Arne Elofsson

Publication Activity (10 Years)

Years Active: 1999-2024
Publications (10 Years): 28

Top Topics

Quality Assessment

Protein Interaction

Subcellular Localization

Top Venues

PLoS Comput. Biol.

Nucleic Acids Res.

Publications

Christopher Iliffe Sprague, Arne Elofsson, Hossein Azizpour
Stable Autonomous Flow Matching. CoRR (2024)
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
Opportunities for machine learning in scientific discovery. CoRR (2024)
Aditi Shenoy, Yogesh Kalakoti, Durai Sundar, Arne Elofsson
M-Ionic: prediction of metal-ion-binding sites from sequence using residue embeddings. Bioinform. 40 (1) (2024)
Yanlei Kang, Arne Elofsson, Yunliang Jiang, Weihong Huang, Minzhe Yu, Zhong Li
AFTGAN: prediction of multi-type PPI based on attention free transformer and graph attention network. Bioinform. 39 (2) (2023)
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, Erzsébet Fichó, Maria Cristina Aspromonte, Claudio Bassot, Anastasia Chasapi, Norman E. Davey, Radoslav Davidovic, Laszlo Dobson, Arne Elofsson, Gábor Erdös, Pascale Gaudet, Michelle G. Giglio, Juliana Glavina, Javier Iserte, Valentín Iglesias, Zsófia L. Kálmán, Matteo Lambrughi, Emanuela Leonardi, Sonia Longhi, Sandra Macedo-Ribeiro, Emiliano Maiani, Julia Marchetti, Cristina Marino Buslje, Attila Meszaros, Alexander Miguel Monzon, Giovanni Minervini, Suvarna Nadendla, Juliet F. Nilsson, Marián Novotný, Christos A. Ouzounis, Nicolas Palopoli, Elena Papaleo, Pedro J. Barbosa Pereira, Gabriele Pozzati, Vasilis J. Promponas, Jordi Pujols, Alma Carolina Sanchez Rocha, Martin Salas, Luciana Rodriguez Sawicki, Éva Schád, Aditi Shenoy, Tamás Szaniszló, Konstantinos D. Tsirigos, Nevena Veljkovic, Gustavo D. Parisi, Salvador Ventura, Zsuzsanna Dosztányi, Peter Tompa, Silvio C. E. Tosatto, Damiano Piovesan
DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation. Nucleic Acids Res. 50 (D1) (2022)
Gabriele Pozzati, Wensi Zhu, Claudio Bassot, John Lamb, Petras Kundrotas, Arne Elofsson
Limits and potential of combined folding and docking. Bioinform. 38 (4) (2022)
Zhong Li, Kaiyancheng Jiang, Shengwei Qin, Yijun Zhong, Arne Elofsson
GCSENet: A GCN, CNN and SENet ensemble model for microRNA-disease association prediction. PLoS Comput. Biol. 17 (6) (2021)
John Lamb, Arne Elofsson
pyconsFold: a fast and easy tool for modeling and docking using distance predictions. Bioinform. 37 (21) (2021)
Govindarajan Sudha, Claudio Bassot, John Lamb, Nanjiang Shu, Yan Huang, Arne Elofsson
The evolutionary history of topological variations in the CPA/AT transporters. PLoS Comput. Biol. 17 (8) (2021)
Federico Baldassarre, David Menéndez Hurtado, Arne Elofsson, Hossein Azizpour
GraphQA: protein model quality assessment using graph convolutional networks. Bioinform. 37 (3) (2021)
Arne Elofsson
Toward Characterising the Cellular 3D-Proteome. Frontiers Bioinform. 1 (2021)
Claudio Bassot, Arne Elofsson
Accurate contact-based modelling of repeat proteins predicts the structure of new repeats protein families. PLoS Comput. Biol. 17 (4) (2021)
Elodie Laine, Stephan Eismann, Arne Elofsson, Sergei Grudinin
Protein sequence-to-structure learning: Is this the end(-to-end revolution)? CoRR (2021)
Lifan Chen, Xiaoqin Tan, Dingyan Wang, Feisheng Zhong, Xiaohong Liu, Tianbiao Yang, Xiaomin Luo, Kaixian Chen, Hualiang Jiang, Mingyue Zheng, Arne Elofsson
TransformerCPI: improving compound-protein interaction prediction by sequence-based deep learning with self-attention mechanism and label reversal experiments. Bioinform. 36 (16) (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, Radoslav Davidovic, A. Keith Dunker, Arne Elofsson, Julien Gobeill, Nicolás S. González Foutel, Govindarajan Sudha, Mainak Guharoy, Tamás Horváth, Valentin Iglesias, Andrey V. Kajava, Orsolya P. Kovács, John Lamb, Matteo Lambrughi, Tamas Lazar, Jeremy Y. Leclercq, Emanuela Leonardi, Sandra Macedo-Ribeiro, Mauricio Macossay-Castillo, Emiliano Maiani, José A. Manso, Cristina Marino Buslje, Elizabeth Martínez-Pérez, Bálint Mészáros, Ivan Micetic, Giovanni Minervini, Nikoletta Murvai, Marco Necci, Christos A. Ouzounis, Mátyás Pajkos, Lisanna Paladin, Rita Pancsa, Elena Papaleo, Gustavo D. Parisi, Emilie Pasche, Pedro J. Barbosa Pereira, Vasilis J. Promponas, Jordi Pujols, Federica Quaglia, Patrick Ruch, Marco Salvatore, Éva Schád, Beáta Szabó, Tamás Szaniszló, Stella Tamana, Ágnes Tantos, Nevena Veljkovic, Salvador Ventura, Wim F. Vranken, Zsuzsanna Dosztányi, Peter Tompa, Silvio C. E. Tosatto, Damiano Piovesan
DisProt: intrinsic protein disorder annotation in 2020. Nucleic Acids Res. 48 (Database-Issue) (2020)
Arne Elofsson, Berk Hess, Erik Lindahl, Alexey Onufriev, David van der Spoel, Anders Wallqvist
Ten simple rules on how to create open access and reproducible molecular simulations of biological systems. PLoS Comput. Biol. 15 (1) (2019)
Mirco Michel, David Menéndez Hurtado, Arne Elofsson
PconsC4: fast, accurate and hassle-free contact predictions. Bioinform. 35 (15) (2019)
Walter Basile, Marco Salvatore, Claudio Bassot, Arne Elofsson
Why do eukaryotic proteins contain more intrinsically disordered regions? PLoS Comput. Biol. 15 (7) (2019)
Mirco Michel, David Menéndez Hurtado, Karolis Uziela, Arne Elofsson
Large-scale structure prediction by improved contact predictions and model quality assessment. Bioinform. 33 (14) (2017)
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, András Hatos, Andrey V. Kajava, Lajos Kalmár, Emanuela Leonardi, Tamas Lazar, Sandra Macedo-Ribeiro, Mauricio Macossay-Castillo, Attila Meszaros, Giovanni Minervini, Nikoletta Murvai, Jordi Pujols, Daniel B. Roche, Edoardo Salladini, Éva Schád, Antoine Schramm, Beáta Szabó, Ágnes Tantos, Fiorella Tonello, Konstantinos D. Tsirigos, Nevena Veljkovic, Salvador Ventura, Wim F. Vranken, Per Warholm, Vladimir N. Uversky, A. Keith Dunker, Sonia Longhi, Peter Tompa, Silvio C. E. Tosatto
DisProt 7.0: a major update of the database of disordered proteins. Nucleic Acids Res. 45 (Database-Issue) (2017)
Mirco Michel, Marcin J. Skwark, David Menéndez Hurtado, Magnus Ekeberg, Arne Elofsson
Predicting accurate contacts in thousands of Pfam domain families using PconsC3. Bioinform. 33 (18) (2017)
Walter Basile, Oxana Sachenkova, Sara Light, Arne Elofsson
High GC content causes orphan proteins to be intrinsically disordered. PLoS Comput. Biol. 13 (3) (2017)
Marco Salvatore, Per Warholm, Nanjiang Shu, Walter Basile, Arne Elofsson
SubCons: a new ensemble method for improved human subcellular localization predictions. Bioinform. 33 (16) (2017)
Karolis Uziela, David Menéndez Hurtado, Nanjiang Shu, Björn Wallner, Arne Elofsson
ProQ3D: improved model quality assessments using deep learning. Bioinform. 33 (10) (2017)
Niki L. Dimou, Konstantinos D. Tsirigos, Arne Elofsson, Pantelis G. Bagos
GWAR: robust analysis and meta-analysis of genome-wide association studies. Bioinform. 33 (10) (2017)
Christoph Peters, Konstantinos D. Tsirigos, Nanjiang Shu, Arne Elofsson
Improved topology prediction using the terminal hydrophobic helices rule. Bioinform. 32 (8) (2016)
Sikander Hayat, Christoph Peters, Nanjiang Shu, Konstantinos D. Tsirigos, Arne Elofsson
Inclusion of dyad-repeat pattern improves topology prediction of transmembrane β-barrel proteins. Bioinform. 32 (10) (2016)
Konstantinos D. Tsirigos, Arne Elofsson, Pantelis G. Bagos
PRED-TMBB2: improved topology prediction and detection of beta-barrel outer membrane proteins. Bioinform. 32 (17) (2016)
Konstantinos D. Tsirigos, Christoph Peters, Nanjiang Shu, Lukas Käll, Arne Elofsson
The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides. Nucleic Acids Res. 43 (Webserver-Issue) (2015)
Marcin J. Skwark, Daniele Raimondi, Mirco Michel, Arne Elofsson
Improved Contact Predictions Using the Recognition of Protein Like Contact Patterns. PLoS Comput. Biol. 10 (11) (2014)
Mirco Michel, Sikander Hayat, Marcin J. Skwark, Chris Sander, Debora S. Marks, Arne Elofsson
PconsFold: improved contact predictions improve protein models. Bioinform. 30 (17) (2014)
Marcin J. Skwark, Abbi Abdel-Rehim, Arne Elofsson
PconsC: combination of direct information methods and alignments improves contact prediction. Bioinform. 29 (14) (2013)
Marcin J. Skwark, Arne Elofsson
PconsD: ultra rapid, accurate model quality assessment for protein structure prediction. Bioinform. 29 (14) (2013)
Sikander Hayat, Arne Elofsson
BOCTOPUS: improved topology prediction of transmembrane β barrel proteins. Bioinform. 28 (4) (2012)
Sikander Hayat, Arne Elofsson
-barrel proteins using Z-coordinate predictions. Bioinform. 28 (12) (2012)
Per Larsson, Marcin J. Skwark, Björn Wallner, Arne Elofsson
Improved predictions by Pcons.net using multiple templates. Bioinform. 27 (3) (2011)
Nanjiang Shu, Arne Elofsson
KalignP: Improved multiple sequence alignments using position specific gap penalties in Kalign2. Bioinform. 27 (12) (2011)
Aron Hennerdal, Arne Elofsson
Rapid membrane protein topology prediction. Bioinform. 27 (9) (2011)
Kristoffer Illergård, Simone Callegari, Arne Elofsson
MPRAP: An accessibility predictor for alpha-helical transmembrane proteins that performs well inside and outside the membrane. BMC Bioinform. 11 (2010)
Andreas Bernsel, Håkan Viklund, Aron Hennerdal, Arne Elofsson
TOPCONS: consensus prediction of membrane protein topology. Nucleic Acids Res. 37 (Web-Server-Issue) (2009)
Håkan Viklund, Andreas Bernsel, Marcin J. Skwark, Arne Elofsson
SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology. Bioinform. 24 (24) (2008)
Håkan Viklund, Arne Elofsson
OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar. Bioinform. 24 (15) (2008)
Björn Wallner, Per Larsson, Arne Elofsson
Pcons.net: protein structure prediction meta server. Nucleic Acids Res. 35 (Web-Server-Issue) (2007)
Åsa K. Björklund, Diana Ekman, Arne Elofsson
Expansion of Protein Domain Repeats. PLoS Comput. Biol. 2 (8) (2006)
Tomas Ohlson, Varun Aggarwal, Arne Elofsson, Robert M. MacCallum
Improved alignment quality by combining evolutionary information, predicted secondary structure and self-organizing maps. BMC Bioinform. 7 (2006)
Erik Granseth, Håkan Viklund, Arne Elofsson
ZPRED: Predicting the distance to the membrane center for residues in alpha-helical membrane proteins. ISMB (Supplement of Bioinformatics) (2006)
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
PONGO: a web server for multiple predictions of all-alpha transmembrane proteins. Nucleic Acids Res. 34 (Web-Server-Issue) (2006)
Tomas Ohlson, Arne Elofsson
ProfNet, a method to derive profile-profile alignment scoring functions that improves the alignments of distantly related proteins. BMC Bioinform. 6 (2005)
Björn Wallner, Arne Elofsson
Pcons5: combining consensus, structural evaluation and fold recognition scores. Bioinform. 21 (23) (2005)
Krzysztof Ginalski, Arne Elofsson, Daniel Fischer, Leszek Rychlewski
3D-Jury: A Simple Approach to Improve Protein Structure Predictions. Bioinform. 19 (8) (2003)
Pierre Dönnes, Arne Elofsson
Prediction of MHC class I binding peptides, using SVMHC. BMC Bioinform. 3 (2002)
Susana Cristobal, Adam T. Zemla, Daniel Fischer, Leszek Rychlewski, Arne Elofsson
A study of quality measures for protein threading models. BMC Bioinform. 2 (2001)
Olivia Eriksson, Yishao Zhou, Arne Elofsson
Side Chain-Positioning as an Integer Programming Problem. WABI (2001)
Janusz M. Bujnicki, Arne Elofsson, Daniel Fischer, Leszek Rychlewski
Structure prediction meta server. Bioinform. 17 (8) (2001)
Naomi Siew, Arne Elofsson, Leszek Rychlewski, Daniel Fischer
MaxSub: an automated measure for the assessment of protein structure prediction quality. Bioinform. 16 (9) (2000)
Arne Elofsson, Erik L. L. Sonnhammer
A comparison of sequence and structure protein domain families as a basis for structural genomics. Bioinform. 15 (6) (1999)