Dihydroartemisinin inhibits prostate cancer via JARID2/miR-7/miR-34a-dependent downregulation of Axl.
Abstract Axl expression is deregulated in several cancer types, predicts poor overall patient survival and is linked to resistance to drug therapy. Here, we evaluated a library of natural compounds for inhibitors of Axl and identified dihydroartemisinin, the active principle of the anti-malarial drug artemisinin, as an Axl-inhibitor in prostate cancer. Dihydroartemisinin blocks Axl expression leading to apoptosis, decrease in cell proliferation, migration, and tumor development of prostate cancer cells. Dihydroartemisinin treatment synergizes with docetaxel, a standard of care in metastatic prostate cancer increas...
Source: Genomics Proteomics ... - February 19, 2019 Category: Genetics & Stem Cells Authors: Paccez JD, Duncan K, Sekar D, Correa RG, Wang Y, Gu X, Bashin M, Chibale K, Libermann TA, Zerbini LF Tags: Oncogenesis Source Type: research

Translating transcription: proteomics in chronic rhinosinusitis with nasal polyps reveals significant discordance with messenger RNA expression.
Abstract BACKGROUND: Much of the literature examining chronic rhinosinusitis with nasal polyps (CRSwNP) immunopathology has been predicated on messenger RNA (mRNA) analysis with the assumption that transcriptional changes would reflect end-effector protein expression. The purpose of this study was to test this hypothesis using matched transcriptomic and proteomic data sets. METHODS: Matched tissue proteomic and transcriptomic arrays were quantified in CRSwNP polyp tissue and control inferior turbinate tissue (n = 10/group). Mucus samples were additionally collected in 6 subjects from each group. Proteins were...
Source: Genomics Proteomics ... - February 18, 2019 Category: Genetics & Stem Cells Authors: Workman AD, Nocera AL, Mueller SK, Otu HH, Libermann TA, Bleier BS Tags: Int Forum Allergy Rhinol Source Type: research

Delirium and Alzheimer's Disease: A Proposed Model for Shared Pathophysiology.
PMID: 30773695 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - February 17, 2019 Category: Genetics & Stem Cells Authors: Fong TG, Vasunilashorn SM, Libermann T, Marcantonio ER, Inouye SK Tags: Int J Geriatr Psychiatry Source Type: research

Quantitative label-free mass spectrometry using contralateral and adjacent breast tissues reveal differentially expressed proteins and their predicted impacts on pathways and cellular functions in breast cancer.
In this study, the mass spectrometry-based label-free quantification followed by functional annotation was performed to investigate the most significant deregulated proteins among tissues of primary breast tumor (PT) and axillary metastatic lymph node (LN) and corresponding non-tumor tissues contralateral (NCT) and adjacent (ANT) from patients diagnosed with invasive ductal carcinoma. A total of 462 proteins was observed as differentially expressed (DEPs) among the groups analyzed. A high level of similarity was observed in the proteome profile of both non-tumor breast tissues and DEPs (n = 12) were mainly predicted in...
Source: Genomics Proteomics ... - February 14, 2019 Category: Genetics & Stem Cells Authors: Gomig THB, Cavalli IJ, de Souza RLR, Vieira E, Lucena ACR, Batista M, Machado KC, Marchini FK, Marchi FA, Lima RS, de Andrade Urban C, Cavalli LR, de Souza Fonseca Ribeiro EM Tags: J Proteomics Source Type: research

Rice Genomics: Over the Past Two Decades and Into the Future.
Abstract Domestic rice (Oryza sativa L.) is one of the most important cereal crops, feeding a large number of worldwide populations. Along with various high-throughput genome sequencing projects, rice genomics has been making great headway toward direct field applications of basic research advances in understanding the molecular mechanisms of agronomical traits and utilizing diverse germplasm resources. Here, we briefly review its achievements over the past two decades and present the potential for its bright future. PMID: 30771506 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - February 13, 2019 Category: Genetics & Stem Cells Authors: Song S, Tian D, Zhang Z, Hu S, Yu J Tags: Genomics Proteomics Bioinformatics Source Type: research

Biomolecular Reaction & Interaction Dynamics Global Environment (BRIDGE).
We present the foundations of BRIDGE developed on the Galaxy platform that makes possible fundamental molecular dynamics of proteins through workflows and pipelines via commonly used packages such as NAMD, GROMACS and CHARMM. BRIDGE can be used to set up and simulate biological macromolecules, perform conformational analysis from trajectory data and conduct data analytics of large scale protein motions using statistical rigor. We illustrate the basic BRIDGE simulation and analytics capabilities on a previously reported CBH1 protein simulation. Availability: Publicly available at https://github.com/scientificomputing/B...
Source: Genomics Proteomics ... - February 13, 2019 Category: Genetics & Stem Cells Authors: Senapathi T, Bray S, Barnett CB, Grüning B, Naidoo KJ Tags: Bioinformatics Source Type: research

Enhanced Growth of Pilin-Deficient Geobacter sulfurreducens Mutants in Carbon Poor and Electron Donor Limiting Conditions.
Abstract Geobacter sulfurreducens pili enable extracellular electron transfer and play a role in secretion of c-type cytochromes such as OmcZ. PilA-deficient mutants of G. sulfurreducens have previously been shown to accumulate cytochromes within their membranes. This cytochrome retaining phenotype allowed for enhanced growth of PilA-deficient mutants in electron donor and carbon-limited conditions where formate and fumarate are provided as the sole electron donor and acceptor with no supplementary carbon source. Conversely, wild-type G. sulfurreducens, which has normal secretion of cytochromes, has comparative li...
Source: Genomics Proteomics ... - February 13, 2019 Category: Genetics & Stem Cells Authors: Semenec L, Vergara IA, Laloo AE, Mathews ER, Bond PL, Franks AE Tags: Microb Ecol Source Type: research

An immunoproteomic approach to characterize the CAR interactome and signalosome.
B, Abate-Daga D Abstract Adoptive transfer of T cells that express a chimeric antigen receptor (CAR) is an approved immunotherapy that may be curative for some hematological cancers. To better understand the therapeutic mechanism of action, we systematically analyzed CAR signaling in human primary T cells by mass spectrometry. When we compared the interactomes and the signaling pathways activated by distinct CAR-T cells that shared the same antigen-binding domain but differed in their intracellular domains and their in vivo antitumor efficacy, we found that only second-generation CARs induced the expression of a c...
Source: Genomics Proteomics ... - February 12, 2019 Category: Genetics & Stem Cells Authors: Ramello MC, Benzaïd I, Kuenzi BM, Lienlaf-Moreno M, Kandell WM, Santiago DN, Pabón-Saldaña M, Darville L, Fang B, Rix U, Yoder S, Berglund A, Koomen JM, Haura EB, Abate-Daga D Tags: Sci Signal Source Type: research

Metformin Treatment Suppresses Melanoma Cell Growth and Motility Through Modulation of microRNA Expression.
Abstract Melanoma is a highly aggressive cancer with high mortality in advanced stages.Metformin is an oral biguanide drug used for diabetes and has demonstrated positive effects oncancer prevention and treatment. Herein, we found that metformin significantly suppressedmelanoma cancer cell motility and growth through inducing cell cycle arrest at the G2/M phase andpromoting cell apoptosis. Using the next-generation sequencing approach, we identified threeupregulated microRNAs (miRNA; miR-192-5p, miR-584-3p, and miR-1246) in melanoma cellstreated with metformin. Among these, we examined the roles of miR-192-5p and ...
Source: Genomics Proteomics ... - February 11, 2019 Category: Genetics & Stem Cells Authors: Tseng HW, Li SC, Tsai KW Tags: Cancers (Basel) Source Type: research

A Time for Celebration: 40th Anniversary of GSC and 15th Anniversary of BIG, CAS.
PMID: 30743051 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - February 8, 2019 Category: Genetics & Stem Cells Authors: Yu J Tags: Genomics Proteomics Bioinformatics Source Type: research

An Exome-seq Based Tool for Mapping and Selection of Candidate Genes in Maize Deletion Mutants.
This study demonstrates the efficiency and cost-effectiveness of BSEx-seq for causal mutation mapping and candidate gene selection, providing a new option in mapping-by-sequencing for maize functional genomics studies. PMID: 30743052 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - February 8, 2019 Category: Genetics & Stem Cells Authors: Jia S, Morton K, Zhang C, Holding D Tags: Genomics Proteomics Bioinformatics Source Type: research

The application of omics techniques to understand the role of the gut microbiota in inflammatory bowel disease.
Abstract The aetiopathogenesis of inflammatory bowel diseases (IBD) involves the complex interaction between a patient's genetic predisposition, environment, gut microbiota and immune system. Currently, however, it is not known if the distinctive perturbations of the gut microbiota that appear to accompany both Crohn's disease and ulcerative colitis are the cause of, or the result of, the intestinal inflammation that characterizes IBD. With the utilization of novel systems biology technologies, we can now begin to understand not only details about compositional changes in the gut microbiota in IBD, but increasingl...
Source: Genomics Proteomics ... - February 6, 2019 Category: Genetics & Stem Cells Authors: Segal JP, Mullish BH, Quraishi MN, Acharjee A, Williams HRT, Iqbal T, Hart AL, Marchesi JR Tags: Therap Adv Gastroenterol Source Type: research

Progress and Challenges for Live-cell Imaging of Genomic Loci Using CRISPR-based Platforms.
Abstract Chromatin conformation, localization, and dynamics are crucial regulators of cellular behaviors. Although fluorescence in situ hybridization-based techniques have been widely utilized for investigating chromatin architectures in healthy and diseased states, the requirement for cell fixation precludes the comprehensive dynamic analysis necessary to fully understand chromatin activities. This has spurred the development and application of a variety of imaging methodologies for visualizing single chromosomal loci in the native cellular context. In this review, we describe currently-available approaches for i...
Source: Genomics Proteomics ... - January 30, 2019 Category: Genetics & Stem Cells Authors: Wu X, Mao S, Ying Y, Krueger CJ, Chen AK Tags: Genomics Proteomics Bioinformatics Source Type: research

Proteome-wide onco-proteogenomic somatic variant identification in ER-positive breast cancer.
CONCLUSIONS: While proteomics fails to identify the vast majority of exome DNA variants in the resulting proteome, its ability to detect a small subset of SAAVs could prove valuable for precision medicine applications. PMID: 30684468 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - January 23, 2019 Category: Genetics & Stem Cells Authors: Dimitrakopoulos L, Prassas I, Sieuwerts AM, Diamandis EP, Martens JWM, Charames GS Tags: Clin Biochem Source Type: research

Combating Diseases with Computational Strategies used for Drug Design and Discovery.
Abstract Computer-aided drug discovery (CADD) tools have provided an effective way in the drug discovery pipeline for expediting of this long process and economizing the cost of research and development. Because of the dramatic increase in the availability of human proteins as drug targets and small molecule information due to the advances in bioinformatics, cheminformatics, genomics, proteomics, and structural information, the applicability of in silico drug discovery has been extended. Computational approaches have been used at almost all stages in the drug discovery pipeline including target identification and ...
Source: Genomics Proteomics ... - January 21, 2019 Category: Genetics & Stem Cells Authors: Makhouri FR, Ghasemi JB Tags: Curr Top Med Chem Source Type: research

Enhancer hijacking activates oncogenic transcription factor NR4A3 in acinic cell carcinomas of the salivary glands.
gaimy A Abstract The molecular pathogenesis of salivary gland acinic cell carcinoma (AciCC) is poorly understood. The secretory Ca-binding phosphoprotein (SCPP) gene cluster at 4q13 encodes structurally related phosphoproteins of which some are specifically expressed at high levels in the salivary glands and constitute major components of saliva. Here we report on recurrent rearrangements [t(4;9)(q13;q31)] in AciCC that translocate active enhancer regions from the SCPP gene cluster to the region upstream of Nuclear Receptor Subfamily 4 Group A Member 3 (NR4A3) at 9q31. We show that NR4A3 is specifically upregulate...
Source: Genomics Proteomics ... - January 21, 2019 Category: Genetics & Stem Cells Authors: Haller F, Bieg M, Will R, Körner C, Weichenhan D, Bott A, Ishaque N, Lutsik P, Moskalev EA, Mueller SK, Bähr M, Woerner A, Kaiser B, Scherl C, Haderlein M, Kleinheinz K, Fietkau R, Iro H, Eils R, Hartmann A, Plass C, Wiemann S, Agaimy A Tags: Nat Commun Source Type: research

PIM1 kinase promotes gallbladder cancer cell proliferation via inhibition of proline-rich Akt substrate of 40  kDa (PRAS40).
This study also elucidates phospho-PRAS40 as a clinical marker in GBC and the role of PIM1 as a therapeutic target in GBC. PMID: 30666556 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - January 21, 2019 Category: Genetics & Stem Cells Authors: Subbannayya T, Leal-Rojas P, Zhavoronkov A, Ozerov IV, Korzinkin M, Babu N, Radhakrishnan A, Chavan S, Raja R, Pinto SM, Patil AH, Barbhuiya MA, Kumar P, Guerrero-Preston R, Navani S, Tiwari PK, Kumar RV, Prasad TSK, Roa JC, Pandey A, Sidransky D, Gowda H Tags: J Cell Commun Signal Source Type: research

Antibiotic collateral sensitivity is contingent on the repeatability of evolution.
Abstract Antibiotic resistance represents a growing health crisis that necessitates the immediate discovery of novel treatment strategies. One such strategy is the identification of collateral sensitivities, wherein evolution under a first drug induces susceptibility to a second. Here, we report that sequential drug regimens derived from in vitro evolution experiments may have overstated therapeutic benefit, predicting a collaterally sensitive response where cross-resistance ultimately occurs. We quantify the likelihood of this phenomenon by use of a mathematical model parametrised with combinatorially complete fi...
Source: Genomics Proteomics ... - January 18, 2019 Category: Genetics & Stem Cells Authors: Nichol D, Rutter J, Bryant C, Hujer AM, Lek S, Adams MD, Jeavons P, Anderson ARA, Bonomo RA, Scott JG Tags: Nat Commun Source Type: research

Peptimapper: proteogenomics workflow for the expert annotation of eukaryotic genomes.
CONCLUSIONS: Peptimapper is a complementary tool for the expert annotation of genomes. It is suitable for any organism and is distributed through a Docker image available on two public bioinformatics docker repositories: Docker Hub and BioShaDock. This workflow is also accessible through the Galaxy framework and for use by non-computer scientists at https://galaxy.protim.eu . Data are available via ProteomeXchange under identifier PXD010618. PMID: 30654742 [PubMed - in process] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - January 17, 2019 Category: Genetics & Stem Cells Authors: Guillot L, Delage L, Viari A, Vandenbrouck Y, Com E, Ritter A, Lavigne R, Marie D, Peterlongo P, Potin P, Pineau C Tags: BMC Genomics Source Type: research

Characterization of the Src-regulated kinome identifies SGK1 as a key mediator of Src-induced transformation.
Abstract Despite significant progress, our understanding of how specific oncogenes transform cells is still limited and likely underestimates the complexity of downstream signalling events. To address this gap, we use mass spectrometry-based chemical proteomics to characterize the global impact of an oncogene on the expressed kinome, and then functionally annotate the regulated kinases. As an example, we identify 63 protein kinases exhibiting altered expression and/or phosphorylation in Src-transformed mammary epithelial cells. An integrated siRNA screen identifies nine kinases, including SGK1, as being essential ...
Source: Genomics Proteomics ... - January 17, 2019 Category: Genetics & Stem Cells Authors: Ma X, Zhang L, Song J, Nguyen E, Lee RS, Rodgers SJ, Li F, Huang C, Schittenhelm RB, Chan H, Chheang C, Wu J, Brown KK, Mitchell CA, Simpson KJ, Daly RJ Tags: Nat Commun Source Type: research

Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity.
Abstract Rapid innovation in sequencing technologies and improvement in assembly algorithms have enabled the creation of highly contiguous mammalian genomes. Here we report a chromosome-level assembly of the water buffalo (Bubalus bubalis) genome using single-molecule sequencing and chromatin conformation capture data. PacBio Sequel reads, with a mean length of 11.5 kb, helped to resolve repetitive elements and generate sequence contiguity. All five B. bubalis sub-metacentric chromosomes were correctly scaffolded with centromeres spanned. Although the index animal was partly inbred, 58% of the genome was ha...
Source: Genomics Proteomics ... - January 16, 2019 Category: Genetics & Stem Cells Authors: Low WY, Tearle R, Bickhart DM, Rosen BD, Kingan SB, Swale T, Thibaud-Nissen F, Murphy TD, Young R, Lefevre L, Hume DA, Collins A, Ajmone-Marsan P, Smith TPL, Williams JL Tags: Nat Commun Source Type: research

Systems Biology Approach to Identify Novel Genomic Determinants for Pancreatic Cancer Pathogenesis.
Abstract Pancreatic ductal adenocarcinoma (PDAC) is a lethal malignancy with a 5-year survival rate of
Source: Genomics Proteomics ... - January 15, 2019 Category: Genetics & Stem Cells Authors: Khatri I, Ganguly K, Sharma S, Carmicheal J, Kaur S, Batra SK, Bhasin MK Tags: Sci Rep Source Type: research

Integration of microbiology, molecular pathology, and epidemiology: a new paradigm to explore the pathogenesis of microbiome-driven neoplasms.
Abstract Molecular pathological epidemiology (MPE) is an integrative transdisciplinary field that addresses heterogeneous effects of exogenous and endogenous factors (collectively termed "exposures"), including microorganisms, on disease occurrence and consequence utilising molecular pathological signatures of the disease. In parallel with the paradigm of precision medicine, findings from MPE research can provide aetiological insights into tailored strategies of disease prevention and treatment. Due to the availability of molecular pathological tests on tumours, the MPE approach has been utilised predomi...
Source: Genomics Proteomics ... - January 11, 2019 Category: Genetics & Stem Cells Authors: Hamada T, Nowak JA, Milner DA, Song M, Ogino S Tags: J Pathol Source Type: research

OMeta: an ontology-based, data-driven metadata tracking system.
CONCLUSIONS: We present, OMeta, a web-based software application that is built on data-driven principles for configuring and customizing data standards, capturing, curating, and sharing metadata. PMID: 30612540 [PubMed - in process] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - January 7, 2019 Category: Genetics & Stem Cells Authors: Singh I, Kuscuoglu M, Harkins DM, Sutton G, Fouts DE, Nelson KE Tags: BMC Bioinformatics Source Type: research

Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set.
We describe how this resource was built, the formats in which the data is provided and offer a descriptive analysis of the data set. The data set is publicly available through the IntAct website and is enhanced with every monthly release. PMID: 30602777 [PubMed - in process] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - January 2, 2019 Category: Genetics & Stem Cells Authors: Del-Toro N, Duesbury M, Koch M, Perfetto L, Shrivastava A, Ochoa D, Wagih O, Piñero J, Kotlyar M, Pastrello C, Beltrao P, Furlong LI, Jurisica I, Hermjakob H, Orchard S, Porras P, IMEx Consortium contributing authors Tags: Nat Commun Source Type: research

Plasma proteome profiling of high-altitude polycythemia using TMT-based quantitative proteomics approach.
Abstract High-altitude polycythemia (HAPC) is one of the classic chronic mountain sicknesses and has been a serious public health problem in high-altitude regions. Despite numerous studies on HAPC via genomics or transcriptomics approaches, the pathogenesis of HAPC is still unclear. Here, we performed a TMT- based comparative quantitative proteomics analysis to reveal the changes of plasma proteomics profiles between HAPC subjects and healthy controls. Of identified 818 proteins, 7 and 12 proteins were up-regulated and down-accumulated, respectively, compared HAPC patients with healthy controls. GO and KEGG pathwa...
Source: Genomics Proteomics ... - December 31, 2018 Category: Genetics & Stem Cells Authors: Wang Z, Liu F, Ye S, Jiang P, Yu X, Xu J, Du X, Ma L, Cao H, Yuan C, Shen Y, Lin F, Zhang R, Li C Tags: J Proteomics Source Type: research

Bayesian generalized biclustering analysis via adaptive structured shrinkage.
Abstract Biclustering techniques can identify local patterns of a data matrix by clustering feature space and sample space at the same time. Various biclustering methods have been proposed and successfully applied to analysis of gene expression data. While existing biclustering methods have many desirable features, most of them are developed for continuous data and few of them can efficiently handle -omics data of various types, for example, binomial data as in single nucleotide polymorphism data or negative binomial data as in RNA-seq data. In addition, none of existing methods can utilize biological information ...
Source: Genomics Proteomics ... - December 31, 2018 Category: Genetics & Stem Cells Authors: Li Z, Chang C, Kundu S, Long Q Tags: Biostatistics Source Type: research

Recent Advances in Function-based Metagenomic Screening.
Abstract Metagenomes from uncultured microorganisms are rich resources for novel enzyme genes. The methods used to screen the metagenomic libraries fall into two categories, which are based on sequence or function of the enzymes. The sequence-based approaches rely on the known sequences of the target gene families. In contrast, the function-based approaches do not involve the incorporation of metagenomic sequencing data and, therefore, may lead to the discovery of novel gene sequences with desired functions. In this review, we discuss the function-based screening strategies that have been used in the identificatio...
Source: Genomics Proteomics ... - December 28, 2018 Category: Genetics & Stem Cells Authors: Ngara TR, Zhang H Tags: Genomics Proteomics Bioinformatics Source Type: research

From Basic Research to Molecular Breeding, Chinese Scientists Play A Central Role in Boosting World Rice Production.
Abstract On Nov.18, 2018, the Future Science Prize Award Ceremony presented awards to this year's winners. In the area of life science, Professors Jiayang Li, Longping Yuan, and Qifa Zhang shared the prize for their pioneering contributions in producing high-yield, superior-quality rice through systematic study of molecular mechanisms associated with specific rice features and application of novel approaches in rice breeding. The Future Science Prize is also touted as "China's Nobel Prize", fully affirming their achievements in rice basic research and breeding. PMID: 30594646 [PubMed - as supplied b...
Source: Genomics Proteomics ... - December 27, 2018 Category: Genetics & Stem Cells Authors: Tang D, Cheng Z Tags: Genomics Proteomics Bioinformatics Source Type: research

RGAAT: A Reference-based Genome Assembly and Annotation Tool for New Genomes and Upgrade of Known Genomes.
Abstract The rapid development of high-throughput sequencing technologies has led to a dramatic decrease in the money and time required for de novo genome sequencing or genome resequencing projects, with new genome sequences constantly released every week. Among such projects, the plethora of updated genome assemblies induces the requirement of version-dependent annotation files and other compatible public dataset for downstream analysis. To handle these tasks in an efficient manner, we developed the reference-based genome assembly and annotation tool (RGAAT), a flexible toolkit for resequencing-based consensus bu...
Source: Genomics Proteomics ... - December 21, 2018 Category: Genetics & Stem Cells Authors: Liu W, Wu S, Lin Q, Gao S, Ding F, Zhang X, Aljohi HA, Yu J, Hu S Tags: Genomics Proteomics Bioinformatics Source Type: research

GlyConnect: glycoproteomics goes visual, interactive and analytical.
Abstract Knowledge of glycoproteins, their site-specific glycosylation patterns and the glycan structures that they present to their recognition partners in health and disease are gradually being built on using a range of experimental approaches. The data from these analyses are increasingly being standardised and presented in various sources, from supplemental tables in publications to localised servers in investigator laboratories. Bioinformatics tools are now needed to collect this data and enable the user to search, display and connect glycomics and glycoproteomics to other sources of related proteomics, genom...
Source: Genomics Proteomics ... - December 21, 2018 Category: Genetics & Stem Cells Authors: Alocci D, Mariethoz J, Gastaldello A, Gasteiger E, Karlsson NG, Kolarich D, Packer NH, Lisacek F Tags: J Proteome Res Source Type: research

TICA: Transcriptional Interaction and Coregulation Analyzer.
We present our method and test it on ENCODE ChIP-seq datasets, using three cell lines as reference including HepG2, GM12878, and K562. TICA positive predictions on ENCODE ChIP-seq data are strongly enriched when compared to protein complex (CORUM) and functional interaction (BioGRID) databases. We also compare TICA against both motif/ChIP-seq based methods for physical TF-TF interaction prediction and published literature. Based on our results, TICA offers significant specificity (average 0.902) while maintaining a good recall (average 0.284) with respect to CORUM, providing a novel technique for fast analysis of regulator...
Source: Genomics Proteomics ... - December 19, 2018 Category: Genetics & Stem Cells Authors: Perna S, Pinoli P, Ceri S, Wong L Tags: Genomics Proteomics Bioinformatics Source Type: research

Machine Learning Models for Genetic Risk Assessment of Infants with Non-syndromic Orofacial Cleft.
In this study, we collected blood samples from control and NSCL/P infants in Han and Uyghur Chinese populations to validate the diagnostic effectiveness of 43 candidate SNPs previously detected using GWAS. We then built predictive models with the validated SNPs using different machine learning algorithms and evaluated their prediction performance. Our results showed that logistic regression had the best performance for risk assessment according to the area under curve. Notably, defective variants in MTHFR and RBP4, two genes involved in folic acid and vitamin A biosynthesis, were found to have high contributions to NSCL/P ...
Source: Genomics Proteomics ... - December 19, 2018 Category: Genetics & Stem Cells Authors: Zhang SJ, Meng P, Zhang J, Jia P, Lin J, Wang X, Chen F, Wei X Tags: Genomics Proteomics Bioinformatics Source Type: research

TELS: A Novel Computational Framework for Identifying Motif Signatures of Transcribed Enhancers.
Abstract In mammalian cells, transcribed enhancers (TrEns) play important roles in the initiation of gene expression and maintenance of gene expression levels in a spatiotemporal manner. One of the most challenging questions is how the genomic characteristics of enhancers relate to enhancer activities. To date, only a limited number of enhancer sequence characteristics have been investigated, leaving space for exploring the enhancers' DNA code in a more systematic way. To address this problem, we developed a novel computational framework, Transcribed Enhancer Landscape Search (TELS), aimed at identifying predictiv...
Source: Genomics Proteomics ... - December 19, 2018 Category: Genetics & Stem Cells Authors: Kleftogiannis D, Ashoor H, Bajic VB Tags: Genomics Proteomics Bioinformatics Source Type: research

VASC: Dimension Reduction and Visualization of Single-cell RNA-seq Data by Deep Variational Autoencoder.
In this study, we proposed the deep variational autoencoder for scRNA-seq data (VASC), a deep multi-layer generative model, for the unsupervised dimension reduction and visualization of scRNA-seq data. VASC can explicitly model the dropout events and find the nonlinear hierarchical feature representations of the original data. Tested on over 20 datasets, VASC shows superior performances in most cases and exhibits broader dataset compatibility compared to four state-of-the-art dimension reduction and visualization methods. In addition, VASC provides better representations for very rare cell populations in the 2D visualizati...
Source: Genomics Proteomics ... - December 18, 2018 Category: Genetics & Stem Cells Authors: Wang D, Gu J Tags: Genomics Proteomics Bioinformatics Source Type: research

Polyphyly in 16S rRNA-based LVTree Versus Monophyly in Whole-genome-based CVTree.
In this study, we reconstructed phylogenetic relationship for more than ten thousand prokaryote genomes by using the CVTree method, which is based on whole-genome information. And many such genera, which are polyphyletic in 16S rRNA-based trees, are well resolved as monophyletic clusters by CVTree. We believe that with genome sequencing of prokaryotes becoming a commonplace, genome-based phylogeny is doomed to play a definitive role in the construction of a natural and objective taxonomy. PMID: 30550857 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - December 11, 2018 Category: Genetics & Stem Cells Authors: Zuo G, Qi J, Hao B Tags: Genomics Proteomics Bioinformatics Source Type: research

Social Stress Affects Colonic Inflammation, the Gut Microbiome, and Short Chain Fatty Acid Levels and Receptors.
CONCLUSIONS: Social stress can have a significant effect on infection-induced colonic inflammation, and stress-induced changes in microbial-produced metabolites and their receptors may be involved. PMID: 30540706 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - December 11, 2018 Category: Genetics & Stem Cells Authors: Maltz RM, Keirsey J, Kim SC, Mackos AR, Gharaibeh RZ, Moore CC, Xu J, Somogyi A, Bailey MT Tags: J Pediatr Gastroenterol Nutr Source Type: research

Improve your Galaxy text life: The Query Tabular Tool.
Abstract Galaxy provides an accessible platform where multi-step data analysis workflows integrating disparate software can be run, even by researchers with limited programming expertise.  Applications of such sophisticated workflows are many, including those which integrate software from different 'omic domains (e.g. genomics, proteomics, metabolomics). In these complex workflows, intermediate outputs are often generated as tabular text files, which must be transformed into customized formats which are compatible with the next software tools in the pipeline.  Consequently, many text manipulation steps a...
Source: Genomics Proteomics ... - December 8, 2018 Category: Genetics & Stem Cells Authors: Johnson JE, Kumar P, Easterly C, Esler M, Mehta S, Eschenlauer AC, Hegeman AD, Jagtap PD, Griffin TJ Tags: F1000Res Source Type: research

Hypervirulent group A Streptococcus emergence in an acaspular background is associated with marked remodeling of the bacterial cell surface.
ne SA Abstract Inactivating mutations in the control of virulence two-component regulatory system (covRS) often account for the hypervirulent phenotype in severe, invasive group A streptococcal (GAS) infections. As CovR represses production of the anti-phagocytic hyaluronic acid capsule, high level capsule production is generally considered critical to the hypervirulent phenotype induced by CovRS inactivation. There have recently been large outbreaks of GAS strains lacking capsule, but there are currently no data on the virulence of covRS-mutated, acapsular strains in vivo. We investigated the impact of CovRS inac...
Source: Genomics Proteomics ... - December 7, 2018 Category: Genetics & Stem Cells Authors: Galloway-Peña J, DebRoy S, Brumlow C, Li X, Tran TT, Horstmann N, Yao H, Chen K, Wang F, Pan BF, Hawke DH, Thompson EJ, Arias CA, Fowler VG, Bhatti MM, Kalia A, Flores AR, Shelburne SA Tags: PLoS One Source Type: research

Agronomic Linked Data (AgroLD): A knowledge-based system to enable integrative biology in agronomy.
We present some integration results of the project, which initially focused on genomics, proteomics and phenomics. AgroLD is now an RDF (Resource Description Format) knowledge base of 100M triples created by annotating and integrating more than 50 datasets coming from 10 data sources-such as Gramene.org and TropGeneDB-with 10 ontologies-such as the Gene Ontology and Plant Trait Ontology. Our evaluation results show users appreciate the multiple query modes which support different use cases. AgroLD's objective is to offer a domain specific knowledge platform to solve complex biological and agronomical questions related to t...
Source: Genomics Proteomics ... - December 4, 2018 Category: Genetics & Stem Cells Authors: Venkatesan A, Tagny Ngompe G, Hassouni NE, Chentli I, Guignon V, Jonquet C, Ruiz M, Larmande P Tags: PLoS One Source Type: research

De novo annotation of the transcriptome of the Northern Wheatear (Oenanthe oenanthe).
n F, Wink M Abstract We have sequenced a partial transcriptome of the Northern Wheatear (Oenanthe oenanthe), a species with one of the longest migrations on Earth. The transcriptome was constructed de novo using RNA-Seq sequence data from the pooled mRNA of six different tissues: brain, muscle, intestine, liver, adipose tissue and skin. The samples came from nine captive-bred wheatears collected at three different stages of the endogenous autumn migratory period: (1) lean birds prior the onset of migration, (2) during the fattening stage and (3) individuals at their migratory body mass plateau, when they have almo...
Source: Genomics Proteomics ... - December 1, 2018 Category: Genetics & Stem Cells Authors: Frias-Soler RC, Villarín Pildaín L, Hotz-Wagenblatt A, Kolibius J, Bairlein F, Wink M Tags: PeerJ Source Type: research

Noninvasive exosomal proteomic biosignatures, including cystatin SN, peroxiredoxin-5, and glycoprotein VI, accurately predict chronic rhinosinusitis with nasal polyps.
Abstract BACKGROUND: Exosomes are secreted epithelial-derived vesicles that contain a conserved protein array representative of their parent cell. Exosomes may be reproducibly and noninvasively purified from nasal mucus. The exosomal proteome can be quantified using SOMAscanTM , a highly multiplexed, aptamer-based proteomic platform. The purpose of this study was to determine whether chronic rhinosinusitis with nasal polyps (CRSwNP) has a unique predictive exosomal proteomic biosignature. METHODS: Exosomes were isolated from whole mucus sampled from control and CRSwNP patients (n = 20 per group) by differenti...
Source: Genomics Proteomics ... - November 28, 2018 Category: Genetics & Stem Cells Authors: Mueller SK, Nocera AL, Dillon ST, Gu X, Wendler O, Otu HH, Libermann TA, Bleier BS Tags: Int Forum Allergy Rhinol Source Type: research

AncestryPainter: A Graphic Program for Displaying Ancestry Composition of Populations and Individuals.
Abstract Ancestry composition of populations and individuals has been extensively investigated in recent years due to advances in the genotyping and sequencing technologies. As the number of populations and individuals used for ancestry inference increases remarkably, say more than 100 populations or 1000 individuals, it is usually challenging to present the ancestry composition in a traditional way using a rectangular graph. To address this issue, we developed a program, AncestryPainter, which can illustrate the ancestry composition of populations and individuals with a rounded and nice-looking graph to save spac...
Source: Genomics Proteomics ... - November 22, 2018 Category: Genetics & Stem Cells Authors: Feng Q, Lu D, Xu S Tags: Genomics Proteomics Bioinformatics Source Type: research

Genome sequence of the non-conventional wine yeast Hanseniaspora guilliermondii UTAD222 unveils relevant traits of this species and of the Hanseniaspora genus in the context of wine fermentation.
NP Abstract Hanseanispora species, including H. guilliermondii, are long known to be abundant in wine grape-musts and to play a critical role in vinification by modulating, among other aspects, the wine sensory profile. Despite this, the genetics and physiology of Hanseniaspora species remains poorly understood. The first genomic sequence of a H. guilliermondii strain (UTAD222) and the discussion of its potential significance are presented in this work. Metabolic reconstruction revealed that H. guilliermondii is not equipped with a functional gluconeogenesis or glyoxylate cycle, nor does it harbours key enzymes f...
Source: Genomics Proteomics ... - November 20, 2018 Category: Genetics & Stem Cells Authors: Seixas I, Barbosa C, Mendes-Faia A, Güldener U, Tenreiro R, Mendes-Ferreira A, Mira NP Tags: DNA Res Source Type: research

Connecting Proteomics to Next-Generation Sequencing (NGS): Proteogenomics and its Current Applications in Biology.
This article is protected by copyright. All rights reserved. PMID: 30431238 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - November 15, 2018 Category: Genetics & Stem Cells Authors: Low TY, Mohtar MA, Ang MY, Jamal R Tags: Proteomics Source Type: research

HAHap: a read-based haplotyping method using hierarchical assembly.
This study presents HAHap, a new phasing algorithm based on hierarchical assembly. HAHap leverages high-confident variant pairs to build haplotypes progressively. The phasing results by HAHap on both real and simulated data, compared to other MEC-based methods, revealed better phasing error rates for constructing haplotypes using short reads from whole-genome sequencing. We compared the number of error corrections (ECs) on real data with other methods, and it reveals the ability of HAHap to predict haplotypes with a lower number of ECs. We also used simulated data to investigate the behavior of HAHap under different sequen...
Source: Genomics Proteomics ... - November 7, 2018 Category: Genetics & Stem Cells Authors: Lin YY, Wu PC, Chen PL, Oyang YJ, Chen CY Tags: PeerJ Source Type: research

Loose ends: almost one in five human genes still have unresolved coding status.
PMID: 30395326 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - November 5, 2018 Category: Genetics & Stem Cells Authors: Abascal F, Juan D, Jungreis I, Kellis M, Martinez L, Rigau M, Rodriguez JM, Vazquez J, Tress ML Tags: Nucleic Acids Res Source Type: research

Recent Development in Omics Studies.
Abstract The central dogma of molecular biology (DNA, RNA, protein and metabolite) has engraved our understanding of genetics in all living organisms. While the concept has been embraced for many decades, the development of high-throughput technologies particularly omics (genomics, transcriptomics, proteomics and metabolomics) has revolutionised the field to incorporate big data analysis including bioinformatics and systems biology as well as synthetic biology area. These omics approaches as well as systems and synthetic biology areas are now increasingly popular as seen by the growing numbers of publication throu...
Source: Genomics Proteomics ... - November 3, 2018 Category: Genetics & Stem Cells Authors: Aizat WM, Ismail I, Noor NM Tags: Adv Exp Med Biol Source Type: research

Multiomics analyses identified epigenetic modulation of the S100A gene family in Kawasaki disease and their significant involvement in neutrophil transendothelial migration.
CONCLUSIONS: This is the first study to integrate genome-wide DNA methylation with gene expression assays in KD and showed that the S100A family plays important roles in the pathogenesis of KD. PMID: 30382880 [PubMed - in process] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - November 1, 2018 Category: Genetics & Stem Cells Authors: Huang LH, Kuo HC, Pan CT, Lin YS, Huang YH, Li SC Tags: Clin Epigenetics Source Type: research

Novel Combination of Arsenic Trioxide (As2O3) Plus Resveratrol in Inducing Programmed Cell Death of Human Neuroblastoma SK-N-SH Cells.
CONCLUSION: Combined treatment at extremely low concentration of two agents from natural products, As2O3 and resveratrol, has high potential as a cocktail of anticancer drugs for neuroblastoma. PMID: 30343279 [PubMed - in process] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - October 22, 2018 Category: Genetics & Stem Cells Authors: Yen CM, Tsai CW, Chang WS, Yang YC, Hung YW, Lee HT, Shen CC, Sheu ML, Wang JY, Gong CL, Cheng WY, Bau DT Tags: Cancer Genomics Proteomics Source Type: research