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  1. 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
  2. Prostate tumor heterogeneity is a major factor in disease management. Heterogeneity could be due to multiple cancer cell types with distinct gene expression. Of clinical importance is the so-called cancer stem...

    Authors: Laura E Pascal, Ricardo ZN Vêncio, Robert L Vessella, Carol B Ware, Eneida F Vêncio, Gareth Denyer and Alvin Y Liu
    Citation: BMC Medical Genomics 2011 4:46
  3. Bladder cancer is the sixth most common cancer in the world and the incidence is particularly high in southwestern Taiwan. Previous studies have identified several tumor-related genes that are hypermethylated ...

    Authors: Pi-Che Chen, Ming-Hsuan Tsai, Sidney KH Yip, Yeong-Chin Jou, Chi-Fai Ng, Yanning Chen, Xiaoling Wang, Wei Huang, Chun-Liang Tung, Gary CW Chen, Martin MS Huang, Joanna HM Tong, Eing-Ju Song, De-Ching Chang, Cheng-Da Hsu, Ka-Fai To…
    Citation: BMC Medical Genomics 2011 4:45
  4. Cancer is a disease of genome alterations that arise through the acquisition of multiple somatic DNA sequence mutations. Some of these mutations can be critical for the development of a tumor and can be useful...

    Authors: Jan Küntzer, Daniela Maisel, Hans-Peter Lenhof, Stefan Klostermann and Helmut Burtscher
    Citation: BMC Medical Genomics 2011 4:43
  5. Recent studies have identified thousands of sense-antisense gene pairs across different genomes by computational mapping of cDNA sequences. These studies have shown that approximately 25% of all transcriptiona...

    Authors: Rintaro Saito, Keisuke Kohno, Yuki Okada, Yuko Osada, Koji Numata, Chihiro Kohama, Kazufumi Watanabe, Hajime Nakaoka, Naoyuki Yamamoto, Akio Kanai, Hiroshi Yasue, Soichiro Murata, Kuniya Abe, Masaru Tomita, Nobuhiro Ohkohchi and Hidenori Kiyosawa
    Citation: BMC Medical Genomics 2011 4:42
  6. The zebrafish is recognized as a versatile cancer and drug screening model. However, it is not known whether the estrogen-responsive genes and signaling pathways that are involved in estrogen-dependent carcino...

    Authors: Siew Hong Lam, Serene GP Lee, Chin Y Lin, Jane S Thomsen, Pan Y Fu, Karuturi RK Murthy, Haixia Li, Kunde R Govindarajan, Lin CH Nick, Guillaume Bourque, Zhiyuan Gong, Thomas Lufkin, Edison T Liu and Sinnakaruppan Mathavan
    Citation: BMC Medical Genomics 2011 4:41
  7. Diabetic retinopathy (DR) is a leading cause of blindness in working age adults. Approximately 95% of patients with Type 1 diabetes develop some degree of retinopathy within 25 years of diagnosis despite norma...

    Authors: Georgina V Bixler, Heather D VanGuilder, Robert M Brucklacher, Scot R Kimball, Sarah K Bronson and Willard M Freeman
    Citation: BMC Medical Genomics 2011 4:40
  8. The gene CHEK2 encodes a checkpoint kinase playing a key role in the DNA damage pathway. Though CHEK2 has been identified as an intermediate breast cancer susceptibility gene, only a small proportion of high-risk...

    Authors: Tú Nguyen-Dumont, Lars P Jordheim, Jocelyne Michelon, Nathalie Forey, Sandrine McKay-Chopin, Olga Sinilnikova, Florence Le Calvez-Kelm, Melissa C Southey, Sean V Tavtigian and Fabienne Lesueur
    Citation: BMC Medical Genomics 2011 4:39
  9. Traditional Chinese Medicine (TCM) has been used for thousands of years to treat or prevent diseases, including cancer. Good manufacturing practices (GMP) and sophisticated product analysis (PhytomicsQC) to en...

    Authors: Ena Wang, Scott Bussom, Jinguo Chen, Courtney Quinn, Davide Bedognetti, Wing Lam, Fulan Guan, Zaoli Jiang, Yichao Mark, Yingdong Zhao, David F Stroncek, Jeffrey White, Francesco M Marincola and Yung-Chi Cheng
    Citation: BMC Medical Genomics 2011 4:38
  10. Recent observations point towards the existence of a large number of neighborhoods composed of functionally-related gene modules that lie together in the genome. This local component in the distribution of the...

    Authors: Eva Alloza, Fátima Al-Shahrour, Juan C Cigudosa and Joaquín Dopazo
    Citation: BMC Medical Genomics 2011 4:37
  11. Myostatin is a potent muscle growth inhibitor that belongs to the Transforming Growth Factor-β (TGF-β) family. Mutations leading to non functional myostatin have been associated with hypermuscularity in severa...

    Authors: Dwi U Kemaladewi, Willem MH Hoogaars, Sandra H van Heiningen, Samuel Terlouw, David JJ de Gorter, Johan T den Dunnen, Gert Jan B van Ommen, Annemieke Aartsma-Rus, Peter ten Dijke and Peter AC 't Hoen
    Citation: BMC Medical Genomics 2011 4:36
  12. Neuroblastoma (NB) tumors are well known for their pronounced clinical and molecular heterogeneity. The global gene expression and DNA copy number alterations have been shown to have profound differences in tu...

    Authors: Xiang Guo, Qing-Rong Chen, Young K Song, Jun S Wei and Javed Khan
    Citation: BMC Medical Genomics 2011 4:35
  13. 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
  14. Cancer shows a great diversity in its clinical behavior which cannot be easily predicted using the currently available clinical or pathological markers. The identification of pathways associated with lymph nod...

    Authors: Anna EL Coló, Ana CQ Simoes, André L Carvalho, Camila M Melo, Lucas Fahham, Luiz P Kowalski, Fernando A Soares, Eduardo J Neves, Luiz FL Reis and Alex F Carvalho
    Citation: BMC Medical Genomics 2011 4:33
  15. 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
  16. Several DNA microarray based expression signatures for the different clinically relevant thyroid tumor entities have been described over the past few years. However, reproducibility of these signatures is gene...

    Authors: Klemens Vierlinger, Markus H Mansfeld, Oskar Koperek, Christa Nöhammer, Klaus Kaserer and Friedrich Leisch
    Citation: BMC Medical Genomics 2011 4:30
  17. Postmenopausal hormone therapy (HT) influences endogenous hormone concentrations and increases the risk of breast cancer. Gene expression profiling may reveal the mechanisms behind this relationship.

    Authors: Marit Waaseth, Karina S Olsen, Charlotta Rylander, Eiliv Lund and Vanessa Dumeaux
    Citation: BMC Medical Genomics 2011 4:29
  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
  19. Diagnostic accuracy of lymphoma, a heterogeneous cancer, is essential for patient management. Several ancillary tests including immunophenotyping, and sometimes cytogenetics and PCR are required to aid histolo...

    Authors: To Ha Loi, Anna Campain, Adam Bryant, Tim J Molloy, Mark Lutherborrow, Jennifer Turner, Yee Hwa Jean Yang and David DF Ma
    Citation: BMC Medical Genomics 2011 4:27
  20. Alterations in gene expression in peripheral blood cells have been shown to be sensitive to the presence and extent of coronary artery disease (CAD). A non-invasive blood test that could reliably assess obstru...

    Authors: Michael R Elashoff, James A Wingrove, Philip Beineke, Susan E Daniels, Whittemore G Tingley, Steven Rosenberg, Szilard Voros, William E Kraus, Geoffrey S Ginsburg, Robert S Schwartz, Stephen G Ellis, Naheem Tahirkheli, Ron Waksman, John McPherson, Alexandra J Lansky and Eric J Topol
    Citation: BMC Medical Genomics 2011 4:26
  21. Clinical laboratories are adopting array genomic hybridization as a standard clinical test. A number of whole genome array genomic hybridization platforms are available, but little is known about their compara...

    Authors: Tracy Tucker, Alexandre Montpetit, David Chai, Susanna Chan, Sébastien Chénier, Bradley P Coe, Allen Delaney, Patrice Eydoux, Wan L Lam, Sylvie Langlois, Emmanuelle Lemyre, Marco Marra, Hong Qian, Guy A Rouleau, David Vincent, Jacques L Michaud…
    Citation: BMC Medical Genomics 2011 4:25
  22. Proteomic technologies applied for profiling human biofluids and blood cells are considered to reveal new biomarkers of exposure or provide insights into novel mechanisms of adaptation.

    Authors: Freek G Bouwman, Baukje de Roos, Isabel Rubio-Aliaga, L Katie Crosley, Susan J Duthie, Claus Mayer, Graham Horgan, Abigael C Polley, Carolin Heim, Susan LM Coort, Chris T Evelo, Francis Mulholland, Ian T Johnson, Ruan M Elliott, Hannelore Daniel and Edwin CM Mariman
    Citation: BMC Medical Genomics 2011 4:24
  23. An understanding of the relation of commensal microbiota to health is essential in preventing disease. Here we studied the oral microbial composition of children (N = 74, aged 3 - 18 years) in natural transiti...

    Authors: Wim Crielaard, Egija Zaura, Annemarie A Schuller, Susan M Huse, Roy C Montijn and Bart JF Keijser
    Citation: BMC Medical Genomics 2011 4:22
  24. 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
  25. The vascular disease in-stent restenosis (ISR) is characterized by formation of neointima and adverse inward remodeling of the artery after injury by coronary stent implantation. We hypothesized that the analy...

    Authors: Santhi K Ganesh, Jungnam Joo, Kimberly Skelding, Laxmi Mehta, Gang Zheng, Kathleen O'Neill, Eric M Billings, Anna Helgadottir, Karl Andersen, Gudmundur Thorgeirsson, Thorarinn Gudnason, Nancy L Geller, Robert D Simari, David R Holmes, William W O'Neill and Elizabeth G Nabel
    Citation: BMC Medical Genomics 2011 4:20
  26. Myelodysplastic Syndromes (MDSS) are pre-leukemic disorders with increasing incident rates worldwide, but very limited treatment options. Little is known about small regulatory RNAs and how they contribute to ...

    Authors: Dominik Beck, Steve Ayers, Jianguo Wen, Miriam B Brandl, Tuan D Pham, Paul Webb, Chung-Che Chang and Xiaobo Zhou
    Citation: BMC Medical Genomics 2011 4:19
  27. Paclitaxel is a microtubule-stabilizing drug that has been commonly used in treating cancer. Due to genetic heterogeneity within patient populations, therapeutic response rates often vary. Here we used the NCI...

    Authors: Lawson Eng, Irada Ibrahim-zada, Hamdi Jarjanazi, Sevtap Savas, Mehran Meschian, Kathleen I Pritchard and Hilmi Ozcelik
    Citation: BMC Medical Genomics 2011 4:18
  28. Uric acid is the primary byproduct of purine metabolism. Hyperuricemia is associated with body mass index (BMI), sex, and multiple complex diseases including gout, hypertension (HTN), renal disease, and type 2 di...

    Authors: Bashira A Charles, Daniel Shriner, Ayo Doumatey, Guanjie Chen, Jie Zhou, Hanxia Huang, Alan Herbert, Norman P Gerry, Michael F Christman, Adebowale Adeyemo and Charles N Rotimi
    Citation: BMC Medical Genomics 2011 4:17
  29. Molecular alterations critical to development of cancer include mutations, copy number alterations (amplifications and deletions) as well as genomic rearrangements resulting in gene fusions. Massively parallel...

    Authors: Ewa Przybytkowski, Cristiano Ferrario and Mark Basik
    Citation: BMC Medical Genomics 2011 4:16
  30. 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
  31. 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
  32. The eMERGE (electronic MEdical Records and GEnomics) Network is an NHGRI-supported consortium of five institutions to explore the utility of DNA repositories coupled to Electronic Medical Record (EMR) systems ...

    Authors: Catherine A McCarty, Rex L Chisholm, Christopher G Chute, Iftikhar J Kullo, Gail P Jarvik, Eric B Larson, Rongling Li, Daniel R Masys, Marylyn D Ritchie, Dan M Roden, Jeffery P Struewing and Wendy A Wolf
    Citation: BMC Medical Genomics 2011 4:13
  33. Readthrough fusions across adjacent genes in the genome, or transcription-induced chimeras (TICs), have been estimated using expressed sequence tag (EST) libraries to involve 4-6% of all genes. Deep transcript...

    Authors: Serban Nacu, Wenlin Yuan, Zhengyan Kan, Deepali Bhatt, Celina Sanchez Rivers, Jeremy Stinson, Brock A Peters, Zora Modrusan, Kenneth Jung, Somasekar Seshagiri and Thomas D Wu
    Citation: BMC Medical Genomics 2011 4:11
  34. 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
  35. Colon cancer has been classically described by clinicopathologic features that permit the prediction of outcome only after surgical resection and staging.

    Authors: Andre Loboda, Michael V Nebozhyn, James W Watters, Carolyne A Buser, Peter Martin Shaw, Pearl S Huang, Laura Van't Veer, Rob AEM Tollenaar, David B Jackson, Deepak Agrawal, Hongyue Dai and Timothy J Yeatman
    Citation: BMC Medical Genomics 2011 4:9
  36. The molecular pathways involved in the interstitial lung diseases (ILDs) are poorly understood. Systems biology approaches, with global expression data sets, were used to identify perturbed gene networks, to g...

    Authors: Ji-Hoon Cho, Richard Gelinas, Kai Wang, Alton Etheridge, Melissa G Piper, Kara Batte, Duaa Dakhlallah, Jennifer Price, Dan Bornman, Shile Zhang, Clay Marsh and David Galas
    Citation: BMC Medical Genomics 2011 4:8
  37. Infection with H. pylori is important in the etiology of gastric cancer. Gastric cancer is infrequent in Africa, despite high frequencies of H. pylori infection, referred to as the African enigma. Variation in en...

    Authors: Tineke E Buffart, Melanie Louw, Nicole CT van Grieken, Marianne Tijssen, Beatriz Carvalho, Bauke Ylstra, Heike Grabsch, Chris JJ Mulder, Cornelis JH van de Velde, Schalk W van der Merwe and Gerrit A Meijer
    Citation: BMC Medical Genomics 2011 4:7
  38. 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
  39. Aortic root diameter is a clinically relevant trait due to its known relationship with the pathogenesis of aortic regurgitation and risk for aortic dissection. African Americans are an understudied population ...

    Authors: Nathan E Wineinger, Amit Patki, Kristin J Meyers, Ulrich Broeckel, Charles C Gu, DC Rao, Richard B Devereux, Donna K Arnett and Hemant K Tiwari
    Citation: BMC Medical Genomics 2011 4:4
  40. Multiple breast cancer gene expression profiles have been developed that appear to provide similar abilities to predict outcome and may outperform clinical-pathologic criteria; however, the extent to which see...

    Authors: Cheng Fan, Aleix Prat, Joel S Parker, Yufeng Liu, Lisa A Carey, Melissa A Troester and Charles M Perou
    Citation: BMC Medical Genomics 2011 4:3
  41. Tetralogy of Fallot (TOF) is the most commonly observed conotruncal congenital heart defect. Treatment of these patients has evolved dramatically in the last few decades, yet a genetic explanation is lacking f...

    Authors: Douglas C Bittel, Merlin G Butler, Nataliya Kibiryeva, Jennifer A Marshall, Jie Chen, Gary K Lofland and James E O'Brien Jr
    Citation: BMC Medical Genomics 2011 4:1
  42. The onset of birth in humans, like other apes, differs from non-primate mammals in its endocrine physiology. We hypothesize that higher primate-specific gene evolution may lead to these differences and target ...

    Authors: Jevon Plunkett, Scott Doniger, Thomas Morgan, Ritva Haataja, Mikko Hallman, Hilkka Puttonen, Ramkumar Menon, Edward Kuczynski, Errol Norwitz, Victoria Snegovskikh, Aarno Palotie, Leena Peltonen, Vineta Fellman, Emily A DeFranco, Bimal P Chaudhari, John Oates…
    Citation: BMC Medical Genomics 2010 3:62
  43. Obesity results from an imbalance between food intake and energy expenditure, which leads to an excess of adipose tissue. The excess of adipose tissue and adipocyte dysfunction associated with obesity are link...

    Authors: Sara Rodríguez-Acebes, Nuria Palacios, José I Botella-Carretero, Nuria Olea, Lorena Crespo, Roberto Peromingo, Diego Gómez-Coronado, Miguel A Lasunción, Clotilde Vázquez and Javier Martínez-Botas
    Citation: BMC Medical Genomics 2010 3:61
  44. The cDNA-mediated Annealing, extension, Selection and Ligation (DASL) assay has become a suitable gene expression profiling system for degraded RNA from paraffin-embedded tissue. We examined assay characteristics...

    Authors: Monica M Reinholz, Jeanette E Eckel-Passow, S Keith Anderson, Yan W Asmann, Michael A Zschunke, Ann L Oberg, Ann E McCullough, Amylou C Dueck, Beiyun Chen, Craig S April, Eliza Wickham-Garcia, Robert B Jenkins, Julie M Cunningham, Jin Jen, Edith A Perez, Jian-Bing Fan…
    Citation: BMC Medical Genomics 2010 3:60

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