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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Quantitative Assessment of Tissue Biomarkers and Construction of a Model to Predict Outcome in Breast Cancer Using Multiple Imputation
John W. Emerson, Marisa Dolled-Filhart, Lyndsay Harris, David L. Rimm and David P. Tuck
Cancer Informatics 2009:7 29-40
Original research | Published on 23 Dec 2008

Applications of Microarray Technology to Acute Myelogenous Leukemia
Rashmi S. Goswami, Mahadeo A. Sukhai, Mariam Thomas, Patricia P. Reis and Suzanne Kamel-Reid
Cancer Informatics 2009:7 13-28
Review | Published on 22 Dec 2008

Simulation of Different Truncated p16INK4a Forms and In Silico Study of Interaction with Cdk4
Najmeh Fahham, Mohammad Hossein Ghahremani, Soroush Sardari, Behrouz Vaziri and Seyed Nasser Ostad
Cancer Informatics 2009:7 1-11
Original research | Published on 03 Dec 2008

Modeling and Analyzing Gene Co-Expression in Hepatocellular Carcinoma Using Actor-Semiotic Networks and Centrality Signatures
David C.Y. Fung
Cancer Informatics 2008:6 463-474
Published on 05 Nov 2008

An Analysis Pipeline for Genome-wide Association Studies
Stefan Stefanov, James Lautenberger and Bert Gold
Cancer Informatics 2008:6 455-461
Published on 24 Sep 2008

Algorithmic Discovery of Methylation “Hot Spots” in DNA from Lymphoma Patients
Chris Papageorgio, Robert Harrison, Farahnaz B. Rahmatpanah, Kristen Taylor, Wade Davis and Charles W. Caldwell
Cancer Informatics 2008:6 449-453
Published on 04 Sep 2008

Grammatical Immune System Evolution for Reverse Engineering Nonlinear Dynamic Bayesian Models
B.A. McKinney and D. Tian
Cancer Informatics 2008:6 433-447
Published on 28 Aug 2008

What Does PLIER Really Do?
Terry M.Therneau and Karla V.Ballman
Cancer Informatics 2008:6 423-431
Published on 27 Aug 2008

Efficiency Analysis of Competing Tests for Finding Differentially Expressed Genes in Lung Adenocarcinoma
Rick Jordan, Satish Patel, Hai Hu, and James Lyons-Weiler
Cancer Informatics 2008:6 389-421

Published on 14 Jul 2008

A Biological Evaluation of Six Gene Set Analysis Methods for Identification of Differentially Expressed Pathways in Microarray Data
Irina Dinu, Qi Liu, John D. Potter, Adeniyi J. Adewale, Gian S. Jhangri, Thomas Mueller, Gunilla Einecke, Konrad Famulsky, Philip Halloran and Yutaka Yasui
Cancer Informatics 2008:6 357-368
Published on 20 Jun 2008

An Integrative Analysis of microRNA and mRNA Expression - A Case Study
Li-Xuan Qin
Cancer Informatics 2008:6 369-379
Published on 17 Jun 2008

The Anti-tumour Agent, Cisplatin, and its Clinically Ineffective Isomer, Transplatin, Produce Unique Gene Expression Profiles in Human Cells
Anne M. Galea and Vincent Murray
Cancer Informatics 2008:6 315-355

Published on 10 Jun 2008

Non-Negative Matrix Factorization for the Analysis of Complex Gene Expression Data: Identification of Clinically Relevant Tumor Subtypes
Attila Frigyesi and Mattias Höglund
Cancer Informatics 2008:6 275-292
Published on 29 May 2008

Detecting Role Errors in the Gene Hierarchy of the NCI Thesaurus
Hua Min, Barry Cohen, Michael Halper, Marc Oren and Yehoshua Perl
Cancer Informatics 2008:6 293-313
Published on 27 May 2008

An Analysis of Risk Factors for Developing Hepatocellular Carcinoma in a Group of Hepatitis C Patients with Stage 3 Fibrosis following Interferon Therapy
Sabina Mahmood , Kazumi Togawa, Miwa Kawanaka, Gouichi Niiyama, Gotaro Yamada
Cancer Informatics 2008:6 381-387
Published on 23 Apr 2008

Connections Between ETV6-Modulated Genes: Identification of Shared Features
Gino Boily, Patrick Beaulieu, Jasmine Healy and Daniel Sinnett
Cancer Informatics 2008:6 183-201
Published on 21 Apr 2008

BRB-ArrayTools Data Archive for Human Cancer Gene Expression: A Unique and Efficient Data Sharing Resource
Yingdong Zhao and Richard Simon
Cancer Informatics 2008:6 9-15
Published on 21 Apr 2008

Classifying Variants of Undetermined Significance in BRCA2 with Protein Likelihood Ratios
Rachel Karchin, Mukesh Agarwal, Andrej Sali, Fergus Couch and Mary S. Beattie
Cancer Informatics 2008:6 203-216
Published on 18 Apr 2008

Comparison of a Label-Free Quantitative Proteomic Method Based on Peptide Ion Current Area to the Isotope Coded Affinity Tag Method
Soyoung Ryu, Byron Gallis, Young Ah Goo, Scott A. Shaffer, Dragan Radulovic, David R. Goodlett
Cancer Informatics 2008:6 243-255
Published on 17 Apr 2008

Uncovering Biological Network Function via Graphlet Degree Signatures
Tijana Milenković and Nataša Pržulj
Cancer Informatics 2008:6 257-273

Published on 14 Apr 2008

Bayesian Mass Spectra Peak Alignment from Mass Charge Ratios
Junfeng Liu, Weichuan Yu, Baolin Wu and Hongyu Zhao
Cancer Informatics 2008:6 217-241
Published on 11 Apr 2008

A Standards based Ontological Approach to Information Handling for use by Organizations Providing Human Tissue for Research
Mary E. Edgerton, Carl Morrison, Virginia A. LiVolsi, Christopher A. Moskaluk, Stephen J. Qualman, M. Kay Washington and William E. Grizzle
Cancer Informatics 2008:6 127-137
Published on 10 Apr 2008

Sample Preparation for in vitro Analysis of Iodine in Thyroid Tissue using X-ray Fluorescence
Marie Hansson, Mats Isaksson and Gertrud Berg
Cancer Informatics 2008:6 51-57
Published on 10 Apr 2008

An Application of a Service-oriented System to Support ArrayAnnotation in Custom Chip Design for Epigenomic Analysis
Junghee Han, Dustin Potter, Tahsin Kurc, Greg Singer, Pearlly S. Yan, Sun Hao, Shannon Hastings, Stephen Langella, Scott Oster, Ramana V. Davuluri,Tim H.-M. Huang and Joel H. Saltz
Cancer Informatics 2008:6 111-125
Published on 10 Apr 2008

MCAM: A Database to Accelerate the Identification of Functional Cell Adhesion Molecules
Anguraj Sadanandam, Sudipendra Nath Pal, Joe Ziskovsky, Prathibha Hegde and Rakesh K. Singh
Cancer Informatics 2008:6 47-50
Published on 31 Mar 2008

Comparisons of Robustness and Sensitivity between Cancer and Normal Cells by Microarray Data
Liang-Hui Chu and Bor-Sen Chen
Cancer Informatics 2008:6 165-181
Published on 28 Mar 2008

DNA Copy Number Analysis in Gastrointestinal Stromal Tumors Using Gene Expression Microarrays
Cristina R. Antonescu, Kai Wu, Guoliang Leon Xing, Manqiu Cao, Yaron Turpaz, Margaret A. Leversha, Earl Hubbell, Robert G. Maki, C. Garrett Miyada, and Raji Pillai
Cancer Informatics 2008:6 59-75
Published on 27 Mar 2008

Chromosome 20q Amplification Regulates in Vitro Response to Kinesin-5 Inhibitor
Aimee L. Jackson, Mao Mao, Sumire Kobayashi, Teresa Ward, Matthew Biery, Hongyue Dai, Steven R. Bartz and Peter S. Linsley
Cancer Informatics 2008:6 147-164
Published on 26 Mar 2008

A Computational Model of Quantitative Chromatin Immunoprecipitation (ChIP) Analysis
Jingping Xie, Philip S. Crooke, Brett A. McKinney, Joel Soltman and Stephen J. Brandt
Cancer Informatics 2008:6 138-146
Published on 12 Mar 2008

Effect of Quantitative Nuclear Image Features on Recurrence of Ductal Carcinoma In Situ (DCIS) of the Breast
David E. Axelrod, Naomi A. Miller, H. Lavina Lickley, Jin Qian, William A. Christens-Barry, Yan Yuan, Yuejiao Fu and Judith-Anne W. Chapman
Cancer Informatics 2008:6 99-109
Published on 01 Mar 2008

Evaluating Microarray-based Classifiers: An Overview
A.-L. Boulesteix, C. Strobl, T. Augustin and M. Daumer
Cancer Informatics 2008:6 77-97
Published on 29 Feb 2008

Estimating the Proportion of True Null Hypotheses for Multiple Comparisons
Hongmei Jiang and R.W. Doerge
Cancer Informatics 2008:6 25-32
Published on 14 Feb 2008

Bayesian Estimation of Performance Measures of Cervical Cancer Screening Tests in the Presence of Covariates and Absence of a Gold Standard
Edson Zangiacomi Martinez, Francisco Louzada-Neto, Sophie Françoise Mauricette Derchain, Jorge Alberto Achcar, Renata Clementino Gontijo, Luis Otávio Zanatta Sarian and Kari Juhani Syrjänen
Cancer Informatics 2008:6 33-46
Published on 14 Feb 2008

Global Associations between Copy Number and Transcript mRNA Microarray Data: An Empirical Study
Wenjuan Gu, Hyungwon Choi and Debashis Ghosh
Cancer Informatics 2008:6 17-23
Published on 09 Feb 2008

Constructing Tumor Progression Pathways and Biomarker Discovery with Fuzzy Kernel Kmeans and DNA Methylation Data
Zhenqiu Liu, Zhongmin Guo and Ming Tan
Cancer Informatics 2008:6 1-7
Published on 25 Jan 2008

Estimating the False Discovery Rate Using Mixed Normal Distribution for Identifying Differentially Expressed Genes in Microarray Data Analysis
Akihiro Hirakawa, Yasunori Sato, Takashi Sozu, Chikuma Hamada, Isao Yoshimura
Cancer Informatics 2007:3 140-148
Published on 22 Jan 2008

A Practical Multifaceted Approach to Selecting Differentially Expressed Genes
Yingye Zheng and Margaret Pepe
Cancer Informatics 2007:3 203-212
Published on 15 Jan 2008

Common Peak Approach Using Mass Spectrometry Data Sets for Predicting the Effects of Anticancer Drugs on Breast Cancer
Masaru Ushijima, Satoshi Miyata, Shinto Eguchi, Masanori Kawakita, Masataka Yoshimoto, Takuji Iwase, Futoshi Akiyama, Goi Sakamoto, Koichi Nagasaki, Yoshio Miki, Tetsuo Noda, Yutaka Hoshikawa and Masaaki Matsuura
Cancer Informatics 2007:3 285-293
Published on 14 Dec 2007

Germinal Center B Cell-Like (GCB) and Activated B Cell-Like (ABC) Type of Diffuse Large B Cell Lymphoma (DLBCL): Analysis of Molecular Predictors, Signatures, Cell Cycle State and Patient Survival
S. Blenk, J. Engelmann, M. Weniger, J. Schultz, M. Dittrich, A. Rosenwald, H.K. Müller-Hermelink, T. Müller and T. Dandekar
Cancer Informatics 2007:3 399-420
Published on 12 Dec 2007

Public Databases and Software for the Pathway Analysis of Cancer Genomes
Ivy F.L. Tsui, Raj Chari, Timon P.H. Buys and Wan L. Lam
Cancer Informatics 2007:3 379-397
Published on 12 Dec 2007

Systems Level Modeling of the Cell Cycle Using Budding Yeast
B.P. Ingalls, B.P. Duncker, D.R. Kim and B.J. McConkey
Cancer Informatics 2007:3 357-370
Published on 11 Dec 2007

Comparison of Computational Algorithms for the Classification of Liver Cancer using SELDI Mass Spectrometry: A Case Study
Changyu Shen, Timothy E Breen, Lacey E Dobrolecki, C. Max Schmidt, George W. Sledge , Kathy D. Miller and Robert J Hickey
Cancer Informatics 2007:3 329-339
Published on 11 Dec 2007

Combining Clinical and Genomic Covariates via Cov-TGDR
Shuangge Ma and Jian Huang
Cancer Informatics 2007:3 371-378
Published on 15 Oct 2007

Tumor Genome Wide DNA Alterations Assessed by Array CGH in Patients with Poor and Excellent Survival Following Operation for Colorectal Cancer
Kristina K. Lagerstedt, Johan Staaf, Göran Jönsson, Elisabeth Hansson, Christina Lönnroth, Ulf Kressner, Lars Lindström, Svante Nordgren, Åke Borg and Kent Lundholm
Cancer Informatics 2007:3 341-355
Published on 12 Oct 2007

Parametric Power Spectral Density Analysis of Noise from Instrumentation in MALDI TOF Mass Spectrometry
Hyunjin Shin, Miray Mutlu, John M. Koomen and Mia K. Markey
Cancer Informatics 2007:3 219-230
Published on 17 Sep 2007

Normalized, Segmented or Called aCGH Data?
Wessel N. van Wieringen, Mark A. van de Wiel and Bauke Ylstra
Cancer Informatics 2007:3 321-327
Published on 17 Sep 2007

Overlay Tool© for aCGHViewer©: An Analysis Module Built for aCGHViewer© used to Perform Comparisons of Data Derived from Different Microarray Platforms
Ken C. Lo, Ganesh Shankar, Yaron Turpaz, Dione Bailey, Michael R. Rossi, Tania Burkhardt, Ping Liang and John K. Cowell
Cancer Informatics 2007:3 307-319
Published on 08 Aug 2007

Comparison of Supervised Classification Methods for Protein Profiling in Cancer Diagnosis
Nadège Dossat, Alain Mangé, Jérôme Solassol, William Jacot, Ludovic Lhermitte, Thierry Maudelonde, Jean-Pierre Daurès and Nicolas Molinari
Cancer Informatics 2007:3 295-305
Published on 19 Jul 2007

Simultaneous EGFR and VEGF Alterations in Non-Small Cell Lung Carcinoma Based on Tissue Microarrays
Evangelos Tsiambas, Athanasios Stamatelopoulos, Andreas Karameris, Ioannis Panagiotou, Dimitrios Rigopoulos, Antonios Chatzimichalis, Demosthenes Bouros and Efstratios Patsouris
Cancer Informatics 2007:3 275-284
Published on 12 Jun 2007

A Novel Cross-Disciplinary Multi-Institute Approach to Translational Cancer Research: Lessons Learned from Pennsylvania Cancer Alliance Bioinformatics Consortium (PCABC)
Ashokkumar A. Patel, John R. Gilbertson, Louise C. Showe, Jack W. London, Eric Ross, Michael F. Ochs, Joseph Carver, Andrea Lazarus, Anil V. Parwani, Rajiv Dhir, J. Robert Beck, Michael Liebman, Fernando U. Garcia, Jeff Prichard, Myra Wilkerson, Ronald B. Herberman, Michael J. Becich, and the PCABC.
Cancer Informatics 2007:3 255-274
Published on 08 Jun 2007

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