List of works - Johannes Köster

A Bayesian model for single cell transcript expression analysis on MERFISH data

scientific article published on 01 July 2019

A Bayesian model for single cell transcript expression analysis on MERFISH data

scientific article published on 01 March 2019

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

scientific article published on 18 November 2021

Bioconda

scientific article published on 01 July 2018

Bioconda: sustainable and comprehensive software distribution for the life sciences

scientific article published on 01 July 2018

CRISPR-DO for genome-wide CRISPR design and optimization

scientific article published on 10 July 2016

Cancer evolution, mutations, and clonal selection in relapse neuroblastoma

scientific article published on 24 February 2018

Differential turnover of isoflavone 7-O-glucoside-6″-O-malonates in Cicer arietinum roots

scientific article published on 25 July 2002

Efficiently mining protein interaction dependencies from large text corpora

scientific article published on 15 June 2012

Eleven grand challenges in single-cell data science

scientific article published on 07 February 2020

Full-length de novo viral quasispecies assembly through variation graph construction

scientific article published on 01 December 2019

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

scientific article published on 12 April 2021

Identifying transcriptional miRNA biomarkers by integrating high-throughput sequencing and real-time PCR data

scientific article

Life threatening neuroleptic malignant syndrome due to olanzapine

scientific article published in July 2003

Machine learning reveals a PD-L1-independent prediction of response to immunotherapy of non-small cell lung cancer by gene expression context

scientific article published on 12 October 2020

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

scientific article published on 30 September 2014

MiR-137 functions as a tumor suppressor in neuroblastoma by downregulating KDM1A.

scientific article published on 7 March 2013

Modeling and simulating networks of interdependent protein interactions

scientific article published on 20 April 2018

Mutational dynamics between primary and relapse neuroblastomas.

scientific article

New Flavone Glucoside Malonylesters from Bryum capillare

scientific article published in 2018

Next-generation RNA sequencing reveals differential expression of MYCN target genes and suggests the mTOR pathway as a promising therapy target in MYCN-amplified neuroblastoma

scientific article published on 26 September 2012

Practical Computational Reproducibility in the Life Sciences

scientific article published on 01 June 2018

Practical computational reproducibility in the life sciences

scientific article published on 10 October 2017

Protein complex similarity based on Weisfeiler-Lehman labeling

Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR.

scientific article

Rust-Bio: a fast and safe bioinformatics library. ⬇️

scientific article published on 6 October 2015

Sensitivity to cdk1-inhibition is modulated by p53 status in preclinical models of embryonal tumors

scientific article

SimLoRD: Simulation of Long Read Data

scientific article

Snakemake-a scalable bioinformatics workflow engine

scientific article published on 01 October 2018

Snakemake—a scalable bioinformatics workflow engine ⬇️

scientific article published on August 20, 2012

Sustainable data analysis with Snakemake

scientific article

Targeting the innate immunoreceptor RIG-I overcomes melanoma-intrinsic resistance to T cell immunotherapy

scientific article published on 19 May 2020

The Public Repository of Xenografts Enables Discovery and Randomized Phase II-like Trials in Mice

scientific article published on April 2016

The Public Repository of Xenografts Enables Discovery and Randomized Phase II-like Trials in Mice

scientific article published on 11 July 2016

The first identification of isoflavones from a bryophyte

scientific article published on 25 July 2002

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

scientific article published on 12 April 2018

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

scientific article published on 28 April 2020

List of works by Johannes Köster

A Bayesian model for single cell transcript expression analysis on MERFISH data

A Bayesian model for single cell transcript expression analysis on MERFISH data

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

Bioconda

Bioconda: sustainable and comprehensive software distribution for the life sciences

CRISPR-DO for genome-wide CRISPR design and optimization

Cancer evolution, mutations, and clonal selection in relapse neuroblastoma

Differential turnover of isoflavone 7-O-glucoside-6″-O-malonates in Cicer arietinum roots

Efficiently mining protein interaction dependencies from large text corpora

Eleven grand challenges in single-cell data science

Full-length de novo viral quasispecies assembly through variation graph construction

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

Identifying transcriptional miRNA biomarkers by integrating high-throughput sequencing and real-time PCR data

Life threatening neuroleptic malignant syndrome due to olanzapine

Machine learning reveals a PD-L1-independent prediction of response to immunotherapy of non-small cell lung cancer by gene expression context

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

MiR-137 functions as a tumor suppressor in neuroblastoma by downregulating KDM1A.

Modeling and simulating networks of interdependent protein interactions

Mutational dynamics between primary and relapse neuroblastomas.

New Flavone Glucoside Malonylesters from Bryum capillare

Next-generation RNA sequencing reveals differential expression of MYCN target genes and suggests the mTOR pathway as a promising therapy target in MYCN-amplified neuroblastoma

Practical Computational Reproducibility in the Life Sciences

Practical computational reproducibility in the life sciences

Protein complex similarity based on Weisfeiler-Lehman labeling

Protein complex similarity based on Weisfeiler-Lehman labeling

Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR.

Rust-Bio: a fast and safe bioinformatics library. ⬇️

Sensitivity to cdk1-inhibition is modulated by p53 status in preclinical models of embryonal tumors

SimLoRD: Simulation of Long Read Data

Snakemake-a scalable bioinformatics workflow engine

Snakemake—a scalable bioinformatics workflow engine ⬇️

Sustainable data analysis with Snakemake

Targeting the innate immunoreceptor RIG-I overcomes melanoma-intrinsic resistance to T cell immunotherapy

The Public Repository of Xenografts Enables Discovery and Randomized Phase II-like Trials in Mice

The Public Repository of Xenografts Enables Discovery and Randomized Phase II-like Trials in Mice

The first identification of isoflavones from a bryophyte

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

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