Hassan Foroughi @hassanforoughi
Exceptionally average bioinformatician | All tweets are my own Stockholm, Sweden Joined March 2014-
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Time to celebrate! 🥂Our new agoTRIBE method to detect microRNA targets transcriptome-wide in single cells has just been published in @NatureBiotech! 🧬 Thanks to @scilifelab @Stockholm_Uni @Vetenskapsradet and @ERC_Research nature.com/articles/s4158…
Open #postdoc position in #RNA #genomics to study RNA-protein interaction and subcellular localization at single-cell level. Apply and join us at @karolinskainst @scilifelab Link here: ki.varbi.com/en/what:job/jo… Deadline 27 May 2023
My new favorite thing - Bing's new ChatGPT bot argues with a user, gaslights them about the current year being 2022, says their phone might have a virus, and says "You have not been a good user" Why? Because the person asked where Avatar 2 is showing nearby
. @SAS what is going with your system. I can see other people's accounts and their flights. Even change their bookings.
this is what happens when you don’t recycle your pizza boxes
Please spread the word. Assistant Professor in Integrative structural biology with focus on structural dynamics Stockholm Deadline Dec 28. su.se/english/about-…
I got it! Mars reappearing after being temporarily hidden by the moon. I got a ton of footage, I'm going to clean it up and share images soon!
Amazing resources.
When men refer to themselves as "alpha males", I hear that in the context of software, where alpha versions are unstable, missing important features, filled with flaws, and not fit for the public.
Please RT! We're looking for a bioinformatician in our Boston office. This is a long-term industry role, so no grant writing or any of that other academia annoyance. More details and how to apply here: genedata.com/careers/open-p…
When it comes to the field of genomics, visualization of genomics data becomes critical. The authors here provide a comprehensive review of published genomic visualization tools. #datascience #dataviz #bioinformatics #genomics #R #Python #AI link: ncbi.nlm.nih.gov/pmc/articles/P…
Liquid biopsy and cfDNA profiling via NGS is dominated by Illumina sequencers. Are there are companies or services available that use other sequencers, e.g. MGI, ONT, or PACB?
A hierarchy of alienness: Pictures of animals from least to most related to you. Least-related animal: Sponges. You and sponges are both animals. That's basically all you've got in common.
1/. In today's @ScienceMagazine, we report bioadhesive ultrasound (BAUS) for long-term continuous imaging of diverse organs --- An ultrasound sticker capable of continuous, on-the-go, high-quality imaging of most parts of the human body. science.org/doi/10.1126/sc…
Very happy to share our first molecular motor made of DNA, open access to everyone to read @Nature nature.com/articles/s4158… . It is a ratchet! And it can wind a spindle.
When your linear regression model outperforms a deep learning model #RStats
No biomedical organization should hold a conference in a state that outlaws abortion.
@lpachter So what does it take to land in one of these journals? Often 6+ complex multi-panel figures, an onslaught of results and data, and a 40+ page supplemental PDF to back up the findings. These papers are written for editors, not other scientists.
The exciting reveal of Ultima Genomics last week was accompanied by the publication of four preprints. Intrigued by the potential of the technology, @sinabooeshaghi & I decided to take a look at the data. A 🧵 about our findings & a preprint we posted: biorxiv.org/content/10.110… 1/
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166K Followers 3K Following Back off man, I'm a scientist. President of @Humanists_UK Lecturer in Genetics @UCL Genetics, race, eugenics, history of science, movies, books, cricket, +–=÷×TFW you’re white knuckled nervous worried the day before important news and a major new release… > over 400 new genome assemblies for the ATCC Genome Portal. > transitioning to Supporting Memberships > launch of a new NGS discrepancy tool for authenticated genomes…
Spatial transcriptomics reveals discrete tumour microenvironments and autocrine loops within ovarian cancer subclones | Nature Communications nature.com/articles/s4146…
What if the fundamental building blocks of reality were not physical matter, but consciousness? In the research article, “Objects of Consciousness,” Donald Hoffman and Chetan Prakash presented a different theoretical framework for understanding the nature of reality. Their…
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What I’m reading this week in genome assembly, synthetic biology, genAI/LLMs in bioinformatics, microbial genomics, biosecurity, etc, … 🧬🖥️🧵
Also: "L %||% R newly in base is an expressive idiom for the phrases if(!is.null(L)) L else R or if(is.null(L)) R else L." #Rstats cran.r-project.org/src/base/NEWS
The complete manuscript cycle will take place on pubpub.org, where I will respond and revise according to public feedback. In addition, @RauchLab has kindly agreed to serve as editor. She will solicit/curate anonymous peer review that we will append to the manuscript
Thank you to @MTranchero for telling me about this observation from this paper: journals.plos.org/plosbiology/ar…
PacBio Plummets omicsomics.blogspot.com/2024/04/pacbio…
Karl Popper (1902-1994) on what it means to be a rationalist ✍️ When I speak of reason or rationalism, all I mean is the conviction that we can learn through criticism of our mistakes and errors, especially through criticism by others, and eventually also through self-criticism.…
Amen. When I interviewed at Bell Labs at the end of graduate school, I was asked to prepare a 45 min talk that took me 90 min to deliver -- thanks to all the interrupting questions and debate that ensued. It was fantastic! It meant that they cared, and they pushed me in…
Karl Popper (1902-1994) on what it means to be a rationalist ✍️ When I speak of reason or rationalism, all I mean is the conviction that we can learn through criticism of our mistakes and errors, especially through criticism by others, and eventually also through self-criticism.…
It has been estimated that the anti-vaccine online industry accumulates annual revenues of $35 million, and that their audience of 62 million followers may be worth upward of a billion dollars a year for the big social media platforms. sciencedirect.com/science/articl… By @johnfocook…
Foldseek-Multimer is a protein complex aligner that is up to 10,000x times faster than SOTA methods without sacrificing quality, enabling the comparison of billions of complex pairs per day. 1/5 📄 biorxiv.org/content/10.110… 💾 github.com/steineggerlab/… 🌐 search.foldseek.com
Another paper on utility of polygenic risk scores: nature.com/articles/s4146… tl;dr: polygenic risk scores have no utility.
does that man look familiar to you
This single-cell paper has no UMAPs. Instead, it's main results are in the form of several small tables. Because those are the results for any single-cell RNA-seq experiment.
Candidate drug targets with #scRNAseq support defined as 👉cell type specific expression in disease-relevant tissue OR 👉cell type specific over-expression in disease patients are more likely to successfully advance from research to clinic medrxiv.org/content/10.110…
Candidate drug targets with #scRNAseq support defined as 👉cell type specific expression in disease-relevant tissue OR 👉cell type specific over-expression in disease patients are more likely to successfully advance from research to clinic medrxiv.org/content/10.110…
Would you believe me if I told you that a single variant in a non-coding RNA explains ~0.5% of all undiagnosed individuals with neurodevelopmental disorders (NDD) in @GenomicsEngland ??? I didn’t initially either, but here is the story of RNU4-2 🧵1/9
Thrilled to share our latest discovery on a spliceosomal snRNA gene causing neurodevelopmental disorders: medrxiv.org/content/10.110… Thank you to everyone who contributed; it’s been a phenomenal effort to collaborate with clinicians and researchers for what would help many families!
Thrilled to share our latest discovery on a spliceosomal snRNA gene causing neurodevelopmental disorders: medrxiv.org/content/10.110… Thank you to everyone who contributed; it’s been a phenomenal effort to collaborate with clinicians and researchers for what would help many families!
1/ We are extremely excited to share our new manuscript published @Cancer_Cell! Kudos to co-first authors @AvishaySpitzer, @GritschSimon and @M_Nomura for seminal work, to co-PIs @MarioSuva, Dan P. Cahill and @KeithLigon5 and to all contributors.
Online Now: Mutant IDH inhibitors induce lineage differentiation in IDH-mutant oligodendroglioma dlvr.it/T57X2F