Publications by authors named "Marcin Skwark"

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Volatile Organic Compounds Induced upon Viral Infection in Cell Culture: Uniform Background Study with Use of Viruses from Different Families.
Anna Karolina Matczuk, Julia Wolska, Maria Olszowy, Agata Kublicka, Adam Szumowski, Marcin J Skwark

Molecules· December 2025

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Nucleotide Transformer: building and evaluating robust foundation models for human genomics.
Hugo Dalla-Torre, Liam Gonzalez, Javier Mendoza-Revilla, Nicolas Lopez Carranza, Adam Henryk Grzywaczewski, Marcin Skwark

Nat Methods· February 2025

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A foundational large language model for edible plant genomes.
Javier Mendoza-Revilla, Evan Trop, Liam Gonzalez, Maša Roller, Hugo Dalla-Torre, Marcin Skwark

Commun Biol· July 2024

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Urinary Proteins of Female Domestic Dog () during Ovarian Cycle.
Martyna Woszczyło, Paweł Pasikowski, Sankarganesh Devaraj, Agata Kokocińska, Antoni Szumny, Marcin J Skwark

Vet Sci· April 2023

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Early computational detection of potential high-risk SARS-CoV-2 variants.
Karim Beguir, Marcin J Skwark, Yunguan Fu, Thomas Pierrot, Nicolas Lopez Carranza

Comput Biol Med· March 2023

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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.
Martyna Woszczyło, Antoni Szumny, Piotr Knap, Tadeusz Jezierski, Wojciech Niżański, Marcin J Skwark

PLoS One· February 2023

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Mycobacterium abscessus pathogenesis identified by phenogenomic analyses.
Lucas Boeck, Sophie Burbaud, Marcin Skwark, Will H Pearson, Jasper Sangen

Nat Microbiol· September 2022

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The structural basis of Cdc7-Dbf4 kinase dependent targeting and phosphorylation of the MCM2-7 double hexamer.
Almutasem Saleh, Yasunori Noguchi, Ricardo Aramayo, Marina E Ivanova, Kathryn M Stevens, Marcin J Skwark

Nat Commun· May 2022

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The Collagen Receptor Discoidin Domain Receptor 1b Enhances Integrin β1-Mediated Cell Migration by Interacting With Talin and Promoting Rac1 Activation.
Corina M Borza, Gema Bolas, Xiuqi Zhang, Mary Beth Browning Monroe, Ming-Zhi Zhang, Marcin J Skwark

Front Cell Dev Biol· March 2022

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HARP: a database of structural impacts of systematic missense mutations in drug targets of .
Sundeep Chaitanya Vedithi, Sony Malhotra, Marcin J Skwark, Asma Munir, Marta Acebrón-García-De-Eulate

Comput Struct Biotechnol J· November 2020

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Genome3D: integrating a collaborative data pipeline to expand the depth and breadth of consensus protein structure annotation.
Ian Sillitoe, Antonina Andreeva, Tom L Blundell, Daniel W A Buchan, Robert D Finn, Marcin J Skwark

Nucleic Acids Res· January 2020

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Computational saturation mutagenesis to predict structural consequences of systematic mutations in the beta subunit of RNA polymerase in .
Sundeep Chaitanya Vedithi, Carlos H M Rodrigues, Stephanie Portelli, Marcin J Skwark, Madhusmita Das

Comput Struct Biotechnol J· January 2020

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Mycobacterial genomics and structural bioinformatics: opportunities and challenges in drug discovery.
Vaishali P Waman, Sundeep Chaitanya Vedithi, Sherine E Thomas, Bridget P Bannerman, Asma Munir, Marcin J Skwark

Emerg Microbes Infect· July 2019

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Mabellini: a genome-wide database for understanding the structural proteome and evaluating prospective antimicrobial targets of the emerging pathogen Mycobacterium abscessus.
Marcin J Skwark, Pedro H M Torres, Liviu Copoiu, Bridget Bannerman, R Andres Floto

Database (Oxford)· January 2019

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

Bioinformatics· September 2017

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Membrane protein contact and structure prediction using co-evolution in conjunction with machine learning.
Pedro L Teixeira, Jeff L Mendenhall, Sten Heinze, Brian Weiner, Marcin J Skwark

PLoS One· September 2017

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Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis.
Marcin J Skwark, Nicholas J Croucher, Santeri Puranen, Claire Chewapreecha, Maiju Pesonen

PLoS Genet· February 2017

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Discoidin domain receptor 1 kinase activity is required for regulating collagen IV synthesis.
Corina M Borza, Yan Su, Truc-Linh Tran, Ling Yu, Nick Steyns, Marcin J Skwark

Matrix Biol· January 2017

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Improved contact predictions using the recognition of protein like contact patterns.
Marcin J Skwark, Daniele Raimondi, Mirco Michel, Arne Elofsson

PLoS Comput Biol· November 2014

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Improving contact prediction along three dimensions.
Christoph Feinauer, Marcin J Skwark, Andrea Pagnani, Erik Aurell

PLoS Comput Biol· October 2014

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PconsFold: improved contact predictions improve protein models.
Mirco Michel, Sikander Hayat, Marcin J Skwark, Chris Sander, Debora S Marks

Bioinformatics· September 2014

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Membrane remodeling capacity of a vesicle-inducing glycosyltransferase.
Changrong Ge, Jordi Gómez-Llobregat, Marcin J Skwark, Jean-Marie Ruysschaert, Ake Wieslander

FEBS J· August 2014

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

Bioinformatics· July 2013

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PconsD: ultra rapid, accurate model quality assessment for protein structure prediction.
Marcin J Skwark, Arne Elofsson

Bioinformatics· July 2013

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Membrane protein shaving with thermolysin can be used to evaluate topology predictors.
Maria Bendz, Marcin Skwark, Daniel Nilsson, Viktor Granholm, Susana Cristobal

Proteomics· May 2013

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