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Benchmarking Studies

Benchmarking

Guest Editors: Olga Vitek and Mark D. Robinson

Genome Biology is currently inviting submissions for our upcoming special issue on Benchmarking Studies.

The issue, which is planned for the second half of 2019, will be guest edited by Professor Olga Vitek from Northeastern University and Professor Mark D. Robinson from University of Zurich.

Bioinformatics tools are essential for all kinds of genomic and post-genomic studies. As increasing numbers of methods are published in certain fields, it can be difficult to keep track of best practices for their use. Large scale studies that benchmark these methods on a wide range of datasets can be extremely useful to the scientific community. Genome Biology is issuing a call for papers reporting in-depth analyses of state-of-the-art computational tools on a wide range of datasets, with clear guidelines and recommendations given for the user.

The special issue will accept manuscripts presenting:

- in-depth analyses of advantages

-limitations of state-of-the-art methods

-demonstration on a variety of representative datasets and simulations

-clear guidelines/recommendations for the end-user

-insight into future directions for methods

Submission deadline: 18 May 2019

Please use the online submission system and indicate in your covering letter that you would like the manuscript to be considered for the ‘Benchmarking Studies’ special issue. If you would like to inquire about the suitability of a manuscript for consideration, please email a pre-submission inquiry to editorial@genomebiology.com.

The guest editors will have an advisory role to guide the scope of the issue and provide advice on commissioned content, but will not be involved in the editorial decision making on all papers submitted.

 

Yixin Yao
Special Issue Editor, Genome Biology

Barbara Cheifet
Chief Editor, Genome Biology

Olga Vitek

Mark D. Robinson

Guest Editors

 

  1. Content type: Open Letter

    Challenges are achieving broad acceptance for addressing many biomedical questions and enabling tool assessment. But ensuring that the methods evaluated are reproducible and reusable is complicated by the dive...

    Authors: Kyle Ellrott, Alex Buchanan, Allison Creason, Michael Mason, Thomas Schaffter, Bruce Hoff, James Eddy, John M. Chilton, Thomas Yu, Joshua M. Stuart, Julio Saez-Rodriguez, Gustavo Stolovitzky, Paul C. Boutros and Justin Guinney

    Citation: Genome Biology 2019 20:195

    Published on:

  2. Content type: Research

    Single-cell transcriptomics is rapidly advancing our understanding of the cellular composition of complex tissues and organisms. A major limitation in most analysis pipelines is the reliance on manual annotati...

    Authors: Tamim Abdelaal, Lieke Michielsen, Davy Cats, Dylan Hoogduin, Hailiang Mei, Marcel J. T. Reinders and Ahmed Mahfouz

    Citation: Genome Biology 2019 20:194

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  3. Content type: Research

    The combination of experimental evolution with whole-genome resequencing of pooled individuals, also called evolve and resequence (E&R) is a powerful approach to study the selection processes and to infer the ...

    Authors: Christos Vlachos, Claire Burny, Marta Pelizzola, Rui Borges, Andreas Futschik, Robert Kofler and Christian Schlötterer

    Citation: Genome Biology 2019 20:169

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  4. Content type: Research

    Alignment-free (AF) sequence comparison is attracting persistent interest driven by data-intensive applications. Hence, many AF procedures have been proposed in recent years, but a lack of a clearly defined be...

    Authors: Andrzej Zielezinski, Hani Z. Girgis, Guillaume Bernard, Chris-Andre Leimeister, Kujin Tang, Thomas Dencker, Anna Katharina Lau, Sophie Röhling, Jae Jin Choi, Michael S. Waterman, Matteo Comin, Sung-Hou Kim, Susana Vinga, Jonas S. Almeida, Cheong Xin Chan, Benjamin T. James…

    Citation: Genome Biology 2019 20:144

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  5. Content type: Review

    In computational biology and other sciences, researchers are frequently faced with a choice between several computational methods for performing data analyses. Benchmarking studies aim to rigorously compare th...

    Authors: Lukas M. Weber, Wouter Saelens, Robrecht Cannoodt, Charlotte Soneson, Alexander Hapfelmeier, Paul P. Gardner, Anne-Laure Boulesteix, Yvan Saeys and Mark D. Robinson

    Citation: Genome Biology 2019 20:125

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  6. Content type: Research

    In high-throughput studies, hundreds to millions of hypotheses are typically tested. Statistical methods that control the false discovery rate (FDR) have emerged as popular and powerful tools for error rate co...

    Authors: Keegan Korthauer, Patrick K. Kimes, Claire Duvallet, Alejandro Reyes, Ayshwarya Subramanian, Mingxiang Teng, Chinmay Shukla, Eric J. Alm and Stephanie C. Hicks

    Citation: Genome Biology 2019 20:118

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  7. Content type: Research

    Structural variations (SVs) or copy number variations (CNVs) greatly impact the functions of the genes encoded in the genome and are responsible for diverse human diseases. Although a number of existing SV det...

    Authors: Shunichi Kosugi, Yukihide Momozawa, Xiaoxi Liu, Chikashi Terao, Michiaki Kubo and Yoichiro Kamatani

    Citation: Genome Biology 2019 20:117

    Published on: