A5022280742- Gene expression and cancer classification
- Single-cell and spatial transcriptomics
- RNA Research and Splicing
- Genomics and Phylogenetic Studies
- Molecular Biology Techniques and Applications
- RNA modifications and cancer
- SARS-CoV-2 detection and testing
- RNA and protein synthesis mechanisms
- Cancer-related molecular mechanisms research
- Cancer Genomics and Diagnostics
- Genomics and Chromatin Dynamics
- Epigenetics and DNA Methylation
- Bioinformatics and Genomic Networks
- Chronic Lymphocytic Leukemia Research
- Advanced Proteomics Techniques and Applications
- Biosensors and Analytical Detection
- interferon and immune responses
- Protein Degradation and Inhibitors
- Advanced biosensing and bioanalysis techniques
- Mass Spectrometry Techniques and Applications
- Cell Image Analysis Techniques
- Lymphoma Diagnosis and Treatment
- Acute Myeloid Leukemia Research
- Immune cells in cancer
- SARS-CoV-2 and COVID-19 Research
Heidelberg University
2017-2024
Heidelberg University
2020-2022
DKFZ-ZMBH Alliance
2019-2021
Institute for Molecular Medicine Finland
2015-2019
University of Helsinki
2016-2019
Finland University
2019
European Molecular Biology Laboratory
2011-2017
European Molecular Biology Organization
2013-2017
European Molecular Biology Laboratory
2010-2015
European Bioinformatics Institute
2009-2013
In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and presence outliers require suitable statistical approach. We present DESeq2, method differential using shrinkage estimation dispersions fold to improve stability interpretability estimates. This enables more quantitative focused...
Abstract Motivation: A large choice of tools exists for many standard tasks in the analysis high-throughput sequencing (HTS) data. However, once a project deviates from workflows, custom scripts are needed. Results: We present HTSeq, Python library to facilitate rapid development such scripts. HTSeq offers parsers common data formats HTS projects, as well classes represent data, genomic coordinates, sequences, reads, alignments, gene model information and variant calls, provides structures...
High-throughput sequencing assays such as RNA-Seq, ChIP-Seq or barcode counting provide quantitative readouts in the form of count data. To infer differential signal data correctly and with good statistical power, estimation variability throughout dynamic range a suitable error model are required. We propose method based on negative binomial distribution, variance mean linked by local regression present an implementation, DESeq, R/Bioconductor package.
RNA-seq is a powerful tool for the study of alternative splicing and other forms isoform expression. Understanding regulation these processes requires sensitive specific detection differential abundance in comparisons between conditions, cell types, or tissues. We present DEXSeq, statistical method to test exon usage data. DEXSeq uses generalized linear models offers reliable control false discoveries by taking biological variation into account. detects with high sensitivity genes, many...
ABSTRACT Motivation: A large choice of tools exists for many standard tasks in the analysis high-throughput sequencing (HTS) data. However, once a project deviates from work flows, custom scripts are needed. Results: We present HTSeq, Python library to facilitate rapid development such scripts. HTSeq offers parsers common data formats HTS projects, as well classes represent genomic coordinates, sequences, reads, alignments, gene model information, variant calls, and provides structures that...
Abstract *Motivation:* High-throughput nucleotide sequencing provides quantitative readouts in assays for RNA expression (RNA-Seq), protein-DNA binding (ChIP-Seq) or cell counting (barcode sequencing). Statistical inference of differential signal such data requires estimation their variability throughout the dynamic range. When number replicates is small, error modelling needed to achieve statistical power. Results: We propose an model that uses negative binomial distribution, with variance...
In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq for evidence systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and presence outliers require suitable statistical approach. We present DESeq2, method differential data. DESeq2 uses shrinkage estimation dispersions fold to improve stability interpretability estimates. This enables more...
HTSeq 2.0 provides a more extensive API including new representation for sparse genomic data, enhancements in htseq-count to suit single cell omics, script data using and molecular barcodes, improved documentation, testing deployment, bug fixes, Python 3 support.HTSeq is released as an open-source software under the GNU General Public License available from Package Index at https://pypi.python.org/pypi/HTSeq. The source code on Github https://github.com/htseq/htseq.Supplementary are...
A colorimetric isothermal RNA amplification method was shown to detect SARS-CoV-2 in clinical samples with excellent sensitivity and specificity.
Abstract Summary: ShortRead is a package for input, quality assessment, manipulation and output of high-throughput sequencing data. provided in the R Bioconductor environments, allowing ready access to additional facilities advanced statistical analysis, data transformation, visualization integration with diverse genomic resources. Availability Implementation: This implemented available at web site; contains ‘vignette’ outlining typical work flows. Contact: mtmorgan@fhcrc.org
There are ∼650,000 Alu elements in transcribed regions of the human genome. These contain cryptic splice sites, so they constant danger aberrant incorporation into mature transcripts. Despite posing a major threat to transcriptome integrity, little is known about molecular mechanisms preventing their inclusion. Here, we present mechanism for protecting from exonization transposable elements. Quantitative iCLIP data show that RNA-binding protein hnRNP C competes with splicing factor U2AF65 at...
Here we walk through an end-to-end gene-level RNA-Seq differential expression workflow using Bioconductor packages. We will start from the FASTQ files, show how these were aligned to reference genome, and prepare a count matrix which tallies number of RNA-seq reads/fragments within each gene for sample. perform exploratory data analysis (EDA) quality assessment explore relationship between samples, analysis, visually results.
Abstract Motivation: High throughput nucleotide sequencing provides quantitative readouts in assays for RNA expression (RNA-Seq), protein-DNA binding (ChIP-Seq), cell counting. Statistical inference of differential signal these data needs to take into account their natural variability throughout the dynamic range. When number replicates is small, error modeling needed achieve statistical power. Results: We propose an model that uses negative binomial distribution, with variance and mean...
Quantitative proteomics by mass spectrometry is widely used in biomarker research and basic biology for investigation of phenotype level cellular events. Despite the wide application, methodology statistical analysis differentially expressed proteins has not been unified. Various methods such as t test, linear model mixed effect models are to define changes experiments. However, none these consider specific structure MS-data. Choices between methods, often originally developed other types...
The expansion of the neocortex, a hallmark mammalian evolution
Sexually dimorphic traits are common among mammals and specified during development through the deployment of sex-specific genetic programs. Because little is known about these programs, we investigated them using a resource gene expression profiles in males females throughout five organs (human, mouse, rat, rabbit, opossum) bird (chicken). We found that sex-biased varied considerably across species was often cell-type specific. Sex differences increased abruptly around sexual maturity...