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Paul Theodor Pyl
Researcher at Lund University
Publications - 18
Citations - 17807
Paul Theodor Pyl is an academic researcher from Lund University. The author has contributed to research in topics: Python (programming language) & Proteogenomics. The author has an hindex of 6, co-authored 15 publications receiving 13163 citations. Previous affiliations of Paul Theodor Pyl include Science for Life Laboratory & European Bioinformatics Institute.
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Journal ArticleDOI
HTSeq—a Python framework to work with high-throughput sequencing data
TL;DR: This work presents HTSeq, a Python library to facilitate the rapid development of custom scripts for high-throughput sequencing data analysis, and presents htseq-count, a tool developed with HTSequ that preprocesses RNA-Seq data for differential expression analysis by counting the overlap of reads with genes.
Journal ArticleDOI
Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer
Jakob Wirbel,Paul Theodor Pyl,Paul Theodor Pyl,Ece Kartal,Konrad Zych,Alireza Kashani,Alessio Milanese,Jonas S. Fleck,Anita Y. Voigt,Albert Pallejà,Ruby Ponnudurai,Shinichi Sunagawa,Luis Pedro Coelho,Petra Schrotz-King,Emily Vogtmann,Nina Habermann,Emma Niméus,Andrew Maltez Thomas,Andrew Maltez Thomas,Paolo Manghi,Sara Gandini,Davide Serrano,Sayaka Mizutani,Sayaka Mizutani,Hirotsugu Shiroma,Satoshi Shiba,Tatsuhiro Shibata,Shinichi Yachida,Takuji Yamada,Takuji Yamada,Levi Waldron,Alessio Naccarati,Nicola Segata,Rashmi Sinha,Cornelia M. Ulrich,Hermann Brenner,Manimozhiyan Arumugam,Manimozhiyan Arumugam,Peer Bork,Georg Zeller +39 more
TL;DR: A meta-analysis of eight geographically and technically diverse fecal shotgun metagenomic studies of colorectal cancer identified a core set of 29 species significantly enriched in CRC metagenomes, establishing globally generalizable, predictive taxonomic and functional microbiome CRC signatures as a basis for future diagnostics.
Posted ContentDOI
HTSeq - A Python framework to work with high-throughput sequencing data
TL;DR: This work presents HTSeq, a Python library to facilitate the rapid development of custom scripts for high-throughput sequencing data analysis and presents htseq-count, a tool developed with HTSequ that preprocesses RNA-Seq data for differential expression analysis by counting the overlap of reads with genes.
Journal ArticleDOI
Recovery of gut microbiota of healthy adults following antibiotic exposure
Albert Pallejà,Kristian Hallundbæk Mikkelsen,Sofia K. Forslund,Alireza Kashani,Kristine H. Allin,Kristine H. Allin,Trine Nielsen,Tue H. Hansen,Suisha Liang,Qiang Feng,Chenchen Zhang,Paul Theodor Pyl,Luis Pedro Coelho,Huanming Yang,Jian Wang,Athanasios Typas,Morten Frost Munk Nielsen,Henrik Nielsen,Peer Bork,Jun Wang,Tina Vilsbøll,Torben Hansen,Torben Hansen,Filip K. Knop,Manimozhiyan Arumugam,Oluf Pedersen +25 more
TL;DR: It is shown that the human gut microbiome can recover after a clinically relevant, broad-spectrum antibiotic treatment and characterization of the resistome indicates that antibiotic resistance genes can impact the recovery process.
Journal ArticleDOI
The Genomic and Transcriptomic Landscape of a HeLa Cell Line
Jonathan J M Landry,Paul Theodor Pyl,Tobias Rausch,Thomas Zichner,Manu M. Tekkedil,Adrian M. Stütz,Anna Jauch,Raeka S. Aiyar,Gregoire Pau,Nicolas Delhomme,Julien Gagneur,Jan O. Korbel,Wolfgang Huber,Lars M. Steinmetz +13 more
TL;DR: This study performed DNA and RNA sequencing of a HeLa Kyoto cell line and analyzed its mutational portfolio and gene expression profile, providing the first detailed account of genomic variants in the HeLa genome.