Cassie Manrique

okay y'all, i'm compiling a list of suggested readings for students in my Biology, Society and Culture class to use as a starting point for choosing papers for our weekly discussions. i obvs have a long list, but always looking for more suggestions!

here's the weeks i need suggestions for:

1/ No, you do not always need single-cell RNA-seq.
Here's why bulk RNA-seq might still be the smarter move for your experiment.

Four images of a tabby cat named Freckles. In the top left, she is lying down on a grey pillow. She is quite small. In the top right, she is sitting on the kitchen floor with her mouth open like she is yelling. In the bottom left, she is grown up and wearing a strawberry collar. Cassie, a brunette woman with glasses, is peering over from behind Freckles. In the bottom right, Freckles is lying down with a paw out, looking at the camera.

Happy Gotcha Day to my best feline friend, Freckles. 🍓 When I adopted her 4 years ago, the closest she would get is sitting on a designated pillow on the couch. Now, she’s my cuddle buddy; most nights she’s asleep on top of my head on “our” pillow, 💕 But she still yells at me if I’m home too late 😆

Freckles has chosen to demonstrate a left-sided sleeping position! (She often alternates between sides)

Cannot emphasize enough that, if you dislike doing the things academics do (reading, writing, developing and expressing opinions about things you've read) enough to try to make a chatbot do them for you, there are lots of actual humans who would be happy to take that unpleasant job off your hands

Cassie, a short brunette, is wearing a bright pink linen dress with her hair pulled back in a clip. She is wearing glasses and a lanyard with her name. She is smiling and standing in front of a pixelated scientific poster with the title “Multi-Omic Analysis to Identify Barriers to hPSC-derived Skeletal Muscle Maturation”. The title is white font on a sky blue background.

A photograph of the ocean of El Escambrón beach in San Juan, Puerto Rico. The sky is partially cloudy and light blue. The ocean is a blue-green color with a few peaceful waves. In the background are palm trees.

A photograph over a cliff near the fortress Bastión de San Sebastian in San Juan, Puerto Rico. The grass of the cliff is a vibrant green with dark green foliage. The sky is clear and a pale blue. The ocean is calm and a medium blue color. The edge of the brick fortress is barely visible along the right edge of the photograph.

So thankful to have spent the past week in Puerto Rico at #2025ICDB #2025SDB! 🌴 This was my first conference outside of NYC, and it was great to hear from so many renowned developmental biologists and receive feedback on my research.

Congrats!!! 🔥

PSA: around 5-8% of the population has a color vision impairment for red/green.

Many talks at #2025ICDB still use red-green LUTs on slides that are not accessible to everyone.

Changing to more accessible colors is doable and easy.

We can do better.
#devbio
#ICDB2025 #WeTheColorBlind

A selfie of Isabelle and Cassie, two young adult women, sitting in front of steps in Old San Juan. Both are smiling at the camera.

So excited to be in Puerto Rico for #2025ICDB #2025SDB! Come visit me at my poster (#C36) Saturday to hear about multi-omic sequencing to mature hPSC-derived skeletal muscle, and see my lab mate and friend Isabelle’s talk (session 4.1) on lamin B loss in muscle nuclei! 💪

Freckles, a brown tabby cat, is standing on a pink bedspread with her front paws on a sealed early voting ballot envelope. Her mouth is open, like she is talking to the screen. She is also wearing a pink strawberry collar charm.

Freckles would like to remind everyone to VOTE in your local elections! 🗳️ They might not be as publicized as federal elections, but local and state elections influence your schools, taxes, infrastructure, and more.

My ongoing request:

If your NSF or NIH grant was terminated--whether at Harvard or elsewhere--please report it here.

NSF: grant-watch.us/submit-nsf.h...

NIH: grant-watch.us/submit-nih.h...

Our trackers are actively used in lawsuits and are often the only record that terminations ever occurred.

I’m glad someone has finally quantified this! I was looking at some specific SRA ATAC data and spent a while thinking something was wrong with my processing or pipeline when I kept getting really poor QC results (duplication rates, non-mitochondrial reads, etc). I was pretty frustrated for a bit 😅

PSA: We just finished processing nearly all public ATAC-seq datasets from SRA (about 22,000 datasets). (Not?) Surprisingly, we had to throw-out nearly ~50% because they were low-quality (low signal-to-noise, duplicate rate, etc.). Check quality before analysis (TSS-enrichment is not sufficient!).

Top 5 is hard, but “Tango Till They’re Sore” is certainly my number one, closely followed by “Cemetery Polka”

Not a playhouse for the children

A schematic of the nucleosome, but the core histone proteins are replaced with four tabby cats in circular formation. The histone tails are represented by lines coming out of each histone or tabby cat, with letters indicating the amino acids and their modifications.

The basic subunit of chromatin, the nucleosome, consists of a segment of DNA wrapped around eight HISStone proteins 🐱

Which FDA-approved vaccines had randomized, placebo-controlled trials?

ALL OF THEM.

Polio?
Measles, mumps, rubella?
Haemophilus influenzae B?
Diphtheria, tetanus, pertussis?
Meningococcus?
Varicella?
Pneumococcus?
Rotavirus?
RSV?
Hepatitis B?
Influenza?
HPV?
COVID-19?
Shingles?

YEP.

A thread🧵
1/

The average American has 3 friends

An important point getting overlooked:

When NIH cancels "diversity" grants (e.g., diversity supplements, Fs, Ks, etc), they aren't canceling the grants based on *what* the grant studies.

They're cancelling them based on *who* is doing the research. And that disallowed "who" is anyone not white.

KEYTRUDA IS AN IMMUNOTHERAPY KEYTRUDA® Need help with medication costs? Visit keytruda.com or call 855-257-3932 Keytruda commercial

Live thread on @60minutes.bsky.social coverage of #NIH.

First, it’s ironic that one of the first commercials was for Keytruda, the cancer therapy developed with heavy NIH investment over decades.

Without NIH, there would be no Keytruda. 1/ 🧵

I'm sorry, but rich, privileged women going on a space fieldtrip is not inspiring. The people are who ARE inspiring are the hardworking women working in STEM. You know, the ones who are at risk of losing their jobs and grants. #SaveOurScience

Plot of chromosome alignments from recent paper

Does anyone know what software/packages generate these nice color-coded visualizations of structural rearrangements (this one from Jeong et al. 2025 Nature Genetics)?

Massive, Unarchivable Datasets of Cancer, Covid, and Alzheimer's Research Could Be Lost Forever Days before Robert F. Kennedy Jr. announced that 10,000 HHS staffers would lose their jobs, a message appeared on NIH research repository sites saying they were "under review."

Petabytes of critical government research that is marked for possible deletion cannot be archived because of technical and legal restrictions, meaning it is very likely to be lost forever:

www.404media.co/nih-archives...

NIH PC members, We are extremely disappointed to hear of drastic cuts across NIH. It is unfortunate that the Office of Pain Policy and Planning did not survive the cuts. NINDS will need some time to recover and plans to continue to support the broad NIH pain research agenda over time. Linda, Laura, Jackie, Leah, Janelle, Giulia, Jess, Anthony J, and Natasha from OPPP were selected for the RIF,. They have created an amazing team, each of whom will be sorely missed. The remaining office members will be settled into new offices and continue to support pain research activities as best they can. I will retire at the end of the month and would have been saying goodbye regardless of the RIF. For others in our team, the loss is devastating. The NIH PC has been an incredibly supportive and valuable resource for the pain research agenda at NIH. It was an amazing journey to have watched the expansion of the PC, the incredible commitment and creativity of the members, and the progress the consortium made in enhancing and integrating pain research across NIH over the years. Nice work everyone- carry on. It is always difficult to say goodbye, but especially under such circumstances. Linda

All staff at the NIH Office of Pain Policy and Planning were let go due to today's cuts.

This devastating loss will have significant negative impacts on the health of millions.

Pain is the leading cause of disability and the top reason for seeking medical care.

we need a totally revised constitution and I think we should call it the Consti2tion

I'm not a "we should teach every kid to code" person but dear lord can we at least teach basic computational concepts or something, this is *embarrassing*

My F31 diversity keeps getting unassigned and reassigned and unassigned to study section… all this limbo is so nerve wracking (especially for young scientists whose first experience with funding submissions and the NIH is *this*).

TO: <ALL STAFF>

Please respond to this email confirming that I am cool and funny. Failure to do so will be taken as confirmation of the same.

a poster that says if life gives you lemon make lemonade on it ALT: a poster that says if life gives you lemon make lemonade on it

ATTENTION (PLEASE SHARE)

If anyone has or knows of any positions that might be appropriate for the NIH staff members who were terminated, please post the information in this thread.

There are lots of talented and accomplished people who may be looking for new opportunities.

Happy International Day of Women in Science. The National Science Foundation’s list of flagged words includes both “Women” and “Female.”