Daniel Blankenberg

Daniel Blankenberg

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Daniel Blankenberg

Daniel Blankenberg

Publications by authors named "Daniel Blankenberg"

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Galaxy External Display Applications: closing a dataflow interoperability loop.

Nat Methods 2020 02;17(2):123-124

Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania, USA.

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http://dx.doi.org/10.1038/s41592-019-0727-xDOI Listing
February 2020

Software engineering for scientific big data analysis.

Gigascience 2019 05;8(5)

Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue / NE50, Cleveland, OH, USA.

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http://dx.doi.org/10.1093/gigascience/giz054DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6532757PMC
May 2019

Biology Needs Evolutionary Software Tools: Let's Build Them Right.

Mol Biol Evol 2018 06;35(6):1372-1375

Lerner Research Institute, Cleveland Clinic, Cleveland, OH.

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http://dx.doi.org/10.1093/molbev/msy084DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5967460PMC
June 2018

Online resources for genomic analysis using high-throughput sequencing.

Cold Spring Harb Protoc 2015 Feb 5;2015(4):324-35. Epub 2015 Feb 5.

Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania 16802;

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http://dx.doi.org/10.1101/pdb.top083667DOI Listing
February 2015

Analysis of next-generation sequencing data using Galaxy.

Methods Mol Biol 2014 ;1150:21-43

Department of Biochemistry and Molecular Biology, Penn State University, 505 Wartik Laboratory, University Park, PA, 16802, USA,

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http://dx.doi.org/10.1007/978-1-4939-0512-6_2DOI Listing
November 2014

Wrangling Galaxy's reference data.

Bioinformatics 2014 Jul 28;30(13):1917-9. Epub 2014 Feb 28.

Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA 16802, USA, http://www.galaxyproject.org, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA, Department of Biology and Department of Mathematics and Computer Science, Emory University, Atlanta, GA 30322, USADepartment of Biochemistry and Molecular Biology, Penn State University, University Park, PA 16802, USA, http://www.galaxyproject.org, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA, Department of Biology and Department of Mathematics and Computer Science, Emory University, Atlanta, GA 30322, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4071198PMC
July 2014

CloudMap: a cloud-based pipeline for analysis of mutant genome sequences.

Genetics 2012 Dec 10;192(4):1249-69. Epub 2012 Oct 10.

Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University Medical Center, New York, NY 10032, USA.

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http://dx.doi.org/10.1534/genetics.112.144204DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3512137PMC
December 2012

An encyclopedia of mouse DNA elements (Mouse ENCODE).

August 2012

Using Galaxy to perform large-scale interactive data analyses.

Curr Protoc Bioinformatics 2012 Jun;Chapter 10:Unit10.5

Penn State University, University Park, PA, USA.

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http://dx.doi.org/10.1002/0471250953.bi1005s38DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4282168PMC
June 2012

Making whole genome multiple alignments usable for biologists.

Bioinformatics 2011 Sep 19;27(17):2426-8. Epub 2011 Jul 19.

The Huck Institutes for the Life Sciences and Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btr398DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3157923PMC
September 2011

Manipulation of FASTQ data with Galaxy.

Bioinformatics 2010 Jul 18;26(14):1783-5. Epub 2010 Jun 18.

Huck Institute for the Life Sciences, Penn State University, University Park, PA 16803, USA.

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http://dx.doi.org/10.1093/bioinformatics/btq281DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2894519PMC
July 2010

Galaxy: a web-based genome analysis tool for experimentalists.

Curr Protoc Mol Biol 2010 Jan;Chapter 19:Unit 19.10.1-21

The Huck Institutes for the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA.

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http://dx.doi.org/10.1002/0471142727.mb1910s89DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4264107PMC
January 2010

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

BMC Bioinformatics 2007 Aug 8;8:294. Epub 2007 Aug 8.

Department of Biochemistry and Molecular Biology, Center of Computational Biology and Genomics, The Huck Institute for Genomics, Proteomics and Bioinformatics, The Pennsylvania State University, University Park, PA 16802, USA.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-8-294DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1976327PMC
August 2007

A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly.

Genome Res 2007 Jun;17(6):960-4

Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania 16802, USA.

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http://dx.doi.org/10.1101/gr.5578007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1891355PMC
June 2007

Galaxy: a platform for interactive large-scale genome analysis.

Genome Res 2005 Oct 16;15(10):1451-5. Epub 2005 Sep 16.

Center for Comparative Genomics and Bioinformatics, Huck Institutes for Life Sciences, Penn State University, University Park, Pennsylvania 16802, USA.

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http://dx.doi.org/10.1101/gr.4086505DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1240089PMC
October 2005