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Bioinformatic and algorithmical studies

Section edited by Youping Deng

This section considers studies on the development, refinement and application of novel computational and statistical methods for the analysis of genetic and genomic data for the study of human health and disease, as well as the application of population genetic approaches.

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  1. The identification of genes involved in human complex diseases remains a great challenge in computational systems biology. Although methods have been developed to use disease phenotypic similarities with a pro...

    Authors: Yong Chen, Xuebing Wu and Rui Jiang

    Citation: BMC Medical Genomics 2013 6:57

    Content type: Research article

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  2. Colorectal cancer is the third leading cause of cancer deaths in the United States. The initial assessment of colorectal cancer involves clinical staging that takes into account the extent of primary tumor inv...

    Authors: HoJoon Lee, Patrick Flaherty and Hanlee P Ji

    Citation: BMC Medical Genomics 2013 6:54

    Content type: Research article

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  3. Neurodegenerative diseases (NDs) are characterized by the progressive loss of neurons in the human brain. Although the majority of NDs are sporadic, evidence is accumulating that they have a strong genetic com...

    Authors: Dokyun Na, Mushfiqur Rouf, Cahir J O’Kane, David C Rubinsztein and Jörg Gsponer

    Citation: BMC Medical Genomics 2013 6:52

    Content type: Database

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  4. Decades of research strongly suggest that the genetic etiology of autism spectrum disorders (ASDs) is heterogeneous. However, most published studies focus on group differences between cases and controls. In co...

    Authors: Malcolm G Campbell, Isaac S Kohane and Sek Won Kong

    Citation: BMC Medical Genomics 2013 6:34

    Content type: Research article

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  5. Neutrophil antigens are involved in a variety of clinical conditions including transfusion-related acute lung injury (TRALI) and other transfusion-related diseases. Recently, there are five characterized group...

    Authors: Hsueh-Ting Chu, Han Lin, Theresa Tsun-Hui Tsao, Chun-Fan Chang, William WL Hsiao, Tze-Jung Yeh, Ching-Mao Chang, Yen-Wenn Liu, Tse-Yi Wang, Ko-Chun Yang, Tsung-Jui Chen, Jen-Chih Chen, Kuang-Chi Chen and Cheng-Yan Kao

    Citation: BMC Medical Genomics 2013 6:31

    Content type: Software

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  6. The accumulation of somatic mutations in genes and molecular pathways is a major factor in the evolution of oral squamous cell carcinoma (OSCC), which sparks studies to identify somatic mutations with clinical...

    Authors: Qu Zhang, Jun Zhang, Hong Jin and Sitong Sheng

    Citation: BMC Medical Genomics 2013 6:28

    Content type: Research article

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  7. Alternative exon usage (AEU) is an important component of gene regulation. Exon expression platforms allow the detection of associations between AEU and phenotypes such as cancer. Numerous studies have identif...

    Authors: Ahmed Sadeque, Nicola VL Serão, Bruce R Southey, Kristin R Delfino and Sandra L Rodriguez-Zas

    Citation: BMC Medical Genomics 2012 5:59

    Content type: Research article

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  8. Being able to visualize multivariate biological treatment effects can be insightful. However the axes in visualizations are often solely defined by variation and thus have no biological meaning. This makes the...

    Authors: Jildau Bouwman, Jack TWE Vogels, Suzan Wopereis, Carina M Rubingh, Sabina Bijlsma and Ben van Ommen

    Citation: BMC Medical Genomics 2012 5:1

    Content type: Research article

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  9. Genome-wide methylation profiling has led to more comprehensive insights into gene regulation mechanisms and potential therapeutic targets. Illumina Human Methylation BeadChip is one of the most commonly used ...

    Authors: Zhifu Sun, High Seng Chai, Yanhong Wu, Wendy M White, Krishna V Donkena, Christopher J Klein, Vesna D Garovic, Terry M Therneau and Jean-Pierre A Kocher

    Citation: BMC Medical Genomics 2011 4:84

    Content type: Research article

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  10. Until recently, genome-wide association studies (GWAS) have been restricted to research groups with the budget necessary to genotype hundreds, if not thousands, of samples. Replacing individual genotyping with...

    Authors: Madalene A Earp, Maziar Rahmani, Kevin Chew and Angela Brooks-Wilson

    Citation: BMC Medical Genomics 2011 4:81

    Content type: Research article

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  11. The accurate diagnosis of idiopathic pulmonary fibrosis (IPF) is a major clinical challenge. We developed a model to diagnose IPF by applying Bayesian probit regression (BPR) modelling to gene expression profi...

    Authors: Eric B Meltzer, William T Barry, Thomas A D'Amico, Robert D Davis, Shu S Lin, Mark W Onaitis, Lake D Morrison, Thomas A Sporn, Mark P Steele and Paul W Noble

    Citation: BMC Medical Genomics 2011 4:70

    Content type: Research article

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  12. Incidence of hepatitis C virus (HCV) induced hepatocellular carcinoma (HCC) has been increasing in the United States and Europe during recent years. Although HCV-associated HCC shares many pathological charact...

    Authors: Siyuan Zheng, William P Tansey, Scott W Hiebert and Zhongming Zhao

    Citation: BMC Medical Genomics 2011 4:62

    Content type: Research article

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  13. A molecular characterization of Alzheimer's Disease (AD) is the key to the identification of altered gene sets that lead to AD progression. We rely on the assumption that candidate marker genes for a given dis...

    Authors: Margherita Squillario and Annalisa Barla

    Citation: BMC Medical Genomics 2011 4:55

    Content type: Research article

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  14. Cancer cells are characterized by massive dysegulation of physiological cell functions with considerable disruption of transcriptional regulation. Genome-wide transcriptome profiling can be utilized for early ...

    Authors: Markus Krupp, Thorsten Maass, Jens U Marquardt, Frank Staib, Tobias Bauer, Rainer König, Stefan Biesterfeld, Peter R Galle, Achim Tresch and Andreas Teufel

    Citation: BMC Medical Genomics 2011 4:53

    Content type: Research article

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  15. Copy number variants (CNV) are a potentially important component of the genetic contribution to risk of common complex diseases. Analysis of the association between CNVs and disease requires that uncertainty i...

    Authors: Isaac Subirana, Ramon Diaz-Uriarte, Gavin Lucas and Juan R Gonzalez

    Citation: BMC Medical Genomics 2011 4:47

    Content type: Software

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  16. Assays of multiple tumor samples frequently reveal recurrent genomic aberrations, including point mutations and copy-number alterations, that affect individual genes. Analyses that extend beyond single genes a...

    Authors: Christopher A Miller, Stephen H Settle, Erik P Sulman, Kenneth D Aldape and Aleksandar Milosavljevic

    Citation: BMC Medical Genomics 2011 4:34

    Content type: Research article

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  17. Comparative Genomic Hybridization (CGH) is a molecular approach for detecting DNA Copy Number Alterations (CNAs) in tumor, which are among the key causes of tumorigenesis. However in the post-genomic era, most...

    Authors: Huimin Geng, Javeed Iqbal, Wing C Chan and Hesham H Ali

    Citation: BMC Medical Genomics 2011 4:32

    Content type: Research article

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  18. The immune contribution to cancer progression is complex and difficult to characterize. For example in tumors, immune gene expression is detected from the combination of normal, tumor and immune cells in the t...

    Authors: Trevor Clancy, Marco Pedicini, Filippo Castiglione, Daniele Santoni, Vegard Nygaard, Timothy J Lavelle, Mikael Benson and Eivind Hovig

    Citation: BMC Medical Genomics 2011 4:28

    Content type: Research article

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  19. Copy number alterations (CNA) play a key role in cancer development and progression. Since more than one CNA can be detected in most tumors, frequently co-occurring genetic CNA may point to cooperating cancer ...

    Authors: Nitin Kumar, Hubert Rehrauer, Haoyang Cai and Michael Baudis

    Citation: BMC Medical Genomics 2011 4:21

    Content type: Research article

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  20. In the post-genomic era, multi-faceted research on complex disorders such as autism has generated diverse types of molecular information related to its pathogenesis. The rapid accumulation of putative candidat...

    Authors: Ajay Kumar, Rachna Wadhawan, Catherine Croft Swanwick, Ravi Kollu, Saumyendra N Basu and Sharmila Banerjee-Basu

    Citation: BMC Medical Genomics 2011 4:15

    Content type: Database

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  21. Genomic instability in cancer leads to abnormal genome copy number alterations (CNA) as a mechanism underlying tumorigenesis. Using microarrays and other technologies, tumor CNA are detected by comparing tumor...

    Authors: Alex Lisovich, Uma R Chandran, Maureen A Lyons-Weiler, William A LaFramboise, Ashley R Brown, Regina I Jakacki, Ian F Pollack and Robert W Sobol

    Citation: BMC Medical Genomics 2011 4:14

    Content type: Software

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  22. Molecular classification of tumors can be achieved by global gene expression profiling. Most machine learning classification algorithms furnish global error rates for the entire population. A few algorithms pr...

    Authors: Lee K Jones, Fei Zou, Alexander Kheifets, Konstantin Rybnikov, Damon Berry and Aik Choon Tan

    Citation: BMC Medical Genomics 2011 4:10

    Content type: Research article

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  23. In cancer prognosis studies with gene expression measurements, an important goal is to construct gene signatures with predictive power. In this study, we describe the coordination among genes using the weighte...

    Authors: Shuangge Ma, Michael R Kosorok, Jian Huang and Ying Dai

    Citation: BMC Medical Genomics 2011 4:5

    Content type: Research article

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  24. The nuclear transcription factor estrogen receptor alpha (ER-alpha) is the target of several antiestrogen therapeutic agents for breast cancer. However, many ER-alpha positive patients do not respond to these ...

    Authors: Jaesik Jeong, Lang Li, Yunlong Liu, Kenneth P Nephew, Tim Hui-Ming Huang and Changyu Shen

    Citation: BMC Medical Genomics 2010 3:55

    Content type: Research article

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  25. The advent of gene expression profiling was expected to dramatically improve cancer diagnosis. However, despite intensive efforts and several successful examples, the development of profile-based diagnostic sy...

    Authors: Satoru Kawarazaki, Kazuya Taniguchi, Mitsuaki Shirahata, Yoji Kukita, Manabu Kanemoto, Nobuhiro Mikuni, Nobuo Hashimoto, Susumu Miyamoto, Jun A Takahashi and Kikuya Kato

    Citation: BMC Medical Genomics 2010 3:52

    Content type: Technical advance

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  26. Despite extensive research, the details of the biological mechanisms by which cancer cells acquire motility and invasiveness are largely unknown. This study identifies an invasion associated gene signature she...

    Authors: Hoon Kim, John Watkinson, Vinay Varadan and Dimitris Anastassiou

    Citation: BMC Medical Genomics 2010 3:51

    Content type: Research article

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  27. Reactive oxygen species (ROS) are known mediators of cellular damage in multiple diseases including diabetic complications. Despite its importance, no comprehensive database is currently available for the gene...

    Authors: Junguk Hur, Kelli A Sullivan, Adam D Schuyler, Yu Hong, Manjusha Pande, David J States, H V Jagadish and Eva L Feldman

    Citation: BMC Medical Genomics 2010 3:49

    Content type: Research article

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