Special Issue "Application of Bioinformatics in Cancers"
A special issue of Cancers (ISSN 2072-6694).
Deadline for manuscript submissions: 31 March 2019
Dr. J. Chad Brenner
Assistant Professor, Department of Otolaryngology-Head and Neck Surgery
Director, Michigan Otolaryngology and Translational Oncology Laboratory
University of Michigan Health Systems, Ann Arbor, MI 48109, USA
Website | E-Mail
Interests: functional genomic, proteomic and bioinformatics approaches in cancer, sequencing the exomes and transcriptomes of head and neck cancer; drug sensitivities
Bioinformatics applications in cancer have rapidly evolved over the past several years. Ever since its initial implementation, next generation sequencing has altered our understanding of cancer biology, and the approaches to analyze more and more complex datasets have also become increasingly complex. Routine bioinformatics pipelines now range from those that rapidly detect and predict functional impact of molecular alterations to those that quantify changes to the tumor microenvironment. For example, several tools that analyze tumor-immune interactions have been successfully developed to assess tumor infiltrating lymphocyte content, microsatellite instability, total mutational burden and neoantigen presentation. Further complexity of integrated omics-based analysis is also now coupled with the emergence of modern machine learning and network-based approaches to analyze large datasets in the context of publicly available resources, such as the cancer genome atlas.
While much of the focus has so far been on annotating molecular alterations as well as infiltrating cell types or cell states in ideal sequencing conditions, alternative and application-specific approaches are now emerging that improve on a wide variety of established analysis techniques. These include techniques that range from improved quantification of copy number and gene expression from formalin fixed tissues as well as applications that require high sensitivity such as the quantification of tumor mutations from liquid biopsies (circulating cell free DNA). Further novel applications attempt to improve the ability to analyze the distribution and molecular impact of complicated genetic features such as repetitive or transposable endogenous elements (e.g., LINE-1) as well as exogenous genetic elements (e.g., human papilloma virus).
As we develop a better understanding of the limitations of these new informatics approaches, we can ultimately hope to apply these techniques to existing datasets and build well-annotated databases of easily accessible information that can be leveraged in multi-variable analysis pipelines. Similar to the success of SIGdb and cBioPortal, this should help yield new diagnostic and prognostic/predictive biomarkers for standard interventional modalities as well as emerging areas like immuno-oncology, and areas of unmet clinical need. This Special Issue will highlight the current state of the art in bioinformatics applications in cancer biology, and infer future prospects for improving informatics applications through artificial intelligence and machine learning approaches.
Dr. J. Chad Brenner
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. Cancers 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.
- Machine learning
- Artificial Intelligence
- Network Analysis
- Single cell sequencing
- Circulating tumor DNA (ctDNA)
- Neoantigen Prediction
- Precision medicine
- Computational Immunology