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Single Cell Genomics Day 2026 (SCGD26)

The Satija Lab's annual one-day, free, virtual single-cell meeting — captured this year from a full livestream transcript. Single Cell Genomics Day (SCGD) is hosted by the Satija Lab at the New York Genome Center (NYGC), runs as a single-track day of keynotes + talks, and is streamed live on YouTube with global virtual attendance. Rahul Satija MCs and runs the live Q&A.

  • Event: Single Cell Genomics Day 2026 — "keynote talks and AI in biology"
  • Date: June 12, 2026 (one day)
  • Host: Satija Lab / New York Genome Center
  • Format: Free virtual livestream (YouTube) + live/written Q&A
  • Site: satijalab.org/scgd26

Status: ✅ built from transcript, speakers verified. Unlike most of the corpus (pre-meeting scaffolds), this vault is populated from an actual session transcript of the SCGD26 livestream — nine talks including three keynotes. Content is extracted from what speakers said on the day; all nine speaker names, affiliations, talk titles, and (where they exist) preprints/DOIs/Addgene IDs were then cross-checked against the official SCGD26 schedule and published sources — see the Sources section on each talk page. A few residual items (archived video link, a handful of lab-member name spellings) remain open and are flagged below.

Brand disambiguation (read this first)

SCGD is not the same meeting as the single-cell-genomics-2026/ vault. That vault is a compound scaffold for the two 2026 academic-society flagships — the GRC Single-Cell Genomics (Les Diablerets, May 10–15, off-the-record) and the Wellcome Single Cell Biology (Hinxton, Jun 10–12). Single Cell Genomics Day is a separate, distinct event: a free one-day NYGC livestream organized by Rahul Satija's group, running annually since the mid-2010s. Same sub-discipline, different meeting, different organizers, different format (fully public + recorded, vs. GRC's closed-door rule). The two vaults are siblings and cross-link, but should not be merged.

Why this is in the vault

  • Real delivered-talk content, not a scaffold. This is one of the few corpus entries built from a verbatim transcript. It gives ground-truth previews of methods that will be cited at AACR 2027 and that overlap heavily with the AACR 2026 single-cell + spatial and virtual-cells topics.
  • Dense AACR-axis fit. The day spans molecular recorders, in vivo Perturb-seq at whole-brain scale, single-cell genotyping, sequencing-based connectomics, sequence-to-function foundation models, the "virtual cell / lab-in-the-loop" program, and ultra-scalable combinatorial-indexing methods — direct overlap with aacr-2026/topics/single-cell-spatial-omics/ and aacr-2026/topics/virtual-cells/.
  • The "AI in biology" turn, stated explicitly. Two of the three keynotes (Regev, and the Kundaje methods talk) are squarely about sequence/expression foundation models, interpretability, and using models to design experiments rather than just predict — the same thread the AACR virtual-cells and agentic-AI dossiers track.

Program (Jun 12, 2026) — as delivered

Single track. Order below is the order of delivery on the livestream. Keynotes marked ★.

# Speaker Affiliation Talk / method Page
1 Dingchang Lin Johns Hopkins (David Baker Lab collab) GEMINI — genetically encoded protein-assembly molecular recorder molecular-recorder-gemini
2 ★ Xin Jin Scripps Research In vivo Perturb-seq → whole-brain genome-scale CRISPR screen xin-jin-in-vivo-perturbseq
3 Sydney B. Blattman MSKCC (Pe'er / Chaligné / LaReau labs) GIFT — Genotyping In Fixed Transcriptomes sydney-blattman-gift
4 Amanda Urke Macosko Lab, Broad / Harvard Synapse-seq — sequencing-based synaptic connectomics amanda-urke-synapseseq
5 Anshul Kundaje Stanford ChromBPNet + fibroblast reprogramming dynamics anshul-kundaje-chrombpnet
6 ★ Aviv Regev Genentech "From Cell Atlases to Medicines, with AI" — virtual cell / lab-in-the-loop aviv-regev-virtual-cell
7 Alexandra (Alex) Bradu Satija Lab, NYGC VIPerturb-seq + the GuEST-List library alex-vip-perturbseq
8 Kevin (Yu-Kai) Chao Harvard / Fei Chen Lab, Broad TimeVault — vault-protein transcriptome recorder kevin-chao-timevault
9 ★ Junyue Cao Rockefeller University Scalable combinatorial-indexing single-cell + temporal/spatial junyue-cao-scalable-singlecell

See talks/ for the per-talk index.

What we have to work with

Source Coverage Notes
SCGD26 livestream transcript all 9 talks + Q&A (two contiguous segments) primary artifact — content extracted into per-talk pages
satijalab.org/scgd26 event page, schedule, registration link
YouTube livestream / chat recording + audience Q&A (speakers answered some questions in chat after sign-off) check the Satija Lab / NYGC YouTube channel for the archived stream
Speaker preprints / papers confirmed for most talks — GIFT (bioRxiv), Synapse-seq (bioRxiv), VIPerturb-seq (bioRxiv + GuEST-List on Addgene), TimeVault (Science 2026 + Addgene), ChromBPNet reprogramming (Nature Genetics / interactive browser), whole-brain Perturb-seq atlas (Hugging Face) DOIs/links on each talk page's Sources section

Cross-vault targets

Verified post-stream

All nine speakers confirmed against the official SCGD26 schedule. Notable transcript→reality corrections:

  • Talk 1 — the unidentified GEMINI speaker is Dingchang Lin (Johns Hopkins); paper in Nature 2026 + bioRxiv.
  • Talk 3 — "Sydney Blackman" → Sydney B. Blattman (MSKCC); GIFT preprint on bioRxiv.
  • Talk 4 — "Amanda Urkey" → Amanda Urke; method published as Synapse-seq (senior author Evan Z. Macosko).
  • Talk 7 — "Alex" → Alexandra (Alex) Bradu (Satija Lab); method is VIPerturb-seq and the library is GuEST-List (Addgene #248188/#248189).
  • Talk 8 — "Kevin Chow" → Kevin (Yu-Kai) Chao (Fei Chen Lab, Broad); TimeVault published in Science 2026.
  • Talks 2, 5, 6, 9 — Xin Jin, Anshul Kundaje, Aviv Regev, Junyue Cao all confirmed as attributed.

Still open

  • Archived video link — the SCGD26 livestream recording URL (the event is live today, Jun 12, 2026; check the NYGC/Satija Lab YouTube once posted).
  • A few lab-member name spellings inside individual talk pages (flagged per page) and the exact identity of the MOSCATO integration layer in the Regev talk.
  • Edition slug — filed as 2026 / scgd26 per the event URL.

Sources