{"record_type":"pith_number_record","schema_url":"https://pith.science/schemas/pith-number/v1.json","pith_number":"pith:2016:DDFOEKM2TEQJND2D4V5KIJ6QIA","short_pith_number":"pith:DDFOEKM2","schema_version":"1.0","canonical_sha256":"18cae2299a9920968f43e57aa427d040146ff5c8e1dc1f9eb86a07bd880a79a2","source":{"kind":"arxiv","id":"1603.01994","version":1},"attestation_state":"computed","paper":{"title":"SCOTTI: Efficient Reconstruction of Transmission within Outbreaks with the Structured Coalescent","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":[],"primary_cat":"q-bio.PE","authors_text":"Chieh-Hsi Wu, Daniel J Wilson, Nicola De Maio","submitted_at":"2016-03-07T10:15:36Z","abstract_excerpt":"Exploiting pathogen genomes to reconstruct transmission represents a powerful tool in the fight against infectious disease. However, their interpretation rests on a number of simplifying assumptions that regularly ignore important complexities of real data, in particular within-host evolution and non-sampled patients.\n  Here we propose a new approach to transmission inference called SCOTTI (Structured COalescent Transmission Tree Inference). This method is based on a statistical framework that models each host as a distinct population, and transmissions between hosts as migration events. Our c"},"verification_status":{"content_addressed":true,"pith_receipt":true,"author_attested":false,"weak_author_claims":0,"strong_author_claims":0,"externally_anchored":false,"storage_verified":false,"citation_signatures":0,"replication_records":0,"graph_snapshot":true,"references_resolved":false,"formal_links_present":false},"canonical_record":{"source":{"id":"1603.01994","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.PE","submitted_at":"2016-03-07T10:15:36Z","cross_cats_sorted":[],"title_canon_sha256":"3f2db5d3ea2df774f1dacd68b9d1d48344f6a294bbbfac8866d5527c301f7966","abstract_canon_sha256":"fca734476098d027cd751324a8ddac541785eb703c1de413defa2278e28ffcf5"},"schema_version":"1.0"},"receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-05-18T00:51:17.853475Z","signature_b64":"k/XsyU+s54SeLQu74v0dpr2CVQdhLeEHXVXVud5sVfGjkKzgtz5vraCpFLLTY9wqV36N0FT0SOGXV+2gHKCWCg==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"18cae2299a9920968f43e57aa427d040146ff5c8e1dc1f9eb86a07bd880a79a2","last_reissued_at":"2026-05-18T00:51:17.852767Z","signature_status":"signed_v1","first_computed_at":"2026-05-18T00:51:17.852767Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"graph_snapshot":{"paper":{"title":"SCOTTI: Efficient Reconstruction of Transmission within Outbreaks with the Structured Coalescent","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":[],"primary_cat":"q-bio.PE","authors_text":"Chieh-Hsi Wu, Daniel J Wilson, Nicola De Maio","submitted_at":"2016-03-07T10:15:36Z","abstract_excerpt":"Exploiting pathogen genomes to reconstruct transmission represents a powerful tool in the fight against infectious disease. However, their interpretation rests on a number of simplifying assumptions that regularly ignore important complexities of real data, in particular within-host evolution and non-sampled patients.\n  Here we propose a new approach to transmission inference called SCOTTI (Structured COalescent Transmission Tree Inference). This method is based on a statistical framework that models each host as a distinct population, and transmissions between hosts as migration events. Our c"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1603.01994","kind":"arxiv","version":1},"verdict":{"id":null,"model_set":{},"created_at":null,"strongest_claim":"","one_line_summary":"","pipeline_version":null,"weakest_assumption":"","pith_extraction_headline":""},"references":{"count":0,"sample":[],"resolved_work":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","internal_anchors":0},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"author_claims":{"count":0,"strong_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"builder_version":"pith-number-builder-2026-05-17-v1"},"aliases":[{"alias_kind":"arxiv","alias_value":"1603.01994","created_at":"2026-05-18T00:51:17.852881+00:00"},{"alias_kind":"arxiv_version","alias_value":"1603.01994v1","created_at":"2026-05-18T00:51:17.852881+00:00"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1603.01994","created_at":"2026-05-18T00:51:17.852881+00:00"},{"alias_kind":"pith_short_12","alias_value":"DDFOEKM2TEQJ","created_at":"2026-05-18T12:30:12.583610+00:00"},{"alias_kind":"pith_short_16","alias_value":"DDFOEKM2TEQJND2D","created_at":"2026-05-18T12:30:12.583610+00:00"},{"alias_kind":"pith_short_8","alias_value":"DDFOEKM2","created_at":"2026-05-18T12:30:12.583610+00:00"}],"events":[],"event_summary":{},"paper_claims":[],"inbound_citations":{"count":0,"internal_anchor_count":0,"sample":[]},"formal_canon":{"evidence_count":0,"sample":[],"anchors":[]},"links":{"html":"https://pith.science/pith/DDFOEKM2TEQJND2D4V5KIJ6QIA","json":"https://pith.science/pith/DDFOEKM2TEQJND2D4V5KIJ6QIA.json","graph_json":"https://pith.science/api/pith-number/DDFOEKM2TEQJND2D4V5KIJ6QIA/graph.json","events_json":"https://pith.science/api/pith-number/DDFOEKM2TEQJND2D4V5KIJ6QIA/events.json","paper":"https://pith.science/paper/DDFOEKM2"},"agent_actions":{"view_html":"https://pith.science/pith/DDFOEKM2TEQJND2D4V5KIJ6QIA","download_json":"https://pith.science/pith/DDFOEKM2TEQJND2D4V5KIJ6QIA.json","view_paper":"https://pith.science/paper/DDFOEKM2","resolve_alias":"https://pith.science/api/pith-number/resolve?arxiv=1603.01994&json=true","fetch_graph":"https://pith.science/api/pith-number/DDFOEKM2TEQJND2D4V5KIJ6QIA/graph.json","fetch_events":"https://pith.science/api/pith-number/DDFOEKM2TEQJND2D4V5KIJ6QIA/events.json","actions":{"anchor_timestamp":"https://pith.science/pith/DDFOEKM2TEQJND2D4V5KIJ6QIA/action/timestamp_anchor","attest_storage":"https://pith.science/pith/DDFOEKM2TEQJND2D4V5KIJ6QIA/action/storage_attestation","attest_author":"https://pith.science/pith/DDFOEKM2TEQJND2D4V5KIJ6QIA/action/author_attestation","sign_citation":"https://pith.science/pith/DDFOEKM2TEQJND2D4V5KIJ6QIA/action/citation_signature","submit_replication":"https://pith.science/pith/DDFOEKM2TEQJND2D4V5KIJ6QIA/action/replication_record"}},"created_at":"2026-05-18T00:51:17.852881+00:00","updated_at":"2026-05-18T00:51:17.852881+00:00"}