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ECCB 2026 — Program Notes (working file)

Internal-use working file. Source for the bulk tool-page generation pass that will run after the meeting closes Sep 4, 2026 and the Bioinformatics OUP supplement is fully online. Not for end-reader consumption — formatting is utilitarian. Compiled from the public ECCB 2026 web pages (eccb2026.org), fetched 2026-05-11 (~16 weeks pre-meeting).

Tag legend: - [PROC] — proceedings paper (peer-reviewed in Bioinformatics OUP supplement); has a DOI when supplement posts - [HIGHLIGHT] — highlight talk; recently published research (post Mar 1, 2025); preprint or journal DOI exists - [ELIXIR] — talk in the ELIXIR Track (community / infrastructure stream embedded in main program) - [INDUSTRY] — Industry Track talk (one session, Monday) - [FOCUS] — Focus session talk (4 sessions across Tue + Wed; topical themes) - [TUTORIAL] — Thursday Sep 3 tutorial / workshop - [SCS] — ISCB Student Council Symposium (Thu Sep 3) - [COMMUNITIES] — Communities Day satellite (Fri Sep 4) - [KEYNOTE] — distinguished keynote - [?] — placeholder; populated post-meeting

Sparse-coverage flags: - Accepted proceedings list not yet public. Proceedings notifications went to authors mid-May 2026 (current cycle). The Bioinformatics OUP supplement typically posts in late-July or August 2026 (~3–6 weeks before the meeting). Until then, per-paper titles + authors are not extractable from a public source. Monitor: academic.oup.com/bioinformatics — ECCB 2026 special issue, expected Jul–Aug 2026. - Highlight-talk acceptances trickle in. Submissions closed Apr 20, 2026; acceptance notifications go to authors early-June 2026. Recheck the highlight-talks page in mid-June. - ELIXIR Track program not yet public. Four ELIXIR Track sessions are scheduled (3 on Mon Aug 31, 1 on Tue Sep 1, 1 on Wed Sep 2 — total 5 by the day-by-day program, but consistently described as "ELIXIR Track" across 3 days). Session topics typically firm up in June via ELIXIR Europe's events calendar. - Tutorial / workshop list not yet public. Tutorials & Workshops chairs (Patricia Palagi + Diana Marek, SIB) typically post the tutorial list 6–8 weeks pre-meeting (late-June / early-July). - Communities Day (Sep 4) satellite list not yet public. SIB Communities organizes independent events; each Community typically posts its own program 4–6 weeks pre-meeting on the SIB Communities pages. - Slide deposits. No central ECCB Zenodo community historically. Bioconductor speakers deposit to zenodo.org/communities/bioconductor. SIB speakers may deposit to a SIB Zenodo community. Others ad-hoc. - Recordings. ECCB historically uneven on recordings. ISCB Nucleus may host some content; recheck post-meeting.

Verified high-level facts (2026-05-11)

  • Conference: ECCB 2026 — 25th European Conference on Computational Biology
  • Dates: Mon Aug 31 – Fri Sep 4, 2026
  • Venue: Geneva, Switzerland (specific venue not yet named on public site; SIB-organized)
  • Theme: "Biodiversity, AI & Health: computational biology to address the challenges of our time"
  • Organizer: SIB Swiss Institute of Bioinformatics
  • Joint year? NO. This is ECCB-only. ISMB/ECCB joint year was 2025 (Liverpool, Jul 20–24). ISMB 2026 is a separate event: Washington DC, Jul 12–16. We treat ECCB 2026 and ISMB 2026 as sibling vaults, not merged.
  • Scale: ~1,000–2,000 attendees historical baseline (between EuroBioC's ~250 and ISMB's ~3,000)
  • Proceedings: Online-only OUP Bioinformatics special issue. CC-BY. $715 USD APC. Submissions closed; notifications mid-May 2026. Author registration deadline Jun 30, 2026. Expected supplement online Jul–Aug 2026.
  • Highlight talks: Window closed Apr 20, 2026. Notifications early-June 2026. Eligibility: published post Mar 1, 2025.
  • Posters: Same submission cycle as highlight talks (closed Apr 20, 2026; notifications early-June 2026).
  • Distinguished Keynotes: 4 confirmed (Farrar, Malaspinas, Quake, Walczak)
  • Scientific Areas: 5 (Genomics, Transcriptomics, Proteins/Structural Biology, Systems Biology, Biodiversity/Sustainability)
  • ELIXIR Track: embedded in Mon/Tue/Wed main program (count ≈4 sessions)
  • Tutorials & Workshops: Thu Sep 3 (count not yet public; SIB Training chairs)
  • ISCB Student Council Symposium: Thu Sep 3
  • Communities Day: Fri Sep 4 — independent SIB Communities satellites

Distinguished Keynotes (4)

Day Speaker Affiliation Title Notes
Mon Aug 31 (opening) Jeremy Farrar WHO Assistant Director-General for Health Promotion, Switzerland (TBD — likely "AI & Global Health" framing) Ex-WHO Chief Scientist, ex-Wellcome Director; not a methods talk — policy/global-health framing; sets up theme "AI & Health"
Tue Sep 1 Stephen Quake Stanford University, USA (Bioengineering + Applied Physics) "Understanding the mysteries of the cell: How do many cell types arise from one genome?" Single-cell biology pioneer; ex-CZI Science Head; ex-CZ Biohub co-founder; elected to all three US National Academies
Tue Sep 1 Anna-Sapfo Malaspinas UNIL + SIB, Switzerland "Tracing human history through DNA" (working title from outreach page) Ancient-DNA / population genetics; PhD UC Berkeley (Slatkin lab); SIB-affiliated; aligns with biodiversity area
Wed Sep 2 (closing) Aleksandra Walczak CNRS / Physics Laboratory of ENS, France "Learning about immune response from large-scale data" Physics-trained; immune-repertoire modeling; French Academy of Sciences (2024); CNRS medals

Keynote-level overlap to flag: - Stephen Quake (Stanford) is highly likely to be cited at ISMB 2026 MLCSB (single-cell foundation models, scGPT-class) and at AACR 2026 (CZ Biohub cell-type catalog). His ECCB → ISMB → AACR cross-link is the strongest tool-overlap thread on the keynote roster. - Anna-Sapfo Malaspinas's ancient-DNA / population genetics work overlaps with ISMB EvolCompGen COSI and RECOMB Phylogeny sessions. - Aleksandra Walczak's immune-repertoire framework overlaps with ISMB CSi (Computational and Systems Immunology) COSI and possibly with SITC 2026 immune-repertoire vendors (CZ Biohub spillover). - Jeremy Farrar's keynote is a policy framing, not a methods talk — set up the keynote page as a policy/context entry, not a methods entry.

Day-by-day skeleton (from the public Programme page)

Monday Aug 31, 2026 — Day 1: Opening + Industry + ELIXIR-heavy

  • 10:00–11:00: Opening Ceremony — Guy Parmelin (President of the Swiss Confederation) address
  • (slot TBD): Opening Keynote — Jeremy Farrar (WHO)
  • 3 Scientific sessions: Proceedings + Highlight talks across Genomics / Transcriptomics / Proteins-Structural / Systems Biology / Biodiversity (one area per session, in parallel with special tracks)
  • 3 Special-track sessions: 2 ELIXIR + 1 Industry
  • 14:00–17:15: Public outreach event (in French) — distinct from main scientific program; SIB civic-engagement layer
  • 17:15–18:30: Welcome Reception

Tuesday Sep 1, 2026 — Day 2: 2 keynotes + Quake-anchor

  • (slot TBD): Distinguished Keynote — Anna-Sapfo Malaspinas (UNIL/SIB)
  • (slot TBD): Distinguished Keynote — Stephen Quake (Stanford) "Understanding the mysteries of the cell: How do many cell types arise from one genome?"
  • 3 Scientific sessions: Proceedings + Highlight talks
  • 3 Special-track sessions: 1 ELIXIR + 2 Focus sessions
  • Poster Session 1
  • 18:15–00:00: Conference Party

Wednesday Sep 2, 2026 — Day 3: Close + Walczak

  • 3 Scientific sessions: Proceedings + Highlight talks
  • 3 Special-track sessions: 1 ELIXIR + 2 Focus sessions
  • Poster Session 2 + Career Workshop (parallel)
  • (closing slot): Distinguished Keynote — Aleksandra Walczak (CNRS/ENS) "Learning about immune response from large-scale data"
  • Best-paper / best-student-paper award announcement (assumed; ECCB precedent)
  • 16:00: Conference Closing

Thursday Sep 3, 2026 — Day 4: Tutorials + Student Council + SIB SAB

  • Tutorials & Workshops — full-day track; count not yet public; chairs Palagi + Marek (SIB)
  • ISCB Student Council Symposium (European edition) — early-career
  • SIB Scientific Advisory Board meeting (closed / invitation only)

Friday Sep 4, 2026 — Day 5: Communities Day

  • Independent satellite events organized by SIB Communities
  • Themes: biodiversity, pathogen surveillance, research infrastructures
  • Each Community runs its own format (half-day workshop / hackathon / training day)
  • Specific satellite list TBD; SIB Communities pages typically post 4–6 weeks pre-meeting

Scientific Areas + Area Chairs (5)

Area Chair Institution AACR-axis fit
Genomics Knut Reinert Free University of Berlin High — sequencing methods, pangenome, structural variants
Transcriptomics Uwe Ohler Max Delbrück Center, Berlin High — RNA-seq, single-cell, regulatory genomics
Proteins / Structural Biology Ivet Bahar Stony Brook University, USA High — drug-target, AlphaFold-class, dynamics
Systems Biology Alfonso Valencia Barcelona Supercomputing Center High — pathway, multi-omics, network methods
Biodiversity / Sustainability Katja Bärenfaller University of Zurich / SIB Low (for AACR per se) but high for One-Health / pathogen / environmental axes

Programme Committee Chair: Christophe Dessimoz (SIB Executive Director) — OMA orthology project lead; comparative genomics.

Scientific Committee co-chairs: Anne-Florence Bitbol (EPFL Lausanne) + Niko Beerenwinkel (ETH Zurich, D-BSSE Basel) — Beerenwinkel especially relevant: cancer-clonal-evolution / tumor phylogeny methods (e.g., SCITE, OncoNEM) used in AACR-axis work.

Cross-vault speaker overlap watch

Expected ECCB 2026 speakers based on (a) typical EuroBioC → GBCC → ISMB → ECCB → BioC annual rotation, (b) European-side lab activity in proceedings-paper-class methods, (c) past ECCB participation, (d) SIB / EMBL / EPFL / ETH proximity. Not confirmed — pending public proceedings + highlight-talk lists.

Person Lab / institution Where they appeared (in corpus) Likely ECCB 2026 venue Likely topic
Charlotte Soneson Friedrich Miescher Institute, Basel EuroBioC2025 (footprintR), GBCC2025 (keynote), ISMB 2026 (predicted BOSC/RegSys) Proceedings or ELIXIR or Transcriptomics highlight footprintR / Bioconductor maintenance; Basel adjacency makes ECCB a natural stop
Stefano Mangiola Adelaide University (Australia, but EU-collab heavy) EuroBioC2025, GBCC2025, ISMB 2026 (predicted BOSC + MLCSB) Highlight or ELIXIR Tidyomics scaling; HCA-scale tidy analysis
Helena Crowell CNAG-CRG Barcelona EuroBioC2025 (CRC whole-tx imaging keynote) Proceedings or Highlight or Transcriptomics Spatial CRC follow-up
Luca Marconato EMBL Heidelberg EuroBioC2025 (SpatialData) Proceedings or Transcriptomics SpatialData v2 / multimodal imaging
Tuomas Borman University of Turku EuroBioC2025 (mia workshop), GBCC2025 (mia/miaverse) ELIXIR or Biodiversity or Tutorial mia / miaverse — Microbiome COSI analogue
Robert Castelo Pompeu Fabra Barcelona GBCC2025 (atena) Highlight or ELIXIR atena / TE analysis
Federico Marini IMBEI Mainz EuroBioC2025 (iSEE workshop) Tutorial or Highlight iSEE / DeeDeeExperiment
Najla Abassi IMBEI Mainz EuroBioC2025 (DeeDeeExperiment) Highlight DeeDeeExperiment update
Mark D. Robinson + lab (Gunz, Cai, Emons, Wang) University of Zurich EuroBioC2025 (DESpace, spatialFDA, ATAC-seq bias), GBCC2025 (sosta) Proceedings × multiple sosta / DESpace / spatialFDA — Zurich adjacency strong
Niko Beerenwinkel + lab ETH Zurich, D-BSSE Basel Scientific Committee co-chair this year will not present (chair role), but lab members likely tumor phylogeny / clonal evolution methods
Christophe Dessimoz + lab UNIL + SIB Programme Chair this year will not present (chair role) OMA / orthology
Anne-Florence Bitbol + lab EPFL Lausanne Scientific Committee co-chair will not present (chair role) Protein co-evolution / sequence-structure
Patricia Palagi + lab SIB Tutorials chair likely Tutorial slot Training infrastructure
Olga Vitek Northeastern (US, but EU-collab heavy) Adjacent to ISMB CompMS / MS proteomics community Possible Proteomics highlight MSstats
Laurent Gatto UCLouvain (Brussels) Bioconductor MS proteomics core ELIXIR or Tutorial MSnbase / RforMassSpectrometry
Wolfgang Huber EMBL Heidelberg Bioconductor founder; Heidelberg adjacency Highlight or Proceedings DESeq2 / multi-omics infra
Alfonso Valencia + lab BSC Barcelona Systems Biology area chair Plenary or chair-introduction; lab members likely Network methods
Anaïs Baudot Aix-Marseille / CNRS Network biology, multilayer networks Systems Biology highlight MultilayerNetworks
Mihaela Pertea / Steven Salzberg (USA-EU bridge) Johns Hopkins Genomics; Reinert area Genomics highlight StringTie / HISAT successor
Knut Reinert + lab Free University of Berlin Genomics area chair will not present (chair role); lab members likely SeqAn / variant-calling infra
Uwe Ohler + lab Max Delbrück Center Transcriptomics area chair will not present (chair role); lab members likely regulatory genomics / single-cell
Ivet Bahar + lab Stony Brook (USA, with strong EU collabs) Proteins/Structural area chair will not present (chair role); lab members likely ProDy / dynamics
Yoshihide Hayashizaki / FANTOM consortium RIKEN (Japan) — long-standing ECCB visitors — possible plenary CAGE / non-coding RNA

Sustained "Europe-heavy" prediction: EuroBioC 2025 → ECCB 2026 has the highest single-vault speaker overlap of any two vaults in the corpus, because both are SIB / EMBL / Robinson-lab / Soneson / Crowell / Marconato / Borman / Marini / Castelo-adjacent. We expect ~60–80% of EuroBioC2025 tool-page entries to have an ECCB 2026 update line.

Tool/package shortlist for the bulk extraction pass

Existing-in-corpus tools with high probability of an ECCB 2026 slot (proceedings paper, highlight talk, ELIXIR demo, or tutorial):

  1. SpatialData (scverse, Marconato et al., EMBL Heidelberg) — proceedings paper or highlight talk; Heidelberg adjacency. Last full release covered at EuroBioC 2025; ECCB 2026 is the natural European venue for the v1.x → v2 update.
  2. footprintR (Soneson, FMI Basel) — Transcriptomics highlight or ELIXIR Bioconductor session.
  3. Tidyomics / tidySingleCellExperiment family (Mangiola, Adelaide+European collab) — highlight talk or ELIXIR; published 2025 in Nat Methods-class venues makes it eligible for the highlight track.
  4. mia / miaverse (Borman, Lahti, Turku) — Biodiversity area highlight or ELIXIR or Tutorial; ECCB Biodiversity area is the natural slot.
  5. iSEE + DeeDeeExperiment (Marini, Abassi, IMBEI Mainz) — Tutorial or Highlight.
  6. DESpace / spatialFDA / sosta (Robinson lab, Zurich) — Proceedings paper × multiple; Zurich adjacency strong; same speaker pattern as their ISMB 2026 / EuroBioC 2025 / GBCC 2025 cycle.
  7. MultiAssayExperiment / curatedTCGAData (Ramos Pérez, CUNY/Roswell) — possible ELIXIR Bioconductor session.
  8. atena (Castelo, UPF Barcelona) — Highlight or ELIXIR.
  9. plyxp / fishpond (Love lab, UNC — with European collabs) — Transcriptomics highlight.
  10. signifinder (Pirrotta, Padova) — Systems Biology or Transcriptomics highlight.
  11. OSTA / Bioconductor spatial book (Dong, Patrick) — Tutorial track candidate.
  12. OMA orthology (Dessimoz lab, SIB) — Programme Chair's home project; possibly Plenary/ELIXIR rather than contributed slot.
  13. Bio.tools registry (ELIXIR Norway / EMBL-EBI) — ELIXIR Track infrastructure entry.
  14. BioContainers (ELIXIR / Galaxy) — ELIXIR Track infrastructure entry.
  15. Galaxy Europe (Freiburg / ELIXIR) — ELIXIR Track infrastructure entry; bridges to Galaxy + GBCC 2025 vault.
  16. Ensembl / UniProt / IntAct / Reactome (EMBL-EBI core resources) — ELIXIR Track infrastructure entries; bridge to multiple AACR-axis tool pages.
  17. OncoNEM / SCITE / clonal-evolution methods (Beerenwinkel lab, ETH Zurich) — Scientific Committee co-chair home; lab-member proceedings paper likely; cancer-clonal-evolution AACR-axis fit.

New ECCB-debuting candidates (predicted from current preprint flow / SIB / EMBL / EPFL pipelines; not confirmed):

  1. Pangenome graph tooling (Reinert lab Berlin, Soueidan, Beller) — Genomics area.
  2. Long-read isoform discovery successors (Ohler lab Berlin, Patro lab USA-EU bridge) — Transcriptomics area.
  3. AlphaFold-class downstream tooling (Bahar lab, EPFL Bitbol lab) — Proteins/Structural area.
  4. Multilayer / multi-omics network methods (Valencia lab Barcelona, Baudot lab Marseille) — Systems Biology area.
  5. Ancient-DNA tooling (Malaspinas lab UNIL — keynote sets agenda) — likely highlight talks on damageprofiler, ANGSD, qpAdm-class methods.
  6. Single-cell foundation-model European spinouts (post-scGPT / Geneformer; Crowell lab, Ohler lab) — Transcriptomics highlight.
  7. Pathogen-surveillance genomic tooling (Beerenwinkel lab, Stadler lab — Swiss SARS-CoV-2 lineage tracking heritage) — Communities Day satellite or Genomics highlight.
  8. One-Health / biodiversity-genomics tooling (Bärenfaller area + Communities Day) — likely environmental microbiome / pollinator-genomics tools; novel category for AACR vault.
  9. Immune-repertoire modeling tools (Walczak keynote sets agenda) — IGoR, OLGA, sonia-class — relevant to ISMB CSi COSI and SITC 2026 cross-link.

Tutorials as tool pages (Thu Sep 3, count TBD — typically 6–10 at ECCB):

27.–34+. Populated once the Tutorials & Workshops chairs publish the list (expected late-June 2026).

ELIXIR Track entries (count ≈4 sessions × ~3 talks per session):

35.–46+. Populated once the ELIXIR Track program firms up; treated as infrastructure entries in topics/elixir-infra/ rather than full tool pages.

Communities Day satellites (Fri Sep 4, count TBD — typically 5–10 SIB Communities):

47.+. Populated from SIB Communities pages 4–6 weeks pre-meeting; each Community gets its own short entry; tool pages only when the satellite produces an AACR-axis-relevant tool.

Excluded from initial tool-page pass:

  • Keynotes (handled in keynotes/ directory, not tools/) — 4 entries
  • Industry Track talk (Mon Aug 31) — vendor demos; selectively triage based on open-source artifacts
  • Career Workshop (Wed Sep 2) — not a tools venue
  • Public outreach event (Mon Aug 31 PM, in French) — civic engagement; not a tools venue
  • Opening-ceremony political address (Parmelin) — context entry, not a tool entry

Open follow-ups before bulk extraction

  1. Watch for accepted-proceedings list — author notifications mid-May 2026; OUP Bioinformatics supplement typically posts late-July or August 2026. URL to monitor: academic.oup.com/bioinformatics + ECCB 2026 announcements feed at eccb2026.org/news (the public site has a news section that posts paper-list announcements).
  2. Highlight-talk acceptances — notifications early-June 2026. Recheck eccb2026.org/call-highlight-talk-poster.
  3. ELIXIR Track program — typically firms up in June via ELIXIR Europe's events calendar at elixir-europe.org/events. Recheck mid-to-late June.
  4. Tutorial / workshop list — Palagi + Marek (SIB Training) typically post 6–8 weeks pre-meeting; recheck late-June / early-July.
  5. Communities Day satellite programs — SIB Communities pages typically post 4–6 weeks pre-meeting; check via sib.swiss Communities listings.
  6. bioRxiv "to appear in ECCB 2026" preprints — cross-search bioRxiv for the "Comments: To appear in ECCB 2026 proceedings" tag; useful for getting paper-and-code links before the OUP supplement is online.
  7. ISMB 2026 ↔ ECCB 2026 cross-link prep — since both use the same Bioinformatics OUP proceedings track but with separate program committees, identify any authors with papers in both supplements (unlikely but possible for dual-submission edge cases); annotate cross-link in the tool page Proceedings row.
  8. Slide DOIs (post-meeting). No ECCB-wide Zenodo community; check (a) zenodo.org/communities/bioconductor for Bioconductor speakers, (b) a SIB Zenodo community if one exists, (c) individual lab sites.
  9. Cross-link map. Build the EuroBioC2025 ↔ GBCC2025 ↔ ISMB 2026 ↔ ECCB 2026 ↔ BioC2026 cross-link table after both ISMB (Jul 16) and ECCB (Sep 4) close. Heaviest expected re-up traffic: Soneson, Marconato, Crowell, Borman, Castelo, Marini, Robinson lab, Beerenwinkel lab, Dessimoz lab, Mangiola.
  10. AACR cross-link mirror policy. Decide (see tools/index.md Open Q2) whether ECCB highlight-talk tools (which by definition are already-published 2025 papers) get fresh entries or "ECCB 2026 highlight" sections appended to existing entries. Proposed default: append to existing entry.