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  1. Research

    Identification and characterization of a FOXA2-regulated transcriptional enhancer at a type 2 diabetes intronic locus that controls GCKR expression in liver cells

    Genome-wide association studies (GWAS) have identified more than 100 genetic loci associated with type 2 diabetes (T2D). However, the underlying biological mechanisms for many of these associations remain unkn...

    Maykel López Rodríguez, Dorota Kaminska, Kati Lappalainen, Jussi Pihlajamäki, Minna U. Kaikkonen and Markku Laakso

    Genome Medicine 2017 9:63

    Published on: 6 July 2017

  2. Research

    Linked read sequencing resolves complex genomic rearrangements in gastric cancer metastases

    Genome rearrangements are critical oncogenic driver events in many malignancies. However, the identification and resolution of the structure of cancer genomic rearrangements remain challenging even with whole ...

    Stephanie U. Greer, Lincoln D. Nadauld, Billy T. Lau, Jiamin Chen, Christina Wood-Bouwens, James M. Ford, Calvin J. Kuo and Hanlee P. Ji

    Genome Medicine 2017 9:57

    Published on: 19 June 2017

  3. Comment

    Dissecting the human microbiome with single-cell genomics

    Recent advances in genome sequencing of single microbial cells enable the assignment of functional roles to members of the human microbiome that cannot currently be cultured. This approach can reveal the genom...

    Andrew C. Tolonen and Ramnik J. Xavier

    Genome Medicine 2017 9:56

    Published on: 14 June 2017

  4. Research

    The genomic road to invasion—examining the similarities and differences in the genomes of associated oral pre-cancer and cancer samples

    It is frequently assumed that pre-invasive lesions are simpler precursors of cancer and will contain a limited subset of the genomic changes seen in their associated invasive disease. Driver mutations are thou...

    Henry M. Wood, Catherine Daly, Rebecca Chalkley, Burcu Senguven, Lisa Ross, Philip Egan, Preetha Chengot, Jennifer Graham, Neeraj Sethi, Thian K. Ong, Kenneth MacLennan, Pamela Rabbitts and Caroline Conway

    Genome Medicine 2017 9:53

    Published on: 7 June 2017

  5. Research

    Seed-effect modeling improves the consistency of genome-wide loss-of-function screens and identifies synthetic lethal vulnerabilities in cancer cells

    Genome-wide loss-of-function profiling is widely used for systematic identification of genetic dependencies in cancer cells; however, the poor reproducibility of RNA interference (RNAi) screens has been a majo...

    Alok Jaiswal, Gopal Peddinti, Yevhen Akimov, Krister Wennerberg, Sergey Kuznetsov, Jing Tang and Tero Aittokallio

    Genome Medicine 2017 9:51

    Published on: 1 June 2017

  6. Research

    A pharmacogenetic signature of high response to Copaxone in late-phase clinical-trial cohorts of multiple sclerosis

    Copaxone is an efficacious and safe therapy that has demonstrated clinical benefit for over two decades in patients with relapsing forms of multiple sclerosis (MS). On an individual level, patients show variab...

    Colin J. Ross, Fadi Towfic, Jyoti Shankar, Daphna Laifenfeld, Mathis Thoma, Matthew Davis, Brian Weiner, Rebecca Kusko, Ben Zeskind, Volker Knappertz, Iris Grossman and Michael R. Hayden

    Genome Medicine 2017 9:50

    Published on: 31 May 2017

  7. Review

    Genome annotation for clinical genomic diagnostics: strengths and weaknesses

    The Human Genome Project and advances in DNA sequencing technologies have revolutionized the identification of genetic disorders through the use of clinical exome sequencing. However, in a considerable number ...

    Charles A. Steward, Alasdair P. J. Parker, Berge A. Minassian, Sanjay M. Sisodiya, Adam Frankish and Jennifer Harrow

    Genome Medicine 2017 9:49

    Published on: 30 May 2017

  8. Research

    Genomic diagnosis for children with intellectual disability and/or developmental delay

    Developmental disabilities have diverse genetic causes that must be identified to facilitate precise diagnoses. We describe genomic data from 371 affected individuals, 309 of which were sequenced as proband-pa...

    Kevin M. Bowling, Michelle L. Thompson, Michelle D. Amaral, Candice R. Finnila, Susan M. Hiatt, Krysta L. Engel, J. Nicholas Cochran, Kyle B. Brothers, Kelly M. East, David E. Gray, Whitley V. Kelley, Neil E. Lamb, Edward J. Lose, Carla A. Rich, Shirley Simmons, Jana S. Whittle…

    Genome Medicine 2017 9:43

    Published on: 30 May 2017

  9. Research

    GLADIATOR: a global approach for elucidating disease modules

    Understanding the genetic basis of disease is an important challenge in biology and medicine. The observation that disease-related proteins often interact with one another has motivated numerous network-based ...

    Yael Silberberg, Martin Kupiec and Roded Sharan

    Genome Medicine 2017 9:48

    Published on: 26 May 2017

  10. Research

    Type 2 diabetes and obesity induce similar transcriptional reprogramming in human myocytes

    Skeletal muscle is one of the primary tissues involved in the development of type 2 diabetes (T2D). The close association between obesity and T2D makes it difficult to isolate specific effects attributed to th...

    Leif Väremo, Tora Ida Henriksen, Camilla Scheele, Christa Broholm, Maria Pedersen, Mathias Uhlén, Bente Klarlund Pedersen and Jens Nielsen

    Genome Medicine 2017 9:47

    Published on: 25 May 2017

  11. Research

    Multilevel genomics of colorectal cancers with microsatellite instability—clinical impact of JAK1 mutations and consensus molecular subtype 1

    Approximately 15% of primary colorectal cancers have DNA mismatch repair deficiency, causing a complex genome with thousands of small mutations—the microsatellite instability (MSI) phenotype. We investigated m...

    Anita Sveen, Bjarne Johannessen, Torstein Tengs, Stine A. Danielsen, Ina A. Eilertsen, Guro E. Lind, Kaja C. G. Berg, Edward Leithe, Leonardo A. Meza-Zepeda, Enric Domingo, Ola Myklebost, David Kerr, Ian Tomlinson, Arild Nesbakken, Rolf I. Skotheim and Ragnhild A. Lothe

    Genome Medicine 2017 9:46

    Published on: 24 May 2017

  12. Comment

    Pancreatic β-cell regeneration: advances in understanding the genes and signaling pathways involved

    Recent advances in β-cell regeneration in vivo are providing insights into the mechanisms involved in the conversion of distinct pancreatic cell lineages into β cells. These mechanisms mostly involve reactivat...

    Solomon Afelik and Meritxell Rovira

    Genome Medicine 2017 9:42

    Published on: 16 May 2017

    The Erratum to this article has been published in Genome Medicine 2017 9:52

  13. Research

    Lost in translation: returning germline genetic results in genome-scale cancer research

    The return of research results (RoR) remains a complex and well-debated issue. Despite the debate, actual data related to the experience of giving individual results back, and the impact these results may have...

    Amber L. Johns, Skye H. McKay, Jeremy L. Humphris, Mark Pinese, Lorraine A. Chantrill, R. Scott Mead, Katherine Tucker, Lesley Andrews, Annabel Goodwin, Conrad Leonard, Hilda A. High, Katia Nones, Ann-Marie Patch, Neil D. Merrett, Nick Pavlakis, Karin S. Kassahn…

    Genome Medicine 2017 9:41

    Published on: 28 April 2017

  14. Research

    Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson’s disease patients

    Parkinson’s disease (PD) presently is conceptualized as a protein aggregation disease in which pathology involves both the enteric and the central nervous system, possibly spreading from one to another via the...

    J. R. Bedarf, F. Hildebrand, L. P. Coelho, S. Sunagawa, M. Bahram, F. Goeser, P. Bork and U. Wüllner

    Genome Medicine 2017 9:39

    Published on: 28 April 2017

    The Erratum to this article has been published in Genome Medicine 2017 9:61

  15. Research

    Activity of distinct growth factor receptor network components in breast tumors uncovers two biologically relevant subtypes

    The growth factor receptor network (GFRN) plays a significant role in driving key oncogenic processes. However, assessment of global GFRN activity is challenging due to complex crosstalk among GFRN components,...

    Mumtahena Rahman, Shelley M. MacNeil, David F. Jenkins, Gajendra Shrestha, Sydney R. Wyatt, Jasmine A. McQuerry, Stephen R. Piccolo, Laura M. Heiser, Joe W. Gray, W. Evan Johnson and Andrea H. Bild

    Genome Medicine 2017 9:40

    Published on: 26 April 2017

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