Study design and data analysis considerations for the discovery of prognostic molecular biomarkers: a case study of progression free survival in advanced serous ovarian cancer.

abstract：:During June 10-12, 2018, the International Conference on Intelligent Biology and Medicine (ICIBM 2018) was held in Los Angeles, California, USA. The conference included 11 scientific sessions, four tutorials, one poster session, four keynote talks and four eminent scholar talks that covered a wide range of topics rang...

journal_title：BMC medical genomics

authors： Zhi D,Zhao Z,Li F,Wu Z,Liu X,Wang K

更新日期：2019-01-31 00:00:00

abstract：BACKGROUND:Non-small cell lung cancer (NSCLC) is the leading cause of cancer mortality worldwide. At present no reliable biomarkers are available to guide the management of this condition. Microarray technology may allow appropriate biomarkers to be identified but present platforms are lacking disease focus and are thu...

journal_title：BMC medical genomics

authors： Tanney A,Oliver GR,Farztdinov V,Kennedy RD,Mulligan JM,Fulton CE,Farragher SM,Field JK,Johnston PG,Harkin DP,Proutski V,Mulligan KA

更新日期：2008-05-30 00:00:00

abstract：BACKGROUND:Despite their singular origin, monozygotic twin pairs often display discordance for complex disorders including schizophrenia. It is a common (1%) and often familial disease with a discordance rate of ~50% in monozygotic twins. This high discordance is often explained by the role of yet unknown environmental...

journal_title：BMC medical genomics

authors： Castellani CA,Laufer BI,Melka MG,Diehl EJ,O'Reilly RL,Singh SM

更新日期：2015-05-06 00:00:00

abstract：BACKGROUND:DNA methylation is thought to be extensively involved in the pathogenesis of many diseases, including major psychosis. However, most studies focus on DNA methylation alteration at promoters of protein-coding genes, despite the poor correlation between DNA methylation and gene expression. METHODS:We analyzed...

journal_title：BMC medical genomics

authors： Zhao H,Xu J,Pang L,Zhang Y,Fan H,Liu L,Liu T,Yu F,Zhang G,Lan Y,Bai J,Li X,Xiao Y

更新日期：2015-10-14 00:00:00

abstract：BACKGROUND:Head and neck squamous cell carcinoma (HNSCC) is one of the most common malignancies in humans. The average 5-year survival rate is one of the lowest among aggressive cancers, showing no significant improvement in recent years. When detected early, HNSCC has a good prognosis, but most patients present metast...

journal_title：BMC medical genomics

authors： Silveira NJ,Varuzza L,Machado-Lima A,Lauretto MS,Pinheiro DG,Rodrigues RV,Severino P,Nobrega FG,Head and Neck Genome Project GENCAPO.,Silva WA Jr,de B Pereira CA,Tajara EH

更新日期：2008-11-11 00:00:00

abstract：BACKGROUND:Type 1 diabetes (T1D) is a complex disease and harmful to human health, and most of the existing biomarkers are mainly to measure the disease phenotype after the disease onset (or drastic deterioration). Until now, there is no effective biomarker which can predict the upcoming disease (or pre-disease state) ...

journal_title：BMC medical genomics

authors： Liu X,Liu R,Zhao XM,Chen L

更新日期：2013-01-01 00:00:00

abstract：BACKGROUND:In recent years, high-throughput protein interaction identification methods have generated a large amount of data. When combined with the results from other in vivo and in vitro experiments, a complex set of relationships between biological molecules emerges. The growing popularity of network analysis and da...

journal_title：BMC medical genomics

authors： Carson MB,Lu H

更新日期：2015-01-01 00:00:00

abstract：BACKGROUND:DNA methylation levels will be important for detection of epigenetic effects. However, there are few reports showing sex-related differences in the sensitivity to DNA methylation. To evaluate their sex-related individual differences in the sensitivity to methylation rigorously, we performed a systematic anal...

journal_title：BMC medical genomics

authors： Watanabe M,Honda C,Osaka Twin Research Group.,Iwatani Y,Yorifuji S,Iso H,Kamide K,Hatazawa J,Kihara S,Sakai N,Watanabe H,Makimoto K,Watanabe M,Honda C,Iwatani Y

更新日期：2016-08-26 00:00:00

abstract：BACKGROUND:One of the tasks in the 2017 iDASH secure genome analysis competition was to enable training of logistic regression models over encrypted genomic data. More precisely, given a list of approximately 1500 patient records, each with 18 binary features containing information on specific mutations, the idea was f...

journal_title：BMC medical genomics

authors： Chen H,Gilad-Bachrach R,Han K,Huang Z,Jalali A,Laine K,Lauter K

更新日期：2018-10-11 00:00:00

abstract：BACKGROUND:Advanced age-related macular degeneration (AMD) is a leading cause of blindness. While around half of the genetic contribution to advanced AMD has been uncovered, little is known about the genetic architecture of early AMD. METHODS:To identify genetic factors for early AMD, we conducted a genome-wide associ...

journal_title：BMC medical genomics

authors： Winkler TW,Grassmann F,Brandl C,Kiel C,Günther F,Strunz T,Weidner L,Zimmermann ME,Korb CA,Poplawski A,Schuster AK,Müller-Nurasyid M,Peters A,Rauscher FG,Elze T,Horn K,Scholz M,Cañadas-Garre M,McKnight AJ,Quinn N,H

更新日期：2020-08-26 00:00:00

abstract：BACKGROUND:Expression quantitative trait loci (eQTL) are genomic regions regulating RNA transcript expression levels. Genome-wide Association Studies (GWAS) have identified many variants, often in non-coding regions, with unknown functions and eQTL provide a possible mechanism by which these variants may influence obse...

journal_title：BMC medical genomics

authors： McKenzie M,Henders AK,Caracella A,Wray NR,Powell JE

更新日期：2014-06-03 00:00:00

abstract：BACKGROUND:Persistent infection by high risk HPV types (e.g. HPV-16, -18, -31, and -45) is the main risk factor for development of cervical intraepithelial neoplasia and cervical cancer. Tumor necrosis factor (TNF) is a key mediator of epithelial cell inflammatory response and exerts a potent cytostatic effect on norma...

journal_title：BMC medical genomics

authors： Termini L,Boccardo E,Esteves GH,Hirata R Jr,Martins WK,Colo AE,Neves EJ,Villa LL,Reis LF

更新日期：2008-06-27 00:00:00

abstract：:This editorial summarizes eight research articles included in this supplement issue for the 2020 International Conference on Intelligent Biology and Medicine (ICIBM 2020) conference, that was held on August 9-10, 2020 (virtual conference), with a topic on data-driven analytics in biomedical genomics. These articles co...

journal_title：BMC medical genomics

authors： Shi X,Zhao Z,Wang K,Shen L

更新日期：2020-12-28 00:00:00

abstract：BACKGROUND:Inflammation is a hallmark of many human diseases. Elucidating the mechanisms underlying systemic inflammation has long been an important topic in basic and clinical research. When primary pathogenetic events remains unclear due to its immense complexity, construction and analysis of the gene regulatory netw...

journal_title：BMC medical genomics

authors： Chen BS,Yang SK,Lan CY,Chuang YJ

更新日期：2008-09-30 00:00:00

abstract：BACKGROUND:The Cancer Genome Atlas (TCGA) is an important data resource for cancer biologists and oncologists. However, a lack of bioinformatics expertise often hinders experimental cancer biologists and oncologists from exploring the TCGA resource. Although a number of tools have been developed for facilitating cancer...

journal_title：BMC medical genomics

authors： Sun Q,Li M,Wang X

更新日期：2018-08-08 00:00:00

abstract：BACKGROUND:The purpose of this paper is to describe the data collection efforts and validation of PhenX measures in the Personalized Medicine Research Project (PMRP) cohort. METHODS:Thirty-six measures were chosen from the PhenX Toolkit within the following domains: demographics; anthropometrics; alcohol, tobacco and ...

journal_title：BMC medical genomics

authors： McCarty CA,Berg R,Rottscheit CM,Waudby CJ,Kitchner T,Brilliant M,Ritchie MD

更新日期：2014-01-14 00:00:00

abstract：BACKGROUND:Alterations in gene expression in peripheral blood cells have been shown to be sensitive to the presence and extent of coronary artery disease (CAD). A non-invasive blood test that could reliably assess obstructive CAD likelihood would have diagnostic utility. RESULTS:Microarray analysis of RNA samples from...

journal_title：BMC medical genomics

authors： Elashoff MR,Wingrove JA,Beineke P,Daniels SE,Tingley WG,Rosenberg S,Voros S,Kraus WE,Ginsburg GS,Schwartz RS,Ellis SG,Tahirkheli N,Waksman R,McPherson J,Lansky AJ,Topol EJ

更新日期：2011-03-28 00:00:00

abstract：BACKGROUND:Chiari Type I Malformation (CMI) is characterized by herniation of the cerebellar tonsils through the foramen magnum at the base of the skull, resulting in significant neurologic morbidity. As CMI patients display a high degree of clinical variability and multiple mechanisms have been proposed for tonsillar ...

journal_title：BMC medical genomics

authors： Markunas CA,Lock E,Soldano K,Cope H,Ding CK,Enterline DS,Grant G,Fuchs H,Ashley-Koch AE,Gregory SG

更新日期：2014-06-25 00:00:00

abstract：BACKGROUND:A Mendelian transmission produces phenotypic and genetic relatedness between family members, giving family-based analytical methods an important role in genetic epidemiological studies-from heritability estimations to genetic association analyses. With the advance in genotyping technologies, whole-genome seq...

journal_title：BMC medical genomics

authors： Lee S,Choi S,Qiao D,Cho M,Silverman EK,Park T,Won S

更新日期：2018-04-20 00:00:00

abstract：BACKGROUND:Preeclampsia (PE) is a pregnancy-related condition that affects both the infant and the mother. Although the role of various inflammatory molecules in PE has been demonstrated, the importance of pro-inflammatory molecules such as IL-17A, IL-23 is not well understood. In the present investigation, a potential...

journal_title：BMC medical genomics

authors： Lang X,Liu W,Hou Y,Zhao W,Yang X,Chen L,Yan Q,Cheng W

更新日期：2021-01-06 00:00:00

abstract：BACKGROUND:Detection of copy number variants (CNVs) is an important aspect of clinical testing for several disorders, including Duchenne muscular dystrophy, and is often performed using multiplex ligation-dependent probe amplification (MLPA). However, since many genetic carrier screens depend instead on next-generation...

journal_title：BMC medical genomics

authors： Kozareva V,Stroff C,Silver M,Freidin JF,Delaney NF

更新日期：2018-10-20 00:00:00

abstract：BACKGROUND:Nicolaides-Baraitser syndrome (NCBRS) is a neurodevelopmental disorder caused by pathogenic sequence variants in SMARCA2 which encodes the catalytic component of the chromatin remodeling BAF complex. Pathogenic variants in genes that encode epigenetic regulators have been associated with genome-wide changes ...

journal_title：BMC medical genomics

authors： Chater-Diehl E,Ejaz R,Cytrynbaum C,Siu MT,Turinsky A,Choufani S,Goodman SJ,Abdul-Rahman O,Bedford M,Dorrani N,Engleman K,Flores-Daboub J,Genevieve D,Mendoza-Londono R,Meschino W,Perrin L,Safina N,Townshend S,Scherer S

更新日期：2019-07-09 00:00:00

abstract：BACKGROUND:The complexity of genome informatics is a recurring challenge for genome exploration and analysis by students and other non-experts. This complexity creates a barrier to wider implementation of experiential genomics education, even in settings with substantial computational resources and expertise. Reducing ...

journal_title：BMC medical genomics

authors： Linderman MD,McElroy L,Chang L

更新日期：2019-11-27 00:00:00

abstract：BACKGROUND:Host protein-protein interaction networks are altered by invading virus proteins, which create new interactions, and modify or destroy others. The resulting network topology favors excessive amounts of virus production in a stressed host cell network. Short linear peptide motifs common to both virus and host...

journal_title：BMC medical genomics

authors： Evans P,Dampier W,Ungar L,Tozeren A

更新日期：2009-05-18 00:00:00

abstract：BACKGROUND:The HIV viral genome mutates at a high rate and poses a significant long term health risk even in the presence of combination antiretroviral therapy. Current methods for predicting a patient's response to therapy rely on site-directed mutagenesis experiments and in vitro resistance assays. In this bioinforma...

journal_title：BMC medical genomics

authors： Dampier W,Evans P,Ungar L,Tozeren A

更新日期：2009-07-23 00:00:00

abstract：BACKGROUND:While BMPR2 mutation strongly predisposes to pulmonary arterial hypertension (PAH), only 20% of mutation carriers develop clinical disease. This finding suggests that modifier genes contribute to FPAH clinical expression. Since modifiers are likely to be common alleles, this problem is not tractable by tradi...

journal_title：BMC medical genomics

authors： West J,Cogan J,Geraci M,Robinson L,Newman J,Phillips JA,Lane K,Meyrick B,Loyd J

更新日期：2008-09-29 00:00:00

abstract：BACKGROUND:Genomic data is increasingly collected by a wide array of organizations. As such, there is a growing demand to make summary information about such collections available more widely. However, over the past decade, a series of investigations have shown that attacks, rooted in statistical inference methods, can...

journal_title：BMC medical genomics

authors： Wan Z,Vorobeychik Y,Kantarcioglu M,Malin B

更新日期：2017-07-26 00:00:00

abstract：BACKGROUND:Meiotic recombination happens during the process of meiosis when chromosomes inherited from two parents exchange genetic materials to generate chromosomes in the gamete cells. The recombination events tend to occur in narrow genomic regions called recombination hotspots. Its dysregulation could lead to serio...

journal_title：BMC medical genomics

authors： Guo J,Chen H,Yang P,Lee YT,Wu M,Przytycka TM,Kwoh CK,Zheng J

更新日期：2018-04-20 00:00:00

abstract：BACKGROUND:Breast cancer comprises multiple tumor entities associated with different biological features and clinical behaviors, making individualized medicine a powerful tool to bring the right drug to the right patient. Next generation sequencing of RNA (RNA-Seq) is a suitable method to detect targets for individuali...

journal_title：BMC medical genomics

authors： Meißner T,Fisch KM,Gioia L,Su AI

更新日期：2015-05-21 00:00:00

abstract：BACKGROUND:Childhood asthma is a syndrome composed of heterogeneous phenotypes; furthermore, intrinsic biologic variation among racial/ethnic populations suggests possible genetic ancestry variation in childhood asthma. The objective of the study is to identify clinically homogeneous asthma subphenotypes in a diverse s...

journal_title：BMC medical genomics

authors： Ding L,Li D,Wathen M,Altaye M,Mersha TB

更新日期：2018-05-31 00:00:00