Daniel Blankenberg

Scopus Author ID ORCID

Publication Activity (10 Years)

Years Active: 2018-2024
Publications (10 Years): 33

Top Venues

Nature communications

Journal of chemical theory and computation

PLoS computational biology

GigaScience

This page only lists publications with an associated author ORCID identifier.

Publications

Thiruvaimozhi Abimannan, Velayoudame Parthibane, Si-Hung Le, Nagampalli Vijaykrishna, Stephen D Fox, Baktiar O Karim, Govind Kunduri, Daniel Blankenberg, Thorkell Andresson, Takeshi Bamba, Usha R Acharya, Jairaj K Acharya
Sphingolipid biosynthesis is essential for metabolic rewiring during T H 17 cell differentiation. Science advances 10 (17) (2024)
Debjit Khan, Iyappan Ramachandiran, Kommireddy Vasu, Arnab China, Krishnendu Khan, Fabio Cumbo, Dalia Halawani, Fulvia Terenzi, Isaac Zin, Briana Long, Gregory Costain, Susan Blaser, Amanda Carnevale, Valentin Gogonea, Ranjan Dutta, Daniel Blankenberg, Grace Yoon, Paul L Fox
Homozygous EPRS1 missense variant causing hypomyelinating leukodystrophy-15 alters variant-distal mRNA m 6 A site accessibility. Nature communications 15 (1) (2024)
Debjit Khan, Iyappan Ramachandiran, Kommireddy Vasu, Arnab China, Krishnendu Khan, Fabio Cumbo, Dalia Halawani, Fulvia Terenzi, Isaac Zin, Briana Long, Gregory Costain, Susan Blaser, Amanda Carnevale, Valentin Gogonea, Ranjan Dutta, Daniel Blankenberg, Grace Yoon, Paul L Fox
Homozygous EPRS1 missense variant causing hypomyelinating leukodystrophy-15 alters variant-distal mRNA m 6 A site accessibility. Nature communications 15 (1) (2024)
Hakan Doga, Bryan Raubenolt, Fabio Cumbo, Jayadev Joshi, Frank P DiFilippo, Jun Qin, Daniel Blankenberg, Omar Shehab
A Perspective on Protein Structure Prediction Using Quantum Computers. Journal of chemical theory and computation 20 (9) (2024)
Debjit Khan, Iyappan Ramachandiran, Kommireddy Vasu, Arnab China, Krishnendu Khan, Fabio Cumbo, Dalia Halawani, Fulvia Terenzi, Isaac Zin, Briana Long, Gregory Costain, Susan Blaser, Amanda Carnevale, Valentin Gogonea, Ranjan Dutta, Daniel Blankenberg, Grace Yoon, Paul L Fox
Homozygous EPRS1 missense variant causing hypomyelinating leukodystrophy-15 alters variant-distal mRNA m 6 A site accessibility. Nature communications 15 (1) (2024)
Bryan Raubenolt, Daniel Blankenberg
Generalized open-source workflows for atomistic molecular dynamics simulations of viral helicases. GigaScience 13 (2024)
Debjit Khan, Iyappan Ramachandiran, Kommireddy Vasu, Arnab China, Krishnendu Khan, Fabio Cumbo, Dalia Halawani, Fulvia Terenzi, Isaac Zin, Briana Long, Gregory Costain, Susan Blaser, Amanda Carnevale, Valentin Gogonea, Ranjan Dutta, Daniel Blankenberg, Grace Yoon, Paul L Fox
Homozygous EPRS1 missense variant causing hypomyelinating leukodystrophy-15 alters variant-distal mRNA m 6 A site accessibility. Nature communications 15 (1) (2024)
Thiruvaimozhi Abimannan, Velayoudame Parthibane, Si-Hung Le, Nagampalli Vijaykrishna, Stephen D Fox, Baktiar O Karim, Govind Kunduri, Daniel Blankenberg, Thorkell Andresson, Takeshi Bamba, Usha R Acharya, Jairaj K Acharya
Sphingolipid biosynthesis is essential for metabolic rewiring during T H 17 cell differentiation. Science advances 10 (17) (2024)
Hakan Doga, Bryan Raubenolt, Fabio Cumbo, Jayadev Joshi, Frank P DiFilippo, Jun Qin, Daniel Blankenberg, Omar Shehab
A Perspective on Protein Structure Prediction Using Quantum Computers. Journal of chemical theory and computation (2024)
Hakan Doga, Bryan Raubenolt, Fabio Cumbo, Jayadev Joshi, Frank P DiFilippo, Jun Qin, Daniel Blankenberg, Omar Shehab
A Perspective on Protein Structure Prediction Using Quantum Computers. Journal of chemical theory and computation 20 (9) (2024)
Hakan Doga, Bryan Raubenolt, Fabio Cumbo, Jayadev Joshi, Frank P DiFilippo, Jun Qin, Daniel Blankenberg, Omar Shehab
A Perspective on Protein Structure Prediction Using Quantum Computers. Journal of chemical theory and computation 20 (9) (2024)
Bryan Raubenolt, Daniel Blankenberg
Generalized open-source workflows for atomistic molecular dynamics simulations of viral helicases. GigaScience 13 (2024)
Bryan Raubenolt, Daniel Blankenberg
Generalized open-source workflows for atomistic molecular dynamics simulations of viral helicases. GigaScience 13 (2024)
Hakan Doga, Bryan Raubenolt, Fabio Cumbo, Jayadev Joshi, Frank P DiFilippo, Jun Qin, Daniel Blankenberg, Omar Shehab
A Perspective on Protein Structure Prediction Using Quantum Computers. Journal of chemical theory and computation 20 (9) (2024)
Harpreet Kaur, Paige Minchella, David Alvarez-Carbonell, Neeraja Purandare, Nagampalli Vijaykrishna, Daniel Blankenberg, Todd Hulgan, Mariana Gerschenson, Jonathan Karn, Siddhesh Aras, Asha R Kallianpur
Contemporary Antiretroviral Therapy Dysregulates Iron Transport and Augments Mitochondrial Dysfunction in HIV-Infected Human Microglia and Neural-Lineage Cells. International journal of molecular sciences 24 (15) (2023)
Marie Macnee, Eduardo Pérez-Palma, Tobias Brünger, Chiara Klöckner, Konrad Platzer, Arthur Stefanski, Ludovica Montanucci, Allan Bayat, Maximilian Radtke, Ryan L Collins, Michael Talkowski, Daniel Blankenberg, Rikke S Møller, Johannes R Lemke, Michael Nothnagel, Patrick May, Dennis Lal
CNV-ClinViewer: enhancing the clinical interpretation of large copy-number variants online. Bioinformatics (Oxford, England) 39 (5) (2023)
Saskia Hiltemann, Helena Rasche, Simon Gladman, Hans-Rudolf Hotz, Delphine Larivière, Daniel Blankenberg, Pratik D Jagtap, Thomas Wollmann, Anthony Bretaudeau, Nadia Goué, Timothy J Griffin, Coline Royaux, Yvan Le Bras, Subina Mehta, Anna Syme, Frederik Coppens, Bert Droesbeke, Nicola Soranzo, Wendi Bacon, Fotis Psomopoulos, Cristóbal Gallardo-Alba, John Davis, Melanie Christine Föll, Matthias Fahrner, Maria A Doyle, Beatriz Serrano-Solano, Anne Claire Fouilloux, Peter van Heusden, Wolfgang Maier, Dave Clements, Florian Heyl, null null, Björn Grüning, Bérénice Batut
Galaxy Training: A powerful framework for teaching! PLoS computational biology 19 (1) (2023)
Saskia Hiltemann, Helena Rasche, Simon Gladman, Hans-Rudolf Hotz, Delphine Larivière, Daniel Blankenberg, Pratik D Jagtap, Thomas Wollmann, Anthony Bretaudeau, Nadia Goué, Timothy J Griffin, Coline Royaux, Yvan Le Bras, Subina Mehta, Anna Syme, Frederik Coppens, Bert Droesbeke, Nicola Soranzo, Wendi Bacon, Fotis Psomopoulos, Cristóbal Gallardo-Alba, John Davis, Melanie Christine Föll, Matthias Fahrner, Maria A Doyle, Beatriz Serrano-Solano, Anne Claire Fouilloux, Peter van Heusden, Wolfgang Maier, Dave Clements, Florian Heyl, null null, Björn Grüning, Bérénice Batut
Galaxy Training: A powerful framework for teaching! PLoS computational biology 19 (1) (2023)
Michael Reich, Thorin Tabor, John Liefeld, Jayadev Joshi, Forrest Kim, Helga Thorvaldsdottir, Daniel Blankenberg, Jill P Mesirov
Genomics to Notebook (g2nb): extending the electronic notebook to address the challenges of bioinformatics analysis. bioRxiv : the preprint server for biology (2023)
Saskia Hiltemann, Helena Rasche, Simon Gladman, Hans-Rudolf Hotz, Delphine Larivière, Daniel Blankenberg, Pratik D Jagtap, Thomas Wollmann, Anthony Bretaudeau, Nadia Goué, Timothy J Griffin, Coline Royaux, Yvan Le Bras, Subina Mehta, Anna Syme, Frederik Coppens, Bert Droesbeke, Nicola Soranzo, Wendi Bacon, Fotis Psomopoulos, Cristóbal Gallardo-Alba, John Davis, Melanie Christine Föll, Matthias Fahrner, Maria A Doyle, Beatriz Serrano-Solano, Anne Claire Fouilloux, Peter van Heusden, Wolfgang Maier, Dave Clements, Florian Heyl, null null, Björn Grüning, Bérénice Batut
Galaxy Training: A powerful framework for teaching! PLoS computational biology 19 (1) (2023)
Marie Macnee, Eduardo Pérez-Palma, Tobias Brünger, Chiara Klöckner, Konrad Platzer, Arthur Stefanski, Ludovica Montanucci, Allan Bayat, Maximilian Radtke, Ryan L Collins, Michael Talkowski, Daniel Blankenberg, Rikke S Møller, Johannes R Lemke, Michael Nothnagel, Patrick May, Dennis Lal
CNV-ClinViewer: enhancing the clinical interpretation of large copy-number variants online. Bioinformatics (Oxford, England) 39 (5) (2023)
Saskia Hiltemann, Helena Rasche, Simon Gladman, Hans-Rudolf Hotz, Delphine Larivière, Daniel Blankenberg, Pratik D Jagtap, Thomas Wollmann, Anthony Bretaudeau, Nadia Goué, Timothy J Griffin, Coline Royaux, Yvan Le Bras, Subina Mehta, Anna Syme, Frederik Coppens, Bert Droesbeke, Nicola Soranzo, Wendi Bacon, Fotis Psomopoulos, Cristóbal Gallardo-Alba, John Davis, Melanie Christine Föll, Matthias Fahrner, Maria A Doyle, Beatriz Serrano-Solano, Anne Claire Fouilloux, Peter van Heusden, Wolfgang Maier, Dave Clements, Florian Heyl, null null, Björn Grüning, Bérénice Batut
Galaxy Training: A powerful framework for teaching! PLoS computational biology 19 (1) (2023)
Marie Macnee, Eduardo Pérez-Palma, Tobias Brünger, Chiara Klöckner, Konrad Platzer, Arthur Stefanski, Ludovica Montanucci, Allan Bayat, Maximilian Radtke, Ryan L Collins, Michael Talkowski, Daniel Blankenberg, Rikke S Møller, Johannes R Lemke, Michael Nothnagel, Patrick May, Dennis Lal
CNV-ClinViewer: enhancing the clinical interpretation of large copy-number variants online. Bioinformatics (Oxford, England) 39 (5) (2023)
Kommireddy Vasu, Debjit Khan, Iyappan Ramachandiran, Daniel Blankenberg, Paul L Fox
Analysis of nested alternate open reading frames and their encoded proteins. NAR genomics and bioinformatics 4 (4) (2022)
Nagampalli VijayKrishna, Jayadev Joshi, Nate Coraor, Jennifer Hillman-Jackson, Dave Bouvier, Marius van den Beek, Ignacio Eguinoa, Frederik Coppens, John Davis, Michał Stolarczyk, Nathan C Sheffield, Simon Gladman, Gianmauro Cuccuru, Bjoern Andreas Gruening, Nicola Soranzo, Helena Rasche, Bradley W Langhorst, Matthias Bernt, Dan Fornika, David Anderson de Lima Morais, Michel Barrette, Peter van Heusden, Mauro Petrillo, Antonio Puertas Gallardo, Alex Patak, Hans-Rudolf Hotz, Daniel Blankenberg
Expanding the Galaxy's reference data. Bioinformatics advances 2 (1) (2022)
Sehyun Oh, Ludwig Geistlinger, Marcel Ramos, Daniel Blankenberg, Marius van den Beek, Jaclyn N Taroni, Vincent J Carey, Casey S Greene, Levi Waldron, Sean Davis
GenomicSuperSignature facilitates interpretation of RNA-seq experiments through robust, efficient comparison to public databases. Nature communications 13 (1) (2022)
Jayadev Joshi, Daniel Blankenberg
PDAUG: a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling. BMC bioinformatics 23 (1) (2022)
A Murat Eren, Evan Kiefl, Alon Shaiber, Iva A Veseli, Samuel E Miller, Matthew S Schechter, Isaac Fink, Jessica N Pan, Mahmoud Yousef, Emily C Fogarty, Florian Trigodet, Andrea R Watson, Özcan C Esen, Ryan M Moore, Quentin Clayssen, Michael D Lee, Veronika Kivenson, Elaina D Graham, Bryan D Merrill, Antti Karkman, Daniel Blankenberg, John M Eppley, Andreas Sjödin, Jarrod J Scott, Xabier Vázquez-Campos, Luke J McKay, Elizabeth A McDaniel, Sarah L R Stevens, Rika E Anderson, Jessika Fuessel, Antonio Fernandez-Guerra, Lois Maignien, Tom O Delmont, Amy D Willis
Community-led, integrated, reproducible multi-omics with anvi'o. Nature microbiology 6 (1) (2021)
Daniel Blankenberg, John M Chilton, Nate Coraor
Galaxy External Display Applications: closing a dataflow interoperability loop. Nature methods 17 (2) (2020)
Dannon Baker, Marius van den Beek, Daniel Blankenberg, Dave Bouvier, John M Chilton, Nate Coraor, Frederik Coppens, Ignacio Eguinoa, Simon Gladman, Bjoern Andreas Gruening, Nicholas Keener, Delphine Larivière, Andrew J Lonie, Sergei L Kosakovsky Pond, Wolfgang Maier, Anton Nekrutenko, James Taylor, Steven Weaver
No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics. PLoS pathogens 16 (8) (2020)
Bjoern Andreas Gruening, Olivier Sallou, Pablo Moreno, Felipe da Veiga Leprevost, Hervé Ménager, Dan Søndergaard, Hannes Röst, Timo Sachsenberg, Brian O'Connor, Fábio Madeira, Victoria Dominguez Del Angel, Michael R Crusoe, Susheel Varma, Daniel Blankenberg, Rafael C Jimenez, null null, Yasset Perez Riverol
Recommendations for the packaging and containerizing of bioinformatics software. F1000Research 7 (2018)
Sarah J C Craig, Daniel Blankenberg, Alice Carla Luisa Parodi, Ian M Paul, Leann L Birch, Jennifer S Savage, Michele E Marini, Jennifer L Stokes, Anton Nekrutenko, Matthew Reimherr, Francesca Chiaromonte, Kateryna D Makova
Child Weight Gain Trajectories Linked To Oral Microbiota Composition. Scientific reports 8 (1) (2018)
Bjoern Andreas Gruening, Olivier Sallou, Pablo Moreno, Felipe da Veiga Leprevost, Hervé Ménager, Dan Søndergaard, Hannes Röst, Timo Sachsenberg, Brian O'Connor, Fábio Madeira, Victoria Dominguez Del Angel, Michael R Crusoe, Susheel Varma, Daniel Blankenberg, Rafael C Jimenez, null null, Yasset Perez Riverol
Recommendations for the packaging and containerizing of bioinformatics software. F1000Research (2018)

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Publication Activity (10 Years)

Top Topics

Top Venues

Daniel Blankenberg