea Pierleoni; Pier Luigi Martelli; Piero Fariselli; Rita Casadio (ISMB (Supplement of Bioinformatics), 2006)

eSLDB: eukaryotic subcellular localization database. - Andrea Pierleoni; Pier Luigi Martelli; Piero Fariselli; Rita Casadio (Nucleic Acids Res., 2007)

PredGPI: a GPI-anchor predictor. - Andrea Pierleoni; Pier Luigi Martelli; Rita Casadio (BMC Bioinform., 2008)

MemLoci: predicting subcellular localization of membrane proteins in eukaryotes. - Andrea Pierleoni; Pier Luigi Martelli; Rita Casadio (Bioinform., 2011)

Improving the prediction of disulfide bonds in Eukaryotes with machine learning methods and protein subcellular localization. - Castrense Savojardo; Piero Fariselli; Monther Alhamdoosh; Pier Luigi Martelli; Andrea Pierleoni; Rita Casadio (Bioinform., 2011)

MemPype: a pipeline for the annotation of eukaryotic membrane proteins. - Andrea Pierleoni; Valentina Indio; Castrense Savojardo; Piero Fariselli; Pier Luigi Martelli; Rita Casadio (Nucleic Acids Res., 2011)

Open Targets: a platform for therapeutic target identification and validation. - Gautier Koscielny; Peter An; Denise Carvalho-Silva; Jennifer A. Cham; Luca Fumis; Rippa Gasparyan; Samiul Hasan; Nikiforos Karamanis; Michael Maguire; Eliseo Papa; Andrea Pierleoni; Miguel Pignatelli; et al. (Nucleic Acids Res., 2017)

Deep Bidirectional Transformers for Relation Extraction without Supervision. - Yannis Papanikolaou; Ian Roberts; Andrea Pierleoni (DeepLo@EMNLP-IJCNLP, 2019)

Reasoning Over Paths via Knowledge Base Completion. - Saatviga Sudhahar; Andrea Pierleoni; Ian Roberts (TextGraphs@EMNLP, 2019)

Open Targets Platform: new developments and updates two years on. - Denise Carvalho-Silva; Andrea Pierleoni; Miguel Pignatelli; Chuang Kee Ong; Luca Fumis; Nikiforos Karamanis; Miguel Carmona; Adam Faulconbridge; Andrew Hercules; Elaine McAuley; Alfredo Miranda; Gareth Peat; et al. (Nucleic Acids Res., 2019)

DARE: Data Augmented Relation Extraction with GPT-2. - Yannis Papanikolaou; Andrea Pierleoni (CoRR, 2020)

Open Targets Platform: supporting systematic drug-target identification and prioritisation. - David Ochoa; Andrew Hercules; Miguel Carmona; Daniel Suveges; Asier Gonzalez-Uriarte; Cinzia Malangone; Alfredo Miranda; Luca Fumis; Denise Carvalho-Silva; Michaela Spitzer; Jarrod Baker; Javier Ferrer; et al. (Nucleic Acids Res., 2021)

Improving Entity Disambiguation by Reasoning over a Knowledge Base. - Tom Ayoola; Joseph Fisher; Andrea Pierleoni (NAACL-HLT, 2022)

ReFinED: An Efficient Zero-shot-capable Approach to End-to-End Entity Linking. - Tom Ayoola; Shubhi Tyagi; Joseph Fisher; Christos Christodoulopoulos 001; Andrea Pierleoni (NAACL-HLT (Industry Papers), 2022)

WebIE: Faithful and Robust Information Extraction on the Web. - Chenxi Whitehouse; Clara Vania; Alham Fikri Aji; Christos Christodoulopoulos 001; Andrea Pierleoni (ACL (1), 2023)

REXEL: An End-to-end Model for Document-Level Relation Extraction and Entity Linking. - Nacime Bouziani; Shubhi Tyagi; Joseph Fisher; Jens Lehmann 001; Andrea Pierleoni (NAACL (Industry Track), 2024)

HALLUCANA: Fixing LLM Hallucination with A Canary Lookahead. - Tianyi Li; Erenay Dayanik; Shubhi Tyagi; Andrea Pierleoni (NAACL (Findings), 2025)