The EVcouplings Python framework for coevolutionary sequence analysis. - Thomas A. Hopf; Anna G. Green; Benjamin Schubert; Sophia Mersmann; Charlotta Schärfe; John Ingraham; Ágnes Tóth-Petróczy; Kelly Brock; Adam J. Riesselman; Perry Palmedo; Chan Kang; Robert P. Sheridan; et al. (Bioinform., 2019)

Modeling aspects of the language of life through transfer-learning protein sequences. - Michael Heinzinger; Ahmed Elnaggar; Yu Wang; Christian Dallago; Dmitrii Nechaev; Florian Matthes; Burkhard Rost (BMC Bioinform., 2019)

ProtTrans: Towards Cracking the Language of Life's Code Through Self-Supervised Deep Learning and High Performance Computing. - Ahmed Elnaggar; Michael Heinzinger; Christian Dallago; Ghalia Rehawi; Yu Wang; Llion Jones; Tom Gibbs; Tamas Feher; Christoph Angerer; Martin Steinegger; Debsindhu Bhowmik; Burkhard Rost (CoRR, 2020)

AlignmentViewer: Sequence Analysis of Large Protein Families. - Roc Reguant; Yevgeniy Antipin; Robert P. Sheridan; Christian Dallago; Drew Diamantoukos; Augustin Luna; Chris Sander; Nicholas Paul Gauthier (F1000Research, 2020)

Pathway Commons 2019 Update: integration, analysis and exploration of pathway data. - Igor V. Rodchenkov; Ozgun Babur; Augustin Luna; Bülent Arman Aksoy; Jeffrey V. Wong; Dylan Fong; Max Franz; Metin Can Siper; Manfred Cheung; Michael Wrana; Harsh Mistry; Logan Mosier; et al. (Nucleic Acids Res., 2020)

FLIP: Benchmark tasks in fitness landscape inference for proteins. - Christian Dallago; Jody Mou; Kadina E. Johnston; Bruce J. Wittmann; Nicholas Bhattacharya; Samuel Goldman; Ali Madani; Kevin K. Yang (NeurIPS Datasets and Benchmarks, 2021)

Clustering FunFams using sequence embeddings improves EC purity. - Maria Littmann; Nicola Bordin; Michael Heinzinger; Konstantin Schütze; Christian Dallago; Christine A. Orengo; Burkhard Rost (Bioinform., 2021)

A flexible search system for high-accuracy identification of biological entities and molecules. - Max Franz; Jeffrey V. Wong; Metin Can Siper; Christian Dallago; John M. Giorgi; Emek Demir; Chris Sander; Gary D. Bader (J. Open Source Softw., 2021)

PredictProtein - Predicting Protein Structure and Function for 29 Years. - Michael Bernhofer; Christian Dallago; Timothy Karl; Venkata P. Satagopam; Michael Heinzinger; Maria Littmann; Tobias Olenyi; Jiajun Qiu; Konstantin Schütze; Guy Yachdav; Haim Ashkenazy; Nir Ben-Tal; et al. (Nucleic Acids Res., 2021)

3D Infomax improves GNNs for Molecular Property Prediction. - Hannes Stärk; Dominique Beaini; Gabriele Corso; Prudencio Tossou; Christian Dallago; Stephan Günnemann; Pietro Lió (ICML, 2022)

A roadmap for the functional annotation of protein families: a community perspective. - Valérie de Crécy-Lagard; Rocio Amorin de Hegedus; Cecilia N. Arighi; Jill Babor; Alex Bateman; Ian Blaby; Crysten Blaby-Haas; Alan J. Bridge; Stephen K. Burley; Stacey Cleveland; Lucy J. Colwell; Ana Conesa; et al. (Database J. Biol. Databases Curation, 2022)

ProteomicsDB: toward a FAIR open-source resource for life-science research. - Ludwig Lautenbacher; Patroklos Samaras; Julian Müller 007; Andreas Grafberger; Marwin Shraideh; Johannes Rank; Simon T. Fuchs; Tobias K. Schmidt; Matthew The; Christian Dallago; Holger Wittges; Burkhard Rost; et al. (Nucleic Acids Res., 2022)

ProtTrans: Toward Understanding the Language of Life Through Self-Supervised Learning. - Ahmed Elnaggar; Michael Heinzinger; Christian Dallago; Ghalia Rehawi; Yu Wang; Llion Jones; Tom Gibbs; Tamas Feher; Christoph Angerer; Martin Steinegger; Debsindhu Bhowmik; Burkhard Rost (IEEE Trans. Pattern Anal. Mach. Intell., 2022)

DeepSpeed4Science Initiative: Enabling Large-Scale Scientific Discovery through Sophisticated AI System Technologies. - Shuaiwen Leon Song; Bonnie Kruft; Minjia Zhang; Conglong Li; Shiyang Chen 004; Chengming Zhang 006; Masahiro Tanaka; Xiaoxia Wu; Jeff Rasley; Ammar Ahmad Awan; Connor Holmes; Martin Cai; et al. (CoRR, 2023)

GenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary dynamics. - Maxim Zvyagin; Alexander Brace; Kyle Hippe; Yuntian Deng; Bin Zhang; Cindy Orozco Bohorquez; Austin Clyde; Bharat Kale; Danilo Perez-Rivera; Heng Ma; Carla M. Mann; Michael W. Irvin; et al. (Int. J. High Perform. Comput. Appl., 2023)

BioNeMo Framework: a modular, high-performance library for AI model development in drug discovery. - Peter St. John; Dejun Lin; Polina Binder; Malcolm Greaves; Vega Shah; John St. John; Adrian Lange; Patrick D. Hsu; Rajesh Illango; Arvind Ramanathan; Anima Anandkumar; David H. Brookes; et al. (CoRR, 2024)

Proteina: Scaling Flow-based Protein Structure Generative Models. - Tomas Geffner; Kieran Didi; Zuobai Zhang; Danny Reidenbach; Zhonglin Cao; Jason Yim; Mario Geiger; Christian Dallago; Emine Küçükbenli; Arash Vahdat; Karsten Kreis (ICLR, 2025)

La-Proteina: Atomistic Protein Generation via Partially Latent Flow Matching. - Tomas Geffner; Kieran Didi; Zhonglin Cao; Danny Reidenbach; Zuobai Zhang; Christian Dallago; Emine Küçükbenli; Karsten Kreis; Arash Vahdat (CoRR, 2025)