Marcin J. Skwark

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Arne ElofssonScience for Life Laboratory and department of Biochemistry and Biophysics, Stockholm UniversityVerified email at bioinfo.se
Karim BeguirInstaDeepVerified email at instadeep.com
Tom L BlundellEmeritus Professor of Biochemistry, University of CambridgeVerified email at cam.ac.uk
Thomas PierrotStaff Research Scientist, InstaDeepVerified email at instadeep.com
Julian ParkhillUniversity of CambridgeVerified email at cam.ac.uk
Jens MeilerVanderbilt University & University LeipzigVerified email at meilerlab.org
Erik AurellProfessor of Biological Physics, KTH-Royal Institute of TechnologyVerified email at kth.se
Ugur SahinProfessor of ImmunologyVerified email at uni-mainz.de
R. Andres FlotoUniversity of CambridgeVerified email at cam.ac.uk
Stephen BentleyWellcome Sanger InstituteVerified email at sanger.ac.uk
Jukka CoranderUiO, Wellcome Sanger Institute, University of HelsinkiVerified email at medisin.uio.no
Chris SanderHarvard Medical School, Broad Institute, Dana-Farber Cancer Institute, Memorial Sloan KetteringVerified email at sanderlab.org
Paul TurnerProfessor of Paediatric Microbiology, University of OxfordVerified email at tropmedres.ac
Simon R. HarrisSenior Program Officer, Bill & Melinda Gates FoundationVerified email at sanger.ac.uk
Stephen BeresProfessor of Pathology and Genomic Medicine, Houston Methodist Institute for Academic MedicineVerified email at houstonmethodist.org
Craig LindsleyVanderbilt UniversityVerified email at vanderbilt.edu
Christian SpeckProfessor, DNA Replication Group, Imperial College LondonVerified email at imperial.ac.uk
Christine OrengoProfessor of Bioinformatics, University College LondonVerified email at biochem.ucl.ac.uk
David JonesProfessor of Bioinformatics, University College LondonVerified email at ucl.ac.uk
Paul J TurnerImperial College LondonVerified email at doctors.org.uk

Marcin J. Skwark

Other namesMarcin Skwark

Bioinformatics Lead, InstaDeep

Verified email at skwark.pl

Computational Biology Protein Structure Machine Learning


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SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology H Viklund, A Bernsel, M Skwark, A Elofsson Bioinformatics 24 (24), 2928-2929, 2008	278	2008
Improved contact predictions using the recognition of protein like contact patterns MJ Skwark, D Raimondi, M Michel, A Elofsson PLoS computational biology 10 (11), e1003889, 2014	187	2014
Nucleotide Transformer: building and evaluating robust foundation models for human genomics H Dalla-Torre, L Gonzalez, J Mendoza-Revilla, N Lopez Carranza, ... Nature Methods, 1-11, 2024	127	2024
PconsFold: improved contact predictions improve protein models M Michel, S Hayat, MJ Skwark, C Sander, DS Marks, A Elofsson Bioinformatics 30 (17), i482-i488, 2014	115	2014
Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis MJ Skwark, NJ Croucher, S Puranen, C Chewapreecha, M Pesonen, ... PLoS genetics 13 (2), e1006508, 2017	112	2017
PconsC: combination of direct information methods and alignments improves contact prediction MJ Skwark, A Abdel-Rehim, A Elofsson Bioinformatics 29 (14), 1815-1816, 2013	97	2013
Improving contact prediction along three dimensions C Feinauer, MJ Skwark, A Pagnani, E Aurell PLoS computational biology 10 (10), e1003847, 2014	88	2014
Assessment of global and local model quality in CASP8 using Pcons and ProQ P Larsson, MJ Skwark, B Wallner, A Elofsson Proteins: Structure, Function, and Bioinformatics 77 (S9), 167-172, 2009	85	2009
Protein contact prediction from amino acid co-evolution using convolutional networks for graph-valued images V Golkov, MJ Skwark, D Alexey, T Brox, J Meiler, D Cremers Advances in Neural Information Processing Systems, 730-738, 2016	53	2016
Predicting accurate contacts in thousands of Pfam domain families using PconsC3 M Michel, MJ Skwark, D Menéndez Hurtado, M Ekeberg, A Elofsson Bioinformatics 33 (18), 2859-2866, 2017	52	2017
Discoidin domain receptor 1 kinase activity is required for regulating collagen IV synthesis CM Borza, Y Su, TL Tran, L Yu, N Steyns, KJ Temple, MJ Skwark, J Meiler, ... Matrix Biology 57, 258-271, 2017	50	2017
Mycobacterial genomics and structural bioinformatics: opportunities and challenges in drug discovery VP Waman, SC Vedithi, SE Thomas, BP Bannerman, A Munir, MJ Skwark, ... Emerging microbes & infections 8 (1), 109-118, 2019	38	2019
PconsD: ultra rapid, accurate model quality assessment for protein structure prediction MJ Skwark, A Elofsson Bioinformatics 29 (14), 1817-1818, 2013	36	2013
Early computational detection of potential high-risk SARS-CoV-2 variants K Beguir, MJ Skwark, Y Fu, T Pierrot, NL Carranza, A Laterre, I Kadri, ... Computers in biology and medicine 155, 106618, 2023	33	2023
Mycobacterium abscessus pathogenesis identified by phenogenomic analyses L Boeck, S Burbaud, M Skwark, WH Pearson, J Sangen, AW Wuest, ... Nature Microbiology 7 (9), 1431-1441, 2022	29	2022
Computational saturation mutagenesis to predict structural consequences of systematic mutations in the beta subunit of RNA polymerase in Mycobacterium leprae SC Vedithi, CHM Rodrigues, S Portelli, MJ Skwark, M Das, DB Ascher, ... Computational and Structural Biotechnology Journal 18, 271-286, 2020	29	2020
The structural basis of Cdc7-Dbf4 kinase dependent targeting and phosphorylation of the MCM2-7 double hexamer A Saleh, Y Noguchi, R Aramayo, ME Ivanova, KM Stevens, A Montoya, ... Nature communications 13 (1), 2915, 2022	28	2022
Membrane remodeling capacity of a vesicle‐inducing glycosyltransferase C Ge, J Gómez‐Llobregat, MJ Skwark, JM Ruysschaert, Å Wieslander, ... The FEBS journal 281 (16), 3667-3684, 2014	23	2014
3D deep learning for biological function prediction from physical fields V Golkov, MJ Skwark, A Mirchev, G Dikov, AR Geanes, J Mendenhall, ... 2020 International Conference on 3D Vision (3DV), 928-937, 2020	21	2020
Improved predictions by Pcons. net using multiple templates P Larsson, MJ Skwark, B Wallner, A Elofsson Bioinformatics 27 (3), 426-427, 2011	20	2011

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