Daniel J. Blankenberg

According to our database, Daniel J. Blankenberg authored at least 23 papers between 2007 and 2026.

Collaborative distances:

• Dijkstra number of three.
• Erdős number of three.

2026

hdlib 2.0: Extending Machine Learning Capabilities of Vector-Symbolic Architectures.

Fabio Cumbo, Kabir Dhillon, Daniel J. Blankenberg

CoRR, January, 2026

An Automatic Pipeline for the Integration of Python-Based Tools into the Galaxy Platform: Application to the anvi'o Framework.

Fabio Cumbo, Jayadev Joshi, Daniel J. Blankenberg

CoRR, January, 2026

Designing vector-symbolic architectures for biomedical applications: ten tips and common pitfalls.

Fabio Cumbo, Davide Chicco, Sercan Aygun, Daniel J. Blankenberg

PeerJ Comput. Sci., 2026

2025

Quantum Hyperdimensional Computing: a foundational paradigm for quantum neuromorphic architectures.

Fabio Cumbo, Rui-Hao Li, Bryan A. Raubenolt, Jayadev Joshi, Abu Kaisar Mohammad Masum, Sercan Aygun, Daniel J. Blankenberg

CoRR, November, 2025

Feature selection with vector-symbolic architectures: a case study on microbial profiles of shotgun metagenomic samples of colorectal cancer.

Fabio Cumbo, Simone Truglia, Emanuel Weitschek, Daniel J. Blankenberg

Briefings Bioinform., March, 2025

GalaxyQ: A Platform for Reproducible and Provenance-Driven Hybrid Quantum-Classical Scientific Workflows.

Bryan A. Raubenolt, Daniel J. Blankenberg

Proceedings of the IEEE International Conference on Quantum Computing and Engineering, 2025

2023

hdlib: A Python library for designing Vector-Symbolic Architectures.

Fabio Cumbo, Emanuel Weitschek, Daniel J. Blankenberg

J. Open Source Softw., October, 2023

Galaxy Training: A powerful framework for teaching!

Saskia D. Hiltemann, Helena Rasche, Simon L. Gladman, Hans-Rudolf Hotz, Delphine Larivière, Daniel J. Blankenberg, Pratik D. Jagtap, Thomas Wollmann, Anthony Bretaudeau, Nadia Goué, Timothy J. Griffin, Coline Royaux, Yvan Le Bras, Subina P. Mehta, Anna Syme, Frederik Coppens, Bert Droesbeke, Nicola Soranzo, Wendi A. Bacon, Fotis E. Psomopoulos, Cristóbal Gallardo-Alba, John Davis, Melanie Christine Föll, Matthias Fahrner, Maria A. Doyle, Beatriz Serrano-Solano, Anne Fouilloux, Peter van Heusden, Wolfgang Maier, Dave Clements, Florian Heyl, The Galaxy Team, Björn A. Grüning, Bérénice Batut

PLoS Comput. Biol., January, 2023

Evaluating homophily in networks via <i>HONTO</i> (HOmophily Network TOol): a case study of chromosomal interactions in human PPI networks.

Nicola Apollonio, Daniel J. Blankenberg, Fabio Cumbo, Paolo Giulio Franciosa, Daniele Santoni

Bioinform., January, 2023

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, Anup Kumar, Arthur C. Eschenlauer, Assunta D. Desanto, Aysam Guerler, Beatriz Serrano-Solano, Bérénice Batut, Bradley W. Langhorst, Bridget Carr, Bryan A. Raubenolt, Cameron J. Hyde, Catherine J. Bromhead, Christopher B. Barnett, Coline Royaux, Cristóbal Gallardo, Daniel J. Fornika, Dannon Baker, Dave Bouvier, Dave Clements, David A. de Lima Morais, David Lopez Tabernero, Delphine Larivière, Engy Nasr, Federico Zambelli, Florian Heyl, Fotis E. Psomopoulos, Frederik Coppens, Gareth R. Price, Gianmauro Cuccuru, Gildas Le Corguillé, Gregory Von Kuster, Gulsum Gudukbay, Helena Rasche, Hans-Rudolf Hotz, Ignacio Eguinoa, Igor V. Makunin, Isuru Ranawaka, James Taylor, Jayadev Joshi, Jennifer Hillman-Jackson, John Chilton, Kaivan Kamali, Keith Suderman, Krzysztof Poterlowicz, Yvan Le Bras, Lucille Lopez-Delisle, Luke Sargent, Madeline E. Bassetti, Marco Antonio Tangaro, Marius van den Beek, Martin Cech, Matthias Bernt, Matthias Fahrner, Mehmet Tekman, Melanie Christine Föll, Michael R. Crusoe, Miguel Roncoroni, Natalie Kucher, Nate Coraor, Nicholas Stoler, Nick Rhodes, Nicola Soranzo, Niko Pinter, Nuwan Goonasekera, Pablo A. Moreno, Pavankumar Videm, Petera Melanie, Pietro Mandreoli, Pratik D. Jagtap, Qiang Gu, Ralf J. M. Weber, Ross Lazarus, Ruben H. P. Vorderman, Saskia D. Hiltemann, Sergey Golitsynskiy, Shilpa Garg, Simon A. Bray, Simon L. Gladman, Simone Leo, Subina P. Mehta, Timothy J. Griffin, Vahid Jalili, Yves Vandenbrouck, Victor Wen, Vijay K. Nagampalli, Wendi A. Bacon, Willem L. De Koning, Wolfgang Maier, Peter J. Briggs

Nucleic Acids Res., 2022

PDAUG: a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling.

Jayadev Joshi, Daniel J. Blankenberg

BMC Bioinform., 2022

2021

SimText: a text mining framework for interactive analysis and visualization of similarities among biomedical entities.

Marie Macnee, Eduardo Pérez-Palma, Sarah Schumacher-Bass, Jarrod Dalton, Costin Leu, Daniel J. Blankenberg, Dennis Lal

Bioinform., November, 2021

2020

A crowdsourced set of curated structural variants for the human genome.

Lesley M. Chapman, Noah Spies, Patrick Pai, Chun Shen Lim, Andrew Carroll, Giuseppe Narzisi, Christopher M. Watson, Christos Proukakis, Wayne E. Clarke, Naoki Nariai, Eric T. Dawson, Garan Jones, Daniel J. Blankenberg, Christian Brueffer, Chunlin Xiao, Sree Rohit Raj Kolora, Noah Alexander, Paul Wolujewicz, Azza E. Ahmed, Graeme Smith, Saadlee Shehreen, Aaron M. Wenger, Marc L. Salit, Justin M. Zook

PLoS Comput. Biol., 2020

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update.

Vahid Jalili, Enis Afgan, Qiang Gu, Dave Clements, Daniel J. Blankenberg, Jeremy Goecks, James Taylor, Anton Nekrutenko

Nucleic Acids Res., 2020

2019

You Wrote It, Now Get It Used: Publishing Your Software with Galaxy and Bioconda.

Daniel J. Blankenberg, Martin Cech

Proceedings of the 10th ACM International Conference on Bioinformatics, 2019

2018

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update.

Enis Afgan, Dannon Baker, Bérénice Batut, Marius van den Beek, Dave Bouvier, Martin Cech, John Chilton, Dave Clements, Nate Coraor, Björn A. Grüning, Aysam Guerler, Jennifer Hillman-Jackson, Saskia D. Hiltemann, Vahid Jalili, Helena Rasche, Nicola Soranzo, Jeremy Goecks, James Taylor, Anton Nekrutenko, Daniel J. Blankenberg

Nucleic Acids Res., 2018

Recommendations for the packaging and containerizing of bioinformatics software.

Björn A. Grüning, Olivier Sallou, Pablo A. Moreno, Felipe da Veiga Leprevost, Hervé Ménager, Dan Søndergaard, Hannes L. Röst, Timo Sachsenberg, Brian O'Connor, Fábio Madeira, Victoria Dominguez Del Angel, Michael R. Crusoe, Susheel Varma, Daniel J. Blankenberg, Rafael C. Jiménez, Daniel Blankenberg, Yasset Pérez-Riverol

F1000Research, 2018

2016

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update.

Enis Afgan, Dannon Baker, Marius van den Beek, Daniel J. Blankenberg, Dave Bouvier, Martin Cech, John Chilton, Dave Clements, Nate Coraor, Carl Eberhard, Björn A. Grüning, Aysam Guerler, Jennifer Hillman-Jackson, Gregory Von Kuster, Eric Rasche, Nicola Soranzo, Nitesh Turaga, James Taylor, Anton Nekrutenko, Jeremy Goecks

Nucleic Acids Res., 2016

2014

Wrangling Galaxy's reference data.

Daniel J. Blankenberg, James E. Johnson, The Galaxy Team, James Taylor, Anton Nekrutenko

Bioinform., 2014

2011

Making whole genome multiple alignments usable for biologists.

Daniel J. Blankenberg, James Taylor, Anton Nekrutenko

Bioinform., 2011

Integrating diverse databases into an unified analysis framework: a Galaxy approach.

Daniel J. Blankenberg, Nathan Coraor, Gregory Von Kuster, James Taylor, Anton Nekrutenko

Database J. Biol. Databases Curation, 2011

2010

Manipulation of FASTQ data with Galaxy.

Daniel J. Blankenberg, Assaf Gordon, Gregory Von Kuster, Nathan Coraor, James Taylor, Anton Nekrutenko

Bioinform., 2010

2007

Quantitative sequence-function relationships in proteins based on gene ontology.

Vineet Sangar, Daniel J. Blankenberg, Naomi Altman, Arthur M. Lesk

BMC Bioinform., 2007