The Maelstrom: Network Service Debugging via "Ineffective Procedures". - Alva L. Couch; Noah M. Daniels (LISA, 2001)

Touring Protein Space with Matt. - Noah M. Daniels; Anoop Kumar; Lenore Cowen; Matthew Menke (ISBRA, 2010)

Formatt: correcting protein multiple structural alignments by sequence peeking. - Shilpa Nadimpalli; Noah M. Daniels; Lenore Cowen (BCB, 2011)

Experience report: Haskell in computational biology. - Noah M. Daniels; Andrew Gallant; Norman Ramsey (ICFP, 2012)

SMURFLite: combining simplified Markov random fields with simulated evolution improves remote homology detection for beta-structural proteins into the twilight zone. - Noah M. Daniels; Raghavendra Hosur; Bonnie Berger; Lenore J. Cowen (Bioinform., 2012)

Formatt: Correcting Protein Multiple Structural Alignments by Incorporating Sequence Alignment. - Noah M. Daniels; Shilpa Nadimpalli; Lenore J. Cowen (BMC Bioinform., 2012)

Compressive genomics for protein databases. - Noah M. Daniels; Andrew Gallant; Jian Peng 001; Lenore J. Cowen; Michael Baym; Bonnie Berger (Bioinform., 2013)

Remote Homology Detection in Proteins Using Graphical Models - Noah M. Daniels (CoRR, 2013)

Entropy-scaling search of massive biological data. - Yun William Yu; Noah M. Daniels; David Christian Danko; Bonnie Berger (CoRR, 2015)

MRFy: Remote Homology Detection for Beta-Structural Proteins Using Markov Random Fields and Stochastic Search. - Noah M. Daniels; Andrew Gallant; Norman Ramsey; Lenore J. Cowen (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

An Evaluation Framework for Lossy Compression of Genome Sequencing Quality Values. - Claudio Alberti; Noah M. Daniels; Mikel Hernaez; Jan Voges; Rachel L. Goldfeder; Ana A. Hernandez-Lopez; Marco Mattavelli; Bonnie Berger (DCC, 2016)

Computational biology in the 21st century: scaling with compressive algorithms. - Bonnie Berger; Noah M. Daniels (Commun. ACM, 2016)

Analysis of 16S Genomic Data using Graphical Databases. - Olivia M. Ahern; Rebecca J. Stevick; Li Yuan; Noah M. Daniels (BCB, 2017)

Assortative Mixture of English Parts of Speech. - Timothy Leonard; Lutz Hamel; Noah M. Daniels; Natallia V. Katenka (COMPLEX NETWORKS, 2017)

Efficient Distance Calculations Between Genomes Using Mathematical Approximation. - Yana Hrytsenko; Noah M. Daniels; Rachel S. Schwartz (BCB, 2018)

Clustered Hierarchical Entropy-Scaling Search of Astronomical and Biological Data. - Najib Ishaq; George Student; Noah M. Daniels (IEEE BigData, 2019)

Clustered Hierarchical Anomaly and Outlier Detection Algorithms. - Najib Ishaq; Thomas J. Howard III; Noah M. Daniels (IEEE BigData, 2021)

MEtaData Format for Open Reef Data (MEDFORD). - Polina Shpilker; John Freeman; Hailey McKelvie; Jill Ashey; Jay-Miguel Fonticella; Hollie Putnam; Jane Greenberg; Lenore Cowen; Alva L. Couch; Noah M. Daniels (MTSR, 2021)

Determining population structure from k-mer frequencies. - Yana Hrytsenko; Noah M. Daniels; Rachel S. Schwartz (BCB, 2022)

MEDFORD: A human- and machine-readable metadata markup language. - Polina Shpilker; John Freeman; Hailey McKelvie; Jill Ashey; Jay-Miguel Fonticella; Hollie Putnam; Jane Greenberg; Lenore Cowen; Alva L. Couch; Noah M. Daniels (Database J. Biol. Databases Curation, 2022)

Context-Sensitive Editing for the MEDFORD Metadata Language. - Liam Strand; Andrew Powers; Polina Shpilker; Lenore Cowen; Alva L. Couch; Noah M. Daniels (MTSR, 2023)

CLAM-Accelerated K-Nearest Neighbors Entropy-Scaling Search of Large High-Dimensional Datasets via an Actualization of the Manifold Hypothesis. - Morgan E. Prior; Thomas J. Howard III; Oliver McLaughlin; Najib Ishaq; Noah M. Daniels (CoRR, 2023)

Generalized compression and compressive search of large datasets. - Morgan E. Prior; Thomas J. Howard III; Emily Light; Najib Ishaq; Noah M. Daniels (IEEE Big Data, 2024)

AnVILMEDFORD: Documenting Cloud-Based Analysis Projects Using the MEDFORD Metadata Language. - Benjamin Stubbs; Polina Shpilker; Michael Sayers; Shaun Wallace; Noah M. Daniels; Alva L. Couch (IEEE Big Data, 2024)

Cross-Referencing Metadata Through an Extension of the MEDFORD Language. - Polina Shpilker; Benjamin Stubbs; Michael Sayers; Lenore Cowen; Shaun Wallace; Alva L. Couch; Noah M. Daniels (MTSR, 2024)