Papers - Statistical Genomics Foundry

Papers

Faithful research notes on primary papers — own-words synthesis plus short load-bearing quotes, each with full citation and a link to the original. Not reproductions.

A draft human pangenome reference

Liao W-W, Asri M, Ebler J, et al. A draft human pangenome reference. Nature 617(7960):312-324, 2023. DOI 10.1038/s41586-023-05896-x. Summary derived from the open-access PMC full text.
A fully-automated method discovers loss of mouse-lethal and human-monogenic disease genes in 58 mammals

Turakhia Y, Chen HI, Marcovitz A, Bejerano G. A fully-automated method discovers loss of mouse-lethal and human-monogenic disease genes in 58 mammals. Nucleic Acids Research 48(16):e91, 2020. DOI 10.1093/nar/gkaa550. Read via Europe PMC/OUP open-access full text; note records CC BY-NC 4.0 posture.
A New Method of Inference of Ancestral Nucleotide and Amino Acid Sequences

Yang Z, Kumar S, Nei M. A New Method of Inference of Ancestral Nucleotide and Amino Acid Sequences. Genetics 141(4):1641-1650, 1995. DOI 10.1093/genetics/141.4.1641. Read via PMC full text; summarized in own words.
Adaptation or biased gene conversion? Extending the null hypothesis of molecular evolution

Galtier N, Duret L. Trends in Genetics 23(6):273-277, 2007 (Epub 2007 Apr 5). DOI 10.1016/j.tig.2007.03.011. PMID 17418442. Abstract-only: full text behind the Elsevier/Trends in Genetics paywall (HTTP 403); only the NLM/PubMed abstract (via NCBI eutils efetch) was read. All rights reserved.
Ancestral Reconstruction

Joy JB, Liang RH, McCloskey RM, Nguyen T, Poon AFY. Ancestral Reconstruction. PLOS Computational Biology 12(7):e1004763, 2016. DOI 10.1371/journal.pcbi.1004763. Open access under Creative Commons BY.
AnchorWave: Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism, and whole-genome duplication

Song B, Marco-Sola S, Moreto M, Johnson L, Buckler ES, Stitzer MC. AnchorWave: Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism, and whole-genome duplication. PNAS 119(1):e2113075119, 2022. DOI 10.1073/pnas.2113075119. Read via PMC Open-Access BioC API; note records CC BY-NC-ND posture.
Are Large Language Models Good Statisticians? (StatQA)

Zhu Y, Du S, Li B, Luo Y, Tang N. Are Large Language Models Good Statisticians? NeurIPS 2024 Datasets & Benchmarks Track. arXiv:2406.07815. The `license` covers the arXiv paper (the note's load-bearing source); the StatQA code + dataset (GitHub HKUSTDial/StatQA) are separately GPL-3.0. Summarized in own words — no source prose reproduced.
Assessment of false discovery rate control in tandem mass spectrometry analysis using entrapment (Wen et al. 2025)

Wen B, Freestone J, Riffle M, MacCoss MJ, Noble WS, Keich U. Nature Methods 22(7):1454-1463, 2025.
Asymptotic conditional singular value decomposition for high-dimensional genomic data

Leek JT. Asymptotic conditional singular value decomposition for high-dimensional genomic data. Biometrics. 2011;67(2):344–352. doi:10.1111/j.1541-0420.2010.01455.x. PMC3165001 (NIH public-access author manuscript; no Creative Commons grant).
Automated Phylogenetic Detection of Recombination Using a Genetic Algorithm

Kosakovsky Pond SL, Posada D, Gravenor MB, Woelk CH, Frost SDW. Molecular Biology and Evolution 23(10):1891-1901, 2006. DOI 10.1093/molbev/msl051. PMID 16818476. Read via OUP open-access full text; article footer states Open Access under the Creative Commons Attribution Non-Commercial License (CC BY-NC 2.0 UK); own-words summary (NC kept out of casts), functional strings kept verbatim as facts.
Beginner's Guide on the Use of PAML to Detect Positive Selection

Alvarez-Carretero S, Kapli P, Yang Z. Molecular Biology and Evolution 40(4):msad041, 2023. DOI 10.1093/molbev/msad041. PMCID PMC10127084. Targets PAML v4.10.6 (CODEML). Full text read via Europe PMC JATS XML, Open Access under CC-BY 4.0, permitting short verbatim quotes.
CAFE 5 models variation in evolutionary rates among gene families

Mendes FK, Vanderpool D, Fulton B, Hahn MW. CAFE 5 models variation in evolutionary rates among gene families. Bioinformatics 36(22-23):5516-5518, 2020. DOI 10.1093/bioinformatics/btaa1022. Oxford University Press article page; summarized in own words.
CAFE: a computational tool for the study of gene family evolution

De Bie T, Cristianini N, Demuth JP, Hahn MW. CAFE: a computational tool for the study of gene family evolution. Bioinformatics 22(10):1269-1271, 2006. DOI 10.1093/bioinformatics/btl097. Oxford University Press article page; summarized in own words.
Capturing Heterogeneity in Gene Expression Studies by Surrogate Variable Analysis

Leek JT, Storey JD. Capturing Heterogeneity in Gene Expression Studies by Surrogate Variable Analysis. PLoS Genetics 3(9):e161, 2007. https://doi.org/10.1371/journal.pgen.0030161 — PLOS open access under the Creative Commons Attribution License. Read from PLOS full text + article XML (equations recovered from XML; PMC was Cloudflare-blocked).
Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics

Stoeckius M, Zheng S, Houck-Loomis B, Hao S, Yeung BZ, Mauck WM III, Smibert P, Satija R. Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics. Genome Biology. 2018;19:224. doi:10.1186/s13059-018-1603-1. Licensed CC BY 4.0.
CESAR 2.0 substantially improves speed and accuracy of comparative gene annotation

Sharma V, Schwede P, Hiller M. CESAR 2.0 substantially improves speed and accuracy of comparative gene annotation. Bioinformatics 33(24):3985-3987, 2017. DOI 10.1093/bioinformatics/btx527. Oxford University Press article page; summarized in own words.
Circular analysis in systems neuroscience: the dangers of double dipping

Kriegeskorte N, Simmons WK, Bellgowan PSF, Baker CI. Circular analysis in systems neuroscience: the dangers of double dipping. Nature Neuroscience 12(5):535–540, 2009. DOI 10.1038/nn.2303. Read via the NIH-PA author manuscript on PMC; final version © Nature Neuroscience. Summarized in own words — no source text reproduced.
Collider scope: when selection bias can substantially influence observed associations

Munafò MR, Tilling K, Taylor AE, Evans DM, Davey Smith G. Collider scope: when selection bias can substantially influence observed associations. International Journal of Epidemiology 47(1):226–235, 2018. https://doi.org/10.1093/ije/dyx206 — open access under CC BY 4.0. Read from the PMC deposit (PMC5837306); Figures 1–3 are images (captions only) and Supplementary Data not retrieved.
ComBat-seq: batch effect adjustment for RNA-seq count data

Zhang Y, Parmigiani G, Johnson WE. ComBat-seq: batch effect adjustment for RNA-seq count data. NAR Genomics and Bioinformatics 2(3):lqaa078, 2020. https://doi.org/10.1093/nargab/lqaa078 — open access under CC BY 4.0. Read from PMC efetch JATS XML (full body, 17 refs); Supplementary Material S1–S5 not read.
Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotation

Fiddes IT, Armstrong J, Diekhans M, Nachtweide S, Kronenberg ZN, Underwood JG, Gordon D, Earl D, Keane T, Eichler EE, Haussler D, Stanke M, Paten B. Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotation. Genome Research 28(7):1029-1038, 2018. DOI 10.1101/gr.233460.117. Read via PMC open-access full text; note records CC BY-NC 4.0 posture.
Comparative genomics: the bacterial pan-genome

Tettelin H, Riley D, Cattuto C, Medini D. Comparative genomics: the bacterial pan-genome. Current Opinion in Microbiology 11(5):472-477, 2008. DOI 10.1016/j.mib.2008.09.006. Abstract-only own-words summary from PubMed and DOI metadata because the full text was not accessible.
Compositionally Constrained Sites Drive Long-Branch Attraction

Szánthó LL, Lartillot N, Szöllősi GJ, Schrempf D. Compositionally Constrained Sites Drive Long-Branch Attraction. Systematic Biology 72(4):767-780, 2023. DOI 10.1093/sysbio/syad013. Open-access full text on PMC under CC-BY 4.0.
Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood

Csűrös M. Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood. Bioinformatics 26(15):1910-1912, 2010. DOI 10.1093/bioinformatics/btq315. Oxford University Press article page; summarized in own words.
Detecting Hidden Diversification Shifts in Models of Trait-Dependent Speciation and Extinction

Beaulieu JM, O'Meara BC. Detecting Hidden Diversification Shifts in Models of Trait-Dependent Speciation and Extinction. Systematic Biology 65(4):583-601, 2016. DOI 10.1093/sysbio/syw022. Published version is Oxford University Press; abstract/preprint access noted in the source note.
Detecting Individual Sites Subject to Episodic Diversifying Selection

Murrell B, Wertheim JO, Moola S, Weighill T, Scheffler K, Kosakovsky Pond SL. PLoS Genetics 8(7):e1002764, 2012. DOI 10.1371/journal.pgen.1002764. Read via PLoS open-access HTML plus the printable PDF (numeric/symbolic values); open access under the Creative Commons Attribution License (PLoS house license CC BY 4.0), permitting verbatim quotes.
Detecting macroevolutionary genotype-phenotype associations using error-corrected rates of protein convergence

Fukushima K, Pollock DD. Nature Ecology & Evolution 7:155-170, 2023. DOI 10.1038/s41559-022-01932-7. Paywalled primary NOT read; summarized from OPEN surrogates only - the author-written CSUBST repository/wiki (github.com/kfuku52/csubst, MIT License, (c) Kenji Fukushima; primary provenance) and the Barua et al. 2026 application (MBE 43(1):msag015, CC-BY 4.0, via PMC12849823). Mixed posture: dominant source is MIT-licensed docs, one CC-BY surrogate.
Detecting positive selection within genomes: the problem of biased gene conversion

Ratnakumar A, Mousset S, Glemin S, Berglund J, Galtier N, Duret L, Webster MT. Philosophical Transactions of the Royal Society B 365(1552):2571-2580, 2010. DOI 10.1098/rstb.2010.0007. PMID 20643747; PMCID PMC2935097. Full text read via PMC; (c) 2010 The Royal Society, free-to-read, no CC license - all rights reserved.
Detection and accurate false discovery rate control of differentially methylated regions from whole genome bisulfite sequencing

Korthauer K, Chakraborty S, Benjamini Y, Irizarry RA. bioRxiv 183210 (2017). Published: Biostatistics 20(3):367-383, 2019. The CC-BY-4.0 license and this note cover the bioRxiv PREPRINT (v1, 2017-08-31; license=cc_by per bioRxiv API), NOT the paywalled published Biostatistics 2019 version.
Effect of Recombination on the Accuracy of the Likelihood Method for Detecting Positive Selection at Amino Acid Sites

Anisimova M, Nielsen R, Yang Z. Genetics 164(3):1229-1236, 2003. DOI 10.1093/genetics/164.3.1229. PMID 12871927; PMCID PMC1462615. Full-text PDF read via the Europe PMC render endpoint. Bronze OA (free-to-read at publisher; Copyright 2003 Genetics Society of America, license None) - all rights reserved.
Engineering indel and substitution variants of diverse and ancient enzymes using GRASP

Foley G, Sützl L, D'Cunha SA, Gillam EMJ, Bodén M. Engineering indel and substitution variants of diverse and ancient enzymes using GRASP. PLOS Computational Biology 18(10):e1010633, 2022. DOI 10.1371/journal.pcbi.1010633. Open access under the Creative Commons Attribution License.
Estimates of positive Darwinian selection are inflated by errors in sequencing, annotation, and alignment

Schneider A, Souvorov A, Sabath N, Landan G, Gonnet GH, Graur D. Genome Biology and Evolution 1:114-118, 2009. DOI 10.1093/gbe/evp012. PMID 20333182; PMCID PMC2817407. Full text read via Europe PMC fullTextXML; open access under the Creative Commons Attribution Non-Commercial License (CC BY-NC 2.5); own-words summary (NC kept out of casts), functional strings kept verbatim as facts.
Estimating Gene Gain and Loss Rates in the Presence of Error in Genome Assembly and Annotation Using CAFE 3

Han MV, Thomas GWC, Lugo-Martinez J, Hahn MW. Estimating Gene Gain and Loss Rates in the Presence of Error in Genome Assembly and Annotation Using CAFE 3. Molecular Biology and Evolution 30(8):1987-1997, 2013. DOI 10.1093/molbev/mst100. Abstract verified via PubMed; body text retrieved from Oxford page with access boundary; summarized in own words.
Estimating the tempo and mode of gene family evolution from comparative genomic data

Hahn MW, De Bie T, Stajich JE, Nguyen C, Cristianini N. Estimating the tempo and mode of gene family evolution from comparative genomic data. Genome Research 15(8):1153-1160, 2005. DOI 10.1101/gr.3567505. Free full text read via PMC; summarized in own words.
Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level

Zhang J, Nielsen R, Yang Z. Molecular Biology and Evolution 22(12):2472-2479, 2005. DOI 10.1093/molbev/msi237. PMID 16107592. Read as the publisher PDF (msi237.pdf) via an Internet Archive Wayback capture of the OUP article-PDF URL; free PDF classified BRONZE (free-to-read, no CC license) - all rights reserved.
Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes

Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes. PNAS 100(20):11484-11489, 2003. DOI 10.1073/pnas.1932072100. Free full text read via PMC; summarized in own words.
Evolutionary Shortcuts via Multinucleotide Substitutions and Their Impact on Natural Selection Analyses

Lucaci AG, Zehr JD, Enard D, Thornton JW, Kosakovsky Pond SL. Molecular Biology and Evolution 40(7):msad150, 2023. DOI 10.1093/molbev/msad150. PMID 37395787; PMCID PMC10336034. Published MBE version read via Europe PMC full-text XML, Open Access under CC-BY 4.0 (preprint bioRxiv 10.1101/2022.12.02.518889 was CC BY-NC; MBE version is canonical here).
Extensive Error in the Number of Genes Inferred from Draft Genome Assemblies

Denton JF, Lugo-Martinez J, Tucker AE, Schrider DR, Warren WC, Hahn MW. Extensive Error in the Number of Genes Inferred from Draft Genome Assemblies. PLOS Computational Biology 10(12):e1003998, 2014. DOI 10.1371/journal.pcbi.1003998. Open access under CC-BY.
False-Positive Psychology: Undisclosed Flexibility in Data Collection and Analysis Allows Presenting Anything as Significant

Simmons JP, Nelson LD, Simonsohn U. Psychological Science 22(11):1359–1366, 2011 (SAGE / Association for Psychological Science). Version of record read via a UBC-hosted PDF copy.
Fitch 1976 J Mol Evol 7:271 synteny attribution check

Attribution check for the downstream citation 'Fitch WM 1976, J Mol Evol 7:271'. CrossRef and PubMed metadata show page 271 is Zuckerkandl E, Evolutionary processes and evolutionary noise at the molecular level, Journal of Molecular Evolution 7:269-311, 1976. DOI 10.1007/BF01743626. No full text read; note summarized in own words.
Frequent adaptation and the McDonald-Kreitman test

Messer PW, Petrov DA. PNAS 110(21):8615-8620, 2013. DOI 10.1073/pnas.1220835110. PMID 23650353; PMCID PMC3666677. Main text read via PMC HTML (display equations transcribed from served images); freely available through the PNAS open-access option, but the exact license is not printed on the page [summarizer-inferred; unverified, treated as all-rights-reserved]; own-words summary, functional strings retained as facts.
Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants

Qiao X, Li Q, Yin H, Qi K, Li L, Wang R, Zhang S, Paterson AH. Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants. Genome Biology 20:38, 2019. DOI 10.1186/s13059-019-1650-2. Summary also uses DupGen_finder README facts accessed 2026-07-05.
Gene-wide identification of episodic selection

Murrell B, Weaver S, Smith MD, Wertheim JO, Murrell S, Aylward A, Eren K, Pollner T, Martin DP, Smith DM, Scheffler K, Kosakovsky Pond SL. Molecular Biology and Evolution 32(5):1365-1371, 2015. DOI 10.1093/molbev/msv035. PMID 25701167; PMCID PMC4408417. Full text read via PMC; copyright 'The Author 2015 ... All rights reserved', no CC license.
GENESPACE tracks regions of interest and gene copy number variation across multiple genomes

Lovell JT, Sreedasyam A, Schranz ME, Wilson M, Carlson JW, Harkess A, Emms D, Goodstein DM, Schmutz J. GENESPACE tracks regions of interest and gene copy number variation across multiple genomes. eLife 11:e78526, 2022. DOI 10.7554/eLife.78526. Read via eLife and PMC full text under eLife CC-BY posture.
Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial pan-genome

Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, et al. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial pan-genome. PNAS 102(39):13950-13955, 2005. DOI 10.1073/pnas.0506758102. Own-words summary from the PMC full text.
HAL: a hierarchical format for storing and analyzing multiple genome alignments

Hickey G, Paten B, Earl D, Zerbino D, Haussler D. HAL: a hierarchical format for storing and analyzing multiple genome alignments. Bioinformatics 29(10):1341-1342, 2013. DOI 10.1093/bioinformatics/btt128. Read via PMC open-access full text; note flags CC BY 3.0 license discrepancy.
Inference after latent variable estimation for single-cell RNA sequencing data

Neufeld A, Gao LL, Popp J, Battle A, Witten D. Biostatistics 25(1):270–287, 2024. Preprint arXiv:2207.00554v2 (18 Oct 2022).
Inference of Genome Duplications from Age Distributions Revisited

Vanneste K, Van de Peer Y, Maere S. Inference of Genome Duplications from Age Distributions Revisited. Molecular Biology and Evolution 30(1):177-190, 2013. DOI 10.1093/molbev/mss214. Own-words summary from the OUP article page.
Integrating gene annotation with orthology inference at scale

Kirilenko BM, Munegowda C, Osipova E, Jebb D, Sharma V, Blumer M, Morales AE, Ahmed A-W, Kontopoulos D-G, Hilgers L, Zoonomia Consortium, Hiller M. Integrating gene annotation with orthology inference at scale. Science 380(6643):eabn3107, 2023. DOI 10.1126/science.abn3107. Read via PMC author manuscript; summarized in own words under restrictive/unverified license posture.
ksrates: positioning whole-genome duplications relative to speciation events in Ks distributions

Sensalari C, Maere S, Lohaus R. ksrates: positioning whole-genome duplications relative to speciation events in Ks distributions. Bioinformatics 38(2):530-532, 2022. DOI 10.1093/bioinformatics/btab602. Own-words summary of the article metadata plus method facts from GPL-3.0 ksrates docs/repo.
Less is more: an adaptive branch-site random effects model for efficient detection of episodic diversifying selection

Smith MD, Wertheim JO, Weaver S, Murrell B, Scheffler K, Kosakovsky Pond SL. Molecular Biology and Evolution 32(5):1342-1353, 2015. DOI 10.1093/molbev/msv022. PMCID PMC4408413. Full text read via PMC; copyright 'The Author 2015 ... All rights reserved', no CC license.
Liftoff: accurate mapping of gene annotations

Shumate A, Salzberg SL. Liftoff: accurate mapping of gene annotations. Bioinformatics 37(12):1639-1643, 2021. DOI 10.1093/bioinformatics/btaa1016. Oxford University Press article page plus Liftoff GitHub README consulted for tool defaults; paper prose summarized in own words.
Linking pangenomes and metagenomes: the Prochlorococcus metapangenome

Delmont TO, Eren AM. Linking pangenomes and metagenomes: the Prochlorococcus metapangenome. PeerJ 6:e4320, 2018. DOI 10.7717/peerj.4320. Summary derived from the open-access PeerJ/Europe PMC full text.
MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

Wang Y, Tang H, DeBarry JD, Tan X, Li J, Wang X, Lee T-h, Jin H, Marler B, Guo H, Kissinger JC, Paterson AH. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Research 40(7):e49, 2012. DOI 10.1093/nar/gkr1293. Read via PMC open-access full text; note records CC BY-NC 3.0 posture.
Methods that remove batch effects while retaining group differences may lead to exaggerated confidence in downstream analyses

Nygaard V, Rødland EA, Hovig E. Methods that remove batch effects while retaining group differences may lead to exaggerated confidence in downstream analyses. Biostatistics 17(1):29–39, 2016. https://doi.org/10.1093/biostatistics/kxv027
micropan: an R-package for microbial pan-genomics

Snipen L, Liland KH. micropan: an R-package for microbial pan-genomics. BMC Bioinformatics 16:79, 2015. DOI 10.1186/s12859-015-0517-0. Summary also uses the author-written CRAN heaps() documentation accessed 2026-07-05.
Minimap2: pairwise alignment for nucleotide sequences

Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34(18):3094-3100, 2018. DOI 10.1093/bioinformatics/bty191. Read from arXiv:1708.01492v5 via ar5iv plus minimap2 manual v2.28 for preset table; summarized in own words.
Model Inadequacy and Mistaken Inferences of Trait-Dependent Speciation

Rabosky DL, Goldberg EE. Model Inadequacy and Mistaken Inferences of Trait-Dependent Speciation. Systematic Biology 64(2):340-355, 2015. DOI 10.1093/sysbio/syu131. Read from arXiv:1412.7082; summarized in own words under arXiv's nonexclusive distribution license.
Multibatch TMT Reveals False Positives, Batch Effects and Missing Values

Brenes A, Hukelmann J, Bensaddek D, Lamond AI. 'Multibatch TMT Reveals False Positives, Batch Effects and Missing Values.' Mol Cell Proteomics 2019;18(10):1967–1980. © 2019 Brenes et al. Licensed CC BY 4.0.
Multiple hypothesis testing to detect lineages under positive selection that affects only a few sites

Anisimova M, Yang Z. Molecular Biology and Evolution 24(5):1219-1228, 2007. DOI 10.1093/molbev/msm042. PMID 17339634. Abstract read verbatim from Europe PMC; body/tables read via WebFetch against the OUP free-to-read HTML (direct access Cloudflare-blocked). BRONZE OA (free-to-read, license null) - all rights reserved.
Multiplexed droplet single-cell RNA-sequencing using natural genetic variation

Kang HM, Subramaniam M, Targ S, Nguyen M, Maliskova L, McCarthy E, Wan E, Wong S, Byrnes L, Lanata CM, Gate RE, Mostafavi S, Marson A, Zaitlen N, Criswell LA, Ye CJ. Multiplexed droplet single-cell RNA-sequencing using natural genetic variation. Nat Biotechnol 36(1):89-94, 2018. DOI 10.1038/nbt.4042. Read via the NIHMS author manuscript on PMC (PMC5784859, NIHMSID NIHMS921103); Nature author manuscript = all rights reserved, NOT Creative Commons. Summarized in own words.
MUMmer4: A fast and versatile genome alignment system

Marçais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, Zimin A. MUMmer4: A fast and versatile genome alignment system. PLOS Computational Biology 14(1):e1005944, 2018. DOI 10.1371/journal.pcbi.1005944. Article page states CC0 public domain dedication.
OSAT: a tool for sample-to-batch allocations in genomics experiments

Yan L, Ma C, Wang D, Hu Q, Qin M, Conroy JM, Sucheston LE, Ambrosone CB, Johnson CS, Wang J, Liu S. OSAT: a tool for sample-to-batch allocations in genomics experiments. BMC Genomics 13:689, 2012. https://doi.org/10.1186/1471-2164-13-689 — open access under CC BY 2.0. Read from the BMC HTML + PDF mirror (PMC was blocked); figures and Additional file 1 not read.
Pangenome graph construction from genome alignments with Minigraph-Cactus

Hickey G, Monlong J, Ebler J, Novak AM, Eizenga JM, Gao Y, Human Pangenome Reference Consortium, Marschall T, Li H, Paten B. Pangenome graph construction from genome alignments with Minigraph-Cactus. Nature Biotechnology 42(4):663-673, 2024. DOI 10.1038/s41587-023-01793-w. Own-words summary from the PMC NIHPA author manuscript.
PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph

Gautreau G, Bazin A, Gachet M, Planel R, Burlot L, Dubois M, Perrin A, Medigue C, Calteau A, Cruveiller S, Matias C, Ambroise C, Rocha EPC, Vallenet D. PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph. PLoS Computational Biology 16(3):e1007732, 2020. DOI 10.1371/journal.pcbi.1007732.
Producing polished prokaryotic pangenomes with the Panaroo pipeline

Tonkin-Hill G, MacAlasdair N, Ruis C, Weimann A, Horesh G, Lees JA, Gladstone RA, Lo S, Beaudoin C, Floto RA, Frost SDW, Corander J, Bentley SD, Parkhill J. Producing polished prokaryotic pangenomes with the Panaroo pipeline. Genome Biology 21:180, 2020. DOI 10.1186/s13059-020-02090-4. Read via PMC open-access full text under CC-BY 4.0.
Progressive Cactus is a multiple-genome aligner for the thousand-genome era

Armstrong J, Hickey G, Diekhans M, Fiddes IT, Novak AM, Deran A, Fang Q, Xie D, Feng S, Stiller J, et al. Progressive Cactus is a multiple-genome aligner for the thousand-genome era. Nature 587(7833):246-251, 2020. DOI 10.1038/s41586-020-2871-y. Read via PMC open-access full text under CC-BY 4.0.
Randomization in Laboratory Procedure Is Key to Obtaining Reproducible Microarray Results

Yang H, Harrington CA, Vartanian K, Coldren CD, Hall R, Churchill GA. Randomization in Laboratory Procedure Is Key to Obtaining Reproducible Microarray Results. PLoS ONE 2008;3(11):e3724. Copyright 2008 Yang et al. NOTE: the article prints the CC-BY license WITHOUT a version number (see Access note); CC-BY-4.0 is taken from PLOS's own CrossRef license deposit for this DOI. Either candidate version (2.5 or 4.0) resolves to verbatim-ok, so posture is unaffected.
Reconstructing Ancient Proteins to Understand the Causes of Structure and Function

Hochberg GKA, Thornton JW. Reconstructing Ancient Proteins to Understand the Causes of Structure and Function. Annual Review of Biophysics 46:247-269, 2017. DOI 10.1146/annurev-biophys-070816-033631. Read via NIH Public Access author manuscript on PMC; summarized in own words.
Roary: rapid large-scale prokaryote pan genome analysis

Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S, Holden MTG, Fookes M, Falush D, Keane JA, Parkhill J. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 31(22):3691-3693, 2015. DOI 10.1093/bioinformatics/btv421. Summary derived from the open-access PMC full text.
Selective Inference for Hierarchical Clustering

Gao LL, Bien J, Witten D. "Selective Inference for Hierarchical Clustering." Journal of the American Statistical Association 119(545):332–342, 2024. DOI 10.1080/01621459.2022.2116331. Read via arXiv:2012.02936v3 (31 Oct 2022, "Final accepted version"). Own-words summary; restrictive license.
Some Limitations of Ancestral Character-State Reconstruction When Testing Evolutionary Hypotheses

Cunningham CW. Some Limitations of Ancestral Character-State Reconstruction When Testing Evolutionary Hypotheses. Systematic Biology 48(3):665-674, 1999. DOI 10.1080/106351599260238. Read from accessible first-page preview only; summarized in own words.
SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies

Goel M, Sun H, Jiao W-B, Schneeberger K. SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies. Genome Biology 20:277, 2019. DOI 10.1186/s13059-019-1911-0. Read via PMC/Europe PMC open-access full text under CC-BY 4.0.
Tackling the widespread and critical impact of batch effects in high-throughput data

Leek JT, Scharpf RB, Corrada Bravo H, Simcha D, Langmead B, Johnson WE, Geman D, Baggerly K, Irizarry RA. Tackling the widespread and critical impact of batch effects in high-throughput data. Nature Reviews Genetics 11(10):733–739, 2010. https://doi.org/10.1038/nrg2825 (© Macmillan Publishers Limited; open NIH author manuscript PMC3880143). Summarized in own words — no source text reproduced.
The garden of forking paths: Why multiple comparisons can be a problem, even when there is no 'fishing expedition' or 'p-hacking' and the research hypothesis was posited ahead of time

Andrew Gelman (Dept. of Statistics, Columbia University) and Eric Loken (Dept. of Human Development and Family Studies, Penn State), dated 14 Nov 2013. Published version: American Scientist 102(6):460, 2014, 'The Statistical Crisis in Science.'
Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps

Tang H, Wang X, Bowers JE, Ming R, Alam M, Paterson AH. Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps. Genome Research 18(12):1944-1954, 2008. DOI 10.1101/gr.080978.108. Free full text read via PMC; summarized in own words.
wgd v2: a suite of tools to uncover and date ancient polyploidy and whole-genome duplication

Chen H, Zwaenepoel A, Van de Peer Y. wgd v2: a suite of tools to uncover and date ancient polyploidy and whole-genome duplication. Bioinformatics 40(5):btae272, 2024. DOI 10.1093/bioinformatics/btae272. Summary also uses wgd v2.0.38 CLI source facts.