JULIO SOLIS-Bioinformatician & Molecular Biologist

Bioinformatics is shaping all life sciences and my world on Andean lupins...

[JULIO SOLIS-Bioinformatician & Molecular Biologist @Jsolis_s]

FIVE STEPS TO STARTING YOUR CAREER TO BECOME A BIOINFORMATICIAN https://t.co/9PFLXJMdX8

[Ming "Tommy" Tang @tangming2005]

Best Practice for R :: Cheat Sheet #rstats
https://t.co/7TjqoW4fox

[Biotech-Spain.com @Biotech_Spain]

.@IBECBarcelona Un nuevo estudio revela cómo el comportamiento de las proteínas impulsa la especialización de la barrera hematoencefálica https://t.co/KksIroINRI

[TrendsPlantSci @TrendsPlantSci]

Multitasking mediators: revealing the secret jobs of plant metacaspases https://t.co/cNh4sqjG7V #plantscience

[Prof. Nikolai Slavov @slavov_n]

Paying peer reviewers led to faster first editorial decisions — an average of 5.5 working days, down from nearly 38 for unpaid reviews.

The review quality, as judged by handling editors on the basis of helpfulness in making an editorial decision, went up.

1/

[Ming "Tommy" Tang @tangming2005]

1/ Public datasets feel like a goldmine.
But look closer—there are landmines hidden inside.
Especially for single-cell RNA-seq.
A thread 🧵

[Ming "Tommy" Tang @tangming2005]

read my full blog post on it
https://t.co/kx4RKT3ya2

[Ming "Tommy" Tang @tangming2005]

4/
Example sequence: ATCGAT
0-based: A(0)T(1)C(2)G(3)A(4)T(5)
1-based: A(1)T(2)C(3)G(4)A(5)T(6)

[Science Magazine @ScienceMagazine]

Some bacteria that are harmful to humans escape elimination by antibiotics because they carry resistance genes. However, antibiotic-susceptible bacterial populations often harbor rare persister cells that survive antibiotic exposure without being resistant. Antibiotic persistence favors recurrent infections and resistance emergence and is a public health threat.

Persister cells are thought to be metabolically dormant. Decreased activity of antibiotic targets would enable them to remain alive when antibiotics are present and to regrow after antibiotic removal.

In a new Science study, researchers report that Escherichia coli persister cells do not simply enter a dormant state upon antibiotic treatment. Instead, genetically identical cells diverge into two physiological states.

Some cells produce membrane vesicles that are loaded with specific proteins, which are taken up by other cells to enhance survival. Therefore, vesicle donors and recipients actively cooperate to benefit the entire bacterial population.

Learn more in a new #SciencePerspective: https://t.co/be5JNwqHJa

[Prof. Nikolai Slavov @slavov_n]

A deeper dive into the article we published last week in @Nature.

I will start with the framing and methodology as they are key to understanding the surprising results:

Proteomics experiments usually begin with an assumption.

https://t.co/XhD0ROD4jR

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[Ming "Tommy" Tang @tangming2005]

solid foundation in statistics is even more important in the age of AI.
This interactive app explaining statistic concepts is great
https://t.co/dO0YSMF9hf

[Daniel J Drucker @DanielJDrucker]

A metabolic update and perspective on #MASLD #MASH @DiabetologiaJnl https://t.co/IJGS7urfBI

[IberianCitizen @IberianCitizen]

Una mitocondria que no funciona bien produce una energía mas "sucia", menos ATP y mas especies reactivas de oxigeno (ROS).
https://t.co/HxOt94pfos (infografía)

[Mark @Sanbomics]

#Python is amazing for #Bioinformatics but it still lacks simple quality of life tools that are found on R/Bioconductor. I've updated my package to include a super fast mapper between ensembl, entrez, and symbols ids. 1) Initialize mapper; 2) use mapper. 🧵(1/3).

[Diego del Alamo @DdelAlamo]

"An atlas of protein homo-oligomerization across domains of life"

Mass prediction of proteins that interact with each other across multiple proteomes

https://t.co/dxae4cC38y

[Veera Rajagopal  @doctorveera]

A new exciting preprint from my colleagues (Rodriguez-Flores et al.) at Regeneron Genetics Center reports the discovery of a major genetic risk factor of stroke in South Asians—a missense variant (Arg1231Cys) in NOTCH3 that is seen in ~1% of the Pakistanis but rare elsewhere in the world.
https://t.co/kHNKn45Skr

NOTCH3 is well known a well-known Mendelian gene for stroke. Pathogenic mutations in NOTCH3 cause an autosomal dominant stroke syndrome called CADASIL (Cerebral Autosomal Dominant Arteriopathy with Subcortical Infacts and Leukoencephalopathy).

NOTCH3 is one of those genes where our knowledge of the disease (CADASIL) is older than our knowledge of the gene itself. It is through the families that suffered from CADASIL we came to know of the existence of NOTCH3 in humans.

History of CADASIL
CADASIL has a fascinating history. The earliest case reports of CADASIL date back to the 1970s when multiple case reports of families suffering from a new type of stroke syndrome surfaced one by one. Each of the research groups came up with their own names for the syndrome based on the clinical features they observed: "hereditary multi-infarct dementia", "chronic familial vascular encephalopathy" etc. (https://t.co/UpPa8qrBsS).

Then they realized that all of these isolated reports were pointing to the same condition. All the patients suffered from early-onset recurrent strokes damaging the brain gradually resulting in dementia, and sensory and motor deficits resulting in death before 60 yrs of age. Looking at the postmortem brain tissues it became clear it's a disease of small blood vessels in the white matter.

Discovery of NOTCH3
In 1993, studying two French families with CADASIL, Tournier-Lasserve et al. triangulated the genomic region (19q12) holding the gene responsible for CADASIL and also coined the acronym CADASIL (https://t.co/QMLbWiVCsJ). Three years later, the same group successfully cloned the causative gene and realized it was a homologue of mouse Notch3 (https://t.co/cBDq5Sy5Ud).

Genetic architecture of CADASIL mutations
NOTCH3 is a huge protein with 2321 amino acids that gets chopped multiple times over its molecular life course. The most characteristic of NOTCH3 is its extracellular domain which contains 34 repeat units, each comprising six cysteine residues. Almost all the CADASIL mutations identified to date fall within these domains, either adding or deleting cysteine residues (cys-altering mutations) that interfere with dimerization resulting in a dominant negative pathology.(https://t.co/ckZz7W6CRZ).

What is exciting about the new discovery?
So far almost all the reported CADASIL mutations have been rare. The recent GWAS of stroke in more than 1 million individuals of predominantly Europeans found no signal around NOTCH3 (https://t.co/bSmZwgVNK2). But studying just 70k Pakistanis, my colleagues found a clear GWAS signal in NOTCH3 driven by a missense variant seen in as much as 1% of the Pakistanis with a large effect size (3.4 fold risk) suggesting this is probably the major genetic risk factor of stroke in South Asians.

If we had not looked at the South Asians and simply used European results to predict the stroke risk in South Asians, we would have missed the contribution of this important variant. This is a great demonstration of the value of studying non-European populations and a reminder that there are many more discoveries to be made in largely under-explored populations like South Asians.

This discovery was possible due to the RGC collaboration with Pakistani Genomic Resource built by Danish Saleheen and his team which has made tremendous contributions towards the advancement of South Asian genetics (https://t.co/cB2VFWAHDN).

Some recent posts:
1. Effect of consanguinuity on the risk of common diseases in South Asians (https://t.co/dTkPsl935K)
2. Discovery of the first genetic locus (ADRA2A) for Reynaud's phenomenon (https://t.co/zC7vGRmerb).
2. Gene by sex interactions of PNPLA3 I148M variant (https://t.co/RFegHHRS2z).

[Science Magazine @ScienceMagazine]

In a new Science study, researchers provide the first estimate of the global density and biomass of arbuscular mycorrhizal fungal networks.

Learn more: https://t.co/iHgv5tmG1H

[Ming "Tommy" Tang @tangming2005]

My next newsletter "Will AI replace bioinformaticians?" is coming at 9:30 am. Subscribe to get it and stay in the loop on everything I'm creating.
https://t.co/q70UytZ2C4

[Heng Li @lh3lh3]

minibwa-0.2 released with a few minor bug fixes (please keep bug reports coming). No algorithm changes. Minibwa is also available via bioconda thanks to Thanh Lee.
https://t.co/jgGaN5duWe

[ISCB SC RSG-Spain @RSGSpain]

💼 Bioinformatician (Long-read sequencing)
📍 Lugar: Centre for Genomic Regulation (CRG) — Barcelona, España
🔗 Más información: https://t.co/bEdSFWDNww

[Ming "Tommy" Tang @tangming2005]

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