Results 1-150 of 525 for Genomics

Phenotypic and Genotypic Characteristics of Small Colony Variants and Their Role in Chronic Infection
Benjamin E. Johns, Kevin J. Purdy, Nicholas P. Tucker and Sarah E. Maddocks
Microbiology Insights 2015:8 15-23
Review | Published on 22 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

Aberrant Expression of Cyclin D1 in Cancer
Kazushi Inoue and Elizabeth A. Fry
Signal Transduction Insights 2015:4 1-13
Review | Published on 20 Sep 2015

Distribution of Angiotensin-1 Converting Enzyme Insertion/Deletion and α-Actinin-3 Codon 577 Polymorphisms in Turkish Male Soccer Players
Korkut Ulucan, Canan Sercan and Türker Biyikli
Genetics & Epigenetics 2015:7 1-4
Original Research | 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

tRNA-Derived Short Non-coding RNA as Interacting Partners of Argonaute Proteins
Megumi Shigematsu and Yohei Kirino
Gene Regulation and Systems Biology 2015:9 27-33
Review | Published on 10 Sep 2015 | Highly accessed (previous month)

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

BRAF Mutation in Colorectal Cancer: An Update
David Barras
Biomarkers in Cancer 2015:Suppl. 1 9-12
Review | Published on 06 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

Mutations in Breast Cancer Exome Sequences Predict Susceptibility to Infections and Converge on the Same Signaling Pathways
Bernard Friedenson
Journal of Genomes and Exomes 2015:4 1-28
Original Research | Published on 26 Aug 2015

Histopathological Features of Non-Neoplastic Breast Parenchyma Do Not Predict BRCA Mutation Status of Patients with Invasive Breast Cancer
Soley Bayraktar, Hongming Qiu, Diane Liu, Yu Shen, Angelica M. Gutierrez-Barrera, Banu K. Arun and Aysegul A. Sahin
Biomarkers in Cancer 2015:7 39-49
Original Research | Published on 18 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

Class III Receptor Tyrosine Kinases in Acute Leukemia – Biological Functions and Modern Laboratory Analysis
Rimma Berenstein
Biomarker Insights 2015:Suppl. 3 1-14
Review | Published on 05 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

Analysis of Lung Flute–collected Sputum for Lung Cancer Diagnosis
Jian Su, Nigar Anjuman, Maria A. Guarnera, Howard Zhang, Sanford A. Stass and Feng Jiang
Biomarker Insights 2015:10 55-61
Original Research | Published on 04 Aug 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

DNA Sequence Signatures for Rapid Detection of Six Target Bacterial Pathogens Using PCR Assays
Kenjiro Nagamine, Guo-Chiuan Hung, Bingjie Li and Shyh-Ching Lo
Microbiology Insights 2015:8 7-14
Original Research | Published on 23 Jul 2015

Molecular Heterogeneity in Primary Breast Carcinomas and Axillary Lymph Node Metastases Assessed by Genomic Fingerprinting Analysis
Rachel E. Ellsworth, Allyson L. Toro, Heather L. Blackburn, Alisha Decewicz, Brenda Deyarmin, Kimberly A. Mamula, Nicholas S. Costantino, Jeffrey A. Hooke, Craig D. Shriver and Darrell L. Ellsworth
Cancer Growth and Metastasis 2015:8 15-24
Original Research | Published on 20 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

Single and Multiple Gene Manipulations in Mouse Models of Human Cancer
Heather L. Lehman and Douglas B. Stairs
Cancer Growth and Metastasis 2015:Suppl. 1 1-15
Review | Published on 13 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

A Genetical Genomics Methodology to Identify Genetic Markers of a Bovine Fertility Phenotype Based on CYP19A1 Gene Expression
Nicolas Guillemin, Isabelle Dufort and Marc-André Sirard
Gene Expression to Genetical Genomics 2015:8 9-18
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

Elevated Expression of the Testis-specific Gene WBP2NL in Breast Cancer
Seyedmehdi Nourashrafeddin, Mehdi Dianatpour, Mahmoud Aarabi, Maryam Beigom Mobasheri, Golnesa Kazemi-oula and Mohammad Hossein Modarressi
Biomarkers in Cancer 2015:7 19-24
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

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

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

Molecular Evolutionary Analysis of β-Defensin Peptides in Vertebrates
Jianbo Tu, Diyan Li, Qingqing Li, Long Zhang, Qing Zhu, Uma Gaur, Xiaolan Fan, Huailiang Xu, Yongfang Yao, Xiaoling Zhao and Mingyao Yang
Evolutionary Bioinformatics 2015:11 105-114
Original Research | Published on 01 Jun 2015

p53 Contributes to Differentiating Gene Expression Following Exposure to Acetaminophen and Its Less Hepatotoxic Regioisomer Both In Vitro and In Vivo
Brendan D. Stamper, Michael L. Garcia, Duy Q. Nguyen, Richard P. Beyer, Theo K. Bammler, Frederico M. Farin, Terrance J. Kavanagh and Sidney D. Nelson
Gene Regulation and Systems Biology 2015:9 1-14
Original Research | Published on 01 Jun 2015 | Video abstract

Examination of Single Nucleotide Polymorphisms in Acetylcholine Receptors in Chronic Fatigue Syndrome Patients
Sonya Marshall-Gradisnik, Peter Smith, Bernd Nilius and Donald R. Staines
Immunology and Immunogenetics Insights 2015:7 7-20
Original Research | Published on 26 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

Transcriptome Analysis of Minimal Residual Disease in Subtypes of Pediatric B Cell Acute Lymphoblastic Leukemia
Jitsuda Sitthi-amorn, Betty Herrington, Gail Megason, Jeanette Pullen, Catherine Gordon, Shirley Hogan, Tejaswi Koganti and Chindo Hicks
Clinical Medicine Insights: Oncology 2015:9 51-60
Original Research | Published on 24 May 2015

A Comprehensive Profile of ChIP-Seq-Based Olig2 Target Genes in Motor Neuron Progenitor Cells Suggests the Possible Involvement of Olig2 in the Pathogenesis of Amyotrophic Lateral Sclerosis
Jun-ichi Satoh, Naohiro Asahina, Shouta Kitano and Yoshihiro Kino
Journal of Central Nervous System Disease 2015:7 1-14
Original Research | Published on 18 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

Association of Common Variations on Chromosome 4q25 and Left Atrial Volume in Patients with Atrial Fibrillation
Yuliya Mints, Hirad Yarmohammadi, Irfan M. Khurram, Hana Hoyt, Rozann Hansford, Stefan L. Zimmerman, Steven J. Steinberg, Daniel P. Judge, Gordon F. Tomaselli, Hugh Calkins, Vadim Zipunnikov and Saman Nazarian
Clinical Medicine Insights: Cardiology 2015:9 39-45
Original Research | 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

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

Examination of Single Nucleotide Polymorphisms (SNPs) in Transient Receptor Potential (TRP) Ion Channels in Chronic Fatigue Syndrome Patients
Sonya M. Marshall-Gradisnik, Peter Smith, Ekua W. Brenu, Bernd Nilius, Sandra B. Ramos and Donald R. Staines
Immunology and Immunogenetics Insights 2015:7 1-6
Original Research | Published on 10 May 2015

Polymorphism in Variable Number of Tandem Repeats of Dopamine D4 Gene Is a Genetic Risk Factor in Attention Deficit Hyperactive Egyptian Children: Pilot Study
Ola Shahin, Nagwa A. Meguid, Omnia Raafat, Reham M. Dawood, Malak Doss, Noha G. Bader el Din and Mostafa K. El Awady
Biomarker Insights 2015:10 33-38
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

Changes in Whole Blood Gene Expression after Computed Tomography in Children: A Pilot Study
Brunhild M. Halm, Maarit Tiirikainen, Jennifer F. Lai, Ian Pagano, Robert V. Cooney and Adrian A. Franke
Gene Expression to Genetical Genomics 2015:8 1-8
Original Research | Published on 05 May 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

Reverse enGENEering of Regulatory Networks from Big Data: A Roadmap for Biologists
Xiaoxi Dong, Anatoly Yambartsev, Stephen A. Ramsey, Lina D Thomas, Natalia Shulzhenko and Andrey Morgun
Bioinformatics and Biology Insights 2015:9 61-74
Review | Published on 29 Apr 2015

Genetics of Interstitial Lung Disease: Vol de Nuit (Night Flight)
Hiroshi Furukawa, Shomi Oka, Kota Shimada, Naoyuki Tsuchiya and Shigeto Tohma
Clinical Medicine Insights: Circulatory, Respiratory and Pulmonary Medicine 2015:Suppl. 1 1-7
Review | 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

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

Functions of Peroxisome Proliferator-Activated Receptor Gamma (PPARγ) in Gynecologic Disorders
Ping Ren, Yuquan Zhang, Yan Huang, Yingli Yang, and Ming Jiang
Clinical Medicine Insights: Oncology 2015:9 43-49
Review | 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

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

MicroRNA-Seq Data Analysis Pipeline to Identify Blood Biomarkers for Alzheimer's Disease from Public Data
Jun-ichi Satoh, Yoshihiro Kino and Shumpei Niida
Biomarker Insights 2015:10 21-31
Original Research | Published on 15 Apr 2015

Genomic Analysis of the BMP Family in Glioblastomas
Laura D. Hover, Ty W. Abel and Philip Owens
Translational Oncogenomics 2015:7 1-9
Consise Review | Published on 15 Apr 2015

An Interpretation of the Ancestral Codon from Miller's Amino Acids and Nucleotide Correlations in Modern Coding Sequences
Nicolas Carels and Miguel Ponce de Leon
Bioinformatics and Biology Insights 2015:9 37-47
Original Research | Published on 15 Apr 2015

Gene Delivery Strategies to Promote Spinal Cord Repair
Christopher M. Walthers and Stephanie K. Seidlits
Biomarker Insights 2015:Suppl. 1 11-29
Review | Published on 09 Apr 2015

Altered Sirtuin 7 Expression is Associated with Early Stage Breast Cancer
Ahmad Aljada, Ayman M. Saleh, Moath Alkathiri, Heba Bani Shamsa, Ahmad Al-Bawab and Amre Nasr
Breast Cancer: Basic and Clinical Research 2015:9 3-8
Original Research | Published on 09 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

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

Ad-REIC Gene Therapy: Promising Results in a Patient with Metastatic CRPC Following Chemotherapy
Hiromi Kumon, Katsumi Sasaki, Yuichi Ariyoshi, Takuya Sadahira, Shin Ebara, Takao Hiraki, Susumu Kanazawa, Hiroyuki Yanai, Masami Watanabe and Yasutomo Nasu
Clinical Medicine Insights: Oncology 2015:9 31-38
Case report | Published on 23 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

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

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

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

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

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

Carbonic Anhydrase II Deficiency in a Saudi Woman
Omar N. Alhuzaim, Ohoud M. Almohareb and Safiya M. Sherbeeni
Clinical Medicine Insights: Case Reports 2015:8 7-10
Case report | 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

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

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

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

A Hypothetical Protein of Alteromonas macleodii AltDE1 (amad1_06475) Predicted to be a Cold-Shock Protein with RNA Chaperone Activity
Arafat Rahman Oany, Shah Adil Ishtiyaq Ahmad, KM Kaderi Kibria, Mohammad Uzzal Hossain and Tahmina Pervin Jyoti
Gene Regulation and Systems Biology 2014:8 141-147
Original Research | Published on 18 Dec 2014

Clinicians' Expectations for Gene-Driven Cancer Therapy
Antti Jekunen
Clinical Medicine Insights: Oncology 2014:8 159-164
Review | Published on 18 Dec 2014

Correction to Reference Numbers in: “Many Breast Cancer Mutations Parallel Mutations in Known Viral Cancers”
Bernard Friedenson
Journal of Genomes and Exomes 2014:3 37-37
Correction | 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

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

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

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

A Comprehensive Profile of ChIP-Seq-Based PU.1/Spi1 Target Genes in Microglia
Jun-ichi Satoh, Naohiro Asahina, Shouta Kitano and Yoshihiro Kino
Gene Regulation and Systems Biology 2014:8 127-139
Original Research | Published on 08 Dec 2014

A Role for the Cavin-3/Matrix Metalloproteinase-9 Signaling Axis in the Regulation of PMA-Activated Human HT1080 Fibrosarcoma Cell Neoplastic Phenotype
Chirine Toufaily, Cyndia Charfi, Bayader Annabi and Borhane Annabi
Cancer Growth and Metastasis 2014:7 43-51
Original Research | 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

The Use of Pharmacogenomics for Selection of Therapy in Non-Small-Cell Lung Cancer
Nagla A. Karim, Hai Bui, Peterson Pathrose, Sandra Starnes, Ninad Patil, Mahmoud Shehata, Ahmed Mostafa, MB Rao, Ahmad Zarzour and Marshall Anderson
Clinical Medicine Insights: Oncology 2014:8 139-144
Original Research | Published on 07 Dec 2014

Allele and Genotype Distributions of DNA Repair Gene Polymorphisms in South Indian Healthy Population
Katiboina Srinivasa Rao, Abialbon Paul, Annan Sudarsan Arun Kumar, Gurusamy Umamaheswaran, Biswajit Dubashi, Karunanithi Gunaseelan and Steven Aibor Dkhar
Biomarkers in Cancer 2014:6 29-35
Original Research | Published on 07 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

Evidence for the Influence of the Iron Regulatory MHC Class I Molecule HFE on Tumor Progression in Experimental Models and Clinical Populations
Cody Weston and James Connor
Translational Oncogenomics 2014:6 1-12
Review | 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

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

Genetic Diversity and Allelic Frequency of Glutamate-Rich Protein (GLURP) in Plasmodium falciparum Isolates from Sub-Saharan Africa
Kimberley C. Duru and Bolaji N. Thomas
Microbiology Insights 2014:7 35-39
Short Report | 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

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

Cellular Responses to Cytosolic Double-stranded RNA—The Role of the Inflammasome
Adi Idris
Immunology and Immunogenetics Insights 2014:6 7-11
Consise 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

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

Cloning and Expression Profiling of the Polycomb Gene, Retinoblastoma-related Protein from Tomato Solanum lycopersicum L.
Zainab M. Almutairi and Monther T. Sadder
Evolutionary Bioinformatics 2014:10 177-185
Original Research | Published on 23 Oct 2014

Comparative Study on Sequence–Structure–Function Relationship of the Human Short-chain Dehydrogenases/Reductases Protein Family
Nu Thi Ngoc Tang and Ly Le
Evolutionary Bioinformatics 2014:10 165-176
Original Research | 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

Toolbox for Mobile-Element Insertion Detection on Cancer Genomes
Wan-Ping Lee, Jiantao Wu and Gabor T. Marth
Cancer Informatics 2014:Suppl. 4 45-52
Methodology | Published on 15 Oct 2014

Mapping Splicing Quantitative Trait Loci in RNA-Seq
Cheng Jia, Yu Hu, Yichuan Liu and Mingyao Li
Cancer Informatics 2014:Suppl. 4 35-43
Original Research | Published on 15 Oct 2014

TEGS-CN: A Statistical Method for Pathway Analysis of Genome-wide Copy Number Profile
Yen-Tsung Huang, Thomas Hsu and David C. Christiani
Cancer Informatics 2014:Suppl. 4 15-23
Original Research | Published on 15 Oct 2014

Unsupervised Outlier Profile Analysis
Debashis Ghosh and Song Li
Cancer Informatics 2014:Suppl. 4 25-33
Review | Published on 15 Oct 2014

CORM: An R Package Implementing the Clustering of Regression Models Method for Gene Clustering
Jiejun Shi and Li-Xuan Qin
Cancer Informatics 2014:Suppl. 4 11-13
Review | Published on 15 Oct 2014

Profiling the microRNA Expression in Human iPS and iPS-derived Retinal Pigment Epithelium
Heuy-Ching Wang, Whitney A. Greene, Ramesh R. Kaini, Jane Shen-Gunther, Hung-I H Chen, Hong Cai and Yufeng Wang
Cancer Informatics 2014:Suppl. 5 25-35
Review | Published on 15 Oct 2014

Master Regulators, Regulatory Networks, and Pathways of Glioblastoma Subtypes
Serdar Bozdag, Aiguo Li, Mehmet Baysan, and Howard A. Fine
Cancer Informatics 2014:Suppl. 3 33-44
Original Research | Published on 15 Oct 2014

Network-based Prediction of Cancer under Genetic Storm
Ahmet Ay, Dihong Gong, Tamer Kahveci
Cancer Informatics 2014:Suppl. 3 15-31
Original Research | Published on 15 Oct 2014

Quality Control for RNA-Seq (QuaCRS): An Integrated Quality Control Pipeline
Karl W. Kroll, Nima E. Mokaram, Alexander R. Pelletier, David E. Frankhouser, Maximillian S. Westphal, Paige A. Stump, Cameron L. Stump, Ralf Bundschuh, James S. Blachly and Pearlly Yan
Cancer Informatics 2014:Suppl. 3 7-14
Review | Published on 15 Oct 2014

Hereditary Breast Cancer: Clinical, Pathological and Molecular Characteristics
Martin J. Larsen, Mads Thomassen, Anne-Marie Gerdes and Torben A. Kruse
Breast Cancer: Basic and Clinical Research 2014:8 145-155
Review | Published on 15 Oct 2014

Prediction of MicroRNA Precursors Using Parsimonious Feature Sets
Petra Stepanowsky, Eric Levy, Jihoon Kim, Xiaoqian Jiang and Lucila Ohno-Machado
Cancer Informatics 2014:Suppl. 1 95-102
Review | Published on 14 Oct 2014

Integrated DNA Copy Number and Gene Expression Regulatory Network Analysis of Non-small Cell Lung Cancer Metastasis
Seyed M. Iranmanesh and Nancy L. Guo
Cancer Informatics 2014:Suppl. 5 13-23
Original Research | Published on 14 Oct 2014

CSNK1A1 and Gli2 as Novel Targets Identified Through an Integrative Analysis of Gene Expression Data, Protein-Protein Interaction and Pathways Networks in Glioblastoma Tumors: Can These Two Be Antagonistic Proteins?
Seema Mishra
Cancer Informatics 2014:13 93-108
Original Research | Published on 13 Oct 2014

Text Mining in Cancer Gene and Pathway Prioritization
Yuan Luo, Gregory Riedlinger and Peter Szolovits
Cancer Informatics 2014:Suppl. 1 69-79
Review | Published on 13 Oct 2014

Modeling Signal Transduction from Protein Phosphorylation to Gene Expression
Chunhui Cai, Lujia Chen, Xia Jiang and Xinghua Lu
Cancer Informatics 2014:Suppl. 1 59-67
Review | Published on 13 Oct 2014

RNAseqPS: A Web Tool for Estimating Sample Size and Power for RNAseq Experiment
Yan Guo, Shilin Zhao, Chung-I Li, Quanhu Sheng and Yu Shyr
Cancer Informatics 2014:Suppl. 6 1-5
Review | Published on 13 Oct 2014

Optogenetic Control of Apoptosis in Targeted Tissues of Xenopus laevis Embryos
Kyle Jewhurst, Michael Levin and Kelly A. McLaughlin
Journal of Cell Death 2014:7 25-31
Methodology | Published on 13 Oct 2014

Many Breast Cancer Mutations Parallel Mutations in Known Viral Cancers
Bernard Friedenson
Journal of Genomes and Exomes 2014:3 17-35
Original Research | Published on 13 Oct 2014

RAD51B Activity and Cell Cycle Regulation in Response to DNA Damage in Breast Cancer Cell Lines
Phoebe S. Lee, Jun Fang, Lea Jessop, Timothy Myers, Preethi Raj, Nan Hu, Chaoyu Wang, Philip R. Taylor, Jianjun Wang, Javed Khan, Maria Jasin and Stephen J. Chanock
Breast Cancer: Basic and Clinical Research 2014:8 135-144
Original Research | Published on 12 Oct 2014

Bayesian Disease Classification Using Copy Number Data
Subharup Guha, Yuan Ji, and Veerabhadran Baladandayuthapani
Cancer Informatics 2014:Suppl. 2 83-91
Review | Published on 01 Oct 2014

Computational Methods for CLIP-seq Data Processing
Paula H. Reyes-Herrera and Elisa Ficarra
Bioinformatics and Biology Insights 2014:8 199-207
Review | Published on 01 Oct 2014

The Comparative Genomics and Phylogenomics of Leishmania amazonensis Parasite
Diogo A Tschoeke, Gisele L Nunes, Rodrigo Jardim, Joana Lima, Aline SR Dumaresq, Monete R Gomes, Leandro de Mattos Pereira, Daniel R Loureiro, Patricia H Stoco, Herbert Leonel de Matos Guedes, Antonio Basilio de Miranda, Jeronimo Ruiz, André Pitaluga, Floriano P Silva Jr, Christian M Probst, Nicholas J Dickens, Jeremy C Mottram, Edmundo C Grisard and Alberto MR Dávila
Evolutionary Bioinformatics 2014:10 131-153
Original Research | Published on 23 Sep 2014

Chronic Lymphocytic Leukemia with t(14;18)(q32;q21) As a Sole Cytogenetic Abnormality
Ghaleb Elyamany, Kamal Fadalla, Hatem Elghezal, Omar Alsuhaibani, Hani Osman and Abdulaziz Al-Abulaaly
Clinical Medicine Insights: Pathology 2014:7 21-27
Original Research | Published on 23 Sep 2014

Introductory Editorial: Classification, Predictive Modelling, and Statistical Analysis of Cancer Data (A)
Hongmei Jiang, Lingling An, Veerabhadran Baladandayuthapani, Paul Livermore Auer
Cancer Informatics 2014:Suppl. 2 1-3
Editorial | Published on 21 Sep 2014