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Prognostics and diagnostics/biomarkers

This section considers studies on the use of genomic markers to diagnose, classify, or predict the risk or prognosis of human disease or genetic disorders as well as the analysis of the structure and function of genes and chromosomes and the role of genetic mutations and cytogenetic changes in human genetic disorders.

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  1. Unexpected cholestasis substantially contributes to drug failure in clinical trials. Current models used for safety assessment in drug development do not accurately predict cholestasis in humans. Therefore, it...

    Authors: Ewa Szalowska, Geert Stoopen, Maria J Groot, Peter JM Hendriksen and Ad ACM Peijnenburg

    Citation: BMC Medical Genomics 2013 6:39

    Content type: Research article

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  2. Differential diagnosis between malignant follicular thyroid cancer (FTC) and benign follicular thyroid adenoma (FTA) is a great challenge for even an experienced pathologist and requires special effort. Molecu...

    Authors: Aleksandra Pfeifer, Bartosz Wojtas, Malgorzata Oczko-Wojciechowska, Aleksandra Kukulska, Agnieszka Czarniecka, Markus Eszlinger, Thomas Musholt, Tomasz Stokowy, Michal Swierniak, Ewa Stobiecka, Dagmara Rusinek, Tomasz Tyszkiewicz, Monika Kowal, Michal Jarzab, Steffen Hauptmann, Dariusz Lange…

    Citation: BMC Medical Genomics 2013 6:38

    Content type: Research article

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  3. Pancreatic cancer is a highly lethal cancer with limited diagnostic and therapeutic modalities.

    Authors: Jinping Jia, Hemang Parikh, Wenming Xiao, Jason W Hoskins, Holger Pflicke, Xuelu Liu, Irene Collins, Weiyin Zhou, Zhaoming Wang, John Powell, Snorri S Thorgeirsson, Udo Rudloff, Gloria M Petersen and Laufey T Amundadottir

    Citation: BMC Medical Genomics 2013 6:33

    Content type: Research article

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  4. Currently, diagnosis of affected individuals with rare genetic disorders can be lengthy and costly, resulting in a diagnostic odyssey and in many patients a definitive molecular diagnosis is never achieved des...

    Authors: Darrell L Dinwiddie, Sarah E Soden, Carol J Saunders, Neil A Miller, Emily G Farrow, Laurie D Smith and Stephen F Kingsmore

    Citation: BMC Medical Genomics 2013 6:32

    Content type: Case report

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  5. Small nucleolar RNAs (snoRNAs) and small Cajal body-specific RNAs are non-coding RNAs involved in the maturation of other RNA molecules. Alterations of sno/scaRNA expression may play a role in cancerogenesis. ...

    Authors: Domenica Ronchetti, Laura Mosca, Giovanna Cutrona, Giacomo Tuana, Massimo Gentile, Sonia Fabris, Luca Agnelli, Gabriella Ciceri, Serena Matis, Carlotta Massucco, Monica Colombo, Daniele Reverberi, Anna Grazia Recchia, Sabrina Bossio, Massimo Negrini, Pierfrancesco Tassone…

    Citation: BMC Medical Genomics 2013 6:27

    Content type: Research article

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  6. It is suspected that early gastric carcinoma (GC) is a dormant variant that rarely progresses to advanced GC. We demonstrated that the dormant and aggressive variants of tubular adenocarcinomas (TUBs) of the s...

    Authors: Ayano Sonoda, Ken-ichi Mukaisho, Takahisa Nakayama, Vo Thi Ngoc Diem, Takanori Hattori, Akira Andoh, Yoshihide Fujiyama and Hiroyuki Sugihara

    Citation: BMC Medical Genomics 2013 6:25

    Content type: Research article

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  7. In order to identify miRNAs expression profiling from genome-wide screen for diagnosis of acute myocardial infarction (AMI) and angina pectoris (AP), we investigated the altered profile of serum microRNAs in A...

    Authors: Chunjian Li, Zhijuan Fang, Ting Jiang, Qiu Zhang, Chao Liu, Chenyu Zhang and Yang Xiang

    Citation: BMC Medical Genomics 2013 6:16

    Content type: Research article

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  8. Colorectal cancer (CRC) is a heterogeneous and biologically poorly understood disease. To tailor CRC treatment, it is essential to first model this heterogeneity by defining subtypes of patients with homogeneo...

    Authors: Andreas Schlicker, Garry Beran, Christine M Chresta, Gael McWalter, Alison Pritchard, Susie Weston, Sarah Runswick, Sara Davenport, Kerry Heathcote, Denis Alferez Castro, George Orphanides, Tim French and Lodewyk FA Wessels

    Citation: BMC Medical Genomics 2012 5:66

    Content type: Research article

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  9. Chronic obstructive pulmonary disease (COPD) is influenced by both environmental and genetic factors. Few gene studies of the Chinese population have focused on COPD. We investigated candidate genes associated...

    Authors: Yi Guo, Yi Gong, Chunming Pan, Yanrong Qian, Guochao Shi, Qijian Cheng, Qingyun Li, Lei Ren, Qiuling Weng, Yi Chen, Ting Cheng, Liang Fan, Zhihong Jiang and Huanying Wan

    Citation: BMC Medical Genomics 2012 5:64

    Content type: Research article

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  10. Smoking is the leading cause of preventable death worldwide and has been shown to increase the risk of multiple diseases including coronary artery disease (CAD). We sought to identify genes whose levels of exp...

    Authors: Philip Beineke, Karen Fitch, Heng Tao, Michael R Elashoff, Steven Rosenberg, William E Kraus and James A Wingrove

    Citation: BMC Medical Genomics 2012 5:58

    Content type: Research article

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  11. Despite entering complete remission after primary treatment, a substantial proportion of patients with early stage breast cancer will develop metastases. Prediction of such an outcome remains challenging despi...

    Authors: Françoise Bonnet, Mickael Guedj, Natalie Jones, Sana Sfar, Véronique Brouste, Nabila Elarouci, Guillaume Banneau, Béatrice Orsetti, Charlotte Primois, Christine Tunon de Lara, Marc Debled, Isabelle de Mascarel, Charles Theillet, Nicolas Sévenet, Aurélien de Reynies, Gaëtan MacGrogan…

    Citation: BMC Medical Genomics 2012 5:54

    Content type: Research article

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  12. Leukocyte infiltration plays an important role in the pathogenesis and progression of myositis, and is highly associated with disease severity. Currently, there is a lack of: efficacious therapies for myositis...

    Authors: Wei Zhu, Katie Streicher, Nan Shen, Brandon W Higgs, Chris Morehouse, Lydia Greenlees, Anthony A Amato, Koustubh Ranade, Laura Richman, David Fiorentino, Bahija Jallal, Steven A Greenberg and Yihong Yao

    Citation: BMC Medical Genomics 2012 5:53

    Content type: Research article

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  13. The purpose of this study is to assess the predictive accuracy of a multi-gene predictor of response to docetaxel, 5-fluorouracil, epirubicin and cyclophosphamide combination chemotherapy on gene expression da...

    Authors: Kui Shen, Yuan Qi, Nan Song, Chunqiao Tian, Shara D Rice, Michael J Gabrin, Stacey L Brower, William Fraser Symmans, Joyce A O’Shaughnessy, Frankie A Holmes, Lina Asmar and Lajos Pusztai

    Citation: BMC Medical Genomics 2012 5:51

    Content type: Research article

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  14. Aortopathies are a group of disorders characterized by aneurysms, dilation, and tortuosity of the aorta. Because of the phenotypic overlap and genetic heterogeneity of diseases featuring aortopathy, molecular ...

    Authors: Whitney L Wooderchak-Donahue, Brendan O’Fallon, Larissa V Furtado, Jacob D Durtschi, Parker Plant, Perry G Ridge, Alan F Rope, Angela T Yetman and Pinar Bayrak-Toydemir

    Citation: BMC Medical Genomics 2012 5:50

    Content type: Research article

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  15. Inattentiveness, impulsivity and hyperactivity are the primary behaviors associated with attention-deficit hyperactivity disorder (ADHD). Previous studies showed that peripheral blood gene expression signature...

    Authors: Yingfang Tian, Boryana Stamova, Bradley P Ander, Glen C Jickling, Joan R Gunther, Blythe A Corbett, Netty GP Bos-Veneman, Pieter J Hoekstra, Julie B Schweitzer and Frank R Sharp

    Citation: BMC Medical Genomics 2012 5:49

    Content type: Research article

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  16. Many methodologies have been used in research to identify the “intrinsic” subtypes of breast cancer commonly known as Luminal A, Luminal B, HER2-Enriched (HER2-E) and Basal-like. The PAM50 gene set is often us...

    Authors: Roy RL Bastien, Álvaro Rodríguez-Lescure, Mark TW Ebbert, Aleix Prat, Blanca Munárriz, Leslie Rowe, Patricia Miller, Manuel Ruiz-Borrego, Daniel Anderson, Bradley Lyons, Isabel Álvarez, Tracy Dowell, David Wall, Miguel Ángel Seguí, Lee Barley, Kenneth M Boucher…

    Citation: BMC Medical Genomics 2012 5:44

    Content type: Research article

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  17. Aberrant DNA methylation leads to loss of heterozygosity (LOH) or loss of imprinting (LOI) as the first hit during human carcinogenesis. Recently we developed a new high-throughput, high-resolution DNA methyla...

    Authors: Hitoshi Hiura, Hiroaki Okae, Hisato Kobayash, Naoko Miyauchi, Fumi Sato, Akiko Sato, Fumihiko Suzuki, Satoru Nagase, Junichi Sugawara, Kunihiko Nakai, Nobuo Yaegashi and Takahiro Arima

    Citation: BMC Medical Genomics 2012 5:8

    Content type: Research article

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  18. Gene expression profiling has shown its ability to identify with high accuracy low cytogenetic risk acute myeloid leukemia such as acute promyelocytic leukemia and leukemias with t(8;21) or inv(16). The aim of...

    Authors: Diane Raingeard de la Blétière, Odile Blanchet, Pascale Cornillet-Lefèbvre, Anne Coutolleau, Laurence Baranger, Franck Geneviève, Isabelle Luquet, Mathilde Hunault-Berger, Annaelle Beucher, Aline Schmidt-Tanguy, Marc Zandecki, Yves Delneste, Norbert Ifrah and Philippe Guardiola

    Citation: BMC Medical Genomics 2012 5:6

    Content type: Research article

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  19. Liver fibrosis is caused by chemicals or viral infection. The progression of liver fibrosis results in hepatocellular carcinogenesis in later stages. Recent studies have revealed the importance of DNA hypermet...

    Authors: Yoko Komatsu, Tsuyoshi Waku, Naoya Iwasaki, Wakana Ono, Chie Yamaguchi and Junn Yanagisawa

    Citation: BMC Medical Genomics 2012 5:5

    Content type: Research article

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  20. Prediction of left ventricular (LV) remodeling after acute myocardial infarction (MI) is clinically important and would benefit from the discovery of new biomarkers.

    Authors: Yvan Devaux, Melanie Bousquenaud, Sophie Rodius, Pierre-Yves Marie, Fatiha Maskali, Lu Zhang, Francisco Azuaje and Daniel R Wagner

    Citation: BMC Medical Genomics 2011 4:83

    Content type: Research article

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  21. Identification of patients who likely will or will not benefit from cytotoxic chemotherapy through the use of biomarkers could greatly improve clinical management by better defining appropriate treatment optio...

    Authors: Chang Hee Kim, Hark K Kim, R Luke Rettig, Joseph Kim, Eunbyul T Lee, Olga Aprelikova, Il J Choi, David J Munroe and Jeffrey E Green

    Citation: BMC Medical Genomics 2011 4:79

    Content type: Research article

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  22. Increased understanding of the variability in normal breast biology will enable us to identify mechanisms of breast cancer initiation and the origin of different subtypes, and to better predict breast cancer r...

    Authors: Vilde D Haakensen, Ole Christian Lingjærde, Torben Lüders, Margit Riis, Aleix Prat, Melissa A Troester, Marit M Holmen, Jan Ole Frantzen, Linda Romundstad, Dina Navjord, Ida K Bukholm, Tom B Johannesen, Charles M Perou, Giske Ursin, Vessela N Kristensen, Anne-Lise Børresen-Dale…

    Citation: BMC Medical Genomics 2011 4:77

    Content type: Research article

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  23. A wide variety of high-throughput microarray platforms have been used to identify molecular targets associated with biological and clinical tumor phenotypes by comparing samples representing distinct pathologi...

    Authors: Waleska K Martins, Gustavo H Esteves, Otávio M Almeida, Gisele G Rezze, Gilles Landman, Sarah M Marques, Alex F Carvalho, Luiz F L Reis, João P Duprat and Beatriz S Stolf

    Citation: BMC Medical Genomics 2011 4:76

    Content type: Research article

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  24. Insulin resistance (IR) is accompanied by chronic low grade systemic inflammation, obesity, and deregulation of total body energy homeostasis. We induced inflammation in adipose and liver tissues in vitro in orde...

    Authors: Ewa Szalowska, Martijn Dijkstra, Marieke GL Elferink, Desiree Weening, Marcel de Vries, Marcel Bruinenberg, Annemieke Hoek, Han Roelofsen, Geny MM Groothuis and Roel J Vonk

    Citation: BMC Medical Genomics 2011 4:71

    Content type: Research article

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  25. Massively parallel sequencing technologies have brought an enormous increase in sequencing throughput. However, these technologies need to be further improved with regard to reproducibility and applicability t...

    Authors: Martin Kerick, Melanie Isau, Bernd Timmermann, Holger Sültmann, Ralf Herwig, Sylvia Krobitsch, Georg Schaefer, Irmgard Verdorfer, Georg Bartsch, Helmut Klocker, Hans Lehrach and Michal R Schweiger

    Citation: BMC Medical Genomics 2011 4:68

    Content type: Research article

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  26. Conventional high-grade osteosarcoma is a primary malignant bone tumor, which is most prevalent in adolescence. Survival rates of osteosarcoma patients have not improved significantly in the last 25 years. Aim...

    Authors: Marieke L Kuijjer, Heidi M Namløs, Esther I Hauben, Isidro Machado, Stine H Kresse, Massimo Serra, Antonio Llombart-Bosch, Pancras CW Hogendoorn, Leonardo A Meza-Zepeda, Ola Myklebost and Anne-Marie Cleton-Jansen

    Citation: BMC Medical Genomics 2011 4:66

    Content type: Research article

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  27. It is widely accepted that atherosclerosis and inflammation are intimately linked. Monocytes play a key role in both of these processes and we hypothesized that activation of inflammatory pathways in monocytes...

    Authors: Suthesh Sivapalaratnam, Rosienne Farrugia, Max Nieuwdorp, Cordelia F Langford, Rachel T van Beem, Stephanie Maiwald, Jaap Jan Zwaginga, Arief Gusnanto, Nicholas A Watkins, Mieke D Trip and Willem H Ouwehand

    Citation: BMC Medical Genomics 2011 4:64

    Content type: Research article

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  28. Transgenic mouse tumor models have the advantage of facilitating controlled in vivo oncogenic perturbations in a common genetic background. This provides an idealized context for generating transcriptome-based di...

    Authors: Heather G LaBreche, Joseph R Nevins and Erich Huang

    Citation: BMC Medical Genomics 2011 4:61

    Content type: Research article

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  29. Gene expression signatures developed to measure the activity of oncogenic signaling pathways have been used to dissect the heterogeneity of tumor samples and to predict sensitivity to various cancer drugs that...

    Authors: Jennifer A Freedman, Christina K Augustine, Angelica M Selim, Kirsten C Holshausen, Zhengzheng Wei, Katherine A Tsamis, David S Hsu, Holly K Dressman, William T Barry, Douglas S Tyler and Joseph R Nevins

    Citation: BMC Medical Genomics 2011 4:58

    Content type: Research article

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  30. Pilocytic Astrocytomas (PAs) are common low-grade central nervous system malignancies for which few recurrent and specific genetic alterations have been identified. In an effort to better understand the molecu...

    Authors: Hrishikesh Deshmukh, Jinsheng Yu, Jahangheer Shaik, Tobey J MacDonald, Arie Perry, Jacqueline E Payton, David H Gutmann, Mark A Watson and Rakesh Nagarajan

    Citation: BMC Medical Genomics 2011 4:57

    Content type: Research article

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  31. Metastasis is the number one cause of cancer deaths. Expression microarrays have been widely used to study metastasis in various types of cancer. We hypothesize that a meta-analysis of publicly available gene ...

    Authors: Marla H Daves, Susan G Hilsenbeck, Ching C Lau and Tsz-Kwong Man

    Citation: BMC Medical Genomics 2011 4:56

    Content type: Research article

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  32. Genomic tests are available to predict breast cancer recurrence and to guide clinical decision making. These predictors provide recurrence risk scores along with a measure of uncertainty, usually a confidence ...

    Authors: Fathi Elloumi, Zhiyuan Hu, Yan Li, Joel S Parker, Margaret L Gulley, Keith D Amos and Melissa A Troester

    Citation: BMC Medical Genomics 2011 4:54

    Content type: Research article

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  33. Glioblastoma is a complex multifactorial disorder that has swift and devastating consequences. Few genes have been consistently identified as prognostic biomarkers of glioblastoma survival. The goal of this st...

    Authors: Nicola VL Serão, Kristin R Delfino, Bruce R Southey, Jonathan E Beever and Sandra L Rodriguez-Zas

    Citation: BMC Medical Genomics 2011 4:49

    Content type: Research article

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  34. Gastric cancer samples obtained by histologic macrodissection contain a relatively high stromal content that may significantly influence gene expression profiles. Differences between the gene expression signat...

    Authors: Hark Kyun Kim, Joseph Kim, Susie Korolevich, Il Ju Choi, Chang Hee Kim, David J Munroe and Jeffrey E Green

    Citation: BMC Medical Genomics 2011 4:48

    Content type: Research article

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  35. 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

    Content type: Research article

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  36. 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

    Content type: Research article

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  37. 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

    Content type: Research article

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  38. 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

    Content type: Research article

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  39. 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

    Content type: Research article

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  40. 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

    Content type: Research article

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  41. 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

    Content type: Research article

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  42. 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

    Content type: Research article

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  43. 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

    Content type: Research article

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  44. Germline mutations in the folliculin (FLCN) gene are associated with the development of Birt-Hogg-Dubé syndrome (BHDS), a disease characterized by papular skin lesions, a high occurrence of spontaneous pneumothor...

    Authors: Jeff A Klomp, David Petillo, Natalie M Niemi, Karl J Dykema, Jindong Chen, Ximing J Yang, Annika Sääf, Peter Zickert, Markus Aly, Ulf Bergerheim, Magnus Nordenskjöld, Sophie Gad, Sophie Giraud, Yves Denoux, Laurent Yonneau, Arnaud Méjean…

    Citation: BMC Medical Genomics 2010 3:59

    Content type: Research article

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  45. Urothelial carcinoma (UC) can arise at any location along the urothelial tract, including the urethra, bladder, ureter, or renal pelvis. Although tumors arising in these various locations have similar morpholo...

    Authors: Zhongfa Zhang, Kyle A Furge, Ximing J Yang, Bin T Teh and Donna E Hansel

    Citation: BMC Medical Genomics 2010 3:58

    Content type: Research article

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  46. Immunization of BALB/c mice with a recombinant adenovirus expressing Mycobacterium tuberculosis (M. tuberculosis) antigen 85A (Ad85A) protects against aerosol challenge with M. tuberculosis only when it is admini...

    Authors: Lian N Lee, Dilair Baban, Edward O Ronan, Jiannis Ragoussis, Peter CL Beverley and Elma Z Tchilian

    Citation: BMC Medical Genomics 2010 3:46

    Content type: Research article

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Announcement

As a result of the significant disruption that is being caused by the COVID-19 pandemic we are very aware that many researchers will have difficulty in meeting the timelines associated with our peer review process during normal times.  Please do let us know if you need additional time. Our systems will continue to remind you of the original timelines but we intend to be highly flexible at this time.