Investigations

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121 Investigations visible to you, out of a total of 306

Die Charité – Universitätsmedizin Berlin betreibt gemeinsam mit dem Berlin Institute of Health
Clinical Study Center (BIH-CSC) eine zentrale Registerstudie ("Pa-COVID-19") und Phänotypisierungs-
plattform für alle an der Charité behandelten Patienten mit COVID-19.
Pa-COVID-19 dient der harmonisierten und standardisierten klinischen und molekularen
Phänotypisierung von COVID-19 Patienten. Übergeordnetes Ziel ist die schnelle und umfassende
Charakterisierung von COVID-19 zur Identifikation von
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Governments and policymakers take different measures vis-à-vis the COVID-19 crisis, ranging from advice to reduce social activities, to a complete lock down of society and economy. To support them with tools that enable them to fulfill their tasks we constructed a differential equation model for the COVID-19 epidemics using systems biology methodologies.

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Collection of cross-links to other sites that gather COVID-19 information

No description specified

The raw data generated in the scope of the SysMetEx project for RNAseq, proteomics, and imaging analysis.
The data was generated on single and mixed species cultures of A. Caldus, L.ferriphilum, and/or S.thermosulfidooxidans.
Raw RNA data is combined in an ENA umbrella study summarising all short read data generated in the project.
Raw proteomics data is provided for distinct conditions at the pride repository.
Imaging data is provided for distinct conditions at a zenodo repository.

The oxidative Weimberg pathway for the five-step pentose degradation to α ketoglutarate from Caulobacter crescentus is a key route for sustainable bioconversion of lignocellulosic biomass to added-value products and biofuels. Here, we developed a novel iterative approach involving initial rate kinetics, progress curves, and enzyme cascades, with high resolution NMR analysis of intermediate dynamics, and multiple cycles of kinetic modelling analyses to construct and validate a quantitative model
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Collection of models submitted to PLaSMo by Uriel Urquiza Garcia and automatically transferred to FAIRDOM Hub.

Investigation: _I_STRT
Short Name: STRT
Title: Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato
Description: Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato
Phenodata: ./phenodata_20191022.txt
pISA Investigation creation date: 2019-10-22
pISA Investigation creator: Maja Zagorscak, Ziva Ramsak, Marko Petek
Principal investigator: Kristina Gruden
License: MIT
Sharing permission: Public
Upload to FAIRDOMHub: Yes

RELATED
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1. To develop a whole-cell dynamic model framework of the metabolism of M. pneumoniae
2. To build upon M. pneumoniae models to develop a genome-scale, constraint-based model of M.
hyopneumoniae for vaccine optimization
3. To deploy the metabolic model(s) to: 1) the rational design and optimization of the vaccine chassis; 2)
aid the development of a higher-growth rate chassis; 3) assist the development of a nutrient optimized a
serum-free growth medium and; 4) assess, at genome scale, the metabolic
...

Investigation: _I_STRT
Short Name: STRT
Title: Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato
Description: Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato
Phenodata: ./phenodata_20191022.txt
pISA Investigation creation date: 2019-10-22
pISA Investigation creator: Maja Zagorscak
Principal investigator: Kristina Gruden
License: GPL-3, CC BY 4.0
Sharing permission: Public
Upload to FAIRDOMHub: Yes

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Project to test effects of temperature cycles on expression of Arabidopsis florigen gene FT, and whether these are mediated by temperature-dependent leaf development or temperature-specific FT expression, or both. Re-used and extended Arabidopsis Framework Model v1 to address this question. Led by Hannah Kinmonth-Schultz in Kim and Imaizumi labs, collaborating with Millar lab.

This is a collection of deep eutectic solvent (DES) experimental and simulation data that is stored in CML format and analysed using gradient boosting decision trees.

Data, FMv2 model and simulations for the Chew et al. 2017 paper (bioRxiv https://doi.org/10.1101/105437 ), mostly on the prr7 prr9 double mutant, with controls in lsf1 and prr7 single mutants.

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Collection of models submitted to PLaSMo by Andrew Millar and automatically transferred to FAIRDOM Hub.

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Project to test effects of natural compared to growth chamber 16:8 LD cycles, on expression of Arabidopsis flowering-time genes, and to define the genetic mechanisms and environmental triggers involved. Led by Young-Hun Song and Akane Kubota in the Imaizumi lab, with collaborators testing plants in parallel in Zurich and Edinburgh.

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Supplementary files for the submission:
Reverse Engineering Directed Gene Regulatory Networks from
Transcriptomics and Proteomics Data of Biomining Bacterial
Communities with Approximate Bayesian Computation and
Steady-State Signalling Simulations

Supplementary files for the publication:
Deep Neural Networks Outperform Human Expert’s Capacity in Characterizing Bioleaching Bacterial Biofilm Composition

Time series response of potato cv. Désirée, which is tolerant to PVY infection, was analysed in both inoculated as well as upper non-inoculated leaves. Additionally, transgenic plants deficient in accumulation of salicylic acid (NahG- Désirée) were studied in the same setting.

All the files available are published under the CC BY 4.0 license.

Publication data made available for Biotechnology Reports, supplementary data

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Collection of models submitted to PLaSMo by Jonathan Massheder and automatically transferred to FAIRDOM Hub.

Collection of models submitted to PLaSMo by Rob Smith and automatically transferred to FAIRDOM Hub.

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