Publications by authors named "Jeremy Goecks"

27Publications

A long-read RNA-seq approach to identify novel transcripts of very large genes.

Genome Res 2020 06 6;30(6):885-897. Epub 2020 Jul 6.

Center for Genetic Medicine Research, Children's Research Institute, Children's National Health System, Washington, D.C. 20010, USA.

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http://dx.doi.org/10.1101/gr.259903.119DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7370890PMC
June 2020

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

Nucleic Acids Res 2020 08;48(14):8205-8207

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

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http://dx.doi.org/10.1093/nar/gkaa554DOI Listing
August 2020

G-OnRamp: Generating genome browsers to facilitate undergraduate-driven collaborative genome annotation.

PLoS Comput Biol 2020 06 4;16(6):e1007863. Epub 2020 Jun 4.

Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1007863DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7272004PMC
June 2020

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

Nucleic Acids Res 2020 07;48(W1):W395-W402

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

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http://dx.doi.org/10.1093/nar/gkaa434DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7319590PMC
July 2020

How Machine Learning Will Transform Biomedicine.

Cell 2020 04;181(1):92-101

Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA.

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http://dx.doi.org/10.1016/j.cell.2020.03.022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7141410PMC
April 2020

High-dimensional multiplexed immunohistochemical characterization of immune contexture in human cancers.

Methods Enzymol 2020 2;635:1-20. Epub 2019 Jul 2.

Department of Cell, Developmental & Cancer Biology, Oregon Health and Science University, Portland, OR, United States; Knight Cancer Research Institute, Oregon Health and Science University, Portland, OR, United States. Electronic address:

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http://dx.doi.org/10.1016/bs.mie.2019.05.039DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7390987PMC
July 2019

Cloud bursting galaxy: federated identity and access management.

Bioinformatics 2020 01;36(1):1-9

Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA.

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http://dx.doi.org/10.1093/bioinformatics/btz472DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6956780PMC
January 2020

G-OnRamp: a Galaxy-based platform for collaborative annotation of eukaryotic genomes.

Bioinformatics 2019 11;35(21):4422-4423

Computational Biology Program, Oregon Health and Science University, Portland, OR, USA.

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http://dx.doi.org/10.1093/bioinformatics/btz309DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6821377PMC
November 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

Biocompute Objects-A Step towards Evaluation and Validation of Biomedical Scientific Computations.

PDA J Pharm Sci Technol 2017 Mar-Apr;71(2):136-146. Epub 2016 Dec 14.

Department of Biochemistry and Molecular Medicine, George Washington University, Washington, DC, USA

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http://dx.doi.org/10.5731/pdajpst.2016.006734DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5510742PMC
June 2018

Open pipelines for integrated tumor genome profiles reveal differences between pancreatic cancer tumors and cell lines.

Cancer Med 2015 Mar 4;4(3):392-403. Epub 2015 Jan 4.

Computational Biology Institute, George Washington University, Ashburn, Virginia, 20147.

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http://dx.doi.org/10.1002/cam4.360DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4380965PMC
March 2015

The Bioinformatics Open Source Conference (BOSC) 2013.

Bioinformatics 2015 Jan 14;31(2):299-300. Epub 2014 Jul 14.

Physical Biosciences Division, Lawrence Berkeley National Laboratory, MS 972R525, Berkeley, CA 94720, USA, Information and Computational Sciences, The James Hutton Institute, Dundee DD2 5DA, UK, Bioinformatics Core, Harvard School of Public Health, Boston, MA 02115, USA, The Computational Biology Institute, George Washington University, Washington, DC 20052, USA, Bioinformatics Department, Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland and National Evolutionary Synthesis Center (NESCent), Durham, NC 27705, USA.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btu413DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4287938PMC
January 2015

Web-based visual analysis for high-throughput genomics.

BMC Genomics 2013 Jun 13;14:397. Epub 2013 Jun 13.

Department of Biology, Emory University, 1510 Clifton Road NE, Atlanta, GA 30322, USA.

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http://dx.doi.org/10.1186/1471-2164-14-397DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3691752PMC
June 2013

Integrative approach reveals composition of endoparasitoid wasp venoms.

PLoS One 2013 23;8(5):e64125. Epub 2013 May 23.

Department of Biology, Emory University, Atlanta, Georgia, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0064125PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3662768PMC
January 2014

Parasitoid wasp venom SERCA regulates Drosophila calcium levels and inhibits cellular immunity.

Proc Natl Acad Sci U S A 2013 Jun 20;110(23):9427-32. Epub 2013 May 20.

Department of Biology, Emory University, Atlanta, GA 30322, USA.

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http://dx.doi.org/10.1073/pnas.1222351110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3677475PMC
June 2013

Turning pipe dreams into reality.

Genome Biol 2012 Aug 30;13(8):318. Epub 2012 Aug 30.

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http://dx.doi.org/10.1186/gb4039DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3491365PMC
August 2012

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences.

Genome Biol 2010 25;11(8):R86. Epub 2010 Aug 25.

Department of Biology and Department of Mathematics and Computer Science, Emory University, 1510 Clifton Road NE, Atlanta, GA 30322, USA.

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http://dx.doi.org/10.1186/gb-2010-11-8-r86DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2945788PMC
January 2011