Models

25 Models visible to you, out of a total of 26

Motivation:
The eClaus model can be used to calculate mutation risks for BRCA1/2 as well as life-time risks for breast cancer in women from families with multiple and/or early onset cases of breast and ovarian cancer. The model can be used to assist genetic counselors in clinical decision making regarding genetic testing, intensified surveillance, and prophylatic surgery.

Description:
The Claus model is a genetic breast cancer risk calculation model assuming a single rare, highly penetrant gene.
...

Creators: Silke Zachariae, Christoph Engel, Claus, E.B. et al. (1991 and 1994)

Contributor: Silke Zachariae

Core Ontology of Phenotypes. Contribute to Onto-Med/COP development by creating an account on GitHub.

Creators: Christoph Beger, Alexandr Uciteli, Heinrich Herre

Contributor: Christoph Beger

The Covid‐19 viewer provides an intuitive tool to monitor the development of the pandemic in 188 countries using simple plots. The tool is interactive and enables the user to select different plots for single countries, groups or all of them. It visualizes descriptive features such as slopes or flattening behaviour of epidemic numbers and of their increments to allow a qualitative justification of the current state of the pandemic, e.g. whether it is growing exponentially, stopped due to counter
...

Creators: Henry Löffler-Wirth, Hans Binder

Contributor: Henry Löffler-Wirth

The GC-HBOC BC Risk Explorer (GC-HBOC BC-RE) predicts the breast cancer risk for BRCA1/2 carriers and high-risk non-carriers at risk for first breast cancer (cohort 1), and BRCA1/2 carriers and high-risk non-carriers who were previously diagnosed with unilateral breast cancer, and are at risk for contralateral breast cancer (cohort 2). GC-HBOC BC-RE is based on data from female BRCA1/2 carriers and non-carriers with a family history of breast and ovarian cancer, who participated in the intensified
...

Creators: Silke Zachariae, Christoph Engel

Contributor: Silke Zachariae

Motivation:
The "GC-HBOC Mutation Frequency Explorer" can be used to assist clinicians and genetic counselors in the clinical management of families suspected of having hereditary breast and ovarian cancer and to decide whether genetic testing should be performed.

Description:
The "GC-HBOC Mutation Frequency Explorer" is a tool to determine the observed frequencies of pathogenic BRCA1 and BRCA2 mutations based on familial cancer history data collected since 1996 by the German Consortium for
...

Creators: Silke Zachariae, Christoph Engel

Contributor: Silke Zachariae

Preprocessing Illumina HT12v4 gene expression data including quality filtering, data transformation and normalisation and batch-effect removal as well as visualisation

Creators: Christoph Beger, Holger Kirsten

Contributor: Christoph Beger

Introduction
On this homepage we provide a web-based tool to calculate prognostic scores on haematopoietic toxicity for 6 cycles CHOP-like regimen in patients with aggressive NHL. As we used for this analysis the data collected within the NHL-B1 and NHL-B2 trials of the DSHNHL as described in detail in Pfreundschuh et al. the predictions are valid for similar patient populations.

Description
We offer two types of models. Pre-treatment models include beside the therapy regimen only prognostic
...

Creators: René Hänsel, Marita Ziepert

Contributor: René Hänsel

The platform is intended for visualization of expression- and mutation-driven changes in biological pathway activities in cancer datasets available in ICGC. The impact of somatic mutations on protein-protein interactions were calculated using Mechismo. Overall activity of biological pathway was evaluated using Pathway Signal Flow algorithm. The application provides interactive heatmaps for pathway output sink node activities and pathway images with mapped affected interactions and output node
...

Creators: Christoph Beger, Siras Hakobyan

Contributor: Christoph Beger

Emerging health geography research analyzes and visualizes health behaviors and outcomes in relation to urban environmental data and related official statistics to produce “health reports” for specific areas.

We mapped measured hand grip data of the large LIFE Adult population (10,000 participants) onto the Leipzig map. In particular, we locate each participant at the time of participation in Leipzig and, thus, can derive hand grip strength averages (incl. mean, median) per specific city districts.
...

Creator: René Hänsel

Contributor: René Hänsel

Depending on the calculated mutation probability genetic counsellors can decide whether patients should undergo further analysis of microsatellite instability and immunohistochemistry. The model is recommended for patients with an age at colorectal cancer diagnosis of 55 or younger.

"MMRpredict" is a risk prediction model for patients with colorectal cancer (Barnetson et al. 2006). It calculates the risk of having a mutation in the mismatch repair genes MLH1, MSH2 and MSH6 (overall probability)
...

Creators: Silke Zachariae, Christoph Engel

Contributor: Silke Zachariae

Motivation:
The "Manchester Scoring System" can be used to assist clinicians and genetic counselors in the clinical management of families suspected of having hereditary breast and ovarian cancer and to decide whether genetic testing should be performed.

Description:
The "Manchester Scoring System" is an empirical mutation risk prediction model. In its current form, a risk score for the identification of a pathogenic BRCA1/2 mutation is being calculated based on the number of breast and ovarian
...

Creators: Silke Zachariae, Christoph Engel, Evans, D.G. et al. (2009)

Contributor: Silke Zachariae

The main goal is to provide a principled analysis workflow addressing specific issues of mass-spectrometry metabolite measurements in the context of testing in multiple studies with a high number of hypotheses

Shiny-Application of an analysis pipeline for preprocessing, association and covariate selection of metabolite data with clinical and lifestyle factors in one or more seperate studies. Preprocessing steps include transformation, outlier filtering and batch-adjustment. Analyses include uni-
...

Creator: Carl Beuchel

Contributor: Carl Beuchel

Motivation:
By using the NLP4CR tool, medical facts (e.g. diagnoses, laboratory values) can be extracted from German medical full texts.

Description:
The NLP4CR tool is a prototype that demonstrates the applicability of Apache UIMA and cTakes to medical full texts in German language.

Creators: Christoph Beger, Colleen Goldberg

Contributor: Christoph Beger

This is an interactive version of figure 4 of the publication „Integration of Genome-Wide SNP Data and Gene-Expression Profiles Reveals Six Novel Loci and Regulatory Mechanisms for Amino Acids and Acylcarnitines in Whole Blood“.

Creators: René Hänsel, Markus Scholz

Contributor: René Hänsel

Emerging health geography research analyzes and visualizes health behaviors and outcomes in relation to urban environmental data and related official statistics to produce “health reports” for specific areas. This can be extended to developments in urban planning, e.g., to identify districts or neighborhoods for social investments or restrictions.

We mapped anthropometric data the large LIFE Adult population (10,000 participants) onto the Leipzig map. In particular, we derived the body mass index
...

Creator: René Hänsel

Contributor: René Hänsel

The PREMM1,2,6 has been developed as a pretest to decide whether patients suspected of having Lynch syndrome should be tested for germline mismatch repair gene mutations.
"PREMM1,2,6" is a logistic regression model. It calculates the risk of having a mutation in the mismatch repair genes MLH1, MSH2 and MSH6 (for single genes and overall) based on the personal and familial cancer history of the proband (colorectal, endometrial, and other Lynch syndrome related cancers).

Creators: Christoph Engel, Silke Zachariae, Kastrinos et al.

Contributor: Silke Zachariae

The PREMM5 has been developed as a pretest to decide whether patients suspected of having Lynch syndrome should be tested for germline mismatch repair gene mutations. In contrast to "PREMM1,2,6" it can be used to predict mutation probabilities in unaffected index patients.
"PREMM5" is a logistic regression model. It calculates the risk of having a mutation in the mismatch repair genes MLH1, MSH2/EPCAM, MSH6 and PMS2 (for single genes and overall) based on the personal and familial cancer history
...

Creators: Christoph Engel, Silke Zachariae, Kastrinos et al.

Contributor: Silke Zachariae

This is a set of MATLAB procedures for automated segmentation and counting of macrophages in multiple IHC stained tissue samples.
Execution assumes that three aligned single-channel greyscale images of a given tissue area are available, representing IHC stainings with CD14 and CD163 antibodies (targeting macrophages) as well as DAPI staining (targeting cell cores). After detection of evaluation subregion (based on DAPI channel information), IHC stained macrophages will be masked and counted (based
...

Creators: René Hänsel, Marcus Wagner

Contributor: René Hänsel

Large scale epidemiological studies, such as LIFE-ADULT, including thousands of participants with a multitude of novel QT assessments allow to define reference values. Reference values are typically used in quality control to find outliers in a specified data volume or to evaluate a given measurement value regarding its pathologic value. Measuring the hand grip strength is a standard assessment in LIFE, for which is no or little prior knowledge regarding reference values available.

Based on the
...

Creator: René Hänsel

Contributor: René Hänsel

All studies and research projects those data are hosted by the Leipzig Health Atlas should follow the FAIR standard. Thus, data are findable, accessible, interoperable, and reusable. To follow the FAIS standard, all data need to be described by rich metadata, on the technical and semantical level. These metadata can then be used to query and search for data elements in a single study or over all studies.

We provide the LHA data portal allowing to searching and accessing data elements in single
...

Creator: René Hänsel

Contributor: René Hänsel

Implementation of recently developed dynamic mathematical models of normal and leukemic hematopoiesis to practically impact clinical decision- making.

Fitting available individual patients information, prediction of next-cycle thrombopenia caused by CHOEP treatment based on the individual fits of the preceeding treatment cycles, changing next-cycle relative dosing, posponement of the next cycle, changing follow-up period, visualization of data and simulation

Creator: René Hänsel

Contributor: René Hänsel

This is a Drupal 8 Module to import nodes and taxonomies into Drupal, using the available API. The module is capable of importing a JSON or OWL file. Idea is to enable users to upload a file containing all information about nodes and their relations. The module will then import all contained information with the Drupal 8 API. Nodes can be specified as "articles" or any other custom node type. The node classification becomes one (or multiple) hierachical vocabulary. Supported import formats are
...

Creator: Christoph Beger

Contributor: Christoph Beger

No description specified

Creators: Carl Beuchel, Markus Scholz, Yuri Kheifetz, Sibylle Schirm

Contributor: Carl Beuchel

Analysis of large-scale molecular biological data using self-organizing maps

Comprehensive analysis of genome-wide molecular data challenges bioinformatics methodology in terms of intuitive visualization with single-sample resolution, biomarker selection, functional information mining and highly granular stratification of sample classes. oposSOM combines those functionalities making use of a comprehensive analysis and visualization strategy based on self-organizing maps (SOM) machine learning
...

Creator: Henry Löffler-Wirth

Contributors: Henry Löffler-Wirth, Christoph Beger

Contribute to hloefflerwirth/scrat development by creating an account on GitHub.

Creator: Henry Löffler-Wirth

Contributor: Henry Löffler-Wirth

Powered by
(v.1.9.1)
Copyright © 2008 - 2019 The University of Manchester and HITS gGmbH
Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig