MS
Michael C. Schatz
bioinformaticsgenomicsSoftwareGenome, HumanGenomicsEvolution, MolecularGenomeGenome, PlantHigh-Throughput Nucleotide SequencingAlgorithms
On Valency
published · living versionsW_26xzgw86·v1 · currentpublished
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
with Keith R. Bradnam, Joseph N. Fass, Anton Alexandrov, Paul Baranay +86
1 version
Preprints & journals
240 papers in the corpus · 1997–2026Voices from contributors to Cell Genomics.42874565 · Courtot, Mélanie, Okada, Yukinori, Im, Hae Kyung et al.2026 · 0 citationsCell genomics. 2026;6(10):101396
Gene duplication of SNAPC1 generates transcription factors for snRNAs and sex-specific piRNAs.42922533 · Benner, Lars Kristian, Starostik, Margaret R, Tay, Rebecca J et al.2026 · 0 citationsbioRxiv : the preprint server for biology. 2026
A 515,579-Genome Reference Panel Improves Rare-Variant Imputation Across Multiple Underrepresented Populations.42922788 · Ivankovic, Franjo, Ko, Arthur, Aster, M Morgan et al.2026 · 0 citationsmedRxiv : the preprint server for health sciences. 2026
HPRC2: A human pangenome reference with near-complete coverage of common genetic variation.42539208 · Lucas, Julian K, Hebbar, Prajna, Liao, Wen-Wei et al.2026 · 9 citationsbioRxiv : the preprint server for biology. 2026
Indirect genomic effects shape cancer risk across species.42427579 · Butler, George, Ramakrishnan, Srividya, Collins, Tyler et al.2026 · 0 citationsbioRxiv : the preprint server for biology. 2026
The Vertebrate Genomes Project Phase I: A global reference genome resource.42395566 · Formenti, Giulio, Absolon, Dominic E, Abueg, Linelle Ann L et al.2026 · 10 citationsbioRxiv : the preprint server for biology. 2026
The Common Fund Data Ecosystem (CFDE).41993383 · Jurgens, Julie A, Bueckle, Andreas, Vora, Jeet et al.2026 · 1 citationbioRxiv : the preprint server for biology. 2026
Perseus: Lineage-Aware Refinement of Kraken2 Taxonomic Classification for Long Read Metagenomes.41867767 · Nguyen, Matthew H, Schatz, Michael C2026 · 2 citationsbioRxiv : the preprint server for biology. 2026
A neofunctionalized flowering antagonist created an evolutionary contingency that channeled Solanaceae adaptation.41757091 · Shohat, Hagai, Ciren, Danielle, Arrones, Andrea et al.2026 · 0 citationsbioRxiv : the preprint server for biology. 2026
AniAnn's: alignment-free annotation of tandem repeat arrays using fast average nucleotide identity estimates.41659693 · Sweeten, Alexander, Schatz, Michael C, Phillippy, Adam M2026 · 2 citationsbioRxiv : the preprint server for biology. 2026
Unearthing soil biodiversity through collaborative genomic research and education.41461908 · BioDIGS Consortium, Alberts, Tristen, Albritton, Claude F et al.2026 · 3 citationsNature genetics. 2026;58(1):3-8
Standardizing RNA-seq Analysis of Fungal Pathogens Using BRC-Analytics and Agentic AI: A Candidozyma auris Case Study.41509213 · Nekrutenko, Anton, Callan, Danielle, Van Den Beek, Marius et al.2026 · 0 citationsbioRxiv : the preprint server for biology. 2025
Insights into the Datasets, Tools, and Training Needs of the AnVIL Community: 2024.41332714 · Isaac, Kathryn J, Cox, Katherine E L, Ho, Kai Yin et al.2025 · 0 citationsbioRxiv : the preprint server for biology. 2025
Genomic Next-Token Predictors are In-Context Learners2511.12797v3 · Nathan Breslow, Aayush Mishra, Mahler Revsine et al.2025 · 0 citationsarXiv
Population-scale Long-read Sequencing in the All of Us Research Program.41256123 · Garimella, Kiran V, Li, Qiuhui, Wertz, Julie et al.2025 · 6 citationsmedRxiv : the preprint server for health sciences. 2025
A complete diploid human genome benchmark for personalized genomics.41000953 · Hansen, Nancy F, Dwarshuis, Nathan, Ji, Hyun Joo et al.2026 · 42 citationsbioRxiv : the preprint server for biology. 2025
Learning Explainable Imaging-Genetics Associations Related to a Neurological Disorder.41988634 · Wang, Jueqi, Jacokes, Zachary, Van Horn, John Darrell et al.2026 · 1 citationMedical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention. 2026;15970:347-357
Microbiology Galaxy Lab: The first community-driven gateway for reproducible and FAIR analysis of microbial data.39764050 · Nasr, Engy, Pechlivanis, Nikos, Strepis, Nikolaos et al.2025 · 5 citationsbioRxiv : the preprint server for biology. 2025
Engineering compact Physalis peruviana (goldenberry) to promote its potential as a global crop10.1101/2025.08.15.670557v2 · Santo Domingo, M., Fitzgerald, B., Robitaille, G. M. et al.2025 · 2 citationsbioRxiv
Improving the FAIRness and Sustainability of the NHGRI Resources Ecosystem.40895087 · Babb, Larry, Bult, Carol, Carey, Vincent J et al.2025 · 0 citationsArXiv. 2025
Comparative genomics of the parasite Trichomonas vaginalis reveals genes involved in spillover from birds to humans.40707449 · Sullivan, Steven A, Orosco, Jordan C, Callejas-Hernández, Francisco et al.2025 · 5 citationsNature communications. 2025;16(1):6487
Author Correction: MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication.40702017 · Cahn, Jonathan, Regulski, Michael, Lynn, Jason et al.2025 · 0 citationsNature communications. 2025;16(1):6790
Assembling unmapped reads reveals hidden variation in South Asian genomes.40463162 · Das, Arun, Biddanda, Arjun, McCoy, Rajiv C et al.2026 · 0 citationsbioRxiv : the preprint server for biology. 2025
Unraveling the hidden complexity of cancer through long-read sequencing.40113261 · Li, Qiuhui, Keskus, Ayse G, Wagner, Justin et al.2025 · 14 citationsGenome research. 2025;35(4):599-620
The Farm Animal Genotype-Tissue Expression (FarmGTEx) Project.40097783 · Fang, Lingzhao, Teng, Jinyan, Lin, Qing et al.2025 · 64 citationsNature genetics. 2025;57(4):786-796
Solanum pan-genetics reveals paralogues as contingencies in crop engineering.40044854 · Benoit, Matthias, Jenike, Katharine M, Satterlee, James W et al.2025 · 68 citationsNature. 2025;640(8057):135-145
k-mer approaches for biodiversity genomics.39890468 · Jenike, Katharine M, Campos-Domínguez, Lucía, Boddé, Marilou et al.2025 · 23 citationsGenome research. 2025;35(2):219-230
MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication.39738013 · Cahn, Jonathan, Regulski, Michael, Lynn, Jason et al.2024 · 19 citationsNature communications. 2024;15(1):10854
Comparative genomics of the sexually transmitted parasite Trichomonas vaginalis reveals relaxed and convergent evolution and genes involved in spillover from birds to humans.39763951 · Sullivan, Steven A, Orosco, Jordan C, Callejas-Hernández, Francisco et al.2025 · 2 citationsbioRxiv : the preprint server for biology. 2024
High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation.39358015 · Gustafson, Jonas A, Gibson, Sophia B, Damaraju, Nikhita et al.2024 · 87 citationsGenome research. 2024;34(11):2061-2073
AnVILWorkflow: A runnable workflow package for Cloud-implemented bioinformatics analysis pipelines.39669685 · Oh, Sehyun, Gravel-Pucillo, Kai, Ramos, Marcel et al.2024 · 0 citationsF1000Research. 2024;13:1257
Complete sequencing of ape genomes.39131277 · Yoo, DongAhn, Rhie, Arang, Hebbar, Prajna et al.2026 · 157 citationsbioRxiv : the preprint server for biology. 2024
Differences in activity and stability drive transposable element variation in tropical and temperate maize.39251347 · Ou, Shujun, Scheben, Armin, Collins, Tyler et al.2024 · 74 citationsGenome research. 2024;34(8):1140-1153
Solanum pan-genomics and pan-genetics reveal paralogs as contingencies in crop engineering10.1101/2024.09.10.612244v1 · Benoit, M., Jenike, K. M., Satterlee, J. W. et al.2024 · 3 citationsbioRxiv
BEATRICE: Bayesian Fine-mapping from Summary Data using Deep Variational Inference.36993396 · Ghosal, Sayan, Schatz, Michael C, Venkataraman, Archana2026 · 5 citationsbioRxiv : the preprint server for biology. 2024
Convergent evolution of plant prickles by repeated gene co-option over deep time.39088611 · Satterlee, James W, Alonso, David, Gramazio, Pietro et al.2024 · 76 citationsScience (New York, N.Y.). 2024;385(6708):eado1663
ModDotPlot-rapid and interactive visualization of tandem repeats.39110522 · Sweeten, Alexander P, Schatz, Michael C, Phillippy, Adam M2024 · 63 citationsBioinformatics (Oxford, England). 2024;40(8)
Beyond the Human Genome Project: The Age of Complete Human Genome Sequences and Pangenome References.38663087 · Taylor, Dylan J, Eizenga, Jordan M, Li, Qiuhui et al.2024 · 48 citationsAnnual review of genomics and human genetics. 2024;25(1):77-104
MEM-based pangenome indexing for k-mer queries.38826299 · Hwang, Stephen, Brown, Nathaniel K, Ahmed, Omar Y et al.2025 · 4 citationsbioRxiv : the preprint server for biology. 2024
Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes.37066352 · Xiang, Guanjue, He, Xi, Giardine, Belinda M et al.2026 · 8 citationsbioRxiv : the preprint server for biology. 2024
ModDotPlot-Rapid and interactive visualization of complex repeats.38712106 · Sweeten, Alexander P, Schatz, Michael C, Phillippy, Adam M2024 · 10 citationsbioRxiv : the preprint server for biology. 2024
Guide to k-mer approaches for genomics across the tree of life2404.01519v1 · Katharine M. Jenike, Luc'ia Campos-Dom'inguez, Marilou Bodd'e et al.2024 · 2 citationsarXiv
Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease.38585781 · Jensen, Tanner D, Ni, Bohan, Reuter, Chloe M et al.2026 · 16 citationsmedRxiv : the preprint server for health sciences. 2024
Gapless assembly of complete human and plant chromosomes using only nanopore sequencing.38529488 · Koren, Sergey, Bao, Zhigui, Guarracino, Andrea et al.2026 · 52 citationsbioRxiv : the preprint server for biology. 2024
Uncalled4 improves nanopore DNA and RNA modification detection via fast and accurate signal alignment.38496646 · Kovaka, Sam, Hook, Paul W, Jenike, Katharine M et al.2026 · 62 citationsbioRxiv : the preprint server for biology. 2024
Nanopore sequencing of 1000 Genomes Project samples to build a comprehensive catalog of human genetic variation.38496498 · Gustafson, Jonas A, Gibson, Sophia B, Damaraju, Nikhita et al.2026 · 36 citationsmedRxiv : the preprint server for health sciences. 2024
Convergent evolution of plant prickles is drivenby repeated gene co-option over deep time10.1101/2024.02.21.581474v1 · Satterlee, J. W., Alonso, D., Gramazio, P. et al.2024 · 5 citationsbioRxiv
Utility of long-read sequencing for All of Us.38281971 · Mahmoud, M, Huang, Y, Garimella, K et al.2024 · 116 citationsNature communications. 2024;15(1):837
The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes.38077089 · Makova, Kateryna D, Pickett, Brandon D, Harris, Robert S et al.2026 · 120 citationsbioRxiv : the preprint server for biology. 2023
Long-Read Sequencing Reveals Rapid Evolution of Immunity- and Cancer-Related Genes in Bats.37728212 · Scheben, Armin, Mendivil Ramos, Olivia, Kramer, Melissa et al.2023 · 61 citationsGenome biology and evolution. 2023;15(9)
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