{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2015:YZLBTP3ZGVBPES3ILDH6L7LWR4","short_pith_number":"pith:YZLBTP3Z","canonical_record":{"source":{"id":"1503.04992","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.GN","submitted_at":"2015-03-17T10:56:23Z","cross_cats_sorted":[],"title_canon_sha256":"8834d4045139004e7a53b6e0d2d875b153de14544565f034d5e781136edc8486","abstract_canon_sha256":"ee54d827795527790e0643607d4d024f7772ec7643d61a47f3ea69c139aea2c7"},"schema_version":"1.0"},"canonical_sha256":"c65619bf793542f24b6858cfe5fd768f0169d82afdf77b28ec3a3ee802fb132c","source":{"kind":"arxiv","id":"1503.04992","version":1},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1503.04992","created_at":"2026-05-18T02:22:20Z"},{"alias_kind":"arxiv_version","alias_value":"1503.04992v1","created_at":"2026-05-18T02:22:20Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1503.04992","created_at":"2026-05-18T02:22:20Z"},{"alias_kind":"pith_short_12","alias_value":"YZLBTP3ZGVBP","created_at":"2026-05-18T12:29:52Z"},{"alias_kind":"pith_short_16","alias_value":"YZLBTP3ZGVBPES3I","created_at":"2026-05-18T12:29:52Z"},{"alias_kind":"pith_short_8","alias_value":"YZLBTP3Z","created_at":"2026-05-18T12:29:52Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2015:YZLBTP3ZGVBPES3ILDH6L7LWR4","target":"record","payload":{"canonical_record":{"source":{"id":"1503.04992","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.GN","submitted_at":"2015-03-17T10:56:23Z","cross_cats_sorted":[],"title_canon_sha256":"8834d4045139004e7a53b6e0d2d875b153de14544565f034d5e781136edc8486","abstract_canon_sha256":"ee54d827795527790e0643607d4d024f7772ec7643d61a47f3ea69c139aea2c7"},"schema_version":"1.0"},"canonical_sha256":"c65619bf793542f24b6858cfe5fd768f0169d82afdf77b28ec3a3ee802fb132c","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-05-18T02:22:20.852283Z","signature_b64":"mit+bAOD1wBvj0vIjNI8YBRY0LY+1/q2fe8X/mcsG0r2KdMFqQK5BtPA5Hm0k4BOxgUu9R2h06IWbqg54neiAg==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"c65619bf793542f24b6858cfe5fd768f0169d82afdf77b28ec3a3ee802fb132c","last_reissued_at":"2026-05-18T02:22:20.851608Z","signature_status":"signed_v1","first_computed_at":"2026-05-18T02:22:20.851608Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"1503.04992","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":"2026-05-18T02:22:20Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"uxSUD+cMq22HzNSY4hsvLTy+8MVSq4dLHa7d8H3QUZ/71IgIPANzdDl3dZF0dspPSx2Ak7gktK9EqNQBxc31DA==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-06-03T18:41:12.256357Z"},"content_sha256":"26a2a448bfda684580d5ed1c491fb0857b30426d234e3f40a45aa496e9d727e0","schema_version":"1.0","event_id":"sha256:26a2a448bfda684580d5ed1c491fb0857b30426d234e3f40a45aa496e9d727e0"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2015:YZLBTP3ZGVBPES3ILDH6L7LWR4","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"Reliable scaling of Position Weight Matrices for binding strength comparisons between transcription factors","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":[],"primary_cat":"q-bio.GN","authors_text":"Boris Adryan, Carmen Navarro, Daphne Ezer, Xiaoyan Ma","submitted_at":"2015-03-17T10:56:23Z","abstract_excerpt":"Scoring DNA sequences against Position Weight Matrices (PWMs) is a widely adopted method to identify putative transcription factor binding sites. While common bioinformatics tools produce scores that can reflect the binding strength between a specific transcription factor and the DNA, these scores are not directly comparable between different transcription factors. Here, we provide two different ways to find the scaling parameter $\\lambda$ that allows us to infer binding energy from a PWM score. The first approach uses a PWM and background genomic sequence as input to estimate $\\lambda$ for a "},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1503.04992","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"},"verdict_id":null},"signer":{"signer_id":"pith.science","signer_type":"pith_registry","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"created_at":"2026-05-18T02:22:20Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"QYNZODZ35bEcPyB/sa+MkFflqKPpDv6nii4gZkegiDv66++ymkas8ctpPRL8Mumex06FQZG5/gbEs77NrHemDA==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-06-03T18:41:12.256711Z"},"content_sha256":"fc2b886f9094fea1078415a871428f30bb6c625b486861f3c45154b5d837faff","schema_version":"1.0","event_id":"sha256:fc2b886f9094fea1078415a871428f30bb6c625b486861f3c45154b5d837faff"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/YZLBTP3ZGVBPES3ILDH6L7LWR4/bundle.json","state_url":"https://pith.science/pith/YZLBTP3ZGVBPES3ILDH6L7LWR4/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/YZLBTP3ZGVBPES3ILDH6L7LWR4/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":"2026-06-03T18:41:12Z","links":{"resolver":"https://pith.science/pith/YZLBTP3ZGVBPES3ILDH6L7LWR4","bundle":"https://pith.science/pith/YZLBTP3ZGVBPES3ILDH6L7LWR4/bundle.json","state":"https://pith.science/pith/YZLBTP3ZGVBPES3ILDH6L7LWR4/state.json","well_known_bundle":"https://pith.science/.well-known/pith/YZLBTP3ZGVBPES3ILDH6L7LWR4/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2015:YZLBTP3ZGVBPES3ILDH6L7LWR4","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":"ee54d827795527790e0643607d4d024f7772ec7643d61a47f3ea69c139aea2c7","cross_cats_sorted":[],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.GN","submitted_at":"2015-03-17T10:56:23Z","title_canon_sha256":"8834d4045139004e7a53b6e0d2d875b153de14544565f034d5e781136edc8486"},"schema_version":"1.0","source":{"id":"1503.04992","kind":"arxiv","version":1}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1503.04992","created_at":"2026-05-18T02:22:20Z"},{"alias_kind":"arxiv_version","alias_value":"1503.04992v1","created_at":"2026-05-18T02:22:20Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1503.04992","created_at":"2026-05-18T02:22:20Z"},{"alias_kind":"pith_short_12","alias_value":"YZLBTP3ZGVBP","created_at":"2026-05-18T12:29:52Z"},{"alias_kind":"pith_short_16","alias_value":"YZLBTP3ZGVBPES3I","created_at":"2026-05-18T12:29:52Z"},{"alias_kind":"pith_short_8","alias_value":"YZLBTP3Z","created_at":"2026-05-18T12:29:52Z"}],"graph_snapshots":[{"event_id":"sha256:fc2b886f9094fea1078415a871428f30bb6c625b486861f3c45154b5d837faff","target":"graph","created_at":"2026-05-18T02:22:20Z","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":"Scoring DNA sequences against Position Weight Matrices (PWMs) is a widely adopted method to identify putative transcription factor binding sites. While common bioinformatics tools produce scores that can reflect the binding strength between a specific transcription factor and the DNA, these scores are not directly comparable between different transcription factors. Here, we provide two different ways to find the scaling parameter $\\lambda$ that allows us to infer binding energy from a PWM score. The first approach uses a PWM and background genomic sequence as input to estimate $\\lambda$ for a ","authors_text":"Boris Adryan, Carmen Navarro, Daphne Ezer, Xiaoyan Ma","cross_cats":[],"headline":"","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.GN","submitted_at":"2015-03-17T10:56:23Z","title":"Reliable scaling of Position Weight Matrices for binding strength comparisons between transcription factors"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1503.04992","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":"sha256:26a2a448bfda684580d5ed1c491fb0857b30426d234e3f40a45aa496e9d727e0","target":"record","created_at":"2026-05-18T02:22:20Z","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":"ee54d827795527790e0643607d4d024f7772ec7643d61a47f3ea69c139aea2c7","cross_cats_sorted":[],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.GN","submitted_at":"2015-03-17T10:56:23Z","title_canon_sha256":"8834d4045139004e7a53b6e0d2d875b153de14544565f034d5e781136edc8486"},"schema_version":"1.0","source":{"id":"1503.04992","kind":"arxiv","version":1}},"canonical_sha256":"c65619bf793542f24b6858cfe5fd768f0169d82afdf77b28ec3a3ee802fb132c","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"c65619bf793542f24b6858cfe5fd768f0169d82afdf77b28ec3a3ee802fb132c","first_computed_at":"2026-05-18T02:22:20.851608Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-05-18T02:22:20.851608Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"mit+bAOD1wBvj0vIjNI8YBRY0LY+1/q2fe8X/mcsG0r2KdMFqQK5BtPA5Hm0k4BOxgUu9R2h06IWbqg54neiAg==","signature_status":"signed_v1","signed_at":"2026-05-18T02:22:20.852283Z","signed_message":"canonical_sha256_bytes"},"source_id":"1503.04992","source_kind":"arxiv","source_version":1}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:26a2a448bfda684580d5ed1c491fb0857b30426d234e3f40a45aa496e9d727e0","sha256:fc2b886f9094fea1078415a871428f30bb6c625b486861f3c45154b5d837faff"],"state_sha256":"bd770b93ef06306abae650ffa108316807a8d2356c26ea2221ea11ec7fdf5497"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"5PkZSPO+AKBFPaRbJgn5HsIOFa5An7Sy3+JdBdQl/nCxO9+M2CE6NffQnffli/g4gs+kw+OheK6a6NB/+qn6Bw==","signed_message":"bundle_sha256_bytes","signed_at":"2026-06-03T18:41:12.258576Z","bundle_sha256":"0c6b346f50591b21d077df2182b1d20bb31263eab22d8e0710096962bb7ab081"}}