TY  - JOUR
A1  - Wittig, Alice
A1  - Miranda, Fabio Malcher
A1  - Hölzer, Martin
A1  - Altenburg, Tom
A1  - Bartoszewicz, Jakub Maciej
A1  - Beyvers, Sebastian
A1  - Dieckmann, Marius Alfred
A1  - Genske, Ulrich
A1  - Giese, Sven Hans-Joachim
A1  - Nowicka, Melania
A1  - Richard, Hugues
A1  - Schiebenhoefer, Henning
A1  - Schmachtenberg, Anna-Juliane
A1  - Sieben, Paul
A1  - Tang, Ming
A1  - Tembrockhaus, Julius
A1  - Renard, Bernhard Y.
A1  - Fuchs, Stephan
T1  - CovRadar
BT  - continuously tracking and filtering SARS-CoV-2 mutations for genomic surveillance
JF  - Bioinformatics
N2  - The ongoing pandemic caused by SARS-CoV-2 emphasizes the importance of genomic surveillance to understand the evolution of the virus, to monitor the viral population, and plan epidemiological responses. Detailed analysis, easy visualization and intuitive filtering of the latest viral sequences are powerful for this purpose. We present CovRadar, a tool for genomic surveillance of the SARS-CoV-2 Spike protein. CovRadar consists of an analytical pipeline and a web application that enable the analysis and visualization of hundreds of thousand sequences. First, CovRadar extracts the regions of interest using local alignment, then builds a multiple sequence alignment, infers variants and consensus and finally presents the results in an interactive app, making accessing and reporting simple, flexible and fast.
Y1  - 2022
U6  - https://doi.org/10.1093/bioinformatics/btac411
SN  - 1367-4803
SN  - 1367-4811
VL  - 38
IS  - 17
SP  - 4223
EP  - 4225
PB  - Oxford Univ. Press
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Genske, Ulrich
A1  - Jahnke, Paul
T1  - Human observer net
BT  - a platform tool for human observer studies of Image data
JF  - Radiology
N2  - Background: 
Current software applications for human observer studies of images lack flexibility in study design, platform independence, multicenter use, and assessment methods and are not open source, limiting accessibility and expandability.

Purpose: 
To develop a user-friendly software platform that enables efficient human observer studies in medical imaging with flexibility of study design. 

Materials and Methods: 
Software for human observer imaging studies was designed as an open-source web application to facilitate access, platform-independent usability, and multicenter studies. Different interfaces for study creation, participation, and management of results were implemented. The software was evaluated in human observer experiments between May 2019 and March 2021, in which duration of observer responses was tracked. Fourteen radiologists evaluated and graded software usability using the 100-point system usability scale. The application was tested in Chrome, Firefox, Safari, and Edge browsers. 

Results: 
Software function was designed to allow visual grading analysis (VGA), multiple-alternative forced-choice (m-AFC), receiver operating characteristic (ROC), localization ROC, free-response ROC, and customized designs. The mean duration of reader responses per image or per image set was 6.2 seconds 6 4.8 (standard deviation), 5.8 seconds 6 4.7, 8.7 seconds 6 5.7, and 6.0 seconds 6 4.5 in four-AFC with 160 image quartets per reader, four-AFC with 640 image quartets per reader, localization ROC, and experimental studies, respectively. The mean system usability scale score was 83 6 11 (out of 100). The documented code and a demonstration of the application are available online (https://github.com/genskeu/HON, https://hondemo.pythonanywhere.com/). 

Conclusion: 
A user-friendly and efficient open-source application was developed for human reader experiments that enables study design versatility, as well as platform-independent and multicenter usability.
Y1  - 2022
U6  - https://doi.org/10.1148/radiol.211832
SN  - 0033-8419
VL  - 303
IS  - 3
SP  - 524
EP  - 530
PB  - Radiologgical soc North America (RSNA)
CY  - Oak brook
ER  -