{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2024:4BV7VIJXETAH53YZ2HHZLGKITS","short_pith_number":"pith:4BV7VIJX","canonical_record":{"source":{"id":"2411.04363","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by-nc-sa/4.0/","primary_cat":"q-bio.GN","submitted_at":"2024-11-07T01:44:17Z","cross_cats_sorted":[],"title_canon_sha256":"5cab4f9d2892af4a2e8a3a94bde75bd07ac60147c8417b2c35f641b6043dca8f","abstract_canon_sha256":"f46cad044a63d592a757d6897c0901bff0eb094a931e41f5914c92fd7e64613c"},"schema_version":"1.0"},"canonical_sha256":"e06bfaa13724c07eef19d1cf9599489ca6898587c4e00ce7cf46141c726e9b94","source":{"kind":"arxiv","id":"2411.04363","version":1},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2411.04363","created_at":"2026-07-05T09:32:18Z"},{"alias_kind":"arxiv_version","alias_value":"2411.04363v1","created_at":"2026-07-05T09:32:18Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2411.04363","created_at":"2026-07-05T09:32:18Z"},{"alias_kind":"pith_short_12","alias_value":"4BV7VIJXETAH","created_at":"2026-07-05T09:32:18Z"},{"alias_kind":"pith_short_16","alias_value":"4BV7VIJXETAH53YZ","created_at":"2026-07-05T09:32:18Z"},{"alias_kind":"pith_short_8","alias_value":"4BV7VIJX","created_at":"2026-07-05T09:32:18Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2024:4BV7VIJXETAH53YZ2HHZLGKITS","target":"record","payload":{"canonical_record":{"source":{"id":"2411.04363","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by-nc-sa/4.0/","primary_cat":"q-bio.GN","submitted_at":"2024-11-07T01:44:17Z","cross_cats_sorted":[],"title_canon_sha256":"5cab4f9d2892af4a2e8a3a94bde75bd07ac60147c8417b2c35f641b6043dca8f","abstract_canon_sha256":"f46cad044a63d592a757d6897c0901bff0eb094a931e41f5914c92fd7e64613c"},"schema_version":"1.0"},"canonical_sha256":"e06bfaa13724c07eef19d1cf9599489ca6898587c4e00ce7cf46141c726e9b94","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-07-05T09:32:18.145446Z","signature_b64":"MzNYJE5vVJAAAY/J9+p1N4HAE7NkWE+elScehKt4EVQJKioDF08YfRudy5UKOaYN1JJ9EvJoxnKhC5LdP/u1BQ==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"e06bfaa13724c07eef19d1cf9599489ca6898587c4e00ce7cf46141c726e9b94","last_reissued_at":"2026-07-05T09:32:18.144950Z","signature_status":"signed_v1","first_computed_at":"2026-07-05T09:32:18.144950Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"2411.04363","source_version":1,"attestation_state":"computed"},"signer":{"signer_id":"pith.science","signer_type":"pith_registry","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"created_at":"2026-07-05T09:32:18Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"8duQF76Rk6GfpHruX62h1GGP+ZIsppggMqEsgB2PQHsSqMBMo23Zuqqh4YQlV0Eiw1akEm8ufBYXqo4pERqDDg==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-03T20:48:48.015270Z"},"content_sha256":"a8b94f6bf9cde53346ec8382b866c7da20b8ecbe285770980afdd77e9e102a30","schema_version":"1.0","event_id":"sha256:a8b94f6bf9cde53346ec8382b866c7da20b8ecbe285770980afdd77e9e102a30"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2024:4BV7VIJXETAH53YZ2HHZLGKITS","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"Perspective on recent developments and challenges in regulatory and systems genomics","license":"http://creativecommons.org/licenses/by-nc-sa/4.0/","headline":"","cross_cats":[],"primary_cat":"q-bio.GN","authors_text":"Alejandra Medina-Rivera, Anthony Mathelier, Ferhat Ay, Jason Ernst, Julia Zeiltinger, Saurabh Sinha, Shaun Mahony, Sushmita Roy","submitted_at":"2024-11-07T01:44:17Z","abstract_excerpt":"Predicting how genetic variation affects phenotypic outcomes at the organismal, cellular, and molecular levels requires deciphering the cis-regulatory code, the sequence rules by which non-coding regions regulate genes. In this perspective, we discuss recent computational progress and challenges towards solving this fundamental problem. We describe how cis-regulatory elements are mapped and how their sequence rules can be learned and interpreted with sequence-to-function neural networks, with the goal of identifying genetic variants in human disease. We also discuss how studies of the 3D chrom"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2411.04363","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":""},"integrity":{"clean":true,"summary":{"advisory":0,"critical":0,"by_detector":{},"informational":0},"endpoint":"/pith/2411.04363/integrity.json","findings":[],"available":true,"detectors_run":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938"},"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"},"verdict_id":null},"signer":{"signer_id":"pith.science","signer_type":"pith_registry","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"created_at":"2026-07-05T09:32:18Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"vAjmc7NGYzJSSlOljw9prAyUuTGCH1KOJBDmWaxEfb8Tl4HLrN0poukSDZ761q5IE1LMTWaBrW9uzKVTHDRVBQ==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-03T20:48:48.015650Z"},"content_sha256":"4746b13d5aadef0b8aee93ff0b60d699222dcc6378e6dae7739793958130ff4e","schema_version":"1.0","event_id":"sha256:4746b13d5aadef0b8aee93ff0b60d699222dcc6378e6dae7739793958130ff4e"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/4BV7VIJXETAH53YZ2HHZLGKITS/bundle.json","state_url":"https://pith.science/pith/4BV7VIJXETAH53YZ2HHZLGKITS/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/4BV7VIJXETAH53YZ2HHZLGKITS/bundle.json","status":"primary"}],"public_keys":[{"key_id":"pith-v1-2026-05","algorithm":"ed25519","format":"raw","public_key_b64":"stVStoiQhXFxp4s2pdzPNoqVNBMojDU/fJ2db5S3CbM=","public_key_hex":"b2d552b68890857171a78b36a5dccf368a953413288c353f7c9d9d6f94b709b3","fingerprint_sha256_b32_first128bits":"RVFV5Z2OI2J3ZUO7ERDEBCYNKS","fingerprint_sha256_hex":"8d4b5ee74e4693bcd1df2446408b0d54","rotates_at":null,"url":"https://pith.science/pith-signing-key.json","notes":"Pith uses this Ed25519 key to sign canonical record SHA-256 digests. Verify with: ed25519_verify(public_key, message=canonical_sha256_bytes, signature=base64decode(signature_b64))."}],"merge_version":"pith-open-graph-merge-v1","built_at":"2026-08-03T20:48:48Z","links":{"resolver":"https://pith.science/pith/4BV7VIJXETAH53YZ2HHZLGKITS","bundle":"https://pith.science/pith/4BV7VIJXETAH53YZ2HHZLGKITS/bundle.json","state":"https://pith.science/pith/4BV7VIJXETAH53YZ2HHZLGKITS/state.json","well_known_bundle":"https://pith.science/.well-known/pith/4BV7VIJXETAH53YZ2HHZLGKITS/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2024:4BV7VIJXETAH53YZ2HHZLGKITS","merge_version":"pith-open-graph-merge-v1","event_count":2,"valid_event_count":2,"invalid_event_count":0,"equivocation_count":0,"current":{"canonical_record":{"metadata":{"abstract_canon_sha256":"f46cad044a63d592a757d6897c0901bff0eb094a931e41f5914c92fd7e64613c","cross_cats_sorted":[],"license":"http://creativecommons.org/licenses/by-nc-sa/4.0/","primary_cat":"q-bio.GN","submitted_at":"2024-11-07T01:44:17Z","title_canon_sha256":"5cab4f9d2892af4a2e8a3a94bde75bd07ac60147c8417b2c35f641b6043dca8f"},"schema_version":"1.0","source":{"id":"2411.04363","kind":"arxiv","version":1}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2411.04363","created_at":"2026-07-05T09:32:18Z"},{"alias_kind":"arxiv_version","alias_value":"2411.04363v1","created_at":"2026-07-05T09:32:18Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2411.04363","created_at":"2026-07-05T09:32:18Z"},{"alias_kind":"pith_short_12","alias_value":"4BV7VIJXETAH","created_at":"2026-07-05T09:32:18Z"},{"alias_kind":"pith_short_16","alias_value":"4BV7VIJXETAH53YZ","created_at":"2026-07-05T09:32:18Z"},{"alias_kind":"pith_short_8","alias_value":"4BV7VIJX","created_at":"2026-07-05T09:32:18Z"}],"graph_snapshots":[{"event_id":"sha256:4746b13d5aadef0b8aee93ff0b60d699222dcc6378e6dae7739793958130ff4e","target":"graph","created_at":"2026-07-05T09:32:18Z","signer":{"key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signer_id":"pith.science","signer_type":"pith_registry"},"payload":{"graph_snapshot":{"author_claims":{"count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","strong_count":0},"builder_version":"pith-number-builder-2026-05-17-v1","claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"integrity":{"available":true,"clean":true,"detectors_run":[],"endpoint":"/pith/2411.04363/integrity.json","findings":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938","summary":{"advisory":0,"by_detector":{},"critical":0,"informational":0}},"paper":{"abstract_excerpt":"Predicting how genetic variation affects phenotypic outcomes at the organismal, cellular, and molecular levels requires deciphering the cis-regulatory code, the sequence rules by which non-coding regions regulate genes. In this perspective, we discuss recent computational progress and challenges towards solving this fundamental problem. We describe how cis-regulatory elements are mapped and how their sequence rules can be learned and interpreted with sequence-to-function neural networks, with the goal of identifying genetic variants in human disease. We also discuss how studies of the 3D chrom","authors_text":"Alejandra Medina-Rivera, Anthony Mathelier, Ferhat Ay, Jason Ernst, Julia Zeiltinger, Saurabh Sinha, Shaun Mahony, Sushmita Roy","cross_cats":[],"headline":"","license":"http://creativecommons.org/licenses/by-nc-sa/4.0/","primary_cat":"q-bio.GN","submitted_at":"2024-11-07T01:44:17Z","title":"Perspective on recent developments and challenges in regulatory and systems genomics"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2411.04363","kind":"arxiv","version":1},"verdict":{"created_at":null,"id":null,"model_set":{},"one_line_summary":"","pipeline_version":null,"pith_extraction_headline":"","strongest_claim":"","weakest_assumption":""}},"verdict_id":null}}],"author_attestations":[],"timestamp_anchors":[],"storage_attestations":[],"citation_signatures":[],"replication_records":[],"corrections":[],"mirror_hints":[],"record_created":{"event_id":"sha256:a8b94f6bf9cde53346ec8382b866c7da20b8ecbe285770980afdd77e9e102a30","target":"record","created_at":"2026-07-05T09:32:18Z","signer":{"key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signer_id":"pith.science","signer_type":"pith_registry"},"payload":{"attestation_state":"computed","canonical_record":{"metadata":{"abstract_canon_sha256":"f46cad044a63d592a757d6897c0901bff0eb094a931e41f5914c92fd7e64613c","cross_cats_sorted":[],"license":"http://creativecommons.org/licenses/by-nc-sa/4.0/","primary_cat":"q-bio.GN","submitted_at":"2024-11-07T01:44:17Z","title_canon_sha256":"5cab4f9d2892af4a2e8a3a94bde75bd07ac60147c8417b2c35f641b6043dca8f"},"schema_version":"1.0","source":{"id":"2411.04363","kind":"arxiv","version":1}},"canonical_sha256":"e06bfaa13724c07eef19d1cf9599489ca6898587c4e00ce7cf46141c726e9b94","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"e06bfaa13724c07eef19d1cf9599489ca6898587c4e00ce7cf46141c726e9b94","first_computed_at":"2026-07-05T09:32:18.144950Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-07-05T09:32:18.144950Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"MzNYJE5vVJAAAY/J9+p1N4HAE7NkWE+elScehKt4EVQJKioDF08YfRudy5UKOaYN1JJ9EvJoxnKhC5LdP/u1BQ==","signature_status":"signed_v1","signed_at":"2026-07-05T09:32:18.145446Z","signed_message":"canonical_sha256_bytes"},"source_id":"2411.04363","source_kind":"arxiv","source_version":1}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:a8b94f6bf9cde53346ec8382b866c7da20b8ecbe285770980afdd77e9e102a30","sha256:4746b13d5aadef0b8aee93ff0b60d699222dcc6378e6dae7739793958130ff4e"],"state_sha256":"302f899ebe4698f66a276d29f55383eebeaddc0857ed093c5dc2dc460785b510"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"lOUaimz+G3XE5olAkNpyAIjvU+R6jW9d9dLyhdNUM4+OC58I4NsT2Hf/4j+QQVT5sNQbEuZlgNza2+V15bNLAQ==","signed_message":"bundle_sha256_bytes","signed_at":"2026-08-03T20:48:48.019057Z","bundle_sha256":"cb95f4a1522db2d9f9a1fc16ef1c762be4d1a4130227bcdff229b7fd07fefa4b"}}