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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.

Databases & Indexes:



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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



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





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What Your Colleagues Say About Cancer Informatics
This is the first time for us to submit a manuscript to Cancer Informatics.  We thank the peer reviewers for their insightful comments, which have improved our manuscript markedly. We were pleased to find that the staff were extremely helpful and kept us informed of the progress of the submission step-by-step. Our experience with Cancer Informatics has been tremendous. Thank you very much!
Dr Yirong Wu (University of Wisconsin, Madison, WI, USA)
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