Investigations

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194 Investigations visible to you, out of a total of 583

We further used the transcriptome dataset from the GEO database with accession number GSE147507 (Blanco-Melo et al., 2020) to extract the series number 5 from the dataset, consisting of 2 conditions in triplicate, A549 cells treated with a mock and A549 infected with SARS-CoV-2, measured 24 hours after treatment. Phosphoproteomic data of mock-treated and SARS-CoV2 infected cells were extracted from (Stukalov et al., 2020). We then applied our pipeline described in M&M X. This work notably ...

In this investigation, we aim to develop automatic workflows to pinpoint drug targets carrying genomic variants at high frequency in the population

In this investigation we aim to develop automatic workflows to analyze COVID19 Omics data to understand and predict the molecular pathways depicting host-virus interaction.

No description specified

Submitter: Dikshant Pradhan

Studies: Benthic fluxes of fluorescent dissolved organic material, salt and heat ..., Colorimetric Detection of Aqueous N-Nitrosodimethylamine via Photonitros..., CometChip Enables Parallel Analysis of Multiple DNA Repair Activities, Excision of mutagenic replication-blocking lesions suppresses cancer but..., Interaction of N-Nitroamines with Bincuelar Copper Complexs for Luminsec..., Molecular origins of mutational spectra produced by the environmental ca..., Novel In Vivo CometChip Reveals NDMA-Induced DNA Damage and Repair in Mu..., Optical Detection of Interleukin-6 using Liquid Janus Emulsions using Hy..., Reversible Electrochemical Sensor for NDMA: Leveraging Molecularly Impri...

Assays: Absorption and Emission Spectroscopy - Data Linked, Absorption and Emission Spectroscopy Analysis - Data Linked, Agglutination Assay - Data Linked, All Metadata, All Metadata, Atomic Force Microscopy - Data Linked, Chemical Challenge - Metadata, Chemical Simulations - Data Linked, Chemical Synthesis - Metadata, Chemical Synthesis - Metadata, Chemical Synthesis - Metadata, Chemical Synthesis - Metadata, Comet Chip - Data Linked, Comet Chip Analysis - Data Attached, Comet Chip Analysis - Data Attached, Crystallography - Data Linked, Electrochemical Sensor Testing - Data Linked, Electron Paramagnetic Resonance - Data Linked, Extraction and Library Creation - Metadata, Field Water Sensor Run, Fourier Transform Infrared Spectroscopy - Data Linked, GPT Assay - Data Attached, GPT Assay – Data Attached, Gel Permeation Chromatography - Data Linked, Genome Alignment - Data Linked, High Resolution Mass Spectra - Data Linked, High Resolution Mass Spectra Analysis - Data Linked, Illumina Sequencing - Data Linked, Imaging - Data Linked, Mass Spectrometry Processing – Data Linked, Mass Spectrometry – Data Linked, Mouse Necropsy – Metadata, Mutational Spectral Analysis - Data Attached, Necropsy - Metadata, Nuclear Magnetic Resonance - Data Linked, Nuclear Magnetic Resonance Analysis - Data Linked, Nuclear Magnetic Resonance Spectroscopy - Data Linked, Nuclear Magnetic Resonance Spectroscopy - Data Linked, Nuclear Magnetic Resonance Spectroscopy Analysis - Data Linked, Nuclear Magnetic Resonance Spectroscopy Analysis - Data Linked, Pendant Drop Tensiometry - Data Linked, RaDR Image Machine Learning Analysis – Data Attached, Sensor Creation - Metadata, Single-crystal X-ray Crystallography - Data Linked, Tissue Collection - Metadata, Tissue Imaging – Metadata, Tissue Lysis – Metadata, UV-Vis Spectroscopy - Data Linked, UV-Vis Spectroscopy Analysis - Data Linked, X-ray Photoelectron Spectroscopy - Data Linked

We develop macrophage logical models to represent the activation/polarization of this immune cell. Interactions are manually curated with available macrophage literature. The models are mainly built and analyzed in GINsim. But other resources are used to integrate specific pathways or small modules (CasQ software) and to analyze the logical models (CoLoMoTo Notebooks).

The hallmarks of cancer provide a highly cited and well-used conceptual framework for describing the processes involved in cancer cell development. However, methods for translating these high-level concepts into data-level associations between hallmarks and genes (for high throughput analysis), vary widely between studies. In this investigation we compare cancer hallmark mapping strategies from different studies, based on Gene Ontology and biological pathway annotation. By analysing the semantic ...

The aim of this investigation is to understand molecular mechanisms of PUFA biosynthesis and regulation in order to enable the sustainable use of vegetable oils in aquafeeds as current sources of fish oils are unable to meet increasing demands for omega-3 PUFAs. By generating gene knockouts, we would like to study the genes that are crucial for multi-tissue synthesis of PUFA synthesis in vivo.

Present in many industrial effluents and as intermediate of lignin degradation, phenol is a widespread pollutant causing serious environmental problems, due to its toxicity to animals and humans. Removal of phenol from the environment by bacteria has been studied extensively over the past decades, but only little is known about phenol biodegradation in hostile environments. We combined metabolomics and transcriptomics together with metabolic modelling to elucidate the organism’s response to growth ...

Consortium website: https://covidclinical.net/

Slack: https://c19i2b2.slack.com/ Owner: Nils Gehlenborg (nils@hms.harvard.edu)

i2b2 tranSMART Foundation Call to Action: https://transmartfoundation.org/covid-19-call-to-action/

Objectives: Empowering smooth implementation and fruitful completion of all WPs and tasks. Implementation of a data management plan for efficient dissemination under F.A.I.R. principles.

Description of Work: The PI of the project with the heads of the collaborating groups will closely monitor the progress of the technical and administrative tasks and it will implement actions to correct any deviation from the established work-plan. The whole group will meet regularly every six months or more ...

Submitter: Ioannis Pavlidis

Studies: No Studies

Assays: No Assays

Objectives: Establishment of the chemoenzymatic process with the best GO-ATA hybrid catalysts. Highlighting of the potential of the process in semi-preparative scale.

Description of Work: The best hybrid catalysts identified in WP3 will be investigated in coupled one-pot reactions selected in WP1, in batch and continuous flow reactors. The productivity of the system will be optimized with response surface methodology (RSM), for parameters such as temperature, duration, substrate concentration ...

Submitter: Ioannis Pavlidis

Studies: No Studies

Assays: No Assays

Objectives: Development of efficient ATA immobilization approach. Production of a hybrid catalyst of high catalytic efficiency.

Description of Work: Τhe ATAs selected in WP2 will be expressed, purified and covalently and/or non-covalently immobilized on the GO selected in WP1. The catalytic behavior (in terms of catalytic activity, stability and reusability) and the structural implications of the immobilization will be investigated. For comparison purposes, the non-optimized ATAs (prior to the ...

Submitter: Ioannis Pavlidis

Studies: No Studies

Assays: No Assays

Objectives: Identification of amine transaminases (ATAs) able to catalyze efficiently the amination of a desired set of ketones and aldehydes (expected products of GO oxidation). Optimization of the most potent biocatalysts, in terms of catalytic efficiency, stability, availability of functional groups for covalent immobilization.

Description of Work: ATAs from our construct selection (>30 wild-type and variants of both (R)- and (S)-enantioselectivity) with different substrate selectivity will ...

Submitter: Ioannis Pavlidis

Studies: No Studies

Assays: No Assays

Objectives: Protocol identification and establishment for the synthesis of high-performing catalytic GO in the desired oxidation reactions under mild conditions. Characterization of the most prominent materials synthesized and comparison to commercially available material.

Description of Work: Several established chemical methods will be used for the synthesis of GO. Each batch will be characterized, for instance for its C/O ratio, surface area and conductivity. The catalytic profile of the ...

Submitter: Ioannis Pavlidis

Studies: No Studies

Assays: No Assays

No description specified

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 ...

Submitter: Matthias Löbe

Studies: No Studies

Assays: No Assays

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.

Submitter: Harald Kusch

Studies: No Studies

Assays: No Assays

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

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 ...

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

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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 ...

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.

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