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  1. We report unbiased metagenomic detection of chikungunya virus (CHIKV), Ebola virus (EBOV), and hepatitis C virus (HCV) from four human blood samples by MinION nanopore sequencing coupled to a newly developed, ...

    Authors: Alexander L. Greninger, Samia N. Naccache, Scot Federman, Guixia Yu, Placide Mbala, Vanessa Bres, Doug Stryke, Jerome Bouquet, Sneha Somasekar, Jeffrey M. Linnen, Roger Dodd, Prime Mulembakani, Bradley S. Schneider, Jean-Jacques Muyembe-Tamfum, Susan L. Stramer and Charles Y. Chiu
    Citation: Genome Medicine 2015 7:99
    Content type: Method Published on:

  2. Studies of historical isolates inform on the evolution and emergence of important pathogens and phenotypes, including antimicrobial resistance. Crucial to studying antimicrobial resistance are isolates that pr...

    Authors: Kate S. Baker, Edward Burnett, Hannah McGregor, Ana Deheer-Graham, Christine Boinett, Gemma C. Langridge, Alexander M. Wailan, Amy K. Cain, Nicholas R. Thomson, Julie E. Russell and Julian Parkhill
    Citation: Genome Medicine 2015 7:97
    Content type: Correspondance Published on:

  3. Cystic fibrosis is the most common genetically determined, life-limiting disorder in populations of European ancestry. The genetic basis of cystic fibrosis is well established to be mutations in the cystic fib...

    Authors: Malcolm Brodlie, Iram J. Haq, Katie Roberts and J. Stuart Elborn
    Citation: Genome Medicine 2015 7:101
    Content type: Review Published on:

  4. Carcinoma of the oral tongue (OTSCC) is the most common malignancy of the oral cavity, characterized by frequent recurrence and poor survival. The last three decades has witnessed a change in the OTSCC epidemi...

    Authors: Andre Luiz Vettore, Kalpana Ramnarayanan, Gregory Poore, Kevin Lim, Choon Kiat Ong, Kie Kyon Huang, Hui Sun Leong, Fui Teen Chong, Tony Kiat-Hon Lim, Weng Khong Lim, Ioana Cutcutache, John R. Mcpherson, Yuka Suzuki, Shenli Zhang, Thakshayeni Skanthakumar, Weining Wang…
    Citation: Genome Medicine 2015 7:98
    Content type: Research Published on:

  5. Cancers adapt to immune-surveillance through evasion. Immune responses against carcinoma and melanoma converge on cytotoxic effectors and IFNγ-STAT1-IRF1 signalling. Local IFN-driven immune checkpoint expressi...

    Authors: Matthew A. Care, David R. Westhead and Reuben M. Tooze
    Citation: Genome Medicine 2015 7:96
    Content type: Research Published on:

  8. Each cell type found within the human body performs a diverse and unique set of functions, the disruption of which can lead to disease. However, there currently exists no systematic mapping between cell types ...

    Authors: Alex J. Cornish, Ioannis Filippis, Alessia David and Michael J.E. Sternberg
    Citation: Genome Medicine 2015 7:95
    Content type: Research Published on:

  9. Neurodevelopmental disorders such as autism and intellectual disability have a sex bias skewed towards boys; however, systematic assessment of this bias is complicated by the presence of significant genetic an...

    Authors: Andrew Polyak, Jill A. Rosenfeld and Santhosh Girirajan
    Citation: Genome Medicine 2015 7:94
    Content type: Research Published on:

  12. Epilepsy is a group of disorders characterized by recurrent seizures, and is one of the most common neurological conditions. The genetic basis of epilepsy is clear from epidemiological studies and from rare ge...

    Authors: Candace T. Myers and Heather C. Mefford
    Citation: Genome Medicine 2015 7:91
    Content type: Review Published on:

  13. The prevalence of allergic diseases are increasing worldwide, emphasizing the need to elucidate their pathogeneses. The aims of this study were to use a two-stage design to identify DNA methylation levels at c...

    Authors: Todd M. Everson, Genevieve Lyons, Hongmei Zhang, Nelís Soto-Ramírez, Gabrielle A. Lockett, Veeresh K. Patil, Simon K. Merid, Cilla Sӧderhӓll, Erik Melén, John W. Holloway, S. Hasan Arshad and Wilfried Karmaus
    Citation: Genome Medicine 2015 7:89
    Content type: Research Published on:

  14. Personalized medicine is predicated on the notion that individual biochemical and genomic profiles are relatively constant in times of good health and to some extent predictive of disease or therapeutic respon...

    Authors: Rubina Tabassum, Ambily Sivadas, Vartika Agrawal, Haozheng Tian, Dalia Arafat and Greg Gibson
    Citation: Genome Medicine 2015 7:88
    Content type: Research Published on:

  15. Mucinous ovarian tumors are an unusual group of rare neoplasms with an apparently clear progression from benign to borderline to carcinoma, yet with a controversial cell of origin in the ovarian surface epithe...

    Authors: Georgina L. Ryland, Sally M. Hunter, Maria A. Doyle, Franco Caramia, Jason Li, Simone M. Rowley, Michael Christie, Prue E. Allan, Andrew N. Stephens, David D L Bowtell, Ian G. Campbell and Kylie L. Gorringe
    Citation: Genome Medicine 2015 7:87
    Content type: Research Published on:

    The Erratum to this article has been published in Genome Medicine 2017 9:1

  17. Psoriasis is a chronic disease characterized by the development of scaly red skin lesions and possible co-morbid conditions. The psoriasis lesional skin transcriptome has been extensively investigated, but mRN...

    Authors: William R. Swindell, Henriette A. Remmer, Mrinal K. Sarkar, Xianying Xing, Drew H. Barnes, Liza Wolterink, John J. Voorhees, Rajan P. Nair, Andrew Johnston, James T. Elder and Johann E. Gudjonsson
    Citation: Genome Medicine 2015 7:86
    Content type: Research Published on:

  18. New methods for epigenome editing now make it possible to manipulate the epigenome in living cells with unprecedented specificity and efficiency. These ground-breaking approaches are beginning to yield novel i...

    Authors: Anna Köferle, Stefan H. Stricker and Stephan Beck
    Citation: Genome Medicine 2015 7:59
    Content type: Comment Published on:

    The Erratum to this article has been published in Genome Medicine 2015 7:75

  20. There is a widespread assumption that risk prediction is the major driver of customer interest in personal genomic testing (PGT). However, some customers may also be motivated by finding out whether their exis...

    Authors: Susanne F. Meisel, Deanna Alexis Carere, Jane Wardle, Sarah S. Kalia, Tanya A. Moreno, Joanna L. Mountain, J. Scott Roberts and Robert C. Green
    Citation: Genome Medicine 2015 7:74
    Content type: Research Published on:

  21. Incidental findings are the subject of intense ethical debate in medical genomic research. Every human genome contains a number of potentially disease-causing alterations that may be detected during comprehens...

    Authors: Sebastian Schuol, Christoph Schickhardt, Stefan Wiemann, Claus R. Bartram, Klaus Tanner, Roland Eils, Benjamin Meder, Daniela Richter, Hanno Glimm, Christof von Kalle and Eva C. Winkler
    Citation: Genome Medicine 2015 7:83
    Content type: Opinion Published on:

  24. As a result of multiple technological and practical advances, high-throughput sequencing, known more commonly as “next-generation” sequencing (NGS), can now be incorporated into standard clinical practice. Whe...

    Authors: Jeffrey Gagan and Eliezer M. Van Allen
    Citation: Genome Medicine 2015 7:80
    Content type: Review Published on:

  25. Expanded genetic carrier testing is changing clinical practice. Current experience highlights the need for rigorous curation of tens of thousands of variants as to their pathogenicity and phenotypic effects. T...

    Authors: Arthur L. Beaudet
    Citation: Genome Medicine 2015 7:79
    Content type: Comment Published on:

  26. Next-generation sequencing is revolutionizing medical genetics and in the near future will pervade all medical fields. To maximize the potential clinical utility of this approach, global data sharing and pheno...

    Authors: Joris A. Veltman and James R. Lupski
    Citation: Genome Medicine 2015 7:78
    Content type: Editorial Published on:

  27. Routine clinical application of whole exome sequencing remains challenging due to difficulties in variant interpretation, large dataset management, and workflow integration. We describe a tool named ClinLabGen...

    Authors: Jinlian Wang, Jun Liao, Jinglan Zhang, Wei-Yi Cheng, Jörg Hakenberg, Meng Ma, Bryn D. Webb, Rajasekar Ramasamudram-chakravarthi, Lisa Karger, Lakshmi Mehta, Ruth Kornreich, George A. Diaz, Shuyu Li, Lisa Edelmann and Rong Chen
    Citation: Genome Medicine 2015 7:77
    Content type: Software Published on:

  28. Next-generation sequencing (NGS) offers unprecedented opportunities to expand clinical genomics. It also presents challenges with respect to integration with data from other sequencing methods and historical d...

    Authors: Márton Münz, Elise Ruark, Anthony Renwick, Emma Ramsay, Matthew Clarke, Shazia Mahamdallie, Victoria Cloke, Sheila Seal, Ann Strydom, Gerton Lunter and Nazneen Rahman
    Citation: Genome Medicine 2015 7:76
    Content type: Method Published on:

  30. Reliable detection of somatic copy-number alterations (sCNAs) in tumors using whole-exome sequencing (WES) remains challenging owing to technical (inherent noise) and sample-associated variability in WES data....

    Authors: Vinay Varadan, Salendra Singh, Arman Nosrati, Lakshmeswari Ravi, James Lutterbaugh, Jill S. Barnholtz-Sloan, Sanford D. Markowitz, Joseph E. Willis and Kishore Guda
    Citation: Genome Medicine 2015 7:69
    Content type: Method Published on:

  32. Whole exome sequencing is increasingly used for the clinical evaluation of genetic disease, yet the variation of coverage and sensitivity over medically relevant parts of the genome remains poorly understood. ...

    Authors: Anil Patwardhan, Jason Harris, Nan Leng, Gabor Bartha, Deanna M. Church, Shujun Luo, Christian Haudenschild, Mark Pratt, Justin Zook, Marc Salit, Jeanie Tirch, Massimo Morra, Stephen Chervitz, Ming Li, Michael Clark, Sarah Garcia…
    Citation: Genome Medicine 2015 7:71
    Content type: Research Published on:

  33. The benefits of implementing high throughput sequencing in the clinic are quickly becoming apparent. However, few freely available bioinformatics pipelines have been built from the ground up with clinical geno...

    Authors: Simon P. Sadedin, Harriet Dashnow, Paul A. James, Melanie Bahlo, Denis C. Bauer, Andrew Lonie, Sebastian Lunke, Ivan Macciocca, Jason P. Ross, Kirby R. Siemering, Zornitza Stark, Susan M. White, Graham Taylor, Clara Gaff, Alicia Oshlack and Natalie P. Thorne
    Citation: Genome Medicine 2015 7:68
    Content type: Software Published on:

  34. In an effort to return actionable results from variant data to electronic health records (EHRs), participants in the Electronic Medical Records and Genomics (eMERGE) Network are being sequenced with the target...

    Authors: David R. Crosslin, Peggy D. Robertson, David S. Carrell, Adam S. Gordon, David S. Hanna, Amber Burt, Stephanie M. Fullerton, Aaron Scrol, James Ralston, Kathleen Leppig, Andrea Hartzler, Eric Baldwin, Mariza de Andrade, Iftikhar J. Kullo, Gerard Tromp, Kimberly F. Doheny…
    Citation: Genome Medicine 2015 7:67
    Content type: Research Published on:

  35. High-throughput genetic testing is increasingly applied in clinics. Next-Generation Sequencing (NGS) data analysis however still remains a great challenge. The interpretation of pathogenicity of single variant...

    Authors: Sabine C. Mueller, Christina Backes, Olga V. Kalinina, Benjamin Meder, Daniel Stöckel, Hans-Peter Lenhof, Eckart Meese and Andreas Keller
    Citation: Genome Medicine 2015 7:65
    Content type: Research Published on:

  36. Classifiers based on molecular criteria such as gene expression signatures have been developed to distinguish Burkitt lymphoma and diffuse large B cell lymphoma, which help to explore the intermediate cases wh...

    Authors: Chulin Sha, Sharon Barrans, Matthew A. Care, David Cunningham, Reuben M. Tooze, Andrew Jack and David R. Westhead
    Citation: Genome Medicine 2015 7:64
    Content type: Research Published on:

  37. The oxidative DNA demethylase ALKBH3 targets single-stranded DNA (ssDNA) in order to perform DNA alkylation damage repair. ALKBH3 becomes upregulated during tumorigenesis and is necessary for proliferation. Ho...

    Authors: Robert Liefke, Indra M. Windhof-Jaidhauser, Jochen Gaedcke, Gabriela Salinas-Riester, Feizhen Wu, Michael Ghadimi and Sebastian Dango
    Citation: Genome Medicine 2015 7:66
    Content type: Research Published on:

  38. Evidence from several recent metabolomic studies suggests that increased concentrations of triacylglycerols with shorter (14–16 carbon atoms), saturated fatty acids are associated with insulin resistance and t...

    Authors: Michael Eiden, Albert Koulman, Mensud Hatunic, James A. West, Steven Murfitt, Michael Osei, Claire Adams, Xinzhu Wang, Yajing Chu, Luke Marney, Lee D. Roberts, Stephen O’Rahilly, Robert K. Semple, David B. Savage and Julian L. Griffin
    Citation: Genome Medicine 2015 7:63
    Content type: Research Published on:

  42. The human gut microbiome is associated with the development of colon cancer, and recent studies have found changes in the microbiome in cancer patients compared to healthy controls. Studying the microbial comm...

    Authors: Michael B. Burns, Joshua Lynch, Timothy K. Starr, Dan Knights and Ran Blekhman
    Citation: Genome Medicine 2015 7:55
    Content type: Research Published on:

  43. Age-related macular degeneration (AMD) is a leading cause of blindness. Most vision loss occurs following the transition from a disease of deposit formation and inflammation to a disease of neovascular fibrosi...

    Authors: Monte J. Radeke, Carolyn M. Radeke, Ying-Hsuan Shih, Jane Hu, Dean Bok, Lincoln V. Johnson and Pete J. Coffey
    Citation: Genome Medicine 2015 7:58
    Content type: Research Published on:

  44. Genetic analyses of autoimmune diseases have revealed hundreds of disease-associated DNA variants, but the identity and function of the causal variants are understudied and warrant deeper mechanistic studies. ...

    Authors: John P Ray and Nir Hacohen
    Citation: Genome Medicine 2015 7:57
    Content type: Comment Published on:

  45. The organic cation transporter OCT1 (SLC22A1) mediates the uptake of vitamin B1, cationic drugs, and xenobiotics into hepatocytes. Nine percent of Caucasians lack or have very low OCT1 activity due to loss-of-...

    Authors: Tina Seitz, Robert Stalmann, Nawar Dalila, Jiayin Chen, Sherin Pojar, Joao N. Dos Santos Pereira, Ralph Krätzner, Jürgen Brockmöller and Mladen V. Tzvetkov
    Citation: Genome Medicine 2015 7:56
    Content type: Research Published on:

  46. Besides its growing importance in clinical diagnostics and understanding the genetic basis of Mendelian and complex diseases, whole exome sequencing (WES) is a rich source of additional information of potentia...

    Authors: Tomasz Gambin, Shalini N. Jhangiani, Jennifer E. Below, Ian M. Campbell, Wojciech Wiszniewski, Donna M. Muzny, Jeffrey Staples, Alanna C. Morrison, Matthew N. Bainbridge, Samantha Penney, Amy L. McGuire, Richard A. Gibbs, James R. Lupski and Eric Boerwinkle
    Citation: Genome Medicine 2015 7:54
    Content type: Research Published on:

  48. We describe an approach for genotyping bacterial strains from low coverage genome datasets, including metagenomic data from complex samples. Sequence reads from unknown samples are aligned to a reference genom...

    Authors: Jason W. Sahl, James M. Schupp, David A. Rasko, Rebecca E. Colman, Jeffrey T. Foster and Paul Keim
    Citation: Genome Medicine 2015 7:52
    Content type: Method Published on:

  50. HIV/AIDS is a chronic and debilitating disease that cannot be cured with current antiretroviral drugs. While combinatorial antiretroviral therapy (cART) can potently suppress HIV-1 replication and delay the on...

    Authors: Maggie L Bobbin, John C Burnett and John J Rossi
    Citation: Genome Medicine 2015 7:50
    Content type: Review Published on:
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Genome Medicine

ISSN: 1756-994X

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