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.

Databases & Indexes:

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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

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

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

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

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

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What Your Colleagues Say About Cancer Informatics
Compared with other journals we considered for publishing, Cancer Informatics provided extremely rapid but quality turnaround from draft submission to a flawlessly typeset final publication.  Moreover, sharing the article is now as easy as sharing a link with no subscriptions required, and additional code and data files are equally accessible, supporting reproducible research.  Because it has published many of our references we feel confident that our target readership must follow the journal.  This is further ...
Dr Seppo Karrila (Prince of Songkla University, Thailand)
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