From Mutation Signature to Molecular Mechanism in the RNA World: A Case of SARS-CoV-2.
PMID: 32739507 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - July 30, 2020 Category: Genetics & Stem Cells Authors: Yu J Tags: Genomics Proteomics Bioinformatics Source Type: research

Identification of Key Genes for the Ultrahigh Yield of Rice Using Dynamic Cross-tissue Network Analysis.
This study, which included extensive field phenotyping, cross-tissue systems biology analyses, and functional validation, uncovered the key genes and gene regulatory networks underpinning the ultrahigh yield of rice. The DCT method could be applied to other plant or animal systems if different phenotypes under various environments with the common genome sequences of the examined sample. DCT can be downloaded from https://github.com/ztpub/DCT. PMID: 32736037 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - July 28, 2020 Category: Genetics & Stem Cells Authors: Hu J, Zeng T, Xia Q, Huang L, Zhang Y, Zhang C, Zeng Y, Liu H, Zhang S, Huang G, Wan W, Ding Y, Hu F, Yang C, Chen L, Wang W Tags: Genomics Proteomics Bioinformatics Source Type: research

Status and Potential of Single-cell Transcriptomics for Understanding Plant Development and Functional Biology.
Abstract The advent of modern "omics" technologies (genomics, transcriptomics, proteomics, and metabolomics) are attributed to innovative breakthroughs in genome sequencing, bioinformatics, and analytic tools. An organism's biological structure and function is the result of the concerted action of single cells in different tissues. Single cell genomics has emerged as a ground-breaking technology that has greatly enhanced our understanding of the complexity of gene expression at a microscopic resolution and holds the potential to revolutionize the way we characterize complex cell assemblies and study thei...
Source: Genomics Proteomics ... - July 26, 2020 Category: Genetics & Stem Cells Authors: Iqbal MM, Hurgobin B, Holme AL, Appels R, Kaur P Tags: Cytometry A Source Type: research

Combining Molecular Weight Fractionation and Metabolomics to Elucidate the Bioactivity of Vegetal Protein Hydrolysates in Tomato Plants.
Abstract The comprehension of the bioactive fractions involved in the biostimulant activity of plant derived protein hydrolysates (PH) is a complex task, but it can also lead to significant improvements in the production of more effective plant biostimulants. The aim of this work is to shed light onto the bioactivity of different PH dialysis fractions (PH1 0.5-1 kDa; PH3 8-10 kDa) of a commercial PH-based biostimulant through a combined in vivo bioassay and metabolomics approach. A first tomato rooting bioassay investigated the auxin-like activity of PH and its fractions, each of them at three nitrogen levels (3, ...
Source: Genomics Proteomics ... - July 24, 2020 Category: Genetics & Stem Cells Authors: Lucini L, Miras-Moreno B, Rouphael Y, Cardarelli M, Colla G Tags: Front Plant Sci Source Type: research

A functional genomics approach to investigate the differentiation of iPSCs into lung epithelium at air-liquid interface.
Abstract The availability of robust protocols to differentiate induced pluripotent stem cells (iPSCs) into many human cell lineages has transformed research into the origins of human disease. The efficacy of differentiating iPSCs into specific cellular models is influenced by many factors including both intrinsic and extrinsic features. Among the most challenging models is the generation of human bronchial epithelium at air-liquid interface (HBE-ALI), which is the gold standard for many studies of respiratory diseases including cystic fibrosis. Here, we perform open chromatin mapping by ATAC-seq and transcriptomic...
Source: Genomics Proteomics ... - July 21, 2020 Category: Genetics & Stem Cells Authors: Kerschner JL, Paranjapye A, Yin S, Skander DL, Bebek G, Leir SH, Harris A Tags: J Cell Mol Med Source Type: research

Unraveling the proteomic changes involved in the resistance response of Cajanus platycarpus to herbivory by Helicoverpa armigera.
Abstract The pigeonpea wild relative Cajanus platycarpus is resistant to Helicoverpa armigera, one of the major pests responsible for yield losses in Cajanus cajan. Deciphering the molecular mechanism underlying host plant resistance is pertinent to identify proteins that aid in the mitigation of the insect pest. The present study adopted comparative proteomics as a tool to interpret the resistance mechanism(s) in C. platycarpus vis-à-vis C. cajan during continued herbivory (up to 96 h). Over-representation analysis of the differentially expressed proteins implicated a multi-dimensional resistance response ...
Source: Genomics Proteomics ... - July 20, 2020 Category: Genetics & Stem Cells Authors: Rathinam M, Roschitzki B, Grossmann J, Mishra P, Kunz L, Wolski W, Panse C, Tyagi S, Rao U, Schlapbach R, Sreevathsa R Tags: Appl Microbiol Biotechnol Source Type: research

Enhanced Permutation Tests via Multiple Pruning.
Abstract Big multi-omics data in bioinformatics often consists of a huge number of features and relatively small numbers of samples. In addition, features from multi-omics data have their own specific characteristics depending on whether they are from genomics, proteomics, metabolomics, etc. Due to these distinct characteristics, standard statistical analyses using parametric-based assumptions may sometimes fail to provide exact asymptotic results. To resolve this issue, permutation tests can be a way to exactly analyze multi-omics data because they are distribution-free and flexible to use. In permutation tests, ...
Source: Genomics Proteomics ... - July 18, 2020 Category: Genetics & Stem Cells Authors: Leem S, Huh I, Park T Tags: Front Genet Source Type: research

Population Genetics of SARS-CoV-2: Disentangling Effects of Sampling Bias and Infection Clusters.
In this study, we first present robust estimator for the time to the most recent common ancestor (TMRCA) and the mutation rate, and then apply the approach to analyze 12,909 genomic sequences of SARS-CoV-2. The mutation rate is inferred to be 8.69 × 10-4 per site per year with a 95% confidence interval (CI) of [8.61 × 10-4, 8.77 × 10-4], and the TMRCA of the samples inferred to be Nov 28, 2019 with a 95% CI of [Oct 20, 2019, Dec 9, 2019]. The results indicate that COVID-19 might originate earlier than and outside of Wuhan Seafood Market. We further demonstrate that genetic polymorphism patterns, including...
Source: Genomics Proteomics ... - July 11, 2020 Category: Genetics & Stem Cells Authors: Liu Q, Zhao S, Shi CM, Song S, Zhu S, Su Y, Zhao W, Li M, Bao Y, Xue Y, Chen H Tags: Genomics Proteomics Bioinformatics Source Type: research

Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma.
Cornwell M, Kothadia RB, Ma W, Yoo S, Mannan R, Vats P, Kumar-Sinha C, Kawaler EA, Omelchenko T, Colaprico A, Geffen Y, Maruvka YE, da Veiga Leprevost F, Wiznerowicz M, Gümüş ZH, Veluswamy RR, Hostetter G, Heiman DI, Wyczalkowski MA, Hiltke T, Mesri M, Kinsinger CR, Boja ES, Omenn GS, Chinnaiyan AM, Rodriguez H, Li QK, Jewell SD, Thiagarajan M, Getz G, Zhang B, Fenyö D, Ruggles KV, Cieslik MP, Robles AI, Clauser KR, Govindan R, Wang P, Nesvizhskii AI, Ding L, Mani DR, Carr SA, Clinical Proteomic Tumor Analysis Consortium Abstract To explore the biology of lung adenocarcinoma (LUAD) and identify new...
Source: Genomics Proteomics ... - July 9, 2020 Category: Genetics & Stem Cells Authors: Gillette MA, Satpathy S, Cao S, Dhanasekaran SM, Vasaikar SV, Krug K, Petralia F, Li Y, Liang WW, Reva B, Krek A, Ji J, Song X, Liu W, Hong R, Yao L, Blumenberg L, Savage SR, Wendl MC, Wen B, Li K, Tang LC, MacMullan MA, Avanessian SC, Kane MH, Newton CJ, Tags: Cell Source Type: research

Proteogenomics of Non-smoking Lung Cancer in East Asia Delineates Molecular Signatures of Pathogenesis and Progression.
av L, Lin CY, Chen YS, Wu PS, Lai CT, Weng SH, Su KY, Chang WH, Tsai PY, Robles AI, Rodriguez H, Hsiao YJ, Chang WH, Sung TY, Chen JS, Yu SL, Choudhary JS, Chen HY, Yang PC, Chen YJ Abstract Lung cancer in East Asia is characterized by a high percentage of never-smokers, early onset and predominant EGFR mutations. To illuminate the molecular phenotype of this demographically distinct disease, we performed a deep comprehensive proteogenomic study on a prospectively collected cohort in Taiwan, representing early stage, predominantly female, non-smoking lung adenocarcinoma. Integrated genomic, proteomic, and phosphop...
Source: Genomics Proteomics ... - July 9, 2020 Category: Genetics & Stem Cells Authors: Chen YJ, Roumeliotis TI, Chang YH, Chen CT, Han CL, Lin MH, Chen HW, Chang GC, Chang YL, Wu CT, Lin MW, Hsieh MS, Wang YT, Chen YR, Jonassen I, Ghavidel FZ, Lin ZS, Lin KT, Chen CW, Sheu PY, Hung CT, Huang KC, Yang HC, Lin PY, Yen TC, Lin YW, Wang JH, Rag Tags: Cell Source Type: research

Integrative Proteomic Characterization of Human Lung Adenocarcinoma.
ng F, Wang G, Zhang Y, Cheng S, Qin J, Qian X, Wang Y, Li J, He F, Xiao T, Tan M Abstract Genomic studies of lung adenocarcinoma (LUAD) have advanced our understanding of the disease's biology and accelerated targeted therapy. However, the proteomic characteristics of LUAD remain poorly understood. We carried out a comprehensive proteomics analysis of 103 cases of LUAD in Chinese patients. Integrative analysis of proteome, phosphoproteome, transcriptome, and whole-exome sequencing data revealed cancer-associated characteristics, such as tumor-associated protein variants, distinct proteomics features, and clinical ...
Source: Genomics Proteomics ... - July 9, 2020 Category: Genetics & Stem Cells Authors: Xu JY, Zhang C, Wang X, Zhai L, Ma Y, Mao Y, Qian K, Sun C, Liu Z, Jiang S, Wang M, Feng L, Zhao L, Liu P, Wang B, Zhao X, Xie H, Yang X, Zhao L, Chang Y, Jia J, Wang X, Zhang Y, Wang Y, Yang Y, Wu Z, Yang L, Liu B, Zhao T, Ren S, Sun A, Zhao Y, Ying W, W Tags: Cell Source Type: research

Network-Based Analysis of OMICs Data to Understand the HIV-Host Interaction.
Abstract The interaction of human immunodeficiency virus with human cells is responsible for all stages of the viral life cycle, from the infection of CD4+ cells to reverse transcription, integration, and the assembly of new viral particles. To date, a large amount of OMICs data as well as information from functional genomics screenings regarding the HIV-host interaction has been accumulated in the literature and in public databases. We processed databases containing HIV-host interactions and found 2910 HIV-1-human protein-protein interactions, mostly related to viral group M subtype B, 137 interactions between hu...
Source: Genomics Proteomics ... - July 8, 2020 Category: Genetics & Stem Cells Authors: Ivanov S, Lagunin A, Filimonov D, Tarasova O Tags: Front Microbiol Source Type: research

Microarray-based Analysis of Genes, Transcription Factors, and Epigenetic Modifications in Lung Cancer Exposed to Nitric Oxide.
CONCLUSION: Through this comprehensive approach, the present study illustrated the scheme of how NO affects molecular events in lung cancer cells. PMID: 32576585 [PubMed - in process] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - June 25, 2020 Category: Genetics & Stem Cells Authors: Maiuthed A, Prakhongcheep O, Chanvorachote P Tags: Cancer Genomics Proteomics Source Type: research

Targeted Sequencing of Circulating Cell Free DNA Can Be Used to Monitor Therapeutic Efficacy of Tyrosine Kinase Inhibitors in Non-small Cell Lung Cancer Patients.
CONCLUSION: The mutation count of tumor-specific mutations can be a monitoring marker of TKI treatment in NSCLC patients. PMID: 32576586 [PubMed - in process] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - June 25, 2020 Category: Genetics & Stem Cells Authors: Chiou CC, Wang CL, Luo JD, Liu CY, Ko HW, Yang CT Tags: Cancer Genomics Proteomics Source Type: research

Antibacterial and NF- κB Inhibitory Lumazine Peptides, Aspochalasin, γ-Butyrolactone Derivatives, and Cyclic Peptides from a Hawaiian Aspergillus flavipes.
Antibacterial and NF-κB Inhibitory Lumazine Peptides, Aspochalasin, γ-Butyrolactone Derivatives, and Cyclic Peptides from a Hawaiian Aspergillus flavipes. J Nat Prod. 2020 Jun 22;: Authors: Wang C, Wu X, Bai H, Zaman KAU, Hou S, Saito J, Wongwiwatthananukit S, Kim KS, Cao S Abstract Five new lumazine peptides (1-5), a new aspochalasin derivative (6), and a new γ-butyrolactone derivative (7), together with seven known compounds (8-14), were isolated from a Hawaiian fungal strain, Aspergillus flavipes FS888. Compound 1 is an uncommon natural product containing an isocyano group. The st...
Source: Genomics Proteomics ... - June 22, 2020 Category: Genetics & Stem Cells Authors: Wang C, Wu X, Bai H, Zaman KAU, Hou S, Saito J, Wongwiwatthananukit S, Kim KS, Cao S Tags: J Nat Prod Source Type: research

Diverse proteins aggregate in mild cognitive impairment and Alzheimer's disease brain.
CONCLUSIONS: Diverse proteins became more detergent-insoluble in the brains of both MCI and AD patients compared to age-matched controls, suggesting that multiple proteins aggregate in these diseases, likely posing a direct toxic insult to neurons. Furthermore, detergent-insoluble proteins included those with important biological activities for critical cellular processes such as energetics, proteolysis, and DNA damage repair. Thus, reduced protein solubility likely promotes aggregation and limits functionality, reducing the efficiency of multiple aspects of cell physiology. Pharmaceutical interventions that increase autop...
Source: Genomics Proteomics ... - June 19, 2020 Category: Genetics & Stem Cells Authors: Kepchia D, Huang L, Dargusch R, Rissman RA, Shokhirev MN, Fischer W, Schubert D Tags: Alzheimers Res Ther Source Type: research

Proteomic analysis in lupus mice identifies Coronin-1A as a potential biomarker for lupus nephritis.
CONCLUSIONS: These preliminary findings suggest that serum Coronin-1A may serve as a promising non-invasive biomarker for LN and, upon validation in larger cohorts, may be employed in the future as a screening test for renal disease in SLE patients. PMID: 32552896 [PubMed - in process] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - June 18, 2020 Category: Genetics & Stem Cells Authors: Nicolaou O, Sokratous K, Makowska Z, Morell M, De Groof A, Montigny P, Hadjisavvas A, Michailidou K, Oulas A, Spyrou GM, Demetriou C, Alarcón-Riquelme ME, Psarellis S, Kousios A, Lauwerys B, Kyriacou K Tags: Arthritis Res Ther Source Type: research

Inflammatory Drivers of Cardiovascular Disease: Molecular Characterization of Senescent Coronary Vascular Smooth Muscle Cells.
Abstract The senescence of vascular smooth muscle cells (VSMCs) has been implicated as a causal pro-inflammatory mechanism for cardiovascular disease development and progression of atherosclerosis, the instigator of ischemic heart disease. Contemporary limitations related to studying this cellular population and senescence-related therapeutics are caused by a lack of specific markers enabling their detection. Therefore, we aimed to profile a phenotypical and molecular signature of senescent VSMCs to allow reliable identification. To achieve this goal, we have compared non-senescent and senescent VSMCs from two in ...
Source: Genomics Proteomics ... - June 12, 2020 Category: Genetics & Stem Cells Authors: Stojanović SD, Fuchs M, Kunz M, Xiao K, Just A, Pich A, Bauersachs J, Fiedler J, Sedding D, Thum T Tags: Front Physiol Source Type: research

IRESbase: A Comprehensive Database of Experimentally Validated Internal Ribosome Entry Sites.
In this study, we present IRESbase, a comprehensive database of IRESs, by curating the experimentally validated functional minimal IRES elements from literature and annotating their host linear and circular RNAs. The current version of IRESbase contains 1328 IRESs, including 774 eukaryotic IRESs and 554 viral IRESs from 11 eukaryotic organisms and 198 viruses, respectively. As IRESbase collects only IRES of minimal length with functional evidence, the median length of IRESs in IRESbase is 174 nucleotides. By mapping IRESs to human circular RNAs (circRNAs) and long non-coding RNAs (lncRNAs), 2191 circRNAs and 168 lncRNAs we...
Source: Genomics Proteomics ... - June 5, 2020 Category: Genetics & Stem Cells Authors: Zhao J, Li Y, Wang C, Zhang H, Zhang H, Jiang B, Guo X, Song X Tags: Genomics Proteomics Bioinformatics Source Type: research

Proteomic analysis revealed ROS-mediated growth inhibition of Aspergillus terreus by shikonin.
In this report, we employed nLC-ESI-MS/MS to identify the differential proteome in A. terreus in response to shikonin. The identified proteins involved in pathways influenced by shikonin could be helpful to understand the molecular mechanism on how shikonin/ phytochemicals or other antifungal agents inhibit fungal growth and may enable the discovery of novel or synergistic drug targets. PMID: 32485396 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - May 30, 2020 Category: Genetics & Stem Cells Authors: Shishodia SK, Shankar J Tags: J Proteomics Source Type: research

Cdc42-Dependent Transfer of mir301 from Breast Cancer-Derived Extracellular Vesicles Regulates the Matrix Modulating Ability of Astrocytes at the Blood-Brain Barrier.
Abstract Breast cancer brain metastasis is a major clinical challenge and is associated with a dismal prognosis. Understanding the mechanisms underlying the early stages of brain metastasis can provide opportunities to develop efficient diagnostics and therapeutics for this significant clinical challenge. We have previously reported that breast cancer-derived extracellular vesicles (EVs) breach the blood-brain barrier (BBB) via transcytosis and can promote brain metastasis. Here, we elucidate the functional consequences of EV transport across the BBB. We demonstrate that brain metastasis-promoting EVs can be inter...
Source: Genomics Proteomics ... - May 28, 2020 Category: Genetics & Stem Cells Authors: Morad G, Daisy CC, Otu HH, Libermann TA, Dillon ST, Moses MA Tags: Int J Mol Sci Source Type: research

Metabolomic Responses of Maize Shoots and Roots Elicited by Combinatorial Seed Treatments With Microbial and Non-microbial Biostimulants.
Abstract Microbial and non-microbial plant biostimulants have been successfully used to improve agriculture productivity in a more sustainable manner. Since the mode of action of biostimulants is still largely unknown, the present work aimed at elucidating the morpho-physiological and metabolomic changes occurring in maize (Zea mays L.) leaves and roots following seed treatment with (i) a consortium of two beneficial fungi [arbuscular mycorrhizal fungi (AMF) and Trichoderma koningii TK7] and rhizobacteria, (ii) a protein hydrolyzate-based biostimulant (PH) alone, or (iii) in combination with a consortium of T. kon...
Source: Genomics Proteomics ... - May 23, 2020 Category: Genetics & Stem Cells Authors: Rouphael Y, Lucini L, Miras-Moreno B, Colla G, Bonini P, Cardarelli M Tags: Front Microbiol Source Type: research

Drosophila SWR1 and NuA4 complexes are defined by DOMINO isoforms.
Abstract Histone acetylation and deposition of H2A.Z variant are integral aspects of active transcription. In Drosophila, the single DOMINO chromatin regulator complex is thought to combine both activities via an unknown mechanism. Here we show that alternative isoforms of the DOMINO nucleosome remodeling ATPase, DOM-A and DOM-B, directly specify two distinct multi-subunit complexes. Both complexes are necessary for transcriptional regulation but through different mechanisms. The DOM-B complex incorporates H2A.V (the fly ortholog of H2A.Z) genome-wide in an ATP-dependent manner, like the yeast SWR1 complex. The DO...
Source: Genomics Proteomics ... - May 20, 2020 Category: Genetics & Stem Cells Authors: Scacchetti A, Schauer T, Reim A, Apostolou Z, Campos Sparr A, Krause S, Heun P, Wierer M, Becker PB Tags: Elife Source Type: research

Identification of Transient Receptor Potential Channel 4-Associated Protein as a Novel Candidate Gene Causing Congenital Primary Hypothyroidism.
CONCLUSION: TRPC4AP was identified as a novel candidate gene in TD, but further studies are needed to validate its role in thyroid function. PMID: 32428920 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - May 19, 2020 Category: Genetics & Stem Cells Authors: Choukair D, Eberle B, Vick P, Hermanns P, Weiss B, Paramasivam N, Schlesner M, Lornsen K, Roeth R, Klutmann C, Kreis J, Hoffmann GF, Pohlenz J, Rappold GA, Bettendorf M Tags: Horm Res Paediatr Source Type: research

SinoDuplex: An Improved Duplex Sequencing Approach to Detect Low-frequency Variants in Plasma cfDNA Samples.
Abstract Accurate detection of low frequency mutations from plasma cell-free DNA in blood using targeted next generation sequencing technology has shown promising benefits in clinical settings. Duplex sequencing technology is the most commonly used approach in liquid biopsies. Unique molecular identifiers are attached to each double-stranded DNA template, followed by production of low-error consensus sequences to detect low frequency variants. However, high sequencing costs have hindered application of this approach in clinical practice. Here, we have developed an improved duplex sequencing approach called SinoDup...
Source: Genomics Proteomics ... - May 16, 2020 Category: Genetics & Stem Cells Authors: Ren Y, Zhang Y, Wang D, Liu F, Fu Y, Xiang S, Su L, Li J, Dai H, Huang B Tags: Genomics Proteomics Bioinformatics Source Type: research

The Birth of Bio-data Science: Trends, Expectations, and Applications.
PMID: 32428604 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - May 16, 2020 Category: Genetics & Stem Cells Authors: Goh WWB, Wong L Tags: Genomics Proteomics Bioinformatics Source Type: research

Something old, something new: Teaching the BMB lab.
Abstract Lab courses are a significant component of biochemistry and molecular biology (BMB) education. In teaching the labs, we combine established techniques with novel approaches. Lab formats have also moved from traditional cookbook style labs to guided inquiry to course-based undergraduate research experiences (CUREs), where faculty bring their own research interests into the course setting with a larger number of students in a much more restricted time frame. This presentation is designed to explore some of these ideas and challenge the reader to introduce research opportunities to all students, not just the...
Source: Genomics Proteomics ... - May 13, 2020 Category: Genetics & Stem Cells Authors: Craig PA Tags: Biochem Mol Biol Educ Source Type: research

Comparative analysis of affected and unaffected areas of systemic sclerosis skin biopsies by high-throughput proteomic approaches.
CONCLUSION: Using MS-based proteomics analysis of human skin biopsies from patients with SSc, we identified a number of proteins and pathways that might be involved in SSc progression and pathogenesis. Fifteen of these proteins were further validated, and results suggest that five of them may serve as potential biomarkers for SSc. PMID: 32381114 [PubMed - in process] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - May 7, 2020 Category: Genetics & Stem Cells Authors: Chairta P, Nicolaou P, Sokratous K, Galant C, Houssiau F, Oulas A, Spyrou GM, Alarcon-Riquelme ME, Lauwerys BR, Christodoulou K Tags: Arthritis Res Ther Source Type: research

Bioinformatics Resources for Plant Abiotic Stress Responses: State of the Art and Opportunities in the Fast Evolving -Omics Era.
Abstract Abiotic stresses are among the principal limiting factors for productivity in agriculture. In the current era of continuous climate changes, the understanding of the molecular aspects involved in abiotic stress response in plants is a priority. The rise of -omics approaches provides key strategies to promote effective research in the field, facilitating the investigations from reference models to an increasing number of species, tolerant and sensitive genotypes. Integrated multilevel approaches, based on molecular investigations at genomics, transcriptomics, proteomics and metabolomics levels, are now fea...
Source: Genomics Proteomics ... - May 6, 2020 Category: Genetics & Stem Cells Authors: Ambrosino L, Colantuono C, Diretto G, Fiore A, Chiusano ML Tags: Plants (Basel) Source Type: research

The omics discovery REST interface.
l Y Abstract The Omics Discovery Index is an open source platform that can be used to access, discover and disseminate omics datasets. OmicsDI integrates proteomics, genomics, metabolomics, models and transcriptomics datasets. Using an efficient indexing system, OmicsDI integrates different biological entities including genes, transcripts, proteins, metabolites and the corresponding publications from PubMed. In addition, it implements a group of pipelines to estimate the impact of each dataset by tracing the number of citations, reanalysis and biological entities reported by each dataset. Here, we present the Omic...
Source: Genomics Proteomics ... - May 6, 2020 Category: Genetics & Stem Cells Authors: Dass G, Vu MT, Xu P, Audain E, Hitz MP, Grüning BA, Hermjakob H, Perez-Riverol Y Tags: Nucleic Acids Res Source Type: research

Adapting Biased Gene Conversion theory to account for intensive GC-content deterioration in the human genome by novel mutations.
We examined seventy million well-characterized human mutations, and their impact on G+C-compositional dynamics, in order to understand the formation and maintenance of major genomic nucleotide sequence patterns. Among novel mutations, those that change a strong (S) base pair G:C/C:G to a weak (W) pair A:T/T:A occur at nearly twice the frequency of the opposite mutations. Such imbalance puts strong downward pressure on overall GC-content. However, along protracted paths to fixation, S→W mutations are much less likely to propagate than W→S mutations. The magnitude of relative propagation disadvantages for S→W ...
Source: Genomics Proteomics ... - May 2, 2020 Category: Genetics & Stem Cells Authors: Paudel R, Fedorova L, Fedorov A Tags: PLoS One Source Type: research

Prognostic Biomarkers in Early-stage Gastric Adenocarcinoma Treated With Adjuvant Chemoradiotherapy.
CONCLUSION: PTEN protein expression and KRAS mutations may predict disease outcome in early-stage gastric cancer. These results need to be further validated in larger cohorts. PMID: 32345669 [PubMed - in process] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - April 30, 2020 Category: Genetics & Stem Cells Authors: Pectasides E, Chatzidakis I, Kotoula V, Koliou GA, Papadopoulou K, Giannoulatou E, Giannouzakos VG, Bobos M, Papavasileiou C, Chrisafi S, Florou A, Pectasides D, Fountzilas G Tags: Cancer Genomics Proteomics Source Type: research

QUATgo: Protein quaternary structural attributes predicted by two-stage machine learning approaches with heterogeneous feature encoding.
Abstract Many proteins exist in natures as oligomers with various quaternary structural attributes rather than as single chains. Predicting these attributes is an essential task in computational biology for the advancement of proteomics. However, the existing methods do not consider the integration of heterogeneous coding and the accuracy of subunit categories with limited data. To this end, we proposed a tool that can predict more than 12 subunit protein oligomers, QUATgo. Meanwhile, three kinds of sequence coding were used, including dipeptide composition, which was used for the first time to predict protein qua...
Source: Genomics Proteomics ... - April 30, 2020 Category: Genetics & Stem Cells Authors: Tung CH, Chien CH, Chen CW, Huang LY, Liu YN, Chu YW Tags: PLoS One Source Type: research

Editorial: Artificial Intelligence Bioinformatics: Development and Application of Tools for Omics and Inter-Omics Studies.
PMID: 32328085 [PubMed] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - April 26, 2020 Category: Genetics & Stem Cells Authors: Chicco D, Heider D, Facchiano A Tags: Front Genet Source Type: research

Key steps and methods in the experimental design and data analysis of highly multi-parametric flow and mass cytometry.
tilde;ón C Abstract High-dimensional, single-cell cell technologies revolutionized the way to study biological systems, and polychromatic flow cytometry (FC) and mass cytometry (MC) are two of the drivers of this revolution. As up to 30-50 dimensions respectively can be measured per single-cell, they allow deep phenotyping combined with cellular functions studies, like cytokine production or protein phosphorylation. In parallel, the bioinformatics field develops algorithms that are able to process incoming data and extract the most useful and meaningful biological information. However, the success of automa...
Source: Genomics Proteomics ... - April 25, 2020 Category: Genetics & Stem Cells Authors: Rybakowska P, Alarcón-Riquelme ME, Marañón C Tags: Comput Struct Biotechnol J Source Type: research

BioHackathon 2015: Semantics of data for life sciences and reproducible research.
We report on the activities of the 2015 edition of the BioHackathon, an annual event that brings together researchers and developers from around the world to develop tools and technologies that promote the reusability of biological data. We discuss issues surrounding the representation, publication, integration, mining and reuse of biological data and metadata across a wide range of biomedical data types of relevance for the life sciences, including chemistry, genotypes and phenotypes, orthology and phylogeny, proteomics, genomics, glycomics, and metabolomics. We describe our progress to address ongoing challenges to the r...
Source: Genomics Proteomics ... - April 22, 2020 Category: Genetics & Stem Cells Authors: Vos RA, Katayama T, Mishima H, Kawano S, Kawashima S, Kim JD, Moriya Y, Tokimatsu T, Yamaguchi A, Yamamoto Y, Wu H, Amstutz P, Antezana E, Aoki NP, Arakawa K, Bolleman JT, Bolton E, Bonnal RJP, Bono H, Burger K, Chiba H, Cohen KB, Deutsch EW, Fernández-B Tags: F1000Res Source Type: research

Structural Database for Lectins and the UniLectin Web Platform.
Abstract The search for new biomolecules requires a clear understanding of biosynthesis and degradation pathways. This view applies to most metabolites as well as other molecule types such as glycans whose repertoire is still poorly characterized. Lectins are proteins that recognize specifically and interact noncovalently with glycans. This particular class of proteins is considered as playing a major role in biology. Glycan-binding is based on multivalence, which gives lectins a unique capacity to interact with surface glycans and significantly contribute to cell-cell recognition and interactions. Lectins have be...
Source: Genomics Proteomics ... - April 20, 2020 Category: Genetics & Stem Cells Authors: Bonnardel F, Perez S, Lisacek F, Imberty A Tags: Methods Mol Biol Source Type: research

Gene-Based Clustering Algorithms: Comparison Between Denclue, Fuzzy-C, and BIRCH.
The objective was to compare the efficacy of the 3 algorithms and determine their strength and drawbacks. Result of the review showed that unlike Denclue and Fuzzy-C which are more efficient in handling noisy data, BIRCH can handle data set with outliers and have a better time complexity. PMID: 32284672 [PubMed] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - April 16, 2020 Category: Genetics & Stem Cells Authors: Nwadiugwu MC Tags: Bioinform Biol Insights Source Type: research

The molecular landscape and microenvironment of salivary duct carcinoma reveal new therapeutic opportunities.
Conclusions: Together our data significantly increase the understanding of SDC biology and open new perspectives for SDC tumor treatment. Before applying immunotherapy, patient stratification according to the immune infiltrate should be taken into account. Immune-infiltrated SDC could benefit from immune checkpoint-targeting therapy, with novel options such as anti-CTLA-4. Macrophages or NK cells could also be targeted. The dense stroma, i.e., fibroblasts or hyaluronic acid, may also be the focus for immune-poor SDC therapies, e.g. in combination with Notch or TGF-β inhibitors, or molecules targeting SDC mutations. ...
Source: Genomics Proteomics ... - April 16, 2020 Category: Genetics & Stem Cells Authors: Alame M, Cornillot E, Cacheux V, Tosato G, Four M, De Oliveira L, Gofflot S, Delvenne P, Turtoi E, Cabello-Aguilar S, Nishiyama M, Turtoi A, Costes-Martineau V, Colinge J Tags: Theranostics Source Type: research

Sparse multiple co-Inertia analysis with application to integrative analysis of multi -Omics data.
CONCLUSION: Proposed sparse mCIA achieves simultaneous model estimation and feature selection and yields analysis results that are more interpretable than the existing mCIA. Furthermore, proposed structured sparse mCIA can effectively incorporate prior network information among genes, resulting in improved feature selection and enhanced interpretability. PMID: 32293260 [PubMed - as supplied by publisher] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - April 15, 2020 Category: Genetics & Stem Cells Authors: Min EJ, Long Q Tags: BMC Bioinformatics Source Type: research

Adaptive Evolution of Geobacter sulfurreducens in Coculture with Pseudomonas aeruginosa.
This study brings to light the multifaceted nature of interactions between just two microorganisms within a controlled environment and will aid in improving metabolic models of microbial communities comprising these two bacteria. PMID: 32265334 [PubMed - in process] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - April 7, 2020 Category: Genetics & Stem Cells Authors: Semenec L, Vergara IA, Laloo AE, Petrovski S, Bond PL, Franks AE Tags: mBio Source Type: research

Metabolic Insights into the Anion-Anion Antagonism in Sweet Basil: Effects of Different Nitrate/Chloride Ratios in the Nutrient Solution.
Abstract Sweet basil (Ocimum basilicum L.) is a highly versatile and globally popular culinary herb, and a rich source of aromatic and bioactive compounds. Particularly for leafy vegetables, nutrient management allows a more efficient and sustainable improvement of crop yield and quality. In this work, we investigated the effects of balanced modulation of the concentration of two antagonist anions (nitrate and chlorine) in basil. Specifically, we evaluated the changes in yield and leaf metabolic profiles in response to four different NO3-:Cl- ratios in two consecutive harvests, using a full factorial design. Our w...
Source: Genomics Proteomics ... - April 3, 2020 Category: Genetics & Stem Cells Authors: Corrado G, Lucini L, Miras-Moreno B, Chiaiese P, Colla G, De Pascale S, Rouphael Y Tags: Int J Mol Sci Source Type: research

Stem cell-derived polarized hepatocytes.
Abstract Human stem cell-derived hepatocyte-like cells (HLCs) offer an attractive platform to study liver biology. Despite their numerous advantages, HLCs lack critical in vivo characteristics, including cell polarity. Here, we report a stem cell differentiation protocol that uses transwell filters to generate columnar polarized HLCs with clearly defined basolateral and apical membranes separated by tight junctions. We show that polarized HLCs secrete cargo directionally: Albumin, urea, and lipoproteins are secreted basolaterally, whereas bile acids are secreted apically. Further, we show that enterically tra...
Source: Genomics Proteomics ... - April 3, 2020 Category: Genetics & Stem Cells Authors: Dao Thi VL, Wu X, Belote RL, Andreo U, Takacs CN, Fernandez JP, Vale-Silva LA, Prallet S, Decker CC, Fu RM, Qu B, Uryu K, Molina H, Saeed M, Steinmann E, Urban S, Singaraja RR, Schneider WM, Simon SM, Rice CM Tags: Nat Commun Source Type: research

ProGeo-neo: a customized proteogenomic workflow for neoantigen prediction and selection.
CONCLUSIONS: The pipeline was constructed based on the genomics and proteomics data of Jurkat leukemia cell line but is generally applicable to other solid cancer research. With massively parallel sequencing and proteomics profiling increasing, this proteogenomics workflow should be useful for neoantigen oriented research and immunotherapy. PMID: 32241270 [PubMed - in process] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - April 3, 2020 Category: Genetics & Stem Cells Authors: Li Y, Wang G, Tan X, Ouyang J, Zhang M, Song X, Liu Q, Leng Q, Chen L, Xie L Tags: BMC Med Genomics Source Type: research

Multi-omics Visualization Platform: An extensible Galaxy plug-in for multi-omics data visualization and exploration.
CONCLUSIONS: MVP provides a powerful, extensible platform for automated, interactive visualization of proteogenomic results within the Galaxy environment, adding a unique and critically needed tool for empowering exploration and interpretation of results. The platform is extensible, providing a basis for further development of new functionalities for proteogenomic data visualization. PMID: 32236523 [PubMed - in process] (Source: Genomics Proteomics ...)
Source: Genomics Proteomics ... - April 1, 2020 Category: Genetics & Stem Cells Authors: McGowan T, Johnson JE, Kumar P, Sajulga R, Mehta S, Jagtap PD, Griffin TJ Tags: Gigascience Source Type: research

No Evidence of Persistence or Inheritance of Mitochondrial DNA Copy Number in Holocaust Survivors and Their Descendants.
In this study, we used qPCR to quantify mtDNA copy number in 15 Holocaust survivors and 102 of their second- and third-generation descendants from the Czech Republic, many of whom suffer from PTSD, and compared them to controls in the respective generations. We found no significant difference in mtDNA copy number in the Holocaust survivors compared to controls, whether they have PTSD or not, and no significant elevation in descendants of female Holocaust survivors as compared to descendants of male survivors or controls. Our results showed no evidence of persistence or inheritance of mtDNA changes in Holocaust survivors, t...
Source: Genomics Proteomics ... - March 28, 2020 Category: Genetics & Stem Cells Authors: Cai N, Fňašková M, Konečná K, Fojtová M, Fajkus J, Coomber E, Watt S, Soranzo N, Preiss M, Rektor I Tags: Front Genet Source Type: research

Developing and applying computational resources for biochemistry education.
Abstract Biochemistry is about structure and function, but it is also about data and this is where computers come in. From my time as a graduate student and post doc, whenever I encountered data I thought, "I can work this up by hand, but I think a computer could do a better job." Since that time, I have been working at the interface of biochemistry and computers, by attracting talented students and collaborating with colleagues with complementary skills. This has resulted in several exciting projects: a simulation of 2D electrophoresis and tandem mass spectrometry, the human visualization project, and t...
Source: Genomics Proteomics ... - March 23, 2020 Category: Genetics & Stem Cells Authors: Craig PA Tags: Biochem Mol Biol Educ Source Type: research

GPS 5.0: An Update on the Prediction of Kinase-specific Phosphorylation Sites in Proteins.
Abstract In eukaryotes, protein phosphorylation is specifically catalyzed by numerous protein kinases (PKs), faithfully orchestrates various biological processes, and reversibly determines cellular dynamics and plasticity. Here we report an updated algorithm of Group-based Prediction System (GPS) 5.0 to improve the performance for predicting kinase-specific phosphorylation sites (p-sites). Two novel methods, position weight determination (PWD) and scoring matrix optimization (SMO), were developed. Compared with other existing tools, GPS 5.0 exhibits a highly competitive accuracy. Besides serine/threonine or tyrosi...
Source: Genomics Proteomics ... - March 18, 2020 Category: Genetics & Stem Cells Authors: Wang C, Xu H, Lin S, Deng W, Zhou J, Zhang Y, Shi Y, Peng D, Xue Y Tags: Genomics Proteomics Bioinformatics Source Type: research

Wikidata as a knowledge graph for the life sciences.
, Slenter D, Stephan R, Thornton K, Tsueng G, Tu R, Ul-Hasan S, Willighagen E, Wu C, Su AI Abstract Wikidata is a community-maintained knowledge base that has been assembled from repositories in the fields of genomics, proteomics, genetic variants, pathways, chemical compounds, and diseases, and that adheres to the FAIR principles of findability, accessibility, interoperability and reusability. Here we describe the breadth and depth of the biomedical knowledge contained within Wikidata, and discuss the open-source tools we have built to add information to Wikidata and to synchronize it with source databases. We al...
Source: Genomics Proteomics ... - March 17, 2020 Category: Genetics & Stem Cells Authors: Waagmeester A, Stupp G, Burgstaller-Muehlbacher S, Good BM, Griffith M, Griffith OL, Hanspers K, Hermjakob H, Hudson TS, Hybiske K, Keating SM, Manske M, Mayers M, Mietchen D, Mitraka E, Pico AR, Putman T, Riutta A, Queralt-Rosinach N, Schriml LM, Shafee Tags: Elife Source Type: research

Machine learning prediction of oncology drug targets based on protein and network properties.
CONCLUSIONS: We developed a machine learning approach to prioritize proteins according to their similarity to approved drug targets. We have shown that the method proposed is highly predictive on a validation dataset consisting of 277 targets of clinical trial drug confirming that our computational approach is an efficient and cost-effective tool for drug target discovery and prioritization. Our predictions were based on oncology targets and cancer relevant biological functions, resulting in significantly higher scores for targets of oncology clinical trial drugs compared to the scores of targets of trial drugs for other i...
Source: Genomics Proteomics ... - March 14, 2020 Category: Genetics & Stem Cells Authors: Dezső Z, Ceccarelli M Tags: BMC Bioinformatics Source Type: research