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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.



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Cross-platform Comparison of Two Pancreatic Cancer Phenotypes
Robert B. Scharpf, Christine A. Iacobuzio-Donahue, Leslie Cope, Ingo Ruczinski, Elizabeth Garrett-Mayer, Sindhu Lakkur, Domenico Campagna and Giovanni Parmigiani
Cancer Informatics 2010:9 257-264
Original Research | Published on 01 Nov 2010



Blasted Cell Line Names
Jing Wang, Lauren A. Byers, John S. Yordy, Wenbin Liu, Li Shen, Keith A. Baggerly, Uma Giri, Jeffrey N. Myers, K. Kian Ang, Michael D. Story, Luc Girard, John D. Minna, John V. Heymach and Kevin R. Coombes
Cancer Informatics 2010:9 251-255
Short Report | Published on 14 Oct 2010



Estimating Shared Copy Number Aberrations for Array CGH Data: The Linear-Median Method
Y.-X. Lin, V. Baladandayuthapani, V. Bonato and K.-A. Do
Cancer Informatics 2010:9 229-249
Original Research | Published on 12 Oct 2010



BeadDataPackR: A Tool to Facilitate the Sharing of Raw Data from Illumina BeadArray Studies
Mike L. Smith and Andy G. Lynch
Cancer Informatics 2010:9 217-227
Short Report | Published on 29 Sep 2010



Heterogeneity Between Ducts of the Same Nuclear Grade Involved by Duct Carcinoma In Situ (DCIS) of the Breast
Naomi A. Miller, Judith-Anne W. Chapman, Jin Qian, William A. Christens-Barry, Yuejiao Fu, Yan Yuan, H. Lavina A. Lickley and David E. Axelrod
Cancer Informatics 2010:9 209-216
Original Research | Published on 07 Sep 2010



LTR: Linear Cross-Platform Integration of Microarray Data
Paul C. Boutros
Cancer Informatics 2010:9 197-208
Original Research | Published on 27 Aug 2010



Professional Networks in the Life Sciences: Linking the Linked
Thomas S. Deisboeck and Jonathan Sagotsky
Cancer Informatics 2010:9 189-195
Perspective | Published on 25 Aug 2010



Weibull-like Model of Cancer Development in Aging
Tengiz Mdzinarishvili and Simon Sherman
Cancer Informatics 2010:9 179-188
Original Research | Published on 24 Aug 2010



Inhibition of Antiapoptotic BCL-XL, BCL-2, and MCL-1 Proteins by Small Molecule Mimetics
D.S. Dalafave and G. Prisco
Cancer Informatics 2010:9 169-177
Original Research | Published on 12 Aug 2010



Relationship between Selected Socio-Demographic Factors and Cancer of Oral Cavity - A Case Control Study
Abdoul Hossain Madani, Madhurima Dikshit, Debanshu Bhaduri, Abdolreza Sotoodeh Jahromi and Teamur Aghamolaei
Cancer Informatics 2010:9 163-168
Original Research | Published on 11 Aug 2010



Clinical Omics Analysis of Colorectal Cancer Incorporating Copy Number Aberrations and Gene Expression Data
Tsuyoshi Yoshida, Takumi Kobayashi, Masaya Itoda, Taika Muto, Ken Miyaguchi, Kaoru Mogushi, Satoshi Shoji, Kazuro Shimokawa, Satoru Iida, Hiroyuki Uetake, Toshiaki Ishikawa, Kenichi Sugihara, Hiroshi Mizushima and Hiroshi Tanaka
Cancer Informatics 2010:9 147-161
Original Research | Published on 29 Jul 2010



Rough Set Soft Computing Cancer Classification and Network: One Stone, Two Birds
Yue Zhang
Cancer Informatics 2010:9 139-145
Short Commentary | Published on 15 Jul 2010



Optimal Network Alignment with Graphlet Degree Vectors
Tijana Milenković, Weng Leong Ng, Wayne Hayes and Nataša Pržulj
Cancer Informatics 2010:9 121-137
Original Research | Published on 30 Jun 2010



An Efficient Gatekeeper Algorithm for Detecting GxE
Jimmy T. Efird
Cancer Informatics 2010:9 115-120
Published on 12 May 2010



Development and Validation of Predictive Indices for a Continuous Outcome Using Gene Expression Profiles
Yingdong Zhao and Richard Simon
Cancer Informatics 2010:9 105-114
Original Research | Published on 07 May 2010



A Penalized Mixture Model Approach in Genotype/Phenotype Association Analysis for Quantitative Phenotypes
Lang Li, Silvana Borges, Robarge D. Jason, Changyu Shen, Zeruesenay Desta and David Flockhart
Cancer Informatics 2010:9 93-103
Original Research | Published on 27 Apr 2010



Genes with Relevance for Early to Late Progression of Colon Carcinoma Based on Combined Genomic and Transcriptomic Information from the Same Patients
Kristina K. Lagerstedt, Erik Kristiansson, Christina Lönnroth, Marianne Andersson, Britt-Marie Iresjö, Annika Gustafsson, Elisabeth Hansson, Ulf Kressner, Svante Nordgren, Fredrik Enlund and Kent Lundholm
Cancer Informatics 2010:9 79-91
Original Research | Published on 23 Apr 2010



Estimation of Hazard Functions in the Log-Linear Age-Period-Cohort Model: Application to Lung Cancer Risk Associated with Geographical Area
Tengiz Mdzinarishvili, Michael X. Gleason and Simon Sherman
Cancer Informatics 2010:9 67-78
Original Research | Published on 14 Apr 2010



Protein-protein Interaction Reveals Synergistic Discrimination of Cancer Phenotype
Jianghui Xiong, Juan Liu, Simon Rayner, Yinghui Li and Shanguang Chen
Cancer Informatics 2010:9 61-66
Original Research | Published on 26 Mar 2010



Characterization of the Effectiveness of Reporting Lists of Small Feature Sets Relative to the Accuracy of the Prior Biological Knowledge
Chen Zhao, Michael L. Bittner, Robert S. Chapkin and Edward R. Dougherty
Cancer Informatics 2010:9 49-60
Methodology | Published on 18 Mar 2010



Comparison of Two Output-Coding Strategies for Multi-Class Tumor Classification Using Gene Expression Data and Latent Variable Model as Binary Classifier
Sandeep J. Joseph, Kelly R. Robbins, Wensheng Zhang and Romdhane Rekaya
Cancer Informatics 2010:9 39-48
Methodology | Published on 10 Mar 2010



Expression a La Bimode
James C. Willey
Cancer Informatics 2010:9 37-38
Editorial | Published on 03 Mar 2010



The Power of the Web in Cancer Drug Discovery and Clinical Trial Design: Research without a Laboratory?
Christine Galustian and Angus G. Dalgleish
Cancer Informatics 2010:9 31-35
Commentary | Published on 18 Feb 2010



Bimodal Gene Expression and Biomarker Discovery
Adam Ertel
Cancer Informatics 2010:9 11-14
Short Commentary | Published on 04 Feb 2010



A Robust Gene Selection Method for Microarray-based Cancer Classification
Xiaosheng Wang and Osamu Gotoh
Cancer Informatics 2010:9 15-30
Original Research | Published on 04 Feb 2010



Dual KS: Defining Gene Sets with Tissue Set Enrichment Analysis
Yarong Yang, Eric J. Kort, Nader Ebrahimi, Zhongfa Zhang and Bin T. Teh
Cancer Informatics 2010:9 1-9
Methodology | Published on 21 Jan 2010



Modeling Prognostic Factors in Resectable Pancreatic Adenocarcinomas
Taxiarchis Botsis, Valsamo K. Anagnostou, Gunnar Hartvigsen, George Hripcsak and Chunhua Weng
Cancer Informatics 2009:7 281-291
Original Research | Published on 20 Jan 2010



A Novel Approach for Analysis of the Log-Linear Age-Period-Cohort Model: Application to Lung Cancer Incidence
Tengiz Mdzinarishvili, Michael X. Gleason and Simon Sherman
Cancer Informatics 2009:7 271-280
Original Research | Published on 14 Dec 2009



In silico Analysis of Human Telomerase Reverse Transcriptase (hTERT ) Gene: Identification of a Distant Homolog of Melanoma Antigen Family Gene (MAGE)
Ruhul Amin, Jesmin, Hasan Jamil and M. Anwar Hossain
Cancer Informatics 2009:7 171-181
Hypothesis | Published on 24 Nov 2009



Discrimination of Carcinogens by Hepatic Transcript Profiling in Rats Following 28-day Administration
Hiroshi Matsumoto, Yoshikuni Yakabe, Koichi Saito, Kayo Sumida, Masaru Sekijima, Koji Nakayama, Hideki Miyaura, Fumiyo Saito, Masanori Otsuka and Tomoyuki Shirai
Cancer Informatics 2009:7 253-269
Original Research | Published on 13 Nov 2009



Introduction of Hypermatrix and Operator Notation into a Discrete Mathematics Simulation Model of Malignant Tumour Response to Therapeutic Schemes In Vivo. Some Operator Properties
Georgios S. Stamatakos and Dimitra D. Dionysiou
Cancer Informatics 2009:7 239-251
Original Research | Published on 21 Oct 2009



Unblocking Blockbusters: Using Boolean Text-Mining to Optimise Clinical Trial Design and Timeline for Novel Anticancer Drugs
Richard J. Epstein
Cancer Informatics 2009:7 231-238

Original Research | Published on 17 Aug 2009



New Advanced Technologies to Provide Decentralised  and Secure Access to Medical Records: Case Studies  in Oncology
Catherine Quantin, Gouenou Coatrieux, François André Allaert, Maniane Fassa, Karima Bourquard, Jean-Yves Boire, Paul de Vlieger, Lydia Maigne and Vincent Breton
Cancer Informatics 2009:7 217-229
Case Report | Published on 07 Aug 2009



The Bimodality Index: A Criterion for Discovering  and Ranking Bimodal Signatures from Cancer Gene Expression Profiling Data
Jing Wang, Sijin Wen, W. Fraser Symmans, Lajos Pusztai and Kevin R. Coombes
Cancer Informatics 2009:7 199-216
Original Research | Published on 05 Aug 2009



A Generalized Beta Model for the Age Distribution of Cancers: Application to Pancreatic and Kidney Cancer
Tengiz Mdzinarishvili, Michael X. Gleason, Leo Kinarsky and Simon Sherman
Cancer Informatics 2009:7 183-197
Original Research | Published on 04 Aug 2009



Linguistic Processing and Classification of Semi Structured Bibliographic Data on Complementary Medicine
Thomas Ostermann, Christa K. Raak, Peter F. Matthiessen, Arndt Büssing and Hartmut Zillmann
Cancer Informatics 2009:7 159-169

Review | Published on 06 Jul 2009



Robust Model Selection for Classification of Microarrays
Ikumi Suzuki, Takashi Takenouchi, Miki Ohira, Shigeyuki Oba and Shin Ishii
Cancer Informatics 2009:7 141-157
Original Research | Published on 25 Jun 2009



Integration of Neuroimaging and Microarray Datasets  through Mapping and Model-Theoretic Semantic Decomposition of Unstructured Phenotypes
Spiro P. Pantazatos, Jianrong Li, Paul Pavlidis and Yves A. Lussier
Cancer Informatics 2009:8 75-94
Original Research | Published on 08 Jun 2009



Microarray-Based Cancer Prediction Using Soft Computing Approach
Xiaosheng Wang and Osamu Gotoh
Cancer Informatics 2009:7 123-139
Original Research | Published on 26 May 2009



Using Semantic Web Technologies to Annotate and Align Microarray Designs
Sebastian Szpakowski, James McCusker and Michael Krauthammer
Cancer Informatics 2009:8 65-73
Methodology | Published on 13 May 2009



Estrogen Exposure, Metabolism, and Enzyme Variants in a Model for Breast Cancer Risk Prediction
Fritz F. Parl, Kathleen M. Egan, Chun Li and Philip S. Crooke
Cancer Informatics 2009:7 109-121
Original Research | Published on 05 May 2009



Dedication: Joan Elaine Althouse Weiler
James Lyons-Weiler
Cancer Informatics 2009:7 105-107
Dedication | Published on 30 Apr 2009



Development of the Lymphoma Enterprise Architecture Database: A caBIG(TM) Silver Level Compliant System
Taoying Huang, Pareen J. Shenoy, Rajni Sinha, Michael Graiser, Kevin W. Bumpers and Christopher R. Flowers
Cancer Informatics 2009:8 45-64
Published on 03 Apr 2009 | Highly accessed (previous month)



Combining Chromosomal Arm Status and Significantly Aberrant Genomic Locations Reveals New Cancer Subtypes
Tal Shay, Wanyu L. Lambiv, Anat Reiner-Benaim, Monika E. Hegi and Eytan Domany
Cancer Informatics 2009:7 91-104
Methodology | Published on 12 Mar 2009



An Algorithm for Identifying Novel Targets of Transcription Factor Families: Application to Hypoxia-inducible Factor 1 Targets
Yue Jiang, Bojan Cukic, Donald A. Adjeroh, Heath D. Skinner, Jie Lin, Qingxi J. Shen and Bing-Hua Jiang
Cancer Informatics 2009:7 75-89
Original research | Published on 04 Mar 2009



Use of Gene Expression Profiles of Peripheral Blood Lymphocytes to Distinguish BRCA1 Mutation Carriers in High Risk Breast Cancer Families
Marie-Laure Vuillaume, Nancy Uhrhammer, Véronique Vidal, Valérie Sylvain Vidal, Valérie Chabaud, Beline Jesson, Fabrice Kwiatkowski and Yves-Jean Bignon
Cancer Informatics 2009:7 41-56
Published on 02 Mar 2009



A Novel Information Retrieval Model for High-Throughput Molecular Medicine Modalities
Firas H. Wehbe, Steven H. Brown, Pierre P. Massion, Cynthia S. Gadd, Daniel R. Masys and Constantin F. Aliferis
Cancer Informatics 2009:8 1-17
Methodology | Published on 09 Feb 2009



Staging of Prostate Cancer Using Automatic Feature Selection, Sampling and Dempster-Shafer Fusion
Sandeep Chandana, Henry Leung and Kiril Trpkov
Cancer Informatics 2009:7 57-73
Original research | Published on 03 Feb 2009



Semantic Integration of Cervical Cancer Data Repositories to Facilitate Multicenter Association Studies: The ASSIST Approach
Theodoros Agorastos, Vassilis Koutkias, Manolis Falelakis, Irini Lekka, Themistoklis Mikos, Anastasios Delopoulos, Pericles A. Mitkas, Antonios Tantsis, Steven Weyers, Pascal Coorevits, Andreas M. Kaufmann, Roberto Kurzeja and Nicos Maglaveras
Cancer Informatics 2009:8 31-44
Original research | Published on 03 Feb 2009



Semantic Web-Based Integration of Cancer Pathways and Allele Frequency Data
Matthew E. Holford, Haseena Rajeevan, Hongyu Zhao, Kenneth K. Kidd and Kei-Hoi Cheung
Cancer Informatics 2009:8 19-30
Methodology | Published on 15 Jan 2009





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