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Bioinformatics

Range of open access peer reviewed Bioinformatics journals & associated research articles. Read full text articles or submit your research for publishing


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Results 1-150 of 791 for Bioinformatics

The Widening Gulf between Genomics Data Generation and Consumption: A Practical Guide to Big Data Transfer Technology
Frank A. Feltus, Joseph R. Breen III, Juan Deng, Ryan S. Izard, Christopher A. Konger, Walter B. Ligon III, Don Preuss and Kuang-Ching Wang
Bioinformatics and Biology Insights 2015:Suppl. 1 9-19
Review | Published on 23 Sep 2015



PPCheck: A Webserver for the Quantitative Analysis of Protein–Protein Interfaces and Prediction of Residue Hotspots
Anshul Sukhwal and Ramanathan Sowdhamini
Bioinformatics and Biology Insights 2015:9 141-151
Original Research | Published on 21 Sep 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



Expression Divergence of Duplicate Genes in the Protein Kinase Superfamily in Pacific Oyster
Dahai Gao, Dennis C. Ko, Xinmin Tian, Guang Yang and Liuyang Wang
Evolutionary Bioinformatics 2015:Suppl. 1 57-65
Review | Published on 13 Sep 2015



Molecular Dynamics Approach in the Comparison of Wild-Type and Mutant Paraoxonase-1 Apoenzyme Form
Khadija Amine, Lamia Miri, Adil Naimi, Rachid Saile, Abderrahmane El Kharrim, Afaf Mikou and Anass Kettani
Bioinformatics and Biology Insights 2015:9 129-140
Original Research | 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



BioImg.org: A Catalog of Virtual Machine Images for the Life Sciences
Martin Dahlö, Frédéric Haziza, Aleksi Kallio, Eija Korpelainen, Erik Bongcam-Rudloff and Ola Spjuth
Bioinformatics and Biology Insights 2015:9 125-128
Technical Advance | Published on 10 Sep 2015



Genomic, Proteomic, and Metabolomic Data Integration Strategies
Kwanjeera Wanichthanarak, Johannes F. Fahrmann and Dmitry Grapov
Biomarker Insights 2015:Suppl. 4 1-6
Review | Published on 07 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



Introductory Editorial: Computer Simulation, Bioinformatics, and Statistical Analysis of Cancer Data and Processes
Kellie J. Archer, Kevin Dobbin, Swati Biswas, Roger S. Day, David C. Wheeler, Hao Wu
Cancer Informatics 2015:Suppl. 2 247-251
Editorial | Published on 01 Sep 2015



CoGNaC: A Chaste Plugin for the Multiscale Simulation of Gene Regulatory Networks Driving the Spatial Dynamics of Tissues and Cancer
Simone Rubinacci, Alex Graudenzi, Giulio Caravagna, Giancarlo Mauri, James Osborne, Joe Pitt-Francis and Marco Antoniotti
Cancer Informatics 2015:Suppl. 4 53-65
Technical Advance | Published on 01 Sep 2015



In Silico Characterization of Functional Divergence of Two Cathelicidin Variants in Indian Sheep
Kamaljeet K. Dhaliwal, Jaspreet S. Arora, Chandra S. Mukhopadhyay and Prem P. Dubey
Evolutionary Bioinformatics 2015:11 189-196
Published on 01 Sep 2015 | Highly accessed (previous month)



Development and Validation of a Clinical Risk-Assessment Tool Predictive of All-Cause Mortality
Ghalib A. Bello, Gerard G. Dumancas and Chris Gennings
Bioinformatics and Biology Insights 2015:Suppl. 3 1-10
Original Research | Published on 01 Sep 2015



Antigenic Determinants of Possible Vaccine Escape by Porcine Circovirus Subtype 2b Viruses
Megan Constans, Marvin Ssemadaali, Oleksandr Kolyvushko and Sheela Ramamoorthy
Bioinformatics and Biology Insights 2015:Suppl. 2 1-12
Original Research | Published on 23 Aug 2015 | Video abstract



Assessing Treatment Response Through Generalized Pharmacokinetic Modeling of DCE-MRI Data
Eleftherios Kontopodis, Georgia Kanli, Georgios C. Manikis, Sofie Van Cauter and Kostas Marias
Cancer Informatics 2015:Suppl. 4 41-51
Original Research | Published on 12 Aug 2015



In Silico Neuro-Oncology: Brownian Motion-Based Mathematical Treatment as a Potential Platform for Modeling the Infiltration of Glioma Cells into Normal Brain Tissue
Markos Antonopoulos and Georgios Stamatakos
Cancer Informatics 2015:Suppl. 4 33-40
Review | Published on 10 Aug 2015



How Many Genes are Needed to Resolve Phylogenetic Incongruence?
Bin Ai and Ming Kang
Evolutionary Bioinformatics 2015:11 185-188
Rapid Communication | Published on 10 Aug 2015



HMPL: A Pipeline for Identifying Hemimethylation Patterns by Comparing Two Samples
Shuying Sun and Peng Li
Cancer Informatics 2015:Suppl. 2 235-245
Original Research | Published on 09 Aug 2015



Genome-wide Identification of WRKY Genes in the Desert Poplar Populus euphratica and Adaptive Evolution of the Genes in Response to Salt Stress
Jianchao Ma, Jing Lu, Jianmei Xu, Bingbing Duan, Xiaodong He and Jianquan Liu
Evolutionary Bioinformatics 2015:Suppl. 1 47-55
Review | Published on 05 Aug 2015



Secondary Data Analytics of Aquaporin Expression Levels in Glioblastoma Stem-Like Cells
Raphael D. Isokpehi, Katharina C. Wollenberg Valero, Barbara E. Graham, Maricica Pacurari, Jennifer N. Sims, Udensi K. Udensi and Kenneth Ndebele
Cancer Informatics 2015:14 95-103
Original Research | Published on 30 Jul 2015



A Visualization Tool for Calculating the Genetic Substitution Patterns Between Two Different Groups
Insung Ahn, Jin-Hwa Jang, Ha-Yeon Kim, Ji-Hae Lee, and Hyeon Seok Son
Evolutionary Bioinformatics 2015:11 179-183
Original Research | Published on 27 Jul 2015



Medical Image Retrieval: A Multimodal Approach
Yu Cao, Shawn Steffey, Jianbiao He, Degui Xiao, Cui Tao, Ping Chen and Henning Müller
Cancer Informatics 2014:Suppl. 3 125-136
Original Research | Published on 22 Jul 2015



Using Nonlinear Stochastic Evolutionary Game Strategy to Model an Evolutionary Biological Network of Organ Carcinogenesis Under a Natural Selection Scheme
Bor-Sen Chen, Kun-Wei Tsai and Cheng-Wei Li
Evolutionary Bioinformatics 2015:11 155-178
Original Research | Published on 19 Jul 2015



A Single-Array-Based Method for Detecting Copy Number Variants Using Affymetrix High Density SNP Arrays and its Application to Breast Cancer
Ming Li, Yalu Wen and Wenjiang Fu
Cancer Informatics 2014:Suppl. 4 95-103
Technical Advance | Published on 16 Jul 2015



A Simple Rank Product Approach for Analyzing Two Classes
Tae Young Yang
Bioinformatics and Biology Insights 2015:9 119-123
Methodology | Published on 16 Jul 2015



The Impact of Microenvironmental Heterogeneity on the Evolution of Drug Resistance in Cancer Cells
Shannon M. Mumenthaler, Jasmine Foo, Nathan C. Choi, Nicholas Heise, Kevin Leder, David B. Agus, William Pao, Franziska Michor, and Parag Mallick
Cancer Informatics 2015:Suppl. 4 19-31
Original Research | Published on 15 Jul 2015



Effective Population Size and Signatures of Selection Using Bovine 50K SNP Chips in Korean Native Cattle (Hanwoo)
Yi Li and Jong-Joo Kim
Evolutionary Bioinformatics 2015:11 143-153
Original Research | Published on 08 Jul 2015



The Origin of Land Plants: A Phylogenomic Perspective
Bojian Zhong, Linhua Sun and David Penny
Evolutionary Bioinformatics 2015:11 137-141
Consise Review | Published on 08 Jul 2015



De Novo Transcriptome Assembly and Development of Novel Microsatellite Markers for the Traditional Chinese Medicinal Herb, Veratrilla baillonii Franch (Gentianaceae)
Lei Wang, Zhengkun Wang, Jianbing Chen, Chunyan Liu, Wanlong Zhu, Liuyang Wang and Lihua Meng
Evolutionary Bioinformatics 2015:Suppl. 1 39-45
Original Research | Published on 08 Jul 2015



High-Throughput miRNA Sequencing Reveals a Field Effect in Gastric Cancer and Suggests an Epigenetic Network Mechanism
Monica B. Assumpção, Fabiano C. Moreira, Igor G. Hamoy, Leandro Magalhães, Amanda Vidal, Adenilson Pereira, Rommel Burbano, André Khayat, Artur Silva, Sidney Santos, Samia Demachki, Ândrea Ribeiro-dos-Santos, and Paulo Assumpção
Bioinformatics and Biology Insights 2015:9 111-117
Original Research | Published on 06 Jul 2015



Prediction of O-glycosylation Sites Using Random Forest and GA-Tuned PSO Technique
Hebatallah Hassan, Amr Badr and M. B. Abdelhalim
Bioinformatics and Biology Insights 2015:9 103-109
Original Research | Published on 05 Jul 2015



Identification of Genetic Mutations in Human Lung Cancer by Targeted Sequencing
Hongxiang Feng, Xiaowei Wang, Zhenrong Zhang, Chuanning Tang, Hua Ye, Lindsey Jones, Feng Lou, Dandan Zhang, Shouwen Jiang, Hong Sun, Haichao Dong, Guangchun Zhang, Zhiyuan Liu, Zhishou Dong, Baishuai Guo, He Yan, Chaowei Yan, Lu Wang, Ziyi Su, Yangyang Li, Vijayalakshmi Nandakumar, Xue F. Huang, Si-Yi Chen and Deruo Liu
Cancer Informatics 2015:14 83-93
Original Research | Published on 29 Jun 2015



High-Throughput Sequencing of miRNAs Reveals a Tissue Signature in Gastric Cancer and Suggests Novel Potential Biomarkers
Sylvain Darnet, Fabiano C Moreira, Igor G Hamoy, Rommel Burbano, André Khayat, Aline Cruz, Leandro Magalhães, Artur Silva, Sidney Santos, Samia Demachki, Monica Assumpção, Paulo Assumpção, and Ândrea Ribeiro-dos-Santos
Bioinformatics and Biology Insights 2015:Suppl. 1 1-8
Original Research | Published on 28 Jun 2015



MSL: A Measure to Evaluate Three-dimensional Patterns in Gene Expression Data
David Gutiérrez-Avilés and Cristina Rubio-Escudero
Evolutionary Bioinformatics 2015:11 121-135
Original Research | Published on 23 Jun 2015



RNA-seq Reveals Complicated Transcriptomic Responses to Drought Stress in a Nonmodel Tropic Plant, Bombax ceiba L.
Zhili Zhou, Huancheng Ma, Kevin Lin, Youjie Zhao, Yuan Chen, Zhi Xiong, Liuyang Wang and Bin Tian
Evolutionary Bioinformatics 2015:Suppl. 1 27-37
Original Research | Published on 23 Jun 2015



Time-Frequency Analysis of Peptide Microarray Data: Application to Brain Cancer Immunosignatures
Brian O'Donnell, Alexander Maurer, Antonia Papandreou-Suppappola and Phillip Stafford
Cancer Informatics 2015:Suppl. 2 219-233
Original Research | Published on 18 Jun 2015



MITOSCISSOR: A Useful Tool for Auto-Assembly of Mitogenomic Datasets in the Evolutionary Analysis of Fishes
Zheng Sun, Yuanzhi Cheng and Junbin Zhang
Evolutionary Bioinformatics 2015:11 115-120
Technical Advance | Published on 14 Jun 2015



Characterization of Plasmodium falciparum Proteome at Asexual Blood Stages for Screening of Effective Vaccine Candidates: An Immunoinformatics Approach
Satarudra Prakash Singh, Vishal Verma and Bhartendu Nath Mishra
Immunology and Immunogenetics Insights 2015:7 21-30
Original Research | Published on 14 Jun 2015



Managing Multi-center Flow Cytometry Data for Immune Monitoring
Scott White, Karoline Laske, Marij J.P. Welters, Nicole Bidmon, Sjoerd H. van der Burg, Cedrik M. Britten, Jennifer Enzor, Janet Staats, Kent J. Weinhold, Cécile Gouttefangeas and Cliburn Chan
Cancer Informatics 2014:Suppl. 7 111-122
Review | Published on 10 Jun 2015



A Proposed Paradigm Shift in Initializing Cancer Predictive Models with DCE-MRI Based PK Parameters: A Feasibility Study
Alexandros Roniotis, Mariam-Eleni Oraiopoulou, Eleftheria Tzamali, Eleftherios Kontopodis, Sofie Van Cauter, Vangelis Sakkalis, Kostas Marias
Cancer Informatics 2015:Suppl. 4 7-18
Original Research | Published on 10 Jun 2015



Bioinformatics Data Mining Approach Suggests Coexpression of AGTPBP1 with an ALS-linked Gene C9orf72
Shouta Kitano, Yoshihiro Kino, Yoji Yamamoto, Mika Takitani, Junko Miyoshi, Tsuyoshi Ishida, Yuko Saito, Kunimasa Arima and Jun-ichi Satoh
Journal of Central Nervous System Disease 2015:7 15-26
Original Research | Published on 08 Jun 2015



Gene Expression Signatures Based on Variability can Robustly Predict Tumor Progression and Prognosis
Wikum Dinalankara and Héctor Corrada Bravo
Cancer Informatics 2015:14 71-81
Original Research | Published on 07 Jun 2015



Powerful Tukey’s One Degree-of-Freedom Test for Detecting Gene–Gene and Gene–Environment Interactions
Yaping Wang, Donghui Li and Peng Wei
Cancer Informatics 2015:Suppl. 2 209-218
Review | Published on 04 Jun 2015



Penalized Ordinal Regression Methods for Predicting Stage of Cancer in High-Dimensional Covariate Spaces
Amanda Elswick Gentry, Colleen K. Jackson-Cook, Debra E. Lyon and Kellie J. Archer
Cancer Informatics 2015:Suppl. 2 201-208
Review | Published on 27 May 2015



Inferring Stable Acquisition Durations for Applications of Perfusion Imaging in Oncology
Brian P. Hobbs and Chaan S. Ng
Cancer Informatics 2015:Suppl. 2 193-199
Review | Published on 25 May 2015



Identifying CDKN3 Gene Expression as a Prognostic Biomarker in Lung Adenocarcinoma via Meta-analysis
Xiao Zang, Min Chen, Yunyun Zhou, Guanghua Xiao, Yang Xie, and Xinlei Wang
Cancer Informatics 2015:Suppl. 2 183-191
Original Research | Published on 24 May 2015



TRUFA: A User-Friendly Web Server for de novo RNA-seq Analysis Using Cluster Computing
Etienne Kornobis, Luis Cabellos, Fernando Aguilar, Cristina Frías-López, Julio Rozas, Jesús Marco and Rafael Zardoya
Evolutionary Bioinformatics 2015:11 97-104
Technical Advance | Published on 24 May 2015



A Hypothesis-Directed Approach to the Targeted Development of a Multiplexed Proteomic Biomarker Assay for Cancer
Emily M. Mackay, Jennifer Koppel, Pooja Das, Joanna Woo, David C. Schriemer and Oliver F. Bathe
Cancer Informatics 2015:14 65-70
Technical Advance | Published on 17 May 2015



Integrative Analyses of Cancer Data: A Review from a Statistical Perspective
Yingying Wei
Cancer Informatics 2015:Suppl. 2 173-181
Review | Published on 14 May 2015



Assessment of Weighted Quantile Sum Regression for Modeling Chemical Mixtures and Cancer Risk
Jenna Czarnota, Chris Gennings and David C. Wheeler
Cancer Informatics 2015:Suppl. 2 159-171
Review | Published on 13 May 2015



PathoQC: Computationally Efficient Read Preprocessing and Quality Control for High-Throughput Sequencing Data Sets
Changjin Hong, Solaiappan Manimaran and William Evan Johnson
Cancer Informatics 2014:Suppl. 1 167-176
Review | Published on 12 May 2015



The Standardized Histogram Shift of T2 Magnetic Resonance Image (MRI) Signal Intensities of Nephroblastoma Does Not Predict Histopathological Diagnostic Information
Sabine Müller, Ruslan David, Kostas Marias and Norbert Graf
Cancer Informatics 2015:Suppl. 4 1-5
Review | Published on 12 May 2015



Computational and in vitro Investigation of miRNA-Gene Regulations in Retinoblastoma Pathogenesis: miRNA Mimics Strategy
Nalini Venkatesan, Perinkulam Ravi Deepa, Vikas Khetan and Subramanian Krishnakumar
Bioinformatics and Biology Insights 2015:9 89-101
Original Research | Published on 12 May 2015



Recent Enhancements to the Genetic Risk Prediction Model BRCAPRO
Emanuele Mazzola, Amanda Blackford, Giovanni Parmigiani and Swati Biswas
Cancer Informatics 2015:Suppl. 2 147-157
Review | Published on 10 May 2015



Identifying Molecular Features Associated with Psychoneurological Symptoms in Women with Breast Cancer Using Multivariate Mixed Models
Qing Zhou, Colleen Jackson-Cook, Debra Lyon, Robert Perera and Kellie J. Archer
Cancer Informatics 2015:Suppl. 2 139-145
Original Research | Published on 07 May 2015



Evaluating Geographically Weighted Regression Models for Environmental Chemical Risk Analysis
Jenna Czarnota, David C. Wheeler and Chris Gennings
Cancer Informatics 2015:Suppl. 2 117-127
Original Research | Published on 05 May 2015



Prediction of Early Breast Cancer Metastasis from DNA Microarray Data Using High-Dimensional Cox Regression Models
Christophe Zemmour, François Bertucci, Pascal Finetti, Bernard Chetrit, Daniel Birnbaum, Thomas Filleron and Jean-Marie Boher
Cancer Informatics 2015:Suppl. 2 129-138
Original Research | Published on 05 May 2015



Metagenomics: Tools and Insights for Analyzing Next-Generation Sequencing Data Derived from Biodiversity Studies
Anastasis Oulas, Christina Pavloudi, Paraskevi Polymenakou, Georgios A. Pavlopoulos, Nikolas Papanikolaou, Georgios Kotoulas, Christos Arvanitidis and Ioannis Iliopoulos
Bioinformatics and Biology Insights 2015:9 75-88
Review | Published on 05 May 2015



Generalized Monotone Incremental Forward Stagewise Method for Modeling Count Data: Application Predicting Micronuclei Frequency
Mateusz Makowski and Kellie J. Archer
Cancer Informatics 2015:Suppl. 2 97-105
Review | Published on 29 Apr 2015



Evaluation of the Performance of Smoothing Functions in Generalized Additive Models for Spatial Variation in Disease
Umaporn Siangphoe and David C. Wheeler
Cancer Informatics 2015:Suppl. 2 107-116
Review | Published on 29 Apr 2015



Roles of Solvent Accessibility and Gene Expression in Modeling Protein Sequence Evolution
Kuangyu Wang, Shuhui Yu, Xiang Ji, Clemens Lakner, Alexander Griffing and Jeffrey L. Thorne
Evolutionary Bioinformatics 2015:11 85-96
Original Research | Published on 29 Apr 2015



Next Generation Distributed Computing for Cancer Research
Pankaj Agarwal and Kouros Owzar
Cancer Informatics 2014:Suppl. 7 97-109
Review | Published on 27 Apr 2015



Selecting Spatial Scale of Covariates in Regression Models of Environmental Exposures
Lauren P. Grant, Chris Gennings and David C. Wheeler
Cancer Informatics 2015:Suppl. 2 81-96
Review | Published on 27 Apr 2015



BIR Pipeline for Preparation of Phylogenomic Data
Surendra Kumar, Anders K. Krabberød, Ralf S. Neumann, Katerina Michalickova, Sen Zhao, Xiaoli Zhang and Kamran Shalchian-Tabrizi
Evolutionary Bioinformatics 2015:11 79-83
Methodology | Published on 27 Apr 2015



BioMiner: Paving the Way for Personalized Medicine
Chris Bauer, Karol Stec, Alexander Glintschert, Kristina Gruden, Christian Schichor, Michal Or-Guil, Joachim Selbig and Johannes Schuchhardt
Cancer Informatics 2015:14 55-63
Technical Advance | Published on 20 Apr 2015



Profiling Age-Related Epigenetic Markers of Stomach Adenocarcinoma in Young and Old Subjects
Byoung-Chul Kim, Hyoung Oh Jeong, Daeui Park, Chul-Hong Kim, Eun Kyeong Lee, Dae Hyun Kim, Eunok Im, Nam Deuk Kim, Sunghoon Lee, Byung Pal Yu, Jong Bhak and Hae Young Chung
Cancer Informatics 2015:14 47-54
Original Research | Published on 20 Apr 2015



Computing Molecular Signatures as Optima of a Bi-Objective Function: Method and Application to Prediction in Oncogenomics
Vincent Gardeux, Rachid Chelouah, Maria F. Barbosa Wanderley, Patrick Siarry, Antônio P. Braga, Fabien Reyal, Roman Rouzier, Lajos Pusztai and René Natowicz
Cancer Informatics 2015:14 33-45
Methodology | Published on 19 Apr 2015



Catchment Area Analysis Using Bayesian Regression Modeling
Aobo Wang and David C. Wheeler
Cancer Informatics 2015:Suppl. 2 71-79
Review | Published on 19 Apr 2015



Cross-Disciplinary Detection and Analysis of Network Motifs
Ngoc Tam L. Tran, Luke DeLuccia, Aidan F. McDonald and Chun-Hsi Huang
Bioinformatics and Biology Insights 2015:9 49-60
Original Research | Published on 19 Apr 2015



CNL Disease Resistance Genes in Soybean and Their Evolutionary Divergence
Madhav P. Nepal and Benjamin V. Benson
Evolutionary Bioinformatics 2015:11 49-63
Original Research | Published on 07 Apr 2015



Synonymous Codon Usage Bias in the Plastid Genome is Unrelated to Gene Structure and Shows Evolutionary Heterogeneity
Yueying Qi, Wenjing Xu, Tian Xing, Mingming Zhao, Nana Li, Li Yan, Guangmin Xia and Mengcheng Wang
Evolutionary Bioinformatics 2015:11 65-77
Original Research | Published on 07 Apr 2015



RNA-Seq and Network Analysis Revealed Interacting Pathways in TGF-β-Treated Lung Cancer Cell Lines
Yan Li, Omid Rouhi, Hankui Chen, Rolando Ramirez, Jeffrey A. Borgia and Youping Deng
Cancer Informatics 2014:Suppl. 5 129-140
Review | Published on 01 Apr 2015



Prioritization of Cancer-Related Genomic Variants by SNP Association Network
Changning Liu and Zhenyu Xuan
Cancer Informatics 2015:Suppl. 2 57-70
Review | Published on 01 Apr 2015



Some Correlates of Electronic Health Information Management System Success in Nigerian Teaching Hospitals
Adebowale I. Ojo and Sunday O. Popoola
Biomedical Informatics Insights 2015:7 1-9
Original Research | Published on 01 Apr 2015



Expression of Polarity Genes in Human Cancer
Wan-Hsin Lin, Yan W. Asmann and Panos Z. Anastasiadis
Cancer Informatics 2015:Suppl. 3 15-28
Original Research | Published on 30 Mar 2015



Design and Implementation of a Comprehensive Web-based Survey for Ovarian Cancer Survivorship with an Analysis of Prediagnosis Symptoms via Text Mining
Jiayang Sun, Kath M. Bogie, Joe Teagno, Yu-Hsiang (Sam) Sun, Rebecca R. Carter, Licong Cui and Guo-Qiang Zhang
Cancer Informatics 2014:Suppl. 3 113-123
Review | Published on 23 Mar 2015



HCsnip: An R Package for Semi-supervised Snipping of the Hierarchical Clustering Tree
Askar Obulkasim and Mark A. van de Wiel
Cancer Informatics 2015:14 1-19
Software or database review | Published on 22 Mar 2015



Case-Based Retrieval Framework for Gene Expression Data
Ali Anaissi, Madhu Goyal, Daniel R. Catchpoole, Ali Braytee and Paul J. Kennedy
Cancer Informatics 2015:14 21-31
Methodology | Published on 19 Mar 2015



GeneMed: An Informatics Hub for the Coordination of Next-Generation Sequencing Studies that Support Precision Oncology Clinical Trials
Yingdong Zhao, Eric C. Polley, Ming-Chung Li, Chih-Jian Lih, Alida Palmisano, David J. Sims, Lawrence V. Rubinstein, Barbara A. Conley, Alice P. Chen, P. Mickey Williams, Shivaani Kummar, James H. Doroshow and Richard M. Simon
Cancer Informatics 2015:Suppl. 2 45-55
Review | Published on 19 Mar 2015



A RESTful API for Access to Phylogenetic Tools via the CIPRES Science Gateway
Mark A. Miller, Terri Schwartz, Brett E. Pickett, Sherry He, Edward B. Klem, Richard H. Scheuermann, Maria Passarotti, Seth Kaufman and Maureen A. O’Leary
Evolutionary Bioinformatics 2015:11 43-48
Software or database review | Published on 16 Mar 2015



Introductory Editorial: Network and Pathway Analysis of Cancer Susceptibility (A)
Nancy Guo, Russell S. Schwartz, Jiang Qian, Peilin Jia, Youping Deng
Cancer Informatics 2014:Suppl. 5 125-127
Editorial | Published on 12 Mar 2015



IVisTMSA: Interactive Visual Tools for Multiple Sequence Alignments
Muhammad Tariq Pervez, Masroor Ellahi Babar, Asif Nadeem, Naeem Aslam, Nasir Naveed, Sarfraz Ahmad, Shah Muhammad, Salman Qadri, Muhammad Shahid, Tanveer Hussain and Maryam Javed
Evolutionary Bioinformatics 2015:11 35-42
Software or database review | Published on 12 Mar 2015



Extensive Genomic Variability of Knops Blood Group Polymorphisms Is Associated with Sickle Cell Disease in Africa
Kimberley C. Duru, Jenelle A. Noble, Aldiouma Guindo, Li Yi, Ikhide G. Imumorin, Dapa A. Diallo and Bolaji N. Thomas
Evolutionary Bioinformatics 2015:11 25-33
Original Research | Published on 09 Mar 2015



A Systems Biology Approach Reveals the Dose- and Time-Dependent Effect of Primary Human Airway Epithelium Tissue Culture After Exposure to Cigarette Smoke In Vitro
Carole Mathis, Stephan Gebel, Carine Poussin, Vincenzo Belcastro, Alain Sewer, Dirk Weisensee, Arnd Hengstermann, Sam Ansari, Sandra Wagner, Manuel C. Peitsch and Julia Hoeng
Bioinformatics and Biology Insights 2015:9 19-35
Original Research | Published on 09 Mar 2015



Identification of Medium-Sized Copy Number Alterations in Whole-Genome Sequencing
Hatice Gulcin Ozer, Aisulu Usubalieva, Adrienne Dorrance, Ayse Selen Yilmaz, Michael Caligiuri, Guido Marcucci and Kun Huang
Cancer Informatics 2014:Suppl. 3 105-111
Review | Published on 05 Mar 2015



Introductory Editorial: Sequencing Platform Modeling and Analysis
Li-Xuan Qin and Yen-Tsung Huang
Cancer Informatics 2015:Suppl. 1 55-56
Editorial | Published on 02 Mar 2015



Modeling Discrete Survival Time Using Genomic Feature Data
Kyle Ferber and Kellie J. Archer
Cancer Informatics 2015:Suppl. 2 37-43
Review | Published on 02 Mar 2015



Comprehensive Evaluation of Composite Gene Features in Cancer Outcome Prediction
Dezhi Hou and Mehmet Koyutürk
Cancer Informatics 2014:Suppl. 3 93-104
Methodology | Published on 24 Feb 2015



What Tumor Dynamics Modeling Can Teach us About Exploiting the Stem-Cell View for Better Cancer Treatment
Roger S. Day
Cancer Informatics 2015:Suppl. 2 25-36
Review | Published on 24 Feb 2015



Apparent microRNA-Target-specific Histone Modification in Mammalian Spermatogenesis
Y-H Taguchi
Evolutionary Bioinformatics 2015:Suppl. 1 13-26
Original Research | Published on 24 Feb 2015



A Novel Approach to Identify Candidate Prognostic Factors for Hepatitis C Treatment Response Integrating Clinical and Viral Genetic Data
Alicia Amadoz and Fernando González-Candelas
Evolutionary Bioinformatics 2015:11 15-24
Methodology | Published on 23 Feb 2015



Network Analysis of Circular Permutations in Multidomain Proteins Reveals Functional Linkages for Uncharacterized Proteins
Donald Adjeroh, Yue Jiang, Bing-Hua Jiang and Jie Lin
Cancer Informatics 2014:Suppl. 5 109-124
Methodology | Published on 19 Feb 2015



Introductory Editorial: Array Platform Modeling and Analysis (A)
Li-Xuan Qin, Shuangge Ma, Yen-Tsung Huang, Hui Zhang, Hongyuan Cao
Cancer Informatics 2014:Suppl. 4 91-93
Editorial | Published on 17 Feb 2015



Mapping Splicing Quantitative Trait Loci in RNA-Seq
Cheng Jia, Yu Hu, Yichuan Liu and Mingyao Li
Cancer Informatics 2015:Suppl. 1 45-53
Original Research | Published on 16 Feb 2015



Toolbox for Mobile-Element Insertion Detection on Cancer Genomes
Wan-Ping Lee, Jiantao Wu, and Gabor T. Marth
Cancer Informatics 2015:Suppl. 1 37-44
Methodology | Published on 12 Feb 2015



windex: Analyzing Convergent Evolution Using the Wheatsheaf Index in R
Kevin Arbuckle and Amanda Minter
Evolutionary Bioinformatics 2015:11 11-14
Short Report | Published on 12 Feb 2015



Extending Information Retrieval Methods to Personalized Genomic-Based Studies of Disease
Shuyun Ye, John A. Dawson and Christina Kendziorski
Cancer Informatics 2014:Suppl. 7 85-95
Review | Published on 10 Feb 2015



Evaluating Methods for Modeling Epistasis Networks with Application to Head and Neck Cancer
Rajesh Talluri and Sanjay Shete
Cancer Informatics 2015:Suppl. 2 17-23
Review | Published on 10 Feb 2015



An Improved Version of Logistic Bayesian LASSO for Detecting Rare Haplotype-Environment Interactions with Application to Lung Cancer
Yuan Zhang and Swati Biswas
Cancer Informatics 2015:Suppl. 2 11-16
Review | Published on 09 Feb 2015



Regulation of Epithelial-Mesenchymal Transition in Breast Cancer Cells by Cell Contact and Adhesion
Magdalena A. Cichon, Celeste M. Nelson, and Derek C. Radisky
Cancer Informatics 2015:Suppl. 3 1-13
Review | Published on 09 Feb 2015 | Video abstract



Identification and Expression Analysis of Ribosome Biogenesis Factor Co-orthologs in Solanum lycopersicum
Stefan Simm, Sotirios Fragkostefanakis, Puneet Paul, Mario Keller, Jens Einloft, Klaus-Dieter Scharf and  Enrico Schleiff
Bioinformatics and Biology Insights 2015:9 1-17
Original Research | Published on 09 Feb 2015



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



Classification of Metagenomics Data at Lower Taxonomic Level Using a Robust Supervised Classifier
Tao Hou, Fu Liu, Yun Liu, Qing Yu Zou, Xiao Zhang and Ke Wang
Evolutionary Bioinformatics 2015:11 3-10
Methodology | 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



Genome-Wide Characterization of miRNAs Involved in N Gene-Mediated Immunity in Response to Tobacco Mosaic Virus in Nicotiana benthamiana
Kangquan Yin, Yang Tang and Jinping Zhao
Evolutionary Bioinformatics 2015:Suppl. 1 1-11
Original Research | Published on 07 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



Computational Analysis Reveals a Successive Adaptation of Multiple Inositol Polyphosphate Phosphatase 1 in Higher Organisms Through Evolution
Surya P. Kilaparty, Awantika Singh, William H. Baltosser and Nawab Ali
Evolutionary Bioinformatics 2014:10 239-250
Original Research | Published on 22 Dec 2014



POEAS: Automated Plant Phenomic Analysis Using Plant Ontology
Khader Shameer, Mahantesha BN Naika, Oommen K. Mathew, and Ramanathan Sowdhamini
Bioinformatics and Biology Insights 2014:8 209-214
Original Research | Published on 21 Dec 2014



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



In Silico Detection of Virulence Gene Homologues in the Human Pathogen Sphingomonas Spp.
Amr T. M. Saeb, Satish Kumar David and Hissa Al-Brahim
Evolutionary Bioinformatics 2014:10 229-238
Original Research | Published on 11 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



Functional Implications of RNA Splicing for Human Long Intergenic Noncoding RNAs
Feng-Chi Chen, Chia-Lin Pan and Hsuan-Yu Lin
Evolutionary Bioinformatics 2014:10 219-228
Original Research | 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



Genome-wide Analysis of Mycoplasma hominis for the Identification of Putative Therapeutic Targets
Md. Masud Parvege, Monzilur Rahman and Mohammad Shahnoor Hossain
Drug Target Insights 2014:8 51-62
Original Research | 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



Evaluating the Accuracy and Efficiency of Multiple Sequence Alignment Methods
Muhammad Tariq Pervez, Masroor Ellahi Babar, Asif Nadeem, Muhammad Aslam, Ali Raza Awan, Naeem Aslam, Tanveer Hussain, Nasir Naveed, Salman Qadri, Usman Waheed and Muhammad Shoaib
Evolutionary Bioinformatics 2014:10 205-217
Original Research | 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



SWAMP: Sliding Window Alignment Masker for PAML
Peter W. Harrison, Gregory E. Jordan and Stephen H. Montgomery
Evolutionary Bioinformatics 2014:10 197-204
Technical Advance | Published on 01 Dec 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



Evaluative Profiling of Arsenic Sensing and Regulatory Systems in the Human Microbiome Project Genomes
Raphael D. Isokpehi, Udensi K. Udensi, Shaneka S. Simmons, Antoinesha L. Hollman, Antia E. Cain, Samson A. Olofinsae, Oluwabukola A. Hassan, Zainab A. Kashim, Ojochenemi A. Enejoh, Deborah E. Fasesan and Oyekanmi Nashiru
Microbiology Insights 2014:7 25-34
Original Research | Published on 11 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



Evolutionary Analysis and Prediction of Peptide Vaccine Candidates for Foot-and-Mouth-Disease Virus Types A and O in Bangladesh
Samina Momtaz, Arafat Rahman, Munawar Sultana and M. Anwar Hossain
Evolutionary Bioinformatics 2014:10 187-196
Original Research | Published on 03 Nov 2014




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