Network and Pathway Analysis of Cancer Susceptibility (A)

Supplement Aims and Scope

Cancer Informatics represents a hybrid discipline encompassing the fields of oncology, computer science, bioinformatics, statistics, computational biology, genomics, proteomics, metabolomics, pharmacology, and quantitative epidemiology. The common bond or challenge that unifies the various disciplines is the need to bring order to the massive amounts of data generated by researchers and clinicians attempting to find the underlying causes and effective means of treating cancer.

The future cancer informatician will need to be well-versed in each of these fields and have the appropriate background to leverage the computational, clinical, and basic science resources necessary to understand their data and separate signal from noise. Knowledge of and the communication among these specialty disciplines, acting in unison, will be the key to success as we strive to find answers underlying the complex and often puzzling diseases known as cancer.

The focus of bioinformatics in cancer research has shifted from generating ranked lists of genes associated with a particular clinical outcome to systematic analysis of critical signaling pathways and molecular networks in pathogenesis (1;2). This Supplement Issue of Cancer Informatics introduces cutting-edge computational methods developed for pathway and network-based analysis of cancer susceptibility and metastasis, including integrative regulatory networks of DNA copy number and expression profiles (3;4), co-expression network analysis of lncRNAs (5) and E2F-responsive genes (6), modeling the Notch signaling pathway in colon cancer therapy (7), functional genomic analysis in cancer prognosis (8), dysregulated pathways (9), and microRNA profiling of induced pluripotent stem (iPS) cells (10). As pointed out in the comprehensive review of molecular network analysis provided in this Supplement Issue (11), the future directions of systematic analysis of cancer susceptibility and metastasis are to utilize multi-level molecular profiles and to combine different computational methods in the analysis, in order to dissect important biological pathways and network modules in cancer initiation and progression.

Lead Guest Editor Dr Nancy Guo

Dr. Nancy Guo is an Associate Professor of Occupational and Environmental Health Science at West Virginia University. She completed her PhD at West Virginia University in 2004 and has previously worked at the University of Southern Mississippi. She now works primarily in cancer biomarkers and systematic assessment of nanotoxicity. Dr. Guo is the author or co-author of 39 published papers and has presented at 27 conferences, and holds editorial appointments at PLOS ONE, Oncology Letters, Journal of Tumor, Anatomy & Physiology (OMICS Publishing Group), Annals of Community Medicine and Practice.

lguo@hsc.wvu.edu

http://wvucancer.org/guolab

Guest Editors

DR. RUSSELL S. SCHWARTZ

Dr. Russell S. Schwartz is a Professor of Biological Sciences and Computational Biology at Carnegie Mellon University. He completed his PhD at Massachusetts Institute of Technology and has previously worked at Celera Genomics before joining Carnegie Mellon. He now works primarily in computational genetics/genomics and computational biophysics, with particular focus on application of phylogenetics and genetic variation analysis to studies in cancer biology. Dr. Schwartz is the author or co-author of 85 published papers and has presented at 30 conferences, and holds editorial appointments at the IEEE/ACM Transactions on Computational Biology and Bioinformatics and the INFORMS Journal on Computing.

russells@andrew.cmu.edu

http://www.cmu.edu/bio/faculty/primary/schwartz.html

DR. JIANG QIAN

Dr. Jiang Qian is an Associate Professor of Bioinformatics at Johns Hopkins Medicine. He completed his PhD at the Max Planck Institute for Polymer Research and has previously worked as postdoctoral fellow at Yale University. He now works primarily in computational modeling of regulatory networks in mammals. Dr. Qian is the author or co-author of >80 published papers and has presented at ~20 conferences, and holds editorial appointments at International Journal of Computational Biology and Drug Design.

Jiang.qian@jhmi.edu

http://www.hopkinsmedicine.org/wilmer/ employees/cvs/Qian.html

DR. PEILIN JIA

Dr. Peilin Jia is a Research Assistant Professor of Biomedical Informatics at Vanderbilt University School of Medicine. She completed her PhD at Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, and has previously worked at Virginia Commonwealth University. She now works primarily in computational cancer biology. Dr Jia is the author or co-author of >70 published papers and has presented at >10 conferences, and holds editorial appointments at BioMed Research International.

peilin.jia@vanderbilt.edu

https://medschool.vanderbilt.edu/cqs/people/Peilin/Jia/cqs-faculty-members

YOUPING DENG, Ph.D.,

Youping Deng, Ph.D., is currently the Director of Bioinformatics and Biostatistics, Associate Professor, Department of Internal Medicine and Biochemistry, Rush University Medical Center in Chicago. Dr. Deng received his Ph.D. from Peking Union Medical College. He used to be Associate Director of Bioinformatics, Mississippi Functional Genomics Network as well as adjunct Associate Professor in the Department of Computer Sciences of Georgia State University. From 2004 to 2008, he was a tenure track assistant professor at the University of Southern Mississippi. He has published more than 150 papers in peer-reviewed journals and is serving as editorial board members of 5 international journals.

youping_deng@rush.edu