lab-papers status

Applying In Vitro Cas9 Cleavage Measurements to Guide Design of Targeted Long-Read Sequencing Experiments

drafting nature-methods ? target 2026-11-01 (170d)

path	/home/farnum248/repos/cas9-clc-ce-methods
github	Single-Molecule-Sequencing/cas9-clc-ce-methods
variants	2 (nature-methods-short, preprint)
words (rough)	9,427
tex / md files	30 / 27
figures	20 (100% with provenance)
TODO / FIXME markers	12
last build	2026-05-04 21:52
atom system	23 atoms · 2 variants (nature-methods-short, preprint) · builds: nature-methods-short 2946w 600KB 2026-05-02 23:50 · preprint 3512w 915KB 2026-05-02 23:50
gold standard	📑 4 · 🎨 12 · 🟢b🟢v🟢f🟢a🟢p
canonical README	✓ canonical block · refreshed 2d ago
textbook chapters	— no chapters mapped — sms-textbook-web
related meetings	none indexed
lineage	no lineage data

Predicting Drug Metabolizer Phenotypes Accurately with PacBio Based Cas9 Targeted Sequencing of Pharmacogenes

drafting nature-genetics ? target 2027-01-01 (231d)

path	/home/farnum248/repos/cas9-targeted-sequencing
github	Single-Molecule-Sequencing/cas9-targeted-sequencing
variants	2 (preprint, thesis-chapter)
words (rough)	6,092
tex / md files	6 / 71
figures	8 (50% with provenance)
TODO / FIXME markers	8
last build	2026-05-12 16:05
atom system	24 atoms · 2 variants (preprint, thesis-chapter) · builds: preprint 5665w · thesis-chapter 5665w · ⚠ 2 stale variants
gold standard	📑 4 · 🎨 6 · 🟢b🟢v🟢f🟢a🟢p
canonical README	✓ canonical block · refreshed 2d ago
textbook chapters	✓ 6: canon Ch 2 · canon Ch 7 · canon Ch 8 +3 more · /ask
related meetings	none indexed
lineage	no lineage data

A One Pot, One Step, Precision Library Preparation Method with High Throughput Multiplexing Capability

drafting unknown ? target 2026-09-01 (109d)

path	/home/farnum248/repos/paper-clc-library-prep
github	Single-Molecule-Sequencing/paper-clc-library-prep
variants	2 (preprint, short)
words (rough)	4,586
tex / md files	22 / 29
figures	8 (100% with provenance)
TODO / FIXME markers	13
last build	2026-05-04 21:52
atom system	15 atoms · 2 variants (preprint, short) · builds: preprint 1692w 331KB 2026-05-02 23:51 · short 1692w 321KB 2026-05-02 23:51
gold standard	📑 4 · 🎨 6 · 🟢b🟢v🟢f🟢a🟢p
canonical README	✓ canonical block · refreshed 2d ago
textbook chapters	— no chapters mapped — sms-textbook-web
related meetings	none indexed
lineage	no lineage data

End-reason QC for Oxford Nanopore adaptive sampling

drafting scientific-data ? target 2026-06-01 (17d)

path	/home/farnum248/repos/end-reason-paper
github	Single-Molecule-Sequencing/end-reason-paper
variants	41 (ajhg, bioinformatics, bioinformatics-advances, biorxiv (+37 more))
words (rough)	15,491
tex / md files	67 / 69
figures	40 (42% with provenance)
TODO / FIXME markers	13
last build	2026-04-27 14:56
atom system	99 atoms · 41 variants (ajhg, bioinformatics, bioinformatics-advances) · builds: ajhg 5539w 6082KB 2026-05-12 13:15 · bioinformatics 1318w 4150KB 2026-05-10 17:26 · bioinformatics-advances 4790w 6035KB 2026-05-10 17:27 · biorxiv 4790w 6035KB 2026-05-10 17:27 · bmc-bioinformatics 4790w 6036KB 2026-05-11 15:21 · book-chapter 4790w 6034KB 2026-05-10 17:28 · briefings-in-bioinformatics 4790w 6035KB 2026-05-10 17:28 · cell-genomics 4790w 6035KB 2026-05-10 17:29 · cpt 4790w 6034KB 2026-05-10 17:29 · elife 4790w 6035KB 2026-05-10 17:30 · f1000research 4521w 5995KB 2026-05-10 17:31 · frontiers-bioinformatics 4790w 6035KB 2026-05-11 15:22 · genome-biology 4521w 5992KB 2026-05-10 17:31 · genome-research 4790w 6035KB 2026-05-10 17:31 · gigascience 4790w 6036KB 2026-05-10 17:32 · hgg-advances 4790w 6035KB 2026-05-11 15:21 · iscience 4790w 6035KB 2026-05-11 15:21 · joss 4790w 6035KB 2026-05-10 17:32 · lay-summary 1800w 4606KB 2026-05-10 17:33 · methods-paper 4790w 6035KB 2026-05-10 17:33 · nar-gab 4790w 6035KB 2026-05-11 15:20 · nar-methods 4790w 6036KB 2026-05-10 17:33 · nat-comm 4790w 6034KB 2026-05-10 17:34 · nature-genetics 4790w 6033KB 2026-05-10 17:34 · nature-methods-bc 1318w 4103KB 2026-05-10 17:34 · nature-methods-full 4790w 6035KB 2026-05-10 17:35 · nature-protocols 4790w 6034KB 2026-05-11 15:20 · npj-genomic-medicine 4790w 6027KB 2026-05-10 17:35 · patterns 4790w 6035KB 2026-05-11 15:21 · pharmacogenomics-j 4790w 6035KB 2026-05-10 17:35 · plos-comp-bio 4790w 6035KB 2026-05-10 17:36 · plos-one 4790w 6035KB 2026-05-10 17:36 · pnas 4790w 6034KB 2026-05-10 17:36 · poster-abstract 1800w 4606KB 2026-05-10 17:36 · preprint 4788w 5904KB 2026-05-10 18:10 · press-release 1800w 4605KB 2026-05-10 17:37 · scidata-short 1903w 4610KB 2026-05-12 13:25 · scientific-data 6119w 6099KB 2026-05-12 13:38 · star-protocols 4790w 6035KB 2026-05-11 15:18 · thesis-chapter 4788w 5904KB 2026-05-10 18:10 · twitter-thread 1800w 4606KB 2026-05-10 17:39 · ⚠ 76 orphan-figure refs
gold standard	📑 82 · 🎨 19 · 🟢b🟢v🟢f🟢a🟢p
canonical README	✓ canonical block · refreshed 2d ago
textbook chapters	✓ 3: canon Ch 9 · pgx Ch 24 · pgx Ch 22 · /ask
related meetings	5 meeting(s) · 5 ingested · 1 decision 2026-05-11 End Reason Datasets and Figure 4 2026-05-11 End Reason Datasets and Figure 4 2026-05-11 End Reason Datasets and Figure 4 2026-05-11 End Reason Datasets and Figure 4 2025-13-06 End Reason Paper Writing Intro
lineage	no lineage data

A Scarless Type-IIS Golden Gate Cloning Platform for Rapid Assembly and QC of Arbitrary DNA Sequences

drafting acs-synthetic-biology ? target 2026-12-01 (200d)

path	/home/farnum248/repos/golden-gate
github	Single-Molecule-Sequencing/golden-gate
variants	2 (acs-synbio-submit, preprint)
words (rough)	8,143
tex / md files	18 / 32
figures	6 (50% with provenance)
TODO / FIXME markers	71
last build	2026-05-03 18:23
atom system	18 atoms · 2 variants (acs-synbio-submit, preprint) · builds: acs-synbio-submit 2970w 236KB 2026-05-03 21:17 · preprint 2970w 238KB 2026-05-03 21:17
gold standard	📑 4 · 🎨 5 · 🟢b🟢v🟢f🔴a🟢p
canonical README	✓ canonical block · refreshed 2d ago
textbook chapters	✓ 3: canon Ch 7 · pgx Ch 18 · pgx Ch 47 · /ask
related meetings	none indexed
lineage	no lineage data

Living Longer, Living Better: Navigating, Leveraging and Measuring the Pathways to Longevity

drafting grant grant-multi-target ? target 2027-02-05 (266d)

path	/home/farnum248/repos/longevity-platform-grant
github	Single-Molecule-Sequencing/longevity-platform-grant
variants	26 (afar-grant, aims-page, arpa-h, astera-5pg (+22 more))   rolling release →
grant readiness	PHS398 100% sub-atom split 0% 6 biosketches project_summary 31% wired
words (rough)	3,086
tex / md files	21 / 121
figures	0 (0% with provenance)
TODO / FIXME markers	14
last build	2026-05-10 15:26
atom system	39 atoms · 26 variants (afar-grant, aims-page, arpa-h) · ⚠ 26 stale variants, 11 orphan-figure refs
gold standard	📑 52 · 🎨 13 · 🟢b🟢v🟢f🟢a🔴p
canonical README	✓ canonical block · refreshed 2d ago
textbook chapters	— no chapters mapped — sms-textbook-web
related meetings	none indexed
lineage	no lineage data

CYP2D6 Diplotyping in Breast Cancer Pharmacogenomics via Targeted Long-Read Sequencing

drafting pharmacogenomics-journal ? target 2027-01-15 (245d)

path	/home/farnum248/repos/paper-cyp2d6-breast-cancer-targeted
github	Single-Molecule-Sequencing/paper-cyp2d6-breast-cancer-targeted
variants	1 (preprint)
words (rough)	3,381
tex / md files	17 / 26
figures	8 (50% with provenance)
TODO / FIXME markers	9
last build	2026-04-27 15:08
atom system	11 atoms · 1 variants (preprint) · builds: preprint 815w 233KB 2026-05-02 23:52
gold standard	📑 2 · 🎨 6 · 🟢b🟢v🟢f🟢a🟢p
canonical README	✓ canonical block · refreshed 2d ago
textbook chapters	— no chapters mapped — sms-textbook-web
related meetings	none indexed
lineage	no lineage data

Plasmid Standards for SMA-seq: Proof of Concept and Validation

archived nature-methods ? target 2026-09-01 (109d)

path	/home/farnum248/repos/paper-plasmid-standards-proof
github	Single-Molecule-Sequencing/paper-plasmid-standards-proof
variants	1 (preprint)
words (rough)	6,799
tex / md files	20 / 17
figures	8 (50% with provenance)
TODO / FIXME markers	16
last build	2026-04-28 02:01
atom system	9 atoms · 1 variants (preprint) · builds: preprint 0w 215KB 2026-05-02 23:52
gold standard	📑 2 · 🎨 6 · ⚪b🟢v🟢f🟢a🟢p
canonical README	✓ canonical block · refreshed 7d ago
textbook chapters	— no chapters mapped — sms-textbook-web
related meetings	none indexed
lineage	no lineage data

Interlaboratory Proficiency Testing with Multiplexed Plasmid Controls

drafting clinical-chemistry ? target 2027-03-01 (290d)

path	/home/farnum248/repos/paper-proficiency-testing-plasmids
github	Single-Molecule-Sequencing/paper-proficiency-testing-plasmids
variants	1 (preprint)
words (rough)	2,599
tex / md files	17 / 26
figures	8 (50% with provenance)
TODO / FIXME markers	9
last build	2026-04-27 19:11
atom system	11 atoms · 1 variants (preprint) · builds: preprint 842w 229KB 2026-05-02 23:52
gold standard	📑 2 · 🎨 6 · 🟢b🟢v🟢f🟢a🟢p
canonical README	✓ canonical block · refreshed 4d ago
textbook chapters	— no chapters mapped — sms-textbook-web
related meetings	none indexed
lineage	no lineage data

Resolution of CYP2D6 Diplotypes through Oxford Nanopore Adaptive Sampling

drafting clinical-pharmacology-therapeutics ? target 2026-07-01 (47d)

path	/home/farnum248/repos/paper-pgx-adaptive-sampling-v2
github	Single-Molecule-Sequencing/paper-pgx-adaptive-sampling-v2
variants	16 (ajhg, bmc-genomics, cell-reports-med, cpt-short (+12 more))
words (rough)	39,730
tex / md files	119 / 117
figures	36 (44% with provenance)
TODO / FIXME markers	7
last build	2026-05-09 04:16
atom system	164 atoms · 16 variants (ajhg, bmc-genomics, cell-reports-med) · builds: cpt-short 2419w 412KB 2026-05-10 17:41 · genome-medicine 4888w 1030KB 2026-05-10 17:41 · narrative 5241w 998KB 2026-05-13 10:53 · preprint 4876w 1096KB 2026-05-10 17:44 · thesis-chapter 4033w 936KB 2026-05-10 17:44 · ⚠ 11 stale variants
gold standard	📑 33 · 🎨 60 · 🟢b🟢v🟢f🔴a🟢p
canonical README	✓ canonical block · refreshed 2d ago
textbook chapters	✓ 6: canon Ch 1 · canon Ch 3 · canon Ch 8 +3 more · /ask
related meetings	10 meeting(s) · 2 ingested · 5 decisions 2025-10-09 Adaptive Sampling Results 2025-10-09 Adaptive Sampling Results 2024-30-07 UM-NCCS meeting re CYP2D6 2024-30-05 UM-NCCS meeting re CYP2D6 2024-16-07 UM-NCCS meeting re CYP2D6
lineage	no lineage data

SMA-seq labels for neural-network basecaller fine-tuning

drafting nature-methods ? target 2026-10-15 (153d)

path	/home/farnum248/repos/paper-smaseq-basecaller-finetuning
github	Single-Molecule-Sequencing/paper-smaseq-basecaller-finetuning
variants	1 (preprint)
words (rough)	3,779
tex / md files	28 / 26
figures	16 (75% with provenance)
TODO / FIXME markers	7
last build	2026-04-27 14:42
atom system	22 atoms · 1 variants (preprint) · builds: preprint 1138w 391KB 2026-05-03 21:16
gold standard	📑 2 · 🎨 6 · 🟢b🟢v🟢f🟢a🟢p
canonical README	✓ canonical block · refreshed 2d ago
textbook chapters	— no chapters mapped — sms-textbook-web
related meetings	none indexed
lineage	no lineage data

Empirical accuracy measurement in single-molecule sequencing using sequence-defined DNA standards

drafting nature-genetics ? target 2026-09-01 (109d)

path	/home/farnum248/repos/SMAseq_paper
github	Single-Molecule-Sequencing/SMAseq_paper
variants	2 (nature-genetics-short, preprint)
words (rough)	5,218
tex / md files	15 / 34
figures	0 (0% with provenance)
TODO / FIXME markers	7
last build	2026-05-03 18:24
atom system	19 atoms · 2 variants (nature-genetics-short, preprint) · builds: nature-genetics-short 4090w · preprint 4090w 259KB 2026-05-03 20:27 · ⚠ 1 stale variants
gold standard	📑 4 · 🎨 — · 🟢b🟢v🟢f🟢a🟢p
canonical README	✓ canonical block · refreshed 2d ago
textbook chapters	✓ 6: canon Ch 5 · canon Ch 6 · canon Ch 10 +3 more · /ask
related meetings	66 meeting(s) · 58 ingested · 8 decisions 2026-04-13 SMA-seq Results discussion 2026-04-13 SMA-seq Results discussion 2026-04-13 SMA-seq Results discussion 2026-04-13 SMA-seq Results discussion 2026-04-13 SMA-seq Results discussion
lineage	no lineage data

Single-Molecule Long-read Sequencing for Resolution of Structurally Complex Genomic Loci and Accurate Phenotype Prediction

submitted um-rackham-thesis ? target 2026-04-10 (35d late)

path	/home/farnum248/repos/Wolfe_Thesis_final
github	Single-Molecule-Sequencing/Wolfe_Thesis_final
words (rough)	59,083
tex / md files	194 / 16
figures	213 (0% with provenance)
TODO / FIXME markers	9
last build	2026-05-13 21:14
atom system	1 atoms
gold standard	📑 — · 🎨 — · 🟢b🟢v🟢f🔴a🟢p
canonical README	✓ canonical block · refreshed 2d ago
textbook chapters	✓ 6: canon Ch 2 · canon Ch 12 · canon Ch 13 +3 more · /ask
related meetings	20 meeting(s) · 15 ingested 2026-04-01 yisang thesis 2026-04-01 yisang thesis 2026-04-01 yisang thesis 2026-04-01 yisang thesis 2026-03-31 yisang thesis
lineage	no lineage data

Invisible Ends: The Last 10-20 Nucleotides of Oxford Nanopore Reads Are Systematically Missing From Basecalled Output

drafting unknown Athey Lab target 2027-01-15 (245d)

path	C:\Users\gregfar\repos\paper-ont-invisible-ends
github	Single-Molecule-Sequencing/paper-ont-invisible-ends
words (rough)	616
tex / md files	7 / 15
figures	0 (0% with provenance)
TODO / FIXME markers	16
last build	—
atom system	1 atoms
gold standard	📑 — · 🎨 — · ⚫b⚫v🟢f🟢a🟢p
canonical README	✓ canonical block · refreshed 2d ago
textbook chapters	— no chapters mapped — sms-textbook-web
related meetings	none indexed
lineage	no lineage data

Capillary Electrophoresis Methods for Quantitative Characterization of Cas9 Cleavage Products at Single-Base-Pair Resolution

drafting unknown Athey Lab target 2027-03-01 (290d)

path	C:\Users\gregfar\repos\paper-ce-cas9-cleavage-methods
github	Single-Molecule-Sequencing/paper-ce-cas9-cleavage-methods
words (rough)	508
tex / md files	7 / 12
figures	0 (0% with provenance)
TODO / FIXME markers	17
last build	—
atom system	1 atoms
gold standard	📑 — · 🎨 — · ⚫b⚫v🟢f🟢a🟢p
canonical README	✓ canonical block · refreshed 2d ago
textbook chapters	— no chapters mapped — sms-textbook-web
related meetings	none indexed
lineage	no lineage data

Single-Read Single-Cell Diplotyping: An SMA-seq Workflow for Per-Cell Pharmacogene Resolution at CYP2D6

drafting unknown Athey Lab target 2027-04-01 (321d)

path	C:\Users\gregfar\repos\single-read-single-cell-diplotyping
github	Single-Molecule-Sequencing/single-read-single-cell-diplotyping
words (rough)	0
tex / md files	0 / 33
figures	14 (0% with provenance)
TODO / FIXME markers	0
last build	2026-04-15 21:03
atom system	1 atoms
gold standard	📑 — · 🎨 — · 🟢b🟢v🟢f🟢a🟢p
canonical README	✓ canonical block · refreshed 2d ago
textbook chapters	— no chapters mapped — sms-textbook-web
related meetings	none indexed
lineage	no lineage data