CARE 2.0: reducing false-positive sequencing error corrections using machine learning

F Kallenborn, J Cascitti, B Schmidt - BMC bioinformatics, 2022 - Springer
Background Next-generation sequencing pipelines often perform error correction as a
preprocessing step to obtain cleaned input data. State-of-the-art error correction programs …

noisyR: enhancing biological signal in sequencing datasets by characterizing random technical noise

I Moutsopoulos, L Maischak, E Lauzikaite… - Nucleic Acids …, 2021 - academic.oup.com
High-throughput sequencing enables an unprecedented resolution in transcript
quantification, at the cost of magnifying the impact of technical noise. The consistent …

CARE: context-aware sequencing read error correction

F Kallenborn, A Hildebrandt, B Schmidt - Bioinformatics, 2021 - academic.oup.com
Motivation Error correction is a fundamental pre-processing step in many Next-Generation
Sequencing (NGS) pipelines, in particular for de novo genome assembly. However, existing …

CLMB: Deep contrastive learning for robust metagenomic binning

P Zhang, Z Jiang, Y Wang, Y Li - International Conference on Research in …, 2022 - Springer
The reconstruction of microbial genomes from large metagenomic datasets is a critical
procedure for finding uncultivated microbial populations and defining their microbial …

Illumina reads correction: evaluation and improvements

M Długosz, S Deorowicz - Scientific Reports, 2024 - nature.com
The paper focuses on the correction of Illumina WGS sequencing reads. We provide an
extensive evaluation of the existing correctors. To this end, we measure an impact of the …

High-performance processing of next-generation sequencing data on CUDA-enabled GPUs

F Kallenborn - 2024 - openscience.ub.uni-mainz.de
With the technological advances in the field of genomics and sequencing, the processing of
vast amounts of generated data becomes more and more challenging. Nowadays, software …

Statistics for Bioinformatics

MK Gupta, G Gouda, R Donde, S Sabarinathan… - Bioinformatics in Rice …, 2021 - Springer
High-throughput methods are rapidly becoming prevalent in biological sciences and clinical
studies. Thus, more rigorous statistical techniques are required to accurately predict the …

noisyR: Enhancing biological signal in sequencing datasets by characterising random technical noise

I Moutsopoulos, L Maischak, E Lauzikaite, SAV Urbina… - bioRxiv, 2021 - biorxiv.org
High-throughput sequencing enables an unprecedented resolution in transcript
quantification, at the cost of magnifying the impact of technical noise. The consistent …

[PDF][PDF] Korekcja danych z sekwencjonowania genomów

M Długosz - bip.polsl.pl
Wśród licznych odkryć naukowych oraz osiągnięć technicznych XX i XXI wieku szczególną
doniosłością charakteryzują się sukcesy w dziedzinie szeroko pojętych badań nad genetyką …

Manoj Kumar Gupta, Gayatri Gouda, Ravindra Donde, S. Sabarinathan, Goutam Kumar Dash, Menaka Ponnana, Pallabi Pati, Sushil Kumar Rathore, Ramakrishna …

L Behera - Bioinformatics in Rice Research: Theories and …, 2021 - books.google.com
High-throughput methods are rapidly becoming prevalent in biological sciences and clinical
studies. Thus, more rigorous statistical techniques are required to accurately predict the …