{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2012:CIV5IICMBXAMF45BLJVKYEXQNA","short_pith_number":"pith:CIV5IICM","canonical_record":{"source":{"id":"1208.3619","kind":"arxiv","version":2},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.QM","submitted_at":"2012-08-17T15:37:58Z","cross_cats_sorted":["cs.CE","q-bio.GN"],"title_canon_sha256":"f9601f81d79dbeeab48091930acae6c9f613fa7b35ed62b2828c72d59bd0578b","abstract_canon_sha256":"f765af6a3610234b1d1b076f9a1d4e1028cefaa571b68a6fb10c5a9115cc73f1"},"schema_version":"1.0"},"canonical_sha256":"122bd4204c0dc0c2f3a15a6aac12f068165fae8e127586197f1d12e36fcbdac2","source":{"kind":"arxiv","id":"1208.3619","version":2},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1208.3619","created_at":"2026-05-18T03:32:45Z"},{"alias_kind":"arxiv_version","alias_value":"1208.3619v2","created_at":"2026-05-18T03:32:45Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1208.3619","created_at":"2026-05-18T03:32:45Z"},{"alias_kind":"pith_short_12","alias_value":"CIV5IICMBXAM","created_at":"2026-05-18T12:27:01Z"},{"alias_kind":"pith_short_16","alias_value":"CIV5IICMBXAMF45B","created_at":"2026-05-18T12:27:01Z"},{"alias_kind":"pith_short_8","alias_value":"CIV5IICM","created_at":"2026-05-18T12:27:01Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2012:CIV5IICMBXAMF45BLJVKYEXQNA","target":"record","payload":{"canonical_record":{"source":{"id":"1208.3619","kind":"arxiv","version":2},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.QM","submitted_at":"2012-08-17T15:37:58Z","cross_cats_sorted":["cs.CE","q-bio.GN"],"title_canon_sha256":"f9601f81d79dbeeab48091930acae6c9f613fa7b35ed62b2828c72d59bd0578b","abstract_canon_sha256":"f765af6a3610234b1d1b076f9a1d4e1028cefaa571b68a6fb10c5a9115cc73f1"},"schema_version":"1.0"},"canonical_sha256":"122bd4204c0dc0c2f3a15a6aac12f068165fae8e127586197f1d12e36fcbdac2","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-05-18T03:32:45.087790Z","signature_b64":"Cs+rECVqPV/pSbZWA2W4uEKfEngKTYcFEqaxcj9uXo4PY/IpPVR2Kj5HMrM3qFJNSy+WZwRJAvFQhvRR/pDnAQ==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"122bd4204c0dc0c2f3a15a6aac12f068165fae8e127586197f1d12e36fcbdac2","last_reissued_at":"2026-05-18T03:32:45.087115Z","signature_status":"signed_v1","first_computed_at":"2026-05-18T03:32:45.087115Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"1208.3619","source_version":2,"attestation_state":"computed"},"signer":{"signer_id":"pith.science","signer_type":"pith_registry","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"created_at":"2026-05-18T03:32:45Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"4/vPJ+f5pvgftwd3UiTTsFr8ejS1GQiebfCEzcYXnssKxfmkHTSgyiHydDJcR0K9eZMm13uPdn5hAzN6U+N9Bg==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-05-26T12:32:05.410736Z"},"content_sha256":"01d951d60d2db34bf6b0ed7f3ec230640fff02adf1e5c55621b25d221d997827","schema_version":"1.0","event_id":"sha256:01d951d60d2db34bf6b0ed7f3ec230640fff02adf1e5c55621b25d221d997827"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2012:CIV5IICMBXAMF45BLJVKYEXQNA","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"SASeq: A Selective and Adaptive Shrinkage Approach to Detect and Quantify Active Transcripts using RNA-Seq","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":["cs.CE","q-bio.GN"],"primary_cat":"q-bio.QM","authors_text":"Dongxiao Zhu, Nan Deng, Tin Chi Nguyen","submitted_at":"2012-08-17T15:37:58Z","abstract_excerpt":"Identification and quantification of condition-specific transcripts using RNA-Seq is vital in transcriptomics research. While initial efforts using mathematical or statistical modeling of read counts or per-base exonic signal have been successful, they may suffer from model overfitting since not all the reference transcripts in a database are expressed under a specific biological condition. Standard shrinkage approaches, such as Lasso, shrink all the transcript abundances to zero in a non-discriminative manner. Thus it does not necessarily yield the set of condition-specific transcripts. Infor"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1208.3619","kind":"arxiv","version":2},"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"},"verdict_id":null},"signer":{"signer_id":"pith.science","signer_type":"pith_registry","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"created_at":"2026-05-18T03:32:45Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"Lql9qQDFTh9s47K++J/4/u2JjKtS5jfBDh+e741u+cRrn4jgqSZDH3516lQkyhQPIQC3Tb9V0gQrwnHWqCIkBg==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-05-26T12:32:05.411464Z"},"content_sha256":"528628e194ede8a70682f192d04267b72d9d47f97cd6ec04a7ce59310100007b","schema_version":"1.0","event_id":"sha256:528628e194ede8a70682f192d04267b72d9d47f97cd6ec04a7ce59310100007b"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/CIV5IICMBXAMF45BLJVKYEXQNA/bundle.json","state_url":"https://pith.science/pith/CIV5IICMBXAMF45BLJVKYEXQNA/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/CIV5IICMBXAMF45BLJVKYEXQNA/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":"2026-05-26T12:32:05Z","links":{"resolver":"https://pith.science/pith/CIV5IICMBXAMF45BLJVKYEXQNA","bundle":"https://pith.science/pith/CIV5IICMBXAMF45BLJVKYEXQNA/bundle.json","state":"https://pith.science/pith/CIV5IICMBXAMF45BLJVKYEXQNA/state.json","well_known_bundle":"https://pith.science/.well-known/pith/CIV5IICMBXAMF45BLJVKYEXQNA/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2012:CIV5IICMBXAMF45BLJVKYEXQNA","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":"f765af6a3610234b1d1b076f9a1d4e1028cefaa571b68a6fb10c5a9115cc73f1","cross_cats_sorted":["cs.CE","q-bio.GN"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.QM","submitted_at":"2012-08-17T15:37:58Z","title_canon_sha256":"f9601f81d79dbeeab48091930acae6c9f613fa7b35ed62b2828c72d59bd0578b"},"schema_version":"1.0","source":{"id":"1208.3619","kind":"arxiv","version":2}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1208.3619","created_at":"2026-05-18T03:32:45Z"},{"alias_kind":"arxiv_version","alias_value":"1208.3619v2","created_at":"2026-05-18T03:32:45Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1208.3619","created_at":"2026-05-18T03:32:45Z"},{"alias_kind":"pith_short_12","alias_value":"CIV5IICMBXAM","created_at":"2026-05-18T12:27:01Z"},{"alias_kind":"pith_short_16","alias_value":"CIV5IICMBXAMF45B","created_at":"2026-05-18T12:27:01Z"},{"alias_kind":"pith_short_8","alias_value":"CIV5IICM","created_at":"2026-05-18T12:27:01Z"}],"graph_snapshots":[{"event_id":"sha256:528628e194ede8a70682f192d04267b72d9d47f97cd6ec04a7ce59310100007b","target":"graph","created_at":"2026-05-18T03:32:45Z","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"},"paper":{"abstract_excerpt":"Identification and quantification of condition-specific transcripts using RNA-Seq is vital in transcriptomics research. While initial efforts using mathematical or statistical modeling of read counts or per-base exonic signal have been successful, they may suffer from model overfitting since not all the reference transcripts in a database are expressed under a specific biological condition. Standard shrinkage approaches, such as Lasso, shrink all the transcript abundances to zero in a non-discriminative manner. Thus it does not necessarily yield the set of condition-specific transcripts. Infor","authors_text":"Dongxiao Zhu, Nan Deng, Tin Chi Nguyen","cross_cats":["cs.CE","q-bio.GN"],"headline":"","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.QM","submitted_at":"2012-08-17T15:37:58Z","title":"SASeq: A Selective and Adaptive Shrinkage Approach to Detect and Quantify Active Transcripts using RNA-Seq"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1208.3619","kind":"arxiv","version":2},"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":"sha256:01d951d60d2db34bf6b0ed7f3ec230640fff02adf1e5c55621b25d221d997827","target":"record","created_at":"2026-05-18T03:32:45Z","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":"f765af6a3610234b1d1b076f9a1d4e1028cefaa571b68a6fb10c5a9115cc73f1","cross_cats_sorted":["cs.CE","q-bio.GN"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.QM","submitted_at":"2012-08-17T15:37:58Z","title_canon_sha256":"f9601f81d79dbeeab48091930acae6c9f613fa7b35ed62b2828c72d59bd0578b"},"schema_version":"1.0","source":{"id":"1208.3619","kind":"arxiv","version":2}},"canonical_sha256":"122bd4204c0dc0c2f3a15a6aac12f068165fae8e127586197f1d12e36fcbdac2","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"122bd4204c0dc0c2f3a15a6aac12f068165fae8e127586197f1d12e36fcbdac2","first_computed_at":"2026-05-18T03:32:45.087115Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-05-18T03:32:45.087115Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"Cs+rECVqPV/pSbZWA2W4uEKfEngKTYcFEqaxcj9uXo4PY/IpPVR2Kj5HMrM3qFJNSy+WZwRJAvFQhvRR/pDnAQ==","signature_status":"signed_v1","signed_at":"2026-05-18T03:32:45.087790Z","signed_message":"canonical_sha256_bytes"},"source_id":"1208.3619","source_kind":"arxiv","source_version":2}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:01d951d60d2db34bf6b0ed7f3ec230640fff02adf1e5c55621b25d221d997827","sha256:528628e194ede8a70682f192d04267b72d9d47f97cd6ec04a7ce59310100007b"],"state_sha256":"600c89dbe7c6fe754dbad6a553ae9079233082198ef99a5f33ec28ff4ecd0ec7"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"VXIxoPa/6CRkk3O8w6HSycn9fZ60YJPpRveX5HwrUn0NvggdzFtwCOb7iz9QjQaxBB+nlSgiX5g+C5EAcUbrBA==","signed_message":"bundle_sha256_bytes","signed_at":"2026-05-26T12:32:05.415163Z","bundle_sha256":"b7e3f167f3a8745e77963cbc86623b4b8f6776eef997c87f798e538f2aa039b2"}}