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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Analysis of Patterns of Gene Expression Variation within and between Ethnic Populations in Pediatric B-ALL
Chindo Hicks, Lucio Miele, Tejaswi Koganti, LaFarra Young-Gaylor, Deidre Rogers, Vani Vijayakumar and Gail Megason
Cancer Informatics 2013:12 155-173
Original Research | Published on 27 Aug 2013

Improved Sparse Multi-Class SVM and Its Application for Gene Selection in Cancer Classification
Lingkang Huang, Hao Helen Zhang, Zhao-Bang Zeng and Pierre R. Bushel
Cancer Informatics 2013:12 143-153
Original Research | Published on 04 Aug 2013

Novel Integrative Genomics Approach for Associating GWAS Information with Intrinsic Subtypes of Breast Cancer
Chindo Hicks, Tejaswi Koganti, Alexandra S. Brown, Jesus Monico, Kandis Backus and Lucio Miele
Cancer Informatics 2013:12 125-142
Original Research | Published on 15 May 2013

Dealing with Diversity in Computational Cancer Modeling
David Johnson, Steve McKeever, Georgios Stamatakos, Dimitra Dionysiou, Norbert Graf, Vangelis Sakkalis, Konstantinos Marias, Zhihui Wang and Thomas S. Deisboeck
Cancer Informatics 2013:12 115-124
Commentary | Published on 07 May 2013

Prognostic Estimator of Survival for Patients with Localized and Extended Pancreatic Ductal Adenocarcinoma
Michael X. Gleason, Tengiz Mdzinarishvili, Chandrakanth Are, Aaron Sasson, Alexander Sherman, Oleg Shats, and Simon Sherman,
Cancer Informatics 2013:12 103-114
Methodology | Published on 18 Mar 2013

An Empirical Evaluation of Normalization Methods for MicroRNA Arrays in a Liposarcoma Study
Li-Xuan Qin, Tom Tuschl and Samuel Singer
Cancer Informatics 2013:12 83-101
Original Research | Published on 18 Mar 2013

Basic Equations and Computing Procedures for Frailty Modeling of Carcinogenesis: Application to Pancreatic Cancer Data
Tengiz Mdzinarishvili and Simon Sherman
Cancer Informatics 2013:12 67-81
Methodology | Published on 18 Feb 2013

In Silico Discovery of Mitosis Regulation Networks Associated with Early Distant Metastases in Estrogen Receptor Positive Breast Cancers
Yuriy Gusev, Rebecca B. Riggins, Krithika Bhuvaneshwar, Robinder Gauba, Laura Sheahan, Robert Clarke and Subha Madhavan
Cancer Informatics 2013:12 31-51
Original Research | Published on 13 Feb 2013

Classification of Tumor Samples from Expression Data Using Decision Trunks
Benjamin Ulfenborg, Karin Klinga-Levan and Björn Olsson
Cancer Informatics 2013:12 53-66
Original Research | Published on 13 Feb 2013

Design of an Expert System for Mitigating Trace Element Toxicity in Cancer Risk Management
P.T. Krishna Kumar, P.T. Vinod, Vir V. Phoha, S.S. Iyengar and Puneeth Iyengar
Cancer Informatics 2013:12 21-29
Original Research | Published on 04 Feb 2013

An Integrative Genomics Approach for Associating GWAS Information with Triple-Negative Breast Cancer
Chindo Hicks, Ranjit Kumar, Antonio Pannuti, Kandis Backus, Alexandra Brown, Jesus Monico and Lucio Miele
Cancer Informatics 2013:12 1-20
Original Research | Published on 29 Jan 2013

Prediction of Breast Cancer Metastasis by Gene Expression Profiles: A Comparison of Metagenes and Single Genes
Mark Burton, Mads Thomassen, Qihua Tan and Torben A. Kruse
Cancer Informatics 2012:11 193-217
Original Research | Published on 10 Dec 2012

Mapping the Future—Merging the Old with the New Across Disciplines
J.T. Efird
Cancer Informatics 2012:11 191-192
Editorial | Published on 26 Nov 2012

Newton, Laplace, and The Epistemology of Systems Biology
Michael L. Bittner and Edward R. Dougherty
Cancer Informatics 2012:11 185-190
Perspective | Published on 30 Oct 2012

Significance Analysis of Microarrays (SAM) Offers Clues to Differences Between the Genomes of Adult Philadelphia Positive ALL and the Lymphoid Blast Transformation of CML
Colin Grace and Elisabeth P. Nacheva
Cancer Informatics 2012:11 173-183
Original Research | Published on 12 Sep 2012

Haploinsufficiency of Tumor Suppressor Genes is Driven by the Cumulative Effect of microRNAs, microRNA Binding Site Polymorphisms and microRNA Polymorphisms: An In silico Approach
Mayakannan Manikandan, Ganesh Raksha and Arasambattu Kannan Munirajan
Cancer Informatics 2012:11 157-171
Perspective | Published on 29 Aug 2012

TNBCtype: A Subtyping Tool for Triple-Negative Breast Cancer
Xi Chen, Jiang Li, William H. Gray, Brian D. Lehmann, Joshua A. Bauer, Yu Shyr, and Jennifer A. Pietenpol
Cancer Informatics 2012:11 147-156
Case report | Published on 24 Jul 2012

Identification of a Gene Expression Signature Common to Distinct Cancer Pathways
Niklaus Fankhauser, Igor Cima, Peter Wild, and Wilhelm Krek
Cancer Informatics 2012:11 139-146
Original Research | Published on 08 May 2012

In Silico Prediction for Regulation of Transcription Factors onTheir Shared Target Genes Indicates Relevant Clinical Implications in a Breast Cancer Population
Li-Yu D Liu, Li-Yun Chang, Wen-Hung Kuo, Hsiao-Lin Hwa, Ming-Kwang Shyu, King-Jen Chang and Fon-Jou Hsieh
Cancer Informatics 2012:11 113-137
Methodology | Published on 19 Apr 2012

Major Functional Transcriptome of an Inferred Center Regulator of an ER(-) Breast Cancer Model System
Li-Yu Daisy Liu, Li-Yun Chang, Wen-Hung Kuo, Hsiao-Lin Hwa, Yi-Shing Lin, Shiu-Feng Huang, Chiung-Nien Chen, King-Jen Chang, Fon-Jou Hsieh
Cancer Informatics 2012:11 87-111
Rapid Communication | Published on 19 Apr 2012

Surface Adjustment of Reverse Phase Protein Arrays using Positive Control Spots
E. Shannon Neeley, Keith A. Baggerly and Steven M. Kornblau
Cancer Informatics 2012:11 77-86
Original Research | Published on 11 Apr 2012

Integrated Analysis Reveals hsa-miR-142 as a Representative of a Lymphocyte-Specific Gene Expression and Methylation Signature
Bill Andreopoulos and Dimitris Anastassiou
Cancer Informatics 2012:11 61-75
Original Research | Published on 12 Mar 2012

A Systems Biology Approach in Therapeutic Response Study for Different Dosing Regimens—a Modeling Study of Drug Effects on Tumor Growth using Hybrid Systems
Xiangfang Li, Lijun Qian, Michale L. Bittner and Edward R. Dougherty
Cancer Informatics 2012:11 41-60
Original Research | Published on 27 Feb 2012

Gene Selection using a High-Dimensional Regression Model with Microarrays in Cancer Prognostic Studies
Shuhei Kaneko, Akihiro Hirakawa and Chikuma Hamada
Cancer Informatics 2012:11 29-39
Original Research | Published on 27 Feb 2012

Evaluating Translocation Gene Fusions by SNP Array Data
Hong Liu, Asher Zilberstein, Pascal Pannier, Frederic Fleche, Christopher Arendt, Christoph Lengauer and Chang S. Hahn
Cancer Informatics 2012:11 15-27
Original Research | Published on 21 Dec 2011

Linear Discriminant Functions in Connection with the micro-RNA Diagnosis of Colon Cancer
Jason B. Nikas and Walter C. Low
Cancer Informatics 2012:11 1-14
Original Research | Published on 20 Dec 2011

Mouse 11β-Hydroxysteroid Dehydrogenase Type 2 for Human Application: Homology Modeling, Structural Analysis and Ligand-Receptor Interaction
Hideaki Yamaguchi, Tatsuo Akitaya, Yumi Kidachi, Katsuyoshi Kamiie, Toshiro Noshita, Hironori Umetsu and Kazuo Ryoyama
Cancer Informatics 2011:10 287-295
Original Research | Published on 01 Dec 2011

Aberrant Signaling Pathways in Squamous Cell Lung Carcinoma
Ivy Shi, Nooshin Hashemi Sadraei, Zhong-Hui Duan, and Ting Shi
Cancer Informatics 2011:10 273-285
Original Research | Published on 21 Nov 2011

New Short Term Prediction Method for Chemical Carcinogenicity by Hepatic Transcript Profiling Following 28-Day Toxicity Tests in Rats
Hiroshi Matsumoto, Yoshikuni Yakabe, Fumiyo Saito, Koichi Saito, Kayo Sumida, Masaru Sekijima, Koji Nakayama, Hideki Miyaura, Masanori Otsuka and Tomoyuki Shirai
Cancer Informatics 2011:10 259-271
Original Research | Published on 27 Oct 2011

Improved Statistical Analysis for Array CGH-Based DNA Copy Number Aberrations
Hongmei Jiang, Zhong-Zheng Zhu, Yue Yu, Simon Lin and Lifang Hou
Cancer Informatics 2011:10 249-258
Methodology | Published on 19 Oct 2011

Mathematical Prognostic Biomarker Models for Treatment Response and Survival in Epithelial Ovarian Cancer
Jason B. Nikas, Kristin L.M. Boylan, Amy P.N. Skubitz, and Walter C. Low
Cancer Informatics 2011:10 233-247
Original Research | Published on 03 Oct 2011

Cellular Imaging Using Equivalent Cross-Relaxation Rate Technique in Rabbit VX-2 Tumor Model
Hideyuki Nishiofuku, Shigeru Matsushima, Osamu Taguchi, Yoshitaka Inaba, Hidekazu Yamaura, Yozo Sato, Toshihiro Tanaka and Kimihiko Kichikawa
Cancer Informatics 2011:10 227-232
Original Research | Published on 31 Aug 2011

Multicenter Breast Cancer Collaborative Registry
Simon Sherman, Oleg Shats, Elizabeth Fleissner, George Bascom, Kevin Yiee, Mehmet Copur, Kate Crow, James Rooney, Zubeena Mateen, Marsha A. Ketcham, Jianmin Feng, Alexander Sherman, Michael Gleason, Leo Kinarsky, Edibaldo Silva-Lopez, James Edney, Elizabeth Reed, Ann Berger and Kenneth Cowan
Cancer Informatics 2011:10 217-226
Methodology | Published on 31 Aug 2011

On Differential Gene Expression Using RNA-Seq Data
Juhee Lee, Yuan Ji, Shoudan Liang, Guoshuai Cai and Peter Müller
Cancer Informatics 2011:10 205-215
Methodology | Published on 01 Aug 2011

An Integrative Genomics Approach to Biomarker Discovery in Breast Cancer
Chindo Hicks, Rozana Asfour, Antonio Pannuti and Lucio Miele
Cancer Informatics 2011:10 185-204
Original Research | Published on 25 Jul 2011

Metagenes Associated with Survival in Non-Small Cell Lung Cancer
Egon Urgard, Tõnu Vooder, Urmo Võsa, Kristjan Välk, Mingming Liu, Cheng Luo, Fabian Hoti, Retlav Roosipuu, Tarmo Annilo, Jukka Laine, Christopher M. Frenz, Liqing Zhang and Andres Metspalu
Cancer Informatics 2011:10 175-183
Original Research | Published on 02 Jun 2011

Model-Integrated Estimation of Normal Tissue Contamination for Cancer SNP Allelic Copy Number Data
Susann Stjernqvist, Tobias Rydén and Chris D. Greenman
Cancer Informatics 2011:10 159-173
Original Research | Published on 25 May 2011

GENT: Gene Expression Database of Normal and Tumor Tissues
Gwangsik Shin, Tae-Wook Kang, Sungjin Yang, Su-Jin Baek, Yong-Su Jeong and Seon-Young Kim
Cancer Informatics 2011:10 149-157
Database Review | Published on 09 May 2011

A Jackknife and Voting Classifier Approach to Feature Selection and Classification
Sandra L. Taylor and Kyoungmi Kim
Cancer Informatics 2011:10 133-147
Methodology | Published on 27 Apr 2011

Bioinformatic Prediction of Ultraviolet Light Mutagenesis Sensitivity of Human Genes and a Method for Genetically Engineering UVB Resistance
Kevin A. Lease and Chris Papageorgio
Cancer Informatics 2011:10 121-131
Short Report | Published on 18 Apr 2011

A Comparison of Methods for Data-Driven Cancer Outlier Discovery, and An Application Scheme to Semisupervised Predictive Biomarker Discovery
Seppo Karrila, Julian Hock Ean Lee and Greg Tucker-Kellogg
Cancer Informatics 2011:10 109-120
Original Research | Published on 18 Apr 2011

Associating GWAS Information with the Notch Signaling Pathway Using Transcription Profiling
Chindo Hicks, Antonio Pannuti and Lucio Miele
Cancer Informatics 2011:10 93-108
Original Research | Published on 06 Apr 2011

PCCR: Pancreatic Cancer Collaborative Registry
Simon Sherman, Oleg Shats, Marsha A. Ketcham, Michelle A. Anderson, David C. Whitcomb, Henry T. Lynch, Paola Ghiorzo, Wendy S. Rubinstein, Aaron R. Sasson, William E. Grizzle, Gleb Haynatzki, Jianmin Feng, Alexander Sherman, Leo Kinarsky and Randall E. Brand
Cancer Informatics 2011:10 83-91
Original Research | Published on 23 Mar 2011

Self-Calibrated Warping for Mass Spectra Alignment
Q. Peter He, Jin Wang, James A. Mobley, Joshua Richman and William E. Grizzle
Cancer Informatics 2011:10 65-82
Methodology | Published on 22 Mar 2011

Reproducibility of SELDI Spectra Across Time and Laboratories
Lixia Diao, Charlotte H. Clarke, Kevin R. Coombes, Stanley R. Hamilton, Jack Roth, Li Mao, Bogdan Czerniak, Keith A. Baggerly, Jeffrey S. Morris, Eric T. Fung and Robert C. Bast Jr
Cancer Informatics 2011:10 45-64
Original Research | Published on 14 Mar 2011

Extension of Cox Proportional Hazard Model for Estimation of Interrelated Age-Period-Cohort Effects on Cancer Survival
Tengiz Mdzinarishvili, Michael X. Gleason, Leo Kinarsky and Simon Sherman
Cancer Informatics 2011:10 31-44
Methodology | Published on 23 Feb 2011

In silico Analysis of Combinatorial microRNA Activity Reveals Target Genes and Pathways Associated with Breast Cancer Metastasis
Alan A. Dombkowski, Zakia Sultana, Douglas B. Craig and Hasan Jamil
Cancer Informatics 2011:10 13-29
Methodology | Published on 17 Feb 2011

Skin Cancer Recognition by Using a Neuro-Fuzzy System
Bareqa Salah, Mohammad Alshraideh, Rasha Beidas and Ferial Hayajneh
Cancer Informatics 2011:10 1-11
Original Research | Published on 02 Feb 2011

Identification of Predictive Pathways for Non-Hodgkin Lymphoma Prognosis
Xuesong Han, Yang Li, Jian Huang, Yawei Zhang, Theodore Holford, Qing Lan, Nathaniel Rothman, Tongzhang Zheng, Michael R. Kosorok and Shuangge Ma
Cancer Informatics 2010:9 281-292
Methodology | Published on 07 Dec 2010

Sinusoidal Cox Regression—A Rare Cancer Example
Jimmy Thomas Efird
Cancer Informatics 2010:9 265-279
Methodology | Published on 28 Nov 2010

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