Cancer Informatics

An international, peer reviewed, open access journal that focuses on reporting bioinformatic analysis of molecular genetic and/or clinical data pertaining to human cancer risk, prevention, outcome or treatment response.  The journal recognizes that scientific collaborations across traditional disciplines can yield exponential synergistic gains: cancer research benefits from advances in many fields, including genomics and proteomics, mass spectrometry and radio imaging, computer science and biostatistics including machine learning and artificial intelligence, and medical informatics. The journal also recognizes the centrality of computational biology in these synergies.

Editor in Chief: Dr. J. T. Efird

ISSN: 1176-9351

Processing Speed: High quality, constructive peer review and rapid editorial decision within an average of four weeks.

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Toolbox for Mobile-Element Insertion Detection on Cancer Genomes
Wan-Ping Lee, Jiantao Wu and Gabor T. Marth
Cancer Informatics 2014:Suppl. 4 45-52
Methodology | Published on 15 Oct 2014

Mapping Splicing Quantitative Trait Loci in RNA-Seq
Cheng Jia, Yu Hu, Yichuan Liu and Mingyao Li
Cancer Informatics 2014:Suppl. 4 35-43
Original Research | Published on 15 Oct 2014

TEGS-CN: A Statistical Method for Pathway Analysis of Genome-wide Copy Number Profile
Yen-Tsung Huang, Thomas Hsu and David C. Christiani
Cancer Informatics 2014:Suppl. 4 15-23
Original Research | Published on 15 Oct 2014

Unsupervised Outlier Profile Analysis
Debashis Ghosh and Song Li
Cancer Informatics 2014:Suppl. 4 25-33
Review | Published on 15 Oct 2014

CORM: An R Package Implementing the Clustering of Regression Models Method for Gene Clustering
Jiejun Shi and Li-Xuan Qin
Cancer Informatics 2014:Suppl. 4 11-13
Review | Published on 15 Oct 2014

Profiling the microRNA Expression in Human iPS and iPS-derived Retinal Pigment Epithelium
Heuy-Ching Wang, Whitney A. Greene, Ramesh R. Kaini, Jane Shen-Gunther, Hung-I H Chen, Hong Cai and Yufeng Wang
Cancer Informatics 2014:Suppl. 5 25-35
Review | Published on 15 Oct 2014

Master Regulators, Regulatory Networks, and Pathways of Glioblastoma Subtypes
Serdar Bozdag, Aiguo Li, Mehmet Baysan, and Howard A. Fine
Cancer Informatics 2014:Suppl. 3 33-44
Original Research | Published on 15 Oct 2014

Network-based Prediction of Cancer under Genetic Storm
Ahmet Ay, Dihong Gong, Tamer Kahveci
Cancer Informatics 2014:Suppl. 3 15-31
Original Research | Published on 15 Oct 2014

Quality Control for RNA-Seq (QuaCRS): An Integrated Quality Control Pipeline
Karl W. Kroll, Nima E. Mokaram, Alexander R. Pelletier, David E. Frankhouser, Maximillian S. Westphal, Paige A. Stump, Cameron L. Stump, Ralf Bundschuh, James S. Blachly and Pearlly Yan
Cancer Informatics 2014:Suppl. 3 7-14
Review | Published on 15 Oct 2014

Automated Recommendation for Cervical Cancer Screening and Surveillance
Kavishwar B. Wagholikar, Kathy L. MacLaughlin, Petra M. Casey, Thomas M. Kastner, Michael R. Henry, Ronald A. Hankey, Steve G. Peters, Robert A. Greenes, Christopher G. Chute, Hongfang Liu and Rajeev Chaudhry
Cancer Informatics 2014:Suppl. 3 1-6
Original Research | Published on 15 Oct 2014 | Video abstract

Exploiting Literature-derived Knowledge and Semantics to Identify Potential Prostate Cancer Drugs
Rui Zhang, Michael J. Cairelli, Marcelo Fiszman, Halil Kilicoglu, Thomas C. Rindflesch, Serguei V. Pakhomov and Genevieve B. Melton
Cancer Informatics 2014:Suppl. 1 103-111
Original Research | Published on 14 Oct 2014

Prediction of MicroRNA Precursors Using Parsimonious Feature Sets
Petra Stepanowsky, Eric Levy, Jihoon Kim, Xiaoqian Jiang and Lucila Ohno-Machado
Cancer Informatics 2014:Suppl. 1 95-102
Review | Published on 14 Oct 2014

Disease Biomarker Query from RNA-Seq Data
Henry Han and Xiaoqian Jiang
Cancer Informatics 2014:Suppl. 1 81-94
Review | Published on 14 Oct 2014

Integrated DNA Copy Number and Gene Expression Regulatory Network Analysis of Non-small Cell Lung Cancer Metastasis
Seyed M. Iranmanesh and Nancy L. Guo
Cancer Informatics 2014:Suppl. 5 13-23
Original Research | Published on 14 Oct 2014

CSNK1A1 and Gli2 as Novel Targets Identified Through an Integrative Analysis of Gene Expression Data, Protein-Protein Interaction and Pathways Networks in Glioblastoma Tumors: Can These Two Be Antagonistic Proteins?
Seema Mishra
Cancer Informatics 2014:13 93-108
Original Research | Published on 13 Oct 2014

Introductory Editorial: Computational Advances in Cancer Informatics (A)
Xiaoqian Jiang, Rui Chen, Samuel Cheng, Xia Jiang, Bairong Shen, Rong Xu, Song Yi
Cancer Informatics 2014:Suppl. 1 45-48
Editorial | Published on 13 Oct 2014

Inferring Aberrant Signal Transduction Pathways in Ovarian Cancer from TCGA Data
Richard Neapolitan and Xia Jiang
Cancer Informatics 2014:Suppl. 1 29-36
Review | Published on 13 Oct 2014

Optimization of Network Topology in Computer-Aided Detection Schemes Using Phased Searching with NEAT in a Time-Scaled Framework
Maxine Tan, Jiantao Pu and Bin Zheng
Cancer Informatics 2014:Suppl. 1 17-27
Review | Published on 13 Oct 2014

Mining Cancer-Specific Disease Comorbidities from a Large Observational Health Database
Yang Chen and Rong Xu
Cancer Informatics 2014:Suppl. 1 37-44
Review | Published on 13 Oct 2014

Text Mining in Cancer Gene and Pathway Prioritization
Yuan Luo, Gregory Riedlinger and Peter Szolovits
Cancer Informatics 2014:Suppl. 1 69-79
Review | Published on 13 Oct 2014

Modeling Signal Transduction from Protein Phosphorylation to Gene Expression
Chunhui Cai, Lujia Chen, Xia Jiang and Xinghua Lu
Cancer Informatics 2014:Suppl. 1 59-67
Review | Published on 13 Oct 2014

Feasibility and Implementation of a Literature Information Management System for Human Papillomavirus in Head and Neck Cancers with Imaging
Dee H. Wu, Chance L. Matthiesen, Anthony M. Alleman, Aaron L. Fournier and Tyler C. Gunter
Cancer Informatics 2014:Suppl. 1 49-57
Review | Published on 13 Oct 2014

Inferring the Effects of Honokiol on the Notch Signaling Pathway in SW480 Colon Cancer Cells
Michelle L. Wynn, Nikita Consul, Sofia D. Merajver and Santiago Schnell
Cancer Informatics 2014:Suppl. 5 1-12
Original Research | Published on 13 Oct 2014

RNAseqPS: A Web Tool for Estimating Sample Size and Power for RNAseq Experiment
Yan Guo, Shilin Zhao, Chung-I Li, Quanhu Sheng and Yu Shyr
Cancer Informatics 2014:Suppl. 6 1-5
Review | Published on 13 Oct 2014

Combined Benefit of Prediction and Treatment: A Criterion for Evaluating Clinical Prediction Models
Dean Billheimer, Eugene W. Gerner, Christine E. McLaren and Bonnie LaFleur
Cancer Informatics 2014:Suppl. 2 93-103
Review | Published on 05 Oct 2014

Bayesian Disease Classification Using Copy Number Data
Subharup Guha, Yuan Ji, and Veerabhadran Baladandayuthapani
Cancer Informatics 2014:Suppl. 2 83-91
Review | Published on 01 Oct 2014

Introductory Editorial: Classification, Predictive Modelling, and Statistical Analysis of Cancer Data (A)
Hongmei Jiang, Lingling An, Veerabhadran Baladandayuthapani, Paul Livermore Auer
Cancer Informatics 2014:Suppl. 2 1-3
Editorial | Published on 21 Sep 2014

Functional Annotation of Putative Regulatory Elements at Cancer Susceptibility Loci
Stephanie A. Rosse, Paul L. Auer, and Christopher S. Carlson
Cancer Informatics 2014:Suppl. 2 5-17
Review | Published on 21 Sep 2014

A Review of Cancer Risk Prediction Models with Genetic Variants
Xuexia Wang, Michael J. Oldani, Xingwang Zhao, Xiaohui Huang and Dajun Qian
Cancer Informatics 2014:Suppl. 2 19-28
Review | Published on 21 Sep 2014

A Bayesian Integrative Model for Genetical Genomics with Spatially Informed Variable Selection
Alberto Cassese, Michele Guindani and Marina Vannucci
Cancer Informatics 2014:Suppl. 2 29-37
Original Research | Published on 21 Sep 2014

Integrative Bayesian Network Analysis of Genomic Data
Yang Ni, Francesco C. Stingo and Veerabhadran Baladandayuthapani
Cancer Informatics 2014:Suppl. 2 39-48
Original Research | Published on 21 Sep 2014

Integrated Analysis of Whole-Genome Paired-End and Mate-Pair Sequencing Data for Identifying Genomic Structural Variations in Multiple Myeloma
Rendong Yang, Li Chen, Scott Newman, Khanjan Gandhi, Gregory Doho, Carlos S. Moreno, Paula M. Vertino, Leon Bernal-Mizarchi, Sagar Lonial, Lawrence H. Boise, Michael Rossi, Jeanne Kowalski, and Zhaohui S. Qin
Cancer Informatics 2014:Suppl. 2 49-53
Review | Published on 21 Sep 2014

Comparative Study of Computational Methods for Reconstructing Genetic Networks of Cancer-Related Pathways
Nafiseh Sedaghat, Takumi Saegusa, Timothy Randolph and Ali Shojaie
Cancer Informatics 2014:Suppl. 2 55-66
Review | Published on 21 Sep 2014

Review of Current Methods, Applications, and Data Management for the Bioinformatics Analysis of Whole Exome Sequencing
Riyue Bao, Lei Huang, Jorge Andrade, Wei Tan, Warren A. Kibbe, Hongmei Jiang and Gang Feng
Cancer Informatics 2014:Suppl. 2 67-82
Review | Published on 21 Sep 2014

Integrative Pathway Analysis Using Graph-Based Learning with Applications to TCGA Colon and Ovarian Data
Andrew E. Dellinger, Andrew B. Nixon and Herbert Pang
Cancer Informatics 2014:13 Suppl. 4 1-9
Technical Advance | Published on 28 Jul 2014

On the Significance of Fuzzification of the N and M in Cancer Staging
Sara A. Yones, Ahmed S. Moussa, Hesham Hassan and Nelly H. Alieldin
Cancer Informatics 2014:13 85-91
Methodology | Published on 24 Jul 2014

Modeling the Altered Expression Levels of Genes on Signaling Pathways in Tumors As Causal Bayesian Networks
Richard Neapolitan, Diyang Xue, and Xia Jiang
Cancer Informatics 2014:13 77-84
Original Research | Published on 25 May 2014

Nonlinear Optical Microscopy Signal Processing Strategies in Cancer
Javier Adur, Hernandes F. Carvalho, Carlos L. Cesar and Víctor H. Casco
Cancer Informatics 2014:13 67-76
Review | Published on 02 Apr 2014

INsPeCT: INtegrative Platform for Cancer Transcriptomics
Piyush B. Madhamshettiwar, Stefan R. Maetschke, Melissa J. Davis, Antonio Reverter and Mark A. Ragan
Cancer Informatics 2014:13 59-66
Original Research | Published on 12 Mar 2014

A New Method for Predicting Patient Survivorship Using Efficient Bayesian Network Learning
Xia Jiang, Diyang Xue, Adam Brufsky, Seema Khan and Richard Neapolitan
Cancer Informatics 2014:13 47-57
Original Research | Published on 13 Feb 2014

Evaluating Gene Set Enrichment Analysis Via a Hybrid Data Model
Jianping Hua, Michael L. Bittner and Edward R. Dougherty
Cancer Informatics 2014:13(S1)1-16
Original Research | Published on 12 Feb 2014

Prognostic features of signal transducer and activator of transcription 3 in an ER(+) breast cancer model system
Li-Yu D. Liu, Li-Yun Chang, Wen-Hung Kuo, Hsiao-Lin Hwa, Yi-Shing Lin, Meei-Huey Jeng, Don A. Roth, King-Jen Chang and Fon-Jou Hsieh
Cancer Informatics 2014:13 21-45
Original Research | Published on 21 Jan 2014

OmicCircos: A Simple-to-Use R Package for the Circular Visualization of Multidimensional Omics Data
Ying Hu, Chunhua Yan, Chih-Hao Hsu, Qing-Rong Chen, Kelvin Niu, George A. Komatsoulis and Daoud Meerzaman
Cancer Informatics 2014:13 13-20
Technical Advance | Published on 16 Jan 2014

stepwiseCM: An R Package for Stepwise Classification of Cancer Samples Using Multiple Heterogeneous Data Sets
Askar Obulkasim and Mark A van de Wiel
Cancer Informatics 2014:13 1-11
Software or database review | Published on 02 Jan 2014

Are the Somatic Mutation and Tissue Organization Field Theories of Carcinogenesis Incompatible?
Simon Rosenfeld
Cancer Informatics 2013:12 221-229
Debate | Published on 01 Dec 2013

Gene Expression Meta-Analysis Identifies Cytokine Pathways and 5q Aberrations Involved in Metastasis of ERBB2 Amplified and Basal Breast Cancer
Mads Thomassen, Qihua Tan, Mark Burton and Torben A. Kruse
Cancer Informatics 2013:12 203-219
Original Research | Published on 25 Nov 2013

Monitoring of Technical Variation in Quantitative High-Throughput Datasets
Martin Lauss, Ilhami Visne, Albert Kriegner, Markus Ringnér, Göran Jönsson and Mattias Höglund
Cancer Informatics 2013:12 193-201
Original Research | Published on 23 Sep 2013

Comprehensive Assessment and Network Analysis of the Emerging Genetic Susceptibility Landscape of Prostate Cancer
Chindo Hicks, Lucio Miele, Tejaswi Koganti and Srinivasan Vijayakumar
Cancer Informatics 2013:12 175-191
Original Research | Published on 28 Aug 2013

Analysis of Patterns of Gene Expression Variation within and between Ethnic Populations in Pediatric B-ALL
Chindo Hicks, Lucio Miele, Tejaswi Koganti, LaFarra Young-Gaylor, Deidre Rogers, Vani Vijayakumar and Gail Megason
Cancer Informatics 2013:12 155-173
Original Research | Published on 27 Aug 2013

Improved Sparse Multi-Class SVM and Its Application for Gene Selection in Cancer Classification
Lingkang Huang, Hao Helen Zhang, Zhao-Bang Zeng and Pierre R. Bushel
Cancer Informatics 2013:12 143-153
Original Research | Published on 04 Aug 2013

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