High-throughput sequence alignment using Graphics Processing Units. - Michael C. Schatz; Cole Trapnell; Arthur L. Delcher; Amitabh Varshney (BMC Bioinform., 2007)

CloudBurst: highly sensitive read mapping with MapReduce. - Michael C. Schatz (Bioinform., 2009)

Revealing Biological Modules via Graph Summarization. - Saket Navlakha; Michael C. Schatz; Carl Kingsford (J. Comput. Biol., 2009)

Optimizing data intensive GPGPU computations for DNA sequence alignment. - Cole Trapnell; Michael C. Schatz (Parallel Comput., 2009)

Assembly complexity of prokaryotic genomes using short reads. - Carl Kingsford; Michael C. Schatz; Mihai Pop (BMC Bioinform., 2010)

High Performance Computing for DNA Sequence Alignment and Assembly. - Michael C. Schatz (2010)

Genomic dark matter: the reliability of short read mapping illustrated by the genome mappability score. - Hayan Lee; Michael C. Schatz (Bioinform., 2012)

Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies. - Michael C. Schatz; Adam M. Phillippy; Daniel D. Sommer; Arthur L. Delcher; Daniela Puiu; Giuseppe Narzisi; Steven L. Salzberg; Mihai Pop (Briefings Bioinform., 2013)

On Algorithmic Complexity of Biomolecular Sequence Assembly Problem. - Giuseppe Narzisi; Bud Mishra; Michael C. Schatz (AlCoB, 2014)

Large-scale Sequencing and Assembly of Cereal Genomes Using Blacklight. - Philip D. Blood; Shoshana Marcus; Michael C. Schatz (XSEDE, 2014)

SplitMEM: a graphical algorithm for pan-genome analysis with suffix skips. - Shoshana Marcus; Hayan Lee; Michael C. Schatz (Bioinform., 2014)

Answering the demands of digital genomics. - Matthew A. Titmus; James Gurtowski; Michael C. Schatz (Concurr. Comput. Pract. Exp., 2014)

The contribution of de novo coding mutations to autism spectrum disorder. - Ivan Iossifov; Brian J. O'Roak; Stephan J. Sanders; Michael Ronemus; Niklas Krumm; Dan Levy; Holly A. Stessman; Kali T. Witherspoon; Laura Vives; Karynne E. Patterson; Joshua D. Smith; Bryan Paeper; et al. (Nat., 2014)

NanoBLASTer: Fast alignment and characterization of Oxford Nanopore single molecule sequencing reads. - Mohammad Ruhul Amin; Steven Skiena; Michael C. Schatz (ICCABS, 2016)

Assemblytics: a web analytics tool for the detection of variants from an assembly. - Maria Nattestad; Michael C. Schatz (Bioinform., 2016)

GenomeScope: fast reference-free genome profiling from short reads. - Gregory W. Vurture; Fritz J. Sedlazeck; Maria Nattestad; Charles J. Underwood; Han Fang; James Gurtowski; Michael C. Schatz (Bioinform., 2017)

Recovering rearranged cancer chromosomes from karyotype graphs. - Sergey Aganezov; Ilya Zban; Vitaly Aksenov; Nikita Alexeev; Michael C. Schatz (BMC Bioinform., 2019)

Vargas: heuristic-free alignment for assessing linear and graph read aligners. - Charlotte A. Darby; Ravi Gaddipati; Michael C. Schatz; Ben Langmead (Bioinform., 2020)

Skyhawk: an artificial neural network-based discriminator for reviewing clinically significant genomic variants. - Ruibang Luo; Tak Wah Lam; Michael C. Schatz (Int. J. Comput. Biol. Drug Des., 2020)

Sapling: accelerating suffix array queries with learned data models. - Melanie Kirsche; Arun Das 003; Michael C. Schatz (Bioinform., 2021)

Ribbon: intuitive visualization for complex genomic variation. - Maria Nattestad; Robert Aboukhalil; Chen-Shan Chin; Michael C. Schatz (Bioinform., 2021)

Sketching and sampling approaches for fast and accurate long read classification. - Arun Das 003; Michael C. Schatz (BMC Bioinform., 2022)

Diversifying the Genomic Data Science Research Community. - Rosa Alcazar; Maria Alvarez; Rachel Arnold; Mentewab Ayalew; Lyle G. Best; Michael C. Campbell; Kamal Chowdhury; Katherine E. L. Cox; Christina Daulton; Youping Deng; Carla Easter; Karla Fuller; et al. (CoRR, 2022)

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update. - Enis Afgan; Anton Nekrutenko; Björn A. Grüning; Daniel J. Blankenberg; Jeremy Goecks; Michael C. Schatz; Alexander E. Ostrovsky; Alexandru Mahmoud; Andrew J. Lonie; Anna Syme; Anne Fouilloux; Anthony Bretaudeau; et al. (Nucleic Acids Res., 2022)

Fast and accurate genome-wide predictions and structural modeling of protein-protein interactions using Galaxy. - Aysam Guerler; Dannon Baker; Marius van den Beek; Björn A. Grüning; Dave Bouvier; Nate Coraor; Stephen D. Shank; Jordan D. Zehr; Michael C. Schatz; Anton Nekrutenko (BMC Bioinform., 2023)

StephenHwang/MEMO. - Stephen Hwang; Nathaniel K. Brown; Omar Y. Ahmed; Katharine M. Jenike; Sam Kovaka; Michael C. Schatz; Ben Langmead (DROPS Artifacts, 2024)

StephenHwang/MEMO_experiments. - Stephen Hwang; Nathaniel K. Brown; Omar Y. Ahmed; Katharine M. Jenike; Sam Kovaka; Michael C. Schatz; Ben Langmead (DROPS Artifacts, 2024)

Mem-based pangenome indexing for k-mer queries. - Stephen Hwang; Nathaniel K. Brown; Omar Y. Ahmed; Katharine M. Jenike; Sam Kovaka; Michael C. Schatz; Ben Langmead (Algorithms Mol. Biol., 2025)