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List of works by John Boyle

Adaptable data management for systems biology investigations

scientific article

Biology must develop its own big-data systems.

scientific article

Challenging times for bioinformatics

scientific article published in Nature

Cytoscape: a community-based framework for network modeling

scientific article published on 01 January 2009

Decision support system for designing chemotherapeutic regimens.

scientific article published in January 1997

EPEPT: a web service for enhanced P-value estimation in permutation tests.

scientific article

Exploring novel chemotherapy treatments using the WWW.

scientific article

Fastbreak: a tool for analysis and visualization of structural variations in genomic data

scientific article

Gene-Expression Omnibus integration and clustering tools in SeqExpress.

scientific article published on 03 March 2005

Genome-wide analysis of effectors of peroxisome biogenesis

scientific article

Genome-wide analysis of signaling networks regulating fatty acid-induced gene expression and organelle biogenesis

scientific article published on April 2008

Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework

scientific article

Improving the learning of chemical-protein interactions from literature using transfer learning and specialized word embeddings

scientific article published on 01 January 2018

Interfaces to PeptideAtlas: a case study of standard data access systems.

scientific article

Is there a gender gap in chemical sciences scholarly communication?

scientific article published on 28 January 2020

Managing Chaos: Lessons Learned Developing Software in the Life Sciences.

scientific article

Methods for visual mining of genomic and proteomic data atlases

scientific article

Mining PeptideAtlas for biomarkers and therapeutics in human disease

scientific article

QTIPS: a novel method of unsupervised determination of isotopic amino acid distribution in SILAC experiments

scientific article

SAMQA: error classification and validation of high-throughput sequenced read data

scientific article

SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments

scientific article

SeqExpress: desktop analysis and visualization tool for gene expression experiments.

scientific article published on 26 February 2004

Systems biology driven software design for the research enterprise

scientific article

mspecLINE: bridging knowledge of human disease with the proteome

scientific article

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