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  1. Human leukocyte antigen (HLA) typing from next generation sequencing (NGS) data has the potential for widespread applications. Here we introduce a novel tool (HLAreporter) for HLA typing from NGS data based on...

    Authors: Yazhi Huang, Jing Yang, Dingge Ying, Yan Zhang, Vorasuk Shotelersuk, Nattiya Hirankarn, Pak Chung Sham, Yu Lung Lau and Wanling Yang
    Citation: Genome Medicine 2015 7:25
    Content type: Method Published on:

  2. Heart failure (HF) is the most common cause of morbidity and mortality in developed countries. Here, we identify biologically relevant transcripts that are significantly altered in the early phase of myocardia...

    Authors: Agata Maciejak, Marek Kiliszek, Marcin Michalak, Dorota Tulacz, Grzegorz Opolski, Krzysztof Matlak, Slawomir Dobrzycki, Agnieszka Segiet, Monika Gora and Beata Burzynska
    Citation: Genome Medicine 2015 7:26
    Content type: Research Published on:

  4. Urothelial carcinoma of the bladder (UC) is a common malignancy. Although extensive transcriptome analysis has provided insights into the gene expression patterns of this tumor type, the mechanistic underpinni...

    Authors: Mattias Aine, Gottfrid Sjödahl, Pontus Eriksson, Srinivas Veerla, David Lindgren, Markus Ringnér and Mattias Höglund
    Citation: Genome Medicine 2015 7:23
    Content type: Research Published on:

  5. Long non-coding RNAs (lncRNAs) are emerging as molecules that significantly impact many cellular processes and have been associated with almost every human cancer. Compared to protein-coding genes, lncRNA gene...

    Authors: Ewan A Gibb, René L Warren, Gavin W Wilson, Scott D Brown, Gordon A Robertson, Gregg B Morin and Robert A Holt
    Citation: Genome Medicine 2015 7:22
    Content type: Research Published on:

  6. During intra-erythrocytic development, late asexually replicating Plasmodium falciparum parasites sequester from peripheral circulation. This facilitates chronic infection and is linked to severe disease and orga...

    Authors: Karell G Pelle, Keunyoung Oh, Kathrin Buchholz, Vagheesh Narasimhan, Regina Joice, Danny A Milner, Nicolas MB Brancucci, Siyuan Ma, Till S Voss, Ken Ketman, Karl B Seydel, Terrie E Taylor, Natasha S Barteneva, Curtis Huttenhower and Matthias Marti
    Citation: Genome Medicine 2015 7:19
    Content type: Research Published on:

  7. Microbiome-based therapies are moving quickly towards the clinic, with successes including fecal microbial transplants for recurring Clostridium difficile, hints of new antibiotics to come, and possible new micro...

    Authors: Fergus Shanahan
    Citation: Genome Medicine 2015 7:17
    Content type: Comment Published on:

  10. The editors of Genome Medicine are extremely grateful for the time, hard work and support of all our reviewers, and would like to thank everyone who contributed to the journal in Volume 6 (2014).

    Authors: Rebecca Furlong
    Citation: Genome Medicine 2015 7:14
    Content type: Reviewer acknowledgement Published on:

  12. The HHIP gene, encoding Hedgehog interacting protein, has been implicated in chronic obstructive pulmonary disease (COPD) by genome-wide association studies (GWAS), and our subsequent studies identified a functio...

    Authors: Taotao Lao, Kimberly Glass, Weiliang Qiu, Francesca Polverino, Kushagra Gupta, Jarrett Morrow, John Dominic Mancini, Linh Vuong, Mark A Perrella, Craig P Hersh, Caroline A Owen, John Quackenbush, Guo-Cheng Yuan, Edwin K Silverman and Xiaobo Zhou
    Citation: Genome Medicine 2015 7:12
    Content type: Research Published on:

  13. The role played by microRNAs in the deregulation of protein expression in breast cancer is only partly understood. To gain insight, the combined effect of microRNA and mRNA expression on protein expression was...

    Authors: Miriam Ragle Aure, Sandra Jernström, Marit Krohn, Hans Kristian Moen Vollan, Eldri U Due, Einar Rødland, Rolf Kåresen, Prahlad Ram, Yiling Lu, Gordon B Mills, Kristine Kleivi Sahlberg, Anne-Lise Børresen-Dale, Ole Christian Lingjærde and Vessela N Kristensen
    Citation: Genome Medicine 2015 7:21
    Content type: Research Published on:

  14. Breast cancer exhibits significant molecular, pathological, and clinical heterogeneity. Current clinicopathological evaluation is imperfect for predicting outcome, which results in overtreatment for many patie...

    Authors: Lao H Saal, Johan Vallon-Christersson, Jari Häkkinen, Cecilia Hegardt, Dorthe Grabau, Christof Winter, Christian Brueffer, Man-Hung Eric Tang, Christel Reuterswärd, Ralph Schulz, Anna Karlsson, Anna Ehinger, Janne Malina, Jonas Manjer, Martin Malmberg, Christer Larsson…
    Citation: Genome Medicine 2015 7:20
    Content type: Research Published on:

  16. Wilms tumours (WTs) are characterised by several hallmarks that suggest epimutations such as aberrant DNA methylation are involved in tumour progression: loss of imprinting at 11p15, lack of recurrent mutation...

    Authors: Jocelyn Charlton, Richard D Williams, Neil J Sebire, Sergey Popov, Gordan Vujanic, Tasnim Chagtai, Marisa Alcaide-German, Tiffany Morris, Lee M Butcher, Paul Guilhamon, Stephan Beck and Kathy Pritchard-Jones
    Citation: Genome Medicine 2015 7:11
    Content type: Research Published on:

  17. Studies examining whether genetic risk information about common, complex diseases can motivate individuals to improve health behaviors and advance planning have shown mixed results. Examining the influence of ...

    Authors: Kurt D Christensen, J Scott Roberts, Brian J Zikmund-Fisher, Sharon LR Kardia, Colleen M McBride, Erin Linnenbringer and Robert C Green
    Citation: Genome Medicine 2015 7:10
    Content type: Research Published on:

  18. The discovery that ten-eleven translocation (TET) proteins are α-ketoglutarate-dependent dioxygenases involved in the conversion of 5-methylcytosines (5-mC) to 5-hydroxymethylcytosine (5-hmC), 5-formylcytosine...

    Authors: Laurianne Scourzic, Enguerran Mouly and Olivier A Bernard
    Citation: Genome Medicine 2015 7:9
    Content type: Review Published on:

  21. Human cancers are frequently polyploid, containing multiple aneuploid subpopulations that differ in total DNA content. In this study we exploit this property to reconstruct evolutionary histories, by assuming ...

    Authors: Ankit Malhotra, Yong Wang, Jill Waters, Ken Chen, Funda Meric-Bernstam, Ira M Hall and Nicholas E Navin
    Citation: Genome Medicine 2015 7:6
    Content type: Method Published on:

  22. With the advent of affordable and comprehensive sequencing technologies, access to molecular genetics for clinical diagnostics and research applications is increasing. However, variant interpretation remains c...

    Authors: Dace Ruklisa, James S Ware, Roddy Walsh, David J Balding and Stuart A Cook
    Citation: Genome Medicine 2015 7:5
    Content type: Research Published on:

  24. Failure to consider lessons from behavioral economics in the case of whole genome sequencing may cause us to run into the ‘last mile problem’ - the failure to integrate newly developed technology, on which bil...

    Authors: Jennifer S Blumenthal-Barby, Amy L McGuire, Robert C Green and Peter A Ubel
    Citation: Genome Medicine 2015 7:3
    Content type: Comment Published on:

  29. We are only beginning to understand the relationship between host genetics and the gut microbiome. Two recent studies help to disentangle this interaction and show that genetic loci across the human genome sha...

    Authors: Jonathan Jacobs and Jonathan Braun
    Citation: Genome Medicine 2014 6:119
    Content type: Research highlight Published on:

  30. The use of information and communication technology can offer a novel way to promote family-centric initiatives for informed consent, and can address associated ethical challenges in personal genome research.

    Authors: Jusaku Minari, Harriet Teare, Colin Mitchell, Jane Kaye and Kazuto Kato
    Citation: Genome Medicine 2014 6:118
    Content type: Comment Published on:

  31. The use of tumour xenografts is a well-established research tool in cancer genomics but has not yet been comprehensively evaluated for cancer epigenomics.

    Authors: Paul Guilhamon, Lee M Butcher, Nadege Presneau, Gareth A Wilson, Andrew Feber, Dirk S Paul, Moritz Schütte, Johannes Haybaeck, Ulrich Keilholz, Jens Hoffman, Mark T Ross, Adrienne M Flanagan and Stephan Beck
    Citation: Genome Medicine 2014 6:116
    Content type: Research Published on:

  32. Comparative analysis of expression profiles between early and late stage cancers can help to understand cancer progression and metastasis mechanisms and to predict the clinical aggressiveness of cancer. The ob...

    Authors: Qi Liu, Pei-Fang Su, Shilin Zhao and Yu Shyr
    Citation: Genome Medicine 2014 6:117
    Content type: Research Published on:

  33. Improved usage of the repertoires of pancreatic ductal adenocarcinoma (PDAC) profiles is crucially needed to guide the development of predictive and prognostic tools that could inform the selection of treatmen...

    Authors: Syed Haider, Jun Wang, Ai Nagano, Ami Desai, Prabhu Arumugam, Laurent Dumartin, Jude Fitzgibbon, Thorsten Hagemann, John F Marshall, Hemant M Kocher, Tatjana Crnogorac-Jurcevic, Aldo Scarpa, Nicholas R Lemoine and Claude Chelala
    Citation: Genome Medicine 2014 6:105
    Content type: Research Published on:

  34. A number of compelling candidate Alzheimer’s biomarkers remain buried within the literature. Indeed, there should be a systematic effort towards gathering this information through approaches that mine publicly...

    Authors: Ashutosh Malhotra, Erfan Younesi, Shweta Bagewadi and Martin Hofmann-Apitius
    Citation: Genome Medicine 2014 6:97
    Content type: Research Published on:

  35. Designed in collaboration with 23andMe and Pathway Genomics, the Impact of Personal Genomics (PGen) Study serves as a model for academic-industry partnership and provides a longitudinal dataset for studying ps...

    Authors: Deanna Alexis Carere, Mick P Couper, Scott D Crawford, Sarah S Kalia, Jake R Duggan, Tanya A Moreno, Joanna L Mountain, J Scott Roberts and Robert C Green
    Citation: Genome Medicine 2014 6:96
    Content type: Method Published on:

  36. Human genetics and host-associated microbial communities have been associated independently with a wide range of chronic diseases. One of the strongest associations in each case is inflammatory bowel disease (...

    Authors: Dan Knights, Mark S Silverberg, Rinse K Weersma, Dirk Gevers, Gerard Dijkstra, Hailiang Huang, Andrea D Tyler, Suzanne van Sommeren, Floris Imhann, Joanne M Stempak, Hu Huang, Pajau Vangay, Gabriel A Al-Ghalith, Caitlin Russell, Jenny Sauk, Jo Knight…
    Citation: Genome Medicine 2014 6:107
    Content type: Research Published on:

  39. Acute promyelocytic leukemia (APL) is a sub-type of acute myeloid leukemia (AML) characterized by a block of myeloid differentiation at the promyelocytic stage and the predominant t(15:17) chromosomal transloc...

    Authors: Stefano Percio, Nadia Coltella, Sara Grisanti, Rosa Bernardi and Linda Pattini
    Citation: Genome Medicine 2014 6:84
    Content type: Research Published on:

  40. The current therapeutic arsenal against viral infections remains limited, with often poor efficacy and incomplete coverage, and appears inadequate to face the emergence of drug resistance. Our understanding of...

    Authors: Benoît de Chassey, Laurène Meyniel-Schicklin, Jacky Vonderscher, Patrice André and Vincent Lotteau
    Citation: Genome Medicine 2014 6:115
    Content type: Review Published on:

  42. During the latter half of the natural 48-h intraerythrocytic life cycle of human Plasmodium falciparum infection, parasites sequester deep in endothelium of tissues, away from the spleen and inaccessible to perip...

    Authors: Daria Van Tyne, Yan Tan, Johanna P Daily, Steve Kamiza, Karl Seydel, Terrie Taylor, Jill P Mesirov, Dyann F Wirth and Danny A Milner
    Citation: Genome Medicine 2014 6:110
    Content type: Research Published on:

  43. Toxigenic Corynebacterium ulcerans can cause a diphtheria-like illness in humans and have been found in domestic animals, which were suspected to serve as reservoirs for a zoonotic transmission. Additionally, tox...

    Authors: Dominik M Meinel, Gabriele Margos, Regina Konrad, Stefan Krebs, Helmut Blum and Andreas Sing
    Citation: Genome Medicine 2014 6:113
    Content type: Research Published on:

  44. Bacteria have been shown to generate constant genetic variation in a process termed phase variation. We present a tool based on whole genome sequencing that allows detection and quantification of coexisting ge...

    Authors: Amir Goldberg, Ofer Fridman, Irine Ronin and Nathalie Q Balaban
    Citation: Genome Medicine 2014 6:112
    Content type: Method Published on:

  45. Sepsis, a leading cause of morbidity and mortality, is not a homogeneous disease but rather a syndrome encompassing many heterogeneous pathophysiologies. Patient factors including genetics predispose to poor o...

    Authors: Ephraim L Tsalik, Raymond J Langley, Darrell L Dinwiddie, Neil A Miller, Byunggil Yoo, Jennifer C van Velkinburgh, Laurie D Smith, Isabella Thiffault, Anja K Jaehne, Ashlee M Valente, Ricardo Henao, Xin Yuan, Seth W Glickman, Brandon J Rice, Micah T McClain, Lawrence Carin…
    Citation: Genome Medicine 2014 6:111
    Content type: Research Published on:

  46. Dendritic cells localize throughout the body, where they can sense and capture invading pathogens to induce protective immunity. Hence, harnessing the biology of tissue-resident dendritic cells is fundamental ...

    Authors: Dorothée Duluc, Romain Banchereau, Julien Gannevat, Luann Thompson-Snipes, Jean-Philippe Blanck, Sandra Zurawski, Gerard Zurawski, Seunghee Hong, Jose Rossello-Urgell, Virginia Pascual, Nicole Baldwin, Jack Stecher, Michael Carley, Muriel Boreham and SangKon Oh
    Citation: Genome Medicine 2014 6:98
    Content type: Research Published on:

  48. Global gene expression profiling can provide insight into the underlying pathophysiology of disease processes. Kawasaki disease (KD) is an acute, self-limited vasculitis whose etiology remains unknown. Althoug...

    Authors: Long Truong Hoang, Chisato Shimizu, Ling Ling, Ahmad Nazri Mohamed Naim, Chiea Chuen Khor, Adriana H Tremoulet, Victoria Wright, Michael Levin, Martin L Hibberd and Jane C Burns
    Citation: Genome Medicine 2014 6:541
    Content type: Research Published on:

  50. One of the most successful public health applications of next-generation sequencing is whole-genome sequencing of pathogens to not only detect and characterize outbreaks, but also to inform outbreak management...

    Authors: Patrick Tang and Jennifer L Gardy
    Citation: Genome Medicine 2014 6:104
    Content type: Research highlight Published on:
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Genome Medicine

ISSN: 1756-994X

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