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  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. The design of effective antimicrobial therapies for serious eukaryotic pathogens requires a clear understanding of their highly variable genomes. To facilitate analysis of copy number variations, single nucleo...

    Authors: Darren A Abbey, Jason Funt, Mor N Lurie-Weinberger, Dawn A Thompson, Aviv Regev, Chad L Myers and Judith Berman
    Citation: Genome Medicine 2014 6:100
  10. Rapid molecular typing of bacterial pathogens is critical for public health epidemiology, surveillance and infection control, yet routine use of whole genome sequencing (WGS) for these purposes poses significa...

    Authors: Michael Inouye, Harriet Dashnow, Lesley-Ann Raven, Mark B Schultz, Bernard J Pope, Takehiro Tomita, Justin Zobel and Kathryn E Holt
    Citation: Genome Medicine 2014 6:90
  11. Multidrug-resistant Acinetobacter baumannii commonly causes hospital outbreaks. However, within an outbreak, it can be difficult to identify the routes of cross-infection rapidly and accurately enough to inform i...

    Authors: Mihail R Halachev, Jacqueline Z-M Chan, Chrystala I Constantinidou, Nicola Cumley, Craig Bradley, Matthew Smith-Banks, Beryl Oppenheim and Mark J Pallen
    Citation: Genome Medicine 2014 6:70
  12. Advances in genomics are contributing to the development of more effective, personalized approaches to the prevention and treatment of infectious diseases. Genetic sequencing technologies are furthering our un...

    Authors: Gail Geller, Rachel Dvoskin, Chloe L Thio, Priya Duggal, Michelle H Lewis, Theodore C Bailey, Andrea Sutherland, Daniel A Salmon and Jeffrey P Kahn
    Citation: Genome Medicine 2014 6:106
  13. Whole genome sequencing is increasingly used to study phenotypic variation among infectious pathogens and to evaluate their relative transmissibility, virulence, and immunogenicity. To date, relatively little ...

    Authors: Maha R Farhat, B Jesse Shapiro, Samuel K Sheppard, Caroline Colijn and Megan Murray
    Citation: Genome Medicine 2014 6:101
  14. Trachoma, caused by Chlamydia trachomatis, remains the worlds leading infectious cause of blindness. Repeated ocular infection during childhood leads to scarring of the conjunctiva, in-turning of the eyelashes (t...

    Authors: Yanjiao Zhou, Martin J Holland, Pateh Makalo, Hassan Joof, Chrissy h Roberts, David CW Mabey, Robin L Bailey, Matthew J Burton, George M Weinstock and Sarah E Burr
    Citation: Genome Medicine 2014 6:99
  15. Gene finding is a finite exercise, and a means to an end, rather than an end in itself. The field of human genetics should increasingly shift its attention from disease gene identification to following through...

    Authors: Jay Shendure
    Citation: Genome Medicine 2014 6:86
  16. INDELs, especially those disrupting protein-coding regions of the genome, have been strongly associated with human diseases. However, there are still many errors with INDEL variant calling, driven by library p...

    Authors: Han Fang, Yiyang Wu, Giuseppe Narzisi, Jason A ORawe, Laura T Jimenez Barrón, Julie Rosenbaum, Michael Ronemus, Ivan Iossifov, Michael C Schatz and Gholson J Lyon
    Citation: Genome Medicine 2014 6:89
  17. Although genome-wide association studies (GWAS) have identified hundreds of variants associated with a risk for autoimmune and immune-related disorders (AID), our understanding of the disease mechanisms is sti...

    Authors: Barbara Hrdlickova, Vinod Kumar, Kartiek Kanduri, Daria V Zhernakova, Subhash Tripathi, Juha Karjalainen, Riikka J Lund, Yang Li, Ubaid Ullah, Rutger Modderman, Wayel Abdulahad, Harri Lähdesmäki, Lude Franke, Riitta Lahesmaa, Cisca Wijmenga and Sebo Withoff
    Citation: Genome Medicine 2014 6:88
  18. Gene enhancer elements are noncoding segments of DNA that play a central role in regulating transcriptional programs that control development, cell identity, and evolutionary processes. Recent studies have sho...

    Authors: Olivia Corradin and Peter C Scacheri
    Citation: Genome Medicine 2014 6:85
  19. Neoadjuvant chemotherapy for breast cancer leads to considerable variability in clinical responses, with only 10 to 20% of cases achieving complete pathologic responses (pCR). Biological and clinical factors t...

    Authors: Angela Alistar, Jeff W Chou, Srikanth Nagalla, Michael A Black, Ralph D’Agostino and Lance D Miller
    Citation: Genome Medicine 2014 6:80
  20. Many common diseases, such as asthma, diabetes or obesity, involve altered interactions between thousands of genes. High-throughput techniques (omics) allow identification of such genes and their products, but...

    Authors: Mika Gustafsson, Colm E Nestor, Huan Zhang, Albert-László Barabási, Sergio Baranzini, Sören Brunak, Kian Fan Chung, Howard J Federoff, Anne-Claude Gavin, Richard R Meehan, Paola Picotti, Miguel Ángel Pujana, Nikolaus Rajewsky, Kenneth GC Smith, Peter J Sterk, Pablo Villoslada…
    Citation: Genome Medicine 2014 6:82
  21. Recently, a number of large-scale cancer genome sequencing projects have generated a large volume of somatic mutations; however, identifying the functional consequences and roles of somatic mutations in tumori...

    Authors: Huy Vuong, Feixiong Cheng, Chen-Ching Lin and Zhongming Zhao
    Citation: Genome Medicine 2014 6:81
  22. Identifying functional non-coding variants is one of the greatest unmet challenges in genetics. To help address this, we introduce an R package, SuRFR, which integrates functional annotation and prior biologic...

    Authors: Niamh M Ryan, Stewart W Morris, David J Porteous, Martin S Taylor and Kathryn L Evans
    Citation: Genome Medicine 2014 6:79
  23. Common genetic variation and rare mutations in genes encoding calcium channel subunits have pleiotropic effects on risk for multiple neuropsychiatric disorders, including autism spectrum disorder (ASD) and sch...

    Authors: Yuan Tian, Irina Voineagu, Sergiu P Paşca, Hyejung Won, Vijayendran Chandran, Steve Horvath, Ricardo E Dolmetsch and Daniel H Geschwind
    Citation: Genome Medicine 2014 6:75
  24. There are 481 ultra-conserved regions (UCRs) longer than 200 bases in the genomes of human, mouse and rat. These DNA sequences are absolutely conserved and show 100% identity with no insertions or deletions. A...

    Authors: Marco Galasso, Paola Dama, Maurizio Previati, Sukhinder Sandhu, Jeff Palatini, Vincenzo Coppola, Sarah Warner, Maria E Sana, Riccardo Zanella, Ramzey Abujarour, Caroline Desponts, Michael A Teitell, Ramiro Garzon, George Calin, Carlo M Croce and Stefano Volinia
    Citation: Genome Medicine 2014 6:76
  25. Interpretation of the multitude of variants obtained from next generation sequencing (NGS) is labor intensive and complex. Web-based interfaces such as Galaxy streamline the generation of variant lists but lac...

    Authors: Geert Vandeweyer, Lut Van Laer, Bart Loeys, Tim Van den Bulcke and R Frank Kooy
    Citation: Genome Medicine 2014 6:74
  26. Genomic information reported as haplotypes rather than genotypes will be increasingly important for personalized medicine. Current technologies generate diploid sequence data that is rarely resolved into its c...

    Authors: Gustavo Glusman, Hannah C Cox and Jared C Roach
    Citation: Genome Medicine 2014 6:73
  27. As many personal genomes are being sequenced, collaborative analysis of those genomes has become essential. However, analysis of personal genomic data raises important privacy and confidentiality issues. We pr...

    Authors: Amin Ardeshirdavani, Erika Souche, Luc Dehaspe, Jeroen Van Houdt, Joris Robert Vermeesch and Yves Moreau
    Citation: Genome Medicine 2014 6:71
  28. Effectively educating families about the risks and benefits of genomic tests such as whole exome sequencing (WES) offers numerous challenges, including the complexity of test results and potential loss of priv...

    Authors: Sarah Scollon, Katie Bergstrom, Robin A Kerstein, Tao Wang, Susan G Hilsenbeck, Uma Ramamurthy, Richard A Gibbs, Christine M Eng, Murali M Chintagumpala, Stacey L Berg, Laurence B McCullough, Amy L McGuire, Sharon E Plon and D Williams Parsons
    Citation: Genome Medicine 2014 6:69
  29. The evolutionarily conserved DNA mismatch repair (MMR) system corrects base-substitution and insertion-deletion mutations generated during erroneous replication. The mutation or inactivation of many MMR factor...

    Authors: Elena Tosti, Joseph A Katakowski, Sonja Schaetzlein, Hyun-Soo Kim, Colm J Ryan, Michael Shales, Assen Roguev, Nevan J Krogan, Deborah Palliser, Michael-Christopher Keogh and Winfried Edelmann
    Citation: Genome Medicine 2014 6:68
  30. The analysis of the genomic distribution of viral vector genomic integration sites is a key step in hematopoietic stem cell-based gene therapy applications, allowing to assess both the safety and the efficacy ...

    Authors: Andrea Calabria, Simone Leo, Fabrizio Benedicenti, Daniela Cesana, Giulio Spinozzi, Massimilano Orsini, Stefania Merella, Elia Stupka, Gianluigi Zanetti and Eugenio Montini
    Citation: Genome Medicine 2014 6:67
  31. The comparison of DNA methylation patterns across cancer types (pan-cancer methylome analyses) has revealed distinct subgroups of tumors that share similar methylation patterns. Integration of these data with ...

    Authors: Tania Witte, Christoph Plass and Clarissa Gerhauser
    Citation: Genome Medicine 2014 6:66
  32. Next-generation sequencing (NGS) methodology allows for a major expansion in current carrier screening tests. NGS testing has been shown to be analytically accurate and cost-effective, but major challenges inc...

    Authors: Thomas W Prior
    Citation: Genome Medicine 2014 6:62
  33. One of the most provocative recent observations in cancer epigenetics is the discovery of large hypomethylated blocks, including single copy genes, in colorectal cancer, that correspond in location to heteroch...

    Authors: Winston Timp, Hector Corrada Bravo, Oliver G McDonald, Michael Goggins, Chris Umbricht, Martha Zeiger, Andrew P Feinberg and Rafael A Irizarry
    Citation: Genome Medicine 2014 6:61
  34. A relatively large percentage of patients with chronic obstructive pulmonary disease (COPD) develop systemic co-morbidities that affect prognosis, among which muscle wasting is particularly debilitating. Despi...

    Authors: Peter K Davidsen, John M Herbert, Philipp Antczak, Kim Clarke, Elisabet Ferrer, Victor I Peinado, Constancio Gonzalez, Josep Roca, Stuart Egginton, Joan A Barberá and Francesco Falciani
    Citation: Genome Medicine 2014 6:59

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