Jeremy Simon
@jeremymsimon.bsky.social
Senior Research Scientist @dfcidatascience @harvardchanschool
Cancer genomics, bioinformatics, chromatin & epigenetics, single-cell, plus occasional dog, food, and travel photos
AKA @jeremy_m_simon, @[email protected] elsewhere
Cancer genomics, bioinformatics, chromatin & epigenetics, single-cell, plus occasional dog, food, and travel photos
AKA @jeremy_m_simon, @[email protected] elsewhere
Reposted by Jeremy Simon
We are thrilled to announce the first official release (v0.1.8) of #𝗯𝗲𝗱𝗱𝗲𝗿, the successor to one of our flagship tool, #𝗯𝗲𝗱𝘁𝗼𝗼𝗹𝘀! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen.
1/n
1/n
Intro to Bedder – The Quinlan Lab
quinlanlab.org
December 2, 2025 at 2:28 AM
Reposted by Jeremy Simon
📢 We are taking applications for our Postdoctoral Fellows Program at Harvard/DFCI!
🔹Join a research group in our department
🔹Co-mentoring opportunities with 2+ faculty
🔹Collaborate with investigators beyond our department
🔹Salary starts at $75K
Apply here: t.co/B7SLZzQFKu
🔹Join a research group in our department
🔹Co-mentoring opportunities with 2+ faculty
🔹Collaborate with investigators beyond our department
🔹Salary starts at $75K
Apply here: t.co/B7SLZzQFKu
https://ds.dfci.harvard.edu/postdocs/
t.co
December 1, 2025 at 6:59 PM
📢 We are taking applications for our Postdoctoral Fellows Program at Harvard/DFCI!
🔹Join a research group in our department
🔹Co-mentoring opportunities with 2+ faculty
🔹Collaborate with investigators beyond our department
🔹Salary starts at $75K
Apply here: t.co/B7SLZzQFKu
🔹Join a research group in our department
🔹Co-mentoring opportunities with 2+ faculty
🔹Collaborate with investigators beyond our department
🔹Salary starts at $75K
Apply here: t.co/B7SLZzQFKu
Reposted by Jeremy Simon
Many people hours, calls and messages later: OSTA is now “in (pre)print”, though the real thing lives at bioconductor.org/books/OSTA.
Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions).
It’s been a joy working with you @estellayixingdong.bsky.social!
Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions).
It’s been a joy working with you @estellayixingdong.bsky.social!
November 21, 2025 at 5:31 PM
Many people hours, calls and messages later: OSTA is now “in (pre)print”, though the real thing lives at bioconductor.org/books/OSTA.
Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions).
It’s been a joy working with you @estellayixingdong.bsky.social!
Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions).
It’s been a joy working with you @estellayixingdong.bsky.social!
Despite city lights and buildings, clearest view of the Aurora from Somerville I've ever seen!
November 12, 2025 at 2:57 AM
Despite city lights and buildings, clearest view of the Aurora from Somerville I've ever seen!
Reposted by Jeremy Simon
Excited to share our new preprint on molecular gene x treatment interactions led by Jordan Valone, Brandon Le, and @nanamatoba.bsky.social. www.medrxiv.org/content/10.1.... Here, we tried to further develop the "pharmacogenomics in a dish" approach for psychiatry.
Assessing molecular gene by treatment interactions using a population of neural progenitors exposed to valproic acid and lithium
Gene by treatment (GxT) interactions likely contribute to variability in clinical response, but are difficult to identify in population studies. Here, we applied psychiatric and neurological disorder ...
www.medrxiv.org
October 27, 2025 at 3:21 PM
Excited to share our new preprint on molecular gene x treatment interactions led by Jordan Valone, Brandon Le, and @nanamatoba.bsky.social. www.medrxiv.org/content/10.1.... Here, we tried to further develop the "pharmacogenomics in a dish" approach for psychiatry.
Reposted by Jeremy Simon
PSA: Many of you may have noticed a website floating around called formatmypaper(dot)com. People rightly noted something was fishy. I dig into what happened here:
open.substack.com/pub/ubadah/p...
open.substack.com/pub/ubadah/p...
Beware giving this site your unpublished data
Users noticed the website had fake testimonials and a domain name registered seemingly overnight.
open.substack.com
October 23, 2025 at 2:07 PM
PSA: Many of you may have noticed a website floating around called formatmypaper(dot)com. People rightly noted something was fishy. I dig into what happened here:
open.substack.com/pub/ubadah/p...
open.substack.com/pub/ubadah/p...
Reposted by Jeremy Simon
Online now: Pan-cancer spatial characterization of key immune biomarkers in the tumor microenvironment
Pan-cancer spatial characterization of key immune biomarkers in the tumor microenvironment
Lindsay et al. present a pan-cancer spatial characterization of the tumor immune microenvironment using multiplex immunofluorescence data from 2,019 tumors. Spatial factors conserved across cancer types are identified that correlate with genomics and patient outcomes. A spatially resolved single-cell database comprising 39.4 million cells accompanies the findings.
dlvr.it
October 15, 2025 at 7:19 PM
Online now: Pan-cancer spatial characterization of key immune biomarkers in the tumor microenvironment
Reposted by Jeremy Simon
Today at #ASHG25 I will talk about the work of a talented graduate student Dev Raj Bhattarai on cell type-specific isoform expression in Alzheimer's disease at the @nanoporetech.com Education Session (12pm Rm 153). Dev will also present his work today at poster 9228T.
October 16, 2025 at 12:30 PM
Today at #ASHG25 I will talk about the work of a talented graduate student Dev Raj Bhattarai on cell type-specific isoform expression in Alzheimer's disease at the @nanoporetech.com Education Session (12pm Rm 153). Dev will also present his work today at poster 9228T.
Incredible opportunity to go train with the Patro lab @umdscience.bsky.social and develop new genomic methods!
Hi bioinformatics, genomics and CS friends! Please help me spread the word. I'm hiring a postdoc! Come work on cutting edge method development in algorithmic genomics with me and my group at @umdscience.bsky.social! 🖥️🧬
And it's posted! If you're interested and eligible, please consider applying through the UMD portal: umd.wd1.myworkdayjobs.com/en-US/UMCP/j....
If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!
If you're a PI working in algorithmic genomics (& you can recommend my lab to your top graduating students ;P), please let them know!
October 10, 2025 at 1:58 PM
Incredible opportunity to go train with the Patro lab @umdscience.bsky.social and develop new genomic methods!
Reposted by Jeremy Simon
We’re offering free vaccine clinics in Boston. Vaccines are safe, effective, and protect against serious illness. Getting vaccinated keeps you healthy and helps protect your family, friends, and community.
Learn more at boston.gov/vaccine-clinics.
Learn more at boston.gov/vaccine-clinics.
September 24, 2025 at 7:53 PM
We’re offering free vaccine clinics in Boston. Vaccines are safe, effective, and protect against serious illness. Getting vaccinated keeps you healthy and helps protect your family, friends, and community.
Learn more at boston.gov/vaccine-clinics.
Learn more at boston.gov/vaccine-clinics.
Reposted by Jeremy Simon
🧬🖥️ Thrilled that our paper "Tree-based differential testing using inferential uncertainty for RNA-seq" genome.cshlp.org/content/earl..., led by @noorpratap.bsky.social, & in collab with @mikelove.bsky.social, @fennecpaaaw.bsky.social and Jason Fan is now accepted at @genomeresearch.bsky.social. 1/4
Tree-based differential testing using inferential uncertainty for RNA-seq
An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms
genome.cshlp.org
August 21, 2025 at 7:24 PM
🧬🖥️ Thrilled that our paper "Tree-based differential testing using inferential uncertainty for RNA-seq" genome.cshlp.org/content/earl..., led by @noorpratap.bsky.social, & in collab with @mikelove.bsky.social, @fennecpaaaw.bsky.social and Jason Fan is now accepted at @genomeresearch.bsky.social. 1/4
Reposted by Jeremy Simon
Ever wondered what else SETD2 does beyond transcription? 🧬
Check out our new @natcellbio.nature.com study.
Awesome work from Abid Khan in the lab SETD2 moonlights during mitosis to keep the genome safe from chaos.showing how SETD2 moonlights to safeguard the genome during cell division.
Check out our new @natcellbio.nature.com study.
Awesome work from Abid Khan in the lab SETD2 moonlights during mitosis to keep the genome safe from chaos.showing how SETD2 moonlights to safeguard the genome during cell division.
August 11, 2025 at 12:26 PM
Ever wondered what else SETD2 does beyond transcription? 🧬
Check out our new @natcellbio.nature.com study.
Awesome work from Abid Khan in the lab SETD2 moonlights during mitosis to keep the genome safe from chaos.showing how SETD2 moonlights to safeguard the genome during cell division.
Check out our new @natcellbio.nature.com study.
Awesome work from Abid Khan in the lab SETD2 moonlights during mitosis to keep the genome safe from chaos.showing how SETD2 moonlights to safeguard the genome during cell division.
Reposted by Jeremy Simon
A lovely meditation on community.
(Go there, the food is really good!)
(Go there, the food is really good!)
Essay: As a Somerville resident, the Palestinian-owned Yafa Bakery & Café quickly became my “third space,” writes Lydia Begag. I’d find myself wandering there for a cup of chai or piece of baklawa, but it was the owner, Abdulla Awad, who really brought me back.
A Palestinian bakery in Somerville that always feels like home
What continues to make Yafa so special is that what might feel sacred elsewhere is the standard here, writes Lydia Begag. Over time, I started paying attention not just to how Abdulla’s practice of ‘a...
www.wbur.org
August 8, 2025 at 12:24 PM
A lovely meditation on community.
(Go there, the food is really good!)
(Go there, the food is really good!)
This one hurts, truly a legend
Grammy-winning bandleader and pianist Eddie Palmieri, whose pounding rhythms forged a new style for Latin music, has died.
Eddie Palmieri, a trailblazer in Latin music, has died at age 88
The bandleader and pianist was one of the leading Latin musicians of his generation. He won multiple Grammys and was recognized as an NEA Jazz Master.
n.pr
August 7, 2025 at 11:43 AM
This one hurts, truly a legend
Reposted by Jeremy Simon
Files referring to coordinates without genome info should be gone
we should always include genome digests
we should always include genome digests
August 5, 2025 at 9:12 PM
Files referring to coordinates without genome info should be gone
we should always include genome digests
we should always include genome digests
Was out of town when this first dropped, so following up now to call attention to our *extensive* github repo consisting of 7 quarto books (written by Chloe Tu and me) that contain all code to produce the figures shown in this paper:
github.com/jeremymsimon...
github.com/jeremymsimon...
July 18, 2025 at 8:57 PM
Was out of town when this first dropped, so following up now to call attention to our *extensive* github repo consisting of 7 quarto books (written by Chloe Tu and me) that contain all code to produce the figures shown in this paper:
github.com/jeremymsimon...
github.com/jeremymsimon...
Reposted by Jeremy Simon
Very excited this is finally published in the ISMB proceedings. This was @noorpratap.bsky.social's last conference-related paper in my lab (but look out for a new Genome Research paper soon), & a monumental effort. It's already integrated into simpleaf. Noor will be presenting it at ISMB next week!
July 18, 2025 at 11:23 AM
Very excited this is finally published in the ISMB proceedings. This was @noorpratap.bsky.social's last conference-related paper in my lab (but look out for a new Genome Research paper soon), & a monumental effort. It's already integrated into simpleaf. Noor will be presenting it at ISMB next week!
Reposted by Jeremy Simon
Now online! A multi-adjuvant personal neoantigen vaccine generates potent immunity in melanoma
A multi-adjuvant personal neoantigen vaccine generates potent immunity in melanoma
A personalized neoantigen peptide vaccine formulated with Montanide plus poly-ICLC and administered with local ipilimumab plus systemic nivolumab induces robust neoepitope-specific T cell responses and reshapes the T cell repertoire in blood and tumor.
dlvr.it
July 10, 2025 at 2:59 PM
Now online! A multi-adjuvant personal neoantigen vaccine generates potent immunity in melanoma
Reposted by Jeremy Simon
In a study published in @cellpress.bsky.social, @danafarber.bsky.social researchers showed that a modified NeoVax cancer vaccine triggered strong immune responses in melanoma.
Read more: bit.ly/44nz5Wp
Read more: bit.ly/44nz5Wp
July 10, 2025 at 5:15 PM
In a study published in @cellpress.bsky.social, @danafarber.bsky.social researchers showed that a modified NeoVax cancer vaccine triggered strong immune responses in melanoma.
Read more: bit.ly/44nz5Wp
Read more: bit.ly/44nz5Wp
Reposted by Jeremy Simon
The more potent and bespoke immunotherapy vs cancer, the better. Today's example is a neoantigen vaccine vs melanoma
cell.com/cell/fulltex...
cell.com/cell/fulltex...
A multi-adjuvant personal neoantigen vaccine generates potent immunity in melanoma
A personalized neoantigen peptide vaccine formulated with Montanide plus poly-ICLC
and administered with local ipilimumab plus systemic nivolumab induces robust neoepitope-specific
T cell responses an...
cell.com
July 10, 2025 at 3:17 PM
The more potent and bespoke immunotherapy vs cancer, the better. Today's example is a neoantigen vaccine vs melanoma
cell.com/cell/fulltex...
cell.com/cell/fulltex...
Our new study investigating combination neoantigen vaccine plus montanide and Ipi in melanoma is now online in @cellpress.bsky.social !
A multi-adjuvant personal neoantigen vaccine generates potent immunity in melanoma: www.cell.com/cell/fulltex...
A multi-adjuvant personal neoantigen vaccine generates potent immunity in melanoma: www.cell.com/cell/fulltex...
A multi-adjuvant personal neoantigen vaccine generates potent immunity in melanoma
A personalized neoantigen peptide vaccine formulated with Montanide plus poly-ICLC
and administered with local ipilimumab plus systemic nivolumab induces robust neoepitope-specific
T cell responses an...
www.cell.com
July 10, 2025 at 2:56 PM
Our new study investigating combination neoantigen vaccine plus montanide and Ipi in melanoma is now online in @cellpress.bsky.social !
A multi-adjuvant personal neoantigen vaccine generates potent immunity in melanoma: www.cell.com/cell/fulltex...
A multi-adjuvant personal neoantigen vaccine generates potent immunity in melanoma: www.cell.com/cell/fulltex...
Reposted by Jeremy Simon
This is the message. Everyone in the US should have access to life-saving treatments in their state. The value is immense, and we would be throwing away a half century of investment to lose these centers and research hospitals. The risk of losing these is real as we look to a 2026 budget.
Thank you for writing this and standing up for science, Katie.
"Hospitals like the Cleveland Clinic, Cincinnati Children’s, and Children’s Hospital in Columbus rely on NIH funding to run clinical trials, bringing cutting-edge treatments to Ohio patients before they're widely available."
"Hospitals like the Cleveland Clinic, Cincinnati Children’s, and Children’s Hospital in Columbus rely on NIH funding to run clinical trials, bringing cutting-edge treatments to Ohio patients before they're widely available."
Stand up for National Institutes of Health and National Science Foundation | Opinion
Guest essayist Katie Digianantonio urges federal leaders to support funding for the National Institutes of Health and National Science Foundation.
www.indeonline.com
July 6, 2025 at 9:46 AM
This is the message. Everyone in the US should have access to life-saving treatments in their state. The value is immense, and we would be throwing away a half century of investment to lose these centers and research hospitals. The risk of losing these is real as we look to a 2026 budget.
From @kimrynrathmell.bsky.social
Much of my work since joining @danafarber.bsky.social has been focused on this exciting field of personalized immunotherapy and its potential to treat many forms of cancer
Stay tuned as one of these newest stories is in press!
Much of my work since joining @danafarber.bsky.social has been focused on this exciting field of personalized immunotherapy and its potential to treat many forms of cancer
Stay tuned as one of these newest stories is in press!
Yes. The time is now. Vaccines to treat and prevent cancer.
www.jci.org/articles/vie...
www.jci.org/articles/vie...
July 1, 2025 at 6:50 PM
From @kimrynrathmell.bsky.social
Much of my work since joining @danafarber.bsky.social has been focused on this exciting field of personalized immunotherapy and its potential to treat many forms of cancer
Stay tuned as one of these newest stories is in press!
Much of my work since joining @danafarber.bsky.social has been focused on this exciting field of personalized immunotherapy and its potential to treat many forms of cancer
Stay tuned as one of these newest stories is in press!
Reposted by Jeremy Simon
🚀 We are thrilled to introduce QCatch — a fast, command-line QC reporting tool built for alevin-fry & simpleaf single-cell data! Led by @ygao61.bsky.social & in collaboration with Dongze He 🧬🖥️ . The Preprint 📖 is available at bit.ly/4neSznl. Read more below: 1/3
GitHub - COMBINE-lab/QCatch: Quality Control downstream of alevin-fry / simpleaf
Quality Control downstream of alevin-fry / simpleaf - COMBINE-lab/QCatch
github.com
June 23, 2025 at 12:27 PM
🚀 We are thrilled to introduce QCatch — a fast, command-line QC reporting tool built for alevin-fry & simpleaf single-cell data! Led by @ygao61.bsky.social & in collaboration with Dongze He 🧬🖥️ . The Preprint 📖 is available at bit.ly/4neSznl. Read more below: 1/3
A very large proportion of these are HIV related. And many terminated on this list relate to cancer, Alzheimer's, diabetes, etc- despite what some politicians may be saying
Wondering if your grant will be reinstated from Monday's ruling? Check here.
Plaintiffs have uploaded a list of 848 (of the ~2400 total terminated) they say are covered because they're to institutions in the states aforementioned or a part of APHA/UAW.
The judge must approve the list first.
Plaintiffs have uploaded a list of 848 (of the ~2400 total terminated) they say are covered because they're to institutions in the states aforementioned or a part of APHA/UAW.
The judge must approve the list first.
storage.courtlistener.com
June 18, 2025 at 9:41 PM
A very large proportion of these are HIV related. And many terminated on this list relate to cancer, Alzheimer's, diabetes, etc- despite what some politicians may be saying