Call for Papers for 2016 Special Issue
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ACS Publications | Copyright © 2014
In the era of studies of increasing complexity, availability of high-resolution mass spectrometers, and large datasets generated by these experimental workflows, the need for scalable and accurate computational methods is more urgent than ever. In response to this need, this special issue of JPR will collect:
  •  reviews of the state of the art in large-scale computational mass spectrometry,
  • opinion pieces related to computational and statistical issues in mass spectrometric and integrative investigations
  • manuscripts describing new methods in the areas of algorithms, statistics and machine learning
  • manuscripts introducing new tools (software, databases, web servers), or improvements upon the existing tools, for large-scale analysis, and case studies exemplifying best practices in large-scale investigation.
Encouraged topics include (but are not limited to):

Combined large-scale experimentation and computation
  • Computational methods for emerging high-throughput technologies (e.g., single-cell technologies, spatial omics, MS imaging)
  •  Novel approaches to studies of genomic variants produced by alternative splicing (AST) and coding non synonymous single nucleotide polymorphisms (cSNPs).
  • Analysis of heterogeneous populations (e.g., heterogeneous biological groups, cell populations)
  • Personalized omics and personalized biomarker detection

Statistical inference on large-scale datasets and multi-omics datasets
  •  Integrative analysis of multiple omics technologies (including but not limited to genomics, transcriptomics, proteomics, metabolomics)
  •  Integration across scales (multiple temporal and spatial resolutions)
  • Statistical assessment of confidence in identified and quantified peptides, protein groups, and individual protein species
  •  Novel approaches to characterize absent or low-abundant analytes

Scalability and reproducibility

  •  Repeatability and reproducibility of large-scale computational research
  •  Best practices for data exchange, deposition, and processing
  • Grid computing, cloud computing, and scientific workflows
  • Re-analysis of datasets available in comprehensive repositories

Submission Deadline: September 14, 2015
Large-scale Computational Mass Spectrometry and Multi-omics

Guest Editors
Olga Vitek
Northeastern University

Oliver Kohlbacher
University of Tübingen

William S. Hancock
Northeastern University

Susan Weintraub
The University of Texas Health Science Center at San Antonio


Manuscripts must be submitted by September 14, 2015 to be considered for this Special Issue. Manuscripts must be submitted electronically through the ACS Paragon Plus Environment online submission system. Prospective authors should prepare manuscripts according to the JPR guidelines for submission. Authors should indicate in the Comments to the Editor that the manuscript is submitted for publication in the Special Issue: Large-scale computational mass spectrometry and multi-omics. Where applicable, raw data and metadata must be deposited via ProteomeXchange, with the PXD identifier in the final sentence of the Abstract. The target final acceptance date is November 2, 2015.

All submitted manuscripts will be subject to initial editorial review to determine whether they are appropriate for the Special Issue. Those not meeting this criterion may be considered for a regular issue of the journal or returned. All relevant papers will go through full peer review. Due to the publication schedule, only papers requiring no or minor revision will be accepted for this Special Issue. Papers requiring major revision may be considered for later regular issues.