Eric Kernfeld
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ekernf01.bsky.social
Eric Kernfeld
@ekernf01.bsky.social
1.3K followers 420 following 310 posts
Statistician and computational biologist; uw alum; jhu student. He/him. http://ekernf01.github.io
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ekernf01.bsky.social
Found it!!
Photo of Eric with mom, dad, and brother Paul. They are holding flowers and balloons to celebrate after Eric's defense.
August 13, 2025 at 3:45 PM
ekernf01.bsky.social
Job Search Recap
ekernf01.github.io/job_search_2...
Sankey diagram of Eric's job search efforts and opportunities. Source data: Months unemployed [1] Biking Months unemployed [1] Stressing Months unemployed [1] Applying Months unemployed [2] Networking Months unemployed [0] Waiting to joke about "came in a fluffer" Jobs applied to (no referral) [64] No follow up Jobs applied to (with referral) [4] No follow up Jobs applied to (with referral) [3] Interview Jobs applied to (no referral) [1] Interview Info interviews conducted [30] No follow up Info interviews conducted [2] Interview Credible unsolicited inquiries [2] Interview Credible unsolicited inquiries [3] Location mismatch Interview [2] Job offer
August 13, 2025 at 3:26 PM
ekernf01.bsky.social
3) I rode my bike from Washington, DC to Pittsburgh and back, through rain, mud, stiff headwinds, dozens of downed trees, and a couple of sub-freezing nights.
Picture of Eric and his bike in front of tons of unstable rock at the mouth of the Paw-Paw Tunnel, part of the C&O Canal Towpath national park
August 13, 2025 at 3:24 PM
ekernf01.bsky.social
What it felt like to write this series:
Classic "midwit meme" with dummy expanding (a+b)^2 as a^2 + b^2, midwit (superimposed ekernf01 profile pic) crying and expanding (a+b)^2 as a^2 + 2ab + b^2, and wizard (superimposed Sasha Gusev profile pic) expanding E[(a+b)^2] as E[a^2] + E[b^2] because E[ab]=0.
June 26, 2025 at 1:08 PM
ekernf01.bsky.social
Blogpost: ekernf01.github.io/vanilla

Image credits:
Vanilla (Linkage Disequilibrium Score Regression) By B.navez - Own work, CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=436896 Strawberry (stratified LD score regression) By Ivar Leidus - Own work, CC BY-SA 4.0, https://commons.wikimedia.org/w/index.php?curid=114685374 Cranberry (cross-trait LD score regression) By Ɱ - Own work, CC BY-SA 4.0, https://commons.wikimedia.org/w/index.php?curid=42145142 Lime (Signed LD Score Regression) By Ivar Leidus - Own work, CC BY-SA 4.0, https://commons.wikimedia.org/w/index.php?curid=97307282 Melon (Mediated Expression Score Regression) By Filo gèn' - Own work, CC BY-SA 4.0, https://commons.wikimedia.org/w/index.php?curid=68127982
June 26, 2025 at 1:05 PM
ekernf01.bsky.social
BLOG ALERT! 🧬 If you do RNA-seq, ATAC-seq, ChIP-seq, or modeling thereof, you may be overlooking LD score regression methods. These should be standard tools to study genes, variants, and regions en masse, but they are hard to understand. I wrote intros:
(flowery font "Corsiva" with bright colors) The exotic FLAVORS of LD Score Regression Vanilla (Linkage Disequilibrium Score Regression) distinguishes whether bias is from polygenicity or population structure using GWAS summary stats Strawberry (stratified LD score regression) quantifies which genomic regions are enriched for disease risk using GWAS summary stats + functional annotations Cranberry (cross-trait LD score regression) estimates genetic correlations between traits using summary stats from multiple GWAS Lime (Signed LD Score Regression) tests whether predicted allele effects directionally align with per-allele disease risk using GWAS + deep learning Melon (Mediated Expression Score Regression) quantifies how much disease risk is mediated through gene expression using GWAS + eQTL effects
June 26, 2025 at 1:03 PM
ekernf01.bsky.social
Help me understand the definition of genetic covariance from the xt-ldsc paper. If beta is an argmax, then isn't cbeta also an argmax for any positive scalar c?
June 23, 2025 at 6:04 PM
ekernf01.bsky.social
There's a lot going on with transcriptome transformers, virtual cells, and perturbation prediction. I updated my recap:
ekernf01.github.io/perturbation...
table with a rundown of perturbation prediction benchmark papers, describing each study's datasets, baselines, and major findings.
May 25, 2025 at 8:03 PM
ekernf01.bsky.social
New blog post: pitfalls and open questions in GRN inference, ft. Audrey II.

ekernf01.github.io/guiding-ques...
Meme showing Audrey II saying "Why don't you try ... GENE REGULATORY NETWORK INFERENCE"
May 5, 2025 at 4:13 PM
ekernf01.bsky.social
The model also learns that different sets of mutations have different immunogenicity (KRAS vs KRAS/STK).
April 30, 2025 at 1:56 PM
ekernf01.bsky.social
How well does it work? Well, per the report just linked, model has learned that Ifng -> HLA.
April 30, 2025 at 1:55 PM
ekernf01.bsky.social
First, a quick who's-who on Noetik itself, plus a description of the software in their own words.
www.businesswire.com/news/home/20...
Screenshot says: “OCTO-vc is a transformative tool for understanding the hidden biology driving disease progression,” said Ron Alfa, M.D., Ph.D., CEO & Co-Founder, Noetik. “Leveraging its generative capabilities, we can simulate how virtual cells behave in different tissue environments, shedding light on mechanisms that were previously inaccessible. By scaling these simulations to cohorts of patients within our dataset, we can run virtual experiments to discover patient and therapeutic biology.”
April 30, 2025 at 1:53 PM
ekernf01.bsky.social
side by side images of a mundane professionally-lit home electrical panel with ~20 switches and a neon-pink-lit theater lighting panel with ~50 dimmers and a touchscreen. Captioned respectively "prokaryote transcriptional regulation" and "eukaryote transcriptional regulation".
February 26, 2025 at 2:56 PM
ekernf01.bsky.social
Friday shitpost: I wish biologists would italicize *bona fide* the way we italicize *in vitro*.
February 21, 2025 at 5:51 PM
ekernf01.bsky.social
February 9, 2025 at 6:08 PM
ekernf01.bsky.social
My Ph.D.
February 6, 2025 at 9:22 PM
ekernf01.bsky.social
i knew that *looks sideways*
screenshot of a paper saying "NDP kinases (NDPKs) are a textbook case of housekeeping enzymes that have been known for some 60 years to catalyze nonspecific transphosphorylation reactions between nucleoside di- and triphosphates through a conserved histidine residue. It was assumed"
January 31, 2025 at 4:15 PM
ekernf01.bsky.social
Mean of the training data still absolutely crushing it for perturbation prediction.
www.biorxiv.org/content/10.1...
Screenshot of preprint saying "To benchmark the methods, we evaluated the performance of six methods: Linear, Linear-GPT, CellOracle, GEARS, scGPT, and scFoundation (Methods). We also included a basic approach that averages gene expression across all cells within all known perturbations as the prediction of unseen perturbations (referred to as KnownAverage). The benchmarking results across the 17 datasets were summarized in Fig. 2b. Notably, the KnownAverage method consistently demonstrated some of the best overall performance across all four types of metrics."
January 24, 2025 at 12:59 PM
ekernf01.bsky.social
Seeing this in a here's-your-nobel speech makes me a little less embarrassed that I thought transcriptome data might sometimes be causally sufficient.
www.nobelprize.org/prizes/medic...
January 21, 2025 at 7:51 PM
ekernf01.bsky.social
(2/2)
January 13, 2025 at 7:30 PM
ekernf01.bsky.social
I think we can all learn something about persistence from Salgado and Collado-Vides. (1/2)
January 13, 2025 at 7:30 PM
ekernf01.bsky.social
January 8, 2025 at 7:53 PM
ekernf01.bsky.social
Delightful quote from circa 1159AD about kids these days singing *polyphony in church*:

en.wikipedia.org/wiki/Notre-D...

(I'll return to genomics-posting soon, after a short musical interlude.)
December 23, 2024 at 8:02 PM
ekernf01.bsky.social
yadirF tsoptihs: rirrom efil dab, t'not ekam ti!!!

ylsuoires hguoht, t'nod od taht tihs. t'nod tcnitxe em orb.
tohsneercs fo a tsop no x yb ikoN ytraCcM tuoba eht sregnad fo derirrom efil
December 13, 2024 at 3:58 PM
ekernf01.bsky.social
IF they had known the first word was gonna be all caps, they could have rearranged it to be SEGMENTATION instead of ... MUCH!!
Screenshotted abstract of a scientific paper reads "MUCH of our present knowledge of the biological processes involved in pattern formation in Drosophila is derived from segmentation analysis1, 2. Comparatively little is known about the genetic requirement and mechanisms underlying the formation and separation of germ layers by morphogenetic movements during gastrulation3. Here we show that theDrosophila gene huckebein (hkb), a member of the gap-gene class of segmentation genes4, 5, is required for germ-layer formation at blastoderm. Absence of the hkb product, an Sp1/egr-like zinc-finger protein, causes the ectodermal and mesodermal primordia to expand at the expense of endoderm anlagen. Conversely, ectopic expression of hkb inhibits the formation of the major gastrulation fold which gives rise to the mesoderm and prevents normal segmentation in the ectoderm. Thus, hkb is necessary for endoderm development and its activity defines spatial limits within the blastoderm embryo in which the germ layers are established."
November 26, 2024 at 7:11 PM