Special Issue "Computational Advances for Single-Cell Omics Data Analysis"

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Technologies and Resources for Genetics".

Deadline for manuscript submissions: closed (15 January 2019)

Special Issue Editors

Guest Editor
Prof. Ion Mandoiu

Computer Science and Engineering department, University of Connecticut, Storrs, 06269 CT, USA.
Website | E-Mail
Interests: bioinformatics, next-generation sequencing data analysis, metagenomics and metatranscriptomics, computational molecular epidemiology, immunogenomics
Guest Editor
Prof. Alex Zelikovsky

Department of Computer Science, Georgia State University, Atlanta, GA 30303, USA
Website | E-Mail
Guest Editor
Prof. Pavel Skums

Department of Computer Science, Georgia State University, Atlanta, GA 30303, USA
Website | E-Mail
Interests: bioinformatics, computational biology, public health, computational molecular epidemiology computational cancer genomics

Special Issue Information

Dear colleagues,

Recent technological advances have enabled high-throughput profiling of genomes, transcriptomes, epigenomes, and proteomes at single cell resolution. These revolutionary single-cell -omics technologies promise to bring unprecedented insights into tissue heterogeneity and unveil subtle regulatory processes that are undetectable by bulk sample analysis. However, fully realizing their potential requires the development of novel computational and statistical analysis methods capable of handling the massive data sizes and significant levels of technical and biological noise.

The goal of this Special Issue is to publish review and research articles on the latest developments in computing infrastructure, mathematical and statistical modeling, algorithms, and visualization methods for single-cell -omics data. Topics of interest include, but are not limited to, the following topics:

  • Quality control for single-cell sequencing data
  • Single-cell RNA-Seq quantification
  • Variant calling and haplotyping
  • Modeling of missing data and imputation
  • Normalization and batch effect removal
  • Clustering and cell type inference
  • Single-cell spatial reconstruction
  • Lineage inference
  • Single-cell phylogenetics
  • Visualization
  • Single-cell bioinformatics workflows and benchmarking
  • Integration of multi-omics single-cell data
  • Cell atlases

Prospective authors are encouraged to participate in the 1st Workshop on Computational Advances for Single-Cell Omics Data Analysis (CASCODA) held in conjunction with the 8th IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS) at the University of Nevada, Las Vegas on Oct. 18-20, 2018 (see http://www.iccabs.org/iccabs18_workshop.html for details).

Prof. Ion Mandoiu
Prof. Alex Zelikovsky
Prof. Pavel Skums
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

For this Special Issue we are glad to offer a 15% discount from our APC to all planned contributions.


  • single-cell -omics
  • high-throughput sequencing
  • statistical modeling
  • algorithms
  • visualization
  • lineage inference
  • cell atlases

Published Papers

There is no accepted submissions to this special issue at this moment.
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