Daniel Blankenberg Laboratory

Research

Propelling Research through the Omics Age
The massive deluge of biomedical data that has privileged the contemporary scientific community is only the tip of the iceberg. With each technological advance, the wealth of biological data grows at an increasing rate.

Opportunities in biology and human health will exceed anything seen before, but will only bear fruit if researchers have access to the tools and means to analyze ‘big data’ in a reproducible, transparent, and collaborative fashion.

The explosion of data that heralds the ‘omics’ age provides a unique set of challenges and opportunities.

The Blankenberg lab is developing a collaborative computational biology research program that produces new algorithms and tools for the analysis of increasingly large and complex ‘omic’ datasets. This includes:

1. building computational resources and approaches that enable individuals and communities, regardless of their background, to effectively and reproducibly use high-throughput data and analysis tools for data-intensive science
2. empowering collaborative analysis and dissemination of human health datasets across all strata of métier
3. developing new, high-performance, computing-ready tools and algorithms for biomedical applications.

Selected Publications

View publications for Daniel Blankenberg, PhD
(Disclaimer: This search is powered by PubMed, a service of the U.S. National Library of Medicine. PubMed is a third-party website with no affiliation with Cleveland Clinic.)

1. 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, Soranzo N, Turaga N, Taylor J, Nekrutenko A, Goecks J. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Res. 2016 May 2.
2. 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, Kuhn RM, Nekrutenko A, Segal E, Ideker T, Reich M, Regev A, Chang HY, Mesirov JP. Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace. Nat Methods. 2016 Jan 18.
3. Blankenberg D, Taylor J, Nekrutenko A. Online resources for genomic analysis using high-throughput sequencing. Cold Spring Harb Protoc. 2015 Feb 5;2015(4):pdb.top083667.
4. Blankenberg D, Johnson JE; Galaxy Team, Taylor J, Nekrutenko A. Wrangling Galaxy's reference data. Bioinformatics. 2014 Jul 1;30(13):1917-9.
5. Blankenberg D, Von Kuster G, Bouvier E, Baker D, Afgan E, Stoler N; Galaxy Team, Taylor J, Nekrutenko A. Dissemination of scientific software with Galaxy ToolShed. Genome Biol. 2014 Feb 20;15(2):403.
6. 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. Proc Natl Acad Sci USA. 2014 Oct 28;111(43):15474-9.
7. Blankenberg D, Hillman-Jackson J. Analysis of next-generation sequencing data using Galaxy. Methods Mol Biol. 2014;1150:21-43.
8. 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. 2014 Mar 1;56(3):134-6, 138-41.
9. Minevich G, Park DS, Blankenberg D, Poole RJ, Hobert O. CloudMap: a cloudbased pipeline for analysis of mutant genome sequences. Genetics. 2012 Dec;192(4):1249-69.
10. Mouse ENCODE Consortium, 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, Byron R, Roach V, Sabo PJ, Sandstrom R, Stehling AS, Thurman RE, Weissman SM, Cayting P, Hariharan M, Lian J, Cheng Y, Landt SG, Ma Z, Wold BJ, Dekker J, Crawford GE, Keller CA, Wu W, Morrissey C, Kumar SA, Mishra T, Jain D, Byrska-Bishop M, Blankenberg D, Lajoie1 BR, Jain G, Sanyal A, Chen KB, Denas O, Taylor J, Blobel GA, Weiss MJ, Pimkin M, Deng W, Marinov GK, Williams BA, Fisher-Aylor KI, Desalvo G, Kiralusha A, Trout D, Amrhein H, Mortazavi A, Edsall L, McCleary D, Kuan S, Shen Y, Yue F, Ye Z, Davis CA, Zaleski C, Jha S, Xue C, Dobin A, Lin W, Fastuca M, Wang H, Guigo R, Djebali S, Lagarde J, Ryba T, Sasaki T, Malladi VS, Cline MS, Kirkup VM, Learned K, Rosenbloom KR, Kent WJ, Feingold EA, Good PJ, Pazin M, Lowdon RF, Adams LB. An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol. 2012 Aug 13;13(8):418.
11. Hillman-Jackson J, Clements D, Blankenberg D, Taylor J, Nekrutenko A; Galaxy Team. Using Galaxy to perform large-scale interactive data analyses. Curr Protoc Bioinformatics. 2012 Jun;Chapter 10:Unit10.5.
12. Blankenberg D, Taylor J, Nekrutenko A; Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-8.
13. Blankenberg D, Coraor N, Von Kuster G, Taylor J, Nekrutenko A; Galaxy Team. Integrating diverse databases into a unified analysis framework: a Galaxy approach. Database (Oxford). 2011 Apr 29.
14. Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5.
15. 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. Curr Protoc Mol Biol. 2010 Jan;Chapter 19:Unit 19.10.1-21.
16. 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, Diekhans M, Pringle TH, Murphy WJ, Lesk A, Weinstock GM, Lindblad-Toh K, Gibbs RA, Lander ES, Siepel A, Haussler D, Kent WJ. 28-way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome Res. 2007 Dec;17(12):1797-808.
17. Taylor J, Schenck I, Blankenberg D, Nekrutenko A. Using galaxy to perform large-scale interactive data analyses. Curr Protoc Bioinformatics. 2007 Sep;Chapter 10:Unit 10.5.
18. Sangar V, Blankenberg D, Altman N, Lesk AM. Quantitative sequence-function relationships in proteins based on gene ontology. BMC Bioinformatics. 2007 Aug 8;8:294.
19. 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 biologistfriendly. Genome Res. 2007 Jun;17(6):960-4.
20. 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 Res. 2005 Oct;15(10):1451-5.