Bioinformatics Scientist @ Theiagen Genomics| PhD in computational biology | enjoys metagenomic nerd talk | gets mean when hungry
Lisbon, Portugal
Joined January 2018
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I'm happy to share my very first publication with @theiagen entitled "Accelerating bioinformatics implementation in public health". We present the use of @TerraBioApp as an analysis platform to connect public health users to bioinformatics - go.shr.lc/3pLRVVu
Inês Mendes retweeted
Come and do a Master’s with us!
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Inês Mendes retweeted
Recently, @andrewjpage, @ines_cim and @rpetit3 contributed to "Putting everything in its place: using the INSDC compliant Pathogen Data Object Model to better structure genomic data submitted for public health applications."
You can read it here: microbiologyresearch.org/con…
Inês Mendes retweeted
The Pathogen DOM is out now in @MicrobioSoc!
Putting everything in its place: using the INSDC compliant Pathogen Data Object Model to better structure genomic data submitted for public health applications - go.shr.lc/3TnjpNQ
#PHA4GE
Wondering how to submit a new pathogen genome to INSDC? Or, how to build a dashboard to track the evolution of a diverse set of pathogens within the INSDC?🤔 Enter the Pathogen DOM, an open protocol for standardized data sharing.
osf.io/5cyu4
Inês Mendes retweeted
Excited to announce the @HealthHolland project ‘Predict and Prevent’ on the integration of pan-genomics, population dynamics and clinical outcomes to elucidate emerging pathogen threats using machine learning. A partnership between @UniUtrecht, @RIVM and @theiagen.
Inês Mendes retweeted
Happy to share our latest #preprint, presenting the upgraded “#INSaFLU - #TELEVIR: an open web-based bioinformatics suite for #viral #metagenomic #detection and #routine #genomic #surveillance”.
- tool: insaflu.insa.pt/
- preprint:
researchsquare.com/article/r…
👇
Inês Mendes retweeted
#MVIF #23 full program is OUT
We're happy to welcome YOU & speakers⬇️
⭐️ Keynote:
🇩🇪 @merenbey
⭐️ Selected talks:
🇳🇴@AhmedBargheet
🇮🇹 Antonia Bruno (@unimib)
🇨🇭@pscepanovic (@Roche)
⭐️ Highlights:
🇺🇸 @BioBohmann
🇮🇹 @GabrieleGhiotto
FREE registration hopin.com/events/microbiome-…
Inês Mendes retweeted
Day 2 of the #PHA4GECon workshop with @cziscience @czbiohub hosting sessions on using metagenomics to survey vector-based pathogens 🧬🖥️ – at Bellville, South Africa
Inês Mendes retweeted
Unlocking Genomic Insights for Public Health! 🌍
Join this session to explore how infrastructure drives progress in public health research.
Meet our speakers:
Abebe Aseffa Negeri
Jairo Méndez-Rico
Kim Ng
Gerald Mboowa
Joel Sevinsky
Furqan Kabir
#PHA4GEcon
Inês Mendes retweeted
Our paper examining critical errors in a cancer metagenomics study is now live in @mbiojournal. Work carried out with @StevenSalzberg1 @danbrewer @elapertea @YuchenGe1 @JenniferLu717 and others. Errors in bioinformatics can be subtle but important! doi.org/10.1128/mbio.01607-2…
Inês Mendes retweeted
Nothing could make me happier right now that this bioinformatics pipeline-generated csv file full of TB resistance data. All correct and ready for import into LIMS. All thanks to hard work of @theiagen #ClinicalWGS #TB
Inês Mendes retweeted
Have you recently used artificial intelligence (AI) to develop content? Our Director of Technical Innovation, @andrewjpage, recently published an editorial about this tool.
Read it here: microbiologyresearch.org/con…
What are the cool kids using for #metagenomic #binning these days? Still good old CONCOCT? MaxBin2? SemiBin2? 🦠👩💻
#Bioinformatics #help
Inês Mendes retweeted
🚨Funding opportunity 🚨
The Essential #OpenSource Software for Science program supports maintenance, growth, development + community engagement for critical tools used by biomedical scientists globally czi.co/OpenSourceSoftwareRFA
Host removal on #metagenomic sequences is an issue that, in my opinion, not enough attention is given. Bede exposes the major issues simply and beautifully in this blog post. A must read for anyone #sequencing! – at Seixal, Portugal
Inês Mendes retweeted
🆕Vacancy! We’re looking for an enthusiastic and motivated Bioinformatician to join our Food, Microbiome and Health programme.
💷 £35,300 to £43,750
🗓️ Apply by 3 October
➡️ buff.ly/3qFfv6P
ALT A social card with an image of coding. On the right a green quadrangle with the text "Bioinformatician, assisting the interpretation of microbiome research projects generated as part of the Food, Microbiome and Health programme. Salary: £35.300 to £43,750. Contract length : 4 years. Apply by 3 October 2023." One the left the Quadram Institute logo.
Inês Mendes retweeted
The development of a standard pathogen data object model is a huge step forward for public health bioinformatics and data integration.
This should allow for much more flexible interoperability, help with future-proofing and QMS, and advance both research and public health use.
Wondering how to submit a new pathogen genome to INSDC? Or, how to build a dashboard to track the evolution of a diverse set of pathogens within the INSDC?🤔 Enter the Pathogen DOM, an open protocol for standardized data sharing.
osf.io/5cyu4
Inês Mendes retweeted
Wondering how to submit a new pathogen genome to INSDC? Or, how to build a dashboard to track the evolution of a diverse set of pathogens within the INSDC?🤔 Enter the Pathogen DOM, an open protocol for standardized data sharing.
osf.io/5cyu4
Inês Mendes retweeted
On the 3rd episode of The Bioinformatics Lab podcast we discuss if AI Robots are going to replace bioinformaticians. Available from YouTube or your favourite podcast app.
Youtube: youtube.com/watch?v=-l5xy4nJ…
Soundcloud: soundcloud.com/the_bioinform…
very interesting read on the issue of removing host contamination (human) from sequencing reads!! I highly recommend you take a look!
#metagenomics #bioinformatics
The critique of Poore et al’s Nature paper highlights the dangers of i) metagenomic classification using incomplete indexes and ii) human read subtraction using incomplete reference genomes. Some related thoughts 🧵
biorxiv.org/content/10.1101/…
Inês Mendes retweeted
Career highlight to be in some way linked to @donttrythis! Thanks, @molly_j_for the opportunity to highlight @theiagen’s work in public health pathogen genomics
#Bioinformatics is a field that uses principles and approaches from #datascience and #computerscience, which it uses to make sense of large biological data sets.
Join us as we interview @kevinlibuit #CTO, on this latest podcast episode of Data Unchained:
youtu.be/y9P8INaU_ZI