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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Identifying Driver Genes in Cancer by Triangulating Gene Expression, Gene Location, and Survival Data
Sigrid Rouam, Lance D. Miller and R. Krishna Murthy Karuturi
Cancer Informatics 2014:Suppl. 6 35-48
Review | Published on 03 Feb 2015

Empirical Transition Probability Indexing Sparse-Coding Belief Propagation (ETPI-SCoBeP) Genome Sequence Alignment
Aminmohammad Roozgard, Nafise Barzigar, Shuang Wang, Xiaoqian Jiang and Samuel Cheng
Cancer Informatics 2014:Suppl. 1 159-165
Review | Published on 01 Feb 2015

sfDM: Open-Source Software for Temporal Analysis and Visualization of Brain Tumor Diffusion MR Using Serial Functional Diffusion Mapping
Rafael Ceschin, Ashok Panigrahy, Vanathi Gopalakrishnan
Cancer Informatics 2015:Suppl. 2 1-9
Review | Published on 01 Feb 2015

Hidden Markov Model-Based CNV Detection Algorithms for Illumina Genotyping Microarrays
Eric L. Seiser and Federico Innocenti
Cancer Informatics 2014:Suppl. 7 77-83
Review | Published on 27 Jan 2015

Prognostic Gene Signature Identification Using Causal Structure Learning: Applications in Kidney Cancer
Min Jin Ha, Veerabhadran Baladandayuthapani and Kim-Anh Do
Cancer Informatics 2015:Suppl. 1 23-35
Review | Published on 27 Jan 2015

Mitochondrial Variations in Non-Small Cell Lung Cancer (NSCLC) Survival
Zhaoxi Wang, Sojung Choi, Jinseon Lee, Yen-Tsung Huang, Feng Chen, Yang Zhao, Xihong Lin, Donna Neuberg, Jhingook Kim and David C. Christiani
Cancer Informatics 2015:Suppl. 1 1-9
Original Research | Published on 27 Jan 2015

Nonparametric Tests for Differential Histone Enrichment with ChIP-Seq Data
Qian Wu, Kyoung-Jae Won and Hongzhe Li
Cancer Informatics 2015:Suppl. 1 11-22
Review | Published on 27 Jan 2015

Inferring Active and Prognostic Ligand-Receptor Pairs with Interactions in Survival Regression Models
Christina Ruggeri and Kevin H. Eng
Cancer Informatics 2014:Suppl. 7 67-75
Review | Published on 26 Jan 2015

Practical Issues in Screening and Variable Selection in Genome-Wide Association Analysis
Sungyeon Hong, Yongkang Kim and Taesung Park
Cancer Informatics 2014:Suppl. 7 55-65
Review | Published on 14 Jan 2015

Network-Constrained Group Lasso for High-Dimensional Multinomial Classification with Application to Cancer Subtype Prediction
Xinyu Tian, Xuefeng Wang, and Jun Chen
Cancer Informatics 2014:Suppl. 6 25-33
Review | Published on 12 Jan 2015

Detection of Pancreatic Cancer Biomarkers Using Mass Spectrometry
Kiyoun Kim, Soohyun Ahn, Johan Lim, Byong Chul Yoo, Jin-Hyeok Hwang and Woncheol Jang
Cancer Informatics 2014:Suppl. 7 45-53
Review | Published on 06 Jan 2015

Web Tool for Estimating the Cancer Hazard Rates in Aging
Tengiz Mdzinarishvili, Alexander Sherman, Oleg Shats, and Simon Sherman
Cancer Informatics 2014:13 197-205
Methodology | Published on 17 Dec 2014

Statistical Issues in the Design and Analysis of nCounter Projects
Sin-Ho Jung and Insuk Sohn
Cancer Informatics 2014:Suppl. 7 35-43
Review | Published on 14 Dec 2014

ordinalgmifs: An R Package for Ordinal Regression in High-dimensional Data Settings
Kellie J. Archer, Jiayi Hou, Qing Zhou, Kyle Ferber, John G. Layne and Amanda E. Gentry
Cancer Informatics 2014:13 187-195
Methodology | Published on 10 Dec 2014

Bayesian Hierarchical Models for Protein Networks in Single-Cell Mass Cytometry
Riten Mitra, Peter Müller, Peng Qiu and Yuan Ji
Cancer Informatics 2014:Suppl. 4 79-89
Review | Published on 10 Dec 2014

Overcome Support Vector Machine Diagnosis Overfitting
Henry Han and Xiaoqian Jiang
Cancer Informatics 2014:Suppl. 1 145-158
Review | Published on 09 Dec 2014

Normal Cell-Type Epigenetics and Breast Cancer Classification: A Case Study of Cell Mixture–Adjusted Analysis of DNA Methylation Data from Tumors
Eugene Andrés Houseman and Tan A. Ince
Cancer Informatics 2014:Suppl. 4 53-64
Review | Published on 09 Dec 2014

Growth Rate Analysis and Efficient Experimental Design for Tumor Xenograft Studies
Gregory Hather, Ray Liu, Syamala Bandi, Jerome Mettetal, Mark Manfredi, Wen-Chyi Shyu, Jill Donelan and Arijit Chakravarty
Cancer Informatics 2014:Suppl. 4 65-72
Review | Published on 09 Dec 2014

Stratified Pathway Analysis to Identify Gene Sets Associated with Oral Contraceptive Use and Breast Cancer
Herbert Pang and Hongyu Zhao
Cancer Informatics 2014:Suppl. 4 73-78
Technical Advance | Published on 09 Dec 2014

CARAT-GxG: CUDA-Accelerated Regression Analysis Toolkit for Large-Scale Gene–Gene Interaction with GPU Computing System
Sungyoung Lee, Min-Seok Kwon and Taesung Park
Cancer Informatics 2014:Suppl. 7 27-33
Review | Published on 09 Dec 2014

Computational Construction of Antibody–Drug Conjugates Using Surface Lysines as the Antibody Conjugation Site and a Non-cleavable Linker
Arianna Filntisi, Dimitrios Vlachakis, George K. Matsopoulos and Sophia Kossida
Cancer Informatics 2014:13 179-186
Original Research | Published on 08 Dec 2014

Semantically Linking In Silico Cancer Models
David Johnson, Anthony J. Connor, Steve McKeever, Zhihui Wang, Thomas S. Deisboeck, Tom Quaiser and Eliezer Shochat
Cancer Informatics 2014:Suppl. 1 133-143
Methodology | Published on 08 Dec 2014

Bayesian Joint Selection of Genes and Pathways: Applications in Multiple Myeloma Genomics
Lin Zhang, Jeffrey S. Morris, Jiexin Zhang, Robert Z. Orlowski and Veerabhadran Baladandayuthapani
Cancer Informatics 2014:Suppl. 2 113-123
Methodology | Published on 07 Dec 2014

Trial Prospector: Matching Patients with Cancer Research Studies Using an Automated and Scalable Approach
Satya S. Sahoo, Shiqiang Tao, Andrew Parchman, Zhihui Luo, Licong Cui, Patrick Mergler, Robert Lanese, Jill S. Barnholtz-Sloan, Neal J. Meropol and Guo-Qiang Zhang
Cancer Informatics 2014:13 157-166
Methodology | Published on 04 Dec 2014

A Pan-Cancer Analysis of Alternative Splicing Events Reveals Novel Tumor-Associated Splice Variants of Matriptase
Daryanaz Dargahi, Richard D. Swayze, Leanna Yee, Peter J. Bergqvist, Bradley J. Hedberg, Alireza Heravi-Moussavi, Edie M. Dullaghan, Ryan Dercho, Jianghong An, John S. Babcook, and Steven J.M. Jones
Cancer Informatics 2014:13 167-177
Original Research | Published on 04 Dec 2014

Streamlined Genome Sequence Compression using Distributed Source Coding
Shuang Wang, Xiaoqian Jiang, Feng Chen, Lijuan Cui and Samuel Cheng
Cancer Informatics 2014:Suppl. 1 123-131
Review | Published on 02 Dec 2014

Assessment of Subnetwork Detection Methods for Breast Cancer
Biaobin Jiang and Michael Gribskov
Cancer Informatics 2014:Suppl. 6 15-23
Original Research | Published on 02 Dec 2014

FocalCall: An R Package for the Annotation of Focal Copy Number Aberrations
Oscar Krijgsman, Christian Benner, Gerrit A. Meijer, Mark A. van de Wiel and Bauke Ylstra
Cancer Informatics 2014:13 153-156
Technical Advance | Published on 01 Dec 2014

Supervised Classification by Filter Methods and Recursive Feature Elimination Predicts Risk of Radiotherapy-Related Fatigue in Patients with Prostate Cancer
Leorey N. Saligan, Juan Luis Fernández-Martínez, Enrique J. deAndrés-Galiana and Stephen Sonis
Cancer Informatics 2014:13 141-152
Methodology | Published on 01 Dec 2014

Health Information Technology in Oncology Practice: A Literature Review
G. Fasola, M. Macerelli, A. Follador, K. Rihawi, G. Aprile and V. Della Mea
Cancer Informatics 2014:13 131-139
Review | Published on 01 Dec 2014

Revealing Biological Pathways Implicated in Lung Cancer from TCGA Gene Expression Data Using Gene Set Enrichment Analysis
Binghuang Cai and Xia Jiang
Cancer Informatics 2014:Suppl. 1 113-121
Original Research | Published on 01 Dec 2014

Correction to “Master Regulators, Regulatory Networks, and Pathways of Glioblastoma Subtypes”
Serdar Bozdag, Aiguo Li, Mehmet Baysan, and Howard A. Fine
Cancer Informatics 2014:Suppl. 3 91-91
Editorial | Published on 30 Nov 2014

Correction to "Network Analysis of Cancer-focused Association Network Reveals Distinct Network Association Patterns"
Yuji Zhang and Cui Tao
Cancer Informatics 2014:Suppl. 3 89-89
Editorial | Published on 20 Nov 2014

A Bayesian Framework to Improve MicroRNA Target Prediction by Incorporating External Information
Zixing Wang, Wenlong Xu, Haifeng Zhu and Yin Liu
Cancer Informatics 2014:Suppl. 7 19-25
Review | Published on 18 Nov 2014

Type I Error Control for Tree Classification
Sin-Ho Jung, Yong Chen and Hongshik Ahn
Cancer Informatics 2014:Suppl. 7 11-18
Review | Published on 16 Nov 2014

Conducting Retrospective Ontological Clinical Trials in ICD-9-CM in the Age of ICD-10-CM
Neeta K. Venepalli, Ardaman Shergill, Parvaneh Dorestani and Andrew D. Boyd
Cancer Informatics 2014:Suppl. 3 81-88
Review | Published on 09 Nov 2014

In Silico Prediction of Synthetic Lethality by Meta-Analysis of Genetic Interactions, Functions, and Pathways in Yeast and Human Cancer
Min Wu, Xuejuan Li, Fan Zhang, Xiaoli Li, Chee-Keong Kwoh and Jie Zheng
Cancer Informatics 2014:Suppl. 3 71-80
Review | Published on 05 Nov 2014

A Novel Subset of Human Tumors That Simultaneously Overexpress Multiple E2F-responsive Genes Found in Breast, Ovarian, and Prostate Cancers
Stanley E. Shackney, Salim Akhter Chowdhury and Russell Schwartz
Cancer Informatics 2014:Suppl. 5 89-100
Original Research | Published on 03 Nov 2014

Correction to: 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 2014:13 125-129
Corrigendum | Published on 02 Nov 2014

Predicting Cancer Prognosis Using Functional Genomics Data Sets
Jishnu Das, Kaitlyn M. Gayvert and Haiyuan Yu
Cancer Informatics 2014:Suppl. 5 85-88
Review | Published on 02 Nov 2014

Propensity Score Method for Partially Matched Omics Studies
Pei-Fen Kuan
Cancer Informatics 2014:Suppl. 7 1-10
Review | Published on 29 Oct 2014

A Pan-Cancer Modular Regulatory Network Analysis to Identify Common and Cancer-Specific Network Components
Sara A. Knaack, Alireza Fotuhi Siahpirani, and Sushmita Roy
Cancer Informatics 2014:Suppl. 5 69-84
Original Research | Published on 28 Oct 2014

Learning Dysregulated Pathways in Cancers from Differential Variability Analysis
Bahman Afsari, Donald Geman and Elana J. Fertig
Cancer Informatics 2014:Suppl. 5 61-67
Review | Published on 23 Oct 2014

Classification of Images Acquired with Colposcopy Using Artificial Neural Networks
Priscyla W. Simões, Narjara B. Izumi, Ramon S. Casagrande, Ramon Venson, Carlos D. Veronezi, Gustavo P. Moretti, Edroaldo L. da Rocha, Cristian Cechinel, Luciane B. Ceretta, Eros Comunello, Paulo J. Martins, Rogério A. Casagrande, Maria L. Snoeyer and Sandra A. Manenti
Cancer Informatics 2014:13 119-124
Original Research | Published on 21 Oct 2014

eMBI: Boosting Gene Expression-based Clustering for Cancer Subtypes
Zheng Chang, Zhenjia Wang, Cody Ashby, Chuan Zhou, Guojun Li, Shuzhong Zhang and Xiuzhen Huang
Cancer Informatics 2014:Suppl. 2 105-112
Review | Published on 21 Oct 2014

Co-expression Network Analysis of Human lncRNAs and Cancer Genes
Steven B. Cogill and Liangjiang Wang
Cancer Informatics 2014:Suppl. 5 49-59
Review | Published on 19 Oct 2014

The Axis of Progression of Disease
Alan M. Tartakoff and Di Wu
Cancer Informatics 2014:Suppl. 6 7-13
Review | Published on 19 Oct 2014

A Comprehensive Comparison of Normalization Methods for Loading Control and Variance Stabilization of Reverse-Phase Protein Array Data
Wenbin Liu, Zhenlin Ju, Yiling Lu, Gordon B. Mills and Rehan Akbani
Cancer Informatics 2014:13 109-117
Original Research | Published on 16 Oct 2014

Network-Based Identification of Biomarkers Coexpressed with Multiple Pathways
Nancy Lan Guo and Ying-Wooi Wan
Cancer Informatics 2014:Suppl. 5 37-47
Review | Published on 16 Oct 2014

StickWRLD as an Interactive Visual Pre-Filter for Canceromics-Centric Expression Quantitative Trait Locus Data
Robert Wolfgang Rumpf, Samuel L. Wolock and William C. Ray
Cancer Informatics 2014:Suppl. 3 63-69
Review | Published on 16 Oct 2014

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