Quantifying Reproducibility in Computational Biology: The Case of the Tuberculosis Drugome

Enhancing reproducibility

(2013)   NATURE METHODS

CDE: A Tool for Creating Portable Experimental Software Packages

(2012) Philip Guo   COMPUTING IN SCIENCE & ENGINEERING

Case studies in reproducibility

(2011) T. Hothorn et al.   BRIEFINGS IN BIOINFORMATICS

A semantic framework for automatic generation of computational workflows using distributed data and component catalogues

(2011) Yolanda Gil et al.   JOURNAL OF EXPERIMENTAL & THEORETICAL ARTIFICIAL INTELLIGENCE

Repeatability and workability evaluation of SIGMOD 2011

(2011) Philippe Bonnet et al.   SIGMOD RECORD

Deriving chemosensitivity from cell lines: Forensic bioinformatics and reproducible research in high-throughput biology

(2010) Keith A. Baggerly et al.   Annals of Applied Statistics

Pre-calculated protein structure alignments at the RCSB PDB website: Fig. 1.

(2010) Andreas Prlić et al.   BIOINFORMATICS

Transparency and reproducibility in data analysis: the Prostate Cancer Prevention Trial

(2010) S. G. Baker et al.   BIOSTATISTICS

Special Section: The third provenance challenge on using the open provenance model for interoperability

(2010) Yogesh Simmhan et al.   Future Generation Computer Systems-The International Journal of eScience

Wings: Intelligent Workflow-Based Design of Computational Experiments

(2010) Yolanda Gil et al.   IEEE INTELLIGENT SYSTEMS

Accessible Reproducible Research

(2010) J. P. Mesirov   SCIENCE

The Mycobacterium tuberculosis Drugome and Its Polypharmacological Implications

(2010) Sarah L. Kinnings et al.   PLoS Computational Biology

What Do I Want from the Publisher of the Future?

(2010) Philip E. Bourne   PLoS Computational Biology

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

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

Reproducible research in signal processing

(2009) Patrick Vandewalle et al.   IEEE SIGNAL PROCESSING MAGAZINE

Repeatability of published microarray gene expression analyses

(2009) John P A Ioannidis et al.   NATURE GENETICS

A HUPO test sample study reveals common problems in mass spectrometry–based proteomics

(2009) Alexander W Bell et al.   NATURE METHODS

Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments

(2008) L. Xie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Computational Biology Resources Lack Persistence and Usability

(2008) Stella Veretnik et al.   PLoS Computational Biology