2024-03-28T14:12:57Z
https://zenodo.org/oai2d
oai:zenodo.org:10365987
2023-12-21T16:18:30Z
openaire
user-igc
Carolina, Ventura Costa
Tiago, Paixão
2023-12-12
<p>Exploring essential factors at every data life stage we highlight the challenges associated with handling sensitive information, from data planning to data sharing. This encompasses understanding best practices, security measures, and ethical considerations crucial for safeguarding sensitive data throughout its life cycle.</p>
https://doi.org/10.5281/zenodo.10365987
oai:zenodo.org:10365987
Zenodo
https://zenodo.org/communities/igc
https://doi.org/10.5281/zenodo.10365986
info:eu-repo/semantics/openAccess
Creative Commons Attribution Share Alike 4.0 International
https://creativecommons.org/licenses/by-sa/4.0/legalcode
Working with sensitive data: the data life cycle
info:eu-repo/semantics/conferencePoster
oai:zenodo.org:6325980
2022-03-04T01:49:06Z
user-igc
Paixão, Tiago
2021-03-03
<p>This document establishes the first draft of the institutional guidelines for data management of the Instituto Gulbenkian de Ciencia.</p>
https://doi.org/10.5281/zenodo.6325980
oai:zenodo.org:6325980
Zenodo
https://zenodo.org/communities/igc
https://doi.org/10.5281/zenodo.6325979
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Data Management
Policy
FAIR
Institutional Guidelines for Research Data Management
info:eu-repo/semantics/other
oai:zenodo.org:7272281
2022-11-02T10:33:00Z
user-igc
user-eu
Temitope Akhigbe Etibor
Maria João Amorim
2022-11-01
<p>Multiple viral infections form biomolecular condensates in the host cell to compartmentalize viral reactions. Accumulating evidence indicates that these viral condensates may be hardened, a strategy with the potential for exploitation as novel antiviral therapy, given that viral reactions rely on specific material properties for function. However, there is no molecular understanding of how to specifically and efficiently modify the material properties of viral condensates <em>in vivo</em>, a prerequisite for overcoming off-target effects by rational drug design. <em>In vitro</em>, the material properties of biological condensates are modified by different thermodynamic parameters, including free energy, concentration, and type/strength of interactions. Here, we used influenza A virus liquid cytosolic condensates, A.K.A viral inclusions, to provide a proof of concept that modulating the type/strength of transient interactions among the interactome in IAV inclusions is more efficient at hardening these structures than varying the temperature or concentration, both in <em>in vitro </em>and in <em>in vivo </em>models. This stabilization can be achieved by a known pharmacological sticker that, in addition, can specifically change the solubility of the viral proteome without affecting host proteome abundance nor solubility. Our work supports the development of antivirals targeting the material properties of biomolecular condensates in viral infections. It also provides a framework for the selection of compounds with this activity for general application and thus provides an advance in disease therapy.</p>
https://doi.org/10.5281/zenodo.7272281
oai:zenodo.org:7272281
Zenodo
https://zenodo.org/communities/igc
https://zenodo.org/communities/eu
https://doi.org/10.5281/zenodo.7272280
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Phase transition
Biomolecular condensates
Viral inclusions
Influenza A virus
Pharmacological hardening
Thermodynamics
Solubility proteome profiling
Thermal stability
Rules for hardening influenza A virus liquid
info:eu-repo/semantics/article
oai:zenodo.org:1255038
2020-01-24T19:22:29Z
openaire_data
user-igc
Daniel Sobral
2018-05-29
<p>This dataset contains a set of example data for a functional enrichment tutorial.</p>
https://doi.org/10.5281/zenodo.1255038
oai:zenodo.org:1255038
Zenodo
https://doi.org/10.1038/nprot.2012.016
https://doi.org/10.1038/nature10532
https://doi.org/10.1093/nar/gkx1098
https://doi.org/10.1093/nar/gkw1108
https://zenodo.org/communities/igc
https://doi.org/10.5281/zenodo.1255037
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Functional Enrichment
Example Datasets for Functional Enrichment Analysis
info:eu-repo/semantics/other
oai:zenodo.org:5091797
2021-07-13T13:48:22Z
software
user-igc
user-eu
Paixao, Tiago
2021-07-12
<p>Code (and data) to reproduce analysis of centriole size in <em>The 3D architecture and molecular foundations of de novo centriole assembly via bicentrioles, </em>published in Current Biology. Code is in the form of a jupyter notebook and written in Python. A non-interactive version in HTML is provided.</p>
<p>packages used:</p>
<pre>pandas: 1.2.3
numpy: 1.20.1
sklearn: 0.24.1
scipy: 1.6.0</pre>
https://doi.org/10.5281/zenodo.5091797
oai:zenodo.org:5091797
Zenodo
https://zenodo.org/communities/igc
https://zenodo.org/communities/eu
https://doi.org/10.5281/zenodo.5091796
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
python
centriole
Gaussian Misture code for "The 3D architecture and molecular foundations of de novo centriole assembly via bicentrioles"
info:eu-repo/semantics/other
oai:zenodo.org:1193536
2020-01-24T19:23:18Z
openaire_data
user-igc
Sobral, Daniel
2017-11-01
<p>This is a 16S Metagenomics example dataset obtained by transforming data originally from Batista et al. (2015). It consists of data corresponding to 2 conditions (WT untreated and WT after Streptomycin treatment) with 5 replicates each, where exactly 10000 reads were obtained from the original forward raw reads of each sample. This dataset includes a metadata file, sequencing reads as well as the greengenes reference dataset, which is given here for convenience and reproducibility.</p>
https://doi.org/10.5281/zenodo.1193536
oai:zenodo.org:1193536
Zenodo
https://doi.org/10.1038/ncomms9945
http://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA297801
https://zenodo.org/communities/igc
https://doi.org/10.5281/zenodo.1040360
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
16S Metagenomics, Qiime, Antibiotic Resistance
Example 16S Metagenomics Dataset
info:eu-repo/semantics/other
oai:zenodo.org:7473398
2023-01-03T14:26:50Z
user-igc
user-eu
Maria João Amorim
Temitope Akhigbe Etibor
2022-12-22
<p>Descriptive statistics and videos of all my data set.</p>
https://doi.org/10.5281/zenodo.7473398
oai:zenodo.org:7473398
ang
Zenodo
https://zenodo.org/communities/igc
https://zenodo.org/communities/eu
https://doi.org/10.5281/zenodo.7473397
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Influenza A virus inclusions are liquid condensates that can be pharmacologically hardened.
info:eu-repo/semantics/doctoralThesis
oai:zenodo.org:10355037
2023-12-13T09:58:29Z
user-igc
Soares, Miguel
Rebelo, Sofia
2023-12-13
https://doi.org/10.5281/zenodo.10355037
oai:zenodo.org:10355037
eng
Zenodo
https://zenodo.org/communities/igc
https://doi.org/10.5281/zenodo.10355036
info:eu-repo/semantics/restrictedAccess
Creative Commons Attribution Non Commercial Share Alike 4.0 International
https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode
The EMBO Journal, (2023-12-13)
Source.Data #EMBOJ-2023-114293R1
info:eu-repo/semantics/other
oai:zenodo.org:7376908
2022-11-29T14:39:02Z
user-igc
Temitope Akhigbe Etibor
Sílvia Vale-Costa
Sindhuja Sridharan
Daniela Brás
Isabelle Becher
Victor Hugo Mello
Filipe Ferreira
Marta Alenquer
Mikhail M Savitski
Maria João Amorim
2022-11-29
<p>Controlled phase transitions in biomolecular condensates will provide further understanding to cell physiology and diseases as the material properties in these structures are tailored for function. Since native or engineered transitions affect condensate behavior, phase transitions may offer opportunities to block viral infections. The material properties of biological condensates are modified by thermodynamic parameters, including free energy, concentration, and type/strength of interactions, regulated by different processes in cells. Biologically, it is not known whether biomolecular condensates exhibit hierarchical responses to these stimuli. Viral infections are good systems to address this question by forming condensates <em>de novo</em> as part of their replication programmes. Here, we used influenza A virus liquid cytosolic condensates, A.K.A viral inclusions, to provide a proof of concept that condensate hardening via perturbing the type/strength of interactions among the IAV inclusions’ interactome is efficient and specific both <em>in vitro </em>and <em>in vivo </em>and that alterations in temperature and concentration are not. This stabilization, achieved by a known pharmacological sticker, changed the material properties of viral inclusions without affecting host proteome abundance nor solubility. Our work addresses the critical need to identify inducers of controlled phase transitions in biology and may guide strategies to block viral infections.</p>
https://doi.org/10.5281/zenodo.7376908
oai:zenodo.org:7376908
ang
Zenodo
https://zenodo.org/communities/igc
https://doi.org/10.5281/zenodo.7376907
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Phase transition, Biomolecular condensates, Viral inclusions, Influenza A virus, Thermodynamics, Pharmacological hardening, Temperature, Concentration, Molecular interaction, Proteome-wide solubility, Thermal stability.
Rules for hardening influenza a virus liquid condensates: Data and Codes
info:eu-repo/semantics/article
oai:zenodo.org:4773828
2021-05-25T13:48:22Z
openaire_data
user-igc
Brito Santos, Nuno
Vaz da Silva, Zoé E.
Gomes, Catarina
Reis, Celso A.
Amorim, Maria João
2021-05-24
<p>Data generated for the submitted manuscript Complement Decay-Accelerating Factor is a modulator of influenza A virus lung immunopathology (https://doi.org/10.1101/2021.02.16.431406)</p>
https://doi.org/10.5281/zenodo.4773828
oai:zenodo.org:4773828
Zenodo
https://doi.org/10.1101/2021.02.16.431406
https://zenodo.org/communities/igc
https://doi.org/10.5281/zenodo.4773827
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Complement Decay-Accelerating Factor is a modulator of influenza A virus lung immunopathology
info:eu-repo/semantics/other
oai:zenodo.org:1040361
2020-01-24T19:23:18Z
openaire_data
user-igc
Sobral, Daniel
2017-11-01
<p>This is a 16S Metagenomics example dataset obtained by transforming data originally from Batista et al. (2015). It consists of data corresponding to 2 conditions (WT untreated and WT after Streptomycin treatment) with 5 replicates each, where exactly 10000 reads were obtained from the original forward raw reads of each sample. This dataset includes a metadata file, sequencing reads as well as the greengenes reference dataset, which is given here for convenience and reproducibility.</p>
https://doi.org/10.5281/zenodo.1040361
oai:zenodo.org:1040361
Zenodo
https://doi.org/10.1038/ncomms9945
http://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA297801
https://zenodo.org/communities/igc
https://doi.org/10.5281/zenodo.1040360
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
16S Metagenomics, Qiime, Antibiotic Resistance
Example 16S Metagenomics Dataset
info:eu-repo/semantics/other
oai:zenodo.org:849901
2020-01-24T19:24:30Z
openaire_data
user-igc
Daniel Sobral
2017-08-26
<p>This is an RNA-Seq small example dataset by transforming data originally from Guilgur et al. (2012). It consists of data corresponding to a small selection of Drosophila melanogaster genes. This dataset includes sequencing reads as well as gene annotation.</p>
https://doi.org/10.5281/zenodo.849901
oai:zenodo.org:849901
Zenodo
https://doi.org/10.7554/eLife.02181
http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-2321/
https://zenodo.org/communities/igc
https://doi.org/10.5281/zenodo.849900
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Example RNA-Seq Data
info:eu-repo/semantics/other
oai:zenodo.org:2565417
2020-01-24T19:25:55Z
openaire_data
user-igc
Daniel
2019-02-13
<p>This dataset contains a set of example data for a functional enrichment tutorial.</p>
https://doi.org/10.5281/zenodo.2565417
oai:zenodo.org:2565417
Zenodo
https://zenodo.org/communities/igc
https://doi.org/10.5281/zenodo.2564087
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
GO Enrichment
Example Datasets for Functional Enrichment Analysis
info:eu-repo/semantics/other
oai:zenodo.org:6901207
2022-11-02T10:32:58Z
openaire_data
user-igc
Temitope Akhigbe Etibor
Maria João Amorim
2022-07-25
<p>Data generated and codes used for the publication titled "Influenza A virus liquid condensates can undergo pharmacological hardening"</p>
https://doi.org/10.5281/zenodo.6901207
oai:zenodo.org:6901207
eng
Zenodo
https://zenodo.org/communities/igc
https://doi.org/10.5281/zenodo.6901206
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Influenza A virus liquid condensates can undergo pharmacological hardening
info:eu-repo/semantics/other
oai:zenodo.org:1193466
2020-01-24T19:24:30Z
openaire_data
user-igc
Daniel Sobral
2017-08-26
<p>This is an RNA-Seq small example dataset by transforming data originally from Guilgur et al. (2012). It consists of data corresponding to a small selection of Drosophila melanogaster genes. This dataset includes sequencing reads as well as gene annotation.</p>
https://doi.org/10.5281/zenodo.1193466
oai:zenodo.org:1193466
Zenodo
https://doi.org/10.7554/eLife.02181
http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-2321/
https://zenodo.org/communities/igc
https://doi.org/10.5281/zenodo.849900
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Example RNA-Seq Data
info:eu-repo/semantics/other
oai:zenodo.org:1144111
2020-01-24T19:23:19Z
openaire_data
user-igc
Sobral, Daniel
2017-11-01
<p>This is a 16S Metagenomics example dataset obtained by transforming data originally from Batista et al. (2015). It consists of data corresponding to 2 conditions (WT untreated and WT after Streptomycin treatment) with 5 replicates each, where exactly 10000 reads were obtained from the original forward raw reads of each sample. This dataset includes a metadata file, sequencing reads as well as the greengenes reference dataset, which is given here for convenience and reproducibility.</p>
https://doi.org/10.5281/zenodo.1144111
oai:zenodo.org:1144111
Zenodo
https://doi.org/10.1038/ncomms9945
http://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA297801
https://zenodo.org/communities/igc
https://doi.org/10.5281/zenodo.1040360
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
16S Metagenomics, Qiime, Antibiotic Resistance
Example 16S Metagenomics Dataset
info:eu-repo/semantics/other
oai:zenodo.org:2564088
2020-01-24T19:26:02Z
openaire_data
user-igc
Daniel
2019-02-13
<p>This dataset contains a set of example data for a functional enrichment tutorial.</p>
https://doi.org/10.5281/zenodo.2564088
oai:zenodo.org:2564088
Zenodo
https://zenodo.org/communities/igc
https://doi.org/10.5281/zenodo.2564087
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
GO Enrichment
Example Datasets for Functional Enrichment Analysis
info:eu-repo/semantics/other