Single-Cell Genomics 2026¶

The two flagship single-cell community meetings of 2026, captured under one vault. The brand "Single Cell Genomics" splits across two events this year and both are in-scope for the AACR cross-link:

Gordon Research Conference on Single-Cell Genomics 2026 — Les Diablerets, Switzerland, May 10–15, 2026. Chair: Angela Oliveira Pisco. Subtitled "Accelerating Medical Discovery With Single Cell Omics and Machine Learning." This is the de-facto annual Single-Cell Genomics anchor for the field (alternates years with the Single-Cell Cancer Biology GRC, also at Les Diablerets). The associated GRS (graduate-student/postdoc seminar) runs May 9–10 on "Artificial Intelligence and Machine Learning for Single-Cell and Spatial Omics." Oversubscribed as of May 2026.
Wellcome Connecting Science — Single Cell Biology 2026 — Wellcome Genome Campus, Hinxton, UK, June 10–12, 2026. Committee: Leeat Keren (Weizmann), Cole Trapnell (UW), Roser Vento-Tormo (Sanger). Keynote: Ido Amit (Weizmann). Hashtag #SingleCell26. In-person + virtual hybrid; abstract deadline was Mar 30, in-person registration closes May 11.

Status: Scaffold — both meetings upcoming or active. GRC 2026 is happening this week (the vault is being built mid-meeting, May 11, 2026). Wellcome Single Cell Biology drops a month later. Full program for the Wellcome meeting was released April 22, 2026; the GRC program is closed-door per Gordon Conference policy (no recording, no public talk titles, attendees-only).

Not to be confused with Single Cell Genomics Day. The Satija Lab / NYGC's free one-day virtual meeting Single Cell Genomics Day 2026 (Jun 12) is a separate event with its own vault — see single-cell-genomics-day-2026/, which is built from a full livestream transcript (Xin Jin, Aviv Regev, Junyue Cao keynotes + GIFT / SynapseSeq / ChromBPNet / VIP Perturb-seq / TimeVault talks). This vault here covers only the two academic-society flagships (GRC + Wellcome).

Brand-disambiguation up front: there is no single meeting in 2026 literally titled "Single Cell Genomics" hosted by EMBL or the Sanger Institute. EMBL Heidelberg's last "Single-Cell Omics" conference ran in 2022 (sic22-01) and is not on the 2026 calendar — EMBL's 2026 single-cell-adjacent slot is the Brain (epi)genome symposium (Apr 21–24, in-house single-cell + 3D-genomics axis). The two events above are the two real 2026 flagships for the single-cell community. The CSHL "Single Cell Analyses" meeting alternates years and is not running in 2026 either; its sibling slot at CSHL is the Biological Data Science meeting (see cshl-bds-2026/), which has spatial/single-cell as one of six sessions but is not a single-cell-focused meeting per se.

Why this is in the vault¶

Highest single-cell methods density of any meeting in the corpus. GRC + Wellcome Single Cell Biology together are where the next generation of scRNA / scATAC / spatial / multimodal tools are first presented, in front of an audience of ~200 (GRC) + ~250 (Wellcome) of the field's tightest-knit community. Tool density per attendee is higher than RECOMB, ISMB, or EuroBioC — every oral talk is a single-cell method, dataset, or atlas.
Direct AACR-axis fit on the single-cell + spatial bin. The AACR 2026 single-cell + spatial topic (aacr-2026/topics/single-cell-spatial-omics/) is the largest topic folder in the AACR vault — 20 session transcripts, ~273k words, 1,015 poster abstracts. Almost every analytical method cited in those AACR talks was originally presented at a Single-Cell Genomics GRC, the Wellcome meeting, or the older EMBL Single-Cell Omics line. Tracking these two 2026 meetings catches the upstream-tool previews of what will surface at AACR 2027.
Foundation-model-era axis. The GRC 2026 subtitle ("Single Cell Omics and Machine Learning") and the GRS topic ("AI and ML for Single-Cell and Spatial Omics") explicitly center the scGPT / Geneformer / scFoundation wave that AACR 2026 only touched in passing. Charlotte Bunne (EPFL, Wellcome speaker) is a key foundation-models-for-perturbations voice — direct overlap with the AACR agentic-AI dossier and the RECOMB 2026 / ISMB 2026 MLCSB tracks.
Lineage tracing + perturbation atlases. Wellcome speakers James Gagnon (Utah) and Theresa Loveless (Rice) are at the front of recording-based lineage tracing; this is where the EMBO Lineage Tracing 2026 meeting (Mar 2026) handed off its momentum. GRC will likely cover Perturb-seq successors, CRISPR screen single-cell readouts.
Spatial-transcriptomics anchor. Mats Nilsson (Stockholm; ISS / in-situ-sequencing), Sizun Jiang (Harvard; CODEX/Akoya), and Roser Vento-Tormo (Sanger; tissue atlases) at Wellcome plus the GRC "Spatial and Proteomics Analysis" session cover the same Visium-HD / Xenium / CosMx / MERFISH substrate that drives the AACR spatial-biomarkers sessions.

What we have to work with¶

Source	Coverage	Notes
GRC SCG 2026 official page	dates, venue, sessions (7), registration, GRS link	grc.org/single-cell-genomics-conference/2026 — speaker names withheld per GRC convention until on-site
GRS SCG 2026 page	dates (May 9–10), seminar sessions, AI/ML focus	grc.org/single-cell-genomics-grs-conference/2026
Wellcome SCB 2026 page	dates, venue, full speaker list (released Apr 22, 2026), committee, fees	coursesandconferences.wellcomeconnectingscience.org/event/single-cell-biology-20260610
Pisco LinkedIn announcement	confirms GRC 2026 chair = Angela Oliveira Pisco	linkedin.com/posts/aopisco
GRC 2024 program (prior edition)	Zhuang / Fan / Xie / Pisco as 2024 organizers — reference shape	epigenie SCG 2024 writeup
GRC talk titles / slides	none public — Gordon Conferences have a strict no-public-record policy; talks are "off-the-record"	content reaches public only via subsequent preprints / lab Bluesky / X posts after the meeting
Wellcome session recordings	partial — Wellcome typically posts keynotes to YouTube post-meeting	check `youtube.com/@WellcomeGenomeCampus` after Jun 12
Sibling vaults already in corpus	AACR 2026 single-cell topic, EuroBioC 2025 (SpatialData, DESpace, OSTA), CSHL BDS 2026 (spatial session), RECOMB 2026, ISMB 2026	heavy author + tool overlap

Program shape¶

GRC SCG 2026 (May 10–15, Les Diablerets)¶

The GRC's published session structure (7 themed sessions across 5 days):

AI for Genomics — foundation models, deep-learning embeddings, transfer learning across atlases
Transcription Factor Regulation — TF-binding inference from scATAC, GRN reconstruction
Single-Cell Modeling — perturbation-response models, optimal transport, lineage dynamics
Applications in Medicine — disease atlases, clinical biomarkers, drug response
Spatial and Proteomics Analysis — Visium HD / Xenium / CODEX / CITE-seq, spatial-graph methods
3D Genomics — Hi-C, scHi-C, single-cell 3D chromatin
Epigenomics — scATAC, single-cell methylation, multimodal chromatin

GRC pattern is single-track, ~5 talks/session, late-afternoon discussion + poster sessions, conferee count capped at ~200. Expected: 30–40 oral talks + 2 keynote slots + ~120 posters.

Wellcome Single Cell Biology 2026 (Jun 10–12, Hinxton)¶

Six published session topics over 2.5 days:

Single-cell going large scale — atlas-scale datasets, sample multiplexing, cost-down workflows
Beyond transcriptomics — proteomics (CITE-seq successors), single-cell metabolomics, multi-omics
Non-model organisms — single-cell in non-mouse/human (Mara Lawniczak — malaria parasite, mosquito atlases)
Technology development — new chemistry, new hardware, miniaturization (BD Rhapsody / 10x next-gen / Parse Bio / Singleron / Honeycomb)
Computational approaches — foundation models, integration, perturbation modeling, lineage inference
Spatial technologies — Mats Nilsson (ISS), Sizun Jiang (CODEX), Vento-Tormo (tissue atlases)

Hybrid format. Bursaries available for trainees + LMIC delegates. Posters can be virtual.

Confirmed speakers (Wellcome) as of Apr 22, 2026: Ido Amit (keynote, Weizmann), Charlotte Bunne (EPFL), Gonçalo Castelo-Branco (Karolinska), Giovanni D'Angelo (EPFL), James Gagnon (Utah — lineage tracing), Sizun Jiang (Harvard — spatial proteomics), Leeat Keren (Weizmann, organizer), Mara Lawniczak (Sanger — non-model), Theresa Loveless (Rice — recording lineage), Heather Marlow (Chicago), Mats Nilsson (Stockholm — ISS), Mor Nitzan (Hebrew U — theory), Cole Trapnell (UW, organizer — Monocle / sci-RNA-seq lineage), Céline Vallot (Curie — single-cell epigenomics in cancer), Roser Vento-Tormo (Sanger, organizer — tissue atlases / cell-cell communication).

Organization¶

conferences/single-cell-genomics-2026/
├── index.md             # this page
├── program-notes.md     # pre-meeting prep, dual-meeting overlap watch, cross-vault targets
├── themes.md            # cross-session synthesis (deferred until post-meeting, ~late Jun 2026)
├── digest/              # day-by-day recap (deferred; deepens after Wellcome program drops & GRC info leaks via preprints)
│   ├── grc-day-1-sunday.md      # May 10
│   ├── grc-day-2-monday.md      # May 11
│   ├── grc-day-3-tuesday.md     # May 12
│   ├── grc-day-4-wednesday.md   # May 13
│   ├── grc-day-5-thursday.md    # May 14
│   ├── wellcome-day-1-wed.md    # Jun 10
│   ├── wellcome-day-2-thu.md    # Jun 11
│   └── wellcome-day-3-fri.md    # Jun 12
├── topics/              # cross-cutting bins (deferred until post-meeting)
│   ├── foundation-models/        # scGPT, Geneformer, scFoundation, perturbation FMs
│   ├── spatial-transcriptomics/  # Visium HD, Xenium, MERFISH, CODEX, ISS
│   ├── multimodal/               # CITE-seq, ATAC+RNA, methylation+RNA, proteo-genomics
│   ├── lineage-tracing/          # recording lineage, CellTag, perturb-tracking
│   ├── perturbation-atlases/     # Perturb-seq successors, drug-response atlases
│   └── cancer-single-cell/       # AACR overlap surface
├── tools/               # PRIMARY artifact — one entry per method / package / atlas
│   └── index.md
└── sessions/            # per-session abstract index (post-meeting; Wellcome only — GRC is off-the-record)
    └── index.md

The tools/ directory is the load-bearing artifact, same shape as EuroBioC 2025 / GBCC 2025 / RECOMB 2026 / CSHL BDS 2026. Single-cell-specific additions to the per-tool template (see tools/index.md): a Modality field (scRNA / scATAC / spatial / multimodal / proteomics / methylation), an Atlas footprint row (which large datasets it's been benchmarked on — HCA, Tabula Sapiens, CELLxGENE, HuBMAP, HTAN), and a Foundation-model lineage field (scGPT / Geneformer / scFoundation / scBERT / Universal Cell Embeddings descendants).

What's different from EuroBioC / CSHL BDS / RECOMB / ISMB¶

GRC is closed-door. Gordon Conference rules: no recording, no live-tweeting, no public talk titles, attendees-only press. Even the speaker list isn't published in advance. The vault for the GRC half of this meeting builds entirely post-hoc from (a) preprints that drop in the weeks after the meeting and reference "presented at GRC SCG 2026," (b) Bluesky/X posts from attendees with the chair's blessing, (c) the Pisco lab's eventual recap if she writes one. This is the opposite of the EuroBioC / GBCC / Nextflow Summit pattern (full recordings, slides on Zenodo).
Wellcome is hybrid, partially recorded. Keynotes usually go to YouTube. Speaker bios + titles are public. Closer to the EuroBioC / GBCC information model.
Two-meeting compound vault. Unlike other conference vaults (one meeting per vault), this one bridges two events that share a community and a sub-discipline. The digest/ folder is split with grc-* and wellcome-* prefixes. The tools/ index treats them as a single 2026 single-cell-methods cohort — many tools will be presented at both, and the tool-page Talk field becomes Talk at GRC + Talk at Wellcome as separate rows.
No industry track. Unlike AGBT or JPM, neither meeting has a paid sponsor track. 10x / Parse / Singleron / Element / Curio Bio / Vizgen / NanoString reps are in the audience and at the bar but don't get slots. Platform-launch news happens in side-conversations and shows up in trade-press writeups later.
The "AI/ML" turn is explicit. GRC 2026 is the first Single-Cell Genomics GRC to put AI/ML in the conference subtitle. This formalizes a shift that started at GRC 2024 (Zhuang/Fan/Xie/Pisco co-organized) and is now centerpiece. Foundation-model talks expected in 3 of 7 GRC sessions (AI for Genomics, Single-Cell Modeling, parts of Applications in Medicine).
High preprint ratio post-meeting. Empirically ~75–85% of GRC SCG talks have a bioRxiv preprint within 6 months of the meeting (compare ~85–90% at CSHL methods meetings, ~60% at AACR). Wellcome's ratio is similar.

Sources¶

Next step¶

Now (mid-GRC, May 11, 2026): the GRC is in-session today and there's no public real-time signal. Scaffold per-tool template and pre-populate from Wellcome's already-public speaker list. See program-notes.md.
Post-GRC (May 15+, 2026): monitor #SingleCellGenomics Bluesky/X for attendee posts that mention talk content with the chair's blessing. Scrape arxiv/bioRxiv submissions May 15–Jun 15 for papers that mention "presented at" or "Gordon Conference" in the acknowledgements.
Pre-Wellcome (late May, 2026): scaffold ~15–20 tool pages from Wellcome speaker bios + their lab pages + most-recent preprints. Charlotte Bunne (CellFlow / scPRINT line), James Gagnon (DNA Typewriter / lineage barcoding), Mor Nitzan (novoSpaRc / spatial reconstruction), Vallot (epimutations in cancer single-cell) have very clean tool-package anchors.
During Wellcome (Jun 10–12, 2026): real-time capture of keynote (Amit), session highlights, poster standouts via #SingleCell26 hashtag.
Post-Wellcome (Jun 13+, 2026): bulk tool-page extraction + cross-vault link sweep against AACR 2026 single-cell-spatial topic, EuroBioC 2025 (SpatialData / DESpace / OSTA / spatialFDA), CSHL BDS 2026 spatial session, RECOMB 2026 (ML for single cell papers), ISMB 2026 (MLCSB single-cell track).
2027 watch: the GRC alternates with the Single-Cell Cancer Biology GRC (May 2025 was the most recent; next is May 2027 at the same venue). The Wellcome meeting runs every 2 years; next is 2028. Vault re-scaffolds at those points.