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JOURNAL

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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Article Search

Gene-Set Reduction for Analysis of Major and Minor Gleason Scores Based on Differential Gene-Set Expressions and Biological Pathways in Prostate Cancer
Irina Dinu, Surya Poudel, Saumyadipta Pyne
Cancer Informatics 2017:16 1176935117730016
Original Research | Published on 11 Sep 2017



xSyn: A Software Tool for Identifying Sophisticated 3-Way Interactions From Cancer Expression Data
Baishali Bandyopadhyay, Veda Chanda, Yupeng Wang
Cancer Informatics 2017:16 1176935117728516
Methodology | Published on 28 Aug 2017



Adaptive Multiview Nonnegative Matrix Factorization Algorithm for Integration of Multimodal Biomedical Data
Bisakha Ray, Wenke Liu, David Fenyö
Cancer Informatics 2017:16 1176935117725727
Methodology | Published on 18 Aug 2017



Immuno-Oncology Integrative Networks: Elucidating the Influences of Osteosarcoma Phenotypes
Ankush Sharma, Enrico Capobianco
Cancer Informatics 2017:16 1176935117721691
Original Research | Published on 26 Jul 2017
This article is part of the special collection Precision Cancer Medicine through Biomedical Informatics



Prediction With Dimension Reduction of Multiple Molecular Data Sources for Patient Survival
Adam Kaplan, Eric F Lock
Cancer Informatics 2017:16 1176935117718517
Methodology | Published on 11 Jul 2017



The Impact of Collisions on the Ability to Detect Rare Mutant Alleles Using Barcode-Type Next-Generation Sequencing Techniques
Jenna VanLiere Canzoniero, Karen Cravero, Ben Ho Park
Cancer Informatics 2017:16 1176935117719236
Original Research | Published on 10 Jul 2017



An Assessment of Database-Validated microRNA Target Genes in Normal Colonic Mucosa: Implications for Pathway Analysis
Martha L Slattery, Jennifer S Herrick, John R Stevens, Roger K Wolff, Lila E Mullany
Cancer Informatics 2017:16 1176935117716405
Original Research | Published on 23 Jun 2017



A Software Application for Mining and Presenting Relevant Cancer Clinical Trials per Cancer Mutation
Lisa M Gandy, Jordan Gumm, Amanda L Blackford, Elana J Fertig, Luis A Diaz
Cancer Informatics 2017:16 1176935117711940
Original Research | Published on 22 Jun 2017



The Model-Based Study of the Effectiveness of Reporting Lists of Small Feature Sets Using RNA-Seq Data
Eunji Kim, Ivan Ivanov, Jianping Hua, Johanna W Lampe, Meredith AJ Hullar, Robert S Chapkin, Edward R Dougherty
Cancer Informatics 2017:16 1176935117710530
Methodology | Published on 12 Jun 2017



Tumor RAS Gene Expression Levels Are Influenced by the Mutational Status of RAS Genes and Both Upstream and Downstream RAS Pathway Genes
Robert M Stephens, Ming Yi, Bailey Kessing, Dwight V Nissley, Frank McCormick
Cancer Informatics 2017:16 1176935117711944
Original Research | Published on 08 Jun 2017



Lung Cancer Pathological Image Analysis Using a Hidden Potts Model
Qianyun Li, Faliu Yi, Tao Wang, Guanghua Xiao, Faming Liang
Cancer Informatics 2017:16 1176935117711910
Original Research | Published on 05 Jun 2017



Immune Checkpoint Inhibition and the Prevalence of Autoimmune Disorders Among Patients With Lung and Renal Cancer
Sherif M El-Refai, Joshua D Brown, Esther P Black, Jeffery C Talbert
Cancer Informatics 2017:16 1176935117712520
Original Research | Published on 01 Jun 2017



Sequence Analysis and Phylogenetic Studies of Hypoxia-Inducible Factor-1α
Jagadeesha Poyya, Chandrashekhar G Joshi, D Jagadeesha Kumar, HG Nagendra
Cancer Informatics 2017:16 1176935117712242
Original Research | Published on 31 May 2017



Quantitative Study of Thermal Disturbances Due to Nonuniformly Perfused Tumors in Peripheral Regions of Women’s Breast
Akshara Makrariya, Neeru Adlakha
Cancer Informatics 2017:16 1176935117700894
Original Research | Published on 15 May 2017



Time-Based Switching Control of Genetic Regulatory Networks: Toward Sequential Drug Intake for Cancer Therapy
Wasiu Opeyemi Oduola, Xiangfang Li, Chang Duan, Lijun Qian, Fen Wu, Edward R Dougherty
Cancer Informatics 2017:16 1176935117706888
Review | Published on 10 May 2017
This article is part of the special collection Precision Cancer Medicine through Biomedical Informatics



Applying Multivariate Adaptive Splines to Identify Genes With Expressions Varying After Diagnosis in Microarray Experiments
Fenghai Duan, Ye Xu
Cancer Informatics 2017:16 1176935117705381
Review | Published on 04 May 2017



miR-10a and miR-204 as a Potential Prognostic Indicator in Low-Grade Gliomas
Ju Cheol Son, Hyoung Oh Jeong, Deaui Park, Sang Gyoon No, Eun Kyeong Lee, Jaewon Lee, Hae Young Chung
Cancer Informatics 2017:16 1176935117702878
Original Research | Published on 12 Apr 2017



A mixture copula Bayesian network model for multimodal genomic data
Qingyang Zhang, Xuan Shi
Cancer Informatics 2017:16 1176935117702389
Methodology | Published on 12 Apr 2017



Bioinformatics Education in Pathology Training: Current Scope and Future Direction
Michael R Clay, Kevin E Fisher
Cancer Informatics 2017:16 1176935117703389
Review | Published on 10 Apr 2017
This article is part of the special collection Sequencing for the Masses: Another Desktop Revolution



Therapeutic Interventions of Cancers Using Intrinsically Disordered Proteins as Drug Targets: c-Myc as Model System
Deepak Kumar, Nitin Sharma, Rajanish Giri
Cancer Informatics 2017:16 1176935117699408
Review | Published on 16 Mar 2017



Roadmap to a Comprehensive Clinical Data Warehouse for Precision Medicine Applications in Oncology
David J Foran, Wenjin Chen, Huiqi Chu, Evita Sadimin, Doreen Loh, Gregory Riedlinger, Lauri A Goodell, Shridar Ganesan, Kim Hirshfield, Lorna Rodriguez, Robert S DiPaola
Cancer Informatics 2017:16 1176935117694349
Original Research | Published on 02 Mar 2017



Integrative Analysis of Gene Networks and Their Application to Lung Adenocarcinoma Studies
Sangin Lee, Faming Liang, Ling Cai, Guanghua Xiao
Cancer Informatics 2017:16 1176935117690778
Original Research | Published on 23 Feb 2017



Significant Prognostic Features and Patterns of Somatic Mutations in Human Cancers
Wensheng Zhang, Andrea Edwards, Erik K Flemington, Kun Zhang
Cancer Informatics 2017:16 1176935117691267
Original Research | Published on 20 Feb 2017
This article is part of the special collection Precision Cancer Medicine through Biomedical Informatics



Improving Gastric Cancer Outcome Prediction Using Single Time-Point Artificial Neural Network Models
Hamid Nilsaz-Dezfouli, Mohd Rizam Abu-Bakar, Jayanthi Arasan, Mohd Bakri Adam, Mohamad Amin Pourhoseingholi
Cancer Informatics 2017:16 1176935116686062
Original Research | Published on 16 Feb 2017



A Numerical Handling of the Boundary Conditions Imposed by the Skull on an Inhomogeneous Diffusion-Reaction Model of Glioblastoma Invasion Into the Brain: Clinical Validation Aspects
Georgios S Stamatakos, Stavroula G Giatili
Cancer Informatics 2017:16 1176935116684824
Original Research | Published on 03 Feb 2017



Epithelial Ovarian Cancer Diagnosis of Second-Harmonic Generation Images: A Semiautomatic Collagen Fibers Quantification Protocol
Angel A Zeitoune, Johana SJ Luna, Kynthia Sanchez Salas, Luciana Erbes, Carlos L Cesar, Liliana ALA Andrade, Hernades F Carvahlo, Fátima Bottcher-Luiz, Victor H Casco, Javier Adur
Cancer Informatics 2017:16 1176935117690162
Original Research | Published on 03 Feb 2017



Unified Least Squares Methods for the Evaluation of Diagnostic Tests With the Gold Standard
Liansheng Larry Tang, Ao Yuan, John Collins, Xuan Che, Leighton Chan
Cancer Informatics 2017:16 1176935116686063
Review | Published on 03 Feb 2017
This article is part of the special collection Computer Simulation, Bioinformatics, and Statistical Analysis of Cancer Data and Processes



Bayesian ABC-MCMC Classification of Liquid Chromatography–Mass Spectrometry Data
Upamanyu Banerjee and Ulisses M. Braga-Neto
Cancer Informatics 2015:Suppl. 5 175-182
Methodology | Published on 09 Jan 2017



Identification of Genetic and Epigenetic Variants Associated with Breast Cancer Prognosis by Integrative Bioinformatics Analysis
Arunima Shilpi, Yingtao Bi, Segun Jung, Samir K. Patra and Ramana V. Davuluri
Cancer Informatics 2017:16 1-13
Original Research | Published on 09 Jan 2017



A Novel Optical Bioimaging Method for Direct Assessment of Ovarian Cancer Chemotherapy Response at Laparoscopy
Alexandros Laios, Davide Volpi, Rajeev Kumar, Zoe Traill, Borivoj Vojnovic and Ahmed A. Ahmed
Cancer Informatics 2016:15 243-245
Short Report | Published on 08 Jan 2017



ROC Estimation from Clustered Data with an Application to Liver Cancer Data
Joungyoun Kim, Sung-Cheol Yun, Johan Lim, Moo-Song Lee, Won Son and DoHwan Park
Cancer Informatics 2016:Suppl. 4 19-26
Original Research | Published on 22 Dec 2016
This article is part of the special collection Computer Simulation, Bioinformatics, and Statistical Analysis of Cancer Data and Processes



Quantitative Proteomic Approach for MicroRNA Target Prediction Based on 18O/16O Labeling
Xuepo Ma, Ying Zhu, Yufei Huang, Tony Tegeler, Shou-Jiang Gao and Jianqiu Zhang
Cancer Informatics 2015:Suppl. 5 163-173
Original Research | Published on 08 Dec 2016



Comparison of Three Information Sources for Smoking Information in Electronic Health Records
Liwei Wang, Xiaoyang Ruan, Ping Yang and Hongfang Liu
Cancer Informatics 2016:15 237-242
Original Research | Published on 08 Dec 2016



A Modular Repository-based Infrastructure for Simulation Model Storage and Execution Support in the Context of In Silico Oncology and In Silico Medicine
Nikolaos A. Christodoulou, Nikolaos E. Tousert, Eleni Ch. Georgiadi, Katerina D. Argyri, Fay D. Misichroni and Georgios S. Stamatakos
Cancer Informatics 2016:15 219-235
Original Research | Published on 27 Oct 2016



Discovering Outliers of Potential Drug Toxicities Using a Large-scale Data-driven Approach
Jake Luo and Ron A. Cisler
Cancer Informatics 2016:15 211-217
Original Research | Published on 26 Oct 2016



Cluster Analysis of p53 Binding Site Sequences Reveals Subsets with Different Functions
Ji-Hyun Lim, Natasha S. Latysheva, Richard D. Iggo, and Daniel Barker
Cancer Informatics 2016:15 199-209
Original Research | Published on 25 Oct 2016



A Novel Graph-based Algorithm to Infer Recurrent Copy Number Variations in Cancer
Chen Chi, Rasif Ajwad, Qin Kuang and Pingzhao Hu
Cancer Informatics 2016:Suppl. 2 43-50
Methodology | Published on 09 Oct 2016



Discovering MicroRNA-Regulatory Modules in Multi-Dimensional Cancer Genomic Data: A Survey of Computational Methods
Christopher J. Walsh, Pingzhao Hu, Jane Batt, and Claudia C. dos Santos
Cancer Informatics 2016:Suppl. 2 25-42
Review | Published on 03 Oct 2016



Novel Biomarker Candidates for Colorectal Cancer Metastasis: A Meta-analysis of In Vitro Studies
Nguyen Phuoc Long, Wun Jun Lee, Nguyen Truong Huy, Seul Ji Lee, Jeong Hill Park and Sung Won Kwon
Cancer Informatics 2016:Suppl. 4 11-17
Original Research | Published on 22 Sep 2016
This article is part of the special collection Computer Simulation, Bioinformatics, and Statistical Analysis of Cancer Data and Processes



Identifying Significant Features in Cancer Methylation Data Using Gene Pathway Segmentation
Zena M. Hira and Duncan F. Gillies
Cancer Informatics 2016:15 189-198
Methodology | Published on 20 Sep 2016



Overlapping Group Logistic Regression with Applications to Genetic Pathway Selection
Yaohui Zeng and Patrick Breheny
Cancer Informatics 2016:15 179-187
Methodology | Published on 15 Sep 2016



DNA Methylation Heterogeneity Patterns in Breast Cancer Cell Lines
Sunny Tian, Karina Bertelsmann, Linda Yu and Shuying Sun
Cancer Informatics 2016:Suppl. 4 1-9
Original Research | Published on 07 Sep 2016
This article is part of the special collection Computer Simulation, Bioinformatics, and Statistical Analysis of Cancer Data and Processes



Biological Networks for Cancer Candidate Biomarkers Discovery
Wenying Yan, Wenjin Xue, Jiajia Chen and Guang Hu
Cancer Informatics 2016:Suppl. 3 1-7
Review | Published on 04 Sep 2016
This article is part of the special collection Precision Cancer Medicine through Biomedical Informatics



Characterization of Gene Expression Patterns among Artificially Developed Cancer Stem Cells Using Spherical Self-Organizing Map
Akimasa Seno, Tomonari Kasai, Masashi Ikeda, Arun Vaidyanath, Junko Masuda, Akifumi Mizutani, Hiroshi Murakami, Tetsuya Ishikawa and Masaharu Seno
Cancer Informatics 2016:15 163-178
Original Research | Published on 16 Aug 2016



ExSurv: A Web Resource for Prognostic Analyses of Exons Across Human Cancers Using Clinical Transcriptomes
Seyedsasan Hashemikhabir, Gungor Budak and Sarath Chandra Janga
Cancer Informatics 2016:Suppl. 2 17-24
Technical Advance | Published on 07 Aug 2016 | Video abstract



Pathway-Informed Classification System (PICS) for Cancer Analysis Using Gene Expression Data
Michael R Young, and David L Craft
Cancer Informatics 2016:15 151-161
Original Research | Published on 27 Jul 2016



Recursive Partitioning Method on Competing Risk Outcomes
Wei Xu, Jiahua Che, and Qin Kong
Cancer Informatics 2016:Suppl. 2 9-16
Methodology | Published on 26 Jul 2016



Normalized lmQCM: An Algorithm for Detecting Weak Quasi-Cliques in Weighted Graph with Applications in Gene Co-Expression Module Discovery in Cancers
Jie Zhang and Kun Huang
Cancer Informatics 2014:Suppl. 3 137-146
Original Research | Published on 24 Jul 2016



TMAinspiration: Decode Interdependencies in Multifactorial Tissue Microarray Data
Florian Boecker, Horst Buerger, Nikhil V. Mallela and Eberhard Korsching
Cancer Informatics 2016:15 143-149
Methodology | Published on 29 Jun 2016



An Integrated Approach for RNA-seq Data Normalization
Shengping Yang, Donald E. Mercante, Kun Zhang and Zhide Fang
Cancer Informatics 2016:15 129-141
Original Research | Published on 27 Jun 2016



The Melanoma MAICare Framework: A Microsimulation Model for the Assessment of Individualized Cancer Care
Elisabeth van der Meijde, Alfons J. M. van den Eertwegh, Sabine C. Linn, Gerrit A. Meijer, Remond J. A. Fijneman, and Veerle M. H. Coupé
Cancer Informatics 2016:15 115-127
Original Research | Published on 15 Jun 2016



multiClust: An R-package for Identifying Biologically Relevant Clusters in Cancer Transcriptome Profiles
Nathan Lawlor, Alec Fabbri, Peiyong Guan, Joshy George and R. Krishna Murthy Karuturi
Cancer Informatics 2016:15 103-114
Software or Database Review | Published on 12 Jun 2016



A Novel Approach to Predict Core Residues on Cancer-Related DNA-Binding Domains
Ka-Chun Wong
Cancer Informatics 2016:Suppl. 2 1-7
Original Research | Published on 02 Jun 2016



Rational Design of Peptide Vaccines Against Multiple Types of Human Papillomavirus
Sumanta Dey, Antara De and Ashesh Nandy
Cancer Informatics 2016:Suppl. 1 1-16
Original Research | Published on 01 Jun 2016 | Video abstract



A Bayesian Nonparametric Approach for Functional Data Classification with Application to Hepatic Tissue Characterization
Kassandra M. Fronczyk, Michele Guindani, Brian P. Hobbs, Chaan S. Ng and Marina Vannucci
Cancer Informatics 2015:Suppl. 5 151-162
Original Research | Published on 29 May 2016



Bioinformatic Studies to Predict MicroRNAs with the Potential of Uncoupling RECK Expression from Epithelial–Mesenchymal Transition in Cancer Cells
Zhipeng Wang, Ryusuke Murakami, Kanako Yuki, Yoko Yoshida and Makoto Noda
Cancer Informatics 2016:15 91-102
Original Research | Published on 19 May 2016



Selecting Reliable mRNA Expression Measurements Across Platforms Improves Downstream Analysis
Pan Tong, Lixia Diao, Li Shen, Lerong Li, John Victor Heymach, Luc Girard, John D. Minna, Kevin R. Coombes, Lauren Averett Byers and Jing Wang
Cancer Informatics 2016:15 81-89
Original Research | Published on 10 May 2016



Thyroid Cancer and Tumor Collaborative Registry (TCCR)
Oleg Shats, Whitney Goldner, Jianmin Feng, Alexander Sherman, Russell B. Smith and Simon Sherman
Cancer Informatics 2016:15 73-79
Technical Advance | Published on 03 May 2016



A New Approach for Identification of Cancer-related Pathways using Protein Networks and Genomic Data
André Fonseca, Marco D. Gubitoso, Marcelo S. Reis, Sandro J. de Souza, and Junior Barrera
Cancer Informatics 2015:Suppl. 5 139-149
Original Research | Published on 02 May 2016



RefCNV: Identification of Gene-Based Copy Number Variants Using Whole Exome Sequencing
Lun-Ching Chang, Biswajit Das, Chih-Jian Lih, Han Si, Corinne E. Camalier, Paul M. McGregor III and Eric Polley
Cancer Informatics 2016:15 65-71
Methodology | Published on 27 Apr 2016



Immunomediated Pan-cancer Regulation Networks are Dominant Fingerprints After Treatment of Cell Lines with Demethylation
Mariama El Baroudi, Caterina Cinti and Enrico Capobianco
Cancer Informatics 2016:15 45-64
Original Research | Published on 27 Apr 2016



Data Requirements for Model-Based Cancer Prognosis Prediction
Lori A. Dalton and Mohammadmahdi R. Yousefi
Cancer Informatics 2015:Suppl. 5 123-138
Original Research | Published on 21 Apr 2016



High-Dimensional Statistical Learning: Roots, Justifications, and Potential Machineries
Amin Zollanvari
Cancer Informatics 2015:Suppl. 5 109-121
Review | Published on 12 Apr 2016



Flow Cytometry-Based Classification in Cancer Research: A View on Feature Selection
S. Sakira Hassan, Pekka Ruusuvuori, Leena Latonen and Heikki Huttunen
Cancer Informatics 2015:Suppl. 5 75-85
Original Research | Published on 10 Apr 2016



An NGS Workflow Blueprint for DNA Sequencing Data and Its Application in Individualized Molecular Oncology
Jian Li, Aarif Mohamed Nazeer Batcha, Björn Grüning and Ulrich R. Mansmann
Cancer Informatics 2015:Suppl. 5 87-107
Original Research | Published on 10 Apr 2016 | Video abstract



Unraveling the Deleterious Effects of Cancer-Driven STK11 Mutants Through Conformational Sampling Approach
Merlin Lopus, D. Meshach Paul and R. Rajasekaran
Cancer Informatics 2016:15 35-44
Original Research | Published on 04 Apr 2016



Design of Probabilistic Random Forests with Applications to Anticancer Drug Sensitivity Prediction
Raziur Rahman, Saad Haider, Souparno Ghosh and Ranadip Pal
Cancer Informatics 2015:Suppl. 5 57-73
Original Research | Published on 31 Mar 2016



Integrative Analysis of mRNA, microRNA, and Protein Correlates of Relative Cerebral Blood Volume Values in GBM Reveals the Role for Modulators of Angiogenesis and Tumor Proliferation
Arvind Rao, Ganiraju Manyam, Ganesh Rao and Rajan Jain
Cancer Informatics 2016:15 29-33
Original Research | Published on 29 Mar 2016



Optimized Prediction of Extreme Treatment Outcomes in Ovarian Cancer
Burook Misganaw, Eren Ahsen, Nitin Singh, Keith A. Baggerly, Anna Unruh, Michael A. White and M. Vidyasagar
Cancer Informatics 2015:Suppl. 5 45-55
Original Research | Published on 21 Mar 2016



Assessing Combinational Drug Efficacy in Cancer Cells by Using Image-based Dynamic Response Analysis
Chao Sima, Jianping Hua, Milana Cypert, Tasha Miller, Heather M. Wilson-Robles, Jeffrey M. Trent, Edward R. Dougherty and Michael L. Bittner
Cancer Informatics 2015:Suppl. 5 33-43
Original Research | Published on 09 Mar 2016



Detection of Productively Rearranged TcR-α V–J Sequences in TCGA Exome Files: Implications for Tumor Immunoscoring and Recovery of Antitumor T-cells
Thomas R. Gill, Mohammad D. Samy, Shanitra N. Butler, James A. Mauro, Wade J. Sexton and George Blanck
Cancer Informatics 2016:15 23-28
Rapid Communication | Published on 25 Feb 2016



Toward Signaling-Driven Biomarkers Immune to Normal Tissue Contamination
John C. Stansfield, Matthew Rusay, Roger Shan, Conor Kelton, Daria A. Gaykalova, Elana J. Fertig, Joseph A. Califano, and Michael F. Ochs
Cancer Informatics 2016:15 15-21
Original Research | Published on 10 Feb 2016



Correlation between Gene Variants, Signaling Pathways, and Efficacy of Chemotherapy Drugs against Colon Cancers
Swarnendu Tripathi, Louiza Belkacemi, Margaret S. Cheung and Rathindra N. Bose
Cancer Informatics 2016:15 1-13
Original Research | Published on 20 Jan 2016



Integrating Multiscale Modeling with Drug Effects for Cancer Treatment
Xiangfang L. Li, Wasiu O. Oduola, Lijun Qian and Edward R. Dougherty
Cancer Informatics 2015:Suppl. 5 21-31
Review | Published on 13 Jan 2016



Introductory Editorial: Computer Simulation, Visualization, and Image Processing of Cancer Data and Processes
David Johnson, James Osborne, Zhihui Wang, Kostas Marias
Cancer Informatics 2015:Suppl. 4 105-108
Editorial | Published on 12 Jan 2016



Simulation of the Protein-Shedding Kinetics of a Fully Vascularized Tumor
Hermann B. Frieboes, Louis T. Curtis, Min Wu, Kian Kani and Parag Mallick
Cancer Informatics 2015:14 163-175
Original Research | Published on 20 Dec 2015



Improving Cancer Gene Expression Data Quality through a TCGA Data-Driven Evaluation of Identifier Filtering
Kevin K. McDade, Uma Chandran and Roger S. Day
Cancer Informatics 2015:14 149-161
Original Research | Published on 16 Dec 2015



Differential Expression Analysis for RNA-Seq: An Overview of Statistical Methods and Computational Software
Huei-Chung Huang, Yi Niu, and Li-Xuan Qin
Cancer Informatics 2015:Suppl. 1 57-67
Review | Published on 13 Dec 2015



The Impact of Age and Sex in DLBCL: Systems Biology Analyses Identify Distinct Molecular Changes and Signaling Networks
Afshin Beheshti, Donna Neuberg, J. Tyson McDonald, Charles R. Vanderburg and Andrew M. Evens
Cancer Informatics 2015:14 141-148
Rapid Communication | Published on 10 Dec 2015



Predictive Modeling of Drug Treatment in the Area of Personalized Medicine
Lesley A. Ogilvie, Christoph Wierling, Thomas Kessler, Hans Lehrach, and Bodo M. H. Lange
Cancer Informatics 2015:Suppl. 4 95-103
Commentary | Published on 06 Dec 2015



Characterizing Cancer-Specific Networks by Integrating TCGA Data
Yanxun Xu, Yitan Zhu, Peter Müller, Riten Mitra and Yuan Ji
Cancer Informatics 2014:Suppl. 2 125-131
Methodology | Published on 23 Nov 2015



Multigroup Equivalence Analysis for High-Dimensional Expression Data
Celeste Yang, Alfred A. Bartolucci and Xiangqin Cui
Cancer Informatics 2015:Suppl. 2 253-263
Methodology | Published on 23 Nov 2015



Multivariate Boosting for Integrative Analysis of High-Dimensional Cancer Genomic Data
Lie Xiong, Pei-Fen Kuan, Jianan Tian, Sunduz Keles, and Sijian Wang
Cancer Informatics 2014:Suppl. 7 123-131
Methodology | Published on 15 Nov 2015



Cancer Bioinformatic Methods to Infer Meaningful Data From Small-Size Cohorts
Nabila Bennani-Baiti and Idriss M. Bennani-Baiti
Cancer Informatics 2015:14 131-139
Review | Published on 02 Nov 2015



Effectiveness and Usability of Bioinformatics Tools to Analyze Pathways Associated with miRNA Expression
Lila E. Mullany, Roger K. Wolff and Martha L. Slattery
Cancer Informatics 2015:14 121-130
Original Research | Published on 29 Oct 2015



Publication Bias in Methodological Computational Research
Anne-Laure Boulesteix, Veronika Stierle and Alexander Hapfelmeier
Cancer Informatics 2015:Suppl. 5 11-19
Methodology | Published on 15 Oct 2015



FXYD5 is a Marker for Poor Prognosis and a Potential Driver for Metastasis in Ovarian Carcinomas
Pichai Raman, Timothy Purwin, Richard Pestell and Aydin Tozeren
Cancer Informatics 2015:14 113-119
Short Report | Published on 12 Oct 2015



Multiscale Model of Colorectal Cancer Using the Cellular Potts Framework
James M. Osborne
Cancer Informatics 2015:Suppl. 4 83-93
Original Research | Published on 04 Oct 2015



TIN: An R Package for Transcriptome Instability Analysis
Bjarne Johannessen, Anita Sveen, and Rolf I. Skotheim
Cancer Informatics 2015:14 109-112
Software or database review | Published on 20 Sep 2015



Alview: Portable Software for Viewing Sequence Reads in BAM Formatted Files
Richard P. Finney, Qing-Rong Chen, Cu V. Nguyen, Chih Hao Hsu, Chunhua Yan, Ying Hu, Massih Abawi, Xiaopeng Bian and Daoud M. Meerzaman
Cancer Informatics 2015:14 105-107
Software or database review | Published on 13 Sep 2015



An Application of Sequential Meta-Analysis to Gene Expression Studies
Putri W. Novianti, Ingeborg van der Tweel, Victor L. Jong, Kit C. B. Roes and Marinus J. C. Eijkemans
Cancer Informatics 2015:Suppl. 5 1-10
Methodology | Published on 10 Sep 2015



The Importance of Neighborhood Scheme Selection in Agent-based Tumor Growth Modeling
Georgios Tzedakis, Eleftheria Tzamali, Kostas Marias and Vangelis Sakkalis
Cancer Informatics 2015:Suppl. 4 67-81
Original Research | Published on 07 Sep 2015



Preprocessing Steps for Agilent MicroRNA Arrays: Does the Order Matter?
Li-Xuan Qin, Huei-Chung Huang and Qin Zhou
Cancer Informatics 2014:Suppl. 4 105-109
Original Research | Published on 03 Sep 2015



Introductory Editorial: Computer Simulation, Bioinformatics, and Statistical Analysis of Cancer Data and Processes
Kellie J. Archer, Kevin Dobbin, Swati Biswas, Roger S. Day, David C. Wheeler, Hao Wu
Cancer Informatics 2015:Suppl. 2 247-251
Editorial | Published on 01 Sep 2015



CoGNaC: A Chaste Plugin for the Multiscale Simulation of Gene Regulatory Networks Driving the Spatial Dynamics of Tissues and Cancer
Simone Rubinacci, Alex Graudenzi, Giulio Caravagna, Giancarlo Mauri, James Osborne, Joe Pitt-Francis and Marco Antoniotti
Cancer Informatics 2015:Suppl. 4 53-65
Technical Advance | Published on 01 Sep 2015



Assessing Treatment Response Through Generalized Pharmacokinetic Modeling of DCE-MRI Data
Eleftherios Kontopodis, Georgia Kanli, Georgios C. Manikis, Sofie Van Cauter and Kostas Marias
Cancer Informatics 2015:Suppl. 4 41-51
Original Research | Published on 12 Aug 2015



In Silico Neuro-Oncology: Brownian Motion-Based Mathematical Treatment as a Potential Platform for Modeling the Infiltration of Glioma Cells into Normal Brain Tissue
Markos Antonopoulos and Georgios Stamatakos
Cancer Informatics 2015:Suppl. 4 33-40
Review | Published on 10 Aug 2015



HMPL: A Pipeline for Identifying Hemimethylation Patterns by Comparing Two Samples
Shuying Sun and Peng Li
Cancer Informatics 2015:Suppl. 2 235-245
Original Research | Published on 09 Aug 2015



Secondary Data Analytics of Aquaporin Expression Levels in Glioblastoma Stem-Like Cells
Raphael D. Isokpehi, Katharina C. Wollenberg Valero, Barbara E. Graham, Maricica Pacurari, Jennifer N. Sims, Udensi K. Udensi and Kenneth Ndebele
Cancer Informatics 2015:14 95-103
Original Research | Published on 30 Jul 2015



Medical Image Retrieval: A Multimodal Approach
Yu Cao, Shawn Steffey, Jianbiao He, Degui Xiao, Cui Tao, Ping Chen and Henning Müller
Cancer Informatics 2014:Suppl. 3 125-136
Original Research | Published on 22 Jul 2015



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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