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  1. Gut microbiome dysbiosis has been demonstrated in subjects with newly diagnosed and chronic inflammatory bowel disease (IBD). In this study we sought to explore longitudinal changes in dysbiosis and ascertain ...

    Authors: Kelly A. Shaw, Madeline Bertha, Tatyana Hofmekler, Pankaj Chopra, Tommi Vatanen, Abhiram Srivatsa, Jarod Prince, Archana Kumar, Cary Sauer, Michael E. Zwick, Glen A. Satten, Aleksandar D. Kostic, Jennifer G. Mulle, Ramnik J. Xavier and Subra Kugathasan
    Citation: Genome Medicine 2016 8:75
    Content type: Research Published on:

  2. The liver X receptors (LXRs, NR1H2 and NR1H3) and peroxisome proliferator-activated receptor gamma (PPARG, NR1C3) nuclear receptor transcription factors (TFs) are master regulators of energy homeostasis. Intri...

    Authors: Daniel Savic, Ryne C. Ramaker, Brian S. Roberts, Emma C. Dean, Todd C. Burwell, Sarah K. Meadows, Sara J. Cooper, Michael J. Garabedian, Jason Gertz and Richard M. Myers
    Citation: Genome Medicine 2016 8:74
    Content type: Research Published on:

  3. Bloodstream infections remain one of the major challenges in intensive care units, leading to sepsis or even septic shock in many cases. Due to the lack of timely diagnostic approaches with sufficient sensitiv...

    Authors: Silke Grumaz, Philip Stevens, Christian Grumaz, Sebastian O. Decker, Markus A. Weigand, Stefan Hofer, Thorsten Brenner, Arndt von Haeseler and Kai Sohn
    Citation: Genome Medicine 2016 8:73
    Content type: Research Published on:

  4. The human gut microbiota has been implicated in most aspects of health and disease; however, most of the bacteria in this community are considered unculturable, so studies have relied on molecular-based method...

    Authors: Jennifer T. Lau, Fiona J. Whelan, Isiri Herath, Christine H. Lee, Stephen M. Collins, Premysl Bercik and Michael G. Surette
    Citation: Genome Medicine 2016 8:72
    Content type: Research Published on:

  5. Medicine and healthcare are undergoing profound changes. Whole-genome sequencing and high-resolution imaging technologies are key drivers of this rapid and crucial transformation. Technological innovation comb...

    Authors: Charles Auffray, Rudi Balling, Inês Barroso, László Bencze, Mikael Benson, Jay Bergeron, Enrique Bernal-Delgado, Niklas Blomberg, Christoph Bock, Ana Conesa, Susanna Del Signore, Christophe Delogne, Peter Devilee, Alberto Di Meglio, Marinus Eijkemans, Paul Flicek…
    Citation: Genome Medicine 2016 8:71
    Content type: Opinion Published on:

    The Erratum to this article has been published in Genome Medicine 2016 8:118

  8. A diverse B-cell repertoire is essential for recognition and response to infectious and vaccine antigens. High-throughput sequencing of B-cell receptor (BCR) genes can now be used to study the B-cell repertoir...

    Authors: Jacob D. Galson, Johannes Trück, Elizabeth A. Clutterbuck, Anna Fowler, Vincenzo Cerundolo, Andrew J. Pollard, Gerton Lunter and Dominic F. Kelly
    Citation: Genome Medicine 2016 8:68
    Content type: Research Published on:

    The Erratum to this article has been published in Genome Medicine 2016 8:81

  9. Roux-en-Y gastric bypass (RYGB) is an effective means to achieve sustained weight loss for morbidly obese individuals. Besides rapid weight reduction, patients achieve major improvements of insulin sensitivity...

    Authors: Albert Palleja, Alireza Kashani, Kristine H. Allin, Trine Nielsen, Chenchen Zhang, Yin Li, Thorsten Brach, Suisha Liang, Qiang Feng, Nils Bruun Jørgensen, Kirstine N. Bojsen-Møller, Carsten Dirksen, Kristoffer S. Burgdorf, Jens J. Holst, Sten Madsbad, Jun Wang…
    Citation: Genome Medicine 2016 8:67
    Content type: Research Published on:

  10. Patterns in expression data conserved across multiple independent disease studies are likely to represent important molecular events underlying the disease. We present the INSPIRE method to infer modules of co...

    Authors: Safiye Celik, Benjamin A. Logsdon, Stephanie Battle, Charles W. Drescher, Mara Rendi, R. David Hawkins and Su-In Lee
    Citation: Genome Medicine 2016 8:66
    Content type: Method Published on:

  11. Expression quantitative trait loci (eQTL) analysis is a powerful method to detect correlations between gene expression and genomic variants and is widely used to interpret the biological mechanism underlying i...

    Authors: Cornelis Blauwendraat, Margherita Francescatto, J. Raphael Gibbs, Iris E. Jansen, Javier Simón-Sánchez, Dena G. Hernandez, Allissa A. Dillman, Andrew B. Singleton, Mark R. Cookson, Patrizia Rizzu and Peter Heutink
    Citation: Genome Medicine 2016 8:65
    Content type: Research Published on:

  12. Worldwide, over 350 million people are chronically infected with the hepatitis B virus (HBV) and are at increased risk of developing progressive liver diseases. The confinement of HBV replication to the liver,...

    Authors: Johannes C. Schoeman, Jun Hou, Amy C. Harms, Rob J. Vreeken, Ruud Berger, Thomas Hankemeier and Andre Boonstra
    Citation: Genome Medicine 2016 8:64
    Content type: Research Published on:

  14. Personalized therapy provides the best outcome of cancer care and its implementation in the clinic has been greatly facilitated by recent convergence of enormous progress in basic cancer research, rapid advanc...

    Authors: Andrew V. Uzilov, Wei Ding, Marc Y. Fink, Yevgeniy Antipin, Andrew S. Brohl, Claire Davis, Chun Yee Lau, Chetanya Pandya, Hardik Shah, Yumi Kasai, James Powell, Mark Micchelli, Rafael Castellanos, Zhongyang Zhang, Michael Linderman, Yayoi Kinoshita…
    Citation: Genome Medicine 2016 8:62
    Content type: Research Published on:

  15. IL-4-driven alternative macrophage activation and proliferation are characteristic features of both antihelminthic immune responses and wound healing in contrast to classical macrophage activation, which prima...

    Authors: Zsolt Czimmerer, Tamas Varga, Mate Kiss, Cesaré Ovando Vázquez, Quang Minh Doan-Xuan, Dominik Rückerl, Sudhir Gopal Tattikota, Xin Yan, Zsuzsanna S. Nagy, Bence Daniel, Szilard Poliska, Attila Horvath, Gergely Nagy, Eva Varallyay, Matthew N. Poy, Judith E. Allen…
    Citation: Genome Medicine 2016 8:63
    Content type: Research Published on:

  18. The identification of somatic mosaicism in the brain lends a new perspective to our understanding of the role of gene and environment interactions in psychiatric disease risk. Somatic mutations, such as retrot...

    Authors: Tracy A. Bedrosian, Sara Linker and Fred H. Gage
    Citation: Genome Medicine 2016 8:58
    Content type: Comment Published on:

  19. Alterations in genetic and epigenetic landscapes are known to contribute to the development of different types of cancer. However, the mechanistic links between transcription factors and the epigenome which co...

    Authors: Valeriya Malysheva, Marco Antonio Mendoza-Parra, Mohamed-Ashick M. Saleem and Hinrich Gronemeyer
    Citation: Genome Medicine 2016 8:57
    Content type: Research Published on:

  20. There is increasing interest in investigating how the compositions of microbial communities are associated with human health and disease. Although existing methods have identified many associations, a proper c...

    Authors: Chong Wu, Jun Chen, Junghi Kim and Wei Pan
    Citation: Genome Medicine 2016 8:56
    Content type: METHOD Published on:

  22. The effects of probiotic supplementation on fecal microbiota composition in healthy adults have not been well established. We aimed to provide a systematic review of the potential evidence for an effect of pro...

    Authors: Nadja B. Kristensen, Thomas Bryrup, Kristine H. Allin, Trine Nielsen, Tue H. Hansen and Oluf Pedersen
    Citation: Genome Medicine 2016 8:52
    Content type: Research Published on:

  23. The genetic origins of chemotherapy resistance are well established; however, the role of epigenetics in drug resistance is less well understood. To investigate mechanisms of drug resistance, we performed syst...

    Authors: Colin Flinders, Larry Lam, Liudmilla Rubbi, Roberto Ferrari, Sorel Fitz-Gibbon, Pao-Yang Chen, Michael Thompson, Heather Christofk, David B Agus, Daniel Ruderman, Parag Mallick and Matteo Pellegrini
    Citation: Genome Medicine 2016 8:54
    Content type: Research Published on:

  24. The bromodomain containing 1 (BRD1) gene has been implicated with transcriptional regulation, brain development, and susceptibility to schizophrenia and bipolar disorder. To advance the understanding of BRD1 a...

    Authors: Tue Fryland, Jane H. Christensen, Jonatan Pallesen, Manuel Mattheisen, Johan Palmfeldt, Mads Bak, Jakob Grove, Ditte Demontis, Jenny Blechingberg, Hong Sain Ooi, Mette Nyegaard, Mads E. Hauberg, Niels Tommerup, Niels Gregersen, Ole Mors, Thomas J. Corydon…
    Citation: Genome Medicine 2016 8:53
    Content type: Research Published on:

  27. Bacteremia, or bloodstream infection (BSI), is a leading cause of death among patients with certain types of cancer. A previous study reported that intestinal domination, defined as occupation of at least 30 %...

    Authors: Emmanuel Montassier, Gabriel A. Al-Ghalith, Tonya Ward, Stephane Corvec, Thomas Gastinne, Gilles Potel, Philippe Moreau, Marie France de la Cochetiere, Eric Batard and Dan Knights
    Citation: Genome Medicine 2016 8:49
    Content type: Research Published on:

    The Erratum to this article has been published in Genome Medicine 2016 8:61

  28. Humans are virtually identical in their genetic makeup, yet the small differences in our DNA give rise to tremendous phenotypic diversity across the human population. By contrast, the metagenome of the human m...

    Authors: Jason Lloyd-Price, Galeb Abu-Ali and Curtis Huttenhower
    Citation: Genome Medicine 2016 8:51
    Content type: Review Published on:

  29. Obesity, type 2 diabetes, and non-alcoholic fatty liver disease (NAFLD) are serious health concerns, especially in Western populations. Antibiotic exposure and high-fat diet (HFD) are important and modifiable ...

    Authors: Douglas Mahana, Chad M. Trent, Zachary D. Kurtz, Nicholas A. Bokulich, Thomas Battaglia, Jennifer Chung, Christian L. Müller, Huilin Li, Richard A. Bonneau and Martin J. Blaser
    Citation: Genome Medicine 2016 8:48
    Content type: Research Published on:

  30. Recurrent Clostridium difficile infection (CDI) remains problematic, with up to 30 % of individuals diagnosed with primary CDI experiencing at least one episode of recurrence. The success of microbial-based thera...

    Authors: Anna Maria Seekatz, Krishna Rao, Kavitha Santhosh and Vincent Bensan Young
    Citation: Genome Medicine 2016 8:47
    Content type: Research Published on:

  32. A gluten-free diet (GFD) is the most commonly adopted special diet worldwide. It is an effective treatment for coeliac disease and is also often followed by individuals to alleviate gastrointestinal complaints...

    Authors: Marc Jan Bonder, Ettje F. Tigchelaar, Xianghang Cai, Gosia Trynka, Maria C. Cenit, Barbara Hrdlickova, Huanzi Zhong, Tommi Vatanen, Dirk Gevers, Cisca Wijmenga, Yang Wang and Alexandra Zhernakova
    Citation: Genome Medicine 2016 8:45
    Content type: Research Published on:

  33. The oral cavity is home to one of the most diverse microbial communities of the human body and a major entry portal for pathogens. Its homeostasis is maintained by saliva, which fulfills key functions includin...

    Authors: Niklas Grassl, Nils Alexander Kulak, Garwin Pichler, Philipp Emanuel Geyer, Jette Jung, Sören Schubert, Pavel Sinitcyn, Juergen Cox and Matthias Mann
    Citation: Genome Medicine 2016 8:44
    Content type: Research Published on:

  34. The adaptive immune response in rheumatoid arthritis (RA) is influenced by an interaction between host genetics and environment, particularly the host microbiome. Association of the gut microbiota with various...

    Authors: Jun Chen, Kerry Wright, John M. Davis, Patricio Jeraldo, Eric V. Marietta, Joseph Murray, Heidi Nelson, Eric L. Matteson and Veena Taneja
    Citation: Genome Medicine 2016 8:43
    Content type: Research Published on:

  35. The human gut harbors more than 100 trillion microbial cells, which have an essential role in human metabolic regulation via their symbiotic interactions with the host. Altered gut microbial ecosystems have be...

    Authors: Claire L. Boulangé, Ana Luisa Neves, Julien Chilloux, Jeremy K. Nicholson and Marc-Emmanuel Dumas
    Citation: Genome Medicine 2016 8:42
    Content type: Review Published on:

  37. Infections encountered in the cancer setting may arise from intensive cancer treatments or may result from the cancer itself, leading to risk of infections through immune compromise, disruption of anatomic bar...

    Authors: Ying Taur and Eric G. Pamer
    Citation: Genome Medicine 2016 8:40
    Content type: Review Published on:

  39. Colorectal cancer (CRC) is the second leading cause of death among cancers in the United States. Although individuals diagnosed early have a greater than 90 % chance of survival, more than one-third of individ...

    Authors: Nielson T. Baxter, Mack T. Ruffin IV, Mary A. M. Rogers and Patrick D. Schloss
    Citation: Genome Medicine 2016 8:37
    Content type: Research Published on:

  40. There is a growing realization that the gut–brain axis plays a key role in maintaining brain health and the stress response. Recently, the gut microbiota has emerged as a master regulator of this axis. Thus, o...

    Authors: Timothy G. Dinan and John F. Cryan
    Citation: Genome Medicine 2016 8:36
    Content type: Comment Published on:

  41. Management, manipulation, and restoration of a robust vaginal microbiota has the potential to vastly improve women’s health and disease prevention. However, a systems level understanding of how the vaginal mic...

    Authors: Jacques Ravel and Rebecca M. Brotman
    Citation: Genome Medicine 2016 8:35
    Content type: Comment Published on:

  43. More accurate diagnostic methods are pressingly needed to diagnose breast cancer, the most common malignant cancer in women worldwide. Blood-based metabolomics is a promising diagnostic method for breast cance...

    Authors: Sijia Huang, Nicole Chong, Nathan E. Lewis, Wei Jia, Guoxiang Xie and Lana X. Garmire
    Citation: Genome Medicine 2016 8:34
    Content type: Research Published on:

  45. Hepatic fibrosis is the underlying cause of cirrhosis and liver failure in nearly every form of chronic liver disease, and hepatic stellate cells (HSCs) are the primary cell type responsible for fibrosis. Long...

    Authors: Chan Zhou, Samuel R. York, Jennifer Y. Chen, Joshua V. Pondick, Daniel L. Motola, Raymond T. Chung and Alan C. Mullen
    Citation: Genome Medicine 2016 8:31
    Content type: Research Published on:

  48. NF-κB is widely involved in lymphoid malignancies; however, the functional roles and specific transcriptomes of NF-κB dimers with distinct subunit compositions have been unclear.

    Authors: Kivia A. P. de Oliveira, Eva Kaergel, Matthias Heinig, Jean-Fred Fontaine, Giannino Patone, Enrique M. Muro, Stephan Mathas, Michael Hummel, Miguel A. Andrade-Navarro, Norbert Hübner and Claus Scheidereit
    Citation: Genome Medicine 2016 8:28
    Content type: Research Published on:

  50. Limited treatment options are available for patients infected with multidrug (MDR)- or pan-drug (PDR)-resistant bacterial pathogens, resulting in infections that can persist for weeks or months. In order to be...

    Authors: Meredith S. Wright, Alina Iovleva, Michael R. Jacobs, Robert A. Bonomo and Mark D. Adams
    Citation: Genome Medicine 2016 8:26
    Content type: Research Published on:
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Genome Medicine

ISSN: 1756-994X

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