Piotr Wojciech Dąbrowski
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View article: ReadSeeker: A DNABERT based de-novo read-level gene predictor
ReadSeeker: A DNABERT based de-novo read-level gene predictor Open
ReadSeeker, a newly fine-tuned, DNABERT-based model, differentiates NGS short reads into protein-coding (CDS) and non-protein-coding (non-CDS) categories without requiring known reference sequences. For model training, extensive datasets e…
View article: Correction: NGS read classification using AI
Correction: NGS read classification using AI Open
[This corrects the article DOI: 10.1371/journal.pone.0261548.].
View article: PathoLive—Real-Time Pathogen Identification from Metagenomic Illumina Datasets
PathoLive—Real-Time Pathogen Identification from Metagenomic Illumina Datasets Open
Over the past years, NGS has become a crucial workhorse for open-view pathogen diagnostics. Yet, long turnaround times result from using massively parallel high-throughput technologies as the analysis can only be performed after sequencing…
View article: Critical Assessment of Metagenome Interpretation: the second round of challenges
Critical Assessment of Metagenome Interpretation: the second round of challenges Open
Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI II challenge engaged the community to assess methods on r…
View article: NGS read classification using AI
NGS read classification using AI Open
Clinical metagenomics is a powerful diagnostic tool, as it offers an open view into all DNA in a patient’s sample. This allows the detection of pathogens that would slip through the cracks of classical specific assays. However, due to this…
View article: Refseq Test Subsets for Frame Classification with and without Errors
Refseq Test Subsets for Frame Classification with and without Errors Open
These test files extend the 'Refseq datasets for training frame classification' dataset. It provided the original test file and three variations containing erroneous sequences to simulate realistic data. The data is based on randomly selec…
View article: Refseq Test Subsets for Frame Classification with and without Errors
Refseq Test Subsets for Frame Classification with and without Errors Open
These test files extend the 'Refseq datasets for training frame classification' dataset. It provided the original test file and three variations containing erroneous sequences to simulate realistic data. The data is based on randomly selec…
View article: Peer Review #2 of "VGEA: an RNA viral assembly toolkit (v0.1)"
Peer Review #2 of "VGEA: an RNA viral assembly toolkit (v0.1)" Open
Next generation sequencing (NGS)-based studies have vastly increased our understanding of viral diversity.Viral sequence data obtained from NGS experiments are a rich source of information, these data can be used to study their epidemiolog…
View article: Peer Review #2 of "VGEA: an RNA viral assembly toolkit (v0.2)"
Peer Review #2 of "VGEA: an RNA viral assembly toolkit (v0.2)" Open
Next generation sequencing (NGS)-based studies have vastly increased our understanding of viral diversity.Viral sequence data obtained from NGS experiments are a rich source of information, these data can be used to study their epidemiolog…
View article: Peer Review #2 of "VGEA: an RNA viral assembly toolkit (v0.3)"
Peer Review #2 of "VGEA: an RNA viral assembly toolkit (v0.3)" Open
Next generation sequencing (NGS)-based studies have vastly increased our understanding of viral diversity.Viral sequence data obtained from NGS experiments are a rich source of information, these data can be used to study their epidemiolog…
View article: CPXV reads with SNPs for bioinformatics course
CPXV reads with SNPs for bioinformatics course Open
Four samples with CPXV reads for bioinformatics course (mapping and variant calling).
View article: CPXV reads with SNPs for bioinformatics course
CPXV reads with SNPs for bioinformatics course Open
Four samples with CPXV reads for bioinformatics course (mapping and variant calling).
View article: Critical Assessment of Metagenome Interpretation - the second round of challenges
Critical Assessment of Metagenome Interpretation - the second round of challenges Open
Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the community-driven initiative for the Critical Assessment of Metagenome Interpretation (CAMI). In its second challenge, CAMI engaged the communi…
View article: Fostering global data sharing: highlighting the recommendations of the Research Data Alliance COVID-19 working group
Fostering global data sharing: highlighting the recommendations of the Research Data Alliance COVID-19 working group Open
The systemic challenges of the COVID-19 pandemic require cross-disciplinary collaboration in a global and timely fashion. Such collaboration needs open research practices and the sharing of research outputs, such as data and code, thereby …
View article: The virome of German bats: comparing virus discovery approaches
The virome of German bats: comparing virus discovery approaches Open
View article: An environment for sustainable research software in Germany and beyond: current state, open challenges, and call for action
An environment for sustainable research software in Germany and beyond: current state, open challenges, and call for action Open
Research software has become a central asset in academic research. It optimizes existing and enables new research methods, implements and embeds research knowledge, and constitutes an essential research product in itself. Research software…
View article: First detection of bat-borne Issyk-Kul virus in Europe
First detection of bat-borne Issyk-Kul virus in Europe Open
View article: Uniprot datasets with variable patch sizes for testing taxonomic classification
Uniprot datasets with variable patch sizes for testing taxonomic classification Open
These datasets can be used to test the performance of the taxonomic classification model deposited at https://zenodo.org/record/4306499 and trained using the data deposited at https://zenodo.org/record/4306240 with different patch sizes: 3…
View article: Uniprot datasets with variable patch sizes for testing taxonomic classification
Uniprot datasets with variable patch sizes for testing taxonomic classification Open
These datasets can be used to test the performance of the taxonomic classification model deposited at https://zenodo.org/record/4306499 and trained using the data deposited at https://zenodo.org/record/4306240 with different patch sizes: 3…
View article: PyTorch model for frame classification
PyTorch model for frame classification Open
This is a trained PyTorch model for classifying a DNA sequence's (preferably of length 300) frame within an ORF.
View article: PyTorch model for taxonomic classification
PyTorch model for taxonomic classification Open
This is a trained PyTorch model for classifying an amino acid sequence's (preferably of length 100) taxonomic domain as viral (class 0), bacterial (class 1) or mammalian (class 2).
View article: PyTorch model for taxonomic classification
PyTorch model for taxonomic classification Open
This is a trained PyTorch model for classifying an amino acid sequence's (preferably of length 100) taxonomic domain as viral (class 0), bacterial (class 1) or mammalian (class 2).
View article: Refseq datasets for training frame classification
Refseq datasets for training frame classification Open
The data is based on andomly selected viral and bacterial genomes and the human193(GRCh38.p13) reference genome which were downloaded from GenBank. From each original nucleic acid sequences we created mutliple patches of length 300 in all …
View article: PyTorch model for frame classification
PyTorch model for frame classification Open
This is a trained PyTorch model for classifying a DNA sequence's (preferably of length 300) frame within an ORF.
View article: Refseq datasets for training frame classification
Refseq datasets for training frame classification Open
The data is based on andomly selected viral and bacterial genomes and the human193(GRCh38.p13) reference genome which were downloaded from GenBank. From each original nucleic acid sequences we created mutliple patches of length 300 in all …
View article: Uniprot datasets for training taxonomic classification
Uniprot datasets for training taxonomic classification Open
The data is based on the UniProt-Swiss-Prot release 2020-04 dataset and contains data derived from amino acid sequences of human, bacterial and viral origin. From each original sequence we created multiple patches of length 100 using a sli…
View article: Uniprot datasets for training taxonomic classification
Uniprot datasets for training taxonomic classification Open
The data is based on the UniProt-Swiss-Prot release 2020-04 dataset and contains data derived from amino acid sequences of human, bacterial and viral origin. From each original sequence we created multiple patches of length 100 using a sli…
View article: Fostering global data sharing: highlighting the recommendations of the Research Data Alliance COVID-19 working group
Fostering global data sharing: highlighting the recommendations of the Research Data Alliance COVID-19 working group Open
The systemic challenges of the COVID-19 pandemic require cross-disciplinary collaboration in a global and timely fashion. Such collaboration needs open research practices and the sharing of research outputs, such as data and code, thereby …
View article: An environment for sustainable research software in Germany and beyond: current state, open challenges, and call for action
An environment for sustainable research software in Germany and beyond: current state, open challenges, and call for action Open
Research software has become a central asset in academic research. It optimizes existing and enables new research methods, implements and embeds research knowledge, and constitutes an essential research product in itself. Research software…
View article: Zwiesel bat banyangvirus, a potentially zoonotic Huaiyangshan banyangvirus (Formerly known as SFTS)–like banyangvirus in Northern bats from Germany
Zwiesel bat banyangvirus, a potentially zoonotic Huaiyangshan banyangvirus (Formerly known as SFTS)–like banyangvirus in Northern bats from Germany Open