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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A Single-Array-Based Method for Detecting Copy Number Variants Using Affymetrix High Density SNP Arrays and its Application to Breast Cancer
Ming Li, Yalu Wen and Wenjiang Fu
Cancer Informatics 2014:Suppl. 4 95-103
Technical Advance | Published on 16 Jul 2015

The Impact of Microenvironmental Heterogeneity on the Evolution of Drug Resistance in Cancer Cells
Shannon M. Mumenthaler, Jasmine Foo, Nathan C. Choi, Nicholas Heise, Kevin Leder, David B. Agus, William Pao, Franziska Michor, and Parag Mallick
Cancer Informatics 2015:Suppl. 4 19-31
Original Research | Published on 15 Jul 2015

Identification of Genetic Mutations in Human Lung Cancer by Targeted Sequencing
Hongxiang Feng, Xiaowei Wang, Zhenrong Zhang, Chuanning Tang, Hua Ye, Lindsey Jones, Feng Lou, Dandan Zhang, Shouwen Jiang, Hong Sun, Haichao Dong, Guangchun Zhang, Zhiyuan Liu, Zhishou Dong, Baishuai Guo, He Yan, Chaowei Yan, Lu Wang, Ziyi Su, Yangyang Li, Vijayalakshmi Nandakumar, Xue F. Huang, Si-Yi Chen and Deruo Liu
Cancer Informatics 2015:14 83-93
Original Research | Published on 29 Jun 2015

Time-Frequency Analysis of Peptide Microarray Data: Application to Brain Cancer Immunosignatures
Brian O'Donnell, Alexander Maurer, Antonia Papandreou-Suppappola and Phillip Stafford
Cancer Informatics 2015:Suppl. 2 219-233
Original Research | Published on 18 Jun 2015

Managing Multi-center Flow Cytometry Data for Immune Monitoring
Scott White, Karoline Laske, Marij J.P. Welters, Nicole Bidmon, Sjoerd H. van der Burg, Cedrik M. Britten, Jennifer Enzor, Janet Staats, Kent J. Weinhold, Cécile Gouttefangeas and Cliburn Chan
Cancer Informatics 2014:Suppl. 7 111-122
Review | Published on 10 Jun 2015

A Proposed Paradigm Shift in Initializing Cancer Predictive Models with DCE-MRI Based PK Parameters: A Feasibility Study
Alexandros Roniotis, Mariam-Eleni Oraiopoulou, Eleftheria Tzamali, Eleftherios Kontopodis, Sofie Van Cauter, Vangelis Sakkalis, Kostas Marias
Cancer Informatics 2015:Suppl. 4 7-18
Original Research | Published on 10 Jun 2015

Gene Expression Signatures Based on Variability can Robustly Predict Tumor Progression and Prognosis
Wikum Dinalankara and Héctor Corrada Bravo
Cancer Informatics 2015:14 71-81
Original Research | Published on 07 Jun 2015

Powerful Tukey’s One Degree-of-Freedom Test for Detecting Gene–Gene and Gene–Environment Interactions
Yaping Wang, Donghui Li and Peng Wei
Cancer Informatics 2015:Suppl. 2 209-218
Review | Published on 04 Jun 2015

Penalized Ordinal Regression Methods for Predicting Stage of Cancer in High-Dimensional Covariate Spaces
Amanda Elswick Gentry, Colleen K. Jackson-Cook, Debra E. Lyon and Kellie J. Archer
Cancer Informatics 2015:Suppl. 2 201-208
Review | Published on 27 May 2015

Inferring Stable Acquisition Durations for Applications of Perfusion Imaging in Oncology
Brian P. Hobbs and Chaan S. Ng
Cancer Informatics 2015:Suppl. 2 193-199
Review | Published on 25 May 2015

Identifying CDKN3 Gene Expression as a Prognostic Biomarker in Lung Adenocarcinoma via Meta-analysis
Xiao Zang, Min Chen, Yunyun Zhou, Guanghua Xiao, Yang Xie, and Xinlei Wang
Cancer Informatics 2015:Suppl. 2 183-191
Original Research | Published on 24 May 2015

A Hypothesis-Directed Approach to the Targeted Development of a Multiplexed Proteomic Biomarker Assay for Cancer
Emily M. Mackay, Jennifer Koppel, Pooja Das, Joanna Woo, David C. Schriemer and Oliver F. Bathe
Cancer Informatics 2015:14 65-70
Technical Advance | Published on 17 May 2015

Integrative Analyses of Cancer Data: A Review from a Statistical Perspective
Yingying Wei
Cancer Informatics 2015:Suppl. 2 173-181
Review | Published on 14 May 2015

Assessment of Weighted Quantile Sum Regression for Modeling Chemical Mixtures and Cancer Risk
Jenna Czarnota, Chris Gennings and David C. Wheeler
Cancer Informatics 2015:Suppl. 2 159-171
Review | Published on 13 May 2015

PathoQC: Computationally Efficient Read Preprocessing and Quality Control for High-Throughput Sequencing Data Sets
Changjin Hong, Solaiappan Manimaran and William Evan Johnson
Cancer Informatics 2014:Suppl. 1 167-176
Review | Published on 12 May 2015

The Standardized Histogram Shift of T2 Magnetic Resonance Image (MRI) Signal Intensities of Nephroblastoma Does Not Predict Histopathological Diagnostic Information
Sabine Müller, Ruslan David, Kostas Marias and Norbert Graf
Cancer Informatics 2015:Suppl. 4 1-5
Review | Published on 12 May 2015

Recent Enhancements to the Genetic Risk Prediction Model BRCAPRO
Emanuele Mazzola, Amanda Blackford, Giovanni Parmigiani and Swati Biswas
Cancer Informatics 2015:Suppl. 2 147-157
Review | Published on 10 May 2015

Identifying Molecular Features Associated with Psychoneurological Symptoms in Women with Breast Cancer Using Multivariate Mixed Models
Qing Zhou, Colleen Jackson-Cook, Debra Lyon, Robert Perera and Kellie J. Archer
Cancer Informatics 2015:Suppl. 2 139-145
Original Research | Published on 07 May 2015

Evaluating Geographically Weighted Regression Models for Environmental Chemical Risk Analysis
Jenna Czarnota, David C. Wheeler and Chris Gennings
Cancer Informatics 2015:Suppl. 2 117-127
Original Research | Published on 05 May 2015

Prediction of Early Breast Cancer Metastasis from DNA Microarray Data Using High-Dimensional Cox Regression Models
Christophe Zemmour, François Bertucci, Pascal Finetti, Bernard Chetrit, Daniel Birnbaum, Thomas Filleron and Jean-Marie Boher
Cancer Informatics 2015:Suppl. 2 129-138
Original Research | Published on 05 May 2015

Generalized Monotone Incremental Forward Stagewise Method for Modeling Count Data: Application Predicting Micronuclei Frequency
Mateusz Makowski and Kellie J. Archer
Cancer Informatics 2015:Suppl. 2 97-105
Review | Published on 29 Apr 2015

Evaluation of the Performance of Smoothing Functions in Generalized Additive Models for Spatial Variation in Disease
Umaporn Siangphoe and David C. Wheeler
Cancer Informatics 2015:Suppl. 2 107-116
Review | Published on 29 Apr 2015

Next Generation Distributed Computing for Cancer Research
Pankaj Agarwal and Kouros Owzar
Cancer Informatics 2014:Suppl. 7 97-109
Review | Published on 27 Apr 2015

Selecting Spatial Scale of Covariates in Regression Models of Environmental Exposures
Lauren P. Grant, Chris Gennings and David C. Wheeler
Cancer Informatics 2015:Suppl. 2 81-96
Review | Published on 27 Apr 2015

BioMiner: Paving the Way for Personalized Medicine
Chris Bauer, Karol Stec, Alexander Glintschert, Kristina Gruden, Christian Schichor, Michal Or-Guil, Joachim Selbig and Johannes Schuchhardt
Cancer Informatics 2015:14 55-63
Technical Advance | Published on 20 Apr 2015

Profiling Age-Related Epigenetic Markers of Stomach Adenocarcinoma in Young and Old Subjects
Byoung-Chul Kim, Hyoung Oh Jeong, Daeui Park, Chul-Hong Kim, Eun Kyeong Lee, Dae Hyun Kim, Eunok Im, Nam Deuk Kim, Sunghoon Lee, Byung Pal Yu, Jong Bhak and Hae Young Chung
Cancer Informatics 2015:14 47-54
Original Research | Published on 20 Apr 2015

Computing Molecular Signatures as Optima of a Bi-Objective Function: Method and Application to Prediction in Oncogenomics
Vincent Gardeux, Rachid Chelouah, Maria F. Barbosa Wanderley, Patrick Siarry, Antônio P. Braga, Fabien Reyal, Roman Rouzier, Lajos Pusztai and René Natowicz
Cancer Informatics 2015:14 33-45
Methodology | Published on 19 Apr 2015

Catchment Area Analysis Using Bayesian Regression Modeling
Aobo Wang and David C. Wheeler
Cancer Informatics 2015:Suppl. 2 71-79
Review | Published on 19 Apr 2015

RNA-Seq and Network Analysis Revealed Interacting Pathways in TGF-β-Treated Lung Cancer Cell Lines
Yan Li, Omid Rouhi, Hankui Chen, Rolando Ramirez, Jeffrey A. Borgia and Youping Deng
Cancer Informatics 2014:Suppl. 5 129-140
Review | Published on 01 Apr 2015

Prioritization of Cancer-Related Genomic Variants by SNP Association Network
Changning Liu and Zhenyu Xuan
Cancer Informatics 2015:Suppl. 2 57-70
Review | Published on 01 Apr 2015

Expression of Polarity Genes in Human Cancer
Wan-Hsin Lin, Yan W. Asmann and Panos Z. Anastasiadis
Cancer Informatics 2015:Suppl. 3 15-28
Original Research | Published on 30 Mar 2015

Design and Implementation of a Comprehensive Web-based Survey for Ovarian Cancer Survivorship with an Analysis of Prediagnosis Symptoms via Text Mining
Jiayang Sun, Kath M. Bogie, Joe Teagno, Yu-Hsiang (Sam) Sun, Rebecca R. Carter, Licong Cui and Guo-Qiang Zhang
Cancer Informatics 2014:Suppl. 3 113-123
Review | Published on 23 Mar 2015

HCsnip: An R Package for Semi-supervised Snipping of the Hierarchical Clustering Tree
Askar Obulkasim and Mark A. van de Wiel
Cancer Informatics 2015:14 1-19
Software or database review | Published on 22 Mar 2015

Case-Based Retrieval Framework for Gene Expression Data
Ali Anaissi, Madhu Goyal, Daniel R. Catchpoole, Ali Braytee and Paul J. Kennedy
Cancer Informatics 2015:14 21-31
Methodology | Published on 19 Mar 2015

GeneMed: An Informatics Hub for the Coordination of Next-Generation Sequencing Studies that Support Precision Oncology Clinical Trials
Yingdong Zhao, Eric C. Polley, Ming-Chung Li, Chih-Jian Lih, Alida Palmisano, David J. Sims, Lawrence V. Rubinstein, Barbara A. Conley, Alice P. Chen, P. Mickey Williams, Shivaani Kummar, James H. Doroshow and Richard M. Simon
Cancer Informatics 2015:Suppl. 2 45-55
Review | Published on 19 Mar 2015

Introductory Editorial: Network and Pathway Analysis of Cancer Susceptibility (A)
Nancy Guo, Russell S. Schwartz, Jiang Qian, Peilin Jia, Youping Deng
Cancer Informatics 2014:Suppl. 5 125-127
Editorial | Published on 12 Mar 2015

Identification of Medium-Sized Copy Number Alterations in Whole-Genome Sequencing
Hatice Gulcin Ozer, Aisulu Usubalieva, Adrienne Dorrance, Ayse Selen Yilmaz, Michael Caligiuri, Guido Marcucci and Kun Huang
Cancer Informatics 2014:Suppl. 3 105-111
Review | Published on 05 Mar 2015

Introductory Editorial: Sequencing Platform Modeling and Analysis
Li-Xuan Qin and Yen-Tsung Huang
Cancer Informatics 2015:Suppl. 1 55-56
Editorial | Published on 02 Mar 2015

Modeling Discrete Survival Time Using Genomic Feature Data
Kyle Ferber and Kellie J. Archer
Cancer Informatics 2015:Suppl. 2 37-43
Review | Published on 02 Mar 2015

Comprehensive Evaluation of Composite Gene Features in Cancer Outcome Prediction
Dezhi Hou and Mehmet Koyutürk
Cancer Informatics 2014:Suppl. 3 93-104
Methodology | Published on 24 Feb 2015

What Tumor Dynamics Modeling Can Teach us About Exploiting the Stem-Cell View for Better Cancer Treatment
Roger S. Day
Cancer Informatics 2015:Suppl. 2 25-36
Review | Published on 24 Feb 2015

Network Analysis of Circular Permutations in Multidomain Proteins Reveals Functional Linkages for Uncharacterized Proteins
Donald Adjeroh, Yue Jiang, Bing-Hua Jiang and Jie Lin
Cancer Informatics 2014:Suppl. 5 109-124
Methodology | Published on 19 Feb 2015

Introductory Editorial: Array Platform Modeling and Analysis (A)
Li-Xuan Qin, Shuangge Ma, Yen-Tsung Huang, Hui Zhang, Hongyuan Cao
Cancer Informatics 2014:Suppl. 4 91-93
Editorial | Published on 17 Feb 2015

Mapping Splicing Quantitative Trait Loci in RNA-Seq
Cheng Jia, Yu Hu, Yichuan Liu and Mingyao Li
Cancer Informatics 2015:Suppl. 1 45-53
Original Research | Published on 16 Feb 2015

Toolbox for Mobile-Element Insertion Detection on Cancer Genomes
Wan-Ping Lee, Jiantao Wu, and Gabor T. Marth
Cancer Informatics 2015:Suppl. 1 37-44
Methodology | Published on 12 Feb 2015

Extending Information Retrieval Methods to Personalized Genomic-Based Studies of Disease
Shuyun Ye, John A. Dawson and Christina Kendziorski
Cancer Informatics 2014:Suppl. 7 85-95
Review | Published on 10 Feb 2015

Evaluating Methods for Modeling Epistasis Networks with Application to Head and Neck Cancer
Rajesh Talluri and Sanjay Shete
Cancer Informatics 2015:Suppl. 2 17-23
Review | Published on 10 Feb 2015

Pathway-based Biomarkers for Breast Cancer in Proteomics
Fan Zhang, Youping Deng, Mu Wang, Li Cui and Renee Drabier
Cancer Informatics 2014:Suppl. 5 101-108
Review | Published on 09 Feb 2015

An Improved Version of Logistic Bayesian LASSO for Detecting Rare Haplotype-Environment Interactions with Application to Lung Cancer
Yuan Zhang and Swati Biswas
Cancer Informatics 2015:Suppl. 2 11-16
Review | Published on 09 Feb 2015

Regulation of Epithelial-Mesenchymal Transition in Breast Cancer Cells by Cell Contact and Adhesion
Magdalena A. Cichon, Celeste M. Nelson, and Derek C. Radisky
Cancer Informatics 2015:Suppl. 3 1-13
Review | Published on 09 Feb 2015 | Video abstract

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