GeneLab: Omics database for spaceflight experiments.
Abstract Motivation: - To curate and organize expensive spaceflight experiments conducted aboard space stations and maximize the scientific return of investment, while democratizing access to vast amounts of spaceflight related omics data generated from several model organisms. Results: - The GeneLab Data System (GLDS) is an open access database containing fully coordinated and curated "omics" (genomics, transcriptomics, proteomics, metabolomics) data, detailed metadata and radiation dosimetry for a variety of model organisms. GLDS is supported by an integrated data system allowing federated search ...
Source: Genomics Proteomics ... - October 17, 2018 Category: Genetics & Stem Cells Authors: Ray S, Gebre S, Fogle H, Berrios DC, Tran PB, Galazka JM, Costes SV Tags: Bioinformatics Source Type: research

Dark Proteins Important for Cellular Function.
This article is protected by copyright. All rights reserved. PMID: 30318701 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - October 15, 2018 Category: Genetics & Stem Cells Authors: Schafferhans A, O'Donoghue SI, Heinzinger M, Rost B Tags: Proteomics Source Type: research

A joint analysis of metabolomic profiles associated with muscle mass and strength in Caucasian women.
In conclusion, our study identified novel metabolites associated with sarcopenia-related traits, suggesting novel metabolic pathways for muscle regulation. PMID: 30318485 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - October 14, 2018 Category: Genetics & Stem Cells Authors: Zhao Q, Shen H, Su KJ, Tian Q, Zhao LJ, Qiu C, Garrett TJ, Liu J, Kakhniashvili D, Deng HW Tags: Aging (Albany NY) Source Type: research

Genomics and systems biology approaches in the study of lipid disorders.
GENOMICS AND SYSTEMS BIOLOGY APPROACHES IN THE STUDY OF LIPID DISORDERS. Rev Invest Clin. 2018;70(5):217-223 Authors: Rodríguez A, Pajukanta P Abstract Cardiovascular disease (CVD) is a broad definition for diseases of the heart and blood vessels with high mortality and morbidity worldwide. Atherosclerosis and hypertension are the most common causes of CVD, and multiple factors confer the susceptibility. Some of the predisposing factors are modifiable such as diet, smoking, and exercise, whereas others, including age, sex, and individual's genetic variations contributing to the CVD composition ...
Source: Genomics Proteomics ... - October 12, 2018 Category: Genetics & Stem Cells Authors: Rodríguez A, Pajukanta P Tags: Rev Invest Clin Source Type: research

Assessing the Genetic Correlations Between Blood Plasma Proteins and Osteoporosis: A Polygenic Risk Score Analysis.
Abstract Osteoporosis is a common metabolic bone disease. The impact of global blood plasma proteins on the risk of osteoporosis remains elusive now. We performed a large-scale polygenic risk score (PRS) analysis to evaluate the potential effects of blood plasma proteins on the development of osteoporosis in 2286 Caucasians, including 558 males and 1728 females. Bone mineral density (BMD) and bone areas at ulna & radius, hip, and spine were measured using Hologic 4500W DXA. BMD/bone areas values were adjusted for age, sex, height, and weight as covariates. Genome-wide SNP genotyping of 2286 Caucasian subjects ...
Source: Genomics Proteomics ... - October 10, 2018 Category: Genetics & Stem Cells Authors: Liang X, Du Y, Wen Y, Liu L, Li P, Zhao Y, Ding M, Cheng B, Cheng S, Ma M, Zhang L, Shen H, Tian Q, Guo X, Zhang F, Deng HW Tags: Calcif Tissue Int Source Type: research

Increased levels of circulating MMP3 correlate with severe rejection in face transplantation.
Abstract Face transplantation is a viable treatment option for carefully selected patients with devastating injuries to the face. However, acute rejection episodes occur in more than 80% of recipients in the first postoperative year. Unfortunately, neither a correlation between histological grades of rejection and anti-rejection treatment nor systemic surrogate markers of rejection in face transplantation are established in clinical routine. Therefore, we utilized next generation aptamer-based SOMAscan proteomics platform for non-invasive rejection biomarker discovery. Longitudinal serum samples from face transpla...
Source: Genomics Proteomics ... - October 8, 2018 Category: Genetics & Stem Cells Authors: Kollar B, Shubin A, Borges TJ, Tasigiorgos S, Win TS, Lian CG, Dillon ST, Gu X, Wyrobnik I, Murphy GF, Pomahac B, Libermann TA, Riella LV Tags: Sci Rep Source Type: research

α-actinin accounts for the bioactivity of actin preparations in inducing STAT target genes in Drosophila melanogaster.
α-actinin accounts for the bioactivity of actin preparations in inducing STAT target genes in Drosophila melanogaster. Elife. 2018 Sep 27;7: Authors: Gordon O, Henry CM, Srinivasan N, Ahrens S, Franz A, Deddouche S, Chakravarty P, Phillips D, George R, Kjaer S, Frith D, Snijders AP, Valente RS, Simoes da Silva CJ, Teixeira L, Thompson B, Dionne MS, Wood W, Reis E Sousa C Abstract Damage-associated molecular patterns (DAMPs) are molecules exposed or released by dead cells that trigger or modulate immunity and tissue repair. In vertebrates, the cytoskeletal component F-actin is a DAMP specifically...
Source: Genomics Proteomics ... - September 27, 2018 Category: Genetics & Stem Cells Authors: Gordon O, Henry CM, Srinivasan N, Ahrens S, Franz A, Deddouche S, Chakravarty P, Phillips D, George R, Kjaer S, Frith D, Snijders AP, Valente RS, Simoes da Silva CJ, Teixeira L, Thompson B, Dionne MS, Wood W, Reis E Sousa C Tags: Elife Source Type: research

A novel class of viral Ankyrin proteins targeting the host E3 ubiquitin ligase Cullin-2.
Abstract Ankyrin repeat (ANK) domains are one of the most abundant motifs in eukaryotic proteins. ANK proteins are rare amongst viruses with the exception of poxviruses, which presumably acquired them from the host via horizontal gene transfer. The architecture of poxvirus ANK proteins is however different from their cellular counterparts and this precludes a direct acquisition event. Here we combine bioinformatics analysis and quantitative proteomics to discovera new class of viral ANK proteins with a domain organisation that relates to cellular ANK proteins. These non-canonical viral ANK proteins,termed ANK/BC, ...
Source: Genomics Proteomics ... - September 26, 2018 Category: Genetics & Stem Cells Authors: Odon V, Georgana I, Holley J, Morata J, Maluquer de Motes C Tags: J Virol Source Type: research

Sarcoidosis: proteomics and new perspectives for improving personalized medicine.
Abstract INTRODUCTION: Through synergistic approaches integrating biomedical data from omics sciences to the clinical practice, precision medicine aims at more accurate identification of risk factors, characterization of endotypes, patient stratification, establishment of individualized therapy, and prediction of outcomes. Areas covered: This review evaluates the potential role of different -omics approaches for the development and application of Precision Medicine to sarcoidosis patients. This systemic and heterogeneous inflammatory disease is of unknown aetiology, affects people of any age and requires genotypic...
Source: Genomics Proteomics ... - September 25, 2018 Category: Genetics & Stem Cells Authors: Landi C, Carleo A, Cillis G, Rottoli P Tags: Expert Rev Proteomics Source Type: research

Learning and Imputation for Mass-spec Bias Reduction (LIMBR).
Abstract Motivation: Decreasing costs are making it feasible to perform time series proteomics and genomics experiments with more replicates and higher resolution than ever before. With more replicates and time points, proteome and genome-wide patterns of expression are more readily discernible. These larger experiments require more batches exacerbating batch effects and increasing the number of bias trends. In the case of proteomics, where methods frequently result in missing data this increasing scale is also decreasing the number of peptides observed in all samples. The sources of batch effects and missing data...
Source: Genomics Proteomics ... - September 24, 2018 Category: Genetics & Stem Cells Authors: Crowell AM, Greene CS, Loros JJ, Dunlap JC Tags: Bioinformatics Source Type: research

PTMD: A Database of Human Disease-associated Post-translational Modifications.
Abstract Various posttranslational modifications (PTMs) participate in nearly all aspects of biological processes by regulating protein functions, and aberrant states of PTMs are frequently implicated in human diseases. Therefore, an integral resource of PTM-disease associations (PDAs) would be a great help for both academic research and clinical use. In this work, we reported PTMD, a well-curated database containing PTMs that are associated with human diseases. We manually collected 1950 known PDAs in 749 proteins for 23 types of PTMs and 275 types of diseases from the literature. Database analyses show that phos...
Source: Genomics Proteomics ... - September 20, 2018 Category: Genetics & Stem Cells Authors: Xu H, Wang Y, Lin S, Deng W, Peng D, Cui Q, Xue Y Tags: Genomics Proteomics Bioinformatics Source Type: research

\TSNAdb: A Database for Tumor-specific Neoantigens from Immunogenomics Data Analysis.
In this study, we developed a comprehensive tumor-specific neoantigen database (TSNAdb v1.0), based on pan-cancer immunogenomic analyses of somatic mutation data and human leukocyte antigen (HLA) allele information for 16 tumor types with 7748 tumor samples from The Cancer Genome Atlas (TCGA) and The Cancer Immunome Atlas (TCIA). We predicted binding affinities between mutant/wild-type peptides and HLA class I molecules by NetMHCpan v2.8/v4.0, and presented detailed information of 3,707,562/1,146,961 potential neoantigens generated by somatic mutations of all tumor samples. Moreover, we employed recurrent mutations in comb...
Source: Genomics Proteomics ... - September 14, 2018 Category: Genetics & Stem Cells Authors: Wu J, Zhao W, Zhou B, Su Z, Gu X, Zhou Z, Chen S Tags: Genomics Proteomics Bioinformatics Source Type: research

HLBS-PopOmics: an online knowledge base to accelerate dissemination and implementation of research advances in population genomics to reduce the burden of heart, lung, blood, and sleep disorders.
Abstract Recent dramatic advances in multiomics research coupled with exponentially increasing volume, complexity, and interdisciplinary nature of publications are making it challenging for scientists to stay up-to-date on the literature. Strategies to address this challenge include the creation of online databases and warehouses to support timely and targeted dissemination of research findings. Although most of the early examples have been in cancer genomics and pharmacogenomics, the approaches used can be adapted to support investigators in heart, lung, blood, and sleep (HLBS) disorders research. In this article...
Source: Genomics Proteomics ... - September 10, 2018 Category: Genetics & Stem Cells Authors: Mensah GA, Yu W, Barfield WL, Clyne M, Engelgau MM, Khoury MJ Tags: Genet Med Source Type: research

HeteroMeth: A Database of Cell-to-cell Heterogeneity in DNA Methylation.
Abstract DNA methylation is an important epigenetic mark that plays a vital role in gene expression and cell differentiation. The average DNA methylation level among a group of cells has been extensively documented. However, the cell-to-cell heterogeneity in DNA methylation, which reflects the differentiation of epigenetic status among cells, remains less investigated. Here we established a gold standard of the cell-to-cell heterogeneity in DNA methylation based on single-cell bisulfite sequencing (BS-seq) data. With that we optimized a computational pipeline for estimating the heterogeneity in DNA methylation fro...
Source: Genomics Proteomics ... - September 6, 2018 Category: Genetics & Stem Cells Authors: Huan Q, Zhang Y, Wu S, Qian W Tags: Genomics Proteomics Bioinformatics Source Type: research

What We Learned From Big Data for Autophagy Research.
Abstract Autophagy is the process by which cytoplasmic components are engulfed in double-membraned vesicles before being delivered to the lysosome to be degraded. Defective autophagy has been linked to a vast array of human pathologies. The molecular mechanism of the autophagic machinery is well-described and has been extensively investigated. However, understanding the global organization of the autophagy system and its integration with other cellular processes remains a challenge. To this end, various bioinformatics and network biology approaches have been developed by researchers in the last few years. Recently...
Source: Genomics Proteomics ... - September 4, 2018 Category: Genetics & Stem Cells Authors: Jacomin AC, Gul L, Sudhakar P, Korcsmaros T, Nezis IP Tags: Front Cell Dev Biol Source Type: research

Quantitative Proteomics of Xenopus Embryos I, Sample Preparation.
r M Abstract Xenopus oocytes and embryos are model systems optimally suited for quantitative proteomics. This is due to the availability of large amount of protein material and the ease of physical manipulation. Furthermore, facile in vitro fertilization provides superbly synchronized embryos for cell cycle and developmental stages. Here, we detail protocols developed over the last few years for sample preparation of multiplexed proteomics with TMT-tags followed by quantitative mass spectrometry analysis using the MultiNotch MS3 approach. In this approach, each condition is barcoded with an isobaric tag at the pep...
Source: Genomics Proteomics ... - August 29, 2018 Category: Genetics & Stem Cells Authors: Gupta M, Sonnett M, Ryazanova L, Presler M, Wühr M Tags: Methods Mol Biol Source Type: research

Deciphering the oviductal extracellular vesicles content across the estrous cycle: implications for the gametes-oviduct interactions and the environment of the potential embryo.
lod P Abstract BACKGROUND: The success of early reproductive events depends on an appropriate communication between gametes/embryos and the oviduct. Extracellular vesicles (EVs) contained in oviductal secretions have been suggested as new players in mediating this crucial cross-talk by transferring their cargo (proteins, mRNA and small ncRNA) from cell to cell. However, little is known about the oviductal EVs (oEVS) composition and their implications in the reproductive success. The aim of the study was to determine the oEVs content at protein, mRNA and small RNA level and to examine whether the oEVs content is un...
Source: Genomics Proteomics ... - August 22, 2018 Category: Genetics & Stem Cells Authors: Almiñana C, Tsikis G, Labas V, Uzbekov R, da Silveira JC, Bauersachs S, Mermillod P Tags: BMC Genomics Source Type: research

Proteomic analysis of the hypothalamus of broiler-type Taiwan country chickens in response to acute heat stress.
This study investigated global protein changes in the hypothalamus of broiler-type Taiwan country chickens (TCCs) after acute heat stress. Twelve TCC hens aged 30 weeks were allocated to groups subjected to acute heat stress at 38°C for 2 hr without recovery, with 2 hr of recovery, and with 6 hr of recovery; a control group was maintained at 25°C. Hypothalami were collected for protein expression analysis at the end of each time point. The results showed 114 protein spots differentially expressed after acute heat stress. Most of the differentially expressed proteins were involved in cellular pro...
Source: Genomics Proteomics ... - August 20, 2018 Category: Genetics & Stem Cells Authors: Tu WL, Cheng CY, Chen CJ, Chan HL, Wang SH, Tang PC, Chen CF, Chen HH, Lee YP, Chen SE, Huang SY Tags: Anim Sci J Source Type: research

Trends in herbgenomics.
Abstract From Shen Nong's Herbal Classic (Shennong Bencao Jing) to the Compendium of Materia Medica (Bencao Gangmu) and the first scientific Nobel Prize for the mainland of China, each milestone in the historical process of the development of traditional Chinese medicine (TCM) involves screening, testing and integrating. After thousands of years of inheritance and development, herbgenomics (bencaogenomics) has bridged the gap between TCM and international advanced omics studies, promoting the application of frontier technologies in TCM. It is a discipline that uncovers the genetic information and regulatory networ...
Source: Genomics Proteomics ... - August 14, 2018 Category: Genetics & Stem Cells Authors: Xin T, Zhang Y, Pu X, Gao R, Xu Z, Song J Tags: Sci China Life Sci Source Type: research

Identification, Biosynthesis, and Decapping of NAD-Capped RNAs in B.  subtilis.
Identification, Biosynthesis, and Decapping of NAD-Capped RNAs in B. subtilis. Cell Rep. 2018 Aug 14;24(7):1890-1901.e8 Authors: Frindert J, Zhang Y, Nübel G, Kahloon M, Kolmar L, Hotz-Wagenblatt A, Burhenne J, Haefeli WE, Jäschke A Abstract The ubiquitous coenzyme nicotinamide adenine dinucleotide (NAD) decorates various RNAs in different organisms. In the proteobacterium Escherichia coli, the NAD-cap confers stability against RNA degradation. To date, NAD-RNAs have not been identified in any other bacterial microorganism. Here, we report the identification of NAD-RNA in the firmicute ...
Source: Genomics Proteomics ... - August 14, 2018 Category: Genetics & Stem Cells Authors: Frindert J, Zhang Y, Nübel G, Kahloon M, Kolmar L, Hotz-Wagenblatt A, Burhenne J, Haefeli WE, Jäschke A Tags: Cell Rep Source Type: research

Highly multiplexed proteomic analysis reveals significant tissue and exosomal coagulation pathway derangement in chronic rhinosinusitis with nasal polyps.
Abstract BACKGROUND: The coagulation pathway has been previously implicated in the etiopathogenesis of chronic rhinosinusitis with nasal polyps (CRSwNP) through analysis of individual proteins within the cascade. The purpose of this study was to: (1) apply a large-scale proteomic approach to confirm these previous findings; and (2) correlate the protein aberrations between tissue and exosomes to establish exosomal proteomics as a method to probe the pathophysiology of CRSwNP. METHODS: This investigation was an internal review board-approved study in which matched tissue and mucus exosomal proteomes were compa...
Source: Genomics Proteomics ... - August 9, 2018 Category: Genetics & Stem Cells Authors: Mueller SK, Nocera AL, Dillon ST, Wu D, Libermann TA, Bleier BS Tags: Int Forum Allergy Rhinol Source Type: research

The Cancer Omics Atlas: an integrative resource for cancer omics annotations.
CONCLUSIONS: TCOA is a useful tool that supplies a number of unique and new functions complementary to the existing tools to facilitate exploration of the TCGA resource. PMID: 30089500 [PubMed - in process] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - August 8, 2018 Category: Genetics & Stem Cells Authors: Sun Q, Li M, Wang X Tags: BMC Med Genomics Source Type: research

Prolonged restraint stressor exposure in outbred CD-1 mice impacts microbiota, colonic inflammation, and short chain fatty acids.
Abstract Stressor-exposure has been shown to exacerbate inflammation and change the composition of the gastrointestinal microbiota; however stressor-induced effects on microbiota-derived metabolites and their receptors are unknown. Thus, bacterial-produced short chain fatty acids (SCFAs), as well as microbial community composition, were assessed in the colons of mice exposed to stress during infection with Citrobacter rodentium. Mice were exposed to overnight restraint on 7 consecutive nights, or left undisturbed as a control. After the first exposure of restraint, mice were orally challenged with C. rodentium or ...
Source: Genomics Proteomics ... - August 5, 2018 Category: Genetics & Stem Cells Authors: Maltz RM, Keirsey J, Kim SC, Mackos AR, Gharaibeh RZ, Moore CC, Xu J, Bakthavatchalu V, Somogyi A, Bailey MT Tags: PLoS One Source Type: research

Mitochondrial genomics in the cancer cell line encyclopedia and a scoring method to effectively pair cell lines for cytoplasmic hybridization.
Abstract Mitochondrial sequence variants have been associated with many human diseases, including cancer. A well-established experimental strategy to assess the impact of mitochondrial sequence variants is to generate cytoplasmic hybrids (cybrids). Cybridization facilitates the study of mitochondrial DNA (mtDNA) mutations under a controlled nuclear genetic background. However, in generating cybrids, it is important to select most suitable mtDNA donor and recipient cells so that any change in recipient's cellular phenotype may be attributed to the introduction, through the donor, of mutations in the gene of interes...
Source: Genomics Proteomics ... - July 31, 2018 Category: Genetics & Stem Cells Authors: Grandhi S, Gould L, Wang J, Grandhi A, LaFramboise T Tags: Mitochondrion Source Type: research

Whole genome SNP analysis suggests unique virulence factor differences of the Beijing and Manila families of Mycobacterium tuberculosis found in Hawaii.
This study further identified an ancient clade that shared some virulence factor mutations with the Manila family, and investigated the relationship of those and other "Manila-like" spoligotypes to the Manila family with this SNP dataset. This work identified a set of virulence genes that are worth pursuing to determine potential differences in transmission or virulence displayed by these two Mtb families. PMID: 30036392 [PubMed - in process] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - July 25, 2018 Category: Genetics & Stem Cells Authors: Koster K, Largen A, Foster JT, Drees KP, Qian L, Desmond EP, Wan X, Hou S, Douglas JT Tags: PLoS One Source Type: research

Maternal auxin supply contributes to early embryo patterning in Arabidopsis.
haus T, Friml J, Laux T Abstract The angiosperm seed is composed of three genetically distinct tissues: the diploid embryo that originates from the fertilized egg cell, the triploid endosperm that is produced from the fertilized central cell, and the maternal sporophytic integuments that develop into the seed coat1. At the onset of embryo development in Arabidopsis thaliana, the zygote divides asymmetrically, producing a small apical embryonic cell and a larger basal cell that connects the embryo to the maternal tissue2. The coordinated and synchronous development of the embryo and the surrounding integuments, and...
Source: Genomics Proteomics ... - July 16, 2018 Category: Genetics & Stem Cells Authors: Robert HS, Park C, Gutièrrez CL, Wójcikowska B, Pěnčík A, Novák O, Chen J, Grunewald W, Dresselhaus T, Friml J, Laux T Tags: Nat Plants Source Type: research

iSEE: Interactive SummarizedExperiment Explorer.
Abstract Data exploration is critical to the comprehension of large biological data sets generated by high-throughput assays such as sequencing. However, most existing tools for interactive visualisation are limited to specific assays or analyses. Here, we present the iSEE (Interactive SummarizedExperiment Explorer) software package, which provides a general visual interface for exploring data in a SummarizedExperiment object. iSEE is directly compatible with many existing R/Bioconductor packages for analysing high-throughput biological data, and provides useful features such as simultaneous examination of (meta)d...
Source: Genomics Proteomics ... - July 15, 2018 Category: Genetics & Stem Cells Authors: Rue-Albrecht K, Marini F, Soneson C, Lun ATL Tags: F1000Res Source Type: research

Genetic variation of SORBS1 gene is associated with glucose homeostasis and age at onset of diabetes: A SAPPHIRe Cohort Study.
Abstract The SORBS1 gene plays an important role in insulin signaling. We aimed to examine whether common single-nucleotide polymorphisms (SNPs) of SORBS1 are associated with prevalence and incidence of diabetes, age at onset of diabetes, and the related traits of glucose homeostasis. A total of 1135 siblings from 492 ethnic Chinese families were recruited at baseline, and 630 were followed up for 5.19 ± 0.96 years. Nine SNPs including rs7081076, rs2281939, rs3818540, rs2274490, rs61739184, rs726176, rs2296966, rs17849148, and rs3193970 were genotyped and examined. To deal with correlated data...
Source: Genomics Proteomics ... - July 12, 2018 Category: Genetics & Stem Cells Authors: Chang TJ, Wang WC, Hsiung CA, He CT, Lin MW, Sheu WH, Chang YC, Quertermous T, Chen YI, Rotter JI, Chuang LM, SAPPHIRe Study Group Tags: Sci Rep Source Type: research

CD44 glycoprotein in cancer: a molecular conundrum hampering clinical applications.
Abstract CD44 is a heavily glycosylated membrane receptor playing a key role in cell adhesion, signal transduction and cytoskeleton remodelling. It is also one of the most studied glycoproteins in cancer, frequently explored for stem cell identification, and associated with chemoresistance and metastasis. However, CD44 is a general designation for a large family of splicing variants exhibiting different degrees of glycosylation and, potentially, functionally distinct roles. Moreover, structural diversity associated with ambiguous nomenclature has delayed clinical developments. Herein, we attempt to comprehensively...
Source: Genomics Proteomics ... - July 10, 2018 Category: Genetics & Stem Cells Authors: Azevedo R, Gaiteiro C, Peixoto A, Relvas-Santos M, Lima L, Santos LL, Ferreira JA Tags: Clin Proteomics Source Type: research

Genome-wide MicroRNA Expression Profiles in COPD: Early Predictors for Cancer Development.
oup Abstract Chronic obstructive pulmonary disease (COPD) significantly increases the risk for developing cancer. Biomarker studies frequently follow a case-control set-up in which patients diagnosed with a disease are compared to controls. Longitudinal cohort studies such as the COPD-centered German COPD and SYstemic consequences-COmorbidities NETwork (COSYCONET) study provide the patient and biomaterial base for discovering predictive molecular markers. We asked whether microRNA (miRNA) profiles in blood collected from COPD patients prior to a tumor diagnosis could support an early diagnosis of tumor development...
Source: Genomics Proteomics ... - July 5, 2018 Category: Genetics & Stem Cells Authors: Keller A, Fehlmann T, Ludwig N, Kahraman M, Laufer T, Backes C, Vogelmeier C, Diener C, Biertz F, Herr C, Jörres RA, Lenhof HP, Meese E, Bals R, COSYCONET Study Group Tags: Genomics Proteomics Bioinformatics Source Type: research

Proteomic biomarkers of cognitive impairment in obstructive sleep apnea syndrome.
CONCLUSIONS: Proteomic biomarkers in participants with cognitive impairment suggest roles for insulin, and vascular signaling pathways, some of which are similar to findings in Alzheimer's disease. A better understanding of the pathogenic mechanisms of CI in OSAS will help focus clinical trials needed in this patient population. PMID: 29968150 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - July 2, 2018 Category: Genetics & Stem Cells Authors: Lal C, Hardiman G, Kumbhare S, Strange C Tags: Sleep Breath Source Type: research

Community-Driven Data Analysis Training for Biology.
, Le Corguillé G, Manke T, Mareuil F, Ramírez F, Ryan D, Sigloch FC, Soranzo N, Wolff J, Videm P, Wolfien M, Wubuli A, Yusuf D, Galaxy Training Network, Taylor J, Backofen R, Nekrutenko A, Grüning B Abstract The primary problem with the explosion of biomedical datasets is not the data, not computational resources, and not the required storage space, but the general lack of trained and skilled researchers to manipulate and analyze these data. Eliminating this problem requires development of comprehensive educational resources. Here we present a community-driven framework that enables modern, inte...
Source: Genomics Proteomics ... - June 27, 2018 Category: Genetics & Stem Cells Authors: Batut B, Hiltemann S, Bagnacani A, Baker D, Bhardwaj V, Blank C, Bretaudeau A, Brillet-Guéguen L, Čech M, Chilton J, Clements D, Doppelt-Azeroual O, Erxleben A, Freeberg MA, Gladman S, Hoogstrate Y, Hotz HR, Houwaart T, Jagtap P, Larivière D, Le Corgui Tags: Cell Syst Source Type: research

Decreased mitochondrial respiration in aneurysmal aortas of Fibulin-4 mutant mice is linked to PGC1A regulation.
Conclusion: Our data indicate altered mitochondrial function and metabolic dysregulation, leading to increased ROS levels and altered energy production, as a novel mechanism, which may contribute to thoracic aortic aneurysm formation. PMID: 29931197 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - June 21, 2018 Category: Genetics & Stem Cells Authors: van der Pluijm I, Burger J, van Heijningen PM, IJpma A, van Vliet N, Milanese C, Schoonderwoerd K, Sluiter W, Ringuette LJ, Dekkers DHW, Que I, Kaijzel EL, Te Riet L, MacFarlane E, Das D, van der Linden R, Vermeij M, Demmers JA, Mastroberardino PG, Davis Tags: Cardiovasc Res Source Type: research

Sustainable data and metadata management at the BD2K-LINCS Data Coordination and Integration Center.
SC Abstract The NIH-funded LINCS Consortium is creating an extensive reference library of cell-based perturbation response signatures and sophisticated informatics tools incorporating a large number of perturbagens, model systems, and assays. To date, more than 350 datasets have been generated including transcriptomics, proteomics, epigenomics, cell phenotype and competitive binding profiling assays. The large volume and variety of data necessitate rigorous data standards and effective data management including modular data processing pipelines and end-user interfaces to facilitate accurate and reliable data exch...
Source: Genomics Proteomics ... - June 19, 2018 Category: Genetics & Stem Cells Authors: Stathias V, Koleti A, Vidović D, Cooper DJ, Jagodnik KM, Terryn R, Forlin M, Chung C, Torre D, Ayad N, Medvedovic M, Ma'ayan A, Pillai A, Schürer SC Tags: Sci Data Source Type: research

Salivary Exosomes: Emerging Roles in Systemic Disease.
Abstract Saliva, which contains biological information, is considered a valuable diagnostic tool for local and systemic diseases and conditions because, similar to blood, it contains important molecules like DNA, RNA, and proteins. Exosomes are cell-derived vesicles 30-100 nm in diameter with substantial biological functions, including intracellular communication and signalling. These vesicles, which are present in bodily fluids, including saliva, are released upon fusion of multivesicular bodies (MVBs) with the cellular plasma membrane. Salivary diagnosis has notable advantages, which include noninvasiveness, eas...
Source: Genomics Proteomics ... - June 16, 2018 Category: Genetics & Stem Cells Authors: Han Y, Jia L, Zheng Y, Li W Tags: Int J Biol Sci Source Type: research

Author Correction: The landscape of genomic alterations across childhood cancers.
S, Waszak S, Blattmann C, Borkhardt A, Kuhlen M, Eggert A, Fulda S, Gessler M, Wegert J, Kappler R, Baumhoer D, Burdach S, Kirschner-Schwabe R, Kontny U, Kulozik AE, Lohmann D, Hettmer S, Eckert C, Bielack S, Nathrath M, Niemeyer C, Richter GH, Schulte J, Siebert R, Westermann F, Molenaar JJ, Vassal G, Witt H, Burkhardt B, Kratz CP, Witt O, van Tilburg CM, Kramm CM, Fleischhack G, Dirksen U, Rutkowski S, Frühwald M, von Hoff K, Wolf S, Klingebiel T, Koscielniak E, Landgraf P, Koster J, Resnick AC, Zhang J, Liu Y, Zhou X, Waanders AJ, Zwijnenburg DA, Raman P, Brors B, Weber UD, Northcott PA, Pajtler KW, Kool M, Piro RM...
Source: Genomics Proteomics ... - June 6, 2018 Category: Genetics & Stem Cells Authors: Gröbner SN, Worst BC, Weischenfeldt J, Buchhalter I, Kleinheinz K, Rudneva VA, Johann PD, Balasubramanian GP, Segura-Wang M, Brabetz S, Bender S, Hutter B, Sturm D, Pfaff E, Hübschmann D, Zipprich G, Heinold M, Eils J, Lawerenz C, Erkek S, Lambo S, Wasz Tags: Nature Source Type: research

Stability and reproducibility of proteomic profiles measured with an aptamer-based platform.
Abstract The feasibility of SOMAscan, a multiplex, high sensitivity proteomics platform, for use in studies using archived plasma samples has not yet been assessed. We quantified 1,305 proteins from plasma samples donated by 16 Nurses' Health Study (NHS) participants, 40 NHSII participants, and 12 local volunteers. We assessed assay reproducibility using coefficients of variation (CV) from duplicate samples and intra-class correlation coefficients (ICC) and Spearman correlation coefficients (r) of samples processed (i.e., centrifuged and aliquoted into separate components) immediately, 24, and 48 hours afte...
Source: Genomics Proteomics ... - May 30, 2018 Category: Genetics & Stem Cells Authors: Kim CH, Tworoger SS, Stampfer MJ, Dillon ST, Gu X, Sawyer SJ, Chan AT, Libermann TA, Eliassen AH Tags: Sci Rep Source Type: research

Cerebrospinal Fluid Protein Changes in Preeclampsia.
Abstract The molecular mechanisms underlying seizure susceptibility in preeclampsia are unknown. We hypothesized that altered expression of distinct proteins in the cerebrospinal fluid (CSF) may reflect pathophysiological changes in the central nervous system that contribute to the neurological manifestations of severe preeclampsia. We obtained CSF samples from 13 patients with preeclampsia and 14 control patients during spinal anesthesia before delivery and analyzed them by SOMAscan, an aptamer-based proteomics platform for alterations in 1310 protein levels. Ingenuity Pathway Analysis was conducted to highlight ...
Source: Genomics Proteomics ... - May 29, 2018 Category: Genetics & Stem Cells Authors: Ciampa E, Li Y, Dillon S, Lecarpentier E, Sorabella L, Libermann TA, Karumanchi SA, Hess PE Tags: Hypertension Source Type: research

SHMT2 and the BRCC36/BRISC deubiquitinase regulate HIV-1 Tat K63-ubiquitylation and destruction by autophagy.
Abstract HIV-1 Tat is a key regulator of viral transcription, however little is known about the mechanisms that control its turnover in T cells. Here we use a novel proteomics technique, called DiffPOP, to identify the molecular target of JIB-04, a small molecule compound that potently and selectively blocks HIV-1 Tat expression, transactivation, and virus replication in T cell lines. Mass-spectrometry analysis of whole-cell extracts from 2D10 Jurkat T cells revealed that JIB-04 targets Serine Hydroxymethyltransferase 2 (SHMT2), a regulator of glycine biosynthesis and an adaptor for the BRCC36 K63Ub-specific deubi...
Source: Genomics Proteomics ... - May 23, 2018 Category: Genetics & Stem Cells Authors: Xu M, Moresco JJ, Chang M, Mukim A, Smith D, Diedrich JK, Yates JR, Jones KA Tags: PLoS Pathog Source Type: research

EuPathDB: The Eukaryotic Pathogen Genomics Database Resource.
Abstract Fighting infections and developing novel drugs and vaccines requires advanced knowledge of pathogen's biology. Readily accessible genomic, functional genomic, and population data aids biological and translational discovery. The Eukaryotic Pathogen Database Resources ( http://eupathdb.org ) are data mining resources that support hypothesis driven research by facilitating the discovery of meaningful biological relationships from large volumes of data. The resource encompasses 13 sites that support over 170 species including pathogenic protists, oomycetes, and fungi as well as evolutionarily related nonpatho...
Source: Genomics Proteomics ... - May 17, 2018 Category: Genetics & Stem Cells Authors: Warrenfeltz S, Basenko EY, Crouch K, Harb OS, Kissinger JC, Roos DS, Shanmugasundram A, Silva-Franco F Tags: Methods Mol Biol Source Type: research

Author Correction: Kanglaite sensitizes colorectal cancer cells to Taxol via NF- κΒ inhibition and connexin 43 upregulation.
Author Correction: Kanglaite sensitizes colorectal cancer cells to Taxol via NF-κΒ inhibition and connexin 43 upregulation. Sci Rep. 2018 Apr 12;8(1):6141 Authors: Wang Y, Zhang C, Zhang S, Zhao Z, Wang J, Song J, Wang Y, Liu J, Hou S Abstract A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper. PMID: 29643394 [PubMed - in process] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - April 12, 2018 Category: Genetics & Stem Cells Authors: Wang Y, Zhang C, Zhang S, Zhao Z, Wang J, Song J, Wang Y, Liu J, Hou S Tags: Sci Rep Source Type: research

Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions.
CONCLUSIONS: PSI-MI XML3.0 has been developed by the data producers, data users, tool developers and database providers who constitute the PSI-MI workgroup. This group now actively supports PSI-MI XML2.5 as the main interchange format for experimental data, PSI-MI XML3.0 which additionally handles more complex data types, and the simpler, tab-delimited MITAB2.5, 2.6 and 2.7 for rapid parsing and download. PMID: 29642841 [PubMed - in process] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - April 11, 2018 Category: Genetics & Stem Cells Authors: Sivade Dumousseau M, Alonso-López D, Ammari M, Bradley G, Campbell NH, Ceol A, Cesareni G, Combe C, De Las Rivas J, Del-Toro N, Heimbach J, Hermjakob H, Jurisica I, Koch M, Licata L, Lovering RC, Lynn DJ, Meldal BHM, Micklem G, Panni S, Porras P, Ricard- Tags: BMC Bioinformatics Source Type: research

VSClust: Feature-based variance-sensitive clustering of omics data.
We present VSClust that accounts for feature-specific variance. Based on an algorithm derived from fuzzy clustering, VSClust unifies statistical testing with pattern recognition to cluster the data into feature groups that more accurately reflect the underlying molecular and functional behavior. We apply VSClust to artificial and experimental data sets comprising hundreds to more than 80,000 features across 6-20 different conditions including genomics, transcriptomics, proteomics and metabolomics experiments. VSClust avoids arbitrary averaging methods, outperforms standard fuzzy c-means clustering and simplifies the data a...
Source: Genomics Proteomics ... - April 9, 2018 Category: Genetics & Stem Cells Authors: Schwämmle V, Jensen ON Tags: Bioinformatics Source Type: research

Specific Transcriptome Changes Associated with Blood Pressure Reduction in Hypertensive Patients After Relaxation Response Training.
CONCLUSIONS: These findings provide the first insights into the molecular mechanisms that are associated with the beneficial effects of the RR on HTN. PMID: 29616846 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - April 4, 2018 Category: Genetics & Stem Cells Authors: Bhasin MK, Denninger JW, Huffman JC, Joseph MG, Niles H, Chad-Friedman E, Goldman R, Buczynski-Kelley B, Mahoney BA, Fricchione GL, Dusek JA, Benson H, Zusman RM, Libermann TA Tags: J Altern Complement Med Source Type: research

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas.
eghi S, Mungall KL, Robertson AG, Benz C, Schultz A, Kanchi RS, Gay CM, Hegde A, Diao L, Wang J, Ma W, Sumazin P, Chiu HS, Chen TW, Gunaratne P, Donehower L, Rader JS, Zuna R, Al-Ahmadie H, Lazar AJ, Flores ER, Tsai KY, Zhou JH, Rustgi AK, Drill E, Shen R, Wong CK, Cancer Genome Atlas Research Network, Stuart JM, Laird PW, Hoadley KA, Weinstein JN, Peto M, Pickering CR, Chen Z, Van Waes C Abstract This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smoking and/or human papillomavirus (HPV)...
Source: Genomics Proteomics ... - April 3, 2018 Category: Genetics & Stem Cells Authors: Campbell JD, Yau C, Bowlby R, Liu Y, Brennan K, Fan H, Taylor AM, Wang C, Walter V, Akbani R, Byers LA, Creighton CJ, Coarfa C, Shih J, Cherniack AD, Gevaert O, Prunello M, Shen H, Anur P, Chen J, Cheng H, Hayes DN, Bullman S, Pedamallu CS, Ojesina AI, Sa Tags: Cell Rep Source Type: research

The influence of transcript assembly on the proteogenomics discovery of microproteins.
Abstract Proteogenomics methods have identified many non-annotated protein-coding genes in the human genome. Many of the newly discovered protein-coding genes encode peptides and small proteins, referred to collectively as microproteins. Microproteins are produced through ribosome translation of small open reading frames (smORFs). The discovery of many smORFs reveals a blind spot in traditional gene-finding algorithms for these genes. Biological studies have found roles for microproteins in cell biology and physiology, and the potential that there exists additional bioactive microproteins drives the interest in de...
Source: Genomics Proteomics ... - March 28, 2018 Category: Genetics & Stem Cells Authors: Ma J, Saghatelian A, Shokhirev MN Tags: PLoS One Source Type: research

Comparative 'omics analyses differentiate Mycobacterium tuberculosis and Mycobacterium bovis and reveal distinct macrophage responses to infection with the human and bovine tubercle bacilli.
Abstract Members of the Mycobacterium tuberculosis complex (MTBC) are the causative agents of tuberculosis in a range of mammals, including humans. A key feature of MTBC pathogens is their high degree of genetic identity yet distinct host tropism. Notably, while Mycobacterium bovis is highly virulent and pathogenic for cattle, the human pathogen M. tuberculosis is attenuated in cattle. Previous research also suggests that host preference amongst MTBC members has a basis in host innate immune responses. To explore MTBC host tropism, we present in-depth profiling of the MTBC reference strains M. bovis AF2122/97 and ...
Source: Genomics Proteomics ... - March 20, 2018 Category: Genetics & Stem Cells Authors: Malone KM, Rue-Albrecht K, Magee DA, Conlon K, Schubert OT, Nalpas NC, Browne JA, Smyth A, Gormley E, Aebersold R, MacHugh DE, Gordon SV Tags: Microb Genom Source Type: research

Acute Heat Stress Changes Protein Expression in the Testes of a Broiler-Type Strain of Taiwan Country Chickens.
In conclusion, acute heat stress causes a change in protein expression in the testes of broiler-type B strain TCCs and may thus impair cell morphology, spermatogenesis, and apoptosis. The expression of heat shock proteins increased to attenuate the testicular injury induced by acute heat stress. PMID: 29553885 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - March 19, 2018 Category: Genetics & Stem Cells Authors: Wang SH, Cheng CY, Chen CJ, Chan HL, Chen HH, Tang PC, Chen CF, Lee YP, Huang SY Tags: Anim Biotechnol Source Type: research

Systematic Functional Annotation of Somatic Mutations in Cancer.
rchin R, Ding L, Lu Y, Cheung LWT, Chen K, Shaw KR, Meric-Bernstam F, Scott KL, Yi S, Sahni N, Liang H, Mills GB Abstract The functional impact of the vast majority of cancer somatic mutations remains unknown, representing a critical knowledge gap for implementing precision oncology. Here, we report the development of a moderate-throughput functional genomic platform consisting of efficient mutant generation, sensitive viability assays using two growth factor-dependent cell models, and functional proteomic profiling of signaling effects for select aberrations. We apply the platform to annotate>1,000 genomic abe...
Source: Genomics Proteomics ... - March 12, 2018 Category: Genetics & Stem Cells Authors: Ng PK, Li J, Jeong KJ, Shao S, Chen H, Tsang YH, Sengupta S, Wang Z, Bhavana VH, Tran R, Soewito S, Minussi DC, Moreno D, Kong K, Dogruluk T, Lu H, Gao J, Tokheim C, Zhou DC, Johnson AM, Zeng J, Ip CKM, Ju Z, Wester M, Yu S, Li Y, Vellano CP, Schultz N, K Tags: Cancer Cell Source Type: research

Exosomal αvβ6 integrin is required for monocyte M2 polarization in prostate cancer.
We describe a novel αvβ6-mediated signaling pathway that has profound effects on the microenvironment. We show that αvβ6 is transferred from cancer cells to monocytes, including β6-/- monocytes, by exosomes and that monocytes from prostate cancer patients, but not from healthy volunteers, express αvβ6. Cancer cell exosomes, purified via density gradients, promote M2 polarization, whereas αvβ6 down-regulation in exosomes inhibits M2 polarization in recipient monocytes. Also, as evaluated by our proteomic analysis, αvβ6 down-regulation causes a significant increase ...
Source: Genomics Proteomics ... - March 9, 2018 Category: Genetics & Stem Cells Authors: Lu H, Bowler N, Harshyne LA, Craig Hooper D, Krishn SR, Kurtoglu S, Fedele C, Liu Q, Tang HY, Kossenkov AV, Kelly WK, Wang K, Kean RB, Weinreb PH, Yu L, Dutta A, Fortina P, Ertel A, Stanczak M, Forsberg F, Gabrilovich DI, Speicher DW, Altieri DC, Languino Tags: Matrix Biol Source Type: research