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List of works by James Taylor

28-way vertebrate alignment and conservation track in the UCSC Genome Browser

scientific article (publication date: December 2007)

A Novel Long Non-Coding RNA in the hTERT Promoter Region Regulates hTERT Expression

scientific article published on 29 December 2017

A comparative encyclopedia of DNA elements in the mouse genome

scientific article

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

scientific article

A reference model for deploying applications in virtualized environments

A single-cell RNA-sequencing training and analysis suite using the Galaxy framework

scientific article published on 01 October 2020

A sustainable national gateway for biological computation

An encyclopedia of mouse DNA elements (Mouse ENCODE).

scientific article

An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis

scientific article published on 04 March 2020

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome

scientific article published in June 2007

Architectural protein subclasses shape 3D organization of genomes during lineage commitment

scientific article

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

scientific article published on 23 April 2018

Building and provisioning bioinformatics environments on public and private Clouds

Chromosome Conformation Paints Reveal The Role Of Lamina Association In Genome Organization And Regulation

article

Cloud bursting galaxy: federated identity and access management

scientific article published on 01 January 2020

CloudLaunch: Discover and deploy cloud applications

CloudMan as a platform for tool, data, and analysis distribution

scientific article

Community-Driven Data Analysis Training for Biology

scientific article published on 01 June 2018

Comparative analyses of bidirectional promoters in vertebrates

scientific article

Dissemination of scientific software with Galaxy ToolShed

scientific article (publication date: 20 February 2014)

Dynamics of mitochondrial heteroplasmy in three families investigated via a repeatable re-sequencing study

scientific article published on 23 June 2011

Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration

scientific article

ESPERR: learning strong and weak signals in genomic sequence alignments to identify functional elements

scientific article

Enabling cloud bursting for life sciences within Galaxy

Enhancing pre-defined workflows with ad hoc analytics using Galaxy, Docker and Jupyter

Erratum: The anatomy of successful computational biology software

article

Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences

scientific article

Experimental validation of predicted mammalian erythroid cis-regulatory modules

scientific article

Finding cis-regulatory elements using comparative genomics: some lessons from ENCODE data

scientific article

Galaxy CloudMan: delivering cloud compute clusters

scientific article

Galaxy Cluster to Cloud - Genomics at Scale

Galaxy: A Gateway to Tools in e-Science

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

scientific article published on August 25, 2010

Galaxy: a platform for interactive large-scale genome analysis

scientific article

Galaxy: a web-based genome analysis tool for experimentalists

scientific article

Generation and annotation of the DNA sequences of human chromosomes 2 and 4

scientific article

Genome analysis of the platypus reveals unique signatures of evolution

scientific article

Genome analysis of the platypus reveals unique signatures of evolution

scientific article published in Nature

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

scientific article

Genome-wide comparative analysis reveals human- mouse regulatory landscape and evolution

Genome-wide comparative analysis reveals human-mouse regulatory landscape and evolution

scientific article

Genomic approaches towards finding cis-regulatory modules in animals ⬇️

scientific article published on June 18, 2012

Harnessing cloud computing with Galaxy Cloud

scientific article published on 8 November 2011

HiFive: a tool suite for easy and efficient HiC and 5C data analysis

scientific article

HiFive: a tool suite for easy and efficient HiC and 5C data analysis

scholarly article published 3 October 2014

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

scientific article published in June 2007

Integrating diverse databases into an unified analysis framework: a Galaxy approach

scientific article (publication date: 2011)

Integrative approach reveals composition of endoparasitoid wasp venoms

scientific article

Jetstream

Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers.

scientific article

Lamins Organize the Global Three-Dimensional Genome from the Nuclear Periphery

scientific article published on 28 June 2018

Lessons learned from Galaxy, a Web-based platform for high-throughput genomic analyses

Leveraging the national cyberinfrastructure for biomedical research

scientific article (publication date: 2014)

Making whole genome multiple alignments usable for biologists

scientific article (publication date: September 2011)

Manipulation of FASTQ data with Galaxy

scientific article

Measuring the reproducibility and quality of Hi-C data

article by Galip Gürkan Yardımcı et al published 19 March 2019 in Genome Biology

MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis

MetaWRAP-a flexible pipeline for genome-resolved metagenomic data analysis

scientific article published on 15 September 2018

NGS analyses by visualization with Trackster

scientific article

Natural variation in stochastic photoreceptor specification and color preference in Drosophila.

scientific article published on 18 December 2017

Next-generation sequencing data interpretation: enhancing reproducibility and accessibility ⬇️

scientific article published on September 1, 2012

No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics

scientific article published on 13 August 2020

Online resources for genomic analysis using high-throughput sequencing

scientific article published on 5 February 2015

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

scientific article

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

scientific article published on 20 May 2013

Phylogenomic resources at the UCSC Genome Browser

scientific article published in January 2008

Practical Computational Reproducibility in the Life Sciences

scientific article published on 01 June 2018

Practical computational reproducibility in the life sciences

scientific article published on 10 October 2017

Primary sequence and epigenetic determinants of in vivo occupancy of genomic DNA by GATA1.

scientific article

QuASAR: Quality Assessment of Spatial Arrangement Reproducibility in Hi-C Data

Regulatory potential scores from genome-wide three-way alignments of human, mouse, and rat

scientific article published on April 2004

Ribosome A and P sites revealed by length analysis of ribosome profiling data

scientific article

Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

scientific article

Strong and weak male mutation bias at different sites in the primate genomes: insights from the human-chimpanzee comparison

scientific article published on 9 November 2005

Systematic integration of GATA transcription factors and epigenomes via IDEAS paints the regulatory landscape of hematopoietic cells

scientific article published on 25 November 2019

TADs pair homologous chromosomes to promote interchromosomal gene regulation

scientific article published on 16 October 2018

Ten simple rules for reproducible computational research

scientific article

The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications

scientific article

The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies

scientific article (publication date: 11 February 2013)

The DNA60IFX contest

scientific article

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

scientific article

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update.

scientific article published in July 2018

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

scientific article published on 01 June 2020

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

a correction published on 25 June 2020

The anatomy of successful computational biology software

scientific article

The elastic analysis with galaxy on the cloud.

scientific article published on 11 October 2010

The full-length transcriptome of C. elegans using direct RNA sequencing

scientific article published on 05 February 2020

The genome sequence of the leaf-cutter ant Atta cephalotes reveals insights into its obligate symbiotic lifestyle

scientific article

Thyroid hormone signaling specifies cone subtypes in human retinal organoids

scientific article

Topologically associating domains are stable units of replication-timing regulation

scientific article

Toward the commoditization of translational genomic research: Design and implementation features of the Galaxy genomic workbench

scientific article

Using Galaxy to perform large-scale interactive data analyses

scientific article

Using cloud computing infrastructure with CloudBioLinux, CloudMan, and Galaxy

scientific article published on June 2012

Using galaxy to perform large-scale interactive data analyses

scientific article

Web-based analysis of (Epi-) genome data using EpiGRAPH and Galaxy

scientific article

Web-based visual analysis for high-throughput genomics

scientific article

Windshield splatter analysis with the Galaxy metagenomic pipeline

scientific article published on 09 October 2009

Wrangling Galaxy's reference data

scientific article

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