A comparison of sequence and structure protein domain families as a basis for structural genomics. - Arne Elofsson; Erik L. L. Sonnhammer (Bioinform., 1999)

MaxSub: an automated measure for the assessment of protein structure prediction quality. - Naomi Siew; Arne Elofsson; Leszek Rychlewski; Daniel Fischer 001 (Bioinform., 2000)

Side Chain-Positioning as an Integer Programming Problem. - Olivia Eriksson; Yishao Zhou; Arne Elofsson (WABI, 2001)

Structure prediction meta server. - Janusz M. Bujnicki; Arne Elofsson; Daniel Fischer 001; Leszek Rychlewski (Bioinform., 2001)

A study of quality measures for protein threading models. - Susana Cristobal; Adam T. Zemla; Daniel Fischer 001; Leszek Rychlewski; Arne Elofsson (BMC Bioinform., 2001)

Prediction of MHC class I binding peptides, using SVMHC. - Pierre Dönnes; Arne Elofsson (BMC Bioinform., 2002)

3D-Jury: A Simple Approach to Improve Protein Structure Predictions. - Krzysztof Ginalski; Arne Elofsson; Daniel Fischer 001; Leszek Rychlewski (Bioinform., 2003)

Pcons5: combining consensus, structural evaluation and fold recognition scores. - Björn Wallner; Arne Elofsson (Bioinform., 2005)

ProfNet, a method to derive profile-profile alignment scoring functions that improves the alignments of distantly related proteins. - Tomas Ohlson; Arne Elofsson (BMC Bioinform., 2005)

ZPRED: Predicting the distance to the membrane center for residues in alpha-helical membrane proteins. - Erik Granseth; Håkan Viklund; Arne Elofsson (ISMB (Supplement of Bioinformatics), 2006)

Improved alignment quality by combining evolutionary information, predicted secondary structure and self-organizing maps. - Tomas Ohlson; Varun Aggarwal; Arne Elofsson; Robert M. MacCallum (BMC Bioinform., 2006)

PONGO: a web server for multiple predictions of all-alpha transmembrane proteins. - Mauro Amico; Michele Finelli; Ivan Rossi; Andrea Zauli; Arne Elofsson; Håkan Viklund; Gunnar von Heijne; David Jones; Anders Krogh; Piero Fariselli; Pier Luigi Martelli; Rita Casadio (Nucleic Acids Res., 2006)

Expansion of Protein Domain Repeats. - Åsa K. Björklund; Diana Ekman; Arne Elofsson (PLoS Comput. Biol., 2006)

Pcons.net: protein structure prediction meta server. - Björn Wallner; Per Larsson; Arne Elofsson (Nucleic Acids Res., 2007)

SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology. - Håkan Viklund; Andreas Bernsel; Marcin J. Skwark; Arne Elofsson (Bioinform., 2008)

OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar. - Håkan Viklund; Arne Elofsson (Bioinform., 2008)

TOPCONS: consensus prediction of membrane protein topology. - Andreas Bernsel; Håkan Viklund; Aron Hennerdal; Arne Elofsson (Nucleic Acids Res., 2009)

MPRAP: An accessibility predictor for alpha-helical transmembrane proteins that performs well inside and outside the membrane. - Kristoffer Illergård; Simone Callegari; Arne Elofsson (BMC Bioinform., 2010)

Rapid membrane protein topology prediction. - Aron Hennerdal; Arne Elofsson (Bioinform., 2011)

Improved predictions by Pcons.net using multiple templates. - Per Larsson; Marcin J. Skwark; Björn Wallner; Arne Elofsson (Bioinform., 2011)

KalignP: Improved multiple sequence alignments using position specific gap penalties in Kalign2. - Nanjiang Shu; Arne Elofsson (Bioinform., 2011)

BOCTOPUS: improved topology prediction of transmembrane β barrel proteins. - Sikander Hayat; Arne Elofsson (Bioinform., 2012)

Ranking models of transmembrane β-barrel proteins using Z-coordinate predictions. - Sikander Hayat; Arne Elofsson (Bioinform., 2012)

PconsC: combination of direct information methods and alignments improves contact prediction. - Marcin J. Skwark; Abbi Abdel-Rehim; Arne Elofsson (Bioinform., 2013)

PconsD: ultra rapid, accurate model quality assessment for protein structure prediction. - Marcin J. Skwark; Arne Elofsson (Bioinform., 2013)

PconsFold: improved contact predictions improve protein models. - Mirco Michel; Sikander Hayat; Marcin J. Skwark; Chris Sander; Debora S. Marks; Arne Elofsson (Bioinform., 2014)

Improved Contact Predictions Using the Recognition of Protein Like Contact Patterns. - Marcin J. Skwark; Daniele Raimondi; Mirco Michel; Arne Elofsson (PLoS Comput. Biol., 2014)

The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides. - Konstantinos D. Tsirigos; Christoph Peters; Nanjiang Shu; Lukas Käll; Arne Elofsson (Nucleic Acids Res., 2015)

Inclusion of dyad-repeat pattern improves topology prediction of transmembrane β-barrel proteins. - Sikander Hayat; Christoph Peters; Nanjiang Shu; Konstantinos D. Tsirigos; Arne Elofsson (Bioinform., 2016)

Improved topology prediction using the terminal hydrophobic helices rule. - Christoph Peters; Konstantinos D. Tsirigos; Nanjiang Shu; Arne Elofsson (Bioinform., 2016)

PRED-TMBB2: improved topology prediction and detection of beta-barrel outer membrane proteins. - Konstantinos D. Tsirigos; Arne Elofsson; Pantelis G. Bagos (Bioinform., 2016)

GWAR: robust analysis and meta-analysis of genome-wide association studies. - Niki L. Dimou; Konstantinos D. Tsirigos; Arne Elofsson; Pantelis G. Bagos (Bioinform., 2017)

Large-scale structure prediction by improved contact predictions and model quality assessment. - Mirco Michel; David Menéndez Hurtado; Karolis Uziela; Arne Elofsson (Bioinform., 2017)

Predicting accurate contacts in thousands of Pfam domain families using PconsC3. - Mirco Michel; Marcin J. Skwark; David Menéndez Hurtado; Magnus Ekeberg; Arne Elofsson (Bioinform., 2017)

SubCons: a new ensemble method for improved human subcellular localization predictions. - Marco Salvatore; Per Warholm; Nanjiang Shu; Walter Basile; Arne Elofsson (Bioinform., 2017)

ProQ3D: improved model quality assessments using deep learning. - Karolis Uziela; David Menéndez Hurtado; Nanjiang Shu; Björn Wallner; Arne Elofsson (Bioinform., 2017)

DisProt 7.0: a major update of the database of disordered proteins. - Damiano Piovesan; Francesco Tabaro; Ivan Micetic; Marco Necci; Federica Quaglia; Christopher J. Oldfield; Maria Cristina Aspromonte; Norman E. Davey; Radoslav Davidovic; Zsuzsanna Dosztányi; Arne Elofsson; Alessandra Gasparini; et al. (Nucleic Acids Res., 2017)

High GC content causes orphan proteins to be intrinsically disordered. - Walter Basile; Oxana Sachenkova; Sara Light; Arne Elofsson (PLoS Comput. Biol., 2017)

PconsC4: fast, accurate and hassle-free contact predictions. - Mirco Michel; David Menéndez Hurtado; Arne Elofsson (Bioinform., 2019)

Why do eukaryotic proteins contain more intrinsically disordered regions? - Walter Basile; Marco Salvatore; Claudio Bassot; Arne Elofsson (PLoS Comput. Biol., 2019)

Ten simple rules on how to create open access and reproducible molecular simulations of biological systems. - Arne Elofsson; Berk Hess; Erik Lindahl; Alexey Onufriev; David van der Spoel; Anders Wallqvist (PLoS Comput. Biol., 2019)

TransformerCPI: improving compound-protein interaction prediction by sequence-based deep learning with self-attention mechanism and label reversal experiments. - Lifan Chen; Xiaoqin Tan; Dingyan Wang; Feisheng Zhong; Xiaohong Liu 002; Tianbiao Yang; Xiaomin Luo; Kaixian Chen; Hualiang Jiang; Mingyue Zheng; Arne Elofsson (Bioinform., 2020)

DisProt: intrinsic protein disorder annotation in 2020. - András Hatos; Borbála Hajdu-Soltész; Alexander Miguel Monzon; Nicolas Palopoli; Lucía Álvarez; Burcu Aykaç Fas; Claudio Bassot; Guillermo I. Benítez; Martina Bevilacqua; Anastasia Chasapi; Lucía B. Chemes; Norman E. Davey; et al. (Nucleic Acids Res., 2020)

GraphQA: protein model quality assessment using graph convolutional networks. - Federico Baldassarre; David Menéndez Hurtado; Arne Elofsson; Hossein Azizpour (Bioinform., 2021)

pyconsFold: a fast and easy tool for modeling and docking using distance predictions. - John Lamb; Arne Elofsson (Bioinform., 2021)

Protein sequence-to-structure learning: Is this the end(-to-end revolution)? - Elodie Laine; Stephan Eismann; Arne Elofsson; Sergei Grudinin (CoRR, 2021)

Toward Characterising the Cellular 3D-Proteome. - Arne Elofsson (Frontiers Bioinform., 2021)

Accurate contact-based modelling of repeat proteins predicts the structure of new repeats protein families. - Claudio Bassot; Arne Elofsson (PLoS Comput. Biol., 2021)

GCSENet: A GCN, CNN and SENet ensemble model for microRNA-disease association prediction. - Zhong Li; Kaiyancheng Jiang; Shengwei Qin; Yijun Zhong; Arne Elofsson (PLoS Comput. Biol., 2021)

The evolutionary history of topological variations in the CPA/AT transporters. - Govindarajan Sudha; Claudio Bassot; John Lamb; Nanjiang Shu; Yan Huang; Arne Elofsson (PLoS Comput. Biol., 2021)

Limits and potential of combined folding and docking. - Gabriele Pozzati; Wensi Zhu; Claudio Bassot; John Lamb; Petras Kundrotas; Arne Elofsson (Bioinform., 2022)

DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation. - Federica Quaglia; Bálint Mészáros; Edoardo Salladini; András Hatos; Rita Pancsa; Lucía B. Chemes; Mátyás Pajkos; Tamas Lazar; Samuel Peña-Díaz; Jaime Santos; Veronika Ács; Nazanin Farahi; et al. (Nucleic Acids Res., 2022)

AFTGAN: prediction of multi-type PPI based on attention free transformer and graph attention network. - Yanlei Kang; Arne Elofsson; Yunliang Jiang; Weihong Huang; Minzhe Yu; Zhong Li (Bioinform., 2023)

Stable Autonomous Flow Matching. - Christopher Iliffe Sprague; Arne Elofsson; Hossein Azizpour (CoRR, 2024)

Opportunities for machine learning in scientific discovery. - Ricardo Vinuesa; Jean Rabault; Hossein Azizpour; Stefan Bauer; Bingni W. Brunton; Arne Elofsson; Elias Jarlebring; Hedvig Kjellström; Stefano Markidis; David Marlevi; Paola Cinnella; Steven L. Brunton (CoRR, 2024)

Hessian-Informed Flow Matching. - Christopher Iliffe Sprague; Arne Elofsson; Hossein Azizpour (CoRR, 2024)

M-Ionic: prediction of metal-ion-binding sites from sequence using residue embeddings. - Aditi Shenoy; Yogesh Kalakoti; Durai Sundar; Arne Elofsson (Bioinform., 2024)