Marcin J. Skwark

发表

Accurate contact predictions for thousands of protein families using PconsC3

Marcin J. Skwark, Mirco Michel, David Menéndez Hurtado, 2016 .

Designing a Prospective COVID-19 Therapeutic with Reinforcement Learning pdf

Marcin J. Skwark, Alexandre Laterre, Amine Kerkeni, 2020, ArXiv.

PconsD: ultra rapid, accurate model quality assessment for protein structure prediction

Marcin J. Skwark, Arne Elofsson, 2013, Bioinform..

3D Deep Learning for Biological Function Prediction from Physical Fields

Marcin J. Skwark, Daniel Cremers, Jens Meiler, 2017, 2020 International Conference on 3D Vision (3DV).

Predicting accurate contacts in thousands of Pfam domain families using PconsC3

Marcin J. Skwark, Mirco Michel, Magnus Ekeberg, 2017, Bioinform..

Improved Contact Predictions Using the Recognition of Protein Like Contact Patterns

Marcin J. Skwark, Mirco Michel, Arne Elofsson, 2014, PLoS Comput. Biol..

Protein contact prediction from amino acid co-evolution using convolutional networks for graph-valued images

Marcin J. Skwark, Daniel Cremers, Thomas Brox, 2016, NIPS.

Mabellini: a genome-wide database for understanding the structural proteome and evaluating prospective antimicrobial targets of the emerging pathogen Mycobacterium abscessus

Marcin J. Skwark, Tom L. Blundell, Pedro Henrique Monteiro Torres, 2019, Database J. Biol. Databases Curation.

PconsFold: improved contact predictions improve protein models

Marcin J. Skwark, Mirco Michel, Arne Elofsson, 2014, Bioinform..

PconsC: combination of direct information methods and alignments improves contact prediction

Marcin J. Skwark, Arne Elofsson, Abbi Abdel-Rehim, 2013, Bioinform..

Improved predictions by Pcons.net using multiple templates

Marcin J. Skwark, Arne Elofsson, Björn Wallner, 2011, Bioinform..

Improving Contact Prediction along Three Dimensions

Marcin J. Skwark, Erik Aurell, Andrea Pagnani, 2014, PLoS Comput. Biol..

SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology

Marcin J. Skwark, Arne Elofsson, Håkan Viklund, 2008, Bioinform..

Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis

Marcin J. Skwark, Jukka Corander, Paul Turner, 2016, bioRxiv.

PconsFold: improved contact predictions improve protein models

Marcin J. Skwark, Mirco Michel, Arne Elofsson, 2014, Bioinform..

Membrane protein contact and structure prediction using co-evolution in conjunction with machine learning

Marcin J. Skwark, Jens Meiler, Jeffrey L. Mendenhall, 2017, PloS one.

Membrane protein shaving with thermolysin can be used to evaluate topology predictors

Marcin J. Skwark, L. Käll, A. Elofsson, 2013, Proteomics.

Interacting networks of resistance , virulence and core machinery genes identified by genome-wide 1 epistasis analysis 2 Short title : Genome-wide epistasis analysis in bacteria 3

Marcin J. Skwark, J. Corander, E. Aurell, 2016 .

Membrane remodeling capacity of a vesicle‐inducing glycosyltransferase

Marcin J. Skwark, C. Ge, J. Ruysschaert, 2014, The FEBS journal.

Computational saturation mutagenesis to predict structural consequences of systematic mutations in the beta subunit of RNA polymerase in Mycobacterium leprae

Marcin J. Skwark, Carlos H. M. Rodrigues, T. Blundell, 2020, Computational and structural biotechnology journal.

Computational Saturation Mutagenesis of the β subunit of RNA polymerase in Mycobacterium leprae

Marcin J. Skwark, Carlos H. M. Rodrigues, T. Blundell, 2019, bioRxiv.

Computational Saturation Mutagenesis to predict structural consequences of systematic mutations on protein stability and rifampin interactions in the β subunit of RNA polymerase inMycobacterium leprae

Marcin J. Skwark, Carlos H. M. Rodrigues, T. Blundell, 2019 .

HARP: a database of structural impacts of systematic missense mutations in drug targets of Mycobacterium leprae

Marcin J. Skwark, Ali F. Alsulami, T. Blundell, 2020, Computational and structural biotechnology journal.

Computational saturation mutagenesis to predict structural consequences of systematic mutations in the beta subunit of RNA polymerase in Mycobacterium leprae.

Marcin J. Skwark, Carlos H. M. Rodrigues, T. Blundell, 2020 .

Mycobacterial genomics and structural bioinformatics: opportunities and challenges in drug discovery

Marcin J. Skwark, T. Blundell, Vaishali P. Waman, 2019, Emerging microbes & infections.

The structural basis of Cdc7-Dbf4 kinase dependent targeting and phosphorylation of the MCM2-7 double hexamer

Marcin J. Skwark, C. Speck, R. Aramayo, 2022, Nature Communications.

Genome3D: integrating a collaborative data pipeline to expand the depth and breadth of consensus protein structure annotation

Marcin J. Skwark, Gustavo A. Salazar, Daniel W. A. Buchan, 2019, Nucleic Acids Res..

Discoidin domain receptor 1 kinase activity is required for regulating collagen IV synthesis.

Marcin J. Skwark, A. Pozzi, J. Meiler, 2017, Matrix biology : journal of the International Society for Matrix Biology.

Mycobacterium abscessus pathogenesis identified by phenogenomic analyses

Marcin J. Skwark, T. Blundell, J. Parkhill, 2022, Nature Microbiology.

Peptide-MHC Structure Prediction With Mixed Residue and Atom Graph Neural Network

Marcin J. Skwark, Yunguan Fu, U. Şahin, 2022, bioRxiv.

The influence of manual semen collection in male trained dogs (Canis familiaris), in the presence or absence of a female in estrus, on the concentrations of cortisol, oxytocin, prolactin and testosterone

Marcin J. Skwark, A. Szumny, T. Jezierski, 2023, PloS one.

The Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics

Marcin J. Skwark, Christian Dallago, Karim Beguir, 2023, bioRxiv.

The Collagen Receptor Discoidin Domain Receptor 1b Enhances Integrin β1-Mediated Cell Migration by Interacting With Talin and Promoting Rac1 Activation

Marcin J. Skwark, A. Pozzi, J. Meiler, 2022, Frontiers in Cell and Developmental Biology.

The Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics

Marcin J. Skwark, Christian Dallago, Christian Dallago, 2023, bioRxiv.

Early computational detection of potential high-risk SARS-CoV-2 variants

Marcin J. Skwark, Yunguan Fu, U. Şahin, 2021, bioRxiv.

Urinary Proteins of Female Domestic Dog (Canis familiaris) during Ovarian Cycle

Marcin J. Skwark, A. Szumny, A. Kokocińska, 2023, Veterinary sciences.

The pathobiology of Mycobacterium abscessus revealed through phenogenomic analysis

Marcin J. Skwark, T. Blundell, J. Parkhill, 2021, bioRxiv.

Analysis of metabolic pathways in mycobacteria to aid drug-target identification

Marcin J. Skwark, T. Blundell, S. Oliver, 2019, bioRxiv.

Mabellini: a genome-wide database for understanding the structural proteome and evaluating prospective antimicrobial targets of the emerging pathogen Mycobacterium abscessus.

Marcin J. Skwark, T. Blundell, R. Floto, 2019 .