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  1. Periodontitis is a polymicrobial biofilm-induced inflammatory disease that affects 743 million people worldwide. The current model to explain periodontitis progression proposes that changes in the relative abu...

    Authors: Susan Yost, Ana E Duran-Pinedo, Ricardo Teles, Keerthana Krishnan and Jorge Frias-Lopez
    Citation: Genome Medicine 2015 7:27

    The Erratum to this article has been published in Genome Medicine 2015 7:111

  2. There has been considerable progress in the management of acute lymphoblastic leukemia (ALL) but further improvement is needed to increase long-term survival. The thiopurine agent 6-mercaptopurine (6-MP) used ...

    Authors: Laurent Chouchana, Ana Aurora Fernández-Ramos, Florent Dumont, Catherine Marchetti, Irène Ceballos-Picot, Philippe Beaune, David Gurwitz and Marie-Anne Loriot
    Citation: Genome Medicine 2015 7:37
  3. Heritable bleeding and platelet disorders (BPD) are heterogeneous and frequently have an unknown genetic basis. The BRIDGE-BPD study aims to discover new causal genes for BPD by high throughput sequencing usin...

    Authors: Sarah K Westbury, Ernest Turro, Daniel Greene, Claire Lentaigne, Anne M Kelly, Tadbir K Bariana, Ilenia Simeoni, Xavier Pillois, Antony Attwood, Steve Austin, Sjoert BG Jansen, Tamam Bakchoul, Abi Crisp-Hihn, Wendy N Erber, Rémi Favier, Nicola Foad…
    Citation: Genome Medicine 2015 7:36
  4. All cells in an individual are related to one another by a bifurcating lineage tree, in which each node is an ancestral cell that divided into two, each branch connects two nodes, and the root is the zygote. W...

    Authors: Ziming Weng, Noah Spies, Shirley X Zhu, Daniel E Newburger, Dorna Kashef-Haghighi, Serafim Batzoglou, Arend Sidow and Robert B West
    Citation: Genome Medicine 2015 7:28
  5. Preimplantation genetic diagnosis (PGD) enables profiling of embryos for genetic disorders prior to implantation. The majority of PGD testing is restricted in the scope of variants assayed or by the availabili...

    Authors: Akash Kumar, Allison Ryan, Jacob O Kitzman, Nina Wemmer, Matthew W Snyder, Styrmir Sigurjonsson, Choli Lee, Milena Banjevic, Paul W Zarutskie, Alexandra P Lewis, Jay Shendure and Matthew Rabinowitz
    Citation: Genome Medicine 2015 7:35
  6. Applying genomics to patient care demands sensitive, unambiguous and rapid characterization of a known set of clinically relevant variants in patients’ samples, an objective substantially different from the st...

    Authors: Wanding Zhou, Hao Zhao, Zechen Chong, Routbort J Mark, Agda K Eterovic, Funda Meric-Bernstam and Ken Chen
    Citation: Genome Medicine 2015 7:34
  7. With the prevalence of cardio-metabolic disorders reaching pandemic proportions, the search for modifiable causative factors has intensified. One such potential factor is the vast microbial community inhabitin...

    Authors: Tue H Hansen, Rikke J Gøbel, Torben Hansen and Oluf Pedersen
    Citation: Genome Medicine 2015 7:33
  8. Three-dimensional organotypic culture models show great promise as a tool for cancer precision medicine, with potential applications for oncogene modeling, gene discovery and chemosensitivity studies.

    Authors: Michael A Cantrell and Calvin J Kuo
    Citation: Genome Medicine 2015 7:32
  9. Most pediatric tumors have only very few somatic mutations. However, a recent study revealed that a subset of tumors from children with congenital biallelic deficiency of DNA mismatch repair exhibits a mutatio...

    Authors: Matthias Schlesner and Roland Eils
    Citation: Genome Medicine 2015 7:31
  10. RNA-sequencing (RNA-seq) is a powerful technique for the identification of genetic variants that affect gene-expression levels, either through expression quantitative trait locus (eQTL) mapping or through alle...

    Authors: Patrick Deelen, Daria V Zhernakova, Mark de Haan, Marijke van der Sijde, Marc Jan Bonder, Juha Karjalainen, K Joeri van der Velde, Kristin M Abbott, Jingyuan Fu, Cisca Wijmenga, Richard J Sinke, Morris A Swertz and Lude Franke
    Citation: Genome Medicine 2015 7:30
  11. Recent twin studies highlight the astonishing impact of non-heritable contributions to our immune health and wellbeing. Immunologists, long familiar with heterogeneity generated from within cells, must now gra...

    Authors: Alan G Baxter and Philip D Hodgkin
    Citation: Genome Medicine 2015 7:29
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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
  36. 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

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