Nimisha Chaturvedi

[Nimisha Chaturvedi @nimchat12]

Through our collaboration with @syclopseu partners, we are in the process of developing and validating a fully open , accelerated secondary genomic analysis pipeline. A short blog for now. More updates to follow next year. Stay tuned!

[SYCLOPS Project @syclopseu]

SYCLOPS member, Accelom, will work with other partners to develop #SYCL-GAL. This library will enable open, cross-architecture genome sequencing .

It's just one of the ways SYCLOPS will benefit science and innovation.

See more in this blog from Accelom!
https://t.co/CgzGjPzejW

[Nimisha Chaturvedi @nimchat12]

So proud to be a part of this Horizon Europe project and the amazing consortium @HorizonEU

[SYCLOPS Project @syclopseu]

We're excited to launch the SYCLOPS Project, which brings together 8 leading European organisations to democratize AI acceleration using open standards and enable a healthy, innovation-driven ecosystem.

Read the press release here:
https://t.co/cohZN3JqY7
#SYCL #AI

[bioRxiv Genomics @biorxiv_genomic]

Worldwide population genomics reveal long-term stability of the mitochondrial chromosome composition in a keystone marine plant https://t.co/ah8UMFLRNh #biorxiv_genomic

[Raja Appuswamy @raja_appuswamy]

Recently, we (@nimchat12,@yanlolo1) presented #accelalign, our embedding-based #sequencealigner. Now, we have improved embedding accuracy further (https://t.co/4GdIQLH9Lh). Come hear @yanlolo1 present it at #HICOMB @IPDPS today, try it(https://t.co/avipoa3W6B) & give us feedback.

[Nimisha Chaturvedi @nimchat12]

So proud and excited to have ACCELOM be a part of this project. Thank you @EURECOM and @Sapienbio2012 for such an amazing collaboration! Looking forward to doing some ground-breaking research on triple-negative breast cancer together https://t.co/Ni0eA6hyz4

[Heng Li @lh3lh3]

Some of promising short-read mappers this year: accel-align, chromap, dragmap and snap v2. Short-read mapping is not solved yet.

[Raja Appuswamy @raja_appuswamy]

#recombseq2021 just kicked off with amazing attendance! Awesome program! Super excited to talk about #AccelAlign (https://t.co/XbxLnrei8U). Please check it out (https://t.co/k7JDZn0tAG), and reach out for feedback & collab. @nimchat12 @yanlolo1 #sequencealignment #Bioinformatics

[Nimisha Chaturvedi @nimchat12]

Nailed it!

[Sim Kern @sim_kern]

The world is burning, and our billionaires are the people MOST responsible, but at least there's no escape for them. They will live and die (alone, like all of us) on this beautiful, precious, one-in-a-gazillion planet.
We should take our wealth back from them and use it better.

[Nimisha Chaturvedi @nimchat12]

If you are looking for a WGS/exomeseq aligner that is 10x faster than bwa/bowtie2 on just CPUs with a low memory footprint consider #AccelAlign, open source, dockerized, ready to use, now published with @SpringerNature in @BMCBioinfo. Reach out for collaboration/support.

[Raja Appuswamy @raja_appuswamy]

After a rigorous review cycle, our research on sequence alignment(#AccelAlign) has been published with @SpringerNature in @BMCBioinfo (https://t.co/XbxLnrei8U). GPU-accel, splicing support, and more coming soon. Please reach out for collaboration/support. @nimchat12 @yanlolo1

[Thomas Van Boeckel @thvanboeckel]

Dear Colleagues,

The situation in India is haertbreaking. My friends from Delhi, and former advisor at Princeton (@CDDEP) are working round the clock to help bring OXYGEN to those who need it. If you can donate:

https://t.co/SNu9QbwfIW

[Nimisha Chaturvedi @nimchat12]

Short horror story: Your work describes a pipeline to analyze triple negative breast cancer and ovarian cancer data. Reviewer comes back with a comment: How are you going to account for gender bias? What!?!

[Nimisha Chaturvedi @nimchat12]

As if Covid19 anxiety wasn't enough for this year! #Elections2020

[Raja Appuswamy @raja_appuswamy]

For most academics, funding comes via collab, which happens when you are well known in your field, which happens when you have solid publications, which often requires a team of PhDs and postdocs, which in turn requires funding. We need initiatives like these to #breakthecycle.

[Lior Pachter @lpachter]

So I wrote a thread about the lack of representation of women on the SciPy and NumPy papers, and the implications thereof. In return I was blocked by one of the core developers. This is not how one builds open source communities. https://t.co/oamXHMD6s6

[bioRxiv @biorxivpreprint]

Accel-Align: A Fast Sequence Mapper and Aligner based on the Seed-Embed-Extend Method https://t.co/uVefxHv7ep #bioRxiv

[Raja Appuswamy @raja_appuswamy]

Our latest work with @nimchat12 on randomized low distortion embedding for sequence alignment is out. We introduce seed-embed-extend, a new design method, and show that an SEE aligner can provide 10x reduction in exec. time over bwa and bowtie2 without any special hardware.

[Nimisha Chaturvedi @nimchat12]

Thought provoking https://t.co/ShwYHBvxEy

[Nimisha Chaturvedi @nimchat12]

Something to think about while we have self-quarantine time on our hands https://t.co/s0FYIZRTaY

[Nimisha Chaturvedi @nimchat12]

Very interesting ted video on imposter syndrome https://t.co/STUz2FR6dD

[Nimisha Chaturvedi @nimchat12]

Presenting this cool work! Thanks @jacquesfellay and the team for such a fruitful collaboration. Adaptation of hepatitis C virus to interferon lambda polymorphism across multiple viral genotypes https://t.co/uzrw1ijrf3