ಸಮರ್ಥ (Samarth TS, PhD) (@SamarthArya) header
ಸಮರ್ಥ (Samarth TS, PhD) (@SamarthArya) profile picture

ಸಮರ್ಥ (Samarth TS, PhD)

@SamarthArya

Bioinformatician

 Québec, Canada
Joined October 2009
  • Tweets1.2K
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Photo by ಸಮರ್ಥ (Samarth TS, PhD) (@SamarthArya)Photo by ಸಮರ್ಥ (Samarth TS, PhD) (@SamarthArya)Photo by ಸಮರ್ಥ (Samarth TS, PhD) (@SamarthArya)Photo by ಸಮರ್ಥ (Samarth TS, PhD) (@SamarthArya)Photo by ಸಮರ್ಥ (Samarth TS, PhD) (@SamarthArya)
ಕನ್ನಡಿಗರು ಏಳಿಗೆ ಹೊಂದಲು,ಕನ್ನಡದಲ್ಲಿ ವಿಜ್ಞಾನ ತಂತ್ರಜ್ಞಾನದ ಕಲಿಕೆ ಎಲ್ಲಾ ಹಂತಗಳಲ್ಲಿ ಸಾಧ್ಯವಾಗಬೇಕು. ಈ ನಿಟ್ಟಿನಲ್ಲಿ ಆಗಬೇಕಾದ ಮೂಲ ಕೆಲಸವೆಂದರೆ ವಿಜ್ಞಾನ ತಂತ್ರಜ್ಞಾನ ಪದಗಳ ಕಟ್ಟುವಿಕೆ. ಈ ಕೆಲಸ ಎಡೆಬಿಡದೇ ನಡೆಯಬೇಕಿದೆ. ನಿಮಗೂ ಈ ಕೆಲಸದಲ್ಲಿ ಕೈಜೋಡಿಸುವ ಆಸಕ್ತಿ ಇದೆಯೇ? ಹಾಗಿದ್ದರೆ, ಇಲ್ಲಿದೆ ಒಂದು ಪದಗಳ ಪೈಪೋಟಿ.ಪಾಲ್ಗೊಳ್ಳಿ
Image from ಮುನ್ನೋಟ ಟ್ರಸ್ಟ್ Munnota Trust (@Munnota_Trust)
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Krish Ashok (@krishashok) profile picture
Krish Ashok
@krishashok15 Jul 2024
Fun fact: the map of lactose intolerance in India tracks with this migration into the Indian subcontinent and subsequent genetic intermixing and migration patterns within India
Image from Krish Ashok (@krishashok)
Navin Kabra (@NGKabra) profile pictureNavin Kabra@NGKabra15 Jul 2024
Who are Indians descended from? Aryans from Europe? Dravidians who've been "here" forever? The Indus valley civilization? A controversial question for 150+ years, but now we have DNA evidence that answers these questions with a high degree of certainty. 🧵
Image from Navin Kabra (@NGKabra)
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Navin Kabra (@NGKabra) profile picture
Navin Kabra@NGKabra15 Jul 2024
Who are Indians descended from? Aryans from Europe? Dravidians who've been "here" forever? The Indus valley civilization? A controversial question for 150+ years, but now we have DNA evidence that answers these questions with a high degree of certainty. 🧵
Image from Navin Kabra (@NGKabra)
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Samuel Hume (@DrSamuelBHume) profile picture
Samuel Hume
@DrSamuelBHume23 Jun 2024
The 10 biggest cancer papers of the last 10 years (in my opinion) 1. Blocking PD1 activates the immune response against cancer - especially if the cancer has more mutations nejm.org/doi/pdf/10.1056/NEJ…
Image from Samuel Hume (@DrSamuelBHume)
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Lior Pachter (@lpachter) profile picture
Lior Pachter@lpachter5 Apr 2024
The choice of whether to use Seurat or Scanpy for single-cell RNA-seq analysis typically comes down to a preference of R vs. Python. But do they produce the same results? In biorxiv.org/content/10.1101/… w/ @Josephmrich et al. we take a close look. The results are 👀 1/🧵
Image from Lior Pachter (@lpachter)
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Chris Miller (@chrisamiller) profile picture
Chris Miller@chrisamiller6 Mar 2024
Two other resources of note for IGV: - Interactive guide to getting started with IGV: sandbox.bio/tutorials/igv-in… - The supplement to this article, which is an incredibly comprehensive visual guide to reviewing somatic variants: ncbi.nlm.nih.gov/pmc/article…

IGV tutorial

Interactive IGV tutorial: learn to recognize real variants from artifacts using the IGV genome browser

sandbox.bio
Matthew Parker (@bioinfomatt) profile pictureMatthew Parker@bioinfomatt5 Mar 2024
A key skill in bioinfo is assessment of raw seq data. Tools like IGV are useful to view aligned reads & variants. I've manually reviewed 1000s of variants and it's worth knowing what a real variant looks like! From Sirisha in the @nanopore #EPI2ME team: labs.epi2me.io/reviewing-bam
A guide to reviewing BAM files

A guide to reviewing BAM files

In the world of sequencing data analysis, automation reigns supreme. Standardised workflows, such…

epi2me.nanoporetech.com
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AJHG (@AJHGNews) profile picture
AJHG@AJHGNews7 Nov 2023
We're very excited to launch a series of exciting and thought-provoking articles that explore the future of human genetics and genomics. Read more in this launch piece from @girlscientist & @NHGRI_Director cell.com/ajhg/fulltext/S0002…

To boldly go: Unpacking the NHGRI’s bold predictions for human genomics by 2030

The 2020 strategic vision for human genomics, written by the National Human Genome Research Institute (NHGRI), was punctuated by a set of provocatively audacious “bold predictions for human genomics...

cell.com
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sina (@sinabooeshaghi) profile picture
sina
@sinabooeshaghi23 Sep 2023
You're asked to process single-cell sequencing data, what should you do first? Before downloading the data, it is *crucial* to understand the structure of the reads. Where are the barcodes? UMIs? Genomics features?
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Nancy Zhang (@NancyZh60672287) profile picture
Nancy Zhang@NancyZh6067228723 Sep 2023
What gets erased when you integrate #singlecell data across samples/studies, and can you get it back? When samples are from e.g. healthy & disease, should you simply massage cells together? FINALLY, I feel we can answer this question: doi.org/10.1101/2023.05.05.5…
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Support Our Science (@SupportOurSci) profile picture
Support Our Science@SupportOurSci22 Sep 2023
Canada’s federal graduate scholarships and postdoctoral fellowships are not competitive! 😞 For ex, the NSF postdoctoral fellowship is valued at $106,000 CAD 🇺🇸, compared to the $45,000 🇨🇦 offered by the Tri-Agency fellowships 😱🤕 #scholarships #graduate
Image from Support Our Science (@SupportOurSci)
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Rohini Singh (@rohini_sgh) profile picture
Rohini Singh
@rohini_sgh22 Aug 2023
No one does Modi the biggest disservice than the bhakt mandali. A teacher says vote for educated leaders without taking names and bhakt mandali starts to screech that it is an insult to Modi. An actor tweets an old Neil Armstrong joke about finding a Malayali chaiwala on the moon and Bhakt mandali thinks that’s an insult to Modi. Bhakts are bhasmasur basically.
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Alejandro Adem (@alejandroadem) profile picture
Alejandro Adem
@alejandroadem30 Apr 2023
Canada must address this important issue not only because it’s the right thing to do, but also to remain competitive as a global player in science and innovation. nature.com/articles/d41586-0…
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Yun S. Song (@yun_s_song) profile picture
Yun S. Song@yun_s_song17 Nov 2022
Predicting the effects of missense variants is a central problem in human genome interpretation. We are thrilled to share our preprint on using cross-protein transfer (CPT) learning to improve zero-shot prediction of disease variant effects: doi.org/10.1101/2022.11.15.5… (1/8)
Image from Yun S. Song (@yun_s_song)
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TheDoodlingScientist (@deepsud13) profile picture
TheDoodlingScientist@deepsud1327 Oct 2022
Any leads for a company that prints posters on fabric in Quebec/delivers to Quebec?
Emma J Chory (@chorye) profile pictureEmma J Chory@chorye27 Oct 2022
And even with rush shipping it’s more affordable/better quality than a paper poster and they last forever. $40 total with 2 day shipping.
Image from Emma J Chory (@chorye)
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Quirks & Quarks (@CBCQuirks) profile picture
Quirks & Quarks@CBCQuirks7 Oct 2022
Because of low funding, many young scientists are now making less than minimum wage, which means they either have to live in poverty, quit practicing science, or leave Canada. The Support our Science movement is calling for a change. cbc.ca/listen/live-radio/1-5…
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GenSCAPE (aka Raghavan) Lab 🧬 (@GenSCAPE_Lab) profile picture
GenSCAPE (aka Raghavan) Lab 🧬@GenSCAPE_Lab8 Jul 2022
✨ Excited to share our most recent work on population genetics in Southwest India! ✨ 🗣️ We ask: What is the relationship between genetic & oral histories in this region? 🧬 biorxiv.org/content/10.1101/… 🧵 A thread with some highlights …
Integrating genetic and oral histories of Southwest Indian populations

Integrating genetic and oral histories of Southwest Indian populations

India is home to thousands of ethno-linguistically distinct groups, many maintaining strong self-identities that derive from oral traditions and histories. However, these traditions and histories are...

biorxiv.org
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TheDoodlingScientist (@deepsud13) profile picture
TheDoodlingScientist@deepsud1325 Aug 2022
Anyone looking for a roommate in Boston this fall semester? I highly recommend my talented sister @KTsudarshan studying in Berkeley Music Conservatory.
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Parashar Dhapola (@ParasharDhapola) profile picture
Parashar Dhapola@ParasharDhapola8 Aug 2022
✨Scarf✨ got published today🎉 nature.com/articles/s41467-0… 1️⃣ Analyze millions of cells on your laptop 2️⃣ Topology preserving subsampling of cells 3️⃣ Cell projection for label prediction 4️⃣ Graph-based tSNE and hierarchical clustering #Singlecell #Genomics 🧵 1/8
Scarf enables a highly memory-efficient analysis of large-scale single-cell genomics data

Scarf enables a highly memory-efficient analysis of large-scale single-cell genomics data

Nature Communications - As the scale of single-cell genomics experiments grows into the millions, the computational requirements to process this data are beyond the reach of many. Here the authors...

nature.com
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Arjun Raj (@arjunrajlab) profile picture
Arjun Raj
@arjunrajlab1 Jul 2022
Over the years, the lab and I have come up with various materials for science process (writing, presenting, reviewing, etc.). Here they are, loosely organized in a Google Doc. Hope it is useful! docs.google.com/document/d/1…
Tools for science

Tools for science

THE FOLLOWING IS OUT OF DATE MOVED NOW TO: https://arjun-raj-lab.gitbook.io/arjun-rajs-tools-for-science ******************************************************************************** Tools for...

docs.google.com
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Fernando Pozo (@fpozoca) profile picture
Fernando Pozo@fpozoca1 Jun 2022
I'd like to share some personal recommendations if somebody wants to start learning bioinformatics because I still see several (maybe too many) inadequate courses. Below, a 🧵:
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