Mining the literature: new methods to exploit keyword profiles.

abstract：BACKGROUND:Recent highly publicized cases of premature patient assignment into clinical trials, resulting from non-reproducible omics analyses, have prompted many to call for a more thorough examination of translational omics and highlighted the critical need for transparency and reproducibility to ensure patient safet...

journal_title：Genome medicine

authors： Zheng CL,Ratnakar V,Gil Y,McWeeney SK

更新日期：2015-07-25 00:00:00

abstract：BACKGROUND:A comprehensive understanding of the pre-existing genetic variation in genes associated with antibiotic resistance in the Mycobacterium tuberculosis complex (MTBC) is needed to accurately interpret whole-genome sequencing data for genotypic drug susceptibility testing (DST). METHODS:We investigated mutation...

journal_title：Genome medicine

authors： Merker M,Kohl TA,Barilar I,Andres S,Fowler PW,Chryssanthou E,Ängeby K,Jureen P,Moradigaravand D,Parkhill J,Peacock SJ,Schön T,Maurer FP,Walker T,Köser C,Niemann S

更新日期：2020-03-06 00:00:00

abstract：BACKGROUND:Studies of cancer mutations have typically focused on identifying cancer driving mutations that confer growth advantage to cancer cells. However, cancer genomes accumulate a large number of passenger somatic mutations resulting from various endogenous and exogenous causes, including normal DNA damage and rep...

journal_title：Genome medicine

authors： Kim YA,Wojtowicz D,Sarto Basso R,Sason I,Robinson W,Hochbaum DS,Leiserson MDM,Sharan R,Vadin F,Przytycka TM

更新日期：2020-05-29 00:00:00

abstract：: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 has been published on how and how many pathogen strains should be selected for studies associating phenotype a...

journal_title：Genome medicine

authors： Farhat MR,Shapiro BJ,Sheppard SK,Colijn C,Murray M

更新日期：2014-11-15 00:00:00

abstract：:The Killer-cell Immunoglobulin-like Receptor (KIR) gene complex has considerable biomedical importance. Patterns of polymorphism in the KIR region include variability in the gene content of haplotypes and diverse structural arrangements. Droplet digital PCR (ddPCR) was used to identify different haplotype motifs and t...

journal_title：Genome medicine

authors： Roberts CH,Jiang W,Jayaraman J,Trowsdale J,Holland MJ,Traherne JA

更新日期：2014-03-05 00:00:00

abstract：:Primary biliary cirrhosis (PBC) is an autoimmune hepatobiliary disease characterized by immune-mediated injury of small and medium-sized bile ducts, eventually leading to liver cirrhosis. Several studies have addressed PBC immunopathology, and the data support an immune activation leading to autoantibodies and autorea...

journal_title：Genome medicine

authors： Selmi C,Torok NJ,Affronti A,Gershwin ME

更新日期：2010-01-26 00:00:00

abstract：:A report on the 62nd Annual Meeting of the American Society of Human Genetics, San Francisco, California, USA, 6-10 November 2012. ...

journal_title：Genome medicine

authors： Zielinski D,Gymrek M,Erlich Y

更新日期：2012-12-19 00:00:00

abstract：:To help overcome the bottlenecks that limit the development of diagnostic and therapeutic products, academic and industrial researchers, patient organizations and charities, and regulatory and funding institutions should redefine the basis for sharing the knowledge collected in large-scale clinical and experimental st...

journal_title：Genome medicine

authors： Auffray C

更新日期：2009-03-04 00:00:00

abstract：BACKGROUND:As public health interventions drive parasite populations to elimination, genetic epidemiology models that incorporate population genomics can be powerful tools for evaluating the effectiveness of continued intervention. However, current genetic epidemiology models may not accurately simulate the population ...

journal_title：Genome medicine

authors： Wong W,Griggs AD,Daniels RF,Schaffner SF,Ndiaye D,Bei AK,Deme AB,MacInnis B,Volkman SK,Hartl DL,Neafsey DE,Wirth DF

更新日期：2017-01-24 00:00:00

abstract：BACKGROUND:While clinical factors such as age, grade, stage, and histological subtype provide physicians with information about patient prognosis, genomic data can further improve these predictions. Previous studies have shown that germline variants in known cancer driver genes are predictive of patient outcome, but no...

journal_title：Genome medicine

authors： Chatrath A,Przanowska R,Kiran S,Su Z,Saha S,Wilson B,Tsunematsu T,Ahn JH,Lee KY,Paulsen T,Sobierajska E,Kiran M,Tang X,Li T,Kumar P,Ratan A,Dutta A

更新日期：2020-02-17 00:00:00

abstract：BACKGROUND:The human gut microbiome is associated with the development of colon cancer, and recent studies have found changes in the microbiome in cancer patients compared to healthy controls. Studying the microbial communities in the tumor microenvironment may shed light on the role of host-bacteria interactions in co...

journal_title：Genome medicine

authors： Burns MB,Lynch J,Starr TK,Knights D,Blekhman R

更新日期：2015-06-24 00:00:00

abstract：:Recent studies have demonstrated that network approaches are highly appropriate tools for understanding the extreme complexity of the aging process. Moreover, the generality of the network concept helps to define and study the aging of technological and social networks and ecosystems, which may generate novel concepts...

journal_title：Genome medicine

authors： Simkó GI,Gyurkó D,Veres DV,Nánási T,Csermely P

更新日期：2009-09-28 00:00:00

abstract：BACKGROUND:Hepatocellular carcinoma (HCC) is the one of the most common cancers and lethal diseases in the world. DNA methylation alteration is frequently observed in HCC and may play important roles in carcinogenesis and diagnosis. METHODS:Using the TCGA HCC dataset, we classified HCC patients into different methylat...

journal_title：Genome medicine

authors： Cheng J,Wei D,Ji Y,Chen L,Yang L,Li G,Wu L,Hou T,Xie L,Ding G,Li H,Li Y

更新日期：2018-05-30 00:00:00

abstract：BACKGROUND:Efforts to improve research outcomes have resulted in genomic researchers being confronted with complex and seemingly contradictory instructions about how to perform their tasks. Over the past decade, there has been increasing pressure on university researchers to commercialize their work. Concurrently, they...

journal_title：Genome medicine

authors： Caulfield T,Harmon SH,Joly Y

更新日期：2012-02-27 00:00:00

abstract：:With exome sequencing becoming a tool for mutation detection in routine diagnostics there is an increasing need for platform-independent methods of quality control. We present a genotype-weighted metric that allows comparison of all the variant calls of an exome to a high-quality reference dataset of an ethnically mat...

journal_title：Genome medicine

authors： Heinrich V,Kamphans T,Stange J,Parkhomchuk D,Hecht J,Dickhaus T,Robinson PN,Krawitz PM

更新日期：2013-07-31 00:00:00

abstract：:Neoantigens are newly formed peptides created from somatic mutations that are capable of inducing tumor-specific T cell recognition. Recently, researchers and clinicians have leveraged next generation sequencing technologies to identify neoantigens and to create personalized immunotherapies for cancer treatment. To cr...

journal_title：Genome medicine

authors： Richters MM,Xia H,Campbell KM,Gillanders WE,Griffith OL,Griffith M

更新日期：2019-08-28 00:00:00

abstract：BACKGROUND:Profiles of DNA methylation of many tissues relevant in human disease have been obtained from microarrays and are publicly available. These can be used to generate maps of chromatin compartmentalization, demarcating open and closed chromatin across the genome. Additionally, large sets of genome-wide transcri...

journal_title：Genome medicine

authors： Simmonds P,Loomis E,Curry E

更新日期：2017-06-07 00:00:00

abstract：:CRISPR/Cas9 has revolutionized cancer mouse models. Although loss-of-function genetics by CRISPR/Cas9 is well-established, generating gain-of-function alleles in somatic cancer models is still challenging because of the low efficiency of gene knock-in. Here we developed CRISPR-based Somatic Oncogene kNock-In for Cance...

journal_title：Genome medicine

authors： Mou H,Ozata DM,Smith JL,Sheel A,Kwan SY,Hough S,Kucukural A,Kennedy Z,Cao Y,Xue W

更新日期：2019-04-16 00:00:00

abstract：:The pioneering work of Jean Dausset on the HLA system established several principles that were later reflected in the Human Genome Project and contributed to the foundations of predictive, preventive, personalized and participatory (P4) medicine. To effectively develop systems medicine, we should take advantage of the...

journal_title：Genome medicine

authors： Auffray C,Charron D,Hood L

更新日期：2010-08-26 00:00:00

abstract：BACKGROUND:For circadian medicine to influence health, such as when to take a drug or undergo a procedure, a biomarker of molecular clock phase is required--one that is easily measured and generalizable across a broad population. It is not clear that any circadian biomarker yet satisfies these criteria. METHODS:We ana...

journal_title：Genome medicine

authors： Wu G,Ruben MD,Francey LJ,Smith DF,Sherrill JD,Oblong JE,Mills KJ,Hogenesch JB

更新日期：2020-08-21 00:00:00

abstract：:The cancer genome is highly complex, with hundreds of point mutations, translocations, and chromosome gains and losses per tumor. To understand the effects of these alterations, precise models are needed. Traditional approaches to the construction of mouse models are time-consuming and laborious, requiring manipulatio...

journal_title：Genome medicine

authors： Mou H,Kennedy Z,Anderson DG,Yin H,Xue W

更新日期：2015-06-09 00:00:00

abstract：BACKGROUND:DNA methylation changes that accrue in the stem cell pool of an adult tissue in line with the cumulative number of cell divisions may contribute to the observed variation in cancer risk among tissues and individuals. Thus, the construction of epigenetic "mitotic" clocks that can measure the lifetime number o...

journal_title：Genome medicine

authors： Teschendorff AE

更新日期：2020-06-24 00:00:00

abstract：:Rett syndrome is a profound neurological disorder caused by mutations in the MECP2 gene, but preclinical research has indicated that it is potentially treatable. Progress towards this goal depends on the development of increasingly relevant model systems and on our improving knowledge of MeCP2 function in the brain. ...

journal_title：Genome medicine

authors： Shah RR,Bird AP

更新日期：2017-02-17 00:00:00

abstract：:The anticonvulsant carbamazepine has a high incidence of cutaneous adverse drug reactions. A recent prospective clinical trial in Taiwan has indicated that HLA-B*1502 screening will reduce the incidence of life-threatening adverse reactions to carbamazepine, while a genome-wide association study has identified the HLA...

journal_title：Genome medicine

authors： Mushiroda T,Nakamura Y

更新日期：2011-05-30 00:00:00

abstract：BACKGROUND:Wnt signaling is an evolutionarily conserved developmental pathway that is frequently hyperactivated in cancer. While multiple protein-coding genes regulated by Wnt signaling are known, the functional lncRNAs regulated by Wnt signaling have not been systematically characterized. METHODS:We comprehensively m...

journal_title：Genome medicine

authors： Liu S,Harmston N,Glaser TL,Wong Y,Zhong Z,Madan B,Virshup DM,Petretto E

更新日期：2020-10-22 00:00:00

abstract：:Genome-wide association analyses on large patient cohorts are generating large sets of candidate disease genes. This is coupled with the availability of ever-increasing genomic databases and a rapidly expanding repository of biomedical literature. Computational approaches to disease-gene association attempt to harness...

journal_title：Genome medicine

authors： Tiffin N,Andrade-Navarro MA,Perez-Iratxeta C

更新日期：2009-08-07 00:00:00

abstract：BACKGROUND:Metabolomics, the non-targeted interrogation of small molecules in a biological sample, is an ideal technology for identifying diagnostic biomarkers. Current tissue extraction protocols involve sample destruction, precluding additional uses of the tissue. This is particularly problematic for high value sampl...

journal_title：Genome medicine

authors： Brown MV,McDunn JE,Gunst PR,Smith EM,Milburn MV,Troyer DA,Lawton KA

更新日期：2012-04-30 00:00:00

abstract：:Metabolomic analysis will provide the next large set of clues to further our understanding of human health and disease. A recent study has elucidated the significant differences in the metabolomes of adipocytes, serum and an adipocyte cell line after activation of two nuclear receptors, peroxisome proliferator activat...

journal_title：Genome medicine

authors： Patterson AD,Peters JM

更新日期：2011-08-23 00:00:00

abstract：:Stem cell banks are increasingly seen as an essential resource of biological materials for both basic and translational research. Stem cell banks support transnational access to quality-controlled and ethically sourced stem cell lines from different origins and of varying grades. According to the Organisation for Econ...

journal_title：Genome medicine

authors： Knoppers BM,Isasi R

更新日期：2010-10-05 00:00:00

abstract：BACKGROUND:Mycobacterium tuberculosis resistance to anti-tuberculosis drugs is a major threat to global public health. Whole genome sequencing (WGS) is rapidly gaining traction as a diagnostic tool for clinical tuberculosis settings. To support this informatically, previous work led to the development of the widely use...

journal_title：Genome medicine

authors： Phelan JE,O'Sullivan DM,Machado D,Ramos J,Oppong YEA,Campino S,O'Grady J,McNerney R,Hibberd ML,Viveiros M,Huggett JF,Clark TG

更新日期：2019-06-24 00:00:00