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Daniel J. Blankenberg, Ph.D. - Publications

Affiliations: 
2009 Pennsylvania State University, State College, PA, United States 
Area:
Bioinformatics Biology, Evolution and Development Biology, Genetics
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41 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Reich M, Tabor T, Liefeld J, Joshi J, Kim F, Thorvaldsdottir H, Blankenberg D, Mesirov JP. Genomics to Notebook (g2nb): extending the electronic notebook to address the challenges of bioinformatics analysis. Biorxiv : the Preprint Server For Biology. PMID 37066251 DOI: 10.1101/2023.04.04.535621  0.404
2023 Hiltemann S, Rasche H, Gladman S, Hotz HR, Larivière D, Blankenberg D, Jagtap PD, Wollmann T, Bretaudeau A, Goué N, Griffin TJ, Royaux C, Le Bras Y, Mehta S, Syme A, et al. Galaxy Training: A powerful framework for teaching! Plos Computational Biology. 19: e1010752. PMID 36622853 DOI: 10.1371/journal.pcbi.1010752  0.756
2022 Oh S, Geistlinger L, Ramos M, Blankenberg D, van den Beek M, Taroni JN, Carey VJ, Greene CS, Waldron L, Davis S. GenomicSuperSignature facilitates interpretation of RNA-seq experiments through robust, efficient comparison to public databases. Nature Communications. 13: 3695. PMID 35760813 DOI: 10.1038/s41467-022-31411-3  0.305
2022 VijayKrishna N, Joshi J, Coraor N, Hillman-Jackson J, Bouvier D, van den Beek M, Eguinoa I, Coppens F, Davis J, Stolarczyk M, Sheffield NC, Gladman S, Cuccuru G, Grüning B, Soranzo N, ... ... Blankenberg D, et al. Expanding the Galaxy's reference data. Bioinformatics Advances. 2: vbac030. PMID 35669346 DOI: 10.1093/bioadv/vbac030  0.429
2021 Ostrovsky A, Hillman-Jackson J, Bouvier D, Clements D, Afgan E, Blankenberg D, Schatz MC, Nekrutenko A, Taylor J, Team TG, Lariviere D. Using Galaxy to Perform Large-Scale Interactive Data Analyses-An Update. Current Protocols. 1: e31. PMID 33583104 DOI: 10.1002/cpz1.31  0.787
2020 Tekman M, Batut B, Ostrovsky A, Antoniewski C, Clements D, Ramirez F, Etherington GJ, Hotz HR, Scholtalbers J, Manning JR, Bellenger L, Doyle MA, Heydarian M, Huang N, Soranzo N, ... ... Blankenberg D, et al. A single-cell RNA-sequencing training and analysis suite using the Galaxy framework. Gigascience. 9. PMID 33079170 DOI: 10.1093/gigascience/giaa102  0.66
2020 Baker D, van den Beek M, Blankenberg D, Bouvier D, Chilton J, Coraor N, Coppens F, Eguinoa I, Gladman S, Grüning B, Keener N, Larivière D, Lonie A, Kosakovsky Pond S, Maier W, et al. No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics. Plos Pathogens. 16: e1008643. PMID 32790776 DOI: 10.1371/Journal.Ppat.1008643  0.757
2020 Jalili V, Afgan E, Gu Q, Clements D, Blankenberg D, Goecks J, Taylor J, Nekrutenko A. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update. Nucleic Acids Research. PMID 32585001 DOI: 10.1093/Nar/Gkaa554  0.726
2020 Chapman LM, Spies N, Pai P, Lim CS, Carroll A, Narzisi G, Watson CM, Proukakis C, Clarke WE, Nariai N, Dawson E, Jones G, Blankenberg D, Brueffer C, Xiao C, et al. A crowdsourced set of curated structural variants for the human genome. Plos Computational Biology. 16: e1007933. PMID 32559231 DOI: 10.1371/Journal.Pcbi.1007933  0.404
2020 Jalili V, Afgan E, Gu Q, Clements D, Blankenberg D, Goecks J, Taylor J, Nekrutenko A. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update. Nucleic Acids Research. PMID 32479607 DOI: 10.1093/nar/gkaa434  0.706
2020 Blankenberg D, Chilton J, Coraor N. Galaxy External Display Applications: closing a dataflow interoperability loop. Nature Methods. PMID 31959996 DOI: 10.1038/S41592-019-0727-X  0.409
2019 Grüning BA, Lampa S, Vaudel M, Blankenberg D. Software engineering for scientific big data analysis. Gigascience. 8. PMID 31121028 DOI: 10.1093/Gigascience/Giz054  0.469
2019 Craig S, Blankenberg D, Parodi A, Paul I, Birch L, Savage J, Marini M, Stokes J, Nekrutenko A, Reimherr M, Chiaromonte F, Makova K. 172. Child Weight Gain Trajectories Associated With Oral Microbiota Composition Biological Psychiatry. 85: S71. DOI: 10.1016/J.Biopsych.2019.03.186  0.534
2018 Gruening B, Sallou O, Moreno P, da Veiga Leprevost F, Ménager H, Søndergaard D, Röst H, Sachsenberg T, O'Connor B, Madeira F, Dominguez Del Angel V, Crusoe MR, Varma S, Blankenberg D, Jimenez RC, et al. Recommendations for the packaging and containerizing of bioinformatics software. F1000research. 7. PMID 31543945 DOI: 10.12688/F1000Research.15140.2  0.408
2018 Craig SJC, Blankenberg D, Parodi ACL, Paul IM, Birch LL, Savage JS, Marini ME, Stokes JL, Nekrutenko A, Reimherr M, Chiaromonte F, Makova KD. Child Weight Gain Trajectories Linked To Oral Microbiota Composition. Scientific Reports. 8: 14030. PMID 30232389 DOI: 10.1038/S41598-018-31866-9  0.558
2018 Afgan E, Baker D, Batut B, van den Beek M, Bouvier D, Cech M, Chilton J, Clements D, Coraor N, Grüning BA, Guerler A, Hillman-Jackson J, Hiltemann S, Jalili V, Rasche H, ... ... Blankenberg D, et al. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Research. PMID 29790989 DOI: 10.1093/Nar/Gky379  0.725
2018 Nekrutenko A, Team G, Goecks J, Taylor J, Blankenberg D. Biology needs evolutionary software tools: Let's build them right. Molecular Biology and Evolution. PMID 29688462 DOI: 10.1093/Molbev/Msy084  0.651
2018 Čech M, Chilton J, Grüning B, Rasche E, Soranzo N, Nekrutenko A, Bouvier D, Blankenberg D, Coraor N. Galaxy tool shed: tool discovery and repository management F1000research. 7. DOI: 10.7490/F1000Research.1115596.1  0.664
2017 Blankenberg D, Goecks J. 2017 Galaxy community update F1000research. 6. DOI: 10.7490/F1000Research.1114388.1  0.38
2016 Afgan E, Baker D, van den Beek M, Blankenberg D, Bouvier D, Čech M, Chilton J, Clements D, Coraor N, Eberhard C, Grüning B, Guerler A, Hillman-Jackson J, Von Kuster G, Rasche E, et al. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Research. PMID 27137889 DOI: 10.1093/Nar/Gkw343  0.713
2016 Qu K, Garamszegi S, Wu F, Thorvaldsdottir H, Liefeld T, Ocana M, Borges-Rivera D, Pochet N, Robinson JT, Demchak B, Hull T, Ben-Artzi G, Blankenberg D, Barber GP, Lee BT, et al. Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace. Nature Methods. PMID 26780094 DOI: 10.1038/Nmeth.3732  0.702
2016 Blankenberg D, Carnahan-Craig S. Sample Size Does Matter: Scaling Up Analysis in Galaxy with Metagenomics (BOSC2016 version) F1000research. 5. DOI: 10.7490/F1000Research.1112762.1  0.366
2016 Blankenberg D, Carnahan-Craig S. Sample size does matter: scaling up analysis in Galaxy with metagenomics F1000research. 5. DOI: 10.7490/F1000Research.1112712.1  0.364
2015 Blankenberg D, Taylor J, Nekrutenko A. Online resources for genomic analysis using high-throughput sequencing. Cold Spring Harbor Protocols. 2015: 324-35. PMID 25655493 DOI: 10.1101/Pdb.Top083667  0.716
2015 Blankenberg D. Demystifying the interoperability of disparate genomic resources F1000research. 4. DOI: 10.7490/F1000Research.1110122.1  0.377
2014 Rebolledo-Jaramillo B, Su MS, Stoler N, McElhoe JA, Dickins B, Blankenberg D, Korneliussen TS, Chiaromonte F, Nielsen R, Holland MM, Paul IM, Nekrutenko A, Makova KD. Maternal age effect and severe germ-line bottleneck in the inheritance of human mitochondrial DNA. Proceedings of the National Academy of Sciences of the United States of America. 111: 15474-9. PMID 25313049 DOI: 10.1073/Pnas.1409328111  0.569
2014 Blankenberg D, Von Kuster G, Bouvier E, Baker D, Afgan E, Stoler N, Taylor J, Nekrutenko A, Clements D, Coraor N, Eberhard C, Francheteau D, Goecks J, Guerler S, Jackson J, et al. Dissemination of scientific software with Galaxy ToolShed Genome Biology. 15. PMID 25001293 DOI: 10.1186/Gb4161  0.704
2014 Blankenberg D, Hillman-Jackson J. Analysis of next-generation sequencing data using Galaxy. Methods of Molecular Biology. 1150: 21-43. PMID 24743989 DOI: 10.1007/978-1-4939-0512-6_2  0.567
2014 Dickins B, Rebolledo-Jaramillo B, Su MS, Paul IM, Blankenberg D, Stoler N, Makova KD, Nekrutenko A. Controlling for contamination in re-sequencing studies with a reproducible web-based phylogenetic approach. Biotechniques. 56: 134-6, 138-41. PMID 24641477 DOI: 10.2144/000114146  0.654
2014 Blankenberg D, Johnson JE, Taylor J, Nekrutenko A. Wrangling Galaxy's reference data. Bioinformatics (Oxford, England). 30: 1917-9. PMID 24585771 DOI: 10.1093/Bioinformatics/Btu119  0.713
2012 Minevich G, Park DS, Blankenberg D, Poole RJ, Hobert O. CloudMap: a cloud-based pipeline for analysis of mutant genome sequences. Genetics. 192: 1249-69. PMID 23051646 DOI: 10.1534/Genetics.112.144204  0.467
2012 Stamatoyannopoulos JA, Snyder M, Hardison R, Ren B, Gingeras T, Gilbert DM, Groudine M, Bender M, Kaul R, Canfield T, Giste E, Johnson A, Zhang M, Balasundaram G, ... ... Blankenberg D, et al. An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biology. 13: 418. PMID 22889292 DOI: 10.1186/Gb-2012-13-8-418  0.312
2012 Hillman-Jackson J, Clements D, Blankenberg D, Taylor J, Nekrutenko A. Using Galaxy to perform large-scale interactive data analyses. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit10.5. PMID 22700312 DOI: 10.1002/0471250953.bi1005s38  0.731
2011 Blankenberg D, Taylor J, Nekrutenko A. Making whole genome multiple alignments usable for biologists. Bioinformatics (Oxford, England). 27: 2426-8. PMID 21775304 DOI: 10.1093/Bioinformatics/Btr398  0.703
2011 Blankenberg D, Coraor N, Von Kuster G, Taylor J, Nekrutenko A. Integrating diverse databases into an unified analysis framework: a Galaxy approach. Database : the Journal of Biological Databases and Curation. 2011: bar011. PMID 21531983 DOI: 10.1093/Database/Bar011  0.723
2010 Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A. Manipulation of FASTQ data with Galaxy. Bioinformatics (Oxford, England). 26: 1783-5. PMID 20562416 DOI: 10.1093/Bioinformatics/Btq281  0.675
2010 Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R, Mangan M, Nekrutenko A, Taylor J. Galaxy: a web-based genome analysis tool for experimentalists. Current Protocols in Molecular Biology / Edited by Frederick M. Ausubel ... [Et Al.]. Unit 19.10.1-21. PMID 20069535 DOI: 10.1002/0471142727.Mb1910S89  0.746
2007 Taylor J, Schenck I, Blankenberg D, Nekrutenko A. Using galaxy to perform large-scale interactive data analyses. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit 10.5. PMID 18428782 DOI: 10.1002/0471250953.Bi1005S19  0.718
2007 Miller W, Rosenbloom K, Hardison RC, Hou M, Taylor J, Raney B, Burhans R, King DC, Baertsch R, Blankenberg D, Kosakovsky Pond SL, Nekrutenko A, Giardine B, Harris RS, Tyekucheva S, et al. 28-way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome Research. 17: 1797-808. PMID 17984227 DOI: 10.1101/Gr.6761107  0.645
2007 Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Research. 17: 960-4. PMID 17568012 DOI: 10.1101/Gr.5578007  0.705
2005 Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P, Zhang Y, Blankenberg D, Albert I, Taylor J, Miller W, Kent WJ, Nekrutenko A. Galaxy: a platform for interactive large-scale genome analysis. Genome Research. 15: 1451-5. PMID 16169926 DOI: 10.1101/Gr.4086505  0.736
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