Applying the FAIR Principles to computational workflows

Authors: Sean R. Wilkinson, Meznah Aloqalaa, Khalid Belhajjame, Michael R. Crusoe, Bruno de Paula Kinoshita, Luiz Gadelha, Daniel Garijo, Ove Johan Ragnar Gustafsson, Nick Juty, Sehrish Kanwal, Farah Zaib Khan, Johannes Köster, Karsten Peters-von Gehlen, Line Pouchard, Randy K. Rannow, Stian Soiland-Reyes, Nicola Soranzo, Shoaib Sufi, Ziheng Sun, Baiba Vilne, Merridee A. Wouters, Denis Yuen, Carole Goble

Source: Scientific Data, Vol 12, Iss 1, Pp 1-9 (2025)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2052-4463

Access URL: https://doaj.org/article/3602bf33e74a4a9597c6c25e972aedc4

Orthanq: transparent and uncertainty-aware haplotype quantification with application in HLA-typing

Authors: Hamdiye Uzuner, Annette Paschen, Dirk Schadendorf, Johannes Köster

Source: BMC Bioinformatics, Vol 25, Iss 1, Pp 1-18 (2024)

Subject Terms: Haplotype quantification, HLA typing, Bayesian latent variable model, Genomic variants, Uncertainty quantification, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1471-2105

Access URL: https://doaj.org/article/a37634a311bf4a9cae76931a655fd557

UnCoVar: a reproducible and scalable workflow for transparent and robust virus variant calling and lineage assignment using SARS-CoV-2 as an example

Authors: Alexander Thomas, Thomas Battenfeld, Ivana Kraiselburd, Olympia Anastasiou, Ulf Dittmer, Ann-Kathrin Dörr, Adrian Dörr, Carina Elsner, Jule Gosch, Vu Thuy Khanh Le-Trilling, Simon Magin, René Scholtysik, Pelin Yilmaz, Mirko Trilling, Lara Schöler, Johannes Köster, Folker Meyer

Source: BMC Genomics, Vol 25, Iss 1, Pp 1-9 (2024)

Subject Terms: SARS-CoV-2, Workflow, Variant calling, Lineage assignment, Next generation sequencing, Biotechnology, TP248.13-248.65, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1471-2164

Access URL: https://doaj.org/article/7c88bf5065d14a7caf6ac89a4da96eec

NCBench: providing an open, reproducible, transparent, adaptable, and continuous benchmark approach for DNA-sequencing-based variant calling [version 2; peer review: 2 approved]

Authors: Felix Wiegand, Bianca Stöcker, Famke Bäuerle, Susanne Motameny, Andreas Buness, Alexander J. Probst, Fabian Brand, Axel Schmidt, Tyll Stöcker, Sugirthan Sivalingam, Andreas Petzold, Marc Sturm, Janine Altmueller, Johannes Köster, Kerstin Becker, Leon Brandhoff, Anna Ossowski, Christian Mertes, Avirup Guha Neogi, Gisela Gabernet, Nicholas H. Smith, Friederike Hanssen

Source: F1000Research, Vol 12 (2024)

Subject Terms: continuous, benchmarking, NGS, variant calling, eng, Medicine, Science

File Description: electronic resource

Relation: https://f1000research.com/articles/12-1125/v2; https://doaj.org/toc/2046-1402

Access URL: https://doaj.org/article/117f3609dd9e44c58c2a7e52d9ff948e

Pancreatic cancer acquires resistance to MAPK pathway inhibition by clonal expansion and adaptive DNA hypermethylation

Authors: Laura K. Godfrey, Jan Forster, Sven-Thorsten Liffers, Christopher Schröder, Johannes Köster, Leonie Henschel, Kerstin U. Ludwig, David Lähnemann, Marija Trajkovic-Arsic, Diana Behrens, Aldo Scarpa, Rita T. Lawlor, Kathrin E. Witzke, Barbara Sitek, Steven A. Johnsen, Sven Rahmann, Bernhard Horsthemke, Michael Zeschnigk, Jens T. Siveke

Source: Clinical Epigenetics, Vol 16, Iss 1, Pp 1-22 (2024)

Subject Terms: Cancer, Therapy resistance, Epigenetic plasticity, DNA methylation, WGBS, Clonal expansion, Medicine, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1868-7083

Access URL: https://doaj.org/article/d600d9b4f409474cb363cc7b8d335cf3

Accurate and scalable variant calling from single cell DNA sequencing data with ProSolo

Authors: David Lähnemann, Johannes Köster, Ute Fischer, Arndt Borkhardt, Alice C. McHardy, Alexander Schönhuth

Source: Nature Communications, Vol 12, Iss 1, Pp 1-11 (2021)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/8db091b26b934b4bafe06184a93555fe

VISPR-online: a web-based interactive tool to visualize CRISPR screening experiments

Authors: Yingbo Cui, Zihang Wang, Johannes Köster, Xiangke Liao, Shaoliang Peng, Tao Tang, Chun Huang, Canqun Yang

Source: BMC Bioinformatics, Vol 22, Iss 1, Pp 1-7 (2021)

Subject Terms: CRISPR, CRISPR screening, Visualization, VISPR, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1471-2105

Access URL: https://doaj.org/article/a01515760a4f42b39a97e449e9a3f3d5

Go Get Data (GGD) is a framework that facilitates reproducible access to genomic data

Authors: Michael J. Cormier, Jonathan R. Belyeu, Brent S. Pedersen, Joseph Brown, Johannes Köster, Aaron R. Quinlan

Source: Nature Communications, Vol 12, Iss 1, Pp 1-6 (2021)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/229a1630d4cf43f5bf84c23578b10f64

Varlociraptor: enhancing sensitivity and controlling false discovery rate in somatic indel discovery

Authors: Johannes Köster, Louis J. Dijkstra, Tobias Marschall, Alexander Schönhuth

Source: Genome Biology, Vol 21, Iss 1, Pp 1-25 (2020)

Subject Terms: Variant calling, Tumor/normal, Somatic, Bayesian latent variable model, FDR control, Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s13059-020-01993-6; https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/14ba1344d7f441fa9134799fa01e9e97

Detection and Validation of Circular DNA Fragments Using Nanopore Sequencing

Authors: Alicia Isabell Tüns, Till Hartmann, Simon Magin, Rocío Chamorro González, Anton George Henssen, Sven Rahmann, Alexander Schramm, Johannes Köster

Source: Frontiers in Genetics, Vol 13 (2022)

Subject Terms: cancer, circular DNA, nanopore sequencing, algorithm, snakemake, Genetics, QH426-470

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fgene.2022.867018/full; https://doaj.org/toc/1664-8021

Access URL: https://doaj.org/article/66e0271a213b461695eace0945899692

Eleven grand challenges in single-cell data science

Authors: David Lähnemann, Johannes Köster, Ewa Szczurek, Davis J. McCarthy, Stephanie C. Hicks, Mark D. Robinson, Catalina A. Vallejos, Kieran R. Campbell, Niko Beerenwinkel, Ahmed Mahfouz, Luca Pinello, Pavel Skums, Alexandros Stamatakis, Camille Stephan-Otto Attolini, Samuel Aparicio, Jasmijn Baaijens, Marleen Balvert, Buys de Barbanson, Antonio Cappuccio, Giacomo Corleone, Bas E. Dutilh, Maria Florescu, Victor Guryev, Rens Holmer, Katharina Jahn, Thamar Jessurun Lobo, Emma M. Keizer, Indu Khatri, Szymon M. Kielbasa, Jan O. Korbel, Alexey M. Kozlov, Tzu-Hao Kuo, Boudewijn P.F. Lelieveldt, Ion I. Mandoiu, John C. Marioni, Tobias Marschall, Felix Mölder, Amir Niknejad, Alicja Rączkowska, Marcel Reinders, Jeroen de Ridder, Antoine-Emmanuel Saliba, Antonios Somarakis, Oliver Stegle, Fabian J. Theis, Huan Yang, Alex Zelikovsky, Alice C. McHardy, Benjamin J. Raphael, Sohrab P. Shah, Alexander Schönhuth

Source: Genome Biology, Vol 21, Iss 1, Pp 1-35 (2020)

Subject Terms: Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/9368dc7f34b5489abc7fc8743d7a022d

Sustainable data analysis with Snakemake [version 2; peer review: 2 approved]

Authors: Felix Mölder, Kim Philipp Jablonski, Brice Letcher, Michael B. Hall, Christopher H. Tomkins-Tinch, Vanessa Sochat, Jan Forster, Soohyun Lee, Sven O. Twardziok, Alexander Kanitz, Andreas Wilm, Manuel Holtgrewe, Sven Rahmann, Sven Nahnsen, Johannes Köster

Source: F1000Research, Vol 10 (2021)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://f1000research.com/articles/10-33/v2; https://doaj.org/toc/2046-1402

Access URL: https://doaj.org/article/bbd585a540ab405f95b6070a1bbedc3f

VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis

Authors: MacIntosh Cornwell, Mahesh Vangala, Len Taing, Zachary Herbert, Johannes Köster, Bo Li, Hanfei Sun, Taiwen Li, Jian Zhang, Xintao Qiu, Matthew Pun, Rinath Jeselsohn, Myles Brown, X. Shirley Liu, Henry W. Long

Source: BMC Bioinformatics, Vol 19, Iss 1, Pp 1-14 (2018)

Subject Terms: RNA-seq, Analysis, Pipeline, Snakemake, Gene fusion, Immunological infiltrate, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s12859-018-2139-9; https://doaj.org/toc/1471-2105

Access URL: https://doaj.org/article/05f5ce1145074e0bbe0ea6794782fc82

Massively parallel read mapping on GPUs with the q-group index and PEANUT

Authors: Johannes Köster, Sven Rahmann

Source: PeerJ, Vol 2, p e606 (2014)

Subject Terms: Read mapping, Datastructure, Parallel algorithms, GPU programming, Medicine, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://peerj.com/articles/606.pdf; https://peerj.com/articles/606/; https://doaj.org/toc/2167-8359

Access URL: https://doaj.org/article/f3325ee694b64567bd7a61d46a576799

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