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CSHL GI 2026 / BDS 2026 — Program Notes (pre-meeting prep)

Internal working file. Pre-meeting prep notes capturing dates, venue, sources, expected major sessions, and cross-vault overlap watch for CSHL's late-fall 2026 methods meeting. The actual meeting in this slot is Biological Data Science 2026 (Nov 4–7) — Genome Informatics is biennial and runs in odd years; the next GI is Nov 2027. See index.md for the public-facing version of this context.

Verified facts (May 2026)

  • Meeting: Biological Data Science 2026 (CSHL "DATA" meeting code) — the 7th biennial BDS, filling the late-fall methods slot that alternates with Genome Informatics (GI, the "INFO" code, which last ran Nov 2025 and runs again Nov 2027).
  • Dates: Wednesday Nov 4, 2026 (7:30 PM start) → Saturday Nov 7, 2026 (lunch).
  • Venue: Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724. Main program in Grace Auditorium (single-track). Posters in Bush Lecture Hall + adjacent corridors.
  • Organizers (BDS 2026): Elinor Karlsson (UMass Chan Medical School / Broad Institute), Michael Schatz (Johns Hopkins University), Catalina Vallejos (University of Edinburgh / Alan Turing Institute, UK).
  • Reference organizer roster — GI 2025 (last GI): Zamin Iqbal (University of Bath, UK), Ben Langmead (Johns Hopkins University), Camille Marchet (University of Lille, France). Schatz is a recurring CSHL late-fall-methods organizer across both meetings.
  • Six BDS 2026 sessions (announced):
  • Algorithmics — sequence algorithms, indexing, pangenomes, de Bruijn graphs, minimizers
  • Population Genetics and Personalized Medicine — PRS, biobank-scale GWAS, ancestry-aware methods, rare-variant inference
  • Machine Learning — deep learning for regulatory genomics, foundation models, protein/RNA ML, expected agentic-AI presence
  • Tools, Visualization, and Infrastructure — Galaxy/Nextflow/AnVIL/Snakemake-adjacent; JBrowse-class viewers; cloud-native pipelines
  • Functional Genomics — perturbation/CRISPR-screen analysis, regulatory inference, multi-modal integration
  • Spatial Genomics and Spatial Biology — Visium HD, MERFISH/seqFISH/Xenium analysis, spatial-graph methods, tissue-aware deep learning
  • Keynote speakers (2026): not yet announced as of May 2026. GI 2025 had two keynotes (Yana Safonova, Penn State — adaptive immune repertoire methods; Marinka Zitnik, Harvard — therapeutic-graph foundation models). BDS 2024 followed the same 2-keynote pattern. Expect BDS 2026 keynotes to be announced ~July–August 2026.
  • Abstract deadline (2026): not yet posted; historical pattern is early September for a Nov meeting.
  • Recording policy: none (CSHL policy — applies to both GI and BDS). Slides are speaker-deposited (Zenodo / lab sites); social signal lives at #CSHLmeetings on Bluesky + X.

Expected major sessions — shape inference

Inference from BDS 2024 (last BDS), GI 2025 (last GI), and the six announced 2026 sessions. None of the 2026-specific talk titles are public yet — what follows is sessionwise expectation, not extracted content.

Algorithmics

  • Pangenomes — Cuttlefish 3-class assemblies (Rob Patro group; Rayan Chikhi group), VG / GBZ indexing updates, ODGI/PGGB pipeline maturity. Pangenome panel at HG003-class scale.
  • Long-read assembly and polishing — herro-class neural polishing, T2T-CHM13 derivative assemblies, Verkko / hifiasm / HiCanu updates.
  • k-mer / minimizer / sketching infrastructure — mash, sourmash, dashing, KMC successors. High likelihood of a tool talk on space-efficient pangenome indexing.
  • Expected debut tools: ~6–10 talks; ~5–8 likely to get tool pages.

Population Genetics and Personalized Medicine

  • PRS at scale — multi-ancestry PRS portability, PRS-CSx / SBayesRC updates, biobank-PRS pipelines (UK Biobank, All of Us, FinnGen).
  • Statistical genetics methods — rare-variant collapsing, GxE inference, fine-mapping (SuSiE-class), TWAS extensions, conditional/joint analysis at All-of-Us scale.
  • Personalized-medicine bridges — clinical-genomics pipelines, ACMG-class variant interpretation automation.
  • Expected debut tools: ~5–8 talks; ~4–6 likely to get tool pages. Heavy preprint signal.

Machine Learning

  • Foundation models for genomics — Enformer/Borzoi successor work, DNA-language-model variants (Caduceus, HyenaDNA, DNABert-2), single-cell foundation models (Geneformer/scGPT/scFoundation lineage).
  • Deep learning for regulatory — basenji-class enhancer prediction, allele-specific deep models (overlap with RECOMB 2026 paper #19 Mostafavi-coauthored).
  • Protein / RNA ML — ESM-3 derivative work, RNA-FM, AlphaFold3 downstream applications.
  • Agentic AI — if 2025 pattern continues (GI 2025 had agentic-AI track presence), expect 2–3 talks on LLM-driven bioinformatics agents (overlap with GBCC 2025 GalaxyMCP, ISMB 2026 BOSC agentic-pipeline track).
  • Expected debut tools: ~6–10 talks; ~5–7 likely to get tool pages.

Tools, Visualization, and Infrastructure

  • Pipeline frameworks — Nextflow-adjacent work (overlap with Nextflow Summit 2026 Oct slot), Snakemake updates, Galaxy infrastructure (overlap with GBCC 2025).
  • Genome browsers and viewers — JBrowse 3, IGV.js updates, pangenome viewers (Bandage successors, Panagram-class).
  • Cloud-native genomics infrastructure — AnVIL, Terra, Seqera Platform, DNAnexus-adjacent.
  • Reproducibility / packaging — Bioconda updates, container-orchestration, WDL/CWL refresh.
  • Expected debut tools: ~5–8 talks; ~5–7 likely to get tool pages. Highest sibling-vault overlap.

Functional Genomics

  • Perturbation analysis — Perturb-seq / CROP-seq analysis methods (overlap with EuroBioC spatialFDA-class work).
  • Single-cell regulatory inference — multi-modal ATAC + RNA + protein integration, GRN inference (overlap with RECOMB 2026 single-cell papers).
  • CRISPR-screen analysis — MAGeCK successors, dual-guide statistical methods.
  • Expected debut tools: ~5–7 talks; ~4–6 likely to get tool pages.

Spatial Genomics and Spatial Biology

  • Visium HD analysis — sub-spot deconvolution, neighborhood inference, multi-sample comparison (overlap with EuroBioC 2025 DESpace / spatialFDA / SpatialData / OSTA).
  • Imaging-based ST — MERFISH / seqFISH / Xenium analysis pipelines, segmentation-aware quantification (overlap with RECOMB 2026 MOSAICField / DIME / LineageMap).
  • Tissue-aware deep learning — histopathology FMs (overlap with EuroBioC HistoImagePlot, AACR 2026 spatial dossier), Visium-HD-trained transformers.
  • Expected debut tools: ~5–8 talks; ~5–7 likely to get tool pages. Highest AACR-axis fit.

Total expected: ~30–40 tool-pages across the six sessions. Plus posters: ~120–150 posters total, of which ~30–50 have associated preprints and warrant tool entries (or a lighter-weight posters/index.md table).

Cross-vault overlap watch

Authors / labs / tools likely to appear at CSHL BDS 2026 and at another vault'd meeting. This list drives the pre-meeting tool-page scaffolding pass — for each entry below, the BDS 2026 page either is the canonical or links back to the canonical sibling-vault entry.

People expected to appear

Person Lab / institution Sibling-vault appearance BDS 2026 likely session
Michael Schatz JHU BDS 2026 organizer; GBCC 2025 (sibling CSHL); ISMB 2026 (BOSC history) Algorithmics / Spatial (his lab spans both)
Ben Langmead JHU GI 2025 organizer; ISMB 2026 (Bowtie2 lineage); RECOMB 2026 (sequence algorithms) Algorithmics
Rob Patro Maryland RECOMB 2026 (Cuttlefish 3, paper #49); GBCC 2025 (tximeta/fishpond); EuroBioC 2025 sibling Algorithmics
Rayan Chikhi Institut Pasteur RECOMB 2026 PC Chair; ISMB 2026; sequence algorithms Algorithmics
Zamin Iqbal Bath / EMBL-EBI GI 2025 organizer; ISMB 2026 (pangenome track) Algorithmics / Tools-Viz-Infra
Catalina Vallejos Edinburgh / Turing BDS 2026 organizer; EuroBioC (BASiCS scRNA stats) ML / Functional Genomics
Elinor Karlsson UMass / Broad BDS 2026 organizer; AGBT 2026 platform-launch axis (Darwin's Ark) PopGen / Functional Genomics
Olga Troyanskaya Princeton ISMB 2026 keynote (Mon Jul 13); RECOMB 2026 (Aggarwal/Sokolova co-author) ML / Spatial
Anshul Kundaje Stanford ISMB 2026; ML for regulatory genomics; basenji/borzoi lineage ML
Sara Mostafavi UW / Allen RECOMB 2026 keynote (Fri May 29); allele-specific deep models ML
Jingyi Jessica Li UCLA RECOMB 2026 (3 papers: Information-Geometry, Nullstrap-DE, scDesignPop); ISMB 2026 MLCSB ML / Functional Genomics
Bonnie Berger MIT RECOMB 2026 steering chair; ISMB 2026 MLCSB ML
Michael Love UNC GBCC 2025 (Session 4 chair); EuroBioC sibling; RNA-seq stats Tools-Viz-Infra / Functional Genomics
Charlotte Soneson FMI / Basel GBCC 2025 keynote 2; EuroBioC 2025 (footprintR) Tools-Viz-Infra
Lambda Moses Caltech GBCC 2025 (Session 3 chair); Voyager; spatial-omics infra Spatial
Sehyun Oh CUNY GBCC 2025 (Session 1 chair) Tools-Viz-Infra
Marinka Zitnik Harvard GI 2025 keynote 2; therapeutic-graph FMs ML (if invited again)
Yana Safonova Penn State GI 2025 keynote 1; adaptive immune repertoire Algorithmics / Functional Genomics
Tuuli Lappalainen NYGC / KTH ISMB 2026; statistical genetics + functional genomics PopGen / Functional Genomics
Alkes Price Harvard Chan PRS at scale; statistical genetics PopGen
Adam Siepel CSHL home turf CSHL-resident; phylogenetic / population-genetic models PopGen / Algorithmics
Ben Raphael Princeton RECOMB 2026 (3 papers); cancer evolution + spatial Spatial / Functional Genomics
Tool / method Domain Sibling-vault page Expected BDS 2026 angle
Cuttlefish 3 pangenome indexing RECOMB 2026 paper #49 release talk or follow-on benchmark
SpatialData spatial-omics framework EuroBioC 2025 SpatialData entry Python + R interop update
Voyager spatial-omics SpatialFeatureExperiment GBCC 2025 (Lambda Moses) spatial-graph methods extension
DESpace / spatialFDA spatial DE EuroBioC 2025 DESpace / spatialFDA post-EuroBioC follow-on
OSTA spatial book / curriculum EuroBioC 2025 OSTA workshop possible book-launch retrospective
Borzoi / Enformer-class regulatory deep learning ISMB 2026 MLCSB; AACR 2026 FM dossier next-gen successor talk
Geneformer / scGPT / scFoundation single-cell FM AACR 2026 FM dossier; ISMB 2026; RECOMB 2026 scaling + downstream-task benchmarks
VG / GBZ / PGGB pangenome graphs RECOMB-Seq 2026 satellite T2T-pangenome reference panel updates
Galaxy MCP / agentic-AI agents bioinformatics agents GBCC 2025 (GalaxyMCP); ISMB 2026 BOSC cross-platform agent benchmark
PRS-CSx / SBayesRC-class multi-ancestry PRS (new — not yet in corpus) new sibling-vault entry candidate
MAGeCK successors / CRISPR-screen perturbation stats (new — not yet in corpus) new sibling-vault entry candidate
JBrowse 3 genome viewer (new — not yet in corpus) infra-track candidate

When BDS 2026 tool pages get scaffolded post-meeting, the following inbound/outbound links should be checked:

  • EuroBioC 2025 (../eurobioc-2025/tools/) — every spatial-omics talk; every Bioconductor-package-update talk.
  • GBCC 2025 (../gbcc-2025/) — every Galaxy-infra talk; every Bioc-to-Galaxy wrapping update; Schatz / Williams / Soneson sibling appearances.
  • RECOMB 2026 (../recomb-2026/tools/) — every Algorithmics talk (pangenome, sequence indexing); every ML talk (foundation models, protein/RNA ML); every Spatial talk (MOSAICField / DIME / LineageMap follow-ons).
  • ISMB 2026 (../ismb-2026/) — MLCSB co-publications; BOSC tool-release co-announcements; Troyanskaya keynote spillover.
  • Nextflow Summit 2026 (../nextflow-2026/) — every Tools/Viz/Infra pipeline-framework talk; every cloud-native infrastructure talk.
  • AACR 2026 (../aacr-2026/) — every Spatial talk (Visium HD analysis, histopathology FMs); every FM talk (downstream cancer-research applications); every ML-for-regulatory talk with cancer-context examples.
  • JPM 2026 (../jpm-2026/) — sparse overlap, but Seqera Platform / DNAnexus-adjacent infrastructure talks may name-drop platforms covered there.

Pre-meeting checklist

  • [ ] Sep 2026: when the BDS 2026 program drops, populate _program-extracted.md (working file) with the session-by-session schedule + speaker list.
  • [ ] Sep–Oct 2026: preprint sweep — for each oral talk, locate the speaker's most recent bioRxiv preprint. Pre-scaffold tool-page skeletons.
  • [ ] Oct 2026: keynote announcements typically drop ~6–8 weeks pre-meeting. Update index.md when known.
  • [ ] Nov 4–7, 2026: track #CSHLmeetings on Bluesky/X during the meeting for talk-day reactions. CSHL has no recordings, so social is the only real-time signal.
  • [ ] Nov 8+, 2026: post-meeting bulk extraction. Cross-vault link sweep. Abstract book PDF backfill.
  • [ ] Dec 2026: slide-deposit re-sweep (~4 weeks post-meeting). ~30–50% of speakers will have deposited by then.

Sources (verified May 2026)