sina b
@sina.bio
HHMI Hanna Gray Fellow at @UCBerkeley w/ @airstreets. PhD @caltech, Math & ME BS @mit. I enjoy drinking tea, riding bikes, taking photos, and exploring nature.
Pinned
Hi, I’m Sina! A bioinformatics PhD @ucberkeleyofficial.bsky.social developing tools for single-cell data 🧬. When I’m not coding in a café ☕️ or biking around the bay area 🚴♂️, I’m planning experiments, staying active, and building things with my hands. Follow for science and life updates! 🌟
Reposted by sina b
single-cell is a fun field. for instance, one of the heavily curated bixbench scenarios is about interpreting the results of a sc analysis and comparing to ground truth. this ground truth is, of course, based on DE analyses with some truly remarkable p-values for n=5
March 6, 2025 at 2:44 AM
single-cell is a fun field. for instance, one of the heavily curated bixbench scenarios is about interpreting the results of a sc analysis and comparing to ground truth. this ground truth is, of course, based on DE analyses with some truly remarkable p-values for n=5
Reposted by sina b
"No one is coming out of the sky to give you your grant money. Your citation portfolio won’t survive this market crash. Your credentials mean nothing. Everything is going to change."
New for @undark.org
undark.org/2025/03/06/o...
New for @undark.org
undark.org/2025/03/06/o...
How Science Can Adapt to a New Normal
Opinion | In the wake of attacks on the research enterprise, scientists need to focus on protecting its fragile infrastructure.
undark.org
March 6, 2025 at 2:35 PM
"No one is coming out of the sky to give you your grant money. Your citation portfolio won’t survive this market crash. Your credentials mean nothing. Everything is going to change."
New for @undark.org
undark.org/2025/03/06/o...
New for @undark.org
undark.org/2025/03/06/o...
“blocking retro nasal sensation with a nose clip significantly reduces the subjective and objective neural responses to sucrose taste”
Retro Nasal blockade reduces the Neural Processing of Sucrose in the Human Brain https://www.biorxiv.org/content/10.1101/2025.02.11.637706v1
February 12, 2025 at 6:28 PM
“blocking retro nasal sensation with a nose clip significantly reduces the subjective and objective neural responses to sucrose taste”
Reposted by sina b
Amazing to me how useful looking at data in 2D PCA continues to be, even though the approach sounds crazy on paper—"p-dimensional ellipsoid", rantings of a madman. PCA is the cockroach of dimension reduction. I expect it to be present in any advanced galactic civilization.
February 10, 2025 at 9:44 AM
Amazing to me how useful looking at data in 2D PCA continues to be, even though the approach sounds crazy on paper—"p-dimensional ellipsoid", rantings of a madman. PCA is the cockroach of dimension reduction. I expect it to be present in any advanced galactic civilization.
Reposted by sina b
"One thing is certain: The changes we make ourselves will be healthier than the ones our adversaries demand."
New work for @undark.org:
undark.org/2025/02/06/o...
New work for @undark.org:
undark.org/2025/02/06/o...
The End of Science’s Peacetime
Opinion | Defending the practice of science from its adversaries will require dealing with some uncomfortable truths.
undark.org
February 6, 2025 at 1:52 PM
"One thing is certain: The changes we make ourselves will be healthier than the ones our adversaries demand."
New work for @undark.org:
undark.org/2025/02/06/o...
New work for @undark.org:
undark.org/2025/02/06/o...
🧵 On a Friday night, the NIH twitter account announced the most significant change to research funding in decades. What are indirect costs, how are universities funded and what are the impacts?
February 8, 2025 at 12:21 AM
🧵 On a Friday night, the NIH twitter account announced the most significant change to research funding in decades. What are indirect costs, how are universities funded and what are the impacts?
Reminder: there is little evidence that brain computation works in the same way as neural networks.
Quote from "Understanding Deep Learning by Simon Prince (@simonprinceai.bsky.social)"
Quote from "Understanding Deep Learning by Simon Prince (@simonprinceai.bsky.social)"
January 23, 2025 at 11:33 PM
Reminder: there is little evidence that brain computation works in the same way as neural networks.
Quote from "Understanding Deep Learning by Simon Prince (@simonprinceai.bsky.social)"
Quote from "Understanding Deep Learning by Simon Prince (@simonprinceai.bsky.social)"
why is this desirable? Language models are helpful in parsing unstructured data, but QC reports are already structured...
The gold standard in #bioinformatics reporting just got even better! #AI Summaries are now available in @multiqc.info🎉
Find out more: hubs.la/Q033Kjp30
Find out more: hubs.la/Q033Kjp30
January 23, 2025 at 10:54 PM
why is this desirable? Language models are helpful in parsing unstructured data, but QC reports are already structured...
An often overlooked point in genomics:
"Molecular omics resources should require sex annotation: a call for action"
by @gliomath.bsky.social
www.nature.com/articles/s41...
"Molecular omics resources should require sex annotation: a call for action"
by @gliomath.bsky.social
www.nature.com/articles/s41...
Molecular omics resources should require sex annotation: a call for action - Nature Methods
The most commonly used omics databases are a compilation of results from primarily male-only and sex-agnostic studies. The pervasive use of these databases critically hinders progress toward fully acc...
www.nature.com
January 17, 2025 at 6:14 PM
An often overlooked point in genomics:
"Molecular omics resources should require sex annotation: a call for action"
by @gliomath.bsky.social
www.nature.com/articles/s41...
"Molecular omics resources should require sex annotation: a call for action"
by @gliomath.bsky.social
www.nature.com/articles/s41...
TIL about the watch command in the terminal: it reruns a command at set intervals, and is perfect for monitoring GPU usage or tracking real-time system updates.
December 17, 2024 at 8:24 PM
TIL about the watch command in the terminal: it reruns a command at set intervals, and is perfect for monitoring GPU usage or tracking real-time system updates.
Reposted by sina b
In this year's user survey, 89% of respondents said that EMBL-EBI data resources empowered them to undertake work that would otherwise not have been possible 💪
Big thank you to everyone who filled in the survey - we appreciate your input!
Explore further findings: www.ebi.ac.uk/about/news/a...
Big thank you to everyone who filled in the survey - we appreciate your input!
Explore further findings: www.ebi.ac.uk/about/news/a...
Fuelling discovery together: 2024 user survey learnings
Blog post by Eleni Tzampatzopoulou, EMBL-EBI Impact Manager In summer 2024, EMBL-EBI ran a user survey, inviting our community to let us know how they use the open data resources we jointly manage wit...
www.ebi.ac.uk
December 17, 2024 at 4:01 PM
In this year's user survey, 89% of respondents said that EMBL-EBI data resources empowered them to undertake work that would otherwise not have been possible 💪
Big thank you to everyone who filled in the survey - we appreciate your input!
Explore further findings: www.ebi.ac.uk/about/news/a...
Big thank you to everyone who filled in the survey - we appreciate your input!
Explore further findings: www.ebi.ac.uk/about/news/a...
Cool to see our open source syringe pumps being made in the wild !
Original article: www.nature.com/articles/s41...
Original article: www.nature.com/articles/s41...
December 13, 2024 at 7:10 PM
Cool to see our open source syringe pumps being made in the wild !
Original article: www.nature.com/articles/s41...
Original article: www.nature.com/articles/s41...
Reposted by sina b
gonna post up in a cafe and speedrun a new protein diffusion model "from scratch" with Claude
live poasting my way thru it, public Git repo
last did this in June and it's really at the edge of both of our capabilities
live poasting my way thru it, public Git repo
last did this in June and it's really at the edge of both of our capabilities
December 8, 2024 at 4:42 PM
gonna post up in a cafe and speedrun a new protein diffusion model "from scratch" with Claude
live poasting my way thru it, public Git repo
last did this in June and it's really at the edge of both of our capabilities
live poasting my way thru it, public Git repo
last did this in June and it's really at the edge of both of our capabilities
Reposted by sina b
I often make microfluidic emulsions and microparticles for scalable biology experiments, but the other day I was thinking, what if we polymerize the continuous phase of an emulsion?
come learn about a delightful little branch of science, polyHIPEs!
come learn about a delightful little branch of science, polyHIPEs!
December 6, 2024 at 4:38 PM
I often make microfluidic emulsions and microparticles for scalable biology experiments, but the other day I was thinking, what if we polymerize the continuous phase of an emulsion?
come learn about a delightful little branch of science, polyHIPEs!
come learn about a delightful little branch of science, polyHIPEs!
I am honestly stoked by the ability to customize one's algorithm on @bsky.app. It's a killer feature (over Twitter) that makes it actually useable for scientific communication. Simply pick the feed you want to follow and boom you get the relevant content.
November 27, 2024 at 9:25 PM
I am honestly stoked by the ability to customize one's algorithm on @bsky.app. It's a killer feature (over Twitter) that makes it actually useable for scientific communication. Simply pick the feed you want to follow and boom you get the relevant content.
Reposted by sina b
It’s out!! We subjected soils from 30 different locations across Europe to extreme events and found that soil fungal and bacterial communities showed consistent responses that could be predicted from their origin! With @knightjar.bsky.social and many collaborators!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Soil microbiomes show consistent and predictable responses to extreme events - Nature
Soils from 30 grasslands across Europe were subjected to 4 contrasting extreme climatic events under drought, flood, freezing and heat conditions, with the results suggesting that soil microbiomes fro...
www.nature.com
November 27, 2024 at 7:47 PM
It’s out!! We subjected soils from 30 different locations across Europe to extreme events and found that soil fungal and bacterial communities showed consistent responses that could be predicted from their origin! With @knightjar.bsky.social and many collaborators!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by sina b
(1/5) Tired of Excel messing up your gene names? Just released gfix, a simple command-line tool that fixes Excel-converted gene names in spreadsheets. No custom file conversions required- just supply your excel file as is! 🛠️
github.com/sbooeshaghi/gfix
github.com/sbooeshaghi/gfix
GitHub - sbooeshaghi/gfix: Fix Excel-converted gene names in files.
Fix Excel-converted gene names in files. Contribute to sbooeshaghi/gfix development by creating an account on GitHub.
github.com
November 27, 2024 at 12:23 AM
(1/5) Tired of Excel messing up your gene names? Just released gfix, a simple command-line tool that fixes Excel-converted gene names in spreadsheets. No custom file conversions required- just supply your excel file as is! 🛠️
github.com/sbooeshaghi/gfix
github.com/sbooeshaghi/gfix
Car emissions, pollutants, and noise are large drivers of health outcomes and we have the technology to address these issues.
I think the work we do in genetics and genomics is really fundamental to so many aspects of human disease, etc. However, I often worry that as a society we are not doing enough to combat the obvious health implications of things like driving, our food environment etc.
November 27, 2024 at 6:09 PM
Car emissions, pollutants, and noise are large drivers of health outcomes and we have the technology to address these issues.
(1/5) Tired of Excel messing up your gene names? Just released gfix, a simple command-line tool that fixes Excel-converted gene names in spreadsheets. No custom file conversions required- just supply your excel file as is! 🛠️
github.com/sbooeshaghi/gfix
github.com/sbooeshaghi/gfix
GitHub - sbooeshaghi/gfix: Fix Excel-converted gene names in files.
Fix Excel-converted gene names in files. Contribute to sbooeshaghi/gfix development by creating an account on GitHub.
github.com
November 27, 2024 at 12:23 AM
(1/5) Tired of Excel messing up your gene names? Just released gfix, a simple command-line tool that fixes Excel-converted gene names in spreadsheets. No custom file conversions required- just supply your excel file as is! 🛠️
github.com/sbooeshaghi/gfix
github.com/sbooeshaghi/gfix
The dreaded gene name turns date in Excel strikes again (in a published paper!).. this happens because MARCH3 is interpreted as March 3rd by Excel's automatic date formatting. (previously I was bamboozled by SEPT1 (Septin 1)!
November 26, 2024 at 9:54 PM
The dreaded gene name turns date in Excel strikes again (in a published paper!).. this happens because MARCH3 is interpreted as March 3rd by Excel's automatic date formatting. (previously I was bamboozled by SEPT1 (Septin 1)!
This claim in a published paper gives the same energy as "trending towards significance".
"Two additional [cell types] were characterized by gradual expression of genes, such as [gene 1] and [gene 2]"
"Two additional [cell types] were characterized by gradual expression of genes, such as [gene 1] and [gene 2]"
November 26, 2024 at 9:29 PM
This claim in a published paper gives the same energy as "trending towards significance".
"Two additional [cell types] were characterized by gradual expression of genes, such as [gene 1] and [gene 2]"
"Two additional [cell types] were characterized by gradual expression of genes, such as [gene 1] and [gene 2]"