Alan Garfinkel
@agarfinkel.bsky.social
Modeling and Dynamics of Biological Systems
https://modelinginbiology.github.io
https://en.wikipedia.org/wiki/Alan_Garfinkel
https://profiles.ucla.edu/alan.garfinkel
https://modelinginbiology.github.io
https://en.wikipedia.org/wiki/Alan_Garfinkel
https://profiles.ucla.edu/alan.garfinkel
Reposted by Alan Garfinkel
ChatGPT offered to make an image for me of how the cerebellum interacts with other brain predictive processing pathways and this amazingly confused diagram was the result--mislabeling almost every brain structure & even inventing new ones. 😱 Let's hope our future doctors aren't using LLMs to study!
June 21, 2025 at 11:17 AM
ChatGPT offered to make an image for me of how the cerebellum interacts with other brain predictive processing pathways and this amazingly confused diagram was the result--mislabeling almost every brain structure & even inventing new ones. 😱 Let's hope our future doctors aren't using LLMs to study!
Reposted by Alan Garfinkel
#DynamicsClub in June: 𝗖𝗮𝘀𝗲𝘆 𝗔𝗱𝗮𝗺 from Purdue University will share her work on dynamic neuromodulation. www.nature.com/articles/s42...
June 12 (Thur) at 11am PT / 2pm ET
Join in person at UCLA or on Zoom: lingyunxiong.github.io/DynamicsClub/
June 12 (Thur) at 11am PT / 2pm ET
Join in person at UCLA or on Zoom: lingyunxiong.github.io/DynamicsClub/
June 2, 2025 at 10:13 PM
#DynamicsClub in June: 𝗖𝗮𝘀𝗲𝘆 𝗔𝗱𝗮𝗺 from Purdue University will share her work on dynamic neuromodulation. www.nature.com/articles/s42...
June 12 (Thur) at 11am PT / 2pm ET
Join in person at UCLA or on Zoom: lingyunxiong.github.io/DynamicsClub/
June 12 (Thur) at 11am PT / 2pm ET
Join in person at UCLA or on Zoom: lingyunxiong.github.io/DynamicsClub/
Reposted by Alan Garfinkel
Delighted to share that I will give a department seminar at UCSD 𝑺𝒉𝒖 𝑪𝒉𝒊𝒆𝒏 - 𝑮𝒆𝒏𝒆 𝑳𝒂𝒚 𝑫𝒆𝒑𝒂𝒓𝒕𝒎𝒆𝒏𝒕 𝒐𝒇 𝑩𝒊𝒐𝒆𝒏𝒈𝒊𝒏𝒆𝒆𝒓𝒊𝒏𝒈 on Friday, June 6th. be.ucsd.edu/seminar/2025...
Join us in La Jolla at 2pm in The FUNG Auditorium.
Join us in La Jolla at 2pm in The FUNG Auditorium.
Bifurcation theory in physiology | Shu Chien - Gene Lay Department of Bioengineering
be.ucsd.edu
June 2, 2025 at 10:48 PM
Delighted to share that I will give a department seminar at UCSD 𝑺𝒉𝒖 𝑪𝒉𝒊𝒆𝒏 - 𝑮𝒆𝒏𝒆 𝑳𝒂𝒚 𝑫𝒆𝒑𝒂𝒓𝒕𝒎𝒆𝒏𝒕 𝒐𝒇 𝑩𝒊𝒐𝒆𝒏𝒈𝒊𝒏𝒆𝒆𝒓𝒊𝒏𝒈 on Friday, June 6th. be.ucsd.edu/seminar/2025...
Join us in La Jolla at 2pm in The FUNG Auditorium.
Join us in La Jolla at 2pm in The FUNG Auditorium.
Reposted by Alan Garfinkel
I have been selected by the UCLA Molecular Biology Institute for the 2025 Boyer/Parvin Posteoctoral Award. 🥳🥳🥳
Initiated by Paul Boyer since his Nobel Prize in 1997, this honor is now supported by the Parvin foundation to celebrate the legacy of Dr. Boyer, beyond ATP synthase and the sodium pump.
Initiated by Paul Boyer since his Nobel Prize in 1997, this honor is now supported by the Parvin foundation to celebrate the legacy of Dr. Boyer, beyond ATP synthase and the sodium pump.
June 1, 2025 at 3:01 PM
I have been selected by the UCLA Molecular Biology Institute for the 2025 Boyer/Parvin Posteoctoral Award. 🥳🥳🥳
Initiated by Paul Boyer since his Nobel Prize in 1997, this honor is now supported by the Parvin foundation to celebrate the legacy of Dr. Boyer, beyond ATP synthase and the sodium pump.
Initiated by Paul Boyer since his Nobel Prize in 1997, this honor is now supported by the Parvin foundation to celebrate the legacy of Dr. Boyer, beyond ATP synthase and the sodium pump.
Reposted by Alan Garfinkel
#DynamicsClub in May: 𝗡𝗮𝘁𝗮𝗹𝗶𝗲 𝗛𝗮𝘂𝗴𝗹𝘂𝗻𝗱 @ox.ac.uk will share her recent work on the glymphatic system during sleep. pubmed.ncbi.nlm.nih.gov/39788123/
May 7 (Wed) at 9am PT / 5pm BST
Join us on Zoom: lingyunxiong.github.io/DynamicsClub/
May 7 (Wed) at 9am PT / 5pm BST
Join us on Zoom: lingyunxiong.github.io/DynamicsClub/
May 1, 2025 at 3:43 PM
#DynamicsClub in May: 𝗡𝗮𝘁𝗮𝗹𝗶𝗲 𝗛𝗮𝘂𝗴𝗹𝘂𝗻𝗱 @ox.ac.uk will share her recent work on the glymphatic system during sleep. pubmed.ncbi.nlm.nih.gov/39788123/
May 7 (Wed) at 9am PT / 5pm BST
Join us on Zoom: lingyunxiong.github.io/DynamicsClub/
May 7 (Wed) at 9am PT / 5pm BST
Join us on Zoom: lingyunxiong.github.io/DynamicsClub/
Reposted by Alan Garfinkel
I'm aiming to get some thoughtful biologists together (there's no lack of them!) to discuss what kind of narratives might best reflect the nature of their field in the 21st century. Here's a preview of the goals; I'm excited and optimistic about it.
www.marginaliareviewofbooks.com/post/after-t...
www.marginaliareviewofbooks.com/post/after-t...
After the Genetic Paradigm: Why We Need a New Biology
PHILIP BALL | One sign of this shift is that biology is becoming more ready to accept and to speak of concepts long considered taboo...
www.marginaliareviewofbooks.com
April 18, 2025 at 11:25 AM
I'm aiming to get some thoughtful biologists together (there's no lack of them!) to discuss what kind of narratives might best reflect the nature of their field in the 21st century. Here's a preview of the goals; I'm excited and optimistic about it.
www.marginaliareviewofbooks.com/post/after-t...
www.marginaliareviewofbooks.com/post/after-t...
Reposted by Alan Garfinkel
My article with @agarfinkel.bsky.social titled "𝗔𝗿𝗲 𝗽𝗵𝘆𝘀𝗶𝗼𝗹𝗼𝗴𝗶𝗰𝗮𝗹 𝗼𝘀𝗰𝗶𝗹𝗹𝗮𝘁𝗶𝗼𝗻𝘀 𝙥𝙝𝙮𝙨𝙞𝙤𝙡𝙤𝙜𝙞𝙘𝙖𝙡?" has ranked as a Top Viewed Article by Wiley. Check it out if you haven't done so: onlinelibrary.wiley.com/doi/full/10.... #TopViewedArticle
Are physiological oscillations physiological?
Abstract figure legend Mechanisms and functions of physiological oscillations.
onlinelibrary.wiley.com
April 16, 2025 at 1:46 PM
My article with @agarfinkel.bsky.social titled "𝗔𝗿𝗲 𝗽𝗵𝘆𝘀𝗶𝗼𝗹𝗼𝗴𝗶𝗰𝗮𝗹 𝗼𝘀𝗰𝗶𝗹𝗹𝗮𝘁𝗶𝗼𝗻𝘀 𝙥𝙝𝙮𝙨𝙞𝙤𝙡𝙤𝙜𝙞𝙘𝙖𝙡?" has ranked as a Top Viewed Article by Wiley. Check it out if you haven't done so: onlinelibrary.wiley.com/doi/full/10.... #TopViewedArticle
Reposted by Alan Garfinkel
Pleased to host 𝗗𝗿. 𝗔𝗹𝗶𝗰𝗶𝗮 𝗠𝗰𝗗𝗼𝗻𝗼𝘂𝗴𝗵 for the first IBP Departmental Seminar on Thursday, April 3rd. Join us in person at UCLA to find out the 𝘱𝘩𝘺𝘴𝘪𝘰𝘭𝘰𝘨𝘪𝘤𝘢𝘭 𝘣𝘦𝘯𝘦𝘧𝘪𝘵𝘴 𝘰𝘧 𝘵𝘩𝘦 𝘧𝘦𝘮𝘢𝘭𝘦 𝘬𝘪𝘥𝘯𝘦𝘺 and meet members of the Department of Integrative Biology and Physiology!
March 28, 2025 at 6:59 PM
Pleased to host 𝗗𝗿. 𝗔𝗹𝗶𝗰𝗶𝗮 𝗠𝗰𝗗𝗼𝗻𝗼𝘂𝗴𝗵 for the first IBP Departmental Seminar on Thursday, April 3rd. Join us in person at UCLA to find out the 𝘱𝘩𝘺𝘴𝘪𝘰𝘭𝘰𝘨𝘪𝘤𝘢𝘭 𝘣𝘦𝘯𝘦𝘧𝘪𝘵𝘴 𝘰𝘧 𝘵𝘩𝘦 𝘧𝘦𝘮𝘢𝘭𝘦 𝘬𝘪𝘥𝘯𝘦𝘺 and meet members of the Department of Integrative Biology and Physiology!
Reposted by Alan Garfinkel
Quick video summary of my research: We develop computational and experimental methods to discover drugs for heart disease 🧪
youtu.be/nmpFDiE4GSg
youtu.be/nmpFDiE4GSg
Jeff Saucerman, PhD, uses computational and experimental methods to find new drugs for heart disease
YouTube video by UVA - School of Medicine
youtu.be
February 20, 2025 at 1:36 PM
Quick video summary of my research: We develop computational and experimental methods to discover drugs for heart disease 🧪
youtu.be/nmpFDiE4GSg
youtu.be/nmpFDiE4GSg
Reposted by Alan Garfinkel
🚨Our latest preprint: "Continuation methods as a tool for parameter inference in electrophysiology modeling" by @MattJOwen_
and me: doi.org/10.48550/arX...
You fitting models to data related to limit cycles?
Tweetorial follows... 🧵 1/9
and me: doi.org/10.48550/arX...
You fitting models to data related to limit cycles?
Tweetorial follows... 🧵 1/9
Continuation methods as a tool for parameter inference in electrophysiology modeling
Parameterizing mathematical models of biological systems often requires fitting to stable periodic data. In cardiac electrophysiology this typically requires converging to a stable action potential th...
doi.org
January 17, 2025 at 11:48 AM
🚨Our latest preprint: "Continuation methods as a tool for parameter inference in electrophysiology modeling" by @MattJOwen_
and me: doi.org/10.48550/arX...
You fitting models to data related to limit cycles?
Tweetorial follows... 🧵 1/9
and me: doi.org/10.48550/arX...
You fitting models to data related to limit cycles?
Tweetorial follows... 🧵 1/9
Reposted by Alan Garfinkel
Eight years ago, I worked on mathematical modeling of gene regulation. Always, thought why the relevant literature and lessons from this field are not present in popular science. Well, now here it is. A moving piece by @philipcball.bsky.social
#biology #gene #emergence
nautil.us/how-life-rea...
#biology #gene #emergence
nautil.us/how-life-rea...
How Life Really Works
Just as I uncovered a new way to understand life, I got news about my own.
nautil.us
December 23, 2024 at 1:07 PM
Eight years ago, I worked on mathematical modeling of gene regulation. Always, thought why the relevant literature and lessons from this field are not present in popular science. Well, now here it is. A moving piece by @philipcball.bsky.social
#biology #gene #emergence
nautil.us/how-life-rea...
#biology #gene #emergence
nautil.us/how-life-rea...
Reposted by Alan Garfinkel
Thoughts from leaders of systems #immunology how mechanistic models can leverage omics/ML for deeper understanding of how our immune system works #sysbio @cp-cellsystems.bsky.social
www.cell.com/cell-systems...
www.cell.com/cell-systems...
What unique insights can modeling approaches capture about the immune system?
The immune system, optimized by evolution to maintain health and prevent disease, is remarkably good at what it does. It detects pathogens and monitors physiological stresses with a sensitivity and selectivity that far surpasses that of man-made biosensors. It then mounts potent yet precise responses, enabling the body to maintain homeostasis amid varying internal milieu and external threats.
www.cell.com
December 23, 2024 at 6:34 PM
Thoughts from leaders of systems #immunology how mechanistic models can leverage omics/ML for deeper understanding of how our immune system works #sysbio @cp-cellsystems.bsky.social
www.cell.com/cell-systems...
www.cell.com/cell-systems...
The math world lost a giant in September, with the death of Ralph Abraham. Ralph’s paradigm-changing Foundations of Mechanics (with Jerry Marsden) laid out the differential geometric and topological foundations of global analysis. (1/n)
November 26, 2024 at 9:44 PM
The math world lost a giant in September, with the death of Ralph Abraham. Ralph’s paradigm-changing Foundations of Mechanics (with Jerry Marsden) laid out the differential geometric and topological foundations of global analysis. (1/n)
Reposted by Alan Garfinkel
Something that's been bugging me for a while in bioinformatics data analysis is this overreliance on packages, workflows and what's been called "cargo cult science".
Can we have more conceptual thinking, more theory?
Asking for what we really want to achieve and what we need to do gets us there.
Can we have more conceptual thinking, more theory?
Asking for what we really want to achieve and what we need to do gets us there.
November 19, 2024 at 10:58 AM
Something that's been bugging me for a while in bioinformatics data analysis is this overreliance on packages, workflows and what's been called "cargo cult science".
Can we have more conceptual thinking, more theory?
Asking for what we really want to achieve and what we need to do gets us there.
Can we have more conceptual thinking, more theory?
Asking for what we really want to achieve and what we need to do gets us there.
This is priceless! tylervigen.com has long been a wonderful source for spurious correlations, but now it has added these totally bs "explanations" generated by AI!
It's been a while since I've gone on the Spurious Correlations site. The author has added AI explanations, which I think is absolutely delightful. www.tylervigen.com/spurious-cor...
November 25, 2024 at 1:41 AM
This is priceless! tylervigen.com has long been a wonderful source for spurious correlations, but now it has added these totally bs "explanations" generated by AI!
Reposted by Alan Garfinkel
Wild!
UCSF hosted its first food pantry event for postdocs today, where a local food bank gives free food to UCSF employees.
This picture represents about half the line that had formed 10 minutes before the market had opened.
What the fuck are we doing here guys?
This picture represents about half the line that had formed 10 minutes before the market had opened.
What the fuck are we doing here guys?
November 21, 2024 at 6:54 PM
Wild!
thrilled that Ivy Xiong’s poster was chosen to represent basic science at UCLA Dept of Medicine’s annual Research Day: intravital imaging (thanks, Natalie Porat-Shliom!) and mathematical modeling to identify key sex differences in kidney function.
connect.uclahealth.org/dom/2024/10/...
A common pathway to cancer: Oncogenic mutations abolish p53 oscillations
The tumor suppressor p53 oscillates in response to DNA double-strand breaks, a behavior that has been suggested to be essential to its anti-cancer fun…
sciencedirect.com
November 20, 2024 at 9:49 PM
thrilled that Ivy Xiong’s poster was chosen to represent basic science at UCLA Dept of Medicine’s annual Research Day: intravital imaging (thanks, Natalie Porat-Shliom!) and mathematical modeling to identify key sex differences in kidney function.
connect.uclahealth.org/dom/2024/10/...
Delighted to post this article (open access), which takes direct aim at the doctrine of homeostasis, and argues for the fundamental role of oscillatory processes. Also discusses the math needed to understand the mechanisms of oscillatory processes, which is nonlinear dynamics.
Are physiological oscillations physiological?
Abstract figure legend Mechanisms and functions of physiological oscillations.
physoc.onlinelibrary.wiley.com
November 20, 2024 at 9:43 PM
Delighted to post this article (open access), which takes direct aim at the doctrine of homeostasis, and argues for the fundamental role of oscillatory processes. Also discusses the math needed to understand the mechanisms of oscillatory processes, which is nonlinear dynamics.
Reposted by Alan Garfinkel
Why is there no bookmark feature here? It would be really useful to save insightful posts, for our own learning and to refer to when challenging misleading claims and narratives especially those peddled by the ruling class. It’s an essential tool for accountability.
November 18, 2024 at 6:09 AM
Why is there no bookmark feature here? It would be really useful to save insightful posts, for our own learning and to refer to when challenging misleading claims and narratives especially those peddled by the ruling class. It’s an essential tool for accountability.