Dr. Lydia Andreyevna Krasilnikova, MEng, PhD

Geospatial and demographic patterns of SARS-CoV-2 spread in Massachusetts from over 130,000 genomes Despite intensive study, gaps remain in our understanding of SARS-CoV-2 transmission patterns during the COVID-19 pandemic, in part due to limited contextual metadata accompanying most large genomic s...

I’m thrilled to share our latest preprint! We analyzed >130,000 SARS-CoV-2 genomes from MA to investigate complex transmission dynamics—from statewide patterns, within specific facilities, and at the individual level 🦠🧬

Check out the preprint here ⬇️
www.medrxiv.org/content/10.1...

Measles requires 95% vaccination rates for herd immunity.

It has a 16.2% case fatality rate for unvaccinated children under 5 years and 24% for children under 9 months (who are unable to be vaccinated).

30% of the survivors experience severe complications like blindness, deafness, or encephalitis.

Excerpt from a public letter Roald Dahl wrote encouraging people to vaccinate their children. Olivia, my eldest daughter, caught measles when she was seven years old. As the illness took its usual course I can remember reading to her often in bed and not feeling particularly alarmed about it. Then one morning, when she was well on the road to recovery, I was sitting on her bed showing her how to fashion little animals out of coloured pipe-cleaners, and when it came to her turn to make one herself, I noticed that her fingers and her mind were not working together and she couldn’t do anything. “Are you feeling all right?” I asked her. “I feel all sleepy,” she said. In an hour, she was unconscious. In twelve hours she was dead. The measles had turned into a terrible thing called measles encephalitis and there was nothing the doctors could do to save her. That was twenty-four years ago in 1962, but even now, if a child with measles happens to develop the same deadly reaction from measles as Olivia did, there would still be nothing the doctors could do to help her. On the other hand, there is today something that parents can do to make sure that this sort of tragedy does not happen to a child of theirs. They can insist that their child is immunized against measles. I was unable to do that for Olivia in 1962 because in those days a reliable measles vaccine had not been discovered. Today a good and safe vaccine is available to every family and all you have to do is to ask your doctor to administer it.

The measles outbreak in Texas is reminding me of the public letter Roald Dahl wrote about losing his daughter to measles in 1962, just before the vaccine was publicly available.

Reminder for the new semester that you can’t detect AI

Researchers secretly added AI-created papers to the exam pool: “We found that 94% of our AI submissions were undetected. The grades awarded to our AI submissions were on average half a grade boundary higher than that achieved by real students”

Behind the Scenes: Creating the Sabeti Lab's Holiday Take a sneak peek into the magic behind the Sabeti Lab's holiday card! 🎄✨ A huge shoutout to our amazing holiday card crew for bringing this vision to life, and an extra-special thank you to Omayma Dalal for capturing the magic and creating this beautiful video. Happy Holidays from all of us!

✨ Get a glimpse behind the scenes of this year’s holiday card! 🎥💫 Watch the magic come to life here: bit.ly/4gFdvjp

We hope it brings a little extra holiday cheer your way! 🎄💖

What better way to kick off our Bluesky journey than with our annual holiday card? 🌟 Celebrate unity, humanity, and the milestones shaping a brighter future with us. Happy Holidays! 🎄✨ bit.ly/3Dsr6wk

@sabetilab.bsky.social just joined!

(To be completely clear I love my job. It brings me joy, it's rewarding, and it's an honor to get to do this work and get paid to do it—and I had fun at work today. Some days are just some days.)

Losing flexibility has been by far the hardest thing about transitioning to a non-academic job. Proud to say that today, like I'm sure many adults, I woke up miserable, cried on the orange line, and then did my job anyway.

Temporal contact patterns and the implications for predicting superspreaders and planning of targeted outbreak control | Journal of The Royal Society Interface Directly transmitted infectious diseases spread through social contacts that change over time, but outbreak models typically make simplifying assumptions about network structure and dynamics. To assess how common assumptions relate to real-world ...

Are superspreaders always social butterflies? 🦋🦠

Our new study on temporal social contacts showed most people are highly connected only for brief periods. Crucially, this challenges the idea that respi outbreaks naturally subside once highly connected people becomes immune.

doi.org/10.1098/rsif...

I'm seeing some (entirely justified) concern about the possibility of the US no longer having a polio vaccination program given the threat posed by the incoming administration and I feel like this is a really good opportunity to explain some things about polio to clarify what the risks are 🧵

I am now selling my heirloom pumpkins and squashes on Threadless! Come see what RedBubble deemed risqué enough to ban :p

(It's pumpkins. It's just pumpkins.)

lydiakayart.threadless.com/other-things...

I thought it might be worthwhile to do a quick primer on CDC.gov datasets and public data resources.

1. DATA.CDC.GOV (data.cdc.gov/browse)
Datasets from across the agency, in browsable, machine readable format (Socrata system). Other/older collections are on:

2. WONDER.CDC.GOV (wonder.cdc.gov)

65. Good luck.

64. If you are going to quit, quit early. This applies to projects, this applies to classes, and this applies to grad school.

62. If your lab pits trainees against each other, find another lab.
63. If the people in your lab stress you out enough that it is hard to focus on your work, find another lab.

61. To the extent that you have control over authorship, be extremely generous with authorship.

60 (cont.). It also helps you to get to know your colleagues, which leads to friendship, collaboration, and helpful feedback and new ideas as you share what you are each working on.

60. Even if you have the flexibility to work remote, show up to the office at least twice a week. I’ve found that I am much more productive and take fewer breaks and procrastinate less when I am physically in the office

58. Get dental insurance, even if grad school doesn’t supply it, and see a dentist.
59. Ask around and go to the dentist your colleagues go to (that takes your insurance).

55. Show up to departmental happy hours.
56. Bring food to share at work sometimes. Baked goods or Halloween candy.
57. Work out at least once a week.

52. Don’t work for at least one day every weekend.
53. Have hobbies.
54. Maintain friendships, both in your department (especially with your cohort) and from your life before grad school. If you can’t meet in person, meet with coffee or lunch over zoom.

48. Treat your work like a job. Set your hours, show up during your hours, and try to disconnect outside of those hours.
49. Don’t work during vacations.
50. Don’t show up to meetings during vacations.
51. Or during dinner.

47. Don’t listen to music while you work. At the very least try working with music, try working without music, and see which version is more productive and enjoyable.

46 (cont.). As a bonus, it was a lot less work than teaching three semesters would have been, because I simply did the same thing three times in a row each day.

46. If you have teaching requirements and you think that teaching will distract you from your research, consider squeezing your teaching into one semester, and not doing any research during that semester. I taught my required three sections in one very stressful semester.

45. But don’t get distracted from your research!

44. Try to teach at some point, even if your department doesn’t require it. This will help you figure out if you want to be a professor, it will help you identify and correct gaps in your knowledge of your field, and it will make you better at presenting your own work.

43. Be on social media wherever your field is on social media. When you read a paper you enjoyed, follow its authors on social media so that you can learn from them and get notifications about new papers they have published.

42. If you want to, start a TikTok or Instagram about your (published) work and what you learn in grad school. One of my friends from my cohort got Internet famous with his science TikTok, which both is very cool and also probably didn’t not help him land a professorship right out of grad school.