1/n. The travel ban was upheld by the SCOTUS and as an Iranian American I am devastated by this decision. This imposes a blanket ban, no ifs and no buts. Setting aside what it does to my personal life, it will have a catastrophic impact on the lives of grad students and postdocs.
I am deeply grateful to the Vilcek Fdn
@Vilcek
for this recognition. Immigrants are and have long been the backbone of science and technology in the US. I am surrounded by visionary immigrants, and I am excited to be their representative for today...
Joining twitter, my goal was to get exposure to political and scientific discourse. Now, more and more, the scientific questions seem woefully trivial. It's impossible to take a primer on GenBank seriously, when the post above and below outline the ways our society is collapsing.
I am excited to join all the amazing investigators and scientists at
@arcinstitute
! Can't wait to do some cool computational and technology-centric team science! And looking forward to joining forces with the innovation and ignite awardees to expand our community!
We’re thrilled to welcome Hani Goodarzi
@genophoria
, Associate Professor of Biochemistry & Biophysics
@UCSF
, as our newest Core Investigator
His groundbreaking research uses machine learning models and experimental frameworks to dig into cancer progression and metastasis.
Super excited to see the launch of
@exaibio
. When
@lisacfishsci
and I started our search for orphan RNA species (oncRNAs), never did we imagine it will lead us here. Now some of the smartest people I know will be working on this problem!
@babak_alipanahi
@lisacfishsci
The Vilcek Foundation congratulates Hani Goodarzi and the team
@exaibio
on securing $67.5M to finance a new RNA-based platform for early
#cancer
detection.
@genophoria
is the recipient of a 2022
#VilcekPrize
for Creative Promise in Biomedical Science.
As the incoming graduate students start to pick their rotations, this is my take on what they should consider when they pick a lab:
1. One of the key virtues of academia is that you get to choose who you work with, so take full advantage of that.
Excited to announce Vevo’s launch! What started as coffee chats with
@kevansf
close to 7 years ago has now given us an opportunity to rethink how we do drug discovery.
Vevo Therapeutics has officially launched out of stealth today with an oversubscribed and upsized $12M seed financing. We are so excited to reveal what we have been building behind the scenes! 🧵1/6
One of the biggest obstacles to interdisciplinary research is that in the end four reviewers are asked to comment on different aspects of the study. The likelihood of four reviewers from different fields being positive about a single manuscript is exceedingly low.
Read our newest preprint to learn about orphan non-coding RNAs (oncRNAs) and how they form blood-readable digital molecular barcodes that capture the identity of cancer cells. A very long 🧵
11/n. I plead you to check up on those around you. Make sure they are fine. Tell them it will be alright. Tell them they will see their parents again. Tell them they will see their friends soon. Let's make sure we protect the psyche of these young students. Our 1 job today!
I am late to my own party, but I wanted to write a short 🧵 to put this talk in context. First of all, the
@TEDTalks
team was amazing; there is so much that goes into these seemingly short talks. It was an amazing experience and I made some new friends.
A long time ago,
@ElementoLab
and I came up with our solution to the gene-set enrichment analysis. We used mutual information to measure the association between gene-set membership and input. After a decade, a talented undergrad spearheaded an update:
Excited to share our second preprint of the week, courtesy of our former lab specialist Bruce Culbertson and our resident specialist Kristle Garcia, with help and support from many others, most notably Josh Rabinowitz’s group!
Took us a minute, but I am happy to share the final version of this study, now published at
@NatureCancer
, on behalf of Bruce and Kristle. We have it all, regulatory RNA interactions, oxidative stress/ferroptosis, and metastasis:
Excited to share our second preprint of the week, courtesy of our former lab specialist Bruce Culbertson and our resident specialist Kristle Garcia, with help and support from many others, most notably Josh Rabinowitz’s group!
Our first paper and really great work by Dr. Lisa Fish (a postdoc in my lab) and
@at__steven
(former HHMI med student fellow) and great collaboration with
@AndreiGoga_SF
. Below is a thread summarizing our work if you're interested in learning more.
I echo the voices of other Iranians(-Americans) here. Again, discriminating against an entire nation based on poorly conceived notions of security. Both human health and science are borderless...
Genomic interval tools, like bedtools and bedops, have formed the backbone of our analytical pipelines for many years now.
@noamteyssier
has now developed a new package called 'gia' that is order of magnitude faster! Check out our preprint and take gia for a spin.
I'm very excited to release this project I've been working on for about a year or so now!
gia is a high-performance genome interval arithmetic toolkit, written in
#rustlang
🦀, with significant performance increases (2x-20x) over
#bedtools
and
#bedops
.
Does anyone keep track of how many international students, postdocs, and scholars are waiting for their (re)entry visas in the US? It seems like a sort of things us academics should pay more attention to.
In the mist of everything that is happening, I wanted to take a moment and highlight our most recent paper (thread):
RBMS1 suppresses colon cancer metastasis through targeted stabilization of its mRNA regulon.
An opinion I wrote for The Scientist. Please help disseminate this and if you have ideas and platforms that could help deal with this crisis, please DM me.
I have been thinking about the best approaches for building predictive models in liquid biopsies for many years now! Orion, which was built by the
@exaibio
team with input from our advisors
@ElementoLab
and
@james_y_zou
is the culmination of that effort.
4/n. I did not leave the US for the entirety of grad school (+1 year), until I became a permanent resident. During this time, I saw my parents exactly 0 times. I missed countless birthdays and weddings. I lost multiple relatives without getting to say goodbye.
Y'all, check out our latest preprint on determinants of small RNA release. We used machine learning to show much of the information is encoded in the primary RNA sequence and can be leveraged to predict which small RNAs are effectively secreted. See this thread from
@BaharZirak
Super excited to share the results of our highly collaborative project co-led by
@MNaghipourfar
, Ali Saberi,
@DelaramPB
, Amirhossein Zarezadeh and supervised by my incredible mentor
@genophoria
.
Check out this new preprint/white paper from our friends at Entwine bio together with
@vram142
and
@ZaroLab
. We and others have long been interested in sequence-to-function modeling in RNA, especially as it comes to splicing.
I am reviving this thread to announce the final publication of this preprint. Almost a full year after the preprint was first submitted! A clear example of how biorxiv expedites dissemination of science.
I came to this country 15 years ago, and it is unbelievable to me that we haven't managed to improve this system even an iota in these years. It is not just a cruel system, it is also self-defeating. Please read this thread and tag your senators.
@AlexPadilla4CA
@SenFeinstein
I’m quite used to the cruelty students can face when they apply for a US visa but this one broke me. We offered admission to a stellar, talented & hardworking student. After months of work and hundreds of dollars, an embassy officer saw him for 5 mins & said no. why? …
7/n. But even now the scars are there... almost every Iranian student I have talked to shares a common nightmare: you suddenly wake up in Iran and you have no idea what you are doing there, how you got there, where your documents are, and how you can get back.
8/n. This universal nightmare binds us all. It is too late for my generation... we hollowed out our relationships and drastically reshaped our lives for a higher calling. I have personally achieved the goals set by younger self, but there r days that I wonder if it was worth it.
I'm super happy that the UCSF magazine has covered this story.
@FaranakFattahi
's work is nothing short of inspirational.
Cracking the Coronavirus Gender Mystery
3300 subjects across 8 cancers; overall stage I sensitivity of 87% at 95% specificity in the held-out test set. 88% tissue-of-origin accuracy! Watching the
@exaibio
team do their magic has truly been a privilege.
Exai announced compelling new data at
#ASCO23
, demonstrating strong performance in stage I detection of multiple cancers including breast and prostate cancers, overcoming early-stage detection limitations of other blood-based approaches.
☀️It’s a great week at Arc as we welcome our new Core Investigator
@genophoria
and his lab, and our first Science Fellow
@zhou_jingtian
! We’re proud to add these talented minds to our ranks, bringing with them a multidisciplinary approach to human disease research. Welcome, all!
Another movement from
@khorms57
's magnum opus in our lab. A rigorous attempt at systematically annotating functional RNA structural switches that show conformation-dependent regulatory functions 👇
RNA folding affects gene expression, but this link is not well explored in Eukaryotes. We researched RNA structural switches and discovered hundreds of them in the human transcriptome. We even visualized some of their 3D folds with CryoEM. Thread below:
5/n. My mom went through a cancer scare without me by her side (I am a single child). Given the visa restrictions and the expenses, it was difficult if not impossible for my parents to visit either (and they never did).
10/n. People showing up to airports to protest, and lawyers gathering to help was nothing short of miraculous. However, as we have moved on to other daily outrages, and there is no shortage of them, we risk leaving behind students and scholars who are devastated by this decision.
Trump had requested ~20% cuts to NIH year after year! You can’t will scientific progress into existence... it needs sustained prioritization and investment! Let’s not forget that when this is all over...
8. PhD mentors are for life. They will always be your mentor and your best advocate. My advisors are still my go to guys when I have to make tough decisions. And I believe you ask them for letters till the end of time.
6/n. Both my parents and my in-laws and countless friends missed our wedding. I took this emotional isolation in stride and in some sense I even got used to it. By the time restrictions were lifted, I had been isolated for years. Years have passed...
We started this
#RNAyear
by saying goodbye to two longtime amazing postdocs:
@a_navickas
who is off to Institut Curie to start his own "RNA in cancer" lab! And
@MKarimzade
who is joining
@exaibio
to build ML models for disease detection. Certainly a bittersweet moment for our lab
9/n. I say all this not because I think you don't agree that this is bad policy. When we started the "academics against the travel ban" (), we collected close to 50k signatures in a short span of time. It was both heartwarming and reassuring.
Please take a few minutes out of your busy day and read our preprint with the
@FaranakFattahi
lab. Hi-quality in vitro drug screen, supplemented by in silico GCNN screens, followed by targeted validation and clinical confirmation.
Super exciting news! I am happy that our oncRNAs are living their best lives at
@exaibio
! I am also excited for this strong commitment to breast cancer. Breast tumors don't shed a lot of DNA and DNA-based tests show poor performance at low burdens. OncRNAs will change that...
Based on initial positive data, Exai is proud to announce expanded participation in the I-SPY 2 Trial to advance our novel RNA-based liquid biopsy platform for breast cancer. ’s-Novel-RNA-based-Liquid-Biopsy-Platform-in-Breast-Cancer
Shout out to
@sinabooeshaghi
for showing up to our systems biology class (via zoom) and giving one of the best presentations of the whole course! Also I’m told he has some exciting stuff brewing... so, follow him and stay tuned!
I am devastated by this news. She was a fantastic mentor... so kind and generous with her time and resources. A great loss for us at UCSF and the entire cancer research community. She will be missed.
Zena Werb
Today we have lost one of UCSF’s most beloved faculty. Zena Werb died suddenly this morning. A member and VC of the Department of Anatomy, for almost 40 years, Zena was an outstanding scientist. She was one of the world’s leading experts on ECM on cancer development
2/n. A bit of background. I was born in Iran. My visa application for grad school, for which I had to travel twice to Turkey, took close to 4 months to process. I had a single-entry visa, which was valid only for 3 months, meaning when I entered the US, I couldn't leave again.
3/n. I came to the US in 2006 under NSEERS (what is now known as muslim registry). I was questioned once before getting on the plane to Newark and once after. We were checked up on regularly by agents who would show up regularly on campus.
The Bioinformatics team led by Alex Dobin within the Computational Technology Center at the Arc Institute is seeking a Senior Scientist. Come join us and tackle some of the most fundamental problems in the intersection of biology and computation.
UCSF researchers discover new kind of RNA molecule that drives the spread of breast cancer. The discovery may one day lead to non-invasive cancer diagnostics.
@dsboothacosta
Funding for grad students (stipend+tuition+research) should be separated from our grants and be b/w the program & students. Then students can join the labs that best suit them, vs just well-funded labs. It also clarifies our roles as mentors/advisers & not bosses.
Please check out our latest preprint, together with
@FKHM
, and
@halfacrocodile
, along with a detailed Tweetorial from Matvei. Learn about post-transcriptional regulatory modules and how we went about identifying them:
Can’t wait to share the splendid results of the collaboration between the incredible labs of
@genophoria
,
@FKHM
, and
@halfacrocodile
! Tl;dr: we've explored the code on how RNA-binding proteins team up to regulate their target RNAs. Read on for more! (1/15)
It was a lot of fun talking to Frontier Science about my thoughts on multidisciplinary research at the intersection of computational and experimental biology, our work in this space, and our path towards translation.
Frontier Science 🧫 - Modeling Oncological Systems 🧬 w/ Hani Goodarzi - Associate Professor
@UCSF
Learn more about Goodarzi's (
@genophoria
) work & the below...
Grateful to be working with these amazing postdocs. From right, Dr Heather Karner, Dr Sahar Tavakoli, Dr Hossein Asfharian, and Dr Albertas Navickas. Missing a few of our postdocs today.
For all the RNA peeps out there attending
#RNA2020
online. If you are interested in the role of regulatory RNA structural elements in RNA splicing and disease, please check out my talk (15). Happy to answer questions here or any other platform.
4. 5 yrs is a long time... don't think you can just work through it if there are concerns.
5. Don't join a lab to learn a technique; join a lab to learn the fundamentals of how good science is done.
The number of emails I send daily has been growing exponentially... and I have noticed that I am writing shorter emails, often devoid of pleasantries (the PI syndrome!). I think we need a GPT-3 plugin that makes our emails more polite and courteous.
I just came back from my 4th study section and I wanted to share some thoughts. I have served 2x on BDMA (computational) and 2x on MGB (experimental). These are my thoughts from this small n (thread) 👇
Late better than never! We celebrated PAW with our amazing postdocs working on site. With
@a_navickas
& Heather who basically run the lab, and welcoming Benedict and Siyu who just joined recently. Looking forward to next year and all the awesome science they are doing!
Celebrating another year with our awesome postdocs. My life would be insanely more difficult without them! From right: Drs. Fish, Navickas, Asgharian, Baygi.
#ucsfNPAW
#ucsfpostdocs
#NPAW
#NPAW2019
Early access to a perspective by Peter Walter and
@MullinsLab
"From Symbiont to Parasite: Evolution of For-Profit Science Publishing". p7: "what remains puzzling is the lack of more widespread anger in our communities regarding the degree of exploitation"
Had a blast in Bergen! Come for the views, stay for the science. Thank you
@Halberglab1
for the invite. Really, A gem of a place! Extra points for the pride celebration!
We made enteric ganglioids from hPSCs, showed they’re similar to human ENS, used them to find neuromodulators that regulate GI motility and demonstrated their engraftment potential in mouse colon. Check out our new preprint by
@homamajd
et. al.
As our NextGen grant for transformative cancer research comes to an end, I had an interview with
@AACR
on the impact of this grant on our research. Spoiler alert: we may have not transformed cancer res, but certainly tried... and the night is still young.
@s_tavazoie
@PNASNews
I found this sketch from 10 years ago when
@s_tavazoie
first told me about (a version of) this idea! Few in this day and age show this level of stick-to-itiveness! Congratulations Panos and the
@s_tavazoie
lab.
Super excited to see
@FaranakFattahi
on this list...showing the rest of us how it's done!
Also happy to see the strong showing by
@UCSF
. Congratulations to all the awardees.
This morning, I've written and deleted multiple tweets b/c they fail to convey the depth of my frustration! It's one of those weeks that needs an entire book to rant. I'm just so disappointed in everyone and all things! I could use a pep talk from my idealistic 20yr old self.
9. Talk to everyone in the lab. If you can, find those who have left. Learn to read between the lines. But also, understand that it takes two to tango. Someone's heaven can be another's hell.
@eperlste
This reminds me of a story... a friend of ours was asked, a long time ago, how he saw the brain drain problem in Iran; he wisely said: "it can't be that bad, because I am still here"!
Core Investigators are pivotal to Arc’s mission – they’re scientific leaders who are empowered to tackle curiosity driven research. Today, we’re proud to announce a new call for applications in partnership with
@StanfordDBDS
.
Come join us on the sunny side of SF! We promise excellent mentorship, cool science and technology, and ever-flowing coffee (and Covid-permitting Friday lab lunches)!
Please RT! Seeking RAs to support computational & molecular projects in our lab, including collabs with the inimitable
@genophoria
=). A great opp. for recent grads looking for postbac experience. Links below:
Check out our review on the regulatory pathways of translational control that are hijacked by cancer cells. The credit largely goes to
@schen_sc
and
@a_navickas
for putting this together over the holidays!
Thrilled to share our latest review on translational adaptation in breast cancer metastasis and the promising therapeutic opportunities it unveils! Immense thanks to
@genophoria
and
@a_navickas
!
Between GPT-4 and Midjourny-5, I am hit hard by technology envy. Like, how did I spend 4 decades of my life without access to these tools? Last time I felt this way was when smart phones arrived.
2. There aren't universally good/bad PIs; like any other relationship, chemistry matters and it goes both ways.
3. The culture of the lab is really important; make sure you are in a healthy drama-free environment.